Depression marsh intra- and interspecific facilitation in Southeast Florida, dominated by Hypericum fasciculatum, Stillingia aquatica, and Rhynchospora tracyi were studied as a third installment to the author’s ongoing interest in “Hypericum-Stillingia (HS) marsh” vegetation. The project includes a contextual overview in relation to the HS marsh environmental filter, stress-gradient-hypothesis, and harsh-habitat trait convergence vs. divergence. Using field measurements, transects, and quadrats, the effort focused mainly on two research questions: 1. Does the Hypericum fasciculatum microdistribution relate to marsh microtopography? 2. Does H. fasciculatum have positive or negative associations with other species? Tempered by “cause and effect” concerns, the results supported positive feedback autogenic site alteration by H. fasciculatum along with interspecific facilitation.

Galectins are β-galactosyl-binding proteins that fulfill essential physiological functions. Recently, we introduced galectin-1 (Gal-1) and galectin-3 (Gal-3) as fusion proteins of a His6-tag, a SNAP-tag, and a fluorescent protein. We characterized their binding in ELISA-type assays and their application in cell-surface binding. In the present study, we have constructed further fusion proteins of galectins with fluorescent protein color code. The fusion proteins of Gal-1, Gal-3, and Gal-8 were purified by affinity chromatography. For this, we have prepared glycoprotein affinity resins based on asialofetuin (ASF) and fetuin and combined this in a two-step purification with Immobilized Metal Affinity chromatography (IMAC) to get pure and active galectins. Purified galectin fractions were analyzed by size-exclusion chromatography. The binding characteristics to ASF of solely His6-tagged galectins and galectin fusion proteins were compared. As an example, we demonstrate a 1.6-3-fold increase in binding efficiency for HSYGal-3 (His6-SNAP-yellow fluorescent protein-Gal-3) compared to the HGal-3 (His6-Gal-3). Our results reveal an apparent higher binding efficiency for galectin SNAP-tag fusion proteins compared to His6-tagged galectins which are independent of the purification mode. This is also demonstrated by the binding of galectin fusion proteins to extracellular glycoconjugates laminin, fibronectin, and collagen IV. Our results indicate the probable involvement of the SNAP-tag in apparently higher binding signals, which we discuss in this study.

The traditional practice of harvesting and processing raw date palm sap is not only culturally significant but also an essential nutritional source in South Asia. Yet, the potential for bacterial or viral contamination from animals and environmental sources during its collection remains a real and insufficiently studied risk. Implementing improved food safety measures and collection techniques could mitigate the risk of these infections. Additionally, the adoption of advanced food analytical methods has the potential to identify pathogens and uncover the natural bacterial diversity of these products. The advancement of NGS technologies, particularly nanopore sequencing, offers rapid and highly mobile capabilities. In this study, we employed nanopore sequencing for bacterial metabarcoding of a set of raw date palm sap samples collected without protective coverage against animals in Bangladesh in 2021. We identified several bacterial species with importance in the natural fermentation of the product and demonstrated the feasibility of this NGS method in the surveillance of raw palm sap products. We revealed two fermentation directions dominated by either Leuconostoc species or Lactococcus species in these products at the first 6 hours from harvest along with opportunistic human pathogens in the background, represented with low abundance. Plant pathogens, bacteria with the potential for opportunistic human infections and the sequences of the Exiguobacterium genus were also described and their potential role is discussed.

The existing methods of oil palm Fresh Fruit Bunch (FFB) evacuation from in-field to temporary collection point which typically apply medium to large tractors, often result in unexpected soil compaction. Meanwhile, smaller size equipment indicates low working capacity and unable to perform direct unloading to collection bin. This paper addresses the challenge of FFB evacuation by focusing on preventing soil compaction, increasing working capacity and enabling direct unloading to collection bin. For this purpose, a 6x6WD transporter prototype with a scissor lift mechanism was developed. With the design, the transporter could evacuate FFB in both steep mineral terrain and low ground pressure peatland, able to carry FFB with capacity of 750 kg and provide direct unloading into collection bin. The average field working capacity of the transporter was found to be 15 tons day-1. This research offers insights for future designs of medium-sized FFB transporters with advanced unloading mechanisms.

Raman-based Distributed Temperature Sensing (DTS) is a valuable tool for field testing and validating heat transfer models in Borehole Heat Exchanger (BHE) and Ground Source Heat Pump (GSHP) applications. However, temperature uncertainty is rarely reported in the literature. In this paper, a new calibration method is proposed for single-ended DTS configurations, along with a method to remove fictitious temperature drifts due to ambient air variations. The methods are implemented for a Distributed Thermal Response Test case study in an 800 m deep coaxial BHE. The results show that the calibration method and temperature drift correction are robust and give adequate results, with a temperature uncertainty of ± 0.58, 0.74, 1.1 and 1.7 K found at depths of 200, 300, 500 and 800 m, respectively. The temperature uncertainty increases non-linearly with depth and is dominated by the uncertainty in the calibrated parameters for depths larger than 200 m. The paper also offers insights into thermal features observed during the DTRT, including a heat flux inversion along the borehole depth and the slow temperature homogenization under circulation. Distributed temperature measurements and their uncertainties are useful tools in determining the strengths and drawbacks of ground heat transfer models.

Interactions between mobile robots and human operators in common areas require a high safety especially in terms of trajectory planning, obstacle avoidance and mutual cooperation. In this connection the crossings of planned trajectories, their uncertainty based on model fluctuations, system noise and sensor noise,play an outstanding role. This paper discusses the calculation of expected areas of interactions du ring human-robot navigation with respect to fuzzy and noisy information. Expected crossing points of possible trajectories are nonlinearily associated with positions and orientations of robot and human. The nonlinear transformation of a noisy system input, such as directions of motion of human and robot, to a system output, the expected area of intersection of their trajectories, is done by two methods: statistical linearization and the sigma-point-transformation. For both approaches fuzzy approximations are presented and the inverse problem is discussed where the input distribution parameters are computed from given output distribution parameters.

We investigated humoral immune responses in 222 unvaccinated Japanese people after recovery from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2021. Anti-spike protein IgG antibody levels and neutralizing antibody titers were measured in serum samples obtained within 20–180 days after diagnosis. The geometric mean of antibody titers was 1555 ELU/mL (95% confidence interval [CI] = 1257-1923), and the neutralizing activities (50% inhibitory dilution) was 253 (95% CI = 204-313). The antibody titer and neutralizing activity both increased with increasing disease severity, and both values were approximately 4-fold higher for hospitalized patients than for non-hospitalized patients. However, these differences were smaller in older patients. The humoral immune response, which increased with increasing disease severity, gradually decreased over time after SARS-CoV-2 infection. Most patients with mild or moderate symptoms sustained neutralizing activity for up to 180 days after the infection, the decay of the neutralizing activity in the patients with asymptomatic was rather faster than other groups. 11.7% (26/222) of patients had very low neutralizing activity, and half of these were in the age of 20s. Our study results show the importance of measuring the neutralizing activity to confirm the immune status and also estimate the timing of vaccine.

In most Eukaryotes, ubiquitin either exists as free monoubiquitin or as a molecule that is covalently linked to other proteins. These two forms cycle between each other and due to the concerted antagonistic activity of ubiquitylating and deubiquitylating enzymes, an intracellular ubiquitin equilibrium is maintained that is essential for normal biological function. However, measuring the level and ratio of these forms of ubiquitin has been difficult and time consuming. In this paper, we have adapted a simple immunoblotting technique to monitor ubiquitin content and equilibrium dynamics in different developmental stages and tissues of Drosophila. Our data show that the level of total ubiquitin is distinct in different developmental stages, lowest at the larval-pupal transition and in three days old adult males, and highest in first instar larvae. Interestingly, the ratio of free mono-ubiquitin remains within 30-50% range of the total throughout larval development, but peaks to 70-80% at the larval-pupal and the pupal-adult transitions. It stays within the 70-80% range in adults. In developmentally and physiologically active tissues, the ratio of free ubiquitin is similarly high, most likely reflecting a high demand for ubiquitin availability. We also used this method to demonstrate the disruption of the finely tuned ubiquitin equilibrium by the abolition of proteasome function or the housekeeping deubiquitylase, Usp5. Our data support the notion that the ubiquitin equilibrium is regulated by tissue- and developmental stage-specific mechanisms.

This work aimed to develop an anionic cellulose nanofiber (CNF) bio-adsorbent from palm date tree waste and to investigate its removal efficiency against cationic methylene blue dye from contaminated water. Palm date pulp was first prepared from palm date leaves through acid hydrolysis using H2SO4, followed by hydrolysis in a basic medium using KOH, in which the process completely removed the components of hemicellulose, lignin, and silica. To obtain anionic CNF, the resulting pulp was further treated with H2SO4, followed by centrifugation. Biogel formation of the CNF suspension was promoted by sonication, where its removal efficiency of methylene blue dye was studied as a function of dye concentration, temperature, contact time, and pH value. Two equilibrium models, the Langmuir and Freundlich models were employed, and the Langmuir model was found to be consistent with the experimental data. The highest removal efficiency was obtained at 60oC and was 5mg/gm. Furthermore, several kinetic models were used to gain insight into the adsorption mechanism. The pseudo-second-order model provided an accurate description of the adsorption process, while the Elovich equation suggested a chemical reaction between methylene blue dye and CNF. The study’s findings were in agreement with the pseudo-second-order model, indicating general chemical reactions. The study indicates that CNF adsorbents derived from renewable natural waste sources such as palm date leaves can be effective in removing cationic contaminants such as methylene blue dye.

Salmonella is a foodborne pathogen associated with localized outbreaks that potentially pose a huge risk to the public health in some countries such as Africa and India, especially in the regions lacking health care measures. The focus of the present study is the molecular detection method of salmonella. The study was conducted to identify Salmonella strains by PCR targeting flagellin specific gene from suspected patient’s clinical blood samples. Serologically, Widal test results showed that all serum samples except one patient (ID 7) were positive for O antigen. The serum of three patients (ID 4, 5 and 10) were found to be positive for H and O antigens while one patient (ID 9) showed agglutination for antigen H. The PCR approach used in this study was successful for fast and precise detection of clinically related Salmonella Typhi. Seven samples out of 10 were positive for Salmonella Typhi as fragments of 458-497bp were observed on the gel-agarose 0.8% corresponds to flagellin gene of S. Typhi. Relatively, smaller amplicons of 366-343bp were observed utilizing nested PCR as well, which seems more sensitive than the conventional PCR. Therefore, we recommend the PCR approach performed in this study to be used as a fast, cost-effective, and time-consuming tool for diagnostic purposes of Salmonella.

This work aims to investigate systematically the tecno-economic feasibility of ther-mos-catalytic cracking process for two solid waste materials, a lipid-base material (re-sidual fat/scum from retention box of the University Restaurant of UFPA) and a lig-nin-cellulosic material Açaí seed (Euterpe oleracea. Mart). The thermo-catalytic process-es were carried out in pilot scale (THERMTEK/LEQ/UFPA/IME/RJ), and their economic feasibility analyzed. The yields of biofuels produced by fractional distillation were al-so studied. The physicochemical characteristics of the raw materials, the organic liquid product (bio-oil) and the chemical composition of kerosene, light-diesel and heavy-diesel from the lipid-base material, as well as those of kerosene and light-diesel from the Açaí seed were also determined. The economic indicators for the evaluation of the most viable cracking (pyrolysis) and distillation process of bio-oils were: a) the sim-ple payback criterion, b) discounted payback, c) net present value (NPV), d) internal rate of return (IRR), and e) index of profitability (IP). The analysis of the indicators showed the economic viability of crude palm oil (Elaeis guineensis, Jacq) and unfeasibil-ity for the palm oil neutralization. The minimum fuel selling price (MFSP) obtained is this work for the biofuels was of 1.34 US$/L) and the breakeven point obtained was of 1.28 US$/L. The sensibility analysis demonstrated that the pyrolysis and distillation yields are the most important variables to affect the minimum fuel selling price (MFSP).

Background Oil palm (OP), Elaeis guineensis , is by far the most important global oil crop, supplying about 40% of total traded vegetable oil. Palm oils are key dietary components consumed daily by over three billion people, mostly in Asia, and also have a wide range of important non-food uses including in cleansing and sanitising products. Main body Oil palm is a perennial crop with a >25-year life cycle and an exceptionally small land footprint compared to annual oilseed crops. Oil palm crops globally produce an annual 81 million tonnes (Mt) of oil from about 19 million hectares (Mha). In contrast, the second and third largest vegetable oil crops, soybean and rapeseed, yield a combined 84 Mt oil but occupy over 163 Mha of increasingly scarce arable land. Despite this advantage, oil palm has acquired a poor environmental reputation, especially in Europe and North America, although soybean planting is now responsible for more deforestation. Oil palm crops face other challenges in the 2020s. On the demand side, these include changing consumer purchasing habits, threats to global trade systems, and diminishing demand for liquid fuels as transport systems become increasingly electrified. On the supply side, major issues include stagnant yields in ageing plantations, sluggish replanting of improved varieties, labour shortages, diseases and climatic/ environmental threats. The latter include the increasing incidence of new and existing pests/diseases and a general lack of climatic resilience, especially relating to elevated temperatures and increasingly erratic rainfall patterns. This review surveys the oil palm sector in the 2020s and beyond, its major challenges and options for future progress. Conclusions Oil palm crops face many future challenges, including emerging threats from climate change and new pests and diseases, that require more effective international collaboration. Nevertheless, new breeding technologies are providing the promise of improvements, such as much higher yielding varieties, improved oil profiles, enhanced disease resistance and modified crop architecture to enable harvesting mechanisation. The industry also needs to redouble its efforts to engage with global consumers in a constructive dialogue aimed at addressing its image problem and explaining the many benefits of its products.

