This review provides an overview of advancements in plant genomics, emphasizing key stages in genomics projects and addressing associated challenges. Long read sequencing enables the cost-effective sequencing of plant DNA and assembly of highly continuous genome sequences - often even separating haplophases. Incorporating external hints, such as cDNA sequences from RNA-seq or full length cDNA sequencing, enhances the identification of gene models. While these steps enable high-throughput exploration of numerous plant genomes, a significant bottleneck lies in elucidating gene functions. The classical approach based on wet lab methods is impractical when dealing with thousands of genes in a new genome sequence. To overcome this challenge, computational tools harnessing existing information for cross species knowledge transfer are essential for expediting the functional annotation process. In support of researchers entering the field of plant genomics, a collection of recommended tools has been curated and is accessible at https://github.com/bpucker/ToolOverview.

Cisplatin is a widely used anticancer drug for treating solid tumors, but it is associated with severe side effects, including nephrotoxicity. Various studies have suggested that the nephrotoxicity of cisplatin could be overcome; nonetheless, an effective adjuvant drug has not yet been established. Oleanolic acid acetate (OAA), a triterpenoid isolated from Vigna angularis, is commonly used to treat inflammatory and allergic diseases. This study aimed to investigate the protective effects of OAA against cisplatin-induced apoptosis and necroptosis using TCMK-1 cells and a mouse model. In cisplatin-treated TCMK-1 cells, OAA treatment significantly reduced Bax and cleaved-caspase3 expression, whereas increased Bcl-2 expression. Moreover, in cisplatin-induced kidney injury mouse model, OAA treatment alleviated weight loss in the body and major organs and also relieved cisplatin-induced nephrotoxicity symptoms. RNA sequencing analysis of kidney tissues identified lipocalin-2 as the most upregulated gene by cisplatin. Additionally, necroptosis-related genes such as receptor interacting protein kinase (RIPK) and mixed lineage kinase domain like (MLKL) were identified. In vitro study, the phosphorylation of RIPKs and MLKL was reduced by OAA pretreatment in both cisplatin-treated cells and cells boosted by co-treatment with z-VAD-FMK. In conclusion, OAA could protect the kidney from cisplatin-induced nephrotoxicity and may serve as an anticancer adjuvant.

Diacylglycerol kinase (DGK) is a lipid kinase that phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Based on converting one important signaling molecule (DAG) to another (PA), DGK plays an important role in plant responses to abiotic stress including waterlogging stress. However, no studies have been reported on the characterization of the DGK gene family in the waterlogging-tolerant kiwifruit germplasm, Actinidia valvata Dunn. Here, we identified 18 AvDGK genes in the A. valvata genome. The phylogenetic analysis showed that AvDGKs can be classified into three clusters, and members within the same cluster have similar domain distribution, exon-intron structures and conserved motif compositions. Chromosome localization analysis revealed that all the AvDGK genes are located across 18 different chromosomes. There were 29 duplicated gene pairs in kiwifruit and all had undergone purifying selection during evolution. Promoter cis-element analysis revealed that the cis-elements within AvDGK genes are associated with multiple functions, including phytohormone signal transduction, stress response, and plant growth and development. The expression pattern analyses indicated that AvDGK play an important role in the fruit development and plant response to waterlogging stress. AvDGKs gene family in the tetraploid A. valvata genome might promote PA synthesis and subsequent signal transduction both under short-term and long-term waterlogging stress. These results provide information regarding the structural characteristics and potential function of DGK genes within kiwifruit and lay a fundamental basis for further research into breeding for enhancing the kiwifruit’s tolerance to waterlogging stress.

Extracellular vesicles (EVs) hold enormous potential in the diagnosis and treatment of diseases, benefit from their roles in intercellular signaling, as well as their plentiful presence and stability in body fluids. However, conventional EV isolation methods are labor-intensive, and harvest EVs with low purity and compromised recovery. In addition, the drawbacks, such as limited sensitivity and specificity of traditional EV analysis methods hinder the application of EVs in clinical use. Therefore, it is urgent to develop effective and standardized methods for isolating and detecting EVs. Microfluidics technology is a powerful and rapidly developing technology that has been introduced as a potential solution for the above bottlenecks. It holds the advantages of high integration, short analysis time, low consumption of samples and reagents. In this review, we summarize the traditional techniques alongside microfluidic-based methodologies for the isolation and detection of EVs. We emphasize the separation advantages of microfluidic technology in enhancing EV capture efficiency and precise targeting, while summarizing its analytical role in targeted detection and discussing the significance of EV detection in the tumor microenvironment, providing a direction for achieving automated and high-throughput EV detection in clinical samples.

Riparian zones represent ecotones between terrestrial and aquatic ecosystems and are of utmost importance to biodiversity and ecosystem functions. Modelling/mapping of these valuable and fragile areas is needed for an improved ecosystem management, based on an accounting of changes and on monitoring of their functioning in time. In Europe, the main legislative driver behind this goal is the European Commission’s Biodiversity Strategy to 2020, on one hand aiming at reducing biodiversity loss, on the other hand enhancing ecosystem services by 2020, and restoring them as far as feasible. A model, based on Earth Observation data, including Digital Elevation Models, hydrological, soil, land cover/land use data, and vegetation indices is employed in a multi-modular and stratified approach, based on fuzzy logic and object based image analysis, to delineate potential, observed and actual riparian zones. The approach is designed in an open modular way, allowing future modifications and repeatability. The results represent a first step of a future monitoring and assessment campaign for European riparian zones and their implications on biodiversity and on ecosystem functions and services. Considering the complexity and the enormous extent of the area, covering 39 European countries, including Turkey, the level of detail is unprecedented. Depending on the accounting modus, 0.95%–1.19% of the study area can be attributed as actual riparian area (considering Strahler’s stream orders 3-8, based on the Copernicus EU-Hydro dataset), corresponding to 55,558–69.128 km². Similarly depending on the accounting approach, the potential riparian zones are accounted for about 3-5 times larger. Land cover/land use in detected riparian areas was mainly of semi-natural characteristics, while the potential riparian areas are predominately covered by agriculture, followed by semi-natural and urban areas.

Injury to the peritoneum during surgery is followed by a healing process that frequently results in the attachment of adjacent organs by a fibrous mass, referred to commonly as adhesions. Because injuries to the peritoneum during surgery are inevitable, one must understand the mechanisms of adhesion formation to prevent its occurrence. This requires a thorough understanding of the molecular sequence that results in the attachment of injured peritoneum and the development of fibrous tissue. Recent data show that fibroblasts from the injured peritoneum may play a critical role in forming adhesion tissues. Therefore, identifying changes in gene expression patterns in the peritoneal fibroblasts during the process may provide clues to the mechanisms by which adhesion develops. This review presents many papers discussing genes implied in peritoneal adhesion.

To characterize the fecal microbiota of lactating Bactrian camels, this study employed a random selection of camels, assigning them to three groups: the first parity group, the third parity group, and the fifth parity group. The fecal microbial community of lactating camels was assessed using 16S rRNA amplicon sequencing, and the resulting library was sequenced on an Illumina NovaSeq platform. The first parity group was characterized by Verrucomicrobiaceae as a distinctive bi-omarker, whereas Clostridiaceae exhibited a similar role to the third parity group. In terms of functional analysis, the relative abundance of the Steroid biosynthesis pathway was highest in the first parity group, whereas the fifth parity group demonstrated a higher relative abundance of the Tuberculosis pathway compared to the other groups. The first parity group exhibited the greatest presence of seven types of enzymes, whereas the fifth parity group displayed the highest levels of two specific enzymes. Additionally, a positive association was observed between the relative abundance of the Steroid biosynthesis pathway and Verrucomicrobiaceae. Furthermore, the relative abundance of the Tuberculosis pathway displayed positive correlations with 14 enzymes. In conclusion, this study revealed that different parity was associated with distinct fecal microbial ecologies in lactating Bactrian camels.

To enhance the applicability of dual-phase high-entropy alloys (HEAs) like Fe32Cr33Ni29Al3Ti3, fabricated via selective laser melting (SLM), a focus on improving their mechanical properties is essential. As part of this effort, heat treatment was explored. This study compares the microstructure and mechanical properties of the as-printed sample with those cooled in water after undergoing heat treatment at temperatures ranging from 1000 to 1200 ℃ for 1 hour. Both pre- and post-treatment samples reveal a dual-phase microstructure comprising FCC and BCC phases. Although heat treatment led to a reduction in tensile and yield strength, it significantly increased ductility compared to the as-printed sample. This strength-ductility trade-off is related to changes in grain sizes with ultrafine grains enhancing strength and micron grains optimizing ductility, also the influence of the content of FCC/BCC phases and dislocation density. In particular, the sample heat-treated at 1000 °C for 1 hour and then water-cooled exhibited a better combination of strength and ductility, a yield strength of 790 MPa, and an elongation of 13%. This research offers innovative perspectives on crafting dual-phase HEA of Fe32Cr33Ni29Al3Ti3, allowing for tailorable microstructure and mechanical properties through a synergistic approach involving SLM and heat treatment.

Remote Photoplethysmography (rPPG) has emerged as a non-intrusive and promising physiological sensing capability in HCI research, gradually extending its applications in health-monitoring and clinical care contexts. With advanced machine learning models, recent datasets collected in real-world conditions have gradually enhanced the performance of rPPG methods in recovering heart-rate and heart-rate variability metrics. However, the signal quality of reference ground-truth PPG data in existing datasets is by and large neglected, while poor quality references negatively influence models. Here, this work introduces a new imaging blood volume pulse (iBVP) dataset of synchronized RGB and thermal infrared videos with PPG ground-truth signals from the ear and its high resolution signal quality labels, for the first time. Participants perform rhythmic breathing, head-movement, and stress-inducing tasks, which help reflect real-world variations in psycho-physiological states. This work conducts dense (per sample) signal quality assessment to discard noisy segments of ground-truth and corresponding video frames. We further present a novel end-to-end machine learning framework, iBVPNet that features an efficient and effective spatio-temporal feature aggregation for reliable estimation of BVP signals. Finally, this work examines the feasibility of extracting BVP signals from thermal video frames, which is underexplored. The iBVP dataset and source codes are publicly available for research use.

To better understand the shape memory materials and self-healing materials, a new series of liquid-crystalline shape memory polyurethane (LC-SMPU) composites, named SMPU-OOBAm, were successfully prepared by incorporating 4-octyldecyloxybenzoic acid (OOBA) into the PEG-based SMPU. The effect of OOBA on the structure, morphology and properties has been carefully investigated. The results demonstrate that SMPU-OOBAm have liquid crystalline properties, triple-shape memory properties and self-healing properties. The incorporated OOBA promotes the crystallizability of both soft and hard segments of SMPU, and the crystallization rate of the hard segment of SMPU decreases when the OOBA-content increases. Additionally, the SMPU-OOBAm forms a two-phase separated structure (SMPU phase and OOBA phase), and it shows two-step modulus changes upon heating. Therefore, the SMPU-OOBAm shows triple-shape memory behavior, and the shape recovery ratio decreases with an increase in the OOBA content. Finally, SMPU-OOBAm shows self-healing properties. The new mechanism can be ascribed to the heating-induced “bleeding” of OOBA in the liquid crystalline state and the subsequent re-crystallization upon cooling. This successful combination of liquid crystalline properties, triple-shape memory properties and self-healing properties make the SMPU-OOBAm composites with many promise applications in smart optical devices, smart electronic devices and smart sensors.

Honey is a sweet substance extensively consumed in the world for its nutritional and healthy properties. However, residues of pesticides and environmental contaminants can compromise its quality. For this reason, the physicochemical parameters, and the organic contamination of monofloral and multifloral honeys from three regions of Algeria (Tiaret, Laghouat and Tindouf) were monitored to evaluate the quality of honey and the safety for consumers. In general, the results obtained from the physicochemical analyses were in line with the EU standards. In terms of contamination, pesticides authorised and used in Algerian agriculture (matalaxyl-M and cyromazine), as well as banned pesticide (carbaryl), were found in almost all the samples. However, only the concentration of cyromazine was higher than the relative EU maximum residue levels. PCB 180, PCB 189, anthracene, fluorene and phenanthrene were mainly detected. All the honeys show traces of DiBP, DBP, DEHP and DEHT, but no traces of bisphenols were found. Moreover, the dietary exposure assessment shows that a small amount of Algerian honey can be safely consumed. Overall, data from this study should motivate the Algerian government to enhance their monitoring activities in beekeeping and to find solutions for implementing more sustainable agricultural practices harmonizing with the international legislation.

Surface initiated atom transfer radical polymerization (SI-ATRP) is one of the most versatile technique to modify the surface properties of material. Recent developed metal free SI-ATRP makes such technique more widely applicable. Herein photo-induced metal-free SI-ATRP of methacrylates, such as methyl methacrylate, N-isopropanyl acrylamide, and N,N- dimethylaminoethyl methacrylate, on the surface of SBA-15 was reported to fabricate organic-inorganic hybrid materials. SBA-15 based polymeric composite with adjustable graft ratio was obtained. The structure evolution during the SI-ATRP modification of SBA-15 was monitored and verified by FT-IR, XPS, TGA, BET, and TEM. The obtained polymeric composite showed enhanced adsorption ability for the model compound toluene in aqueous. This procedure provides a low cost, ready availability, and facile modification way to synthesize the polymeric composites without the contamination of metal.

Background: The purpuse was to investigate the influence induced by magnesium chloride (MgCl2) and zinc gluconate (ZnG) supplementation on liver and kidney injuries experimentally-induced with acetaminophen (AAPh) and potentiated by ciprofloxacin addition in rats. Material and methods: The experiment was performed on 5 animals groups: group 1 – control, treated for 6 weeks with normal saline, 1mL/kg; group 2 – AAPh, treated for 6 weeks with AAPh, 100 mg/ kg/day; group 3 – AAPh+C, treated AAPh 100 mg/kg/ day for 6 weeks and ciprofloxacin, 50mg /kg/day, only in the last 14 days of the experiment; group 4 – AAPh+C+Mg, with the same treatment as group 3, but, and in the last 14 days, MgCl2 10 mg/ kg/day was added; group 5 – AAPh+C+Zn, with the same treatment as group 3, but, and in the last 14 days, zinc gluconate (ZnG),10 mg/kg/day was added. All administrations were performed by oral gavage. At the end of the experiment, the animals were sacrificed and blood samples were collected for biochemistry examinations. Results: Treatment with AAPh for 6 weeks determined an alteration of the liver function (increases in alanine aminotransferase, aspartate aminotransferase, lactic dehydrogenase and, and gamma-glutamyl transferase) and of renal function (increases in serum urea and creatinine) (P < 0.001 group 2 vs. group 1 for all mentioned parameters). Also, the antioxidant defense capacity was impaired in group 2 vs. group 1 (superoxide dismutase and glutathione peroxidase activity decreased in group 2 vs. group 1, 0.001 < P < 0.01, respectively 0.01 < P < 0.05). The addition of ciprofloxacin, 50 mg/kg/day during the last 14 days resulted in further increases in alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, urea and creatinine (0.01 < P < 0.05, group 3 vs. group 2). MgCl2 provided a slight protection against liver enzymes increase and a more pronounced protection against the increase in serum urea and creatinine (0.001 < P < 0.01 group 4 vs. group 3). MgCl2 provided a slight protection against the decrease in superoxide dismutase (0.01 < P < 0.05 group 4 vs. group 3), but not against decrease of glutathione peroxidase. The improvement of mentioned parameters could also be seen in case of ZnG, to a higher extent especially in the case of alanine aminotransferase and lactic dehydrogenase (0.01 < P < 0.05 group 5 vs. group 4). Conclusions: This study represents a furthermore proof for beneficial effect of magnesium and zinc salts against toxicity induced by different agents, including antibacterials added to the analgesic and antipyretic acetaminophen; the protection is proven on the liver and kidney’s function; the antioxidant profile improvement has a key role, especially in case of zinc gluconate.

In this paper, carbon nanotubes modified screen-printed electrode (CNTs/SPE) was prepared and the CNTs/SPE was employed for the electrochemical determination of antioxidant substance Chlorogenic acids (CGAs). A pair of well-defined redox peak of CGA was observed at the CNTs/SPE in 0.10 mol∙L^-1 acetic acid-sodium acetate buffer (pH 6.2) and electrode process is adsorption-controlled. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) method for the determination of CGA were proposed based on the CNTs/SPE. Under the optimal conditions, the proposed method exhibited linear ranges from 4.73×10^-7 to 4.45×10^-5 mol∙L^-1, the linear regression equation was Ipa(µA) = 4.1993 C (mol∙L^-1)+1.1039 (r = 0.9976) and the detection limit for CGA could reach 3.25×10^-6 mol∙L^-1. The recovery of matrine was 94.74~106.65% (RSD = 2.92%) in coffe beans. The proposed method is quick, sensitive, reliable, and can be used for the determination of CGA.

The aim of this study was to examine the oxidation of human serum albumin (HSA) caused by oxidative stress after an exhaustive exercise such as ultra-marathon race. Thus, blood samples from 12 adult runners who underwent a 103 km mountain ultra-marathon race were collected pre- and 24, 48 and 72 h post race. HSA was partially purified using affinity chromatography and then was subjected to Western blot analysis for disulfide dimers determination, indicating oxidation. The results were correlated with those from a previous study in which the same samples were analyzed using different oxidative