In the main prickly pear (Opuntia ficus-indica) producing region in the State of Mexico, fruit production (tunas) occupies the largest cultivated area with 15,800 ha, while 900 ha are cultivated for fresh consumption (“nopal” or “nopalitos”). Two composite samples consisting of prickly pear cactus cladodes (n=6) and another of nopal vegetable (n=6) showing virus-like symptoms were collected. Both sample sets were subjected to high-throughput sequencing (HTS) to identify the viruses and viroids present. The HTS results were verified using RT-PCR and Sanger sequencing. Subsequently, 86 nopal samples (nopal vegetable, prickly pear cactus, xoconostle and wild) were analyzed via RT-PCR with specific primers for the viruses and viroids previously detected via HTS. Three viruses were discovered [Opuntia virus 2 (OV2), cactus carlavirus 1 (CCV-1), and Opuntia potexvirus A (OPV-A)], along with a previously reported viroid [Opuntia viroid 1 (OPVd-1)]. Additionally, two new viroid species were identified, provisionally named Mexican opuntia viroid (genus Pospiviroid) and Opuntia viroid 2 (OVd-2). Phylogenetic analysis, pairwise identity comparison, and conserved structural elements analysis confirmed the classification of these two viroids as new species within the Pospiviroidae family. This is the first report of a pospiviroid and two apscaviroids infecting prickly pear in the world. Overall, this study enhances our understanding of the virome associated with nopal in Mexico.

Moonmilk are cave carbonate deposits that host a rich microbiome including antibiotic-producing Actinobacteria making these speleothems appealing for bioprospecting. Here we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave “Grotte des Collemboles” via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9 to 23% of the total bacterial population. Next to actinobacterial OTUs attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of OTUs unlinked to the culturable Streptomyces strains previously isolated from the same deposits. 43% of OTUs were shared between the three studied collection points while 34% were exclusive to one deposit indicating that distinct speleothems host their own population despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.

Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants’ growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

Mallard (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there are very few studies on the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis revealed significant differences in the gut microbial communities of domestic and wild mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCOA) plot. In domestic mallards, Firmicutes (67.97%) was the most abundant bacterial phylum, followed by Proteobacteria (24.48%), Bacteroidetes (3.13%), Fusobacteria (2.21%), and Actinobacteria (1.10%). The dominant bacterial phyla in wild mallards were Firmicutes (79.02%), Proteobacteria (12.85%), Fusobacteria (3.37%), and Bacteroidetes (2.79%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogens (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.

Mallard (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there are very few studies on the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis revealed significant differences in the gut microbial communities of domestic and wild mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCOA) plot. In domestic mallards, Firmicutes (67.97%) was the most abundant bacterial phylum, followed by Proteobacteria (24.48%), Bacteroidetes (3.13%), Fusobacteria (2.21%), and Actinobacteria (1.10%). The dominant bacterial phyla in wild mallards were Firmicutes (79.02%), Proteobacteria (12.85%), Fusobacteria (3.37%), and Bacteroidetes (2.79%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogens (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.

Laser machining by ultra-short (sub-ps) pulses at high intensity offers high precision, high throughput in terms of area or volume per unit time, and flexibility to adapt processing protocols to different materials on the same workpiece. Here we consider the challenge of optimization for high throughput: how to use the maximum available laser power and larger focal spots for larger ablation volumes by implementing a fast scan. This implies the use of high-intensity pulses approaching ∼PW/cm2 at the threshold where tunnelling ionization starts to contribute to overall ionization. A custom laser micromachining setup was developed and built to enable high speed, large area processing and easy system reconfiguration for different tasks. The main components include laser, stages, scanners, control system, and software. Machining of metals such as Cu, Al, or stainless steel, and fused silica surfaces at high-fluence and high-exposure doses at high scan speeds up to 3 m/s were tested for the fluence scaling of ablation volume, which was found to be linear. Modified surfaces are color-classified for their appearance, which is dependent on surface roughness and chemical modification. Such colour-coding can be used as a feedback parameter for industrial process control.

Conventional phenotyping breeding approaches for vegetable crops like Solanaceae, Bulb, Root crops, have made a significant contribution by developing many varieties. Despite this, conventional phenotyping approaches are not sufficient due to the longer time taken to develop a variety, low genetic gain, environmental factors and some other externalities that affect the phenotype-based selection. To address the challenges of conventional phenotype, a new recent method of high throughput phenotyping (HTP) is considered a promising tool. The development of high-throughput phenotyping technology began in the preceding decade as advancements in sensor, computer vision, automation, and advanced machine learning technologies. HTP platforms are being utilized to undertake non-destructive assessments of the complete plant system in a range of crops. HTP provides the precise measurements and suggests the collection of high-quality and accurate data which is necessary for standardizing phenotyping for the collection of genetic dissection and genomic assisted breeding such as genome-wide association studies (GWAS), linkage mapping, marker-assisted selection (MAS), genomic selection (GS). The remainder of this chapter discusses how high-throughput phenotyping technologies can be used in genomic-assisted breeding for vegetable crops

For a comprehensive exploration of the Bimolecular Fluorescence Complementation (BiFC) approach, we critically assess whether protein pairs establish direct or indirect interactions within this context. Emphasizing the multifaceted nature of protein interactions, this review underscores the imperative of delineating macromolecular complex characteristics across five distinct levels: composition, stoichiometry, copy number, topology, and dynamics. A pivotal discussion revolves around the challenges introduced by the overexpression of target proteins and the potential artificial ramifications of fusion proteins. The significance of stoichiometry in protein interactions is illuminated, with the HOXA9/PBX1 interaction serving as a pertinent case study. The research identifies and elaborates on the inherent limitations of prevailing large-scale BiFC screenings, advocating for the incorporation of rigorous negative controls. A novel proposition is introduced in the form of a high-throughput multicolor BiFC strategy, exemplified using the HOXA9 and PBX1 proteins. The paper culminates with an insightful discourse on the implications of tags within the BiFC system, presenting the TriFC (Tripartite Fluorescence Complementation) assay as a promising alternative.

The mutton quality of Chinese Tan lambs (Ovis aries) has declined as feeding patterns have shifted from pasturing to pen rationing. Mutton quality is affected by fatty acids, and rumen microorganisms play a role in the synthesis of short-chain fatty acids, long-chain fatty acids, and conjugated linoleic acids. We used 16S rDNA sequencing to analyze the effects of two feeding patterns on the rumen bacteria of Tan lambs. In a randomized block design with 24 newborn Tan lambs, 12 lambs were fed by ewes in pasture and 12 were fed by pen-fed ewes. At 2 months, the biceps femoris and the longissimus dorsi were analyzed by gas chromatography for intramuscular fat content and fatty acid composition, and DNA in the rumen contents was extracted and used to analyze the structure of the bacterial community. Different feeding patterns had no significant effect on the intramuscular fat content of the biceps femoris and longissimus dorsi of the lambs, but there was a significant effect on fatty acid composition. Rumen bacteria were significantly more diverse in the pasture group than in the pen-ration group (P < 0.01). Twenty-one phyla were identified in the pasture group, and 14 phyla were identified in the pen-ration group. The dominant phyla in the pasture group were Bacteroidetes and Fibrobacteres; the dominant phyla in the pen-ration group were Proteobacteria and Bacteroidetes. The relative abundance of Proteobacteria was significantly higher in the pen-ration group than in the pasture group (P < 0.01). Diversity at the genus level was also higher in the pasture group, with 176 genera in the pasture group and 113 genera in the pen-ration group. The dominant genera in the pasture group were Prevotella_1, Rikenellaceae_RC9_gut_group, and Bacteroidales_BS11_gut_group_Na; the dominant genera in the pen-ration group were Prevotella_1, Prevotella_7, Succinivibrionaceae_UCG-001, and Succinivibrionaceae_NA.

The objective was to estimate the correlation between VIs and grain yield and identify the optimal timing and VIs for precise corn grain yield estimation. Furthermore, the study aims to employ photographic quantification to measure corn ear traits and establish their correlation with corn grain yield. Ten corn hybrids were evaluated in CRB with three rep-lications at three locations. Vegetation indices and green leaf area were estimated throughout the cycle using an unmanned aerial vehicle (UAV) and subsequently corre-lated with grain productivity. In addition, photographs were taken of the corn ear to esti-mate their length, width and total number of kernels and compare these values with manual measurements. The experiments consistently demonstrated significant experi-mental quality across sites, with accuracy ranging from 79.07% to 95.94%. UAV flights carried out at the beginning of the crop cycle revealed a positive correlation between grain productivity and the evaluated indices (NGRDI, VARI, GLI). Regarding the phenotyping of corn ears, the regression coefficients for width, length and TNG were 0.92, 0.88 and 0.62, respectively, indicating an association with manual measurements. However, stage V5 in the localities of Lavras and Ijaci and stage V8 in the locality of Nazareno showed a posi-tive correlation with productivity. The use of images for ear phenotyping is promising as a method for measuring corn components.

High throughput multiplex serological systems enable the small developer to set up tests at small cost, for microbes for which there are no commercial tests, and for aspects which have not been addressed by them. An example is testing for Zika and Tick Borne Encephalitis virus antibodies, where antigenic cross-reactions make diagnosis problematic. Our technique variant, Suspension Multiplex Immunoassay (SMIA) allows many samples to be tested for antibodies to many antigens in a short time. Computational compensation for cross-reactions is possible if a SMIA panel contains most of the potentially cross-reacting antigens. Using antibody avidity and pattern of reactivity to whole virus and nonstructural protein, antibodies due to vaccination and infection, respectively, as well as probable degree of protection, can be determined with high throughput. These multiplex techniques hold great promise for future diagnostic development. Theoretically, even large scale serological monitoring, like blood donor pathogen testing, could be done inexpensively and rationally with multiplex serology developed in house. However, the quality control demands are steep and in most cases out of scope for a single laboratory. There remain however a number of clinical applications where in house multiplex serology can be performed with adequate quality control under high throughput conditions.

The hospital indoor environment plays a significant role in shaping the microbial exposures that humans encounter. Resistance to antibiotics is one of the mechanisms employed by bacteria to develop resilience against stress in indoor environments. The extensive usage of antibiotics has been a key factor in driving changes in the ecological function of antibiotic resistance genes (ARGs) and their acquisition by pathogenic bacteria. By integrating the 16S rRNA Illumina sequencing and high throughput-qPCR approaches with water and air dust samples across seven departments at Peking University Shenzhen Hospital, China, this study yielded intriguing findings regarding the department-specific variation, transmission, and correlation of bacteria, ARGs and MGEs within the hospital indoor environment. One notable observation was that the seasonal variation played a vital role in shaping the bacterial composition in the overall hospital indoor environment across seven studied departments. Nevertheless, a similar significant seasonal impact was only observed in the blood test room and emergency departments, rather than in the other five departments. Another intriguing finding was the correlation between ARGs and MGEs abundance. This correlation was evident in the overall hospital indoor environment, which was conversely not found in the emergency, pneumology and gynecology departments. Additionally, while there was no significant relationship that occurred between bacterial communities and ARGs/MGEs within the hospital, the gynecology department demonstrated a close link between bacterial communities and the presence of ARGs/MGEs. Notably, the gynecology department also stood out as an important source of bacteria and ARGs/MGEs for other departments. This study underscores the need for careful surveillance and monitoring of antibiotic resistance, particularly in Legionella spp. in man-made water systems. The findings also show the importance of monitoring and understanding the genetic elements such as Tp614 involved in gene transfer and recombination, as well as their impact on antimicrobial treatment efficacy.

It is an utmost importance to characterize drug candidates as early in the development pipeline as possible. Appropriate application of the emerging high throughput analytical techniques unlocks the opportunities to obtain experimental data for in vitro absorption, distribution, metabolism and elimination (ADME) profiling of large compound libraries which is crucial for selection of lead compounds. In an usual scenario, only one drug candidate will be selected from thousands of early compounds based on several stability and screening results. A high to medium throughput screening approaches could significantly accelerates the subsequent research and production phases. Traditionally, the analysis of metabolic stability assays heavily relies on high throughput LC-MS/MS techniques to meet with the lead profiling demands. In this study presented an innovative experimental approach that can offer a refreshing alternative. Laser Assisted Rapid Evaporative Ionization Mass Spectrometry (LA-REIMS) is a quick and efficient method for characterizing complex biological samples without laborious sample preparation and chemical separation. Therefore, using an automated LA-REIMS well plate reader as fast as 8 seconds per sample, we assessed the oxidative metabolic stability of active agents using biomimetic metalloporphyrin-based oxidative model reactions at various pH for commercially available drug substances and compared stability measurements with traditional HPLC-DAD-MS results.

The accurate virus detection, strain discrimination, and source attribution of contaminated food items remains a persistent challenge because of the high mutation rates anticipated to occur in foodborne RNA viruses, such as Hepatitis A virus (HAV). This has led to predictions of the existence of more than one sequence variant between the hosts (inter-host) or within an individual host (intra-host). However, there have been no reports of intra-host variants from an infected single individual, and little is known about the accuracy of the single nucleotide variations (SNVs) calling with various methods. In this study, the presence and identity of viral SNVs, either between HAV clinical specimens or among a series of samples derived from HAV clone1-infected FRhK4 cells, were determined following analyses of nucleotide sequences generated using next-generation sequencing (NGS) and pyrosequencing methods. The results demonstrate the co-existence of inter- and intra-host variants both in the clinical specimens and the cultured samples. The discovery and confirmation of multi-viral RNAs in an infected individual is dependent on the strain discrimination at the SNV level, and critical for successful outbreak traceback and source attribution investigations. The detection of SNVs in a time series of HAV infected FRhK4 cells improved our understanding on the mutation dynamics determined probably by different selective pressures. Additionally, it demonstrated that NGS could potentially provide a valuable investigative approach toward SNV detection and identification for other RNA viruses.

Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of Escherichia coli O157:H7 from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant formula (PIF) overnight enrichments, where Cronobacter typically dominates the overall microbiome (&gt;90%). In this study, we aimed to test whether using ONT sequencing of overnight PIF enrichments could recover a completely closed Cronobacter genome for further genomic characterization. Ten PIF samples, each inoculated with different Cronobacter strains, covering Cronobacter sakazakii, C. muytjensii, C. dublinensis, C. turicensis, and C. universalis, were processed according to the Bacteriological Analytical Manual (BAM) protocol. qPCR was used for initial screening (detection and quantification) of the overnight enrichments and confirmed that the spiked PIF samples after the overnight enrichment have high levels of Cronobacter (107 to 109 CFU/mL). DNA from overnight PIF enrichments was extracted from the enrichment broth and sequenced using ONT. Results showed that ONT sequencing could accurately identify, characterize, and close the genomes of Cronobacter strains from overnight PIF enrichments in 3 days, much faster than the nearly two weeks required by the current BAM method. Complete genome recovery and species differentiation were achieved. This suggests that combining qPCR with ONT sequencing provides a rapid, cost-effective alternative for detecting and characterizing Cronobacter in PIF, enabling timely corrective actions during outbreaks.

In review, the operating principles of the most common bio sensing devices, detection methods and the identification sensitivity of analyzed molecules were shown. The central focus was done on hybridization analysis of nucleic acids (NA), which are considered to be one of the most important analytes in terms of diagnostic point of view. Constructions enabling to transfer the fact of formation of nucleotide probe/target complex in to detectable signal by optical, electrochemical or micromechanical (piezoelectric) sensors were presented in this review.

Effects of oxygen content on microstructure and creep property of FGH96 superalloy were investigated. When oxygen content increased from 135ppm to 341ppm, prior particle boundary (PPB) rose from degree 2 to degree 3, and the size of γ′ phase on PPB enlarged from 1.07μm to 1.27μm, and MC carbide size grew from 77.4nm to 104.0nm. Meanwhile, the steady creep rate accelerated form 4.34×10-3 h-1 to 1.87×10-2 h-1, and the creep rupture life shortened from 176h to 94h, and the creep rupture mode transferred from intergranular and transgranular mixed fracture to along PPB fracture. During creep, the micro-twins formation and gliding will be restrained by ∑3 boundaries. FGH96 superalloy with higher oxygen content contains less ∑3 boundaries and its micro-twins cross slipped instead of single direction slip in lower oxygen content superalloy. Consequently, specimen with higher oxygen content creeped faster and raptured earlier.

Drug discovery utilizes high-throughput screening (HTS) methods applying target and cell-based assays. This review discusses the challenges and benefits associated with these assays in HTS. Discussed the strategies that can be applied for the development of screening assays through primary and secondary screens for target identification. Further discussion on identify-ing the most efficacious drugs following these approaches in cancer. Even though various drugs have been identified to treat cancer, there is high demand of more relevant phenotypic assays to produce desired diseased phenotype to only highlighting the specific targets instead of off-targets. Hopefully, the new developing strategies could provide innovative drugs to treat cancer patients to reduce mortality rate.

Tumour spheroids are fast becoming commonplace in basic cancer research and drug development. Obtaining high-quality data relating to the inner structure of spheroids is important for analysis, yet existing techniques often use equipment that is not commonly available, are expensive, laborious, cause significant size distortion, or are limited to relatively small spheroids. We present a high-throughput method of mounting, clearing, and imaging tumour spheroids that causes minimal size distortion. Spheroids are mounted in an agarose gel to prevent movement, cleared using a solution prepared from commonly available materials, and imaged using confocal microscopy. We find that our method yields high quality two- and three-dimensional images that provide information about the inner structure of spheroids.

Automated machine learning (AutoML) has been heralded as the next wave in artificial intelligence with its promise to deliver high performance end-to-end machine learning pipelines with minimal effort from the user. However, despite AutoML showing great promise for computer vision tasks, to the best of our knowledge, no study has used AutoML for image-based plant phenotyping. To address this gap in knowledge, we examined the application of AutoML for image-based plant phenotyping using wheat lodging assessment with UAV imagery as an example. We compared the performance of an open-source AutoML framework, AutoKeras in image classification and regression tasks to transfer learning using modern convolutional neural network (CNN) architectures. For image classification which classified plot images as lodged or non-lodged, transfer learning with Xception and DenseNet-201 achieved best classification accuracy of 93.2%, whereas Autokeras had 92.4% accuracy. For image regression which predicted lodging scores from plot images, transfer learning with DenseNet-201 had the best performance (R2=0.8303, RMSE=9.55, MAE=7.03, MAPE=12.54%), followed closely by AutoKeras (R2=0.8273, RMSE=10.65, MAE=8.24, MAPE=13.87%). Interestingly, in both tasks, AutoKeras models had up to 40-fold faster inference times compared to the pretrained CNNs. The merits and drawbacks of AutoML compared to transfer learning for image-based plant phenotyping are discussed.

The importance of both recycling and additive manufacturing (AM) is increasing, however there has been a limited focus on development of AM alloys that are recyclably compatible with the larger scrap loops of wrought 5xxx, 6xxx and cast 3xx aluminium alloys. In this work the powder bed fusion (PBF) printability of AlMgSi alloys in the interval of 0-30wt%Mg and 0-4wt%Si is screened experimentally with a high throughput method. This method produces PBF mimicked material by PVD co-sputtering followed by laser remelting. Strong evidence was found for AlMgSi alloys being printable in two different composition ranges; Si+Mg<0.7wt% or for Si+2/3Mg>4wt% when Mg < 3wt% and Si > 3wt%. Increasing the amount of Mg and Si influence the grain structure by introducing fine columnar grains at the melt pool boundary, although the melt pool interior was unaffected. Hardness in as-built state increased with both Mg and Si, alt-hough Si had neglectable effect at low levels of Mg. Both evaporative loss of Mg and the amount of Mg in solid solution increased linearly with the amount of Mg.

In order to increase the material throughput of aligned discontinuous fibre composites using technologies such as HiPerDiF, stability of the fibres in an aqueous solution needs to be achieved. Subsequently, a range of surfactants, typically employed to disperse carbon-based materials, have been assessed to determine the most appropriate for use in this regard. The optimum stability of the discontinuous fibres was observed when using the anionic surfactant, sodium dodecylbenzene sulfonate, which was superior to a range of other non-ionic and anionic surfactants and single-fibre fragmentation demonstrated that the employment of sodium dodecylbenzene sulfonate did not effect on the interfacial adhesion between fibres. The use of rheometry was used to complement the study to understand the potential mechanisms of the improved stability of discontinuous fibres in aqueous suspension and it led to the understanding that the increased viscosity was a significant factor. For the shear rates employed, fibre deformation was neither expected nor observed.

One of creators of quantum mechanics P. Jordan in his work on quantum biology claimed that life's missing laws were the rules of chance and probability of the quantum world. The article presents author’s results of studying frequencies (or probabilities) of nucleotides on so-called epi-chains of long DNA sequences of various eukaryotic and prokaryotic genomes. DNA epi-chains are algorithmically constructed subsequencies of DNA nucleotide sequences. According to the algorithm of construction of any epi-chain of the order n, the epi-chain is such nucleotide subsequence, in which the numerations of adjacent nucleotides differ by natural number n (n = 1, 2, 3, 4,…). Correspondingly each epi-chain of order n ≥ 2 contains n times less nucleotides than the original DNA sequence. The presented results unexpectedly discover that in long single-stranded and double-stranded DNA of any tested genome its DNA epi-chains of different orders n (values n are not too large) have practically identical frequencies (or probabilities) of each kind of nucleotides. These data allow considering DNA as a regular rich set of epi-chains, which can play a certain role in genetic and epigenetic phenomena as the author belives. Appropriate rules of nucleotide frequencies on epi-chains of long DNA sequences are formulated for further their tests on a wider set of genomes. These results testify on existence of long-range coherence in long DNA and remind the Fröhlich's theory of long-range coherence in biological systems. The phenomenological data are discussed from different standpoints: the DNA double helices and helical antennas with circular polarizations of electromagnetic waves; relations with the Fröhlich's theory; numerical analysis of DNA epi-chains under binary representations of nucleotides. Results are useful for developing quantum and algebraic biology.

This paper presents a new semi-explicit algorithm for parameters estimation in a time-fractional generalization of dual-phase-lag heat conduction model with the Caputo fractional derivatives. It is shown that this model can be derived from a general linear constitutive relation for the heat transfer by conduction when the heat conduction relaxation kernel contains the Mittag-Leffler function. The model can be used to describe heat conduction phenomena in a material with power-law memory. The proposed algorithm of parameters estimation is based on the time integral characteristics method. The explicit representations of the thermal diffusivity and the fractional analogues of the thermal relaxation time and the thermal retardation are obtained via a Laplace transform of the temperature field and utilized in the algorithm. An implicit relation is derived for the order of fractional differentiation. In the algorithm, this relation is resolved numerically. An example illustrates the proposed technique.

Background: Tetanus is an acute, fatal disease caused by exotoxins released from Clostridium tetani during infections. A protective humoral immune response can be induced by vaccinations with pediatric and booster combinatorial vaccines that contain inactivated tetanus neurotoxin (TeNT) as a major antigen. Although some epitopes in NeNT have been described using various ap-proaches, a comprehensive list of its antigenic determinants that are involved with immunity have not been elucidated. To that end, a high resolution analysis of the linear B-cell epitopes in NeNT was performed using antibodies generated in vaccinated children. Methods: Two hundred sixty-four peptides that cover the entire coding sequence of TeNT protein were prepared in situ on a cellulose membrane by SPOT synthesis and probed with sera from children vaccinated (ChVS) with a triple DTP-vaccine to map continuous B-cell epitopes that were further characterized and validated by immunoassays. Results: Forty-three IgG epitopes were identified. Four (TT-215-218) were chemically synthesized as Multiple Antigen Peptides (MAPs) and used in peptide ELISAs to screen post-pandemic DTP vaccinations. The assay displayed a high performance with high sensitivity (99.99%) and specificity (100%). Conclusions: The complete map of linear IgG epitopes induced by vaccination with inactivated TeNT highlights three key epitopes involved in the ef-ficacy of the vaccine. Antibodies against epitope TT-8/G can block enzymatic activity, and those against epitopes TT-40/G and TT-42/G can interfere with TeNT binding to neuronal cell receptors. We further show that four of the epitopes identified can be employed in peptide ELISAs to assess vaccine coverage. Overall, the data suggest a set of select epitopes to engineer new, directed vaccines

Intratumoral heterogeneity associates with more aggressive disease progression and worse patient outcomes. Understanding the reasons enabling the emergence of such heterogeneity remains incomplete, which restricts our ability to manage it from a therapeutic perspective. Technological advancements such as high-throughput molecular imaging, single-cell omics and spatial transcriptomics now allow recording the patterns of spatiotemporal heterogeneity in a longitudinal manner, thus offering insights into the multi-scale dynamics of its evolution. Here, we review latest technological trends and biological insights from molecular diagnostics as well as spatial transcriptomics, both of which have witnessed a burgeoning growth in recent past in terms of mapping heterogeneity within tumor cell types as well as stromal constitution. We also discuss ongoing challenges, indicating possible ways to integrate insights across these methods to have a systems-level spatiotemporal map of heterogeneity in each tumor, and a more systematic investigation of implications of heterogeneity for the patient outcomes.

State-of-the-art dielectrophoretic (DEP) separation techniques provide unique properties to separate particles from a liquid or particles with different properties such as material, morphology or size from each other. However, such separators do not operate at throughput that is sufficient for a vast fraction of separation tasks. The reason for this limitation is that, in order to move particles by dielectrophoresis, high electric field gradients to drive the separation are required. Conventionally, those gradients are generated by electrode microstructures that limit the maximum channel size. Here, we investigate DEP filtration, a technique that uses open porous microstructures instead of microfluidic devices to easily increase the filter cross section and therefore also the processable throughput by several orders of magnitude. Previously, we already separated baker’s yeast by DEP filtration in open porous ceramic structures. Now, we give a more elaborate experimental study about DEP filtration in these open porous structures and separate model particles, that are an order of magnitude smaller (500 nm, polystyrene), from aqueous suspensions. Almost 100% separation at flow rates of up to 9 mL min^-1 was achieved while the majority of the trapped particles could be recovered. We show how particle separation depends on key parameters (voltage, throughput, filter structure size). Further, we work towards selective particle separation and show that particle separation is very dependent on the particle polarizability: This creates the possibility to adjust selectivity by changing the electrical conductivity of the suspension around that of the particle. This study highlights the unique qualities of dielectrophoretic filtration enabling switchable, selective, and scalable particle separation to solve existing problems such as cell separation or precious metal recovery.

Linear mixed models are frequently used for analysing heterogeneous data in a broad range of applications. The restricted maximum likelihood method is often preferred to estimate co-variance parameters in such models due to its unbiased estimation of the underlying variance parameters. The restricted log-likelihood function involves log determinants of a complicated co-variance matrix. An efficient statistical estimate of the underlying model parameters and quantifying the accuracy of the estimation requires the first derivatives and the second derivatives of the restricted log-likelihood function, i.e., the observed information. Standard approaches to compute the observed information and its expectation, the Fisher information, is computationally prohibitive for linear mixed models with thousands random and fixed effects. Customized algorithms are of highly demand to keep mixed models analysis scalable for increasing high-throughput heterogeneous data sets. In this paper, we explore how to leverage an averaged information splitting technique and dedicate matrix transform to significantly reduce computations and to accelerate computing. Together with a fill-in reducing multi-frontal sparse direct solver, the averaged information splitting approach improves the performance of the computation process.

Rapid development of high-throughput omics technologies generates an increasing interests in algorithms for cutoff point identification. Existing cutoff methods and tools identify cutoff points based on association of continuous variables with another variable, such as phenotype, disease state or treatment group. These approaches are not applicable for descriptive studies in which continuous variables are reported without known association with any biologically meaningful variables. The most common shape of the ranked distribution of continuous variables in high-throughput descriptive studies corresponds to a biphasic exponential/super-exponential curve, where the first phase includes big number of variables with values slowly growing with rank and the second phase includes smaller number of variables rapidly growing with rank. This study describes an easy algorithm to identify the boundary between these phases to be used as a cutoff point. The major assumption of that approach is that small number of variables with high values dominate biological system and determine its major processes and functions. This approach was tested on three different datasets: genes in the human cerebral cortex, mammalian genes sensitive to chemical exposures, and proteins expressed in human heart. In every case, the described cutoff identification method produced shortlists of variables (genes, proteins) highly relevant for dominant functions/pathways of the analyzed biological systems. Thus, our described method for cutoff identification may be used to prioritize variables for a focused functional analysis, in situations where other methods of dichotomization of data are inaccessible.

In the post antimicrobial era, increasing attention is paid towards using bacteriophage (phage in short) therapy to control antibiotic-resistant bacteria. The first step in phage therapy applications is isolating highly efficient lytic phages or phage cocktails from various sources. When a double-layer- agar with around 0.7% agar in top agar is employed, it results in a low number of phage isolation with a poor resolution, and in many cases, you miss the phage. To address this problem, a low concentration of agar in top agar is examined for better phage isolation. Here, our results proved the efficiency of isolating phage upon formulating a double-layer agar with 0.3% agar in top agar. A sewage sample was collected then phages were isolated, purified, and spotted on a top layer agar with 0.3% agar. The results showed the possibility of isolating a higher number of phages on 0.3% top agar than 0.7%. The finding advocates using 0.3% top agar for the double-layer agar, as it will provide fast, better, and easy phage screening and isolation.

SARS-CoV-2 is a betacoronavirus that was first identified during the Wuhan COVID-19 epidemic in 2019. It was listed as a potential global health threat by WHO due to high mortality, high basic reproduction number and lack of clinically approved drugs and vaccines for COVID-19. The genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three dimensional structure of the Main protease (Mpro) are available. The reported structure of the target Mpro was utilized in this study to identify potential drugs for COVID-19 using virtual high throughput screening. The results of this study confirm earlier preliminary reports based on studies of homologs that some of the drugs approved for treatment of other viral infections also have the potential for treatment of COVID-19. Approved anti-viral drugs that target proteases were ranked for potential effectiveness against COVID-19 and novel candidates for drug repurposing were identified.

The B169L protein (pB169L) of African swine fever virus (ASFV) is a structural protein with an unidentified function during the virus replication. The sequences of the B169L gene and the downstream B438L gene are separated by short intergenic regions. However, the regulatory mode of the gene transcription remains unknown. Here, we identified two distinct promoter regions and two transcription start sites (TSS) located upstream of the open reading frame (ORF) of B438L. Using the promoter reporter system, we demonstrated that the cis activity of the ORF proximal promoter exhibited significantly higher levels compared with that of the distal promoter located in the B169L gene. Furthermore, transfection with the plasmids with two different promoters for B438L could initiate the transcription and expression of the B438L gene in HEK293T cells, and the cis activity of the ORF proximal promoter also displayed the higher activities compared with the distal promoter. Interestingly, the B438L distal promoter also initiated the transcription of the alternatively spliced B169L mRNA (B169L mRNA2) encoding a truncated pB169L (tpB169L) (amino acids 92–169), and the gene transcription efficiency was increased upon mutation of the initiation codon located upstream of the alternatively spliced B169L gene. Taken together, we demonstrated that the distal promoter of B438L gene initiates the transcription of both the B438L mRNA and B169L mRNA2. Comprehensive analysis of the transcriptional regulatory mode of the B438L gene is beneficial for the understanding of the association of B438L protein and pB169L and the construction of the gene-deleted ASFV.

The domestic ducks (Anas platyrhynchos domesticus) are resistant to most of the highly pathogenic avian influenza virus (HPAIV) infections. In this study, we characterized the lung proteome and phosphoproteome of ducks infected with HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala) at 12 hr, 48 hr and 5 days post infection condition. Total 2082 proteins were differentially expressed and 320 phosphorylation sites mapping to 199 phosphopeptides corresponding to 129 proteins were identified. Functional annotation of proteome data analysis reveals activation of RIG-I-like receptor and Jak-STAT signaling pathways, that lead to induction of interferon stimulated genes (ISGs) expression. The pathway analysis of phosphoproteome datasets also confirms the activation of RIG I, Jak-STAT signaling, NF-kappa B signaling and MAPK signaling pathways in the lung tissues. The induction of ISGs proteins (STAT1, STAT3, STAT5B, STAT6, IFIT5 and PKR) establishes protective antiviral immune response in duck lung tissue. Further, the protein-protein interaction network analysis identified proteins like AKT1, STAT3, JAK2, RAC1, STAT1, PTPN11, RPS27A, NFKB1 and MAPK1 as main hub proteins that might play important roles in disease progression in ducks. Together, functional annotation of proteome and phosphoproteome datasets reveals the molecular basis of the disease progression and disease resistance mechanism in ducks infected with HPAI H5N1 virus.

Microscopic vision plays an important role in automated micro-assembly. However, some uncertain factors in the assembly process, such as occlusion and stains can lead to the mistakes of feature extraction. Herein, to solve the problem, the deep learning techniques are introduced into the feature recognition tasks, focusing on the attention mechanism and visualizing CNNs for DL-based microscopic vision. The main contributions are summarized as follows: The CBAM attention mechanism is combined with the YOLOv5 algorithm to improve the accuracy and robustness of feature extraction. The micropart feature occlusion experiment results show that at 70% occlusion degree, YOLOV5-CBAM can reach 97.9% [email protected], which is 4.6% higher than the original one. Visualization analysis of DL-based model is conducted using Grad-CAM to make the decision result more transparent and avoid potential visual detection risks during assembly. The heatmap matching degree between GT area and high-light area is increased by 27.81% on average, which further verify the effectiveness of attention mechanism in micropart feature localization. Additionally, micropart surface stain and droplet quality classification models based on ResNet50 are trained to replace the manual sorting. The visual results are consistent with human eye discernment and judgement, confirming the reliability of parts and droplets sorting.

Genetic engineering and directed evolution are effective methods to address the low yield and poor industrialization level of microbial target products. The current research focus is on how to efficiently and rapidly screen beneficial mutants from constructed large-scale mutation libraries. Traditional screening methods such as plate screening and well plate screening are severely limited in their development and application due to their low efficiency and high costs. In the past decade, microfluidic technology has become an important high-throughput screening technology due to its fast speed, low cost, high automation, and high screening throughput, and it has developed rapidly. Droplet-based microfluidic high-throughput screening has been widely used in various fields such as strain/enzyme activity screening, pathogen detection, single-cell analysis, drug discovery, and chemical synthesis, and has been widely applied in industries such as materials, food, chemicals, textiles, and biomedicine. In particular, in the field of enzyme research, droplet-based microfluidic high-throughput screening has shown excellent performance in discovering enzymes with new functions, improved catalytic efficiency or stability, acid-base tolerance, etc. Currently, droplet-based microfluidic high-throughput screening technology has achieved high-throughput screening of enzymes such as glycosidase, lipase, peroxidase, protease, amylase, oxidase, and transaminase, as well as high-throughput detection of products such as riboflavin, coumarin, 3-dehydroquinate, lactic acid, and ethanol. This article reviews the application of droplet-based microfluidics in high-throughput screening, with a focus on high-throughput screening strategies based on UV, visible, and fluorescence spectroscopy, including labeled optical signal detection screening, as well as label-free electrochemical detection, mass spectrometry, Raman spectroscopy, nuclear magnetic resonance, etc. Furthermore, the research progress and development trends of droplet-based microfluidic technology in enzyme modification and strain screening are also introduced.

Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges. Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologies have been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) were developed to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture used solves limitations of previous research and can be used at scale in commercial breeding programs.

The Eastern Kunlun Fault Zone (EKFZ) is located in a seismic blank area. This study investigates the hydrogeochemical characteristics of varied-temperature springs in the EKFZ to understand the relationship between fractures, fluids and earthquakes. It aids in establishing their induction mechanisms and assists in monitoring the earthquake precursors of the EKFZ. In this study, the main elements, trace elements, hydrogen and oxygen isotopes and strontium isotopes of 23 varied-temperature springs in the EKFZ were analyzed. The results reveal the source of groundwater recharge, hydrochemical types, mineral saturation, and for a select few springs indicative of geothermal activity, collected geothermal reservoir temperatures. The study also explores the relationship between earthquakes and springs, identifying sensitive chemical indicators. Based on continuous monitoring at Maqu Station, we found that before the occurrence of the Maerkang Ms 6.0 earthquake, the concentration of Cl− rose by 2.9 times, and 46 days before the Gande earthquake (Ms = 4.7), the concentrations of Na+ and SO42− significantly increased. Finally, a conceptual model of the hydrogeochemistry of springs is presented to describe the groundwater circulation in the study area. This research is of great significance for the analysis of fluid geochemistry in this area and for assessing the seismic hazards of the EKFZ.

Functional impairment of the von Hippel-Lindau (pVHL) tumor suppressor is causative of a familiar increased risk to develop cancer. As E3 substrate recognition particle, pVHL marks for degradation the hypoxia inducible factor 1α (HIF-1α) in normoxic conditions, thus acting as a key regulator of both acute and chronic cell adaptation to hypoxia. Further evidence showed pVHL to also play relevant roles in microtubules stabilization, participate in the formation of the extracellular matrix, as well as to regulate cell senescence and apoptosis. Male mice model carrying VHL gene conditional knockout present significative abnormalities in testis development paired with defects in spermatogenesis and infertility, indicating that pVHL exerts testis-specific roles, at least in mice. Here, we describe 55 novel interactors of the human pVHL obtained by testis-tissue library screening. We show that pVHL interacts with multiple human proteins directly involved in spermatogenesis and reproductive metabolism, suggesting that, in addition to its role in cancer formation, pVHL may be pivotal in the correct gonads development also in human.

Selection of biologically relevant genes from high dimensional expression data is a key research problem in gene expression genomics. Most of the available gene selection methods are either based on relevancy or redundancy measure, which are usually adjudged through post selection classification accuracy. Through these methods the ranking of genes was done on a single high-dimensional expression data, which leads to the selection of spuriously associated and redundant genes. Hence, we developed a statistical approach through combining Support Vector Machine with Maximum Relevance and Minimum Redundancy under a sound statistical setup for the selection of biologically relevant genes. Here, the genes are selected through statistical significance values computed using a non-parametric test statistic under a bootstrap based subject sampling model. Further, a systematic and rigorous evaluation of the proposed approach with nine existing competitive methods was carried on six different real crop gene expression datasets. This performance analysis was carried out under three comparison settings, i.e. subject classification, biological relevant criteria based on quantitative trait loci, and gene ontology. Our analytical results showed that the proposed approach selects genes that are more biologically relevant as compared to the existing methods. Moreover, the proposed approach was also found to be better with respect to the competitive existing methods. The proposed statistical approach provides a framework for combining filter, and wrapper methods of gene selection.

In this study, considering the peroxidase-like activity of the SiO₂@AuNPs nanocomposite, their biochemical properties including, pH stability, cycling stability, shelf stability, and kinetic parameters were investigated. The results revealed that the as-mentioned SiO₂@AuNPs nanocomposite reveal its maximal activity at pH=4.0 along with saving 83.3% of its maximal activity at pH=5.0. Besides, the reusability and shelf-storage studies exhibited that the SiO₂@AuNPs nanocomposite retained 90% and 100% of its initial activity after 5 operational cycles and 30 days of storage, in order. The kinetic parameters of the as-prepared nanozymes were calculated using Menten kinetic model, revealing a V_max of 1.35 µM min^-1 and a K_m as low as 0.06 mM for the SiO₂@AuNPs nanocomposite. Based on the results of this work, the as-prepared SiO₂@AuNPs nanocomposite with intrinsic peroxidase-like activity shows high substrate affinity and catalytic efficiency along with excellent cycling- and shelf-stability, making them suitable for application in peroxidase-mediated reactions instead of the native enzyme.

This mini-review provides an overview of traditional, emerging, and future applications of lactic acid bacteria (LAB) and discusses how genome editing tools can be used to overcome current challenges in all these applications. It also describes currently available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for understanding mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack throughput and the number of genetically tractable strains is still rather limited. Further tool development in this direction will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design-Build-Test-Learn workflow cycle for LAB cell factory development based on systems biology, with “cell factory” expanding beyond its traditional meaning of production strains and making use of high-throughput genome editing tools to advance LAB understanding, applications and strain development.

High-throughput research on bimetallic nanoparticles brought a vast overview of their characteristics and catalytic activities.¹ However, traditional bimetallic nano-allloy quantification methods serving catalyst preparations are not suitable for the fast and robust data output of high-throughput experiments. Hence, this work designed and validated a more fast, more neat, and reliable quantitative analysis using X-ray fluorescence spectroscopy for bimetallic nanoparticles synthesized by high-throughput setups. The results demonstrated this method to be accurate with high precision. Furthermore, the agreement to qualitative results from an energy-dispersive X-ray spectrometer equiped on a scanning electron microscope provided an option to quantify a bimetallic nano-alloy by just analyzing one of the two composing elements. Thus, this method is proved to be highly compatible with high-throughput experiments.

Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological systems. However, of the excellent results that the technique has arrogated, this approach remains computationally expensive, but with the emergence of the new supercomputing technologies bases on graphics processing units graphical processing units-based systems GPUs, the perspective has changed. The GPUs allow performing large and complex simulations at a significantly reduced time. In this work, we present recent innovations in the acceleration of molecular dynamics in GPUs to simulate non-Hamiltonian systems. In particular, we show the performance of measure-preserving geometric integrator in the canonical ensemble, that is, at constant temperature. We provide a validation and performance evaluation of the code by calculating the thermodynamic properties of a Lennard-Jones fluid. Our results are in excellent agreement with reported data reported from literature, which were calculated with CPUs. The scope and limitations for performing simulations of high-throughput MD under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.

Artificial intelligence (AI) driven language models have seen a rapid rise in development, deployment, and adoption over the last few years. This surge has sparked many discussions about their societal and political impact, including political bias. Bias is a crucial topic in the context of large models due to its far-reaching consequences on technology, politics, and society. It significantly influences public perception, decision-making, political discourse, and AI policy governance and ethics. This study investigates political bias through a comparative analysis of four prominent AI models: ChatGPT-4, Perplexity, Google Gemini, and Claude.Through a comprehensive analysis by systematically and categorically evaluating their responses to politically and ideologically charged tests and prompts, utilizing the Pew Research Center’s Political Typology Quiz, the Political Compass assessment, and ISideWith political party quiz, this study identifies significant ideological leanings and the nature of political bias within these models. The findings revealed that ChatGPT-4 and Claude exhibit a liberal bias, Perplexity is more conservative, while Google Gemini adopts more centrist stances. The presence of such biases underscores the critical need for transparency in AI development and the incorporation of diverse training datasets, regular audits, and user education to mitigate these biases. This analysis also advocates for more robust practices and comprehensive frameworks to assess and reduce political bias in AI, ensuring these technologies contribute positively to society and support informed, balanced, and inclusive public discourse, which will point towards neutrality.The results of this study add to the ongoing discourse about the ethical implications and development of AI models, highlighting the critical need to build trust and integrity in AI models. Additionally, future research directions have been outlined to explore and address the complex issue of bias in AI.

This study aimed to evaluate the effects of Blazepod technology when incorporated with various training regimens on the essential elements of physical fitness in volleyball, such as agility, speed, visual response time, and vertical leap. Thirty-six participants (age :17.33±0.48 y, height: 183.78±6.34 cm, weight: 77.14±5.16 kg) were in-volved in this study. In randomized design, three equal groups with two experimental groups and one control group were involved in the study over a period of six weeks: (GE1) used Blazepod technology to workout at a low level; (GE2) used Blazepod technology to workout at a higher intensity; (CG) did not employ Blazepod technology, but it adhered to the same fundamental training curriculum. We conducted agility, speed, reaction time, and vertical jump tests before, midway and after the study to determine optimal training volume, intensity, and frequency. A significant main effect of time (P0.01), and time×group interaction (P>0.001) were found for all tests. Post hoc test showed that the two experimental groups gadget significantly improved in all performance variables (P

The numerical simulation of entropy generation at mixed natural free and forced convection flow in a square lid-driven cavity filled with an eletrically conducting binary fluids saturated porous media in the presence of a magnetic field is performed in this investigation. Both the top and bottom horizontal walls of the cavity are kept at constant and different temperatures while the left and right vertical walls are adiabatic and insulated. The magnetic field is applied in normal direction to the cavity. The Darcy model, including Brinkman term relative to viscous effects and Forchheimer term due to inertial forces, is used for the momentum equations, and the SIMPLER algorithm, based on the control volume finite-element method approach is used to solve the pressure –velocity coupling. The flow pattern and the heat transfer characteristics inside the cavity are presented in the form of isotherms, streamlines and isentropic lines and average Nusselt number trend. The entropy generation rate is determined for various values of Darcy number (10^-3 ≤ Da ≤ 1) and for a range of Hartmann number (0 ≤ Ha ≤ 10²). This study is limited to Pr = 7 which corresponds to water. It is observed that entropy generation is very affected by the variations of dimensionless control parameters considered.

Miscanthus holds a great potential in the frame of the bioeconomy and yield prediction can help improving Miscanthus logistic supply chain. Breeding programs in several countries are attempting to produce high-yielding Miscanthus hybrids better adapted to different climates and end-uses. Multispectral images acquired from unmanned aerial vehicles (UAVs) in Italy and in the UK in 2021 and 2022 were used to investigate the feasibility of high-throughput phenotyping (HTP) of novel Miscanthus hybrids for yield prediction and crop traits estimation. An intercalibration procedure was performed using simulated data from the PROSAIL model to link vegetation indices (VIs) derived from two different multispectral sensors. Random forest algorithm estimated with good accuracy yield traits (light interception, plant height, green leaf biomass and standing biomass) using VIs time series and predicted yield using peak descriptor derived from VIs time series with 2.3 Mg DM ha-1 of RMSE. The study demonstrates the potential of UAVs multispectral in HTP applications and in yield prediction for providing important information needed to increase sustainable biomass production.

The management of brain tumors presents numerous challenges, despite the employment of multimodal therapies including surgical intervention, radiotherapy, chemotherapy, and immunotherapy. Owing to the distinct location of brain tumors and the presence of the blood-brain barrier (BBB), these tumors exhibit considerable heterogeneity and invasiveness at a histological level. Recent advancements in hydrogel research for the local treatment of brain tumors have sought to overcome the primary challenge of delivering therapeutics past the BBB, thereby ensuring efficient accumulation within brain tumor tissues. This article elaborates on various hydrogel-based delivery vectors, examining their efficacy in the local treatment of brain tumors. Additionally, it reviews the fundamental principles involved in designing intelligent hydrogels that can circumvent the BBB and penetrate larger tumor areas, thereby facilitating precise, controlled drug release. Hydrogel-based drug delivery systems (DDSs) are posited to offer a groundbreaking approach in addressing the challenges and limitations inherent in traditional oncological therapies, which are significantly impeded by the unique structural and pathological characteristics of brain tumors.

Soccer is the leading cause of all sports-related ocular injuries in Europe and Israel and leads to blindness at a disproportionately high rate, especially among children (Thompson et al., 2019). With soccer being the most popular sport in the world, it is surprising the only solution to ocular injuries are sports glasses which can cause direct damage to the eye and impair peripheral vision by 15%, calling for an alternative (Smith & Jones, 2020). This work, based on an imported facial model, focuses on both the qualitative and quantitative aspects of building a personalized, low-cost (through optimizing material needed), superior apparatus to conventional sports glasses. The quantitative side examines a modified and model-validated (through a SRS of thirty unique extrapolated points) multivariate linear regression equation, based on horizontal and vertical rotation angles (n=60) trained with residual and computer simulation data, that can accurately extrapolate and quantify ocular impact from all horizontal and vertical rotation angles and a modified Hertzian Contact Stress Equation to determine the thickness of the apparatus using the elasticity modulus, impact force, and geometrical facial and soccer-ball features. The qualitative side examines where firstly, ocular impact is most prevalent, and secondly, where most impact is seen from rotating the ball horizontally and vertically through analysis of Pearson’s Correlation Coefficient at the supraorbital, medial canthus, infraorbital, and lateral canthus regions from both regression equations as well as a cost-benefit analysis for comparison with conventional sports glasses. The findings discovered in this work lay the groundwork for future research to build a customized low-cost ocular injury prevention device which can simultaneously ensure complete ocular safety while enhancing athletic performance for over 250,000,000 players (Johnson & Garcia, 2022).

A comprehensive modeling framework for the thermoforming of polymer matrix woven laminate composite was developed. Two numerical indicators, the slip path length and traction magnitude, have been identified to be positively correlated to matrix smearing and wrinkling defects. The material model has been calibrated with picture-frame experimental results, and the prediction accuracy for intra-ply shear and thickness distribution were examined with measurements on the physically formed parts. Finally, a parametric study was conducted to determine the relationship between various process parameters and the quality of the formed part. For the trapezoidal part, orienting the laminate at 45-degrees to the mold axis reduces the likelihood of matrix smear and wrinkling defects. Although this laminate orientation yielded a greater spatial variation of part thickness, the thickness deviation is lower than that for the 0-degree orientation case. Higher forming rates were found to result in more defects due to increased slip path lengths and traction magnitudes. Optimal forming speeds should balance rapid shaping within the operating temperature window while avoiding tear. It was discovered that shallower molds benefit from faster ramp rates, while deeper molds require slower rates to manage extensive shearing, stretching, and bending. Faster forming rates lead to smaller thickness increases at high intra-ply shear regions, indicating a shift from intra-ply shear to out-of-plane bending due to the visco-plastic effect of the molten laminate, and can negatively impact part quality. Lastly, it was shown that a well-conceived strategy using darts could improve the part quality by reducing the magnitude of the defect indicators.

Ab initio density functional theory molecular dynamics extensive calculations were used for the first time to evaluate stability conditions for relevant phases of InN. In particular, thermal decomposition of InN with formation of N2 molecules and pressure induced wurtzite – rocksalt solid-solid phase transition were established. The results consistent with available experimental data allowed a critical evaluation of potential and limitations of the proposed simulation method. The ab initio molecular dynamics as an efficient tool for simulations of phase transformations of InN including solid-solid structural transition and thermal decomposition with formation of N2 molecules has been demonstrated. It is of high interest because InN being important component of epitaxial quantum structures has still not been obtained as a bulk single crystal making difficult a determination of its basic physical properties and designing new applications.

Two-dimensional (2D) materials have been a research hot topic in the passed decades due to their unique and fascinating properties. Among them, mechanical properties plays an important role for their application. However, there lacks an effective tool for high-throughput calculating, analysing and visualizing the mechanical properties of 2D materials. In this work, we present, mech2d package, a highly automated toolkit for calculating and analysing second-order elastic constants (SOECs) tensor and relevant properties of 2D materials with considering their symmetry. In the mech2d, the SOECs can be fitted by both strain-energy and stress-strain approach, where the energy or strain can be calculated by first-principles engine, such as VASP. As a key feature, the mech2d package can automatically submit and collect the tasks from local or remote machine with robust fault-tolerant ability, make it suitable for high-throughput calculation. The present code has been validated by several common 2D materials, including graphene, black phosphorene, GeSe2 and so on.

Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy [1]. When using taxonomy-dependent alignment-based methods to classify and label reads, such as MEGAN [2], the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (i.e., nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX [3]. Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show differences, which can be notorious when working with RNA-seq (Personal observation; Graphical abstract). These inconsistencies led us to develop the HoSeIn workflow to determine the unequivocal taxonomic and functional profile of environmental samples, based on the assumption that the sequences that correspond to a certain taxon are composed of (Graphical abstract): 1) sequences that were assigned to the same taxon by both homology searches, plus 2) sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one, and vice versa.

Simultaneous measurement of different substances from a single sample is an emerging issue to achieve efficient and high-throughput detection in several fields of application. Although immunoanalytical techniques have well-established and prevailing advantages over alternative screening analytical platforms, one of the incoming challenges for immunoassay is exactly multiplexing. The Lateral Flow Immunoassay (LFIA) is a leading immunoanalytical technique for onsite analysis thanks to its simplicity, rapidity and cost-effectiveness. Moreover, LFIA architecture is adaptable to multiplexing and therefore candidates as a possible answer to the pressing demand of multiplexing point-of-need analysis. The review present an overview of diverse approaches for multiplex LFIA, with a special focus on strategies based on new types of magnetic, fluorescent and colored labels

53% of adults in the US acknowledge racial bias as a significant issue, 23% of Asian adults experience cultural and ethnic bias, and more than 60% conceal their cultural heritage after racial abuse. AI models like ChatGPT and Google Bard, trained on historically biased data, inadvertently amplify racial and ethnic bias and stereotypes. This paper addresses the issue of racial bias in AI models using scientific, evidence-based analysis and auditing processes to identify biased responses from AI models and develop a mitigation tool. The methodology involves creating a comprehensive database of racially biased questions, terms, and phrases from thousands of legal cases, Wikipedia, and surveys, and then testing them on AI Models and analyzing the responses through sentiment analysis and human evaluation, and eventually creation of an 'AI-BiasAudit,' tool having a racial-ethnic database for social science researchers and AI developers to identify and prevent racial bias in AI models.

Isothermal interrupted hot compression tests of 5754 aluminum were conducted on Gleeble-3500 thermo-mechanical simulator at temperature 350 °C and 450 °C, strain rate 0.1 s-1 and 1s−1. These tests simulated flat rolling to investigate how softening behaviors respond to controlled parameters, such as deformation temperature, strain rate and delay times. This data allowed the parameters for the hot rolling process to be optimized. The delay times during interrupted compression vary between 5s and 60s. The dynamic softening at each pass and metadynamic recrystallization at the intervals of deformation passes were analyzed in detail. 0.2% offset yield strength is applied to calculate the softening fraction undergoing metadynamic recrystallization. A kinetic model was developed to describe metadynamic recrystallization behaviors of the hot deformed 5754 aluminum alloy. Furthermore, the time constant for 50% recrystallization was expressed as functions related to the temperature and the strain rate. The experimental and calculated results were found to be in close agreement, which verified the developed model.

Many types of banana (Musa spp.)—one of the most economically important horticultural crops—exist, and their ploidy (diploid, triploid, and tetraploid, usually) and genome types (containing A or/and B genome in most cases) differ. At present, observation and genome type detection are commonly used to identify banana germplasm resources. However, the former is tedious, while the latter cannot distinguish categories below genome types. It is therefore urgent that a simple and effective method for identifying banana germplasm resources is established. We sequenced and analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 62 banana germplasm and found that the sequencing peaks, especially the 20 bp region near the 420 bp position (referred to as the “420 bp region”), exhibited relatively recognizable and repeatable polymorphism characteristics. Using the “420 bp region” as a marker, we were able to quickly distinguish bananas belonging to different genome type groups (comprising the AA, AB, AAA, ABB, AAB, ABBB, AAAB, and AAAA groups) or different subgroups in the same genome type group (for example, the Cavendish, Gros Michel, Red, Lakatan, and Ibota Bota subgroups in the AAA group; and the Pisang Raja, Plantain, Pome and Silk subgroups in the AAB group). Moreover, it appeared that Sanger sequencing of ITS could be used for identifying banana hybrid offspring. These results demonstrated that the banana ITS region contains rich genetic information that is useful for genotyping. In general, ITS sequencing simplifies the classification of banana germplasm resources and has potential application in several areas of Musa improvement.

Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Within these niches, dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The extent to which the microbiome surrounding A. carterae affects its growth and secondary metabolite synthesis is still being assessed, as well as the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers, bacterial populations are likely to be present. In this experiment we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9-6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic-treatment. Multiple antibiotic-resistance genes were identified, as well as evidence that the bacterial population do not contribute to toxic secondary metabolite synthesis.

Plasminogen (Plg) is the inactive form of plasmin (Plm) that exists in two major glycoforms, referred to as glycoforms I and II (GI and GII). In the circulation, Plg assumes an activation-resistant 'closed' conformation via interdomain interactions and is mediated by the lysine binding site (LBS) on the kringle (KR) domains. These inter-domain interactions can be readily disrupted when Plg binds to lysine/arginine residues on protein targets or free L-lysine and analogues. This causes Plg to convert into an 'open' form which is crucial for activation by host activators. In this study, we investigated how various ligands affect the kinetics of Plg conformational change using small-angle X-ray scattering (SAXS). We began by examining the open and closed conformations of Plg using size-exclusion chromatography (SEC) coupled with SAXS. Next, we developed a high throughput (HTP) 96-well SAXS assay setup. This method enables us to determine the Kopen value, which is used to compare ligands’ effect on Plg conformation directly. Based on our analysis using Plg GII, we have found that the Kopen for ε-aminocaproic acid (EACA) is approximately three times greater than that of Tranexamic acid (TXA), which is widely recognized as a highly effective ligand. We demonstrated further that Plg undergoes a conformational change when it binds to the C-terminal peptides of the inhibitor α2-antiplasmin and receptor Plg‑RKT. Our findings suggest that, besides the C-terminal lysine, internal lysine(s) are also necessary for the formation of open Plg. Finally, we compared the conformational changes of Plg GI and GII directly and found that the closed form of GI, which has an N-linked glycosylation, is less stable. To summarize, we have successfully determined the response of Plg to various ligand/receptor peptides by directly measuring the kinetics of its conformational changes.

With a longer-term goal of addressing the comparative behavior of the aqueous halides F$^-$, Cl$^-$, Br$^-$, and I$^-$ on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal $(\mathrm{H_2O})_n\mathrm{X}$ clusters, with X = Cl$^-$, Br$^-$, and I$^-$, exhibit \emph{surface} hydration structures. Computed free energies based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (\emph{ab initio} molecular dynamics) simulation stream. This \emph{rough-landscape} procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect corrected. Nevertheless, this procedure can break down when $n \gtrsim 4$, with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of $(\mathrm{H_2O})_n\mathrm{X}$ clusters, including ramified structures natural in \emph{physical cluster theories.} With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction.

Choline is metabolized by the gut microbiota into trimethylamine (TMA), the precursor of pro-atherosclerotic molecule trimethylamine N-oxide (TMAO). Reduction of TMA formation has been shown to provide to cardioprotective effects, and some phytochemicals may produce such reduction. This study aimed to develop an optimized, high-throughput anaerobic fermentation methodology to study inhibition of choline microbial metabolism into TMA by phenolic compounds with healthy human fecal starter. Optimal fermentation conditions were: 20 % fecal slurry (1:10 in PBS), 100 M choline, and 12 h fermentation. Also, 10 mM of 3,3-dimethyl-1-butanol (DMB) was defined as a positive TMA production inhibitor, achieving a ~50 % reduction in TMA production. Gallic acid and chlorogenic acid reported higher TMA inhibitory potential (maximum of 80 -90 % in. TMA production inhibition), with IC50 around 5 mM. Nor DMB neither gallic acid and chlorogenic acid reduced TMA production through cytotoxic effects, indicating mechanisms such as altered TMA lyase activity or expression.

Accurate measurements of tree height and diameter at breast height (DBH) in forests to evaluate the growth rate of cultivars is still a significant challenge, even when using LiDAR and 3-D modeling. We propose an integrated pipeline methodology to measure the biomass of different tree cultivars in plantation forests with high crown density which that combines unmanned aerial vehicles (UAVs), hyperspectral image sensors, and data processing algorithms using machine learning. Using a planation of Cunninghamia lanceolate, commonly known as Chinese fir, in Fujian, China, images were collected using a hyperspectral camera and orthorectified in HiSpectral Stitcher. Vegetation indices and modeling were processed in Python using decision trees, random forests, support vector machine, and eXtreme Gradient Boosting (XGBoost) third-party libraries. Tree height and DBH of 2880 samples were measured manually and clustering into three groups: “fast growth,” “median,” growth and “normal” growth group, and 19 vegetation indices from 12,000 pixels were abstracted as the input of features for the modeling. After modeling and cross-validation, the classifier generated by random forests had the best prediction accuracy compare to other algorisms (75%). This framework can be applied to other tree species to make management and business decisions.

Direct mass spectrometry-based metabolomics has been widely employed in the last years to characterize metabolic alterations underlying to Alzheimer’s disease development and progression. This high-throughput approach presents a great potential for fast and simultaneous fingerprinting of a vast number of metabolites, which can be applied to multiple biological samples such as serum/plasma, urine, cerebrospinal fluid and tissues. In this review article we present the main advantages and drawbacks of metabolomics based on direct mass spectrometry compared with conventional analytical techniques, and provide a comprehensive revision of the literature on the application of these tools in Alzheimer’s disease research.

Powdery mildew is a severe disease causing substantial yield losses in wheat production worldwide. The Chinese wheat landrace Changanhongmai (CAHM) exhibits high resistance to the physiological race E09 of powdery mildew. This study aims to characterize the powdery mildew resistance gene in CAHM, and develop molecular markers for marker-assisted selection of wheat. To investigate the genetic characteristics of this resistant gene, we developed F1 plants, F2 generation population, and F2:3 families from a cross between CAHM and SY225. Genetic analysis demonstrated that all F1 plants were resistant to the disease, while the ratio of resistant to susceptible plants was 3: 1 in both the F2 population and F2:3 families, indicating that CAHM is inherited in a manner of single dominant powdery mildew resistance gene, which was tentatively designated as PmCAHM. By using bulk segregation analysis, we constructed a genetic map encompassing Xgwm273, Xwmc626, Xgwm11, Xgwm18, Xgdm28, Xgpw7812, Xgpw5195, Xwmc694 and PmCAHM. Among these markers, Xgpw7812 and Xgpw5195 were flanking markers tightly linked to PmCAHM at a genetic distance of 2.5 cM and 8.4 cM, respectively. Furthermore, nullisomic-tetrasomic analysis revealed that PmCAHM is located on chromosome 1B. These results indicate that PmCAHM differs from the internationally recognized powdery mildew resistance genes in both location and source. In addition, a new germplasm/line NW1748 with large seeds and powdery mildew resistance was developed from the cross and back cross populations of Fengyou 1718 (FY1718)/CAHM//FY 1718. Therefore, PmCAHM can serve as a novel powdery mildew resistance source for breeding of wheat by using NW1748 as the donor in the future.

Mutual exclusion algorithms are at the heart of concurrent, distributed/parallel, real-time and operating systems. It is well-known that such algorithms are very difficult to analyze and in the literature different conjectures about starvation-freedom and the number of by-passes (also said the overtaking factor), which in turn affects the (hopefully) bounded waiting time that a process competing for entering the critical section has to suffer before accessing the shared resource, have been formulated for specific algorithms. This paper proposes a novel modelling approach based on Timed Automata and the Uppaal toolset, which proves effective for studying all the properties of a mutual exclusion algorithm for N≥2 processes, by exhaustive model checking. Although the approach, as already confirmed by similar experiments reported in the literature, is not scalable due to state explosion problems, and can be practically applied until N≤5, it is of great value for revealing true properties of analyzed algorithms. For dimensions N>5 the statistical model checker of Uppaal can be used which, although based on simulations, can confirm properties by estimations and probabilities. The paper describes the proposed modelling and verification method and applies it to several mutual exclusion algorithms, thus retrieving known properties but also showing new results about properties often studied only by peer-review and intuitive reasoning.

High resolution information on nucleotide arrangement in the genome of any or-ganism is critical to understand its genetic makeup, function, and evolutionary his-tory. For years, DNA sequencing has provided crucial breakthroughs in the field of genomics and molecular biology. With the advent of technology, Next Generation Sequencing has now transformed the whole genome sequencing prospects, thus unveiling the novel and interesting features of an organism genome that can behold. Next generation sequencing platforms offer realistic approach to identify and anal-yses whole genome with high throughput, accuracy, scalability in a very short time span. Information obtained can be further used in improving our existing healthcare systems, designing novel and personalized therapeutic modules, making the envi-ronment sustainable and proactively preparing ourselves for future pandemics and outbreaks. This article discusses the various NGS technologies and approaches, their advantages, drawbacks, and futuristic usage in different fields. Though still in nascent stages and marred with flaws, with ongoing advancement, NGS will indeed have promising impacts in the future.

The study aimed to investigate the impact of incorporating deep learning strategies in mathematics instruction on students' problem-solving abilities, critical thinking skills, academic achievement, and mathematical skills development. The study population consisted of 280 students, with a sample size of 162 participants. Employing a purely quantitative approach, data collection utilized questionnaires and achievement tests as instruments. Data analysis involved simple linear regression, descriptive analysis, and Pearson correlation. The results of the study revealed that there was no significant enhancement observed in students' problem-solving abilities and critical thinking skills when deep learning strategies were incorporated into mathematics instruction. Additionally, students' attitudes towards deep learning activities in mathematics showed no effect on their academic achievement. Furthermore, students' engagement levels in deep learning activities did not impact their development of mathematical skills. Lastly, the frequency of deep learning activities in the mathematics classroom did not show a significant relationship with students' academic performance. These findings suggest that the implementation of deep learning strategies in mathematics instruction did not yield notable improvements in the specified areas based on the study outcomes.

This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the “gateway microbiomes.” Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness.

Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development have not been studied. Here, we conducted a scRNA-seq survey of cells from sheep from the oocyte to the blastocyst developmental stages. We then carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS). We founded that between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis.

As Artificial Intelligence (AI) technology, particularly Machine Learning algorithms, becomes increasingly ubiquitous, our abilities to understand and interpret AI and machine learning algorithms are becoming increasingly desirable. Visualization has been used as a common tool to view and understand complex machine learning processes. In this paper, we will focus on developing a general framework for the visualization of machine learning models as a scalar valued multi-dimensional function to help users understand how the models behave over different viewing spaces. We first give a formal definition of the visualization problem. Interpolation-based morphing and subspace sampling techniques are applied to generate various renderings through projections and cross-sections of the model space as 3D surfaces or heatmap images. This method will be applied to two real-world datasets and applications: the diagnosis of Alzheimer's Disease (AD) using a human brain networks dataset and a real-world benchmark dataset for predicting home credit default risks. The visualizations show that different machine learning algorithms can behave quite differently under different conditions.

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.

Infectivity assays are the key analytical technology for development of manufacturing processes for virus-based therapeutics. Here, we introduce a novel assay format that utilizes label-free bright field images to determine the kinetics of infection-dependent changes in cell morphology. In particular, cell rounding is directly proportional to the amount of infectious virus applied, enabling rapid determination of viral titers in relation to a standard curve. Our kinetic infectious virus titer (KIT) assay is stability-indicating and, due to its sensitive readout method, provides results within 24 hours post-infection. Compared to traditional infectivity assays, which depend on a single readout of an infection endpoint, cumulated analysis of kinetic data by a fit model results in precise results (CV &lt; 20%) based on only three wells per sample. This approach allows for a high throughput with ~400 samples processed by a single operator per week. We demonstrate the applicability of the KIT assay for VSV-GP and NDV, but it can potentially be extended to a wide range of viruses that induce morphological changes upon infection. The versatility of this assay, combined with its independence from specific instruments or software, makes it a promising solution to overcome the analytical bottleneck in infectivity assays within the pharmaceutical industry and as a routine method in academic research.

Stripe rust ​​(caused by Puccinia striiformis f. sp. tritici) is one of the most devastating diseases of wheat and causes large-scale epidemics and severe yield loss. Applying fungicides during early epidemic development is crucial to controlling the disease but is often challenged by resource-limited human visual scouting. Deep learning has the potential to process images and videos captured from affordable devices to empower high-throughput phenotyping for early detection of stripe rust for timely application of fungicides and improve control efficiency. Here, we developed RustNet, a neural network-based image classifier, for efficiently monitoring fields for stripe rust. RustNet was built on a ResNet-18 architecture pre-trained with ImageNet Large-Scale Visual Recognition Challenge (ILSVRC) dataset using transfer learning. RGB images and videos of multiple wheat fields with different wheat types (winter and spring wheat), conditions (irrigated and non-irrigated), and locations were acquired using smartphones or unmanned aerial vehicles near the canopy. A semi-automated image labeling approach was conducted to improve labeling efficiency by combining automated machine labeling and human correction. Cross-validations across multiple categories (sensor platforms, wheat types, and locations) achieved Area Under Curve from 0.72 to 0.87. Independent validation on a published dataset from Germany achieved accuracies ranging from 0.79 to 0.86. The visualization of the last convolutional layer of RustNet demonstrated the identification of pixels with stripe rust. RustNet is freely available at https://zzlab.net/RustNet.

We use state-of-the-art computer-aided drug design (CADD) techniques to identify prospective inhibitors of the main protease enzyme, 3CLpro of the SARS-CoV-2 virus causing COVID-19. From our screening of over one million compounds including approved drugs, investigational drugs, natural products, and organic compounds, and a rescreening protocol incorporating enzyme dynamics via ensemble docking, we have been able to identify a range of prospective 3CLpro inhibitors. Importantly, some of the identified compounds had previously been reported to exhibit inhibitory activities against the 3CLpro enzyme of the closely related SARS-CoV virus. The top- ranking compounds are characterized by the presence of multiple bi- and monocyclic rings, many of them being heterocycles and aromatic, which are flexibly linked allowing the ligands to adapt to the geometry of the 3CLpro substrate site and involve a high amount of functional groups enabling hydrogen bond formation with surrounding amino acid residues, including the catalytic dyad residues H41 and C145. Among the top binding compounds we identified several tyrosine kinase inhibitors, which include a bioflavonoid, the group of natural products that binds best to 3CLpro. Another class of compounds that decently binds to the SARS-CoV-2 main protease are steroid hormones, which thus may be endogenous inhibitors and might provide an explanation for the age-dependent severity of COVID-19. Many of the compounds identified by our work show a considerably stronger binding than found for reference compounds with in vitro demonstrated 3CLpro inhibition and anticoronavirus activity. The compounds determined in this work thus represent a good starting point for the design of inhibitors of SARS-CoV-2 replication.

Three-dimensional (3D) cell culture is considered more clinically relevant in mimicking the structural and physiological conditions of tumors in vivo compared to two-dimensional cell cultures. In recent years, high-throughput screening (HTS) in 3D cell arrays has been extensively used for drug discovery because of its usability and applicability. Herein, we developed a microfluidic spheroid culture device (μFSCD) with a concentration gradient generator (CGG) that enabled cells to form spheroids and grow in the presence of cancer drug gradients. The device is composed of concave microwells with several serpentine micro-channels which generate a concentration gradient. Once the colon cancer cells (HCT116) formed a single spheroid (approximately 120 μm in diameter) in each microwell, spheroids were perfused in the presence of the cancer drug gradient irinotecan for 3 days. The number of spheroids, roundness, and cell viability, were inversely proportional to the drug concentration. These results suggest that the μFSCD with a CGG has the potential to become an HTS platform for screening the efficacy of cancer drugs.

High-throughput screening of samples is the strategy of choice to detect occupational exposure biomarkers, yet it requires user-friendly apparatus that gives relatively prompt results while ensuring high degrees of selectivity, precision, accuracy and automation, particularly in preparation processes. In the last 10 years, miniaturization has attracted much attention in analytical chemistry and has driven solvent and sample savings and easier automation, the latter thanks to the introduction on the market of three axis autosampler. In light of the above, this contribution describes a novel user-friendly solid-phase microextraction (SPME) off- and on-line platform coupled with gas chromatography triple quadrupole-mass spectrometry to determine urinary 1- and 2-hydroxy-napthalene, 9-hydroxy-phenantrene, 1-hydroxy-pyrene, 3- and 9-hydroxy-benzoantracene and 3-hydroxy-benzo[a]pyrene, metabolites of the related polycyclic aromatic hydrocarbons. In this new procedure chromatography’s sensitivity is combined with the user-friendliness of N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide on-fiber SPME derivatization previous direct immersion sampling, to which is added the quantitative accuracy afforded using specific isotope-labelled internal standards. The detection limits for the seven OH-PAHs were ranged from 0.28 to 1.87 ng/L. Intra-(from 2.5 to 3.0%) and inter-session (from 2.4 to 3.9%) repeatability was also evaluated. This method serves to identify suitable risk-control strategies for occupational hygiene conservation programs

The digital model of airborne frequency selective surface radomes (AFSSRs) is the basis of design, simulation analysis, manufacturing, and other related research of AFSSRs. This paper proposes a rapid modeling method of AFSSRs based on dynamic customizable primitives. Firstly, a layered digital model construction scheme of AFSSR is presented based on the typical radome wall structure. Then, according to the characteristics of various surface configurations and complex wireframe information of AFSSRs, the dynamic primitives are raised to express the boundary and contour information of all kinds of radomes. Focusing on the undevelopable characteristics of the aero-dynamic shape surface of the AFSSR, the arrangement solution and mapping method for frequency selective elements on undevelopable surfaces are proposed. Furthermore, the imple-mentation logic of this method on the creation of each layer model and the assembly of the whole machine model is introduced. Finally, according to this method, a rapid modeling system (RMS) is established, and the modeling effect and efficiency of the RMS are demonstrated and compared, which verifies the feasibility and effectiveness of this method.

The performance of OpenFOAM in strong scaling tests on HPC systems with AMD EPYC processors exhibits a pronounced superlinear speedup. Simple test cases show superlinear speedups of over 300%, which significantly impacts the efficient use of computing resources. With the last generation of HPC architectures, a superlinear speedup of about 10% to 20% was well expected and accepted by CFD users. The measured superlinear speedup is much more pronounced and withstands the communication overhead to even larger scales. A detailed performance analysis of OpenFOAM follows, employing various High-Performance Computing (HPC) architectures, including AMD, ARM and Intel systems. The performance metric FVOPS (Finite VOlumes solved Per Second) is introduced to compare the performance of Computational Fluid Dynamics (CFD) applications when varying the grid size, as occurs in a strong scaling test. The achievable FVOPS depends on various factors, including the simulation type, boundary conditions, and especially the grid size of a use case. Analysing FVOPS on a single node level with varying grid size shows a significant difference in performance and cache utilization, which explains the large superlinear speedups seen in the strong scaling tests. Furthermore, FVOPS can be used as a simple benchmark to determine the optimal number of grid elements per rank to simulate a given use case at peak efficiency on a given platform, resulting in time, energy, and cost savings. The FVOPS metric also facilitates the direct comparison between different HPC architectures. The tests using AMD, ARM, and Intel processors show a peak in performance when employing around 10,000 grid elements per core. The presence of a large L3 cache on AMD processors is particularly advantageous, as indicated by L3 cache miss rates observed on AMD EPYC processors. Our results suggest that future HPC architectures with larger caches and higher memory bandwidth would benefit the CFD community.

In this work, a high throughput nanozymatic method was developed for green nanozyme-mediated biodegradation of organic dyes in real water media. The nanozymes were synthesized and characterized for their size and morphology by TEM and DLS analysis. The nanozymatic properties of the as-prepared nanomaterials were evaluated by standard enzyme activity assay, revealing high peroxidase-like performances for the as-prepared nanozymes. Therefore, for exploring more precise, the kinetics behavior of the as-prepared nanozymes was evaluated by the standard Lineweaver-Burk method, revealing a V_max as high as 0.263 µM sec^-1 and a K_m as low as 0.03 mM, revealing high catalytic efficiency and affinity of the as-prepared nanozymes. Hence, the as-prepared nanozymes were utilized for organic dye degradation in real water media using methylene blue as a model organic dye. The effective factors on the dye degradation including pH, ionic strength, degradation time, nanozyme amount, etc. were optimized by the one-factor-at-a-time optimization method. At optimal experimental conditions, the as-prepared nanozymes can degrade about 99.0% of the organic dye within a degradation time as low as 7 min. The developed method was finally employed for the nanozyme-mediated degradation of methylene blue from real water media such as pool, mineral, river, and tap water samples. The results of this study revealed an excellent biodegradation yield of over 94.3%-99.0% for the different real samples, proving the suitability of the developed method for dye degradation in real water media.

Gene editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a five-week period. In the remote-learning version, students perform homology searches, design guide RNAs and primers, and learn the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as closures that have occurred in response to the Covid-19 pandemic. In the in-person version, students design guide RNAs, clone CRISPR-Cas9 constructs, and perform genetic transformation of the model plant Arabidopsis thaliana. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of course sections available. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be readily adapted to other organisms or projects that employ gene editing.

The controllability and consistency in the fabrication of micro-textures on large-scale remains a challenge for existing production processes. Mask electrolyte jet machining (MEJM) is an alternative to Jet-ECM for controllable and high-throughput surface microfabrication with more consistency of dimensional tolerances. This hybrid configuration combines the high-throughput of masked-ECM and the adjustable flow-field of jet-ECM. In this work, a duckbill jet nozzle was introduced to make MEJM more capable of batch micro-structuring. A multiphysics model was built to simulate the distribution of electrochemical reaction ions, the cur- rent density distribution and the evolution of the shape of the machined cavity. Experimental investigations are presented showing the influence of the machining voltage and nozzle moving speed on the micro cavity. Several 35 ×35 micro cavity arrays with a diameter of 24.92 − 11.73 µm and depth of 15.86 − 7.24 µm are generated on 304 stainless steel.

RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like Illumina's next-generation sequencing (NGS) are used to produce the raw data for this experimental procedure. This raw FASTQ data must then be prepared via a complex series of data manipulations by bioinformaticians. This process currently takes place on an unwieldy textual user interface like a terminal/command line that requires the user to install and import multiple program packages, preventing the untrained biologist from initiating data analysis. Open-source platforms like Galaxy have produced a more user-friendly pipeline, yet the visual interface remains cluttered and highly technical, remaining uninviting for the natural scientist. To address this, SeqMate is a user-friendly tool that allows for one-click analytics by utilizing the power of a large language model (LLM) to automate both data preparation and analysis (differential expression, trajectory analysis, etc). Furthermore, by utilizing the power of generative AI, SeqMate is also capable of analyzing such findings and producing written reports of upregulated/downregulated/user-prompted genes with sources cited from known repositories like PubMed, PDB, and Uniprot.

The rapid and accurate detection of viruses and the discovery of single nucleotide polymorphisms (SNPs) are crucial for disease management and understanding viral evolution. In this study, a pipeline for virus detection, validation, and SNP discovery from next-generation sequencing (NGS) data is presented. By integrating state-of-the-art bioinformatics tools with artificial intelligence, the pipeline processes raw sequencing data to identify viral sequences with high accuracy and sensitivity. Before aligning the reads to the reference genomes, quality control measures and adapter trimming are performed to ensure the integrity of the data. Unmapped reads are subjected to de novo assembly to reveal novel viral sequences and genetic elements. The effectiveness of the pipeline is demonstrated by the identification of virus sequences, illustrating its potential for the detection of known and emerging pathogens. SNP discovery is performed using a custom Python script that compares the entire population of sequenced viral reads to a reference genome. This approach provides a comprehensive overview of viral genetic diversity and identifies dominant variants and a spectrum of genetic variations. The robustness of the pipeline is confirmed by the recovery of complete viral sequences, which improves our understanding of viral genomics. This study highlights the synergy between traditional bioinformatics techniques and modern approaches, providing a robust tool for analyzing viral genomes and contributing to the broader field of viral genomics.

In a search for a reliable, inexpensive, and versatile technique for high-throughput kinetic assays of drug metabolism, we elected to rehire an old-school approach based on the determination of formaldehyde (FA) formed in cytochrome P450-dependent demethylation reactions. After evaluating several fluorometric techniques of FA detection, we choose the method based on the Hantzsch reaction with acetoacetanilide as the most sensitive, robust, and adaptable to high-throughput implementation. Here we provide a detailed protocol for the use of our new technique for automatized assays of cytochrome P450-dependent drug demethylations and discuss its applicability for high-throughput scanning of the pathways of drug metabolism in the human liver. To probe our method further, we applied it to re-evaluating the pathways of metabolism of ketamine, a dissociative anesthetic, and potent antidepressant increasingly used in the treatment of alcohol withdrawal syndrome. Probing the kinetic parameters of ketamine demethylation by 11 major cytochrome P450 (CYP) enzymes, we demonstrate that besides CYP2B6 and CYP3A enzymes, which were initially recognized as the primary metabolizers of ketamine, an important role is also played by CYP2C19, and CYP2D6, while the involvement of CYP2C9 suggested in the previous reports deemed insignificant.

Lyme disease (LD) is a tick-transmitted infection caused by Borrelia burgdorferi sensu lato species which includes B. burgdorferi, B. afzelii, and B. garinii. The majority of patients with early LD can be cured by standard treatment, yet some still suffer from post-treatment Lyme disease syndrome (PTLDS). The presence of Borrelia persisters has been proposed as a contributing factor, which cannnot be completely killed by the currently used antibiotics for Lyme disease. Finding new pharmaceuticals targeting Borrelia persisters is crucial in developing more effective treatment. Here, we first confirmed the existence of persisters in cultures of B. garinii and B. afzelii and then conducted high-throughput screening of a custom drug library against persister-rich stationary-phase cultures of B. garinii and B. afzelii. Among 2427 compounds screened, hypocrellin A (HA), anthracycline class of drugs, and topical antibiotics along with some other natural compounds were identified to have strong potential in killing persisters of B. garinii and B. afzelii. HA was the most active anti-Borrelia compound, capable of eradicating stationary-phase Borrelia persisters, in particular when combined with doxycycline and/or ceftriaxone. Liposoluble antioxidant vitamin E was found to antagonize the activity of HA, indicating HA’s target is the cell membrane where HA-triggered reactive oxygen species (ROS) generation took place in the presence of light. HA was found to have distinct bactericidal activity against Borrelia species but had poor or no activity against Gram-positive and Gram-negative bacteria. Identification of the above-mentioned drug candidates may help to develop more effective therapies for LD.

Sideroflexins (SFXN) are evolutionarily conserved mitochondrial carriers belonging to the SCL56 family. Until recently, the metabolites transported by SFXN were unknown and they were thought to be transporters of a metabolite involved in iron homeostasis. SFXN1 is now known as the mitochondrial serine transporter. Because little is known about SFXN1 interactome, we launched a high-throughput search of SFXN1 binding partners with the aim to better understand its mitochondrial functions. Using a large-scale identification of SFXN1 physical partners based on co-immunoprecipitation followed by shotgun mass spectrometry (coIP-MS), we identified 96 putative SFXN1 interactants in the MCF7 human cell line. Our in-silico analysis of the SFXN1 interactome highlights biological processes linked to mitochondrial organization, electron transport chain and transmembrane transport. Among SFXN1 potential physical partners, ATAD3A and 17-HSD10, two proteins associated with neurological disorders and neurodegeneration, were further confirmed as interactants using different human cell lines. Further work will be needed to investigate the significance of these interactions in neurological disorders.

Spontaneous tumours in higher plants can develop depending on plant genotype without any pathogen invasion. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this work, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We have identified numerous single nucleotide variants (amino acid substitutions, insertions or deletions) that are likely to be associated with the spontaneous tumour formation. Furthermore, we performed the identification of CLE and WOX genes the genomic sequences of the radish inbred lines and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

Using the example of III-V nitrides crystallizing in a wurtzite structure (GaN, AlN, InN), this review presents the special role of hydrostatic pressure in studying semiconductor properties. Starting with a brief description of high pressure techniques for growing bulk crystals of nitride compounds, we focus on the use of hydrostatic pressure techniques in both experimental and theoretical investigations of special properties of nitride compounds, their alloys and quantum structures. The band gap pressure coefficient is one of the most important parameters in semiconductor physics. Trends in its behavior in nitride structures, together with trends in pressure-induced phase transitions, are discussed in the context of the behavior of other typical semiconductors. Using InN as an example, the pressure-dependent effects typical of very narrow bandgap materials, such as conduction band filling or effective mass behavior, are described. Interesting aspects of bandgap bowing in In-containing nitride alloys, including pressure and clustering effects, are discussed.Hydrostatic pressure also plays an important role in the study of native defects and impurities, as illustrated by the example of nitride compounds and their quantum structures. Experiments and theoretical studies on this topic are reviewed. Special attention is given to hydrostatic pressure and strain effects in short periods nitride superlattices. The explanation of the discrepancies between theory and experiment in the optical emission and its pressure dependence from InN/GaN superlattices led to the well-documented conclusion that InN growth on the GaN substrate is not possible. The built-in electric field present in InGaN/GaN and AlGaN/GaN heterostructures crystallizing in wurtzite lattice can reach several MV/cm, leading to drastic changes in the physical properties of these structures and related devices. It is shown how hydrostatic pressure modifies these effects and helps to understand their origin.

Despite significant advancements in Artificial Intelligence (AI) and Large Language Models (LLMs), detecting and mitigating bias remains a critical challenge, particularly within social media platforms like X (formerly Twitter) and in addressing cyberbullying present on them. This research investigates the effectiveness of leading LLMs in generating synthetic biased and cyberbullying data and evaluates the proficiency of Transformer AI models in detecting bias and cyberbullying within both authentic and synthetic contexts. The study involves semantic analysis and feature engineering on a dataset of over 48,000 sentences related to cyberbullying collected from Twitter (before it became X). Leveraging state-of-the-art LLMs such as ChatGPT-4o, Pi AI, Claude 3 Opus, and Gemini-1.5, synthetic biased, cyberbullying, and neutral data were generated to deepen the understanding of bias in human-generated data. AI models including DeBERTa, Longformer, BigBird, HateBERT, MobileBERT, DistilBERT, BERT, RoBERTa, ELECTRA, and XLNet were initially trained to classify Twitter cyberbullying data and subsequently fine-tuned, optimized, and quantized for multilabel classification (detecting both biases and cyberbullying). The study's outcomes include a prototype of a hybrid application that combines a Bias Data Detector and a Bias Data Generator, validated through extensive testing.

The statistical analysis of impact of the top 50 solar flares of X-class (1997-2023) on the global seismic activity, as well as on the earthquake preparation zones located in illuminated part of the globe and in the area of 5000 km radius around the subsolar point was carried out. It is shown by a method of epoch superposition that for all cases the increase of seismicity is observed, especially in the region around the subsolar point (up to 38%) during 10 days after the solar flare in comparison with preceding 10 days. The case study of aftershock sequence of strong M=9.1 earthquake (Su-matra-Andaman Islands, 26.12.2004) after the solar flare of X7.2 class (20.01.2005) demonstrated that the number of aftershocks with magnitude M≥2.5 increases more than 20 times after the solar flare with a delay of 7 days. For the case of the Darfield earthquake (M=7.1, 04.09.2010, New Zealand) it was shown that strong solar flares of class X and M probably triggered two strong aftershocks (M>6) with the same delay of 6 days on the Port Hills fault, which is the most sensitive to external electromagnetic impact from point of view of the fault electrical conductivity and orientation. Based on the obtained results the possible application of natural electromagnetic triggering of earthquakes is discussed for a short-term earthquake prediction using confidently recorded strong external electromagnetic triggering impacts on the specific earthquake preparation zones, as well as ionospheric perturbations due to aerosol emission from the earthquake sources recorded by satellites.

DNA sequencing methods were first developed more than 20 years ago with the publication of two approaches to sequencing methodology that became known as Sanger sequencing (1), based on enzymatic synthesis from a single-stranded DNA template with chain termination using dideoxynucleotides (ddNTPs) and Maxim-Gilbert sequencing (2),which involved chemical degradation ofend-radio-labeled DNA fragments. Both methods relied on four-lane,high resolution polyacrylamide gel electrophoresis to separate the labeled fragment and allow the base sequence to be read in a staggered ladder-like fashion. Sanger sequencing was technically easier and faster, and thus became the main DNA sequencing method for the vast majority of applications.

A recently-validated and underexplored drug target in Mycobacterium tuberculosis is PptT, an essential phosphopantetheinyl transferase (PPTase) that plays a critical role in activating enzymes for both primary and secondary metabolism. PptT possesses a deep binding pocket that does not readily accept labelled coenzyme A analogues that have previously been used to screen for PPTase inhibitors. Here we report on the development of a high throughput, colorimetric screen that monitors the PptT-mediated activation of the non-ribosomal peptide synthetase BpsA to a blue pigment (indigoidine) synthesising form in vitro. This screen uses unadulterated coenzyme A, avoiding analogues that may interfere with inhibitor binding, and requires only a single-endpoint measurement. We benchmark the screen using the well-characterised Library of Pharmaceutically Active Compounds (LOPAC1280) collection, and show that it is both sensitive and able to distinguish weak from strong inhibitors. We further show that the BpsA assay can be applied to quantify the level of inhibition and generate consistent EC50 data.

MiRNAs are 20-22 nucleotide long single-stranded non-coding RNA sequences, which can regulate post transcriptional activity of mRNA by binding with it at 3’UTR region (untranslated region). Thus deregulation of miRNA expression is responsible for dysregulating mRNA function which contributes in developing various diseases as well as cancerous phenotypes. Alteration of single nucleotide in miRNA sequence is one of the reasons behind deregulation of miRNA expression. The most frequent carcinoma in current day is breast cancer which causes a high mortality among women around the world as well as India. Despite of the advancement of diagnostic tools, strategies and treatment, the cases of breast cancer is increasing every year. There are plenty of biomarkers like ER, PR, Her2, Ki-67, etc available which are frequently used in diagnosis and treatment of breast cancer. After the discovery of MiRNA in 1993 in Caenorhabiditis elegans, it is attracting all the limelight in diagnosis and treatment of different carcinomas as well as breast cancer. In this review we will discuss on involvement of different types of MiRNAs and miR SNPs in breast cancer occurrence and susceptibility in a detailed manner.

Trio-based exome sequencing and high-resolution HLA typing were employed to analyze three patients with autoimmune adrenal insufficiency (AAI), including those with autoimmune polyglandular syndrome (APS) type 2, as well as their parents. Benign or likely benign variants of the AIRE gene were identified in all participants of the study. These variants, coupled with clinical data and the results of antibody studies to type I interferons, helped to exclude APS-1. Patients with APS-2, in contrast to patient with AAI, inherited distinct variants of unknown significance in the CLEC16A gene, which is associated with autoimmune diseases including AAI. Various risk alleles in other genes associated with autoimmunity were identified in all patients. HLA typing of second class loci revealed alleles related to APS types 2, 3, and 4. Nevertheless, the frequencies of the haplotypes identified are substantial in the healthy Russian population, precluding from regarding these alleles as genetic determinants linked to APS development. Immunological examination can detect antibody carriers and predict the risk of autoimmune disease development. In the future, to identify genetic predictors of autoimmune endocrinopathies, it is recommended to analyze the whole genome of patients and their relatives, examining clinically relevant variants in non-coding regions.

The genetic aetiology of familial glioma is largely unknown. To gain further insight into the role of rare disruptive variants we performed whole exome sequencing (WES) of 17 glioma families, identifying two families where loss of function mutations in dynein axonemal heavy chain 11 (DNAH11) co-segregated with glioma (DNAH11 p.Ser1470ArgfsTer6 and p.Thr3900Lys) and single families implicating Telomere Replication Complex Component 1 (CTC1 p.Leu1058ProfsTer32) and filamin alpha (FLNA p.Ser1356Phe). We complemented linkage analysis by WES of 150 additional unrelated familial glioma cases and conducting gene burden tests leveraging WES data on 691 cases of glioma from TCGA. Our analysis does not provide support for a hitherto unidentified major cancer gene for glioma but highlights a series of novel candidate predisposition variants/genes, worthy of further investigation to shed light on glioma risk.

During the high-speed flight of a vehicle in the atmosphere, surface friction with the air generates aerodynamic heating. The aerodynamic heating phenomenon can create extremely high temperatures near the surface. These high temperatures impact material properties and the structure of the aircraft, so thermal deformation measurement is essential in aerospace engineering. This paper revisits high-temperature deformation measurement using the digital image correlation (DIC) technique under high-intensity blackbody radiation with a precise speckle pattern fabrication and a heat haze reduction method. The effect of speckle pattern on the DIC measurement has been thoroughly studied at room temperature, but high-temperature measurement studies have not reported such effects so far. We found that the commonly used methods to reduce the heat haze effect could produce incorrect results. Hence, we propose a new method to mitigate heat haze effects. An infrared radiation heater was employed to make an experimental setup that could heat a specimen up to 950 ℃. First, we mitigated image saturation using a short-wavelength bandpass filter with blue light illumination, a standard procedure for high-temperature DIC deformation measurement. Second, we studied how to determine the proper size of the speckle pattern under a high-temperature environment. Third, we devised a reduction method for the heat haze effect. As proof of the effectiveness of our developed experimental method, we successfully measured the deformation of stainless steel 304 specimens from 25 ℃ to 800 ℃. The results confirmed that this method can be applied to the research and development of thermal protection systems in the aerospace field.

Species identification and phylogenetic relationships clarification are fundamental goals in species delimitation. Yet these tasks pose challenges when based on morphologies, geographic distribution, and genomic data. Previously, two new species of fern genus Bolbitis, B. × multipinna and B. longiaurita, were described based on morphological traits, are phylogenetically intertwined with B. sinensis and fail to form monophyletic groups. To address the unclear phylogenetic relationships within the B. sinensis species complex, RAD sequencing was performed on 65 individuals from five populations. Our integrated analysis of phylogenetic tree, neighbor net, and genetic structure, indicate that the B. sinensis species complex should not be considered as separate species. Moreover, our findings reveal differences in the degree of genetic differentiation among five populations, ranged from low to moderate, which might be influenced by geographical distance and gene flow. The Fst values also confirmed that genetic differentiation intensifies with increasing geographic distance. Collectively, this study clarifies the complex phylogenetic relationships within the B. sinensis species complex, elucidates the genetic diversity and differentiation across the studied populations, and offers valuable genetic insights that contribute to the broader study of evolutionary relationships and population genetics within the Bolbitis species.

Rapid isolation of white blood cells (WBCs) from whole blood is an essential part of any WBC examination platform. However, most conventional cell separation techniques are labor-intensive and low throughput, require large volumes of samples, need extensive cell manipulation, and have low purity. To address these challenges, we report the design and fabrication of a passive, label-free microfluidic device with a unique U-shaped cross-section to separate WBCs from whole blood using hydrodynamic forces that exist in a microchannel with curvilinear geometry. It is shown that the spiral microchannel with a U-shaped cross-section concentrates larger blood cells (e.g., WBCs) in the inner cross-section of the microchannel by moving smaller blood cells (e.g., red blood cells (RBCs) and platelets) to the outer microchannel section and preventing them from returning to the inner microchannel section. Therefore, it overcomes the major limitation of a rectangular cross-section where secondary Dean vortices constantly enforce particles throughout the entire cross-section and decrease its isolation efficiency. Under optimal settings, more than 95% of WBCs can be isolated from whole blood under high-throughput (6 ml/min), high-purity (88%), and high-capacity (180 ml of sample in 1 hour) conditions. High efficiency, fast processing time, and non-invasive WBC isolation from large blood samples without centrifugation, RBC lysis, cell biomarkers, and chemical pre-treatments make this method an ideal choice for downstream cell study platforms.

In this paper, we focus on the impact of financial liberalization on stability of emerging stock market. We identify crises in a group of Latin American (Argentina, Brazil and Chile) and Asian countries (Philippines, Korea, Taiwan and Thailand) during 1975–2005. This paper aims to apply the methodology of CMAX method. Our results indicate that liberalization triggers more unstable stock market in the short run and generate several crises. Still, liberalization seems to generate more stable financial markets in the long run. Financial liberalization does not increase the frequency of crises in emerging countries and at long-term, crises are less several.

Type 2 diabetes (T2D) is a chronic systemic disease with a complex etiology, characterized by insulin resistance and mitochondrial dysfunction in various cell tissues. To explore this relationship, we conducted a secondary analysis of complete mtDNA sequences from 1,261 T2D patients and 1,105 control individuals. Our findings revealed significant associations between certain single nucleotide polymorphisms (SNPs) and T2D. Notably, the variants m.1438A>G (controls: 32 [27.6%], T2D: 84 [72.4%]; OR: 2.46; 95%CI: 1.64-3.78; p<0.001), m.14766C>T (controls: 498 [36.9%], T2D: 853 [63.1%]; OR: 2.57, 95%CI: 2.18-3.04, p<0.001), and m.16519T>C (controls: 363 [43.4%], T2D: 474 [56.6%]; OR: 1.24, 95%CI: 1.05-1.47, p=0.012) were significantly associated with diabetes probability. The variant m.16189T>C Previously reported in multiple studies in different populations, it was not found to be associated with T2D in our analysis (controls: 148 [13.39] T2D: 171 [13.56%]; OR: 1.03; 95%CI: 0.815-1.31,; p=0.83). These results provide evidence suggesting a link between some mtDNA polymorphisms and T2D, probably related to association rules and topological patterns and three-dimensional confirmation associated to regions where the changes are, rather than to point mutations in the sequence.