The breast holds significant importance in women's lactation process. The breast has diverse tissues such as glandular, Cooper’s ligament, lactiferous ducts, adipose, muscles, and skin with various mechanical properties. Most soft tissues exhibit nonlinear, viscoelastic, and anisotropic mechanical behaviour. Stiffness is one of the commonly used mechanical properties for measuring mechanical behaviour in soft tissues. However, this is typically used in simplifying cases where analysis is limited to within the linear elastic region. Young’s modulus is the prevailing measure for quantifying stiffness in tissues. This systematic review examines commonly used techniques for mechanically characterising breast soft tissues to close the gap in the literature. Additionally, this systematic review summarises the mechanical behaviour of the breast tissues available in the literature and highlights the uncovered areas to understand the mechanical behaviour of breast tissues fully. These include a) more mechanical behaviour studies, allowing more accurate modelling for other applications, b) Viscoelastic analysis studies, and c) mechanical analysis on other breast tissues, such as the lactiferous duct, also known as the milk duct. The data obtained in the review can be used as inputs in computational models to analyse the behaviour of the breast tissues.

In this paper, we introduce a specialized, fully automated experimental arrangement designed for assessing the effectiveness of augmented and virtual reality technologies in healthcare setting and explore its design principles focusing on depth sensor characterization. The main goal of this project is to establish a robust benchtop platform for the quantitative evaluation of extended reality technologies in a controlled environment, emphasizing the practical assessment of augmented reality head-mounted devices. We outline a design concept and considerations for an experimental configuration aimed at creating a realistic testing environment. This apparatus comprises an observation platform mounted on a three-degree-of-freedom motorized system and a test phantom stage. Focusing on real-case scenarios, we utilized a range of sensors, including readily available range-sensing cameras and commercial augmented reality headsets, such as the Intel RealSense L515 LiDAR camera, mounted on the motion control system. The setup enabled automated data collection and facilitates controlled assessments and validation of various facets of augmented reality technologies, including object, hand, and head tracking, as well as static and dynamic image registration. This paper describes the system architecture, the process of automated data collection, and presents several evaluation studies conducted with this setup, providing insights into the quality and temporal noise associated with static or moving objects or observers in augmented reality applications.

Infrared thermography has already been proven to be a significant method in non-destructive evaluation since it gives information with immediacy, rapidity and low cost. However, the thorniest issue for wider application of IRT is the quantification. In this work, we proposed a specific depth quantifying technique by employing the Gated Recurrent Units (GRU) in composite material samples via pulsed thermography (PT). Carbon Fiber Reinforced Polymer(CFRP) embedded with flat bottom holes were designed via Finite Element Method (FEM) modeling in order to precisely control the depth and geometrics of the defects. The GRU model automatically quantified the depth of defects presented in the CFRP material. The proposed method evaluated the accuracy and performance of synthetic CFRP data from FEM for defect depth predictions.

In the field of quality control, the critical challenge of analyzing microdefects in steel filament holds significant importance. This is particularly vital as steel filaments serve as reinforced fibers in the use and applications within various component manufacturing industries. This paper addresses the crucial requirement of identifying and investigating microdefects on steel filaments. Eddy current signals are used for the identification of microdefects, and an in-depth investigation is conducted. The core objective is to establish the relationship between the depth of defects and the signals detected through the eddy current sensing principle. The threshold of eddy current instrument was set at 10%, corresponding to a created depth of 20 µm, to identify defective specimens. A total of 30 defective samples were analyzed, and the phase angles between the experimental and theoretical results were compared. The depths of defects ranged from 20 to 60 µm, with one sample having a depth exceeding 75 µm. The calculated threshold of 10.18% closely aligns with the set threshold of 10%, with a difference of only 1.77%. The resulting root mean square error (RMSE) was found to be 10.53 degrees, equivalent to 3.49 µm for the difference in depth and phase between measured results and estimated results. This underscores the methodology's accuracy and its applicability across diverse manufacturing industries.

Depth-sensing technology has led to broad applications of inexpensive depth cameras that can capture human motion and scenes in 3D space. Background subtraction algorithms can be improved by fusing color and depth cues, thereby allowing many issues encountered in classical color segmentation to be solved. In this paper, we propose a new fusion method that combines depth and color information for foreground segmentation based on an advanced color-based algorithm. First, a background model and a depth model are developed. Then, based on these models, we propose a new updating strategy that can eliminate ghosting and black shadows almost completely. Extensive experiments have been performed to compare the proposed algorithm with other, conventional RGB-D algorithms. The experimental results suggest that our method extracts foregrounds with higher effectiveness and efficiency.

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.

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.

Air pollution is a critical issue impacting urban environments, leading to severe health problems and environmental degradation. This comprehensive review examines the potential of green systems—specifically green walls, active green walls, and urban greenery systems—to mitigate atmospheric pollutants such as particulate matter (PM), volatile organic compounds (VOCs), and carbon dioxide (CO2). By systematically analyzing 44 recent studies, the review highlights the pollutant capture efficiency of various green technologies and plant species in both indoor and outdoor settings. Active green walls, particularly those utilizing plant species such as Chlorophytum comosum and Sansevieria trifasciata, were found to be highly effective, with VOC reduction efficiencies up to 96.34%, PM reductions by 65.42%, and CO2 reduction rates reaching 4.8% under optimal conditions. The review identifies key strengths in current research, including diverse experimental setups and the use of sophisticated measurement techniques, but also notes significant limitations such as variability in experimental conditions and a lack of long-term performance data. The study underscores the importance of proper maintenance to sustain green systems' efficacy and highlights the potential issue of pollutant resuspension, which remains under-researched. Practical implications for urban planning are discussed, advocating for the integration of effective green systems into urban infrastructure to enhance air quality and public health. Recommendations for future research include the need for standardized metrics, long-term studies, economic feasibility analyses, and real-world validation of simulation models to better understand and optimize green systems for urban air pollution mitigation.

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.

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.

Neural radiance fields (NeRF) leverage a neural representation to encode scenes, obtaining photo-realistic rendering of novel views. However, NeRF has notable limitations. A significant drawback is that it does not capture surface geometry and only renders the object surface colors. Furthermore, the training of NeRF is exceedingly time-consuming. We propose Depth-NeRF as a solution to these issues. Specifically, our approach employs a fast depth completion algorithm to denoise and complete the depth maps generated by RGB-D cameras. These improved depth maps guide the sampling points of NeRF to be distributed closer to the scene's surface, benefiting from dense depth information. Furthermore, we have optimized the network structure of NeRF and integrated depth information to constrain the optimization process, ensuring that the termination distribution of the ray is consistent with the scene’s geometry. Compared to NeRF, our method accelerates the training speed by 18% and significantly reduces the RMSE between the rendered scene depth and the ground truth depth, which indicates that our method can better capture the geometric information of the scene. With these improvements, we can train the NeRF model more efficiently and achieve more accurate rendering results.

The advancement in science and technology has led to luffa sponge (LS) being widely used as a natural material in industrial application as its polyporous structure and light texture. In order to enhance the utility of LS fibers as the reinforcement of lightweight composite materials, this study investigate its water absorption, mechanical properties, anatomical characteristic and thermal performance. Hence, moisture regain, tensile properties of LS fiber bundles were measured in accordance with standards and the structural characteristics were investigated via microscopic observation. Scanning electron microscopy (SEM) was used to observe the surface morphology and fracture surface of fiber bundles. Test results shows that the special structure where the phloem tissues degenerate to cavities had a significant influence on the mechanical properties of LS fiber bundles. Additionally, the transverse sectional area occupied by fibers in a fiber bundle (SF), wall thickness and ratio of wall to lumen of fiber cell, and crystallinity of cellulose had an impact on the mechanical properties of LS fiber bundles. Furthermore, the fiber bundles density of LS varies range of 385.46-468.70 kg/m³, much less than that of jute (1360.40 kg/m³) and Arenga engleri (950.20 kg/m³) while LS fiber bundles has superior specific modulus.

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.

(1) Background: The study of microbiome is being crucial for his role in major systemic diseases, in particular the oral and gut microbiota. In the last years the study of microorganism correlated for example with neurodegenerative disease is increasing the prospective of a possible link between gut microbiota and brain. Here we report a new case report about a patient evaluated genetically firstly for dementia and late-onset dyskinesia, and then tested with 16S metagenomics sequencing. (2) Methods: Starting from buccal swab, we extracted bacterial DNA and then we performed a NGS metagenomics sequencing based on the amplification of hypervariable regions of the 16S in bacteria. (3) Results: The sequencing revealed the presence of Spirochaetes Phylum, a pathogenic bacterium generally known to be able to migrate to the Central Nervous System and not only. (4) Conclusions: Oral infections as our results shows could be possible contributing factors to various neurodegenerative conditions.

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.

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.

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.

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.

Due to the extraordinary mechanical properties of ultra-high-performance concrete (UHPC), the shear stirrups in UHPC beams could potentially be removed. The aim of this study is to determine the effect of beam height and steel fiber volume content on the shear behavior of non-stirrup UHPC beams under a larger shear span-depth ratio (up to 2.8). Eight beams were designed and fabricated, including six non-stirrup UHPC beams and two comparing stirrup-reinforced normal concrete (NC) beams. The experimental results demonstrated that the volume content of steel fiber could be a crucial factor affecting the ductility, cracking strength, and shear strength of non-stirrup UHPC beams and altering their failure modes. Additionally, the height of the beam had a considerable effect on its shear resistance. This study revealed that the French standard formulae were more accurate for the UHPC beams with larger shear span-depth ratios and PCI-2021 formulae greatly overestimate the shear capacity of UHPC beams with larger shear span-depth ratios. Xu’s formulae were more accurate for the steel fiber-reinforced UHPC beams with larger shear span-depth ratios.

: In this paper we present an optimization of the planar manufacturing scheme for stretch-free, shape induced metal interconnects to simplify the fabrication with the aim of maximizing the flexibility in the structure regarding to stress and strain. The Formation of trenches between silicon islands are actively used in the lithographic process to create arc shape structures by spin coating resist into the trenches. The resulting resist form is used as a template for the metal lines, which are structured on top. Because this arc shape is beneficial for the flexibility of these bridges. The trench depth as a key parameter for the stress distribution is investigated by applying numerical simulations. The simulated results show that the increase in penetration depth of the metal bridge into the trench increases the tensile load which is converted into a shear Force Q(x), that usually leads to increased strains the structure can generate. For the fabrication the filling of the trenches with resist is optimized by varying the spin speed. Compared to the theoretical resistance, the current-voltage measurements of the metal bridges show a similar behavior and almost every structural variation is capable of functioning as a flexible electrical interconnect in a complete island-bridge array.