Achieving effective control over microbial contamination necessitates the precise and concurrent identification of numerous pathogens. In this research, we have devised a remarkably sensitive duplex droplet digital PCR (dddPCR) reaction system to simultaneously detect Pseudomonas aeruginosa (P. aeruginosa) and Pseudomonas fragi (P. fragi). Employing comparative genomics, we identified four genes of P. fragi. By specific analysis, RS22680 gene was selected as the detection target of P. fragi and LasR gene was chosed as P. aeruginosa, which were applied to construct a dddPCR reaction. In terms of specificity, sensitivity and anti-interference ability, the constructed dddPCR detection system was verified and analyzed. The assay showed excellent sensitivity and applicability, as evidenced by a limit of detection of 100 CFU/mL. When the concentration of natural background bacteria in milk or fresh meat was 100 times that of the target detection bacteria, the method was still capable of completing the absolute quantification. In the simulation of actual sample contamination, P. aeruginosa could be detected after 3 h of enrichment culture, and P. fragi could be detected after 6 h. The established ddPCR detection system exhibits exceptional performance, serving as a foundation for the simultaneous detection of various pathogenic bacteria in food products.

The red palm weevil (Rhynchophorus ferrugineus) inflicts widespread damage in date palm plantations and urban settings, leading to stand loss and safety concerns, intensified by the economic and ecological burdens of synthetic preventive treatments. A novel approach emphasizes detecting weevil-infested palms through sensors and targeting control efforts at colonized trees. The study analyzes two datasets: field manager-reported results from settings with preventive pest control versus seismic sensor-monitored units. Sensor data translates into damage index values, exploring curative treatments, attack likelihood based on infestation history, and the impact of sensor-based management on infestation incidence decline. Findings reveal lower weevil infestation in urban areas and preventive-treated palm settings. A strong correlation exists between sensor indications and grower decisions in date plantations. Palms previously infested are more prone to the damage. Long-term sensor-based management significantly reduces weevil-affected palm numbers. The high infestation in sensor-equipped date palm settings stems from a gap between sensor-identified and preventively treated palms. Controlling weevils based on sensor indications aligns practically with grower curative treatments, preventing significant damage. Weevils target previously infested palms, optimizing pest control through a continuous strategy integrating sensor monitoring with prompt response treatments. This proves highly effective, offering a cost-efficient alternative to preventive treatment reliance.

Sustainable development can only be realised when the social, economic and environmental dimensions are considered altogether. Social capital and local wisdom offer important contributions to the development process and the capabilities of individuals and groups as development actors. This study analyses the role of social capital and local wisdom in managing business partnerships between farmers and palm oil plantation companies in North Konawe, Indonesia. Data were collected via in-depth interviews, field observations and focus group discussions and were analysed descriptively and qualitatively. Results underscore the importance of social capital and local wisdom in organising institutional programmes for strengthening palm oil business partnerships. Trust, social networks and participation negatively affect the sustainability of these partnerships, whilst local wisdom and social solidarity positively influence institutional strengthening. Inconsistency and lack of openness by companies can lead to a trust crisis that can threaten the sustainable operations of palm oil companies. Building a good cooperative commitment and maintaining collaboration play key roles in enhancing community welfare and increasing company profits. The social capital and local wisdom of farmer institutions in villages are expected to significantly contribute to the establishment of sustainable palm oil business partnerships.

Several studies have highlighted the importance and evolution of process safety leadership and culture in various industries. However, none has focused on the palm oil milling industry yet. This paper critically reviews the latest developments in the palm oil milling process and unit operations leading to process safety concerns. It also discusses the Principle of 3C that is applied to explain repeat accidents and the four-level safety culture in the palm oil milling industry. For this purpose, the author presents case studies of two key palm oil companies in Malaysia. Overall, this paper offers guidelines to leaders in the palm oil milling industry about the required process safety leadership and culture to be understood in order to improve their safety outcomes.

This work aims to investigate systematically the tecno-economic feasibility of ther-mos-catalytic cracking process for two solid waste materials, a lipid-base material (re-sidual fat/scum from retention box of the University Restaurant of UFPA) and a lig-nin-cellulosic material Açaí seed (Euterpe oleracea. Mart). The thermo-catalytic process-es were carried out in pilot scale (THERMTEK/LEQ/UFPA/IME/RJ), and their economic feasibility analyzed. The yields of biofuels produced by fractional distillation were al-so studied. The physicochemical characteristics of the raw materials, the organic liquid product (bio-oil) and the chemical composition of kerosene, light-diesel and heavy-diesel from the lipid-base material, as well as those of kerosene and light-diesel from the Açaí seed were also determined. The economic indicators for the evaluation of the most viable cracking (pyrolysis) and distillation process of bio-oils were: a) the sim-ple payback criterion, b) discounted payback, c) net present value (NPV), d) internal rate of return (IRR), and e) index of profitability (IP). The analysis of the indicators showed the economic viability of crude palm oil (Elaeis guineensis, Jacq) and unfeasibil-ity for the palm oil neutralization. The minimum fuel selling price (MFSP) obtained is this work for the biofuels was of 1.34 US$/L) and the breakeven point obtained was of 1.28 US$/L. The sensibility analysis demonstrated that the pyrolysis and distillation yields are the most important variables to affect the minimum fuel selling price (MFSP).

The sweetpotato whitefly, Bemisia tabaci MEAM1, is a pest known to significantly impact tomato development and yields through direct damage and virus transmission. To manage this pest, the current study compared the effectiveness of various insecticide rotations. Field trials included rotations involving synthetic insecticides, biochemicals, and microbial agents, applied according to their labeled highest concentrations. Results indicated that while standard synthetic insecticides consistently reduced whitefly egg and nymph counts significantly, microbial biopesticide rotations also achieved reductions, although less consistently. This study demonstrated that while traditional chemical treatments remain highly effective, integrating microbial biopesticides containing Beauveria bassiana and Cordyceps javanica present a viable alternative that could mitigate resistance development and reduce environmental impact. The findings suggest the potential for optimizing integrated pest management (IPM) and Insecticide Resistance Management (IRM) strategies by incorporating a variety of modes of action to sustainably manage B. tabaci MEAM1 populations in agricultural settings.

This study examined the efficiency of a combined diagnostic approach in which bioamplification of Arizona 861 S1 citron was integrated with RT‒PCR to detect Citrus tristeza virus (CTV) and Hop Stunt Viroid (HSVd) in Citrus plants. The capacity of the combined method to diagnose mixed infections of CTV and HSVd, along with early single infections of both pathogens, was assessed by evaluating the incubation periods and differential detection capabilities between the combined and direct methods. The bioamplification method exhibited high sensitivity (100%) and specificity (100%) for CTV, enabling early detection even in patients with low-titer infections compared to direct RT‒PCR. However, for HSVd, the combined method achieved 50% sensitivity in early infections, highlighting the need for additional replicates to enhance diagnostic reliability. The relative concentrations of pathogens in mixed and simple infections were evaluated; the analysis revealed no significant differences, suggesting minimal interference between CTV and HSVd. This approach allows early detection of CTV but requires further refinement for HSVd diagnosis. These findings underscore the complementary roles of the cost-effectiveness of direct RT‒PCR and the sensitivity of the combined method in implementing effective disease control strategies in citrus crops.

Droplet digital polymerase chain reaction (ddPCR) is a method used to detect and quantify nu-cleic acids even when present in exceptionally low numbers. While it has proven to be valuable for clinical studies, it has failed to be widely adopted for environmental and applied studies. Due to the complexity of the chemical and biological composition of environmental samples, protocols tailored to clinical studies are not appropriate, and results are difficult to interpret. We used en-vironmental DNA samples originating from field studies to determine a protocol for environ-mental samples. Samples included field soils which had been inoculated with the soil fungus Rhizophagus irregularis (environmental positive control), field soils that had not been inoculat-ed and the targeted fungus was not naturally present (environmental negative control), and root samples from both field categories. To control for the effect of soil inhibitors, we also in-cluded DNA samples of an organismal control extracted from pure fungal spores (organismal positive control). Finally, we included a no-template control consisting only of the PCR reaction reagents and nuclease free water instead of template DNA. Using original data, we examined which factors contribute to poor resolution in root and soil samples and propose best practises to ensure accuracy and repeatability. Furthermore, we evaluated manual and automatic threshold determination methods and we propose a novel protocol based on multiple controls that is more appropriate for environmental samples.

Tungiasis is a neglected tropical disease caused by skin-penetrating female Tunga penetrans fleas. Although tungiasis causes severe health problems, its ecology is poorly understood and morphological descriptions of larvae are unavailable. To identify T. penetrans immature stages and sites where they develop, diagnostic PCRs are required. However, flea larvae feed on soil organic matter rich in PCR inhibitors. Here, three DNA preparation methods, a soil DNA kit removing inhibitors, a simple ammonium acetate precipitation approach (AmAcet) and a crude lysate of larvae (CL), were combined with amplification by the highly processive FIREPol® Taq or the inhibitor-resistant Phusion® polymerase. Independent of the polymerase used, frequency of successful amplification, Cq values and PCR efficacies for the low-cost CL and AmAcet methods were superior to the commercial kit for amplification of a 278 bp partial internal transcribed spacer-2 (ITS-2) and a 730 bp pan-Siphonaptera cytochrome oxidase I PCR. For the CL method combined with Phusion® polymerase, costs were approximately 20-fold lower than for methods based on the soil DNA kit, which is a considerable advantage in resource-poor settings. The ITS-2 PCR did not amplify Ctenocephalides felis genomic or Tunga trimammilata ITS-2 plasmid DNA allowing it to be used to specifically identify T. penetrans.

A Infectious diseases account for about 3 million deaths per year. The advent of molecular techniques has led to an enormous improvement in their diagnosis, both in terms of sensitivity and specificity and in terms of the speed with which a clinically useful result can be obtained. Digital PCR, or 3rd generation PCR, is based on a series of technical modifications that result in more sensitive techniques, more resistant to the action of inhibitors and capable of direct quantification, without the need for standard curves.This review presents the main applications that have been developed for the diagnosis of viral, bacterial and parasitic infections, and the potential prospects for the clinical use of this technology.

Palm fatty acid distillate (PFAD) is a by-product from the refining of crude palm oil. It comprises mainly of free fatty acids, having around 45% of palmitic and 33% oleic acids as the major components. Ultra-violet (UV) curable urethane acrylate (UA) oligomers could be synthesized from PFAD by the following procedure. A hydroxyl terminated macromer was first prepared by reacting PFAD with a mixture of isophthalic acid, phthalic anhydride, neopentagylcol (NPG) and pentaerythritol. The macromer is then reacted with 2-hydroxylethylacrylate (2HEA) and toluene diisocynate (TDI) to generate a resin containing acrylate side chains for UV curable application. A series of UA resins were prepared by using 15, 25, 45, 55 and 70% of PFAD respectively. The UA resin has Mw in the range of 3200 to 27,000. They could be cured by UV irradiation at intensity of 225mW/cm². Glass transition temperature (T_g) of the cured film was measured by differential scanning calorimeter (DSC), and hardness of the film was determined by pendulum hardness tester according to ASTM4366. The resins were used in wood coating application. All of the cured films showed good adhesion, hardness and chemical resistant for resins using up to 55% PFAD; however the resin at 70% did not cure properly.

In the oil palm industry, stands age is an important parameter to monitor the sustainability of cultivation, to develop the growth yield model, to identify the disease or stressed area, and to estimate the carbon storage capacity. This research is focused to estimate and distinguish oil palm stands age based on crown/ canopy density obtained using Forest Canopy Density (FCD) model derived from four indices as follows; Advanced Vegetation Index, Bare Soil Index, Shadow Index, and Thermal Index. FCD model employs multi temporal image analysis resulting four classes of oil palm stands age categorized as seed with FCD value of 29–56% (0 years), young with FCD value of 56–63% (1–9 years), teen with FCD value of 63–80% (10–15 years), and mature with FCD value of >80% (>15 years). Minimum canopy density value is 29% even in the zero years old indicates incomplete land clearance or the type of seed planted in the land.

Sepsis is a life-threatening syndrome triggered by infection and accompanied by high mortality, with antimicrobial resistances (AMRs) further escalating clinical challenges. Rapid and reliable detection of causative pathogens and AMRs are key factors for fast and appropriate treatment, in order to improve outcome in septic patients. However, current sepsis diagnostics based on blood culture is limited by low sensitivity and specificity while current molecular approaches fail to enter clinical routine. Therefore, we developed a Suppression PCR-based selective enrichment sequencing approach (SUPSETS), providing a molecular method combining multiplex suppression PCR with Nanopore sequencing to identify most common sepsis-causative pathogens and AMRs using plasma cell-free DNA. Applying only 1 mL of plasma, we target eight pathogens across three kingdoms and ten AMRs in a proof-of-concept study. SUPSETS was successfully tested on first ten clinical samples and revealed comparable results to clinical metagenomics while clearly outperforming blood culture. Several clinically relevant AMRs could be detected additionally. Furthermore, SUPSETS provided first pathogen and AMR-specific sequencing reads within minutes of starting sequencing, thereby potentially decreasing time to results to 11 - 13 hours and suggesting diagnostic potential in sepsis.

A total of five protoclones were successfully cultured on PDA medium out of regenerated twenty two colonies of Termitomyces protoplast and further studied. Liquid MYG grown mycelial tissue is used for protoplast isolation by enzymatic digestionin a mixture containing Lysing enzyme 2% and Cellulase R10 2% in 0.6 M mannitol. The incubation conditions like temperature, shaking and time were standardized at 24ºC, 60 rpm and 10 hours, respectively for healthy protoplasts liberation. The purified protoplasts showed an average yield of 1.2 × 10⁷ cells/gm tissue with 31.60 ± 9.31% regeneration efficiency on specific medium and 77.12 ± 2.72% viability by FDA test. Four ISSR primers were used in this study resulting a total of 27 reproducible bands with mean value of 6.75. They showed similar banding pattern in all the lines with zero percent polymorphism ranged from 280 bp–2700 bp. The amplified rRNA-ITS gene showed ~600 bp size in gel and found a single restriction site for enzyme HaeIII in all the protoclones and parent with similar fragment size in all.

S. aureus is an alarming human pathogen since it triggers numerous diseases, including impetigo and pneumonia. The S. aureus' ability to colonise the upper respiratory tract and other tissues, such as the skin, throat and gut, operate as reservoirs for infection. Indeed, being a carrier of S. aureus in the gut represents a risk factor for developing infection in distinct sites, including an unusual gastrointestinal tract disease. Here, we present an atypical clinical course of staphylococcal enterocolitis (SEC) in a man in his early seventies. After an unforeseen identification of methicillin-resistant Staphylococcus aureus (MRSA), the oral administration of vancomycin was critical in the outcome of the case. Although infrequent, SEC is an underestimated disease and requires a chapter in the treatment recommendations for antibiotic-related diarrhoea. Awareness of the risk factors and diagnostic tests, along with including SEC in algorithms for handling antibiotic-associated diarrhoea, is a step towards new epidemiological information.

This paper presents for the first time the design of a microwave sensing setup for the potential monitoring and identification of red palm weevil (RPW) gender type. The microwave sensor consists of a planar two-port transmission line (TL) with a single complementary split-ring resonant (CSRR) inclusion etched from the bottom metallic layer. The CSRR sensor is placed on top of a customized non-conductive container. The microwave sensing setup has been designed, numerically demonstrated, fabricated and tested experimentally. Simulated results correlate quite well with the experimental data. Moreover, the sensitivity of the CSRR sensor when in close proximity to different RPW gender has been evaluated both numerically and experimentally. Based on the measured results from 15 RPW collected samples with different body sizes, different RPW gender types showed unique microwave signatures. Notable shift to the sensor's resonance frequency has been achieved, where on average a resonant frequency shift of 10% for adult RPWs was achieved, while 2.4% frequency change was obtained for larvae (young) RPWs. Hence, the proposed microwave sensing setup can be adopted in field trials to examine and differentiate between various RPW genders at various development stages.

Increase demand for palm oil production has indirectly increased waste and pollution. Empty fruit bunch (EFB), which is the major solid waste from this industry, has the potential to be further treated into valuable product. In this study, cellulose will be extracted from EFB through alkali treatment and acid hydrolysis treatment with a different approach and further modified via acetylation and silylation technique. The modified samples are to be utilized to reduce pollution due to palm oil mill effluent (POME) and carbon dioxide (CO2) emission from the industry. The characterization of the extracted and modified cellulose was carried out using attenuated total reflectance-Fourier transform infrared (ATR-FTIR), thermogravimetric analysis (TGA) and scanning electron microscope (SEM). ATR-FTIR analysis revealed that the cellulose was successfully extracted from raw EFB and the cellulose-acetyl, nanocrystalline cellulose (NCC) and cellulose-2 has been successfully modified from the cellulose. TGA analysis shows that both modified cellulose have higher thermal stability compared to raw EFB and extracted cellulose. SEM morphology of the modified cellulose shows a higher surface area due to the wrinkled formation while the wax layer and cuticle pore has been diminished clearly. The modified sample gave a significant performance where cellulose-acetyl absorbed 98.5% of oil compared to unmodified cellulose-1 sample that only absorbed 5% of oil from POME. NCC-AEAPDMS adsorbed physically and chemically 3.5 cm3/g CO2 gas compared to NCC sample, which undergoes only physical adsorption with maximum capacity up to 2.4 cm3/g. Thus, modification can enhanced the performance of cellulose for industrial applications.

For the in-house validation of a droplet digital PCR method, a factorial experimental design was implemented. This design serves different purposes. On the one hand, it is an efficient design in relation to the workload involved in achieving a desirable level of reliability of variance estimates. On the other hand, it allows a partitioning of total variance into different components, thus providing information regarding the dominant sources of random variation. The statistical modelling reflects the actual measurement mechanism, establishing relationships between nominal target DNA copies per well, the range of variation of copy numbers per droplet, probability of detection values, and estimated numbers of copies.

The novel COVID-19 pandemic prompted an unprecedented Institutional reaction to aggregate existing capacity from silos of research laboratories to establish a multidisciplinary research laboratory for COVID19 testing. In less than two weeks, resources were mobilized from the community to strengthen public health response and epidemic control. Such strengthening of institutional research capacity to support public health response contributes to a natural knowledge transfer, facilitates collaboration, and generates new frontiers for knowledge production that should ultimately lead to professional development and retention of skilled human resources. This report describes the pre-established mechanisms and involvement of the authors that made it possible to set-up a multidisciplinary laboratory in a remarkably short period of time. We also discuss the opportunities and sustainability of multidisciplinary laboratory research post-COVID19. Existing institutional capacity can be repurposed to establish multidisciplinary research laboratories to support the strengthening of basic and clinical translational research capacity in resource limited settings and impact on public health and scientific knowledge for socioeconomic development.

This study determines the management of downstream oil palm development in the technopolitan areas of Pelalawan Regency. The study object was analyzed qualitatively in stages, including the development, potential, and management of downstream oil palm. The results show that the downstream oil palm facilitates the development of various ideas, innovations, and knowledge from the use of products with high selling value. This supports the government, academia, business, and society in implementing Good Agricultural Practice (GAP). The downstream oil palm development in Pelalawan Regency is managed in an integrated, competitive, and sustainable manner. This allows all stakeholders and society (independent smallholders) to receive economic, social, and environmental benefits.

Photosynthetic activities of the sago palm (Metroxylon sagu Rottb.) were studied to find out its sensitivity to changes in ambient air temperature. The minimum ambient air temperature designed for the experiment was 25–29⁰C, while the higher end was 29–33⁰C. Several photosynthetic parameters were studied to support our analysis in sago photosynthetic activity, including diurnal leaf gas exchange, assimilation rate vs. CO₂ concentration, leaf greenness, leaf chlorophyll content, and photosynthetic rate vs. irradiance. We found that sago palm photosynthetic activity tends to be more sensitive to minimum than to maximum ambient air temperature. The plants exposed to higher air temperatures had dark green leaf color associated with higher rates of diurnal photosynthesis, chlorophyll content, and rubisco limited photosynthetic activity. They also exhibited higher trend in optimum irradiance absorption level. Consequently, maximum light energy dissipation occurred at higher temperatures.

Early onset neonatal sepsis is a significant contributor to neonatal morbidity and mortality. Although blood cultures remain the diagnostic gold standard, they detect pathogens in only a minority of suspected cases. This study compared the accuracy of blood cultures with a rapid multiplex PCR test. Newborns at risk for neonatal sepsis were prospectively screened as recommended per national guidelines. Evaluations included laboratory parameters (CrP, IL6, differential blood count), blood culture, and a molecular multiplex PCR test (ROCHE LightCycler SeptiFast) identifying 20 common microbial agents. Blood samples were taken simultaneously from umbilical cord or venous sources on the first day of life. Of 229 infants included, 69% were born preterm. Blood culture and multiplex PCR sensitivity were 7.4% and 11.1% respectively. Specificity, negative and positive predictive values between methods showed no significant variance, though multiplex PCR had more false positives due to contamination. The limited sensitivity of blood cultures for early onset neonatal sepsis is concerning. Despite quicker results, multiplex PCR does not enhance diagnostic accuracy or antibiotic therapy guidance, thus it can not be recommended for this indication.

In many parts of the Asia, particularly in the arid regions of the middle east the date palm i.e. Phoneix dactylifera L. is considered a significant plant both culturally and economically. Over the past decade numerous biotechnological tools have been applied to revolutionize the date palm research and its cultivation process. In this comprehensive review ,we provided the in depth overview of the cutting edge developments in the date palm biotechnology, mentioning the important areas such as genomics, genetic engineering, in vitro propagation, omics technologies, and the integration of the artificial intelligence and machine learning (AI-ML).Due to these advancements ,in the date palm production how the date palm production lead the production of superior date palm cultivars with the improved yield ,fruit quality and resilience to biotic and abiotic stresses. Also it explores the application of the biotech tools in the enhancing pest and disease management strategies, increasing date palm productivity and developing the date palm based bio-factories for the production of high value compounds. This review highlights the current challenges faced by the date palm industries ,including the limited water resources ,genetic erosion , pests and disease and the need for improved postharvest handling and processing. It examines how these tools coupled with AI-based approaches can be leveraged to address these challenges and ensure the long term sustainability of date palm cultivation.

Red palm weevils (RPWs) are a major pest to coconut and palm trees, causing significant economic losses in many countries. The current control method involves using insecticides, which are unsustainable and environmentally damaging. Thus, it is necessary to develop an eco-friendly and sustainable approach to mitigate the RPW problem. Our studies have revealed that feeding RPWs with food containing specific herbs can affect the weevils' mutualistic relationship with gut microbiota or their growth hormones, resulting in a notable reduction in the metamorphosis rate at the pupation stage. For instance, the addition of Kra-jeab (a roselle Hibiscus sabdariffa) and Kra-pao (a holy basil Ocimum tenuiflorum) led to a reduction of 76.7% and 75.6%, respectively, in the metamorphosis rate, while combining the two herbs resulted in a higher reduction rate of 86.7%. In addition to these findings, altering their pupation nature by reducing the fiber length used in RPW feed to less than 1 centimeter can stop the weevil’s pupation entirely. These findings demonstrate the potential application of biological and physical factors to reduce RPWs' metamorphosis rate and control their destructive impact on palm industries, thus providing a promising solution for the conflict between palm and insect farmers.

Verification of inclusivity of molecular detection methods gives indications on the reliability of viral infections diagnosis because of the tendency of viral pathogens to undergo sequence variation. This study was aimed to select inclusive probe based reverse transcription quantitative PCR (RT-qPCR) assays for the diagnosis of the most widespread and detrimental viruses infecting honeybees, namely the acute bee paralysis virus (ABPV), the black queen cell virus (BQCV), the chronic paralysis bee virus (CBPV), the deformed wing virus variants A (DWVA) and B (DWVB), and the sacbrood virus (SBV). Therefore, detection methods previously described were re-evaluated in silico for specificity and inclusivity. Based on this evaluation, selected methods were modified or new ones were designed and tested in duplex RT-qPCR reactions. The limits of detection (LODs), effect of multiplexing on sensitivity and viral RNA quantification potential in bees and hive debris were assessed. This study made available diagnostic assays able to detect an increased number of virus variants compared to previously described tests and two viral pathogens in a single PCR reaction.

It is important to be able to detect and differentiate between distinct porcine enteric coronaviruses that can cause similar diseases. However, the existence of naturally occurring recombinant coronaviruses such as swine enteric coronavirus (SeCoV) can give misleading results with currently used diagnostic methods. Therefore, we have developed and validated three duplex real-time quantitative RT-PCR assays for the simultaneous detection of, and differentiation between, porcine epidemic diarrhea virus (PEDV) and SeCoV. Transmissible gastroenteritis virus (TGEV) is also detected by two out of these three assays. In addition, a novel triplex assay was set up that was able to detect and differentiate between these alphacoronaviruses and the porcine deltacoronavirus (PDCoV). The validated assays have low limits of detection, close to 100% efficiency and were able to correctly identify the presence of PEDV and SeCoV in 55 field samples, while 20 samples of other pathogens did not give a positive result. Implementing one or more of these multiplex assays into the routine diagnostic surveillance for PEDV will ensure that the presence of SeCoV, TGEV and PDCoV will not go unnoticed.

A brown seaweed consumed worldwide, Fucus vesiculosus, has been used to prevent atherosclerosis and hypercholesterolemia, among other uses, however, the mechanisms of action that lead to these effects are not yet fully understood. An F. vesiculosus aqueous extract, prepared as a soup was characterized as rich in sev-eral bioactive compounds, mainly phlorotannin and peptides. This work aims to study the in vitro effect of this extract on the expression of different proteins involved in the synthesis and transport of cholesterol in HepG2 cells, though a proteomic analysis, western blot and qRT-PCR. The results demonstrated that, in liver cells, the extract decreases the expression of 4 proteins involved in cholesterol biosynthesis process and also decrease the expression of two important transporters proteins of cholesterol, NPC1L1 and ABCG5, as well as decrease the NPC1L1 mRNA levels. Our study demonstrates some mechanisms of action of bioactive com-pounds from F. vesiculosus that may explain its previously reported hypocholesterolemic effect.

Background and Objectives: Most individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are asymptomatic or have mild symptoms of COVID-19, which usually resolve after few days. Regardless of symptoms, infected people can transmit the virus to others especially on the first days of infection. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) is used to confirm SARS-CoV-2 infection; some individuals show persistent PCR-positivity after recovering from COVID-19. In this study, 12 individuals who showed persistence of COVID-19 symptoms and of SARS-CoV-2 PCR-positivity were followed-up. Methods: nasopharyngeal samples were collected for SARS-CoV-2 detection by RT-qPCR; clinical and epidemiological data were analyzed. Results: that persistence of SARS-CoV-2 PCR positivity was associated with duration of symptoms (r_s 0.81338), which varied between one and 49 days, with 75% of the individuals reporting symptoms for more than two weeks; 83.33% of cases remained positive after two weeks of onset of symptoms, despite decreases in viral load. Conclusion: neither RT-qPCR test nor a symptom-based approach alone are sufficient to evaluate discontinuation of patient isolation; other factors such as viral loads and symptom severity should also be considered. Additional studies are needed to understand how RT-PCR-positivity is related to symptoms and the risk of viral transmission, and to better support isolation guidelines.

Abstract: The effect of some weather parameters (rainfall and temperature) on the production of oil palm in Peninsular Malaysia was investigated. Data were analysed using the Statistical Package for Social Sciences (SPSS 20.0 version), with descriptive statistics, time series analysis, and multiple linear regression (MLR) carried out. SPSS and Microsoft Excel 2010 were used to analyse the results. The MLR model determined the strength of the relationship between oil palm yield (dependent variable) and the changing variables of temperature and rainfall (independent variables). The regression output returned three components; regression coefficients, regression statistics and ANOVA. The findings of the study revealed medium to high rainfall variability at the rate of 0.0008. This implies that rainfall is increasing over time with variations in its amount and intensity. As rainfall increases oil palm FFB production is predicted to increase at a slow rate of 0.0009. The estimation of average annual temperature indicated an increase of 5.6℃ at the rate of 0.0357℃ per year with a temperature maximum of 32.01℃ and minimum of 25.45℃. The result also revealed an increase in oil palm yield at the rate of 0.2581 per year with a mean value of 176247.6. Overall, there is a significant difference in the impact of rainfall and temperature on oil palm yield. This signifies that rainfall has a significant impact on oil palm yield (FFB) compared to temperature.

Ubiquitin-specific protease 14 (USP14) is a member of the Deubiquitinating enzymes (DUBs) involved in disrupting the regulation of the ubiquitin-proteasome system, responsible for the degradation of impaired and misfolded proteins which is an essential mechanism in eukaryotic cells. The involvement of USP14 in cancer progression and neurodegenerative disorders has been reported. Thereof USP14 is a prime therapeutic target; hence, designing efficacious inhibitors of USP14 is central in curbing these conditions. Herein, we relied on structural bioinformatics methods incorporating molecular docking, Molecular Mechanics Generalized Born Surface Area (MM-GBSA), Molecular dynamics simulation (MD simulation) and ADME to identify potential allosteric USP14 inhibitors. A library of over 733 compounds from the PubChem repository with >90% match to the IU1 chemical structure was screened in a multi-step framework to attain prospective drug-like inhibitors. Two potential lead compounds (CID 43013232 and CID 112370349) were shown to record better binding affinity compared to IU1, but with subtle difference to IU1-47, a 10-fold potent compound when compared to IU1. The stability of the lead molecules complexed with USP14 was studied via MD simulations. The molecules were found to be stable within the binding site throughout the 50ns simulation time. Moreover, the protein-ligand interactions across the simulation run time suggest Phe331, Tyr476, and Gln197 as crucial residues for USP14 inhibition. Furthermore, in silico pharmacological evaluation revealed the lead compounds as pharmacological sound molecules. Overall, the methods deployed in this study revealed two novel candidates that may show selective inhibitory activity against USP14, which could be exploited to produce potent and harmless USP14 inhibitors.

In recent years, many studies have reported that several distinct families of transcription factor (TF) genes play crucial roles in the response of plants to abiotic stress. Although some of these families got systematically studied in many species, little knowledge exists about these genes in oil palm (Elaeis guineensis Jacq.). In this study, 20 genes differentially expressed in the leaves of oil palm plants subjected to salinity or drought stress and encoding TFs belonging to four families of TFs - MYB, HD-ZIP, NF-Y, and HSFF - got selected for further characterization. The genes underwent a structural and functional annotation, besides having their RNA-Seq expression profile validated by the qPCR technique, and a correlation analysis of their response under both stresses got performed. The annotation analysis of the promoter region showed the presence of seven cis-acting elements, all already reported to be involved in plants' response to abiotic stress. The structural and functional characterization of the proteins encoded by the selected genes showed that some groups present patterns of conserved regions and are orthologs to genes already linked to salinity or drought resistance in other plant species. It was possible to confirm the RNA-Seq expression profile of 19 genes, only gene 4 showed the opposite response when using qPCR. Through correlation analysis, it was possible to observe a high level of similarity in the behavior of the 20 genes in response to drought or salinity stress, a behavior already reported in other species. The results presented here shed light on the role of 20 TFs in the leaves of young oil palm plants under severe levels of soil salinity or water deprivation. The high level of similarity in the molecular response to both stresses allowed the identification of genes that might grant strategies aiming to develop oil palm plants with a tolerance to both salinity and drought at once.

The effects of octadecylamide of alginic acid (amidated alginate) and tetrahydrolipstatin on serum and hepatic cholesterol, and the faecal output of fat and sterols were compared in rats. Amidated alginate is a sorbent of lipids, tetrahydrolipstatin is inhibitor of pancreatic lipase. Rats were fed diets containing cholesterol and palm fat at 10 and 70 g/kg, respectively. Palm fat was provided by coconut meal. Amidated alginate at 40 g/kg diet significantly decreased serum total cholesterol, LDL and hepatic cholesterol, hepatic lipids, and increased faecal output of fat and coprostanol. Tetrahydrolipstatin at 300 mg/kg diet significantly decreased LDL cholesterol, hepatic lipids and increased faecal output of fat. The intake of feed was not significantly influenced, however the weight gains in rats fed amidated alginate was lower than in rats of the control group. Both amidated alginate and tetrahydrolipstatin modified fatty acid profile in excreta lipids. Concentrations of saturated fatty acids were decreased and that of unsaturated fatty acids were increased. Despite different mode of action, amidated alginate and tetrahydrolipstatin were equally efficient in the removing dietary fat from the body.

The quantification of human DNA extracts from forensic samples plays a key role in the forensic genetics process. Quantification guarantees maximum efficiency and avoids repeated analyses, over amplified samples, or unnecessary examinations. Here, we present our experience using an extremely sensitive real-time-based method with the Quantifiler® Trio DNA quantification kit, which we have explored in the ISO/IEC17025 accredited test validation process conducted in our laboratory. In this study, our focus was on establishing a minimum threshold beyond which DNA typing is unnecessary, by defining the correlation of negative quantification results with the absence of genetic profiles resulting from DNA typing. We investigated the results in the range in which the technique is used (50-0.005 ng/μl). In the validation process of the internally accredited method, we used data from the commercial quantification system, based on the average values of the standard curve using a wide range of samples, including artificially degraded samples. This method was extensively used continuously for nine years to quantify the DNA extract coming from a wide range of samples from criminal cases. The validation allowed us to verify the limits of the technique, especially in the use of the minimum quantities necessary to obtain genetic profiles acceptable for sending to the Italian DNA database. This optimization of the protocol for analysing forensic samples allows us to optimise the protocol for analysing forensic samples. However, the technique is used in our laboratory with a completely manual preparative phase, and we have decided to investigate the contribution of human error more accurately. Thus, in our experience, we have found that it is preferable to use quantification ranges rather than exact limits before deciding how to analyse the extracts via PCR. In addition, here we present some preliminary data related to the analysis of certain samples that initially appeared negative during quantification, applying a concentration method for maximum yield from forensic samples of judicial interest. Our aim is to ensure that no source of evidence is lost in the reconstruction of a criminal event.

Klebsiella pneumonia (K. pneumoniae) is a Gram-negative bacterium that causes nosocomial infections in the lung, bloodstream, and urinary tract. Therefore, detecting K. pneumoniae in early time is important in preventing severe infections. However, clinical detection of K. pneumoniae requires a long time of agar plate culture. Nucleic acid detection like qPCR is precise but requires expensive equipment. Recent research reveals that collateral cleavage activity of CRISPR-LbCas12a has been applied in nucleic acid detection. In this study, PCR combined with CRISPR-LbCas12a targeting the K. pneumoniae system was established. This system showed excellent detection specificity and sensitivity in both bench work and clinical samples. Due to its advantages, its application can meet different detection requirements in health centers where qPCR is not accessible.

Numerous protocols have been published for extracting DNA from phlebotomines. Nevertheless, their small size is generally an issue in terms of yield, efficiency, and purity, for large-scale individual sand fly DNA extractions when using traditional methods. Even though this can be circumvented with commercial kits, these are generally cost-prohibitive for developing countries. We encountered these limitations when analysing parasite infection in Lutzomyia spp. by PCR [1] and, for this reason, we evaluated various modifications on a previously published protocol ([2] and Acardi personal communication). The most significant variation was the use of a different lysis buffer [3] to which added Ca2+ (buffer TESCa), because this ion protects proteinase K against autolysis, increases its thermal stability, and could have a regulatory function for its substrate-binding site [4]. Individual sand fly DNA extraction success was confirmed by amplification reactions using internal control primers that amplify a fragment of the cacophony gene [5,6]. To the best of our knowledge, this is the first time a lysis buffer containing Ca2+ has been reported for the extraction of DNA from sand flies.

The Asian weaver ant (Oecophylla smaragdina) is a natural enemy, generalist predator of diverse major pest species (i.e. the highly destructive oriental fruit fly Bactrocera dorsalis) in economically strategic agricultural landscapes in Australia and Southeast Asia countries. For effective implementation of the weaver ant for biological control of the invasive bagworms Metisa plana, the dominant pest in the oil palm plantation, its distribution was investigated in Malaysia. From 2018-2022, censuses were first carried out to record Oecophylla colonies presence. Oecophylla colonies’ occupation patterns were monitored on 8 selected plantations. To distinguish between brood and barracks nests, 26 captured nests were evaluated to define the main predictor variable for its practical visual identification. More than 11000 palms with 10821 nests for over 500 colonies were sampled in this study. Results showed that O. smaragdina colonies distribution pattern exhibited three-dimensional ubiquitous occupation dominance. We also found that by observing the colony’s dense population spatial arrangements, it demonstrates them as spreading by waves featuring interconnected irregular geometrical patches shaped for each colony. The height to the ground nest location in palm canopies was the significant visual discriminant factor between Brood and barrack nests. Moreover, polydomous arboreal nesting behavior occupation occurred irrespective of palms or associated host plants sizes (≥ 3 m), throughout the year. However, colony nesting behaviors were polydomous and monodomous on shorter plants (≥ 2 m), while being strictly monodomous on small plants (≤ 1.5 m). Colonies occupied an average 3 to 4 palms yearly beginning from the newly founding phase up to the stable mature phase (3 to 4 years). Furthermore, we found that matured stable colonies (3 ≥ age ≥13) occupied 10-12 palms on average, on 800 m² to 2500 m² area delimited by a minimum average 20 m² of “no ants land” zone between each colony. Our results suggest that a sustained agriculture system in this area would be possible with the presence of matured colonies nests exploitation which could provide an efficient biological control ecosystem service.

The Herpotrichiellaceae family is an important group of dematiaceous filamentous fungi, associated with a variety of pathogenic fungal species causing Chromoblastomycosis (CBM) and Phaeohyphomycosis (PHM), both with polymorphic clinical manifestations and worldwide incidence. Currently, the identification of this family and determination of the causative agent is challenging due to the subjectivity of morphological identification methods, necessitating the use of molecular techniques to complement diagnosis. In this context, genetic sequencing of the Internal Transcribed Spacer (ITS) has become the norm due to a lack of alternative molecular tools for identifying these agents. Therefore, this study aimed to develop PCR-Multiplex methodologies to address this gap. Sequences from the ITS and Large subunit (LSU) of ribosomal DNA were used, and after manual curation and in vitro analyses, primers were synthesized for the identification of the aforementioned targets. The primers were optimized and validated in vitro, resulting in two PCR-Multiplex methodologies: one for identifying the Herpotrichiellaceae family and the bantiana clade, and another for determining the species Fonsecaea pedrosoi and Fonsecaea monophora. Ultimately, the assays developed in this study aim to complement other identification approaches for these agents, reducing the need for sequencing, improving the management of these infections, and enhancing the accuracy of epidemiological information.

Respiratory tract infections (RTIs) are one of the main causes of hospitalization and mortality causing substantial economic burden to healthcare systems globally. As opposed to the previous belief that respiratory infections are caused by a single pathogen, studies have shown that most RTIs are a result of a combination of bacterial and/or viral pathogens infecting the host. The clinical manifestation of RTIs is very similar (i.e., syndrome), often showing Influenza-like illness (ILI) symptoms. While COVID-19 has dominated ILI over the past few years, there are many other pathogens that are responsible for ILI. In addition, it is not uncommon to have coinfections with multiple pathogens in patients presenting with ILI and that such coinfections can even exacerbate the disease severity of RTIs. Therefore, an insight into coinfections can help with accurate disease prognosis, patient care management and outcomes. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI.

Accurate and timely testing has become an essential measure in combatting the COVID-19 global pandemic. Currently, polymerase chain reaction (PCR) based assays are the most relied on methods for SARS-CoV-2 detection. This traditional workflow involves a viral RNA extraction from the viral transport media storing nasopharyngeal swabs collected from patients, followed by PCR based detection. While accurate, this methodology is time consuming and resource heavy, causing for delays in receiving results or limited access to testing. Herein, we demonstrate a validated method for SARS-CoV-2 detection from viral transport media using a two-step, direct-to-PCR workflow revolving around shaker-mill homogenization. This method completely bypasses the extraction steps of the traditional workflow, replacing it with 30 seconds of mechanical disruption sufficient to allow for COVID-19 detection with a 96.43% sensitivity and 100% specificity when compared to traditional extraction to PCR based methods.

Mosquitoes genus Aedes are the most important arthropod disease vector. Dengue Virus (DENV) and Chikungunya Virus (CHIKV) are the main arboviruses distributed in the world. Based on entomo-virological surveillance, appropriating public health strategies can be addressed to contain cases and control outbreaks. This study aims to show the potential performance of two new molecular methods for detecting DENV serotypes and CHIKV in mosquitoes. Mosquitoes were collected in urban areas and sylvatic areas between July to August 2023, DENV and CHIKV were screened using new multiplex RT-PCR and RT-q PCR. A total of 2150 mosquitoes were trapped including 976 Aedes (959 Ae. egypti, 6 Ae. furcifer and 11 Ae. Vittatus) and 1174 Culex from 39 pools of a maximum of 30 mosquitoes each, tested by molecular screening, 7.7% (3/39) were positive for DENV, DENV-1 was detected in one pool (1/3), and DENV-3 in two pools (2/3). All the pools were negative for CHIKV. The overall minimum infection rate (MIR) of DENV in this study was 3.07 (95% CI: 2.24 —19.86). This study shows the usefulness of our new molecular tools in DENV serotypes and CHIKV surveillance.

Palm oil production involves unit operations that lead to greenhouse gas emissions. A typical mill is estimated to produce greenhouse gas emissions of 637–1,131 kg CO2 eq/t crude palm oil. There has been a huge effort to reduce the carbon footprint of palm oil mills. However, the data from such research have not been consolidated. This paper reviews significant information, results, and conclusions derived from studies in the literature. The latest developments in palm oil milling operations and information on greenhouse gas emissions are presented. Current initiatives in reducing carbon footprint of palm oil mills are discussed along with an assessment of the technologies employed. These include the conventional method of capturing biogas from palm oil mill effluent and emerging approaches such as converting palm sludge oil into biodiesel, deploying enzyme-assisted oil extraction, and converting biomass into fuel for energy generation as an alternative to coal and other fossil fuels. The importance of self-sufficiency is deliberated because a self-sufficient palm oil mill is estimated to reduce emissions by 457 kg CO2 eq/t crude palm oil compared to a mill that requires an external power supply. Methods with the greatest positive effect on the carbon footprint are identified for further investigation.

Oil palm is one of the most important crops in Malaysia. Lately, the production of oil palm has been reduced due to a variety of factors, including the weather and climate. Temperature, wind speed, relative humidity, sunshine, and rainfall distribution all have an impact on palm tree growth and development, which in turn has an impact on oil palm production. This paper aims to investigate the effects of some weather elements (temperature, wind speed, relative humidity, sunshine, and rainfall) on oil palm production in Peninsular Malaysia. Data were analyzed using the Statistical Package for Social Sciences (SPSS 20.0 version), with descriptive statistics, and multiple linear regression (MLR). The MLR model determined the strength of the relationship between oil palm yield (dependent variable) and the changing variables of temperature, sunshine, wind speed, relative humidity, and rainfall (independent variables). The findings revealed that temperature, wind speed, relative humidity, sunshine, and rainfall have a low impact on oil palm production and yield turnover. The R2 value of 0.202 shows that the independent variables explained only 20.2% of the fluctuation in palm oil production. The study recommends working within an integrated approach involving scientific research, planting, improving variety, improving regional academic leadership, and engaging private and public stakeholders, emphasized collaborative efforts with researchers in consumer countries, and strengthening the capacity of growers to best agroecological practices.

Accurately mapping individual tree species in densely forested environments is crucial to forest inventory. When considering only RGB images, this is a challenging task for many automatic photogrammetry processes. The main reason for that is the spectral similarity between species in RGB scenes, which can be a hindrance for most automatic methods. State-of-the-art deep learning methods could be capable of identifying tree species with an attractive cost, accuracy, and computational load in RGB images. This paper presents a deep learning-based approach to detect an important multi-use species of palm trees (Mauritia flexuosa; i.e., Buriti) on aerial RGB imagery. In South-America, this palm tree is essential for many indigenous and local communities because of its characteristics. The species is also a valuable indicator of water resources, which comes as a benefit for mapping its location. The method is based on a Convolutional Neural Network (CNN) to identify and geolocate singular tree species in a high-complexity forest environment, and considers the likelihood of every pixel in the image to be recognized as a possible tree by implementing a confidence map feature extraction. This study compares the performance of the proposed method against state-of-the-art object detection networks. For this, images from a dataset composed of 1,394 airborne scenes, where 5,334 palm-trees were manually labeled, were used. The results returned a mean absolute error (MAE) of 0.75 trees and an F1-measure of 86.9%. These results are better than both Faster R-CNN and RetinaNet considering equal experiment conditions. The proposed network provided fast solutions to detect the palm trees, with a delivered image detection of 0.073 seconds and a standard deviation of 0.002 using the GPU. In conclusion, the method presented is efficient to deal with a high-density forest scenario and can accurately map the location of single species like the M flexuosa palm tree and may be useful for future frameworks.

In the current era of ‘big data’, scientists are able to quickly amass enormous amount of data in a limited number of experiments. The investigators then try to hypothesize about the root cause based on the observed trends for the predictors and the response variable. This involves identifying the discriminatory predictors that are most responsible for explaining variation in the response variable. In the current work, we investigated three related multivariate techniques: Principal Component Regression (PCR), Partial Least Squares or Projections to Latent Structures (PLS), and Orthogonal Partial Least Squares (OPLS). To perform a comparative analysis, we used a publicly available dataset for Parkinson’ disease patien ts. We first performed the analysis using a cross-validated number of principal components for the aforementioned techniques. Our results demonstrated that PLS and OPLS were better suited than PCR for identifying the discriminatory predictors. Since the X data did not exhibit a strong correlation, we also performed Multiple Linear Regression (MLR) on the dataset. A comparison of the top five discriminatory predictors identified by the four techniques showed a substantial overlap between the results obtained by PLS, OPLS, and MLR, and the three techniques exhibited a significant divergence from the variables identified by PCR. A further investigation of the data revealed that PCR could be used to identify the discriminatory variables successfully if the number of principal components in the regression model were increased. In summary, we recommend using PLS or OPLS for hypothesis generation and systemizing the selection process for principal components when using PCR.rewordexplain later why MLR can be used on a dataset with no correlation

During the extraction of palm oil by smallholders in Cameroon, the use of enormous quantities of water results in palm oil mill effluent (POME), which contains substances that are deleterious to the environment at concentrations above the threshold values. A detailed description of the various processes involved is imperative so as to develop methods of reducing loss and minimising the environmental effect caused by the wastes produced. In this study, we characterise the small-holders’ palm oil production sector in Cameroon, along its entire production chain. The main demographics of smallholder farmers are adult males (64.4%) and married (46.7%) with low levels of formal education (51.1% attained only primary education). Plantation establishment involves deforestation of pristine vegetation (46.7%) as well as replacing other farming systems. Processing is carried out by the farmers with their own mills (48.9%) bought at exorbitant prices. Access to finances (51.1%) remains a key limitation to plantation expansion and the adoption of innovations in this sector. Workers’ health issues abound (75.6%) and are treated mainly using ethnomedicine (31.1%), and there is little or no social security; thus, sick workers generally pay their own bills (64.4%). Issues of environmental pollution from production to waste processing abound with solid waste mainly burnt (57.8%) and POME directed into open pits and streams (37.8%) where they become a nuisance and serve as breeding grounds for mosquitoes (51.1%); these issues will require greater state involvement for mitigation. Our findings suggest that farmers in the palm oil sector have deep knowledge base and competence, but government intervention are needed to stimulate further growth in this important sector.

During the recent pandemics of COVID-19, sequencing technics became powerful tool for gaining information about the SARS-CoV-2 virus and using this knowledge in our advantage. Thanks to this advantage, scientists over the world were able to search for emerging variations, watching the virus evolving in real time. Assembly of the virus genomes is crucial part of getting this kind of useful information. In our study, we sequenced 79 samples from nasopharyngeal swabs of COVID-19 patients. Positivity on disease was evaluated by qRT-PCR. By studying assembly success rate, we noticed, that Ct-value of qRT-PCR can predict success of genome assembly and SARS-CoV-2 lineage assignment. In this work we described the relationship between Ct-value and further steps of genome construction and its assignment to specific viral strain.

Wastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence and/or prevalence and trends of coronavirus disease-19 (COVID-19). Surveillance of SARS-CoV-2 in wastewater may provide an early-warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is rapidly increasing. However, there are no standardized protocols nor harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors. Recommendations include, stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, amplification inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly during a low incidence of SARS-CoV-2 in wastewater. Corrective and confirmatory actions must be in place for inconclusive and/or potentially significant results (e.g., initial onset or reemergence of COVID-19 in a community). It will also be prudent to perform inter-laboratory comparisons to ensure results are reliable and interpretable for ongoing and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance was demonstrated during this global crisis. In the future, wastewater will play an important role in the surveillance of a range of other communicable diseases.

Ganoderma boninense is the major causal agent for the basal stem rot (BSR) disease in oil palm, causing the progressive rot of the basal part of the stem. Despite its prominence, key pathogenicity determinants for the aggressive nature of hemibiotrophic infection remain unknown. In this study, genome sequencing and annotation of G. boninense T10 were carried out using the Illumina sequencing platform and comparative genome analysis was performed with previously reported G. boninense strains (NJ3 and G3). The pan-secretome of G. boninense was constructed and comprised of 937 core orthogroups, 243 accessory orthogroups, and 84 strain-specific orthogroups. A set of core candidate effector proteins (CEPs) were found to be enriched with catalytic protein classified as the carbohydrate-active enzymes, hydrolases as well as non-catalytic proteins. Differential expression analysis revealed an upregulation of CEP genes which was linked to the suppression of PTI signaling cascade while the downregulation of CEP genes was linked to the inhibition of PTI by preventing host defense elicitation. Genome architecture analysis revealed the one-speed architecture of the G. boninense genome and the lack of preferential association of CEP genes to the transposable elements. The findings obtained from this study would aid in the characterization of pathogenicity determinants and molecular biomarkers of BSR disease.

Agricultural wastes have posed as a treat to the environment over the years and they are found in large quantities due to domestic and industrial utilization of such materials in under developed and developing countries. The inability to recycle this waste has led to researches on how to use them in carrying out productive industrial activities. The aim of this study is to use Central Composite Design (CCD) to optimize the bleaching effects by snail shell as adsorbents on crude palm oil. The predictive ability of the model was close to accurate using MINITAB 19 software with the design application for the process simulation for % FFA yield to have 75.856% for experimental and 77.587% for predicted yield with just 1.731% residual. The saponification value increased with adsorption, and it indicates that palm oil can be used for soap making.

As the traditional sand fixation measures have many limitations, new sand fixing technologies and methods are urgently needed to be developed. This study demonstrated a new sand fixation method using palm mat geotextile to fix the sand dunes and plant grass. We experimented the physical property of the palm mat geotextile in the laboratory, and observed the vegetation growth in the Hobq Desert. The results showed that (1) The palm mat geotextile is more lighter and tougher than the common straw mat geotextile, the average weight, thickness and tensile strength of palm mat geotextile were 2023 g/m², 20.14 mm, and 842–860 N/m, after a year of field observation, the tensile strength decreased by only 2%. (2) The palm mat geotextile had excellent water retention capacity and scouring resistance, the maximum water content reached 227%, and the substrate lost 2.9% after the simulation of heavy rainfall for 3 hours with rainfall intensity of 30 mm/h in laboratory. (3) The palm mat geotextile significantly decreased the soil temperature and increase the humidity in summer, the observed results shown that the palm mat geotextile had the greatest influence on 5cm depth of the soil temperature and 10cm depth of soil humidity. (4) The field experiment results showed that the vegetation coverage and the biomass of the palm mat geotextile with 2 m × 2 m were 35% and 11.21 g (3.9 times and 4.1 times than that of control group, 1.7 times and 1.8 times than that of high-banded salix psammophila sand-barriers group which is widely used in the Hobq Desert).

The viral nervous necrosis virus (VNNV) is the causative agent of an important disease affecting fish species cultured worldwide. Early and accurate diagnosis is at present the most effective control and prevention tool, and the molecular techniques have been strongly introduced and accepted by official organizations. Among those, real time quantitative polymerase chain reaction (rt-qPCR) is nowadays displacing other molecular techniques. However, another PCR-based technology, the droplet digital PCR (ddPCR), is on the increase. It has many advantages over qPCR, such as higher sensitivity and more reliability of the quantification. Therefore, we decided to design and validate a protocol for diagnosis and quantification of SJ and RG type VNNV, using reverse transcription-ddPCR (RT-ddPCR). We obtained an extremely low limit of detection, 10 to 100-folds lower than with RT-qPCR. Quantification by RT-ddPCR, with a dynamic range of 6.8 – 6.8 x 104 (SJ type) or 1.04 x 101 – 1.04 x 105 (RG) cps/rctn, was more reliable than with RT-qPCR. The procedure was tested and validated in field samples, providing the high clinical sensitivity and negative predictive values. In conclusion, we propose this method to substitute RT-qPCR protocols because it exceeds the expectations of qPCR in the diagnosis and quantification of VNNV.

The co-circulation of duck hepatitis A virus subtypes 1 (DHAV-1) and 3 (DHAV-3) in ducklings has resulted in significant economic losses. Because ducklings infected with DHAV-1 or DHAV-3 show similar clinical signs and gross lesions, it is important to discriminate these subtypes as early as possible for better clinical management. On the basis of multiple alignments of the 5′-noncoding region sequences of strains DHAV-1 and DHAV-3, universal and type-specific primers were designed and synthesized. Using the primers in a one-tube reverse transcription-PCR (RT-PCR) assay, reference strains of DHAV-1 and DHAV-3 (isolated over a span of 60 years and covering many different countries) were successfully amplified, indicating that the primer sequences were completely conserved. The amplicon sequences results and the sizes of amplicons from reference DHAV-1 and DHAV-3 isolates correlated completely with their genotypes. Moreover, with this one-tube RT-PCR system, the amplicon sizes of liver samples of reference DHAV-1- or DHAV-3-infected birds matched perfectly with their respective genotypes, as determined by virus isolation and neutralization tests. No other RNA viruses of duck origin were detected with the synthesized primers. The sensitivity of viral RNA detection was 10 pg. With this system, 20% genotype 1, 45% genotype 3, and 9% co-infection of the two genotypes were detected in 55 clinical samples. This novel approach could be used for the rapid genotyping DHAV-1 and/or DHAV-3 infection in routine clinical surveillance or epidemiologic screening.

This study investigates the impact of temperature-induced quantum proton tunneling probability on DNA amplification during polymerase chain reactions (PCR). Using a simulation model based on a Gaussian wavefunction and finite-difference time-domain method, quantum tunneling of protons across square potential barriers is examined. The results unveil consistent probability distributions for quantum tunneling across various PCR temperatures, with distinct oscillation patterns emerging post-barrier crossing. Acknowledging limitations in initial conditions due to temperature-dependent proton energy, the study highlights the need for refined models and experimental validation. These findings accentuate the potential interplay between quantum mechanics and biological systems, prompting further research to understand quantum tunnelling’s comprehensive effect on genetic variations and molecular processes.

Polymerase chain reaction (PCR) technique is one of the molecular methods in amplifying DNA for the detection of malaria. However, the limitations of PCR especially when used for routine clinical practice can hamper its sensitivity and specificity. With that, this study focuses on designing a microfluidic device that will mimic the function of a conventional genus-specific PCR based on 18S rRNA gene to detect malaria parasites (Plasmodium falciparum) at low grade parasitemia. The design was drawn and simulated using ANSYS 14.5 Computational Fluid Dynamics (CFD). The simulation shows that adding loops to the design increases its relative deviation but to a minimal extent as compared to having only a straight path design, which indicates that looping is acceptable in designing a microfluidic device to minimize chip length. Also, increasing the cross-sectional area of the fluid path decreases the efficiency of the design, thus, the design with a relatively smaller cross-sectional area is favored. And lastly, among the three materials utilized, the chip made of polypropylene is the most efficient with a relative deviation of 0.94 as compared to polycarbonate and polydimethylsiloxane which have relative deviations of 2.78 and 1.92, respectively.

In Kawasaki disease (KD), convulsions are rare and mostly attributed to latent and coexisting encephalitis/encephalopathy due to KD itself. Therefore, we retrospectively investigated concomitant viral infections in patients with KD. Between January 2012 and December 2020, among 523 patients with KD, 7 (1.53%), 1 (0.19%), 6 and 1 (1.15% and 0.19%) were positive for adenovirus (AdV-Ag), respiratory syncytial virus (RSV-Ag), and influenza A or B (Flu A-Ag or Flu B-Ag) antigens, respectively. Among them, two were positive for both AdV-Ag and FluA-Ag. Seven patients with KD (1.3%) presented febrile convulsions, and only one was diagnosed with encephalitis/encephalopathy. Between January 2021 and August 2022, 57 patients with KD were newly diagnosed among whom FilmArray® respiratory panel (FARP) was applied on 24 patients, and 14 (58.3%) were positive for at least one virus. During the same period, 32 out of 45 patients (71.1%) with febrile convulsions examined using the FARP were positive for at least one virus. The trend of viruses in patients with KD and febrile convulsion reflected the regional epidemic viral infection. Respiratory virus detected at a much higher rate using the FARP suggests that most convulsions in patients with KD might be related to concomitant viral infection. The possible involvement and association of concomitant respiratory viral infections in patients with KD with prognosis or encephalopathy/encephalitis remain to be investigated.

The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase–DNA–dNTP complexes. The dUTPs were C5-modified with bulky functional groups (the Cy5 dye analogs) or lighter aromatic groups. Comparing the experimental data and the results of molecular modeling revealed the decrease of PCR efficiency in the presence of modified dUTPs with an increase in the number of non-covalent bonds between the substituents and the DNA polymerase (about 15% decrease per one extra non-covalent bond). Generalization of the revealed patterns to all the studied polymerases of the A and B families is discussed herein. The number of non-covalent bonds between the substituents and polymerase amino acid residues is proposed to be a potentially variable parameter for regulating enzyme activity.

Real-time fluorescent quantitative PCR (RT-qPCR) is the most classic and widely used technology for evaluating the expression level of target gene. In order to select the proper internal reference genes for RT-qPCR analysis in Amorphophallus konjac (Araceae), eight candidate internal reference genes, including 25S ribosomal RNA gene (25S rRNA), 18S ribosomal RNA gene (18S rRNA), actin gene (ACT), glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH), Ubiquitin gene (UBQ), β-tubulin gene (β-TUB), eukaryotic elongation factor 1-αgene(eEF-1α), and eukaryotic translation initiation factor 4α-1 gene (eIF-4α) were selected and tested the corresponding expression level in different tissues at different growing stages. The results showed that 25S rRNA, 18S rRNA, and ACT at the reproductive periods, eEF-1α and eIF-4α at the nutritional periods, and eEF-1α, UBQ, and ACT at different leaf developmental periods had a stable level of gene expression, respectively. These results might be useful for the study of gene function in A. konjac.

Both SARS-CoV-2 and SARS-CoV initially appeared in China and spread to other parts of the world. SARS-CoV-2 has generated a COVID-19 pandemic causing more than 6 million human deaths worldwide while the SARS outbreak quickly ended in six months with a global total of 774 reported deaths. One of the factors contributing to this stunning difference in the outcome between these two outbreaks is the inaccuracy of the RT-qPCR tests for SARS-CoV-2, which generated a large number of false-negative and false-positive test results that have misled patient management and public health policy-makers. This article presented Sanger sequencing evidence to show that the RT-PCR diagnostic protocol established in 2003 for SARS-CoV can in fact detect SARS-CoV-2 accurately due to the well-known nonspecific PCR amplification of DNAs with similar sequences. Using nested RT-PCR followed by Sanger sequencing to retest 50 patient samples collected in January, 2022 and sold as RT-qPCR positive reference confirmed 21 (42%) were false-positive. Although the other 29 positive isolates were categorized as Omicron variant by partial sequencing of the N gene, and the RBD and the NTD of the S gene, 9 (31%) showed focal to complete sequencing failure in the S gene segments due to multi-allelic SNPs. During the course of the study, an Omicron variant isolate containing a BA.1 NTD and a BA.2 RBD in its S gene was also detected. Routine partial S gene sequencing of all PCR-positive samples can timely discover multi-allelic SNPs and viral recombination in the circulating variants for investigation of their impacts on vaccine efficacies, therapeutics and diagnostics.

Indonesia has emerged as one of the leading producers and exporters of palm oil, as supported by data from the Central Bureau of Statistics in 2021, which indicate that Indonesian palm oil exports reached an impressive value of US$ 18.44 billion, or IDR 258 trillion, in 2020, marking an 18.43 percent growth compared to the previous year. Furthermore, the domestic market for palm oil and palm kernel oil remains substantial, despite improvements in export quantities. Various industries, including cooking oil refineries, specialty fats, shortening, margarine, bath soaps, and oleochemicals, present potential markets for palm oil (CPO) and palm kernel oil (PKO). The palm oil industry encompasses four related sub-sectors, namely growers, millers, refiners, and oleochemicals, forming an integrated value chain from upstream to downstream. The current focus on environmental, economic, and social sustainability is driving companies to adopt internal green activities and expand their efforts into sustainability supply chain management (SSCM). Implementing SSCM practices is often seen as economically beneficial, as research has demonstrated their positive impact on firm performance from a resource perspective. Within the palm oil industry, a wide range of green management applications are being utilized. This study aims to examine and highlight the existing sustainable management practices across the entire palm oil supply chain, with a particular emphasis on producing high-quality palm oil. To achieve this objective, the paper utilizes a systematic review methodology, The number of papers analyzed were 62 articles published which involves an extensive review of relevant literature to identify research trends, gaps, and issues. The study seeks to contribute to the body of knowledge by expanding the theory of organizational readiness in preparing globally competitive palm oil products. The research findings hold practical significance for practitioners and academics, providing a comprehensive roadmap for implementing green management applications at the organizational level in the palm oil industry's upstream-to-downstream chain.

: Early and accurate detection of infectious diseases is a key step for surveillance, epidemiology, and control, notably timely disease diagnosis, patient management and follow-up. In this study, we aimed to develop hand-held ultra-fast duplex PCR assays coupled to amplicon detection by lateral flow (LF) immunoassay to deliver a rapid, and simple molecular diagnostic test for con-comitant detection and identification of the main Leishmania parasites encountered in Tunisia and the Old World. We selected two DNA targets to amplify L. major/L. tropica and L. infantum/L. tropica group of species DNAs, respectively. We optimized the experimental conditions of a du-plex ultra-fast PCR. The amplification is performed by a portable Palm convection PCR machine within 18 min and the products are detected by a LF cassette within 10 minutes. The test allows the identification of the infecting species according to the position and number of test lines re-vealed. Tested on a selection of DNAs of representative Leishmania strains of the three studied species (N=37), the ultra-fast duplex PCR-LF showed consistent, stable, and reproducible results. The analytical limit of detection of the test was 0.4pg for L. major, 4pg for L. infantum and 40pg for L. tropica.

Resides derived from liquefaction of oil palm trunk in the presence of polyhydric alcohol with different liquefaction temperature and time were characterized to provide a new approach to understand some fundamental aspects of the liquefaction reaction. Higher temperature and longer reaction time resulted in lower residue content, indicating more decomposition of components of oil palm trunk. The amorphous polymer comprised of lignin, hemicellulose, starch, and cellulose with non-crystalline structure are firstly degraded at low liquefaction temperature, followed by the decomposition of crystalline region of cellulose. Although it was relatively difficult to destroy the ordered structure of cellulose, most of them could be liquefied via prolonging reaction time or enhancing reaction temperature. Nevertheless, it was found that re-condensation of liquefied products occurred during the liquefaction process when higher temperature of 180 oC was used after 60 min, leading to the gradual increase of residue content with increase of reaction time.

DNA extraction for downstream molecular diagnostic applications can be an expensive, time-consuming process. We devised a method to quickly extract genomic DNA from environmental samples based on sodium hydroxide lysis of cells with or without capture by magnetic beads, for subsequent PCR or quantitative PCR. The final DNA extraction method using NaOH is extremely low-cost and can be completed in 10 minutes at room temperature. NaOH extraction was effective for Gram-negative and Gram-positive bacteria in samples from air, soil, sewage, food, laboratory surfaces, and chicken cloacal swabs. The NaOH extraction method was comparable to commercial kits for extraction of DNA from pig fecal samples for 16S amplicon sequencing analyses. We demonstrate that an impinger and portable pump can efficiently capture bacteria in poultry facilities for rapid DNA extraction for quantification of total bacteria and for detection of specific species using qPCR. The air sampling and NaOH extraction procedures are well-suited for routine, high throughput screening, and for metagenomic analyses for specific pathogens, even in resource-limited situations.

Since the outbreak of the COVID-19 pandemic, patients infected with COVID-19 may experience abnormal heart rates, posing potential health risks. This study proposes a non-contact method for measuring heart rate (HR) and heart rate variability (HRV) to effectively reduce the risk of infection and assist healthcare professionals in more accurate diagnosis and treatment. In this study, except for the different image acquisition method, other research processes and methods are similar to the research methods in [15]. The image acquisition method is changed from forehead image to palm image. The new non-contact measurement performance of the proposed method can effectively not only avoid infection concerns but also obtain heart rate and HRV quickly and conveniently, providing higher accuracy for physiological parameters, root mean square error (RMSE), and mean absolute percentage error (MAPE) compared to those in recently published papers.

Porcine pleuropneumonia (PPP) is one of the main causes leading to massive losses in the pig industry, with high economic impacts. Among different etiological agents, Actinobacillus pleuropneumoniae (APP) is responsible for severe fibrinous-necrotizing pleuropneumonia. A total of 19 different APP serotypes are currently recognized. This study aimed to identify APP serotypes isolated from pneumonic lesions in naturally infected and dead pigs in the Piedmont Region and to describe lesions. A total of 107 dead pigs with a suspected PPP diagnosis were included in this study. Lungs were evaluated using gross pathology scoring systems, APP isolation and serotypes identification by multiplex PCR were conducted. Gross lung lesions were mainly represented by fibrinous pneumonia and pleuropneumonia. APP was isolated in 21/107 (19.6%) samples. On the contrary, PCR indicated APP DNA presence in 53/107 (49.5%) of lung samples. The most observed serotypes were serotype 2 in 24/53 (45.3%) and serotype 6 in 13/53 (24.5%) samples. Moreover, multiplex PCR results suggested a coinfection of different serotypes in 5 samples. This study highlights the relevance of the different techniques application (i.e. bacteriological culture, PCR, gross and histopathology) for improving the identification of APP infections.

Cerebellar ataxia, neuronopathy, and vestibular areflexia syndrome (CANVAS) is caused by biallelic pathogenic expansions, or compound heterozygosity with other pathogenic variants in the RFC1 gene. CANVAS is estimated to be underdiagnosed, both because of the lack of formal diagnostic criteria and molecular challenges that translate to lesser access and high cost of routine testing. Our aim was to address the need for making CANVAS genetic testing routine, by designing a streamlined two-step PCR consisting of a short-allele screening PCR and a confirmatory PCR with fragment capillary electrophoresis detection. Exome sequencing of RFC1 was additionally foreseen to resolve potential compound heterozygosity cases. Specificity of our approach was evaluated using ataxia patients with known non-CANVAS diagnoses, and optimized using Southern blot confirmed CANVAS patients. We evaluated our approach by testing patients consecutively referred for clinically suspected CANVAS using first the two-step PCR, followed by exome sequencing. Our approach was able to accurately identify negative and confirm positive cases in prospectively collected suspected CANVAS patients presenting with at least three typical clinical signs. The proposed testing approach provides an alternative method able to clearly distinguish between CANVAS negative and positive cases and can be easily incorporated into the genetic diagnostic laboratory workflow.

Peanut (Arachis hypogaea) contains allergenic proteins, which make it harmful to the sensitised population. The presence of peanut in foods must be indicated on label, to prevent accidental consumption by allergic population. In this work, we use chloroplast markers for specifically detection of peanut by real-time PCR, in order to increase the assay sensitivity. Binary mixtures of raw and processed peanut flour in wheat were performed at concentrations ranging from 100000 to 0.1 mg/kg. DNA isolation from peanut, mixtures and other legumes was carried out following three protocols for obtaining genomic and chloroplast-enrich DNA. Quantity and quality of DNA was evaluated, obtaining better results for protocol 2. Specificity and sensitivity of the method has been assayed with specific primers for three chloroplast markers (mat k, rpl16 and trnH-psbA) and Ara h 6 peanut allergen-coding region was selected as nuclear low-copy target and TaqMan probes. Efficiency and linear correlation of calibration curves were within the adequate ranges. Mat k chloroplast marker yielded the most sensitive and efficient detection for peanut. Moreover, detection of mat K in binary mixtures of processed samples was possible up to 10 mg/kg even after boiling, and autoclave 121°C 15 min, with acceptable efficiency and linear correlation. Applicability of the method has been assayed in several commercial food products.

Malaysia generates significant quantities of lignocellulosic wastes through the production of crude palm oil (CPO). Over the years, the accumulation of the oil palm wastes (OPW) have become an environmental burden. These problems can be addressed by pretreatment and valorisation of OPW in bioenergy as envisioned in the National Biomass Strategy (NBS-2020). However, current strategies for the OPW valorisation are inefficient and unsustainable resulting in increased environmental challenges. Therefore, this paper proposes the pelletization and torrefaction of oil palm empty fruit bunches (OPEFB). Furthermore, the thermal degradation behaviour and potential product yields from OPEFB pellet torrefaction will be examined. The results revealed that the mass yield (M_Y) decreased from 67.89% to 33.11%, whereas energy yield (E_Y) decreased from 88.29% to 49.18% as the torrefaction temperature increased from 250 °C to 350 °C. However, the energy density (D_E) increased from 1.30 to 1.49 due to the increase in higher heating value (HHV) from 22.85 MJ/kg to 26.10 MJ/kg. Likewise, the severity factor (S_F) increased from 5.89 to 8.84 with increasing torrefaction temperature. The results also revealed that effect of temperature on the torrefaction parameters; M_Y, E_Y, D_E, and HHV are slightly reduced after 300 °C. Overall, the findings demonstrate that torrefaction improved the fuel properties and energy recovery potential of the OPEFB pellets.

Our study analyzes the ecology and distribution of fish communities related to the environmental variables of the Alto Madre de Dios River, an Andean-Amazon watershed of southern Peru, between 300 and 2811 m a.s.l. within the Manu Biosphere Reserve. We provide new ecological and diversity data for these highly unknown rivers and new data for palm swamp habitats. With electric fishing techniques, we collected a total of 1934 fish specimens belonging to 78 species, 42 genera and 15 families. To assess main patterns of diversity we combined SIMPER and ANOSIM with canonical correspondence analysis to obtain an overview of the community structure of fish and their distribution related to aquatic habitats. Our results show an important shift on fish diversity at 700 m a.s.l. separating headwater and middle-lowland communities. Electrofishing was a hindrance due to the depth, flow and low conductivity of the rivers, but also allowed us to capture fish not observed with other techniques. We also compared the use of elevation with slope as an alternative variable for statistical analysis. Our results show that slope offers a solid and equivalent explanation for fish distribution variability, avoids redundance, and instead of giving geographical data offers ecologically solid information.

Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for rapid detection of pathogens. A sensitive and specific multiple nanoPCR assay was developed for simultaneous detection of three subgroups avian leucosis virus (ALV). In this study, three pairs of primers that were designed based on gp85 gene sequences of subgroup A, B and J, optimizations were carried out for better performance of the nanoPCR assay and remarkably improved the detection limit of the assay. The detection limit of the assay was 101copies/μl, which was 100-fold more sensitive than conventional PCR assays. The nanoPCR assay amplified the specific 336 bp, 625 bp and 167 bp fragments of ALV-A, -B and –J respectively and no cross-reactivity were found with the genomic DNA or cDNA of Newcastle disease virus, avian infectious laryngotracheitis virus, Marek's disease virus, infectious bronchitis vaccine, infectious bursal disease virus and avian encephalomyelitis Virus. To evaluate the detection ability of the assay, 186 clinical samples were detected by nanoPCR and the detection results were further confirmed by sequencing. The sequencing results were 100% in coincidence with the nanoPCR detection results, suggesting the possibility of clinical application of the newly developed nanoPCR assay. Taking all the results together, a highly specific and sensitive nanoPCR was successfully developed, which could be useful for rapid diagnosis of ALV in poultry farming.

Quantitative polymerase chain reaction (qPCR) is the gold standard approach for detecting a variety of pathogens either via probe-based or SYBR green detection chemistry. Generally, probe-based detection is more specific than SYBR green chemistry. This report describes work done in using a FAM probe targeting a specific segment of the human KRAS gene for detecting presence and relative abundance of the gene in human gastric CloTest samples. Results indicate ineffective detection of the human KRAS gene in samples that are shown to harbor the gene through a similar qPCR assay using SYBR green detection chemistry. Such observations point to inability of the designed FAM probe to bind to target segment of the human KRAS gene that suggests a region of rapid genomic evolution that require close surveillance in the public health community. Given its rapid genomic evolution, this probe region may be an important region in the human KRAS gene playing critical functional roles in either molecular recognition or other structural functions. Overall, human KRAS gene may be undergoing rapid genomic evolution, and qPCR probes targeting specific segment of the gene may be rendered ineffective in short time clinically, thereby, making SYBR green qPCR assay a more reliable choice.

Angelica decursiva is one of the lending traditional Chinese medicinal plants producing coumarins. Notably, several studies have focused on the biosynthesis and not the qRT-PCR (quantitative real-time reverse transcription polymerase chain reaction) study of coumarins. This qRT-PCR technique has been extensively used to investigate gene expression levels in plants and the selection of reference genes which plays a crucial role in standardizing the data form the qRT-PCR analysis. In our study, 11 candidate reference genes were selected from the existing transcriptome data of Angelica decursiva. Here, four different types of statistical algorithms (geNorm, NormFinder, BestKeeper, and Delta Ct) were used to calculate and evaluate the stability of gene expression under different external treatments. Subsequently, RefFinder analysis was used to determine the geometric average of each candidate gene ranking, and to perform comprehensive index ranking. The obtained results showed that among all the 11 candidate reference genes, SAND family protein (SAND), protein phosphatase 2A gene (PP2A), and polypyrimidine tract-binding protein (PTBP) were the most stable reference genes, where Nuclear cap binding protein 2 (NCBP2), TIP41-like protein (TIP41), and Beta-6-tubulin (TUBA) were the least stable genes. To the best of our knowledge, this work is the first to evaluate the stability of reference genes in the Angelica decursiva which has provided an important foundation on the use of qRT-PCR for an accurate and far-reaching gene expression analysis in this medicinal plant.

The emergence of SARS-CoV-2 mutations pose significant challenges to diagnostic tests as these mutations can reduce the sensitivity of commonly used RT-PCR assays. Therefore, there is a need to design diagnostic assays with multiple targets to enhance sensitivity. In this study, we identified a novel diagnostic target, nsp10 gene, using nanopore sequencing. Firstly, we determined the analytical sensitivity and specificity of our COVID-19-nsp10 assay. The COVID-19-nsp10 assay had the limit of detection of 74 copies/mL (95% confidence interval: 48-299 copies/mL) and did not show cross-reactivity with other respiratory viruses. Next, we determined the diagnostic performance of the COVID-19-nsp10 assay using 261 respiratory specimens, including 147 SARS-CoV-2-positive specimens belonging to ancestral strain and Alpha, Beta, Gamma, Delta, Mu, Eta, Kappa, Theta and Omicron lineages. Using the LightMix E-gene RT-PCR assay as the reference method, the diagnostic sensitivity and specificity of the COVID-19-nsp10 assay were 100%. The median Cp values for the LightMix E-gene RT-PCR and our COVID-19-nsp10 RT-PCR were 22.48 (range: 12.95-36.60) and 25.94 (range 16.37-36.87), respectively. The Cp values of the COVID-19-nsp10 RT-PCR assay correlated well with those of the LightMix E-gene RT-PCR assay (Spearman’s ρ = 0.968; P<0.0001). In conclusion, nsp10 is a suitable target for SARS-CoV-2 RT-PCR assay.

Scrub typhus is a life-threatening infectious disease and always creating a diagnostic dilemma in terms of rapid turnaround time and accuracy, qRT PCR can become a very good option to achieve the desired result with the molecular level of accuracy and boost up the rapid patient management. This study was performed to evaluate the performance of qRT PCR in comparison to commonly used IgM ELISA and Weil-Felix tests to diagnose scrub typhus, as well as to look for the demographic and clinical profile of the disease in North-East India. It was a hospital-based prospective study conducted in a tertiary care hospital of north-east India, over a period of 1 year, in which all the samples from suspected scrub typhus cases were screened by Weil-Felix test as per institute’s diagnostic protocol after which IgM ELISA for Scrub Typhus was performed. All the IgM positive samples and 20 highly suspected but ELISA negative samples were subjected to qRT PCR, targeting 56 kDa type-specific gene of O. tsutsugamushi. Statistical analysis was done by MS-Excel for Windows v2013® and MedCalc® v17.9 for Windows (MedCalc Software, Acacialaan 22, B-8400 Ostend, Belgium). In this study, we have successfully evaluated the performance of qRT PCR kit for diagnosis of scrub typhus. Out of 54 samples tested, 24 IgM ELISA positive samples and 3 IgM ELISA negative samples have shown the presence of bacterial DNA with quantification of DNA copies. It has also been observed that 21 out of 27 PCR positive samples (77.8%) were detected within the 1st 7 days of illness. All the demographic, as well as clinical data, were also analysed. The performance of the commercial qRT PCR kit used in our study is satisfactory, which provides the extra advantage of quantification of DNA copies and increases diagnostic accuracy within the 1st week of fever.

Pythium insidiosum causes pythiosis, a fatal infectious disease of humans and animals worldwide. Prompt diagnosis and treatment are essential to improve the clinical outcome of pythiosis. Diagnosis of P. insidiosum relies on immunological, molecular, and proteomic assays. The main treatment of pythiosis aims to surgically remove all affected tissue to prevent recurrent infection. Due to the marked increase in case reports, pythiosis has become a public health concern. Thailand is an endemic area of human pythiosis. To obtain a complete picture of how the pathogen circulates in the environment, we surveyed the presence of P. insidiosum in urban (Bangkok) and rural areas of Thailand. We employed the hair-baiting technique to screen for P. insidiosum in 500 water samples. Twenty-seven culture-positive samples were identified as P. insidiosum by multiplex PCR, multi-DNA barcode (rDNA, cox1, cox2), and mass spectrometric analyses. These environmental strains of P. insidiosum fell into clade-I and -II genotypes and exhibited a close phylogenetic/proteomic relationship with Thai clinical strains. Biodiversity of the environmental strains also existed in a local habitat. In conclusion, P. insidiosum is widespread in Thailand. A better understanding of the ecological niche of P. insidiosum could lead to the effective prevention and control of this pathogen.

In this research, the photocatalytic degradation of cypermethrin using Fe-TiO2 nanoparticles supported in a biomaterial was evaluated. The nanoparticles of TiO2 were synthesized by the green chemistry method assisted by ultrasound and doped by chemical impregnation using molar ratios Fe:Ti of 0, 0.05, 0.075 and 0.1, to make efficient use of direct sunlight (λ>310 nm). All nanoparticles were immobilized on the surface of spathe of coconut palm (Cocos nucifera). The degradation was carried out at room temperature and natural pH in a flat plate solar reactor, on which the composite material was subjected. The concentration of cypermethrin was determined after 12000 J/m2 of accumulated radiation from GC-MS and the resulting material was characterized by Scanning electron microscopy (SEM), Transmission electron microscopy (TEM) image and selected area electron diffraction (SAED), Fourier transform infrared spectroscopy (FTIR), UV-Vis spectrophotometry of diffuse reflectance and BET surface area BET surface area. The best results were achieved with the use of Degussa TiO2 P-25, Fe:Ti=0 and Fe:Ti=0.05 in suspension, with percentages of degradation of cypermethrin of 99.84, 99.62, and 100%, respectively. However, the materials supported on the biomaterial of coconut, they allowed to reach degradation percentages higher than 80% with the advantage that it minimizes operating costs, since they are not necessary filtering or centrifuging processes to separate the catalyst.

Various environmental challenges, related to oil palm commodity has became a major environmental challenge to oil palm production. The aim and objective of this study is to analyze the actual water footprint of oil palm based on root water uptake under varying crop age and soil type. The research was conducted in Pundu Village, Central Kalimantan. The methodology adopted in carrying out this study consists of various stages which includes observing soil moisture, rainfall, and water table, ETo, root water uptake and oil palm water footprint. The highest rate of water consumption was the 13 years oil palm on spodosol soil type with an average daily rate of 3.73 mm/day. The lowest evapotranspiration was represented by the 7th year oil palm on spodosol with an average rate of 3.07 mm/day. The total water footprint value obtained was between 0.56 – 1.14 m3/kg for a variety of plants with various age and soil types. It can be deduced that the water footprint value of oil palm vary for different crop age and soil types on temporal scale. The study also presented that the source of green water from the first root zone of oil palm deliver the highest contribution for oil palm root water uptake.

Escherichia coli O157:H7, a Shiga toxin-producing E. coli (STEC) is an important pathogen related to foodborne disease that is responsible for a growing number of outbreaks worldwide and has been detected in processed meats, dairy, and fresh vegetables. Although culturing is the gold standard method for detection of this bacteria, molecular methods based on nucleic acid amplification techniques such as PCR are becoming more common because of their rapidity, sensitivity, and specificity. However, to ensure reliable results among the several alternative PCR protocols (e.g., commercial kits and reference methods), different measurement assurance tools, including validated methods, reference materials, and proficiency tests among others, are required. Herein, we present a digital PCR method validation for E. coli O157:H7 detection and quantification using seven gene sequences; this method quantified nucleic acids from different E. coli serotypes, with a detection range between 6.6 to 7,900 copies/µL and a repeatability standard deviation over the concentration range of between 1% to 13.6%. The relative standard uncertainty was 3.5%–14.6%, and the detection limit was 0.27 copies/µL. Subsequently two batches of a candidate reference material based on E. coli O157:H7 genomic DNA were then produced and characterized for evaluation of copy number concentration with the validated dPCR method, with assigned values of 164,770 ± 9,251 and 172 ± 9 copies/μL. Thus, this study demonstrated the development a validated method and reference material for dPCR and qPCR detection of E. coli O157:H7, a key STEC responsible for food poisoning.

Quambalaria eucalypti is a fungal pathogen that causes leaf spot, shoot blight, and stem canker disease in Eucalyptus spp. Although the advanced stages of the disease show clear symptoms, diagnosis of the early stages can be challenging. To enable fast and sensitive screening of asymptomatic or latent infected plant material for Q. eucalypti, a specific SYBR green-based real-time PCR assay targeting the partial histone-H3 region was developed. The assay was demonstrated to be specific for Q. eucalypti and did not give cross-reactivity with any of the other Quambalaria species examined or other eucalyptus pathogens. The primers developed in this study ensured high analytical sensitivity, allowing the detection of Q. eucalypti DNA concentrations as low as 10 fg DNA from asymptomatic plants. Comparable results were obtained in interlaboratory testing, demonstrating the assay's robustness and effectiveness in other laboratories. This newly developed quantitative PCR assay can be used for more comprehensive epidemiological investigations, testing plant material in known Q. eucalypti distribution areas for early management strategies, or collecting data for resistance breeding programs.

The device and method in accordance with the constant pressure regulation of micro droplet PCR in microfluidic chips are developed to explore the optimization way for the micro droplet movement, fragmentation, and bubble generation in microfluidic chips in existing digital PCR technology. In the developed device, an air source device is adopted to regulate the pressure in the chip, such that micro droplet generation and PCR amplification without bubbles can be achieved. In 3 min, the sample in 20ul will be distributed into nearly 50,000 water-in-oil droplets exhibiting a diameter of about 87μm, and the micro droplet will be subjected to a close arrangement in the chip without air bubbles. The device and chip are adopted to quantitatively detect the human gene . As indicated by the experimental results, a good linear relationship exists between detection signal and DNA concentration ranging from 101~ 105 copies /μL (R2=0.999). The micro droplet PCR devices based on constant pressure regulation chips exhibit a wide variety of advantages (e.g., achieving high pollution resistance, micro droplet fragmentation and integration avoidance, reducing human interference, and standardizing results). Thus, micro droplet PCR devices based on constant pressure regulation chips have promising applications in nucleic acid quantification.

Phytophthora infestans (Mont.) de Bary causing potato late blight (LB) and potato virus Y (PVY), are serious constraints to cultivated potatoes causing important yield reduction, and phenotyping for resistance is challenging. Breeding operations for vegetatively propagated crops can lead to genotype mislabeling that in turn reduces the genetic gain. Low-density and low-cost molecular marker assessment for phenotype prediction and quality control stands as a viable option for breeding programs. We report here the development of Kompetitive Allele Specific PCR (KASP) markers for LB and PVY resistance, and for quality control assessment, and their routine use in different breeding populations. Two KASP markers for LB resistance and two for PVY Ryadg were validated with an estimated assay power ranging between 0.65 and 0.88. Developed QC KASP markers demonstrated the power of tetraploid calls in discriminating the breeding material, including full sibs and half sibs. The routine implementation of developed markers in a breeding program will allow a better allocation of resources and a precise characterization of the breeding material, leading to an increased genetic gain.

PIK3CA is a gene usually mutated in breast cancer and has an important role in tumor progression and treatment. Therefore, there is required a technique to detect low-rate PIK3CA mutations improving the clinical conduct. This study aimed to compare chip-based dPCR and Sanger sequencing to detect PIK3CA mutations in breast cancer patients. Fifty-seven tumor samples from breast cancer patients were collected and analyzed by Sanger sequencing and dPCR for PIK3CA mutations (E545K, H1047R, and H1047L). Digital PCR sensitivity, specificity, and overall performance were estimated by contingency tables, receptor operator characteristic (ROC), and area under the curve (AUC). Sanger sequencing identified PIK3CA mutations in six patients (10.5%), two with H1047R, and four with E545K. Digital PCR confirmed those mutations and identified 19 additional patients with at least one mutation. Comparison between dPCR and Sanger sequencing showed a sensitivity of 100% (95% CI 53-100%), and a specificity of 84.2% (95% CI 83 - 84.2%). Besides, H1047R mutation showed a significant association with breast cancer phenotype (p =0.019) and lymphatic node infiltration (p =0.046). Digital PCR showed a high sensitivity to detect mutations in tumor samples and it might be capable to detect low-rate mutations and tumor subpopulations not detected by Sanger sequencing.

Several articles have reported that the low number of COVID-19 cases in Japan is attributed to the small number of diagnostic RT-PCR tests performed. The criticism is based on the low number of the tests performed, and they suspected there would be more potential cases in Japan. The use of pre-test probability among tested subjects is proposed in order to evaluate of the sufficiency of test availability instead of the number of the tests. The pre-test probability means the average probability, i.e., ‘suspicion level’, of having coronavirus among the tested subject in a country. The higher pre-test probability is regarded as less sufficient opportunity of the tests, and the test availability could be evaluated by the pre-test probability. Thus, potential problems of underestimation of COVID-19 cases by insufficient amount of the test would be clear by using pre-test probability. The comparison of the pre-test probability could be replaced with that of the positive rate of the test because of the linear relationship between them under the assumption of common sensitivity and specificity. Japan shows the third lowest rate (8.6%), and is considered that the considerably sufficient number of the tests have been performed. In conclusion, the positive rate of the test as a surrogate index of the pre-test probability is useful to evaluate the sufficiency of test amount instead of the number of the tests performed. In present, the potential problem of underestimation by insufficient test availability would be less serious in Japan.

The aim of this study was to examine pathologic complete response (pCR) and overall survival (OS) of patients diagnosed with non-metastatic inflammatory breast cancer (IBC). A total of N=8,550 cases undergoing surgery were identified between 2004-2013, using the National Cancer Database (NCDB). Patients were grouped into 4 biologic subtypes (HR+/HER2-, HR+/HER2+, HR-/HER2+, HR-/HER2-). The median age at diagnosis was 56 years. On average, women were followed for 3.7 years [interquartile range=3.0]. The majority were white (80%), had private health insurance (50%), and presented with poorly differentiated tumors (57%). Approximately 46% of the cancers were >5cm. Most patients underwent mastectomy (94%) and received radiotherapy (71%). Differences by biologic subtypes were observed for grade, lymph node invasion, race, and tumor size (p<.0001). Compared with non-pCR (54%), patients experiencing pCR had superior 5-year survival (77%) (p<.0001). Survival was poor for triple-negative (TN) tumors (37%) vs. other biologic subtypes (60%) (p<.0001). On multivariable analysis, TN-IBC, positive margins, and not receiving either chemotherapy, hormonal therapy or radiotherapy were independently associated with poor 5-year survival (p<.0001). In this large multicentric analysis of IBC, categorized by biologic subtypes, we observed significant differential tumor, patient and treatment characteristics, and OS.

Regional heat capacity change is calculated from the ratio between the addition or subtraction of heat (ΔQ) with the increase or decrease in temperature (ΔT) region. The purpose of this study is to calculate the regional heat capacity change due to the changes of land cover composition with forest, shrubs, oil palm plantation and bare soil using Landsat-5 TM satellite data on 1994, 2000 and 2010. Total area that used on ​​this study is 12971 ha. In 1994-2000, 4 % of forest area and 2% shrubs were increased, followed by additional of biomass forest 4.01 tons/ha and 2.83 tons/ha for shrubs. The increased of forest area and biomass (tons/ha) caused by forest and shrubs growth processing towards climax that added the canopy volume. So that, the regional heat capacity in 1994 amounted 19384 MJC^o-1 increased to 19929 MJC^o-1 in 2000. Data observation for 2000-2010 showed that forest area decreased by 66% due to forest’s clearing into oil palm plantations (47%), shrubs (8%) and bare soil (11%). But, plant’s biomass continue to increased, i.e 1.48 ton/ha for forest, 2.73 tons/ha for shrubs and 4.63 tons/ha for bare soil. Before 2000, there was no land cover by oil palm plantations, so the increasing rate from this land was the biggest than the three other lands, amounting to 122.29 tons/ha. Decreasing in the percentage of forest area does not cause a decrease in the heat capacity of the region. Intensive maintenance on oil plam plantation such as water management, fertilizer and planting space made it biomass productivity and ability to save the heat is greater than the forest. As the result, in 2010 regional heat capacity increased to 22508 MJC^o-1.

Date palm trees generate large amounts of various types of waste, including leaf sheath fibers which can be used as a low-cost, precursor for production of biochar including activated carbon (AC) that can be employed for adsorption of contaminants. In the current study, activated carbon was made from leaf sheath fibers of date palm (LSDPFAC) by use of chemical activation with K2CO3, combined with microwave irradiation, characterized and evaluated for its adsorptive capacity of lead ions (Pb2+). The Brunauer–Emmett–Teller (BET) surface area, Langmuir surface area, total pore volume and average pore diameter of LSDPFAC were 560.20 m2/g, 744.31 m2/g, 0.29 cm3/g and 2.47 nm respectively. When the initial concentrations of Pb2+ were increased from 1 to 10 mg/L, Pb2+ adsorption increased from 0.97 to 8.76 mg/g, dry mass (dm) while the percent of Pb2+ removed decreased from 96.70 to 87.60%. The greatest removal of Pb2+ occurred at pH 13 with adsorption capacity of 9.15 mg/g, dm. Results of isotherm and kinetic studies demonstrated that adsorption of Pb2+ onto LSDPFAC was best described by the Freundlich isotherm and pseudo-second order (PSO) models. Langmuir monolayer adsorption capacity, Qm was 14.10 mg/g. Thermodynamic parameters of H°, S°, G° and Ea were 6.39 kJ/mol, 0.12 kJ/mol.K, -31.28 kJ/mol and 15.90 kJ/mol, respectively, which demonstrated that adsorption of Pb2+ by LSDPFAC was endothermic, spontaneous and governed by physisorption.

Objectives: Human herpes viruses can cause life-threatening diseases in immunocompromised children, especially leukemic patients. Therefore, the aim of this study is to detect the human herpes viruses (HHV1-7) and to investigate its clinical significance in Middle Eastern Pediatric Leukemia Patients by using 2 Independent PCR assays. Methods: Detection of human herpes virus DNA has been done in blood samples of 200 pediatric leukemia patients in addition to 90 blood donors as a control group using multiplex PCR assays. When a ‘‘positive’’ result was observed, real-time PCR was performed to measure the viral load. Results: The most frequent herpes virus infection in Middle Eastern Pediatric Leukemia cases was CMV, followed by EBV, then HHV6, VZV, HHV7, HSV1, and HSV2, where they were 92/200 (46%), 76/200 (38%), 72/200 (36%), 48/200 (24%), 12/200 (6%), 8/200 (4%), and 2/200 (1%) respectively. Also, there was a statistically significance difference between leukemic patients and their controls regarding CMV, EBV, HHV6, and VZV (P <0.05). Correlation between percentage of co-infection, and clinical parameters for the 7 herpes viruses has been studied, and there is an increase in absolute neutrophilic count (ANC), total leukocyte count (TLC) and duration of fever and neutropenia in age group 6-11 years for HHV6/CMV, then in age group 12-18 years especially for EBV/CMV and CMV/HHV6. Also, our results show that multiplex PCR assay is close to single PCR assay in relation to specificity and sensitivity which in turn prove its validity for early diagnosis of herpes viral infection. Conclusions: Adopting multiplex PCR technique is helpful in screening of virus infections. It will save time, effort, cost effective and will assist in rapid diagnosis. However, the clinical relevance of the virus infection needs to be evaluated by quantitative real-time PCR which in turn will help patient's management by using appropriate antiviral treatment.

Tree nuts show nutritional properties and human health benefits. However, they contain allergenic proteins, which make them harmful to the sensitised population. The presence of tree nuts on food labelling is mandatory and, consequently, the development of suitable analytical methodologies to detect nuts in processed foods is advisable. Real-time PCR allowed a specific and accurate amplification of allergen sequences. Some food processing methods could induce structural and/or conformational changes in proteins by altering their allergenic capacity, as well as produce the fragmentation and/or degradation of genomic DNA. In this work, we analysed by means of Real-time PCR, the influence of pressure and thermal processing through Instant Controlled Pressure Drop (DIC) on the detectability of hazelnut,pistachio and cashew allergens have been tested. The detection of targets in hazelnut, pistachio and cashew (Cor a 9, Pis v 1 and Ana o 1, respectively) is affected by the treatment, in different extent depending on the tree nut. Results are compared to those previously obtained by our group in the analysis of different treatments on the amplificability of the same targets. Reduction in amplificability is similar to that reported for some autoclave conditions. Our assays might allow detecting up to 1000 mg/kg of hazelnut, pistachio and cashew flours after being submitted to DIC treatment in food matrices.

The application of quantitative PCR (qPCR) as a routine method to detect and enumerate Paenibacillus larvae in honey and hive debris could greatly speed up the estimation of prevalence and outbreak risk of the American foulbrood (AFB) disease of Apis mellifera. However, none of the qPCR tests described so far has been officially proposed as a standard procedure for P. larvae detection and enumeration for surveillance purposes. Therefore, in this study inclusivity, exclusivity and sensitivity in detection of P. larvae spores directly in samples of honey and hive debris were re-evaluated for the previously published qPCR methods. To this aim recently acquired P. larvae sequence data were considered to assess inclusivity in silico and more appropriate non-target species were used to verify exclusivity experimentally. This led to the modification of one of the previously described methods resulting in a new test capable to allow the detection of P. larvae spores in honey and hive debris down to 1 CFU/g. The application of the qPCR test optimized in this study can allow to reliably detect and quantify P. larvae in honey and hive debris, thus circumventing the disadvantages of late AFB diagnosis based on clinical symptoms and possible underestimation of spore numbers that is the main drawback of culture-dependent procedures.