With the progression of AI, embedding advanced AI technologies into small robotics and mobile devices has become essential, driving research towards lightweighting AI models. Our study enhances the EPINET depth estimation model for light field images, aiming for compactness and faster inference while preserving accuracy. We conducted two-step experiments aimed at enhancing inference efficiency: Initially, by adjusting input streams and convolution layers, we simplified the CNN model, achieving faster inference times at the cost of reduced accuracy. To address this reduction in accuracy, we then applied knowledge distillation, allowing the simplified model to learn from the original model’s more complex patterns. In our quantitative experiments using two error metrics, MSE (Mean Squared Error) and BadPix, we identified optimal knowledge positions and evaluated the required complexity for the student model. As a result, our method improved MSE by 21% and BadPix by 14% compared to training without it. Furthermore, the student model achieved an inference speed 13% faster than the teacher model and surpassed its accuracy by 10% in MSE. Additionally, we demonstrated that repeatedly applying our approach could further enhance both model compactness and accuracy.

In Brazil, Brazilian borreliosis (BB), characterized molecularly, exhibits symptoms akin to Lyme disease (LD) but presents unique epidemiological, clinical, and morphological features. This study explores the incidence, diagnostic challenges, and awareness initiatives regarding this disease in Brazil. Employing a narrative review methodology, data were sourced from Pubmed, Ebsco, Google Scholar, and Web of Science without temporal constraints. Results reveal diagnostic complexities in Brazil due to the low sensitivity of conventional tests and the use of North American B. burgdorferi antigens. Despite challenges, epidemiological studies indicate an upswing in cases in humans and animals. Therefore, there is an urgent need to define new biomarkers, molecular strategies, or new antigenic targets to advance the development of vaccines and diagnostics. Early and accurate pathogen identification is crucial for active surveillance to comprehend and manage this zoonosis.

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 (>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.

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.

The oral microbiome, studied by sampling the saliva or oral rinse, has been long thought to have diagnostic capacity for head and neck cancers (HNC). However, previous reports on the HNC oral microbiome provide inconsistent results. The aim of this study is to consolidate these datasets and determine the oral microbial composition between HNC patients to healthy and premalignant individuals. We analyzed 16 published head and neck cancer (HNC) short-read 16S rRNA sequencing datasets, specifically targeting the V3V4, V4 and V4V5 regions. These datasets included saliva and oral rinse samples from donors with HNC, as well as from healthy and premalignant donors. Differences in diversities and microbial abundance were determined. HNC saliva displayed lower alpha diversity than healthy donors. In contrast, the opposite trend was observed for oral rinse samples. Beta diversity were largely similar across different patient types. Similar oral phyla were detected for all samples, but proportions were largely dependent on sample type (i.e. saliva or oral rinse) and primer set utilised for 16S rRNA sequencing. Neisseria, Leptotrichia and Megasphaera were elevated in healthy saliva, while Mycoplasma was elevated in HNC saliva. Oral rinse and saliva displayed similar enrichment for Fusobacterium, while Veillonella, Alloprevotella, and Campylobacter had conflicting results. The sparse partial least squares discriminant analysis model performed effectively in discriminating HNC from healthy or premalignant patients using V3V4 saliva (AUC = 0.888), and V3V4 oral rinse (AUC = 0.928), while poor discriminative capacity was observed for V4 saliva (AUC = 0.688). In conclusion, our meta-analysis highlighted the limitations of 16S rRNA sequencing, particularly due to variations across study batches, primer sets (i.e. V3V4, V4), and sample types. Hence, caution should be exercised when interpreting 16S rRNA sequencing results across studies, especially when different primer sets and sample types are used.

The Aspergillus genus comprises fungi that are widely distributed in nature. The Terrei section is particularly important due to its functions in recycling organic matter. Aspergillus hortae is a species from this section that has been isolated from clinical samples, but its role as a pathogenic agent is unclear. In this study, three clinical A. hortae isolates from Colombia, initially identified as A. terreus, were characterised by micro and macro-morphological analysis at 26°C and 37°C. A bioinformatic pipeline was used for molecular typing, which included analysis of whole genome sequences for accurate species identification. Susceptibility assays were also conducted using the microdilution broth method (EUCAST). It was confirmed that this species is intrinsically resistant to Amphotericin B with a minimum inhibitory concentration (MIC) of 2-4 mg/L, and is also thermotolerant. We obtained the in vitro susceptibility profiles for three azole drugs (MIC, 0.25-1 mg/L). The three isolates showed phylogenetic divergence from the reference genome strain. A mutation (M769K) in the MelA ortholog of a hypopigmented isolate, which had the lowest MIC value for AmB (2 mg/L), was identified. This study presents the morphological characterization, molecular typing through whole-genome analysis and identification of susceptibility profiles to azoles and amphotericin B of three clinical isolates of A. hortae from Colombia.

Background: Pediatric neurological disorders include neurodegenerative disease causing cognitive impairment, vision loss to mention a few. They are one of the important causes of morbidity and mortality in children with diverse etiology. Diagnosis is difficult in spite of genetic work and in only 60% of cases final diagnosis can be achieved. Case presentation: We explore three cases of pediatric neurological diseases, viz. Arthrogryposis, congenital bilateral cataract and Autism by analyzing clinical exomes. In this work, we attempted to understand rare neurological disorders in an Indian pediatric cohort using exome studies. Conclusions: We used our benchmarked CONVEX pipeline for screening consensus variants, wherein EIF2B2 was found to be inherently pathogenic. We map the association of variants and genes, disease correlation to neuroleptic malignant syndrome which is a matching phenotype to the cases.

A Cu₂ZnSnS₄ (CZTS) film with a thickness of approximately 1.5 μm was fabricated on a Mo-coated glass substrate by annealing a CZTS precursor fabricated from nanoparticle ink. The chemical states of the elements in the CZTS thin film in the depth direction were studied to identify the presence of secondary phases, which are detrimental to the performance of solar cells containing CZTS. X-ray diffraction was unable to detect any secondary phases in CZTS because of their small relative amount. Instead, X-ray photoelectron spectroscopy (XPS), which is highly sensitive to chemical state, was conducted at different depths in the CZTS film to further check the presence of secondary phases. XPS analysis revealed peaks shift consistent with the presence of secondary phases. For the CZTS film annealed in a S atmosphere at 575 °C for 3 h, the film surface consisted of a secondary-phase layer composed of CuS, ZnS, and SnSx (x=1 or 2) originating from the decomposition of CZTS. At depths below 80 nm, the film was pure CZTS. Formation of MoS2 at the CZTS–Mo interface was confirmed by XPS analysis of Mo and S.

Axial resolution is one of the most important characteristics of a microscope. In all microscopes, a high axial resolution is desired in order to discriminate information efficiently along the longitudinal direction. However, when studying thick samples that do not contain laterally overlapping information, a low axial resolution is desirable as information from multiple planes can be recorded simultaneously from a single camera shot instead of plane-by-plane mechanical refocusing. In this study, we increased the focal depth of an infrared microscope non-invasively by introducing a binary axicon fabricated on barium fluoride substrate close to the sample. Preliminary results of imaging thick and sparse silk fibers showed an improved focal depth with a slight decrease in lateral resolution and increase in background noise.

Background: The microbiome of the ocular surface has been characterised, but only limited in-formation is available on a possible silent intraocular microbial colonisation in normal eyes. Therefore, we performed next generation sequencing (NGS) of 16S rDNA genes in aqueous hu-mor. Methods: Aqueous humor was sampled from three patients during cataract surgery. Air swabs, patient’s and healthy donor conjunctival swab served as controls. Following DNA extraction, the V3 and V4 hypervariable regions of the 16S rDNA gene were amplified and sequenced fol-lowed by denoising. The resulting Amplicon Sequence Variants were matched to a subset of the Ribosomal Database Project 16S database. The deduced bacterial community was then statis-tically analysed. Results: DNA content in all samples was low (0-1.49 ng/µl) but sufficient for analysis. Main phyla in all samples were Acinetobacteria (48%), Proteobacteria (26%), Firmicutes (14%), Acidobac-teria (8%) and Bacteroidetes (2%). Patients conjunctival control samples and anterior chamber fluid showed similar patterns of bacterial species containing many waterborne species. Non-disinfected samples showed a different bacterial spectrum than the air swab sample. Conclusions: The data confirm the existence of an ocular surface microbiome. A distinct intraoc-ular microbiome was not discernable from the background, suggesting the absence of an intra-ocular microbiome in normal eyes.

This study examines a case involving a 7-year-old child who developed dengue symptoms following Qdenga vaccination. Despite initial negative diagnostic results, molecular analysis confirmed an infection with DENV4. Next-generation sequencing detected viral RNA from both DENV2 and DENV4 serotypes, which were identified as vaccine-derived strains using specific primers. Phylogenetic analysis further confirmed that these sequences belonged to the Qdenga vaccine rather than circulating wild-type viruses. This case underscores the critical need for precise diagnostic interpretation in vaccinated individuals to avoid misdiagnosis and to strengthen public health surveillance. A comprehensive understanding of vaccine-induced viremia is essential for refining dengue surveillance, improving diagnostic accuracy, and informing public health strategies in endemic regions.

Lecanicillium lecanii KMZW-1, is recognized for its potential as a bio-control agent against agricultural and forestry pests, particularly due to its compatibility with integrated pest management (IPM) strategies. This study aimed to investigate the complete genome of L. lecanii KMZW-1 and assess its pathogenicity against Bactrocera dorsalis. Whole genome sequencing revealed a genome size of 47,239,278 bp, comprising 27 contigs, with a GC content of 51.16%. The genome completeness was assessed as 97.93% using BUSCO analysis, AntiSMASH analysis identified 29 gene clusters associated with secondary metabolite biosynthesis providing insights into the genetic basis of its pathogenic mechanisms and biocontrol potential. The pathogenicity of L. lecanii KMZW-1 was assessed using concentrations ranging from 1×10^4 to 1×10^11 spores/mL. Higher-concentrations (1×10^10 to 1×10^11 spores/mL), resulted in significantly increased cumulative mortality rates of B. dorsalis adults compared to the control group. Notably, the pathogenicity was higher in male adults than in females. Probit regression analysis yielded LogLC50 values as 5.662 for female and 4.486 for male B. dorsalis adults. In summary, L. lecanii KMZW-1 exhibits strong insecticidal activity against B. dorsalis and shows potential as a biocontrol agent with IPM strategies. These findings provide robust genomic evidence supporting the use of L. lecanii KMZW-1in managing against B. dorsalis populations.

Face detection is an important problem in computer vision because it enables a wide range of applications, such as facial recognition and analysis of human behavior. The problem is challenging because of the large variations in facial appearance across different individuals and different lighting and pose conditions. One way to detect faces is to utilize a highly advanced face detection method, such as RetinaFace, which uses deep learning techniques to achieve high accuracy in various datasets. However, even the best face detectors can produce false positives, which can lead to incorrect or unreliable results. In this paper, we propose a method for reducing false positives in face detection by using information from a depth map. A depth map is a two-dimensional representation of the distance of objects in an image from the camera. By using the depth information, the proposed method is able to better differentiate between true faces and false positives. The authors evaluate their method on a combined dataset of 549 images, containing a total of 614 upright frontal faces. The results show that the proposed method is able to significantly reduce the number of false positives without sacrificing the overall detection rate. This indicates that the use of depth information can be a useful tool for improving face detection performance.

Recently concluded, large-scale cancer genomics studies involving multiregion sequencing of primary tumors and paired metastases appear to indicate that many or most cancer patients have one or more “clonal" mutations in their tumors. Clonal mutations are those that are present in all of a patient’s cancer cells. Achilles Therapeutics is currently the only company specifically targeting clonal mutations. However, they are doing so with tumor-derived T cells. To address the potential limitations of immunotherapy, I have devised another approach for exploiting clonal mutations, which I call “Oncolytic Vector Efficient Replication Contingent on Omnipresent Mutation Engagement” (OVERCOME). The ideal version of OVERCOME would likely employ a bioengineered facultative intracellular bacterium. The bacterium would initially be attenuated, but (transiently) reverse its attenuation upon clonal mutation detection.

The ability to read and quantify nucleic acids such as DNA and RNA using sequencing technologies has revolutionized our understanding of life. With the emergence of synthetic biology, these tools are now being put to work in new ways - enabling de novo biological design. Here, we show how sequencing is supporting the creation of a new wave of biological parts and systems, as well as providing the vast data sets needed for the machine learning of design rules for predictive bioengineering. However, we believe this is only the tip of the iceberg and end by providing an outlook on recent advances that will likely broaden the role of sequencing in synthetic biology and its deployment in real-world environments.

The global antibiotic resistance crisis, driven by antibiotic overuse and misuse, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat, including the isolation, antibiotic susceptibility testing (AST), whole genome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 randomly selected retail stores in Gauteng, South Africa. Samples were aseptically separated, with a portion sent to an external laboratory for isolating indicator bacteria and antibiotic residue testing. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system. WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument. The isolated E. coli and enterococci exhibited little phenotypic resistance, with WGS revealing tetracycline resistance genes. Isolated bacteria and meat samples all harboured tetracycline resistance genes, and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin, with the resistome analysis primarily indicating beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance.

A genome represents the complete collection of genetic material in an organism or cell. This genetic information is encoded in nucleic acids, which can be either single or double-stranded and arranged in linear or circular forms. DNA, the most common type of genetic material, consists of just four nucleotides: adenine, guanine, thymine, and cytosine. These nucleotides are organized in a double helix structure, a discovery made by Watson and Crick. The sequence of these nucleotides forms the basic blueprint of a gene or genome. The process of determining this sequence is known as genome sequencing. The field of genome sequencing has evolved dramatically over time, advancing from sequencing short DNA fragments to analyzing millions of base pairs. Initially, efforts were focused on determining the sequence of individual genes, but now whole genome sequencing is both rapid and widely accessible. Recent improvements in sequencing technology emphasize faster, more accurate results, lower costs, and better data analysis. Sanger sequencing, which became the gold standard for DNA sequencing for about thirty years, was instrumental in completing various genome sequences, including the human genome. It laid the groundwork for newer sequencing methods. Today, these newer methods, known collectively as “Next-Generation Sequencing” (NGS), include several generations of technology. Second-generation methods, such as Illumina, Pyrosequencing, ABI/SOLiD, and Ion Torrent Sequencing, and third-generation methods like PacBio and Helicos Sequencing, have advanced the field further. Fourth-generation technology, such as Nanopore sequencing, is also emerging. Most modern research now relies on NGS for analyzing biological sequences, and understanding these technologies offers insight into current methods and future developments.

Salmonella species are important foodborne pathogens worldwide. Salmonella pathogenicity is associated with multiple virulence factors and enhanced antimicrobial resistance. To determine the molecular characteristics and genetic correlations of Salmonella, 24 strains of Salmonella isolated from different sources (raw poultry, human stool, and food) in the Wenzhou area were investigated to determine the distribution of antimicrobial resistance and virulence determinants using whole-genome sequencing (WGS). Aminoglycoside-resistance genes were detected in all samples. Over half of the samples found antimicrobial resistance genes (ARGs) and point mutations for several clinically frequently used antibiotic, β-lactamases, tetracyclines, and fluoroquinolones. Of these strains, 62.5% were predicted to be multidrug-resistant (MDR). The quinolone-modifying enzyme gene aac(6')-Ib-cr, detected in five samples (S1–S4 and S10), were located on integrons. Analysis of Salmonella pathogenicity island (SPI) profiles suggests that serotypes with close genetic relationships share the same distribution of virulence factors, revealing a link between genotype and SPI profiles. CgMLST analysis indicated that five isolates S14–S18 were closely related to strains originating from the UK, suggesting that they may have been introduced from the UK. Data from this study may enrich the molecular traceability database for Salmonella and provide a basis for effective public health policies.

The assessment of soil contamination in the vicinity of integrated siderurgical plants is of outmost importance for agroecosystems and human health, and sensitive techniques should be employed for accurate assessment of chemical elements (metals, potential toxic elements, rare earths, radioelements) in soil and further evaluation of potential ecological and safety risk. In this paper a total of 45 major, minor and trace elements (Al, As, Au, Ba, Br, Ca, Cd, Ce, Co, Cr, Cs, Cu, Dy, Eu, Fe, Hf, Hg, I, K, La, Mg, Mn, Mo, Na, Nd, Ni, Pb, Rb, Sb, Sc, Sm, Sn, Sr, Ta, Tb, Th, Ti, Tm, U, V, W, Y, Yb, Zn and Zr) were quantified in soils located around a large siderurgical works (Galati, SE Romania) using instrumental neutron activation analysis (INAA) in combination with X-ray fluorescence (XRF) and inductively coupled plasma mass spectrometry (ICP-MS). The statistical analysis results and vertical distribution patterns for three depths (0-5 cm, 5-20 cm, 20-30 cm) indicate inputs of toxic elements in the sites close to the ironmaking and steelmaking facilities and industrial wastes dumping site. For selected elements, a comparison with historical, legislated and world reported concentration values in soil was performed and depth migration, contamination and toxic risk indices were assessed. The distribution of major, rock forming elements was closer to the Upper Continental Crust (UCC), and to the Dobrogea loess, finding confirmed by the ternary diagram of the incompatible trace elements Sc, La and Th, as well as by the La to Th rate. At the same time, the La/Th vs. Sc and Th/Sc vs. Zr/Sc bi-plots suggested a felsic origin and a weak recycling of soils mineral components.

Significant advancements have been made in controlled drug delivery systems in recent years, especially for oral administration. Conventional methods, although groundbreaking, encounter significant constraints when handling drugs with weak acidity or alkalinity because of their solubility being influenced by pH. The release rates of these ionizable drugs are subject to variability, which is influenced by factors such as the pH of the gastrointestinal tract (GIT), patient-specific conditions, and whether the patient is in a fed or fasted state. As a result, there is often a lack of correlation between in vitro and in vivo data. Therefore, it is imperative to develop drug delivery systems that are not affected by changes in pH in order to address these limitations. This review delves into different strategies that have been developed to achieve drug release that is not affected by changes in pH. These strategies include the utilisation of Diffucaps technology, the incorporation of pH modifiers and surfactants, the combination of non-ionic and ionic polymers, the implementation of supersaturating techniques with nucleation inhibitors, and the utilisation of osmotic drug delivery systems. We assess the efficacy of these methods in reducing the influence of pH fluctuations on the solubility and release rates of drugs. In addition, we explore the potential of these innovative techniques to enhance the reliability and predictability of drug delivery, ultimately leading to better therapeutic results. This review provides an in-depth information of various pH independent controlled drug delivery based formulation and By summarizing the existing technologies and looking into the future, the importance of innovation in pH independent delivery systems is emphasised, laying a good foundation for the future design of simple drug delivery systems, which will be conducive to achieving a wider range of applications in oral drug delivery system.

Convolutional Neural Networks (CNNs) are largely hand-crafted, which leads to inefficiency in the constructed network. Various other algorithms have been proposed to address this issue, but the inefficiencies resulting from human intervention have not been addressed. Our proposed EvolveNet algorithm is a task-agnostic evolutionary search algorithm that can find optimal depth and width scales automatically in an efficient way. The optimal configurations are not found using grid search, instead evolved from an existing network. This eliminates inefficiencies that emanate from hand-crafting, thus reducing the drop in accuracy. The proposed algorithm is a framework to search through a large search space of subnetworks until a suitable configuration is found. Extensive experiments on the ImageNet dataset demonstrate the superiority of the proposed method by outperforming the state-of-the-art methods.

The medical care and welfare of domestic dogs are now respected worldwide at the same level as that of humans. We previously established a test method to determine whole mitochondrial DNA (mtDNA) using oral mucosal DNA that may be useful for the medical care and welfare of dogs. However, the sample types tested in dogs are not limited to those obtained from the oral mucosa. Therefore, in the present study, we attempted to establish a test method to determine whole mtDNA sequences using feces, which represents the least invasive specimen. Two Japanese domestic dogs were used in the present study. DNA was extracted from approximately 100 mg of fresh feces from each dog, and PCRs were performed using four primer-pairs that can amplify whole mtDNA. Following PCR, amplicons were pooled to create a DNA library using an experimental robot with an original program. Data were then acquired via NGS and data analysis was performed. The results showed that the whole mtDNA sequence of the two dogs was determined with high accuracy. Our results suggest that feces can be adapted for mitochondrial disease and individual identification testing and could serve as a useful testing method for the future medical care and welfare of domestic dogs.

This research work was aimed at investigating and determining the depth resolution of a 500Mhz GPR Antenna. The survey was conducted in an open space at the Physics Department, College of science-KNUST. The MALA GPR equipment with 500MHz shielded Antenna in the common offset-mode was used to investigate the depth at which materials were buried. Concrete block, tree roots, plastic bottle with water, glass bottle and Electric wire were each buried in cavities with five different burial depths. The real depth of each material was measured both along and across the cavity and compared to their corresponding GPR measured depth. The comparison of the Real depth and the GPR depth showed almost identical depth measurements with a root mean square deviation of 0.028m. The implication of this is that the 500 Mhz GPR antenna can accurately locate and detect the position of buried materials in the subsurface at a depth within the range (0.20-0.66) m.

Depth maps produced by LiDAR based approaches are sparse. Even high-end LiDAR sensors produce highly sparse depth maps, which are also noisy around the object boundaries. Depth completion is the task of generating a dense depth map from a sparse depth map. While the traditional approaches focus on directly completing this sparsity from the sparse depth maps, modern techniques use RGB images as a guidance tool to resolve this problem. Whilst many others rely on affinity matrices for depth completion. Based on these approaches, we have sub-divided the literature into two major categories; traditional approaches and backbone-based approaches. The latter is further sub-divided into two-branch, and spatial propagation approaches. The two-branch approaches still have a sub-category named guided-kernel approaches. In this paper, for the first time ever we present a comprehensive survey of depth completion methods. We present a novel taxonomy of depth completion approaches, review and detail different state-of-the art techniques within each category for depth completion of LiDAR data, and provide quantitative results for the approaches on KITTI and NYUv2 depth completion benchmark datasets.

Three-dimensional (3D) imaging has attracted more and more interests because of its widespread applications, especially in information and life science. These techniques can be broadly divided into two types: ray-based and wavefront-based 3D imaging. Issues such as imaging quality and system complexity of these techniques limit the applications significantly, and therefore many investigations have focused on 3D imaging from depth measurements. This paper presents an overview of 3D imaging from depth measurements, and provides a summary of the connection between these the ray-based and wavefront-based 3D imaging techniques.

During the last few years, advancement in the area of biochemistry, science of the material world, engineering and computer-aided testing has directed towards advancement of high-throughput tools for the sake of profiling information encoded in a gene. Single-cell RNA-sequencing (scRNA-seq) tools capable to examine the sequence data from each individual cells and it shows within population variety and permit exploring of cell conditions and transformation by extreme resolution, possibly give out cell sub-types or gene expression fluctuations that are shaded in mass sequencing processes, which shows population-averaged evaluations. Yet, the major disadvantage for this tool is the lack of success to pick out location related details of the RNA transcriptome, as this needs tissue detachment and cell isolation. Location based transcript determination is among the advancements in the area of medical biotechnology as this can find out the molecules like RNA dataset in their intact physical placement in tissue segment with spatial context at the scale of a single-cell, which is very advantageous as compare to single-cell sequencing techniques. These approaches give key observation in the areas of biomedical field sub-disciplines like neurology, embryology, carcinoma study, immune cell investigation and histological activities. Generally, this review mainly focused towards single-cell sequencing methods, technology development, its challenges observed, different expression data analysis mechanisms and their applications in different areas, such as in cancer research, microbes, central nervous system, sex organs and immune-biology, intensifying the essentiality of sequencing tools at single-cell level for the characterization of extremely dynamic individual cells.

Ransomware, a combination of "ransom" and "malware," is a type of malicious software designed to encrypt or block access to a victim's data or system, demanding a ransom for its release Initially targeting individuals, ransomware has evolved to attack businesses for greater financial gain. It mainly exists in two forms: encrypting ransomware, which holds data hostage, and non-encrypting ransomware, which blocks system access and displays a ransom note. The energy sector has been notably targeted by ransomware, exemplified by the 2021 attack on Colonial Pipeline by the DarkSide group, which led to a temporary shutdown and a significant fuel shortage on the US East Coast. Similarly, in 2023, Russian hackers using LockBit ransomware disrupted Royal Mail, halting international deliveries and incurring millions in recovery costs despite no ransom payment. These incidents underscore the need for comprehensive cybersecurity strategies that combine human vigilance with advanced technologies like AI and machine learning. By adopting a multi-layered protection approach, organizations can better prepare for and mitigate the risks posed by ransomware attacks safeguarding sensitive data and ensuring business continuity.

3D object reconstruction from depth image streams using Kinect-style depth cameras has been extensively studied. In this paper, we propose an approach for accurate camera tracking and volumetric dense surface reconstruction assuming a known cuboid reference object is present in the scene. Our contribu¬tion is three-fold. (a) We maintain drift-free camera pose tracking by incorporating the 3D geometric constraints of the cuboid reference object into the image registration process. (b) We reformulate the problem of depth stream fusion as a binary classification problem, enabling high-fidelity surface reconstruction, especially in the con¬cave zones of objects. (c) We further present a surface denoising strategy to mitigate the topological inconsistency (e.g., holes and dangling triangles), which facilitates the generation of a noise-free triangle mesh. We extend our public dataset CU3D with several new image sequences, test our algorithm on these sequences and quantitatively compare them with other state-of-the-art algorithms. Both our dataset and our algorithm are available as open-source content at https://github.com/zhangxaochen/CuFusion for oth-er researchers to reproduce and verify our results.

Low-cost RGB-D cameras are increasingly used in several research fields including human-machine interaction, safety, robotics, biomedical engineering and even Reverse Engineering applications. Among the plethora of commercial devices, the Intel RealSense cameras proved to be among the best suitable devices, providing a good compromise between cost, ease of use, compactness and precision. Released on the market in January 2018, the new Intel model RealSense D415 has a wide acquisition range (i.e. ~160-10000 mm) and a narrow field of view to capture objects in rapid motion. Given the unexplored potential of this new device, especially when used as a 3D scanner, the present work aims to characterize and to provide metrological considerations on the RealSense D415. In particular, tests are carried out to assess the device performances in the near range (i.e. 100-1000 mm). Characterization is performed by integrating the guidelines of the existing standard (i.e. the German VDI/VDE 2634 part 2 normative) with a number of literature-based strategies. Performance analysis is finally compared against latest close-range sensors, thus providing a useful guidance for researchers and practitioners aiming to use RGB-D cameras in Reverse Engineering applications.

Subsoil tillage loosens compacted soil for better plant growth, but promotes water loss, which is a concern in areas commonly irrigated. Therefore, our objective was to determine the physiological responses of high yield spring corn (Zea mays L.) to Subsoil tillage depth when grown in the western plain irrigation area of Inner Mongolia that leads to the best water use efficiency. The experiment during 2014 and 2015 used Zhengdan958 and Xianyu335 with three differing subsoil tillage depths (30, 40, or 50 cm) as trial factor and shallow rotary as a control. Subsoil tillage increased shoot dry matter accumulation, leading to a greater shoot/root ratio. Subsoil tillage helped retain greater leaf area index in each growth stage, increase the leaf area duration, net assimilation rate, and relative growth rate, with greater effects as tillage was deeper, effectively delaying the aging of the blade. Grain yields were increased by 0.7%–8.9% on average in subsoil tillage treatments compared to conventional soil treatment shallow rotary, Water use efficiency were increased by 1.93%–18.49% on average in subsoil tillage treatment compared to shallow rotary, resulting in net income increases by 2.24% to 6.97% compared to shallow rotary. Among the three different subsoil tillage depth treatment, the grain yield, water use efficiency, and net income is the best under the treatment of subsoil tillage depth of 50 cm.

The main goal of the Soil Moisture and Ocean Salinity (SMOS) mission over land surfaces is the production of global maps of soil moisture (SM) and vegetation optical depth (τ) based on multi-angular brightness temperature (TB) measurements at L-band. The operational SMOS Level 2 and Level 3 soil moisture algorithms account for different surface effects, such as vegetation opacity and soil roughness at 4 km resolution, in order to produce global retrievals of SM and τ. In this study, we present an alternative SMOS product which was developed by INRA (Institut National de la Recherche Agronomique) and CESBIO (Centre d’Etudes Spatiales de la BIOsphère). This SMOS-INRA-CESBIO (SMOS-IC) product provides daily SM and τ at the global scale and differs from the operational SMOS Level 3 (SMOSL3) product in the treatment of retrievals over heterogeneous pixels. Specifically, SMOS-IC is much simpler and does not account for corrections associated to the antenna pattern and the complex SMOS viewing angle geometry. It considers pixels as homogeneous to avoid uncertainties and errors linked to inconsistent auxiliary data sets which are used to characterize the pixel heterogeneity in the SMOS L3 algorithm. SMOS-IC also differs from the current SMOSL3 product (Version 300, V300) in the values of the effective vegetation scattering albedo (ω) and soil roughness parameters. An inter-comparison is presented in this study based on the use of ECMWF (European Center for Medium range Weather Forecasting) SM outputs and NDVI (Normalized Difference Vegetation Index) from MODIS (Moderate-Resolution Imaging Spectroradiometer). A 6 year (2010-2015) inter-comparison of the SMOS products SMOS-IC and SMOSL3 SM (V300) with ECMWF SM yielded higher correlations and lower ubRMSD (unbiased root mean square difference) for SMOS-IC over most of the pixels. In terms of τ, SMOS-IC τ was found to be better correlated to MODIS NDVI in most regions of the globe, with the exception of the Amazonian basin and of the northern mid-latitudes.

Idiopathic granulomatous mastitis (IGM) is a rare condition characterised by chronic inflammation and granuloma formation in the breast. The aetiology of IGM is unclear. By focusing on the protein-coding regions of the genome, where most disease-related mutations often occur, whole-exome sequencing (WES) is a powerful approach for investigating rare and complex conditions, like IGM. We report WES results on paired blood and tissue samples from eight IGM patients. Samples were processed using standard genomic protocols. Somatic variants were called with two analytical pipelines: nf-core/sarek with Strelka2 and GATK4 with Mutect2. Our WES study of eight patients did not find evidence supporting a clear genetic component. The discrepancies between variant calling algorithms, along with the considerable genetic heterogeneity observed amongst the eight IGM cases, indicate that common genetic drivers are not readily identifiable. With only three genes, CHIT1, CEP170, and CTR9, recurrently altered in multiple cases, the genetic basis of IGM remains uncertain. The absence of validation for somatic variants by Sanger sequencing raises further questions about the role of genetic mutations in the disease. These observations suggest that IGM may be influenced by non-genetic factors, such as environmental triggers or immune system dysregulation, rather than being primarily a genetic disorder.

Escherichia coli is an indicator microorganism in One Health antibiotic resistance surveillance programmes. The purpose of the study was to describe and compare E. coli isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harboured a richer diversity of antibiotic resistance genes, as compared to human E. coli isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%; 7/169), EPEC (2.96%, 5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169) were detected at low frequencies. Sequence type complex (STc) 10 were the most prevalent (85.51%, 59/169) among human and porcine isolates. Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human-livestock interface according to multilocus sequence typing (MLST). Core genome MLST and hierarchical clustering (HC) showed that human and porcine isolates were overall genetically diverse, but some clustering at HC2 to HC200 were observed. In conclusion, even though the isolates shared a spatio-temporal relationship, there were still differences in the virulence potential, antibiotic resistance profiles, and cgMLST and HC according to the source of isolation.

Deep learning, specifically the supervised approach, has proved to be a breakthrough in depth prediction. However, the generalization ability of deep networks is still limited, and they cannot maintain a satisfactory performance on some inputs. Addressing a similar problem in the segmentation field, a scheme (f-BRS) has been proposed to refine predictions in the inference time. f-BRS adapts an intermediate activation function to each input by using user clicks as sparse labels. Given the similarity between user clicks and sparse depth maps, this paper aims at extending the application of f-BRS to depth prediction. Our experiments show that f-BRS, fused with a depth estimation baseline, is trapped in local optima, and fails to improve the network predictions. To resolve that, we propose a double-stage adaptive refinement scheme (DARS). In the first stage, a Delaunay-based correction module significantly improves the depth generated by a baseline network. In the second stage, a particle swarm optimizer (PSO) delineates the estimation through fine-tuning f-BRS parameters—that is, scales and biases. DARS is evaluated on an outdoor benchmark, KITTI, and an indoor benchmark, NYUv2 while for both the network is pre-trained on KITTI. The proposed scheme outperformed rival methods on both datasets.

Subseasonal-to-seasonal (S2S) weather forecasting has improved in recent years, thanks partly to better representation of physical variables in models. For instance, realistic initializations of snow and soil moisture in models yield enhanced predictability on S2S time scales. Snow depth and soil moisture also mediate month-to-month persistence of near-surface air temperature. Here the role of snow depth as predictor of temperature one month ahead in the Northern Hemisphere is probed via two causal pathways. Through the first pathway, snow depth anomalies in month 1 cause snow depth anomalies in month 2, which then cause temperature anomalies in month 2. This pathway represents the snow–albedo feedback, as well as cooling due to insulation, emissivity and heat loss. It is active from fall to summer, and its effect peaks in March/April in the midlatitudes and in May/June at high latitudes. A complementary second pathway, where snow depth anomalies in month 1 cause soil moisture anomalies in month 2, which then cause temperature anomalies in month 2 through soil moisture–temperature feedbacks, is only active in spring and summer. Its effect peaks later in the warm season than the effect of the first pathway. Geographically, snow depth mediates north of, and soil moisture south of, the areas with the highest temperature predictability from snow depth. These results indicate that the two pathways describe complementary physical mechanisms. The first pathway embodies month-to-month persistence of snow depth, and the second pathway represents melting of snow from one month to the next.

Alfalfa is an important forage crop around the world. LncRNAs are considered to be a class of functional biomacromolecules, while little is known about lncRNAs in alfalfa. In this study, RNAs from different tissues of alfalfa were sequenced and anlyzed with full-length transcriptome sequencing technology, yielding the full-length transcripts dataset of alfalfa. Based on sequencing and public RNA-seq data, lncRNAs of alfalfa were predicted genome-wide by CPC2 and PLEK. The results showed most lncRNAs shared low sequence conservation with those in other plant species, part of which seems originate from plastid genome. We also identified 88563 lncRNAs, approximately 99.8% of total lncRNAs, with possibility of coding small ORFs using two prediction tools. Our research generated the biggest sequence set of alfalfa lncRNAs, and revealed some plastid originated lncRNAs with high sequence conservation.

There have been several developments in the field of nanopore biosensor development and sequencing applications that address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making these platforms a mainstay in contemporary research labs. Equipped with the ability to provide long and short-read sequencing information with quick turn-around times and simple sample preparation, nanopore sequencers are quickly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We conclude with examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.

Genetic disorders are preeminent determinants of infant mortality. The inherited pediatric-onset genetic disorders have consequential stress on child growth and development: several congenital, complex and rare disorders with indistinguishable clinical symptoms where diagnosis always remains a challenging task. Traditional diagnosis methods include biochemical tests followed by chromosomal microarray and sequencing of a single gene or panel of genes. These methods had several limitations, but with the advent of whole-exome sequencing (WES), genetic testing has become cost-effective and transformative. Exome sequencing has been known for its effectiveness, which appropriately elucidates and distinguishes the heterogeneous disorders to avoid misdiagnosis and decode the underlying genetic alterations. WES has led to discovering genes and genomic variants in a broad spectrum of diseases, including autism, epilepsy, congenital heart diseases, neurodevelopmental diseases, cancer, nephrotic disorders, neural tube defects and fetal structural anomalies. WES is significant in producing immense genomic biomarkers that can be made as appropriate pharmacogenomic targets for drug therapy. In this article, we analyze the recent exploration of WES technology to revolutionize not only the process of genetic variation and disease detection but also the convention of preventative and targeted drug discovery.

The world has now entered into a replacement era of genomics due to the continued advancements within the next generation high throughput sequencing technologies, which incorporates sequencing by synthesis-fluorescent in place sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization alongside sequencing by ligation, and nanopore technology. Great impacts of those methods are often seen for solving the genome related problems of plant and Animalia which will open the door of a replacement era of genomics. This might ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is predicted to advance and make the drug discovery process more rapid.

Since the financial crisis in 2008, the U.S. economy has weakened, and the world economy has slowly developed. As the world's leading country, the United States has used many methods to restore the economy. But it does work efficiently. However, there are many issues in developed countries such as domestic social, economic, immigration in the United States/United Kingdom; those are not optimistic. Developed countries have entered a dilemma. The neoliberalism financial system has been unable to move forward. Populists have pointed out that those problems have been causing by globalization. Under the leadership of the Brexit Referendum, President Trump has caused a wave of anti-globalization. Under a series of systems such as the China-US trade war and the US-Mexico border wall repairs, the anti-globalization trend is getting stronger. This article mainly analyzes the in-depth reasons and mechanism research of globalization and anti-globalization alternately—the data obtained from an international method performance study. The results show that anti-globalization is temporary, along with globalization. There are three main factors affecting globalization: the situation of the dominant country, natural disasters, and wars. After so much literature review, I believe that the United States' globalization is gradually weakening, and globalization may return to regionalization under the United States' opposition.

Antibiotic-loaded bone cement (ALBC) plays a pivotal role in infection prevention and treatment related to musculoskeletal surgery. The release efficacy of antibiotics from ALBC is closely tied to its surface area, yet little is known about the effective release depth. To investigate the relationship between surface area, volume, and antibiotic elution, spheric ALBC specimens with consistent outer diameters but different internal metal sphere diameters were prepared. Two vancomycin doses were utilized in ALBC specimens with an outer diameter of 35 mm: high (4 g) and low (1 g). Each dosage group included five specimens containing embedded metal spheres with diameters of 15, 25, 29, 32, or 33 mm. The resulting shell-like ALBC specimens had thicknesses of 10 mm, 5 mm, 3 mm, 1.5 mm, or 1 mm, respectively. The specimens were immersed in sterile phosphate buffer solution, and antibiotic elution was measured at designated sampling times (1, 3, 6, 10, 24, 48, 72, and 168 hours). Methylene blue was employed to visualize penetration depth. Vancomycin elution did not display statistically significant differences between high- and low-dose groups. In both groups, specimens with 1 mm thickness exhibited a higher vancomycin release efficiency (high-dose group: 18560±5474 μg, 6.7%; low-dose group: 2017±419 μg, 2.6%), decreasing sharply in thicker ALBC specimens. Methylene blue penetration depth showed no apparent difference between high-dose and low-dose groups. ALBC thickness does not significantly impact antibiotic elution, while surface area and antibiotic dose exert notable effects. These in vitro findings offer potential applications in clinical treatments for musculoskeletal infections.

Biofilm serves as the residence for bacteria, wherein bacteria attach to surfaces and produce extracellular polymeric substances, including proteins, polysaccharides, and extracellular DNA. In recent years, biofilm reactors have gained increasing significance, playing a crucial role, for instance, in immobilizing heavy metals from waterways. This paper employs a bibliographic study to analyze the most important keywords and organizations in the field of biofilm reactors, identifying recent significant papers. Additionally, the paper discusses the opportunities for the future development of biofilm reactors. Through this study, a better understanding of key factors in biofilm reactor research is achieved, providing valuable guidance for future studies and applications in this field.

Ground penetrating radar (georadar, GPR), widely used in geology, archeology and road construction, is an efficient tool for searching and studying subsurface objects and structures. When planning GPR missions, it is necessary to predict the resolution of the device and the achievable probing depth. The article discusses the methods and results of assessing these characteristics of the Loza-V and Loza-N radars obtained in the course of archaeological and geographical expedition works.

Copernicus is Europe's space-based Earth monitoring asset, which consists of a complex set of systems that collect data from different sources: remote sensing satellites (RS) and in-situ sensors such as ground stations, airborne and marine sensors. This study was originally prepared for the needs of the Czech agricultural community, where we provided an in-depth analysis of articles related to Earth observation in precision agriculture. At a later stage, we extended this study by comparing the recommendations of the European EO4Agri project and scientific articles published in MDPI. We had two important objectives, one was to validate the results of the EO4Agri project and the other was to look for gaps in current research and community needs. To recognize the importance of using Sentinel 1 data, we also added a specific analysis of methods for data fusion of Sentinel 1 and Sentinel 2 data.

Infrared thermography has already been proven to be a significant method in non-destructive evaluation since it gives information with immediacy, rapidity, and low cost. However, the thorniest issue for the wider application of IRT is quantification. In this work, we proposed a specific depth quantifying technique by employing the Gated Recurrent Units (GRU) in composite material samples via pulsed thermography (PT). Finite Element Method (FEM) modeling provides the economic examination of the response pulsed thermography. In this work, Carbon Fiber Reinforced Polymer (CFRP) specimens embedded with flat bottom holes are stimulated by a FEM modeling (COMSOL) with precisely controlled depth and geometrics of the defects. The GRU model automatically quantified the depth of defects presented in the stimulated CFRP material. The proposed method evaluated the accuracy and performance of synthetic CFRP data from FEM for defect depth predictions.

Introduction Meningioma is the second most common primary intracranial tumor of the central nervous system. in Sudan, meningioma is the most common primary brain tumor, among Sudanese patients, Surgical total excision of meningioma offers a better survival, however, Chemotherapy has largely been unsuccessful for meningioma treatment, and therefore, refractory and recurrence meningioma treated with palliative surgery and radiotherapy. Monosomy of chromosome 22 is the utmost common genetic alteration among meningioma and many genes were investigated and described in the development of this tumor of which , NF2 hSNF5/INI1gene, P53. In addition to this, Molecular signal pathways in meningioma, and that contribute to the survival, proliferation, self-renewal, and differentiation properties of normal stem cells which are abnormally activated and nominated as cancerous stem cell (CSCs). Objectives 1/ To identify the possible pathway of candidate genes in both setting and whole genes hypothesis free approach 2/ To assess the presence of mutations in candidate genes among histological subtypes of meningioma in Sudan. Material and methods This is a prospective cross-sectional study done at the National Center of Neurological Sciences (NCNS) Khartoum, from 2018 to 2021. The study included all cerebral tumors that were radio- logically diagnosed preoperatively as meningioma. Ethical approval was taken from Institute of Endemic disease, Khartoum University, and written consent was obtained Three DNA extracts were randomly selected from 20 meningioma tissue samples and processed for WES. All genes harboring exonic and splice site variations stratified into SNVs and INDELs sets were prepared. The 1000G online database was used to explore novel mutations per 3 samples. SIFT and PolyPhen-2 programs were used to predict possible impact of amino acids substitution. To address meticulous genes interaction and particular centrality, all shared genes within the class INDEL and SNVs were used as input on Network Analysis to predict protein- protein interaction and functional gene ontology. Finally, shared mutations within genes of centrality were detected via Sanger sequencing and mutations were correlated between histological sub-types and recurrenceThree non meningioma brain tumor used as control. Results WES analysis revealed high number for mutational signature within 2 classes (INDEL and SNVs) per 3 samples, the findings of 1000 genome online database showed number of novel mutations; 5618 in fibrous , 6032 in meningothelial while in recurrent fibrous sample 5930. Network analysis of shared genes per each class (INDEL, SNVs), showed UBC is the most protein of remarkable degree centrality over thousand of genes. Whereas, all shared genes per 3 samples within the 2 classes (INDEL and SNVs) revealed Akt1 with the highest degree of centrality and betweenness. Akt1 rs17846829was detected in 20% of the samples, while CD44 stemness gene revealed mutation A>G (rs9666607) in all meningioma samples (100%), this mutation was associated with 60% of the recurrence. Conclusions Nevertheless, the present study, highlight how such complex molecular processes might contribute to tumorogenesis, in attempt to shed light over thousands of genes and multifaceted network analysis rather than a solitary gene which is challenging question.

Multiple myeloma (MM) is an incurable, diverse cancer in which abnormal plasma cells produce and release monoclonal immunoglobulin (Ig), also known as monoclonal protein or M protein. MM is always preceded by monoclonal gammaglobulinemia of unknown significance (MGUS) and smoldering multiple myeloma (SMM). Diagnosis of MM is made from a bone marrow sample, which involves analysis of the appearance of plasma cells. Quantification of CD138+ plasma cells in core biopsies is performed using techniques such as immunohistochemistry, flow cytometry, fluorescence in situ hybridization (FISH) and conventional cytogenetics. Urinalysis includes total protein by immunofixation and 24-hour urine by serum protein electrophoresis. FISH probes should detect the presence of at least del 13, del 17p, t(4;14), t(11;14), t(14;16), and 1q21 amplifications. Indeed, next-generation sequencing (NGS) has become an increasingly important tool in the diagnosis and treatment of MM. It can be used to identify genetic mutations, copy number changes, and clonal structures to help determine disease prognosis and treatment strategies. NGS can identify subclonal populations of cancer cells that are resistant to therapy and may lead to disease relapse, and can be used to identify potential targets for personalized therapy. For example, NGS can identify mutations in genes involved in drug resistance, enabling the selection of drugs that may be more effective in treating a patient's cancer. This systematic review analyzes 182 papers to determine the position and role of NGS in the diagnosis of MM. We first analyze the platforms and sample types used in the selected studies, and then start discussing the results.

Growing concerns about the greenhouse effect, global warming, and adverse climate changes primarily stemming from carbon dioxide (CO2) emissions in traditional Portland cement (OPC) used in civil engineering construction, have prompted a shift toward eco-friendly alternatives like geopolymer cement (GPC). Over the last few decades, significant advancements have been made in developing environmentally sustainable pavement construction materials such as GPC to mitigate global CO2 emissions. The success of geopolymer cement (GPC) as an eco-friendly alternative to OPC has garnered attention for its potential to lower carbon emissions and enhance durability. This is attributed to the sustainable production method of GPC, where industrial cementitious waste materials (such as fly ash (FA), metakaolin (MK), mine tailings (MT), slag, etc.) are combined with an eco-friendly alkaline activator and water through the geopolymerization process. Numerous studies on geopolymer concrete indicate that, like OPC, GPC exhibits comparable mechanical properties, including strength, fire resistance, chemical resistance, and durability. This review explores the properties and applications of GPC as a sustainable material in pavement construction, exploring key studies and advancements in geopolymer technology, particularly its suitability for pavement applications. The assessment covers the mechanical properties, long-term performance, and environmental impact of geopolymer-based pavements, providing a comprehensive overview to inform policymakers, engineers, and researchers about the viability of geopolymer-based materials as a sustainable solution for modern pavement construction.

This research presents a comprehensive bibliometric and sentiment analysis of nanocomposite literature from 1990 to 2024. Employing cutting-edge computational methods, the study delves deep into the progression of microstructural characterization, electrical properties, and mechanical behaviors of nanocomposites. The analysis utilizes advanced Boolean search strategies from the Scopus database, ensuring a thorough extraction of thematic content. The results explore various themes and insights, shedding light on trends evident in the Scopus database, particularly the prominence of research on nanocomposite microstructure, electrical attributes, and mechanical performance. The paper also offers textual analytics and bibliometric data, showcasing critical collaborative efforts and influential studies. Significant discoveries encompass the evolution of research language, shifts in thematic focus, and global contributions, providing a comprehensive perspective on the current landscape of nanocomposite research and its dynamic evolution. Moving forward, the "State-of-the-Art and Gaps Extracted from Results and Discussions" section of the paper delves into the most recent advancements in nanocomposite research. It delves into various types of nanocomposites, with a particular emphasis on their microstructural characteristics, electrical properties, mechanical dynamics, and the application of nanocomposite films. This section identifies key research themes, traces historical progress, and highlights emerging trends while underscoring the significance of collaboration and the influence of pivotal studies that have shaped the field. Lastly, in the "Literature Review Guided by Artificial Intelligence" section, the paper introduces a revised approach for researching nanocomposites through AI-guided techniques. This approach prioritizes articles published in 2023 based on citation frequency. Here, the focus is on exploring the relationship between nanocomposites and their electrical properties, emphasizing their fundamental interactions and impact on electrical characteristics. Various nanocomposite systems are covered, highlighting their composition, structure, and functionality. Findings from recent studies are integrated to provide a comprehensive overview of the current state of knowledge in this area. Notably, the sentiment analysis, anchored by an average sentiment score of 0.638771, underscores a positive trajectory in academic discourse, emphasizing the growing recognition of the potential of nanocomposites. The bibliometric exploration maps the intellectual domain, emphasizing pivotal research themes and the influence of crosslinking time on nanocomposite attributes. While this study is thorough, it acknowledges its limitations and advocates for broader database inclusion in future research endeavors. This work elucidates the prevailing trends in nanocomposite research, emphasizing the indispensable role of computational tools in comprehending this vast wealth of information.

(1) Background: The intermediate-depth seismicity in the Vrancea region (Romania) is characterized by localized and persistent earthquake activity that culminates about two or three times in a century with the occurrence of a large event (M 6.5). Here we have revisited some important seismicity characteristics, using earthquake catalog data spanning two different time periods: 2005 – 2013 and 1960 – 2000. (2) Methods: we have determined the b-value of the frequency-magnitude distribution of earthquakes, using a maximum likelihood procedure, and estimated the parameter to quantify anomalous seismicity rate decreases and increases. (3) Results: by using data from the first period, we have confirmed the existence of a decreased b-value in the deepest part of the seismogenic zone; by using data from the second period, we have statistically confirmed the seismic quiescence that preceded the occurrence of the 1977 M7.4 Vrancea earthquake. (4) Conclusions: the decreased b-value has been interpreted either in terms of an increased lithostatic stress with depth or as an indicator of the depth range where the next major Vrancea earthquake may occur. The time variation of the seismicity parameter may reveal anomalous seismic quiescence and increased earthquake rates that may precede the occurrence of large earthquakes.

To understand dynamics in climate change, informing policy decisions and prompting timely action to mitigate its impact, this study provides a comprehensive analysis of the short-term trend of year-on-year CO2 emission changes across ten countries, considering a broad range of factors including socioeconomic, CO2-related industry, and education. This study uniquely goes beyond the common country-based analysis, offering a broader understanding of the interconnected impact of CO2 emissions across countries. Our preliminary regression analysis, using the ten most significant features, could only explain 66% of variations in the target. To capture emissions trend variation, we categorized countries by the change in CO2 emission volatility (high, moderate, low with upward or downward trends), assessed using standard deviation. We employed machine learning techniques, including feature importance analysis, Partial Dependence Plots (PDPs), sensitivity analysis, and Pearson and Canonical correlation analyses, to identify influential factors driving these short-term changes. The Decision Tree Classifier was the most accurate model, with an accuracy of 96%. It revealed population size, CO2 emissions from coal, the three-year average change in CO2 emissions, GDP, CO2 emissions from oil, education level (incomplete primary), and contribution to temperature rise as the most significant predictors, in order of importance. Furthermore, this study estimates the likelihood of a country transitioning to a higher emission category. Our findings provide valuable insights into the temporal dynamics of factors influencing CO2 emissions changes, contributing to global efforts to address climate change

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

The choice of parameters for laser beams used in the treatment of musculoskeletal diseases is of great importance. First, to reach high penetration depths into biological tissue and, secondly, to achieve the required effects on a molecular level. The penetration depth depends on the wavelength since there are multiple light-absorbing and scattering molecules in tissue with different absorption spectra. The present study is the first comparing the penetration depth of 1064 nm laser light with light of a smaller wavelength (905 nm) using high-fidelity laser measurement technology. Penetration depths in two types of tissue (porcine skin and bovine muscle) were investigated. The transmittance of 1064 nm light through both tissue types was consistently higher than of 905 nm light. The largest differences (up to 5.9%) were seen in the upper 10 mm of tissue, while the difference vanished with increasing tissue thickness. The higher penetration was most likely due to a combination of lower absorption in hemoglobin and less scattering at larger wavelengths, and not due to absorption in melanin. Overall, differences in penetration depth were comparably small and high peak power and short pulse lengths of laser light seem to be more important to efficiently treat deep musculoskeletal diseases.

Single molecule de novo protein sequencing based on the 'superspecificity' of amino-acyl tRNA synthetases (aaRS) is proposed. An unfolded protein molecule is threaded through a nanopore in an electrolytic cell (e-cell) to expose the terminal residue in the e-cell's trans chamber. After the residue is cleaved with an exopeptidase, a set of tRNAs, their aaRSs, and ATP are added to trans. An aaRS charges a cognate tRNA molecule with the residue. The charged tRNA (along with the other reactants) is transferred to an extended e-cell with N (20 ≤ N ≤ 61) pores in N individual cis chambers and a single trans chamber. Each pore holds an RNA molecule ending in a unique codon that is exposed in trans. The charged tRNA's anticodon base-pairs with the terminal codon of an RNA. If tRNAs and residues are fluorescently tagged with two different colors, the residue can be identified from the observed position of the resulting color pair. As charging is 'superspecific' identification is unambiguous. The protein molecule in the first e-cell is advanced by one residue and the process repeated. In this approach there is no need for precise pore current or optical intensity measurements. Potential implementation issues are discussed. Other possibilities, including one in which the terminal residue is cleaved after charging, are also examined.

Due to the major impact of climate change on the world's environment, political and economic systems, climate change mitigation has become a pressing priority for the international community and requires rapid action from the whole society. With the continuous advancement of artificial intelligence research, the integration of AI and other technologies makes it more and more used in the whole society. It has become a promising and innovative avenue in the field of climate change mitigation. This paper comprehensively considers the key role of AI technology in the field of climate change mitigation, such as climate modeling, the optimization of renewable energy systems, the development of intelligent solutions for sustainable practices and CSS technology, and affirms its future prospects. It also describes the challenges of AI in the field of climate change mitigation. As researchers, policymakers, and industries collaborate to refine AI methodologies and integrate them into practical applications, a concerted effort is required to establish ethical guidelines, transparency standards, and inclusive governance frameworks.

As the structure of horizontal gas wells is more complicated than that of vertical wells, the form of the liquid-carrying in different sections does not well agree. This makes it problematic to apply the widely used liquid-carrying theory of vertical gas wells in horizontal gas wells. Since the theory focused on the critical gas flow rate, it cannot quantify how much liquid it can remove. Simultaneously, it ignores the fact that the liquid-carrying ability of gas flow is limited and the producing liquid has a certain amount of flowing energy. In this study, the gas-liquid flow law of horizontal gas wells and wellhead drainage stability in different tubing depths were firstly studied. Then, the stability of gas drainage for different tubing depths was analyzed and confirmed. Given the disadvantages of the typical theory of critical gas flow, the mathematical model of different tubing depths for gas drainage is established for horizontal gas wells. The innovative model could take the energy of gas flow and liquid flow into account, and quantify the liquid volume which was removed. By verifying the model with the experiments, the result showed that the relative error of the model is generally less than 10%. It shows the research could provide a scientific basis for the analysis and liquid-carrying capacity for horizontal gas wells.

The change of tire groove depth will have a huge impact on tire performance, and the use of excessively worn tires is not conducive to the driving safety of automobiles. Tire groove depth detection has become one of the annual inspection items of automobiles, but the research on its related detection technology is still relatively backward. Based on the principle of monocular vision ranging (MVR), image processing technology and cloud platform technology, this paper develops a tire groove depth detection system, which realizes non-destructive detection of tire groove depth. In addition, the system uses the cloud platform to store the test results, and builds a multi-level data management system, allowing car owners to keep track of the tire wear status and historical changes, which is of great significance to ensuring driving safety.

We present a new approach to retrieve Aerosol Optical Depth (AOD) from Moderate Resolution Imaging Spectroradiometer (MODIS) over the turbid coastal water. This approach supplements the operational Dark Target (DT) aerosol retrieval algorithm that currently don’t conduct any AOD retrieval in the regions with large water-leaving radiances in the visible spectrum. Over the global coastal water regions in all cloud-free conditions, this unavailability of AOD retrievals due to the inherent limitation in existing DT algorithm is ~20%. Here, we refine the MODIS DT algorithm by considering that water-leaving radiance at 2.1 μm is negligible regardless of water turbidity. This refinement, with the assumption that the aerosol single scattering properties over coastal turbid water are similar to that over the adjacent open-ocean pixels, yields ~18% more of MODIS-AERONET collocated pairs for six AEROENT stations in the coastal water regions. Furthermore, comparison with these AERONET observations show that the new AOD retrievals are in either equivalent or better accuracy than those retrieved by the MODIS operational algorithm (over coastal land and non-turbid coastal water). Combining the new retrievals with the existing MODIS operational retrievals not only yield an overall improvement of AOD over those coastal water regions, but also successfully extend the spatial and temporal coverage of MODIS AOD retrievals over the coastal regions where 60% of human population resides, and thereby, aerosol impacts on regional air quality and climate are expected to be significant.

Optimal conditions for maximum efficacy of photoinitiated polymerization are theoretically presented. Analytic formulas are shown for the crosslink time, crosslink depth and efficacy function. The roles of photoinitiator (PI) concentration, diffusion depth and light intensity on the polymerization spatial and temporal profiles, for both uniform and non-uniform cases, are presented. For optimal efficacy, a strategy via controlled PI concentration is proposed, where re-supply of PI in high light intensity may achieve a combined-efficacy similar to low light intensity, but has a much faster procedure. A new criterion of efficacy based on the polymerization (crosslink) [strength] and [depth] is introduced. Experimental data are analyzed for the role of PI concentration and light intensity on the gelation time and efficacy.

This study was aimed to assess visual performance and overall satisfaction of extended depth of focus (EDOF) contact lenses (CLs) in a presbyopic population. We prospectively investigated visual acuity at all distances (0.3, 0.4, 0.5, 0.7, 1, and 5 m), higher-order aberrations (HOAs), contrast sensitivity function, and, overall satisfaction score, before and during EDOF CL wear. Binocular visual acuity at 0.3, 0.5, 0.7, 1, 2, 3, and 5 m when wearing EDOF CLs was 0.01 ± 0.14, -0.08 ± 0.02, -0.08 ± 0.02, -0.08 ± 0.00, -0.08 ± 0.00, -0.08 ± 0.02, and -0.07 ± 0.02, respectively. We found a significant improvement at near to intermediate distances (0.3, and 0.5 m), but no significant change at intermediate to far distances (0.7, 1, 2, 3, and 5 m) between before and during CL wear. The area under the log contrast sensitivity function was not significantly changed neither under photopic nor mesopic conditions (p=0.099, and p=0.689). Ocular third-order aberrations, fourth-order aberrations or total HOAs for a 4-mm pupil significantly increased. The overall satisfaction score significantly improved by wearing EDOF CLs. EDOF CLs significantly improved visual acuity at near to intermediate dis-tances, while maintaining far vision, and the effect of contrast sensitivity was minimal, suggesting its viability of presbyopic correction in such candidates.

Understanding microbial composition in upper respiratory infections (URIs) is critical for effective diagnosis and treatment. Precision Metagenomic next-generation sequencing p(mNGS) can provide a comprehensive yet clinically relevant profile of respiratory infection. The hybridization capture-based targeted sequencing generated a precision metagenomics profile of 29 patients with acute URIs. Nasopharyngeal samples were collected from the subjects suspected of respiratory infection, and p(mNGS) was performed using the Illumina®/IDbyDNA Respiratory Pathogen ID/AMR Panel (RPIP). The dataset obtained from the mNGS analysis contains a wealth of information on the composition of acute URI microbiota, including the relative abundance of known pathogens and potential clinical implications. The dataset represents a valuable resource for future research endeavors in respiratory medicine, infectious disease epidemiology, and therapeutic interventions. In addition, the dataset offers significant potential for reuse and integration with other omics datasets. The comprehensive nature of the mNGS data allows the exploration of associations between the respiratory microbiota and host factors such as clinical outcomes, immune responses, or genetic predisposition. Combining this dataset with other relevant datasets, such as transcriptomics or metabolomics, could provide a deeper understanding of the complex interactions between the microbiota and the host in acute URIs.

The quickest and easiest way to avoid greenhouse gas (GHG) emissions is to purchase renewable electricity and offset the remaining emissions. However, the industrial sector’s electricity needs already exceed renewable electricity generation. Moreover, electricity accounts for only one third of the industry’s energy needs. Simultaneously, the advance of sectoral coupling and the decarbonisation of industrial processes, as well as the desire to rapidly decrease dependence on fossil fuels, are creating significant additional demand for renewable energy. Neither existing nor planned generation and transmission infrastructure will suffice to meet the expected short-term demand. Based on survey data from the German Industry Energy Efficiency Index, this article therefore examines the share of GHG savings that companies intend to achieve on- and off-site. Understanding how much additional generation and transmission capacity is needed by the industry to decarbonise and by when is crucial to identify and address the extent of excess demand. On average, companies plan to avoid 22 % of their 2019 emissions by 2025 and 27 % by 2030, primarily through on-site measures. In combination with the extrapolation of the entire industry’s needs for off-site capacity, the data calls for a rapid expansion of planning authority and green generation capacities.

BACKGROUND: Glioblastoma (GBM) is driven by various genomic alterations. Next generation sequencing (NGS) could yield targetable alterations that may impact outcomes. The goal of this study was to describe how NGS can inform targeted therapy (TT) in this patient population. METHODS: The medical records of patients (pts) with a diagnosis of GBM from 2017-2019 were reviewed. Records of patients with recurrent GBM and genomic alterations were evaluated. Objective response rates and disease control rates were deter-mined. RESULTS: A total of 87 pts with GBM underwent NGS. Forty percent (n = 35) were considered to have actionable alterations. Of the 35, 40% (n=14) pts had their treatment changed due to an alteration. The objective response rate (ORR) of this population was 43%. The disease control rate (DCR) was 100%. The absolute mean decrease in contrast enhancing disease was 50.7% (95% CI 34.8 – 66.6). CONCLUSION: NGS for GBM, particularly in the recurrent setting, yields a high rate of actionable alterations. We observed a high ORR and DCR, reflecting the value of NGS in deciding on TT to match alterations that are likely to respond. In conclusion, patient selection and availability of NGS may impact outcomes in select pts with recurrent GBM.

Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was performed using the PacBio RS II platform, followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not the L. acidophilus as previously assumed. 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, aight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of the both strains. The expression of some genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages and show some genome-determined resistance to antibiotics, stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.

The scientific community has shown considerable interest in Industry 4.0 due to its capacity to revolutionise the manufacturing sector through digitalisation and data-driven decision-making. However, the actual implementation of Industry 4.0 within complex industrial settings presents obstacles that are typically beyond the scope of mainstream research articles. In this paper, a comprehensive case-study detailing our collaborative partnership with a leading medical device manufacturer is presented. The study traces their evolution from a state of limited digitalisation to the development of a digital intelligence platform that leverages data and machine learning models to enhance operations across a wide range of critical machines and assets. The main business objective was to enhance the energy efficiency of the manufacturing process, thereby improving its sustainability measures while also saving costs. The project encompasses energy modelling and analytics, Fault Detection and Diagnostics (FDD), renewable energy integration and advanced visualisation tools. Together, these components enable informed decision making in the context of energy efficiency.

Background: The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenges. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Results: Here, we propose a computational and experimental protocol for whole genome quantitative metagenomics studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatic protocol to analyse ONT sequences taxonomically and functionally and optimized pre-analytic protocols including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities which reflect naturally occuring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. Conclusion: This protocol can be implemented in the clinical or research setting, bringing rapid personalized whole genome profiling of target microbiome species.

Kluyveromyces marxianus (K. marxianus) is a newly emerging industrially relevant yeast. It is known to possess a highly efficient Non-Homologous End Joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the Gross Chromosomal Rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in Eukaryotes, which could potentially provide insights for cancer research.

This paper investigates the performance of dual hop UAV-assisted communication channels, employing a decode and forward relay architecture. The system utilizes Terahertz (THz) communication in the primary hop and Visible Light Communication (VLC) in the secondary hop. We conduct a thorough analysis by deriving closed-form expressions for end to end bit error rate (BER). Furthermore, we employ a Monte Carlo approach to generate best fitting curves and validate our numerical expressions with simulation results. Evaluation via BER and outage probability demonstrates the proposed system’s effectiveness. The outcomes of this research offer valuable insights into the feasibility and limitations of UAV-assisted THz- VLC systems.

X-ray tomography is an effective non-destructive testing method for industrial quality control. Limited angle tomography can be used to reduce the amount of data that needs to be acquired and thus speed up the process. In some industrial applications, however, objects are flat and layered, and laminography is preferred. It can deliver 2D images of the structure of a layered object at a particular depth from very limited data. An image at a particular depth is obtained by summing those parts of the data that contribute to that slice. This produces a sharp image of that slice while superimposing a blurred version of structures present at other depths. In this paper, we investigate an optimal experimental design (OED) problem for laminography that aims to determine the optimal source positions. Not only can this be used to mitigate imaging artifacts, it can also speed up the acquisition process in case where moving the source and detector is time consuming (e.g., in robotic arm imaging systems). We investigate the imaging artifacts in detail through a modified Fourier Slice Theorem. We address the experimental design problem within the Bayesian risk framework using empirical Bayes risk minimization. Finally, we present numerical experiments on simulated data.

The ocean’s mixed layer depth (MLD) plays an important role in understanding climate dynamics, especially during extreme weather occurrences like hurricanes. This study investigates the effects of Hurricane Katrina (2005) on the MLD in the Gulf of Mexico, using the Delft3D modeling system. By integrating hydrodynamics and wave dynamics modules, we simulate the ocean’s response to extreme weather, focusing on temperature, salinity and MLD variations. Our analysis reveals significant cooling and mixing induced by Katrina, resulting in spatial and temporal fluctuations in temperature (~± 4°C) and salinity (~± 2.5 ppt). The MLD is estimated using a simple threshold method, revealing a substantial deepening to ~120 m on August 29th-30th during Hurricane Katrina in the middle of northern Gulf of Mexico, compared to an average MLD of ~20-40 m during pre-storm conditions. It took about 18-days to recover to ~84% of the pre-storm level after Katrina. Compared to the stand-alone FLOW model, the coupled FLOW+WAVE model yields a deeper MLD of ~5%. The MLD recovery and wave effect on the MLD provide insights from various scientific, environmental and operational perspectives, offering a valuable basis for ocean management, planning and applications, particularly during extreme weather events.

New insights into the causes and mechanisms of congenital heart disease (CHD) have been gained through the use of next-generation sequencing. Examination of the whole exome sequence detects detrimental gene variations modifying single or contiguous nucleotides, that are characterised as pathogenicity based on statistical assessments of families. and correlates with congenital heart disease, elevated expression during heart development, and reduction of harmful protein-coding mutations in the general population. Patients with CHD and extracardiac abnormalities enriched for gene classes meeting these criteria. CHDs and extracardiac defects, supporting a common set of pathways in the organogenesis of CHDs. Single-cell transcriptomics data reveal the expression of genes associated with CHD in specific cell lineages, and emerging evidence suggests that genetic variants disrupt multicellular genes essential for cardiogenesis. Metrics and units are being tracked in whole genome sequence studies.

Scour depth around bridge piers plays a vital role in the safety and stability of the bridges. Existing methods to predict scour depth are mainly based on regression models or black box models in which the first one lacks enough accuracy while the later one does not provide a clear mathematical expression to easily employ it for other situations or cases. Therefore, this paper aims to develop new equations using particle swarm optimization as a metaheuristic approach to predict scour depth around bridge piers. To improve the efficiency of the proposed model, individual equations are derived for laboratory and field data. Moreover, sensitivity analysis is conducted to achieve the most effective parameters in the estimation of scour depth for both experimental and filed data sets. Comparing the results of the proposed model with those of existing regression-based equations reveal the superiority of the proposed method in terms of accuracy and uncertainty. Moreover, the ratio of pier width to flow depth and ratio of d50 (mean particle diameter) to flow depth for the laboratory and field data were recognized as the most effective parameters, respectively. The derived equations can be used as a suitable proxy to estimate scour depth in both experimental and prototype scales.

Newborn screening using biochemical tests is a widespread practice. However, the recent availability of genetic sequencing has enabled the rapid screening of many monogenic disorders. The purpose of our study was to assess the outcomes of whole exome sequencing (WES) and whole genome sequencing (WGS) as the primary newborn screening test. This cohort study enrolled 26 symptomatic neonates and infants exhibiting a spectrum of neurological symptoms and issues. Genome sequencing (GS) identified relevant diagnostic variants in 9 patients (point mutations, CNVs and one case of aneuploidy), suggesting that using GS as the primary newborn screening test in a general newborn population enhances traditional screening's detection capabilities. This evidence-based finding may support considering GS as a critical method for first-tier screening.

Fatigue risk to commercial pilots operating under global pandemic conditions had not been in-vestigated prior to COVID-19. Examining how pilots slept during COVID-19 pandemic-specific flights can provide a precedent for estimating fatigue risk for future public health emergencies. Twenty (n=20) pilots flying across five COVID-19 humanitarian missions between Brazil and China wore a sleep-tracking device (the Zulu watch), which has been validated for the estimation of sleep timing (sleep onset and offset), duration, efficiency, and sleep depth (Wake, Interrupted, Light, or Deep Sleep) throughout the mission period. Pilots also reported sleep timing, duration and subjective quality of their in-flight rest periods using a sleep diary. To our knowledge, this is the first report of commercial pilot sleep behavior during ultra-long-range operations under COVID-19 pandemic conditions. Moreover, these analyses provide an estimate of sleep depth during in-flight sleep, which has not been reported previously in the literature.

A sufficient amount of tissue sample is required to perform next-generation sequencing (NGS) with a high success rate, but the majority of patients with advanced non-small-cell lung cancer (NSCLC) are diagnosed with small biopsy specimens. Biopsy samples were collected from 184 patients with bronchoscopically diagnosed NSCLC. The tissue surface area, tumor cell count, and tumor content rate of each biopsy sample were evaluated. The impact of the cut-off criteria for the tissue surface area (≥ 1 mm2) and tumor content rate (≥ 30%) on the success rate of Oncomine Dx Target Test (ODxTT) was evaluated. The mean tissue surface area of the transbronchial biopsies was 1.23 ± 0.85 mm2 when small endobronchial ultrasonography with a guide sheath (EBUS-GS) was used, 2.16 ± 1.49 mm2 with large EBUS-GS, and 1.81 ± 0.75 mm2 with endobronchial biopsy (EBB). The proportion of samples with a tissue surface area of ≥ 1 mm2 was 48.8% for small EBUS-GS, 79.2% for large EBUS-GS, and 78.6% for EBB. Sixty-nine patients underwent ODxTT. The success rate of DNA sequencing was 84.1% and that of RNA sequencing was 92.7% over all patients. The success rate of DNA (RNA) sequencing was 57.1% (71.4%) for small EBUS-GS (n = 14), 93.4% (96.9%) for large EBUS-GS (n = 32), 62.5% (100%) for EBB (n = 8), and 100% (100%) for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) (n = 15). Regardless of the device used, a tissue surface area of ≥ 1 mm2 is adequate for samples to be tested with NGS.

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencings with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5’-truncated putative mRNAs embedded into larger host mRNAs. A large fraction of these RNA molecules contain in-frame ORFs, which may encode N-terminally truncated polypeptides. These study demonstrates that the PRV transcriptome is much more complex than previously appreciated.

Targeted next-generation sequencing (NGS) technology detects specific mutations that can provide treatment opportunities for colorectal cancer (CRC) patients. We included 145 CRC patients who underwent surgery. We analyzed the mutation frequencies of common actionable genes and their association with clinicopathological characteristics and oncologic outcomes using targeted NGS. Approximately 97.9% (142) of patients showed somatic mutations. Frequent mutations were observed in TP53 (70%), KRAS (49%), and APC (47%). TP53 mutations were significantly linked to higher overall stage (p=0.038) and lower disease-free survival (DFS) (p=0.039). ATM mutation was significantly associated with higher tumor stage (p=0.012) and shorter overall survival (OS) (p=0.041). Stage 3 and 4 patients with ATM mutations (p=0.023) had shorter OS, and FBXW7 mutation was significantly associated with shorter DFS (p=0.002). In multivariate Cox regression analysis, ATM mutation was an independent biomarker for poor prognosis of OS (p=0.022). TP53 and FBXW7 mutations are independent biomarkers for poor prognosis of DFS (p=0.042 and 0.030, respectively). A comprehensive analysis of the molecular markers for CRC can provide insights into the mechanisms underlying disease progression and help optimize a personalized therapy.

Purpose: To evaluate clinical outcomes after bilateral mix-and-match cataract surgery using extended depth of focus (EDOF) and diffractive multifocal (DMF) intraocular lenses (IOLs). Methods: Thirty-seven patients received Tecnis Symfony EDOF IOL (ZXR00) implantation in the dominant eye, and Tecnis +3.25 DMF IOL (ZLB00) in the non-dominant eye. Patients were followed for 3 months, and uncorrected and corrected distance visual acuity (UDVA, CDVA) , uncorrected intermediate and near visual acuity (UIVA, UNVA), contrast sensitivity, defocus curves, stereopsis, and patient satisfaction were assessed. Results: At 3 months, mean logMAR UDVA was 0.07 ± 0.09 in EDOF IOL eyes, 0.12 ± 0.11 in DMF IOL eyes, and 0.02 ± 0.05 in both eyes. UIVA was 0.11 ± 0.11 in EDOF IOL eyes, 0.16 ± 0.12 in DMF IOL eyes, and 0.04 ± 0.07 in both eyes. UNVA was 0.25 ± 0.15 in EDOF IOL eyes, 0.22 ± 0.16 in DMF IOL eyes, and 0.13 ± 0.13 in both eyes. Thirty patients(81.1%) were more than satisfied with near vision, and 8 patients(21.6%) complained of severe glare and halo. Spectacle independence for near vision was achieved in 34 patients(91.9%), and 31 patients(83.8%) had better than a 50 second arc of stereopsis. Conclusion: Mix-and-match cataract surgery with EDOF and DMF IOL implantation provided good visual outcomes through all distances. Also excellent patient satisfaction was achieved with high level of spectacle independence and minimal photic phenomena.

With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Indeed, sequencing techniques but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome-scale is now feasible at the laboratory scale. Current technologies, and especially long-range technologies, are numerous and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range techniques, optical mapping, Omni-C and Pore-C sequencing libraries commercialized by Bionano Genomics, Dovetail Genomics and Oxford Nanopore Technologies respectively, or a combination of the three, in order to evaluate the capability of each technology.

We consider the problem of scheduling $n$ jobs with identical processing times and given release as well as delivery times on $m$ uniform machines. The goal is to minimize the makespan, i.e., the maximum full completion time of any job. This problem is well-known to have an open complexity status even if the number of jobs is fixed. We present a polynomial-time algorithm for the problem which is based on the earlier introduced algorithmic framework blesscmore (``branch less and cut more''). We extend the analysis of the so-called behavior alternatives developed earlier for the version of the problem with identical parallel machines and show how the earlier used technique for identical machines can be extended to the uniform machine environment if a special condition on the job parameters is imposed. The time complexity of the proposed algorithm is $O(\gamma m^2 n\log n)$, where $\gamma$ can be either $n$ or the maximum job delivery time $q_{\max}$. This complexity can even be reduced further by using a smaller number $\kappa<n$ in the estimation describing the number of jobs of particular types. However, this number $\kappa$ becomes only known when the algorithm has terminated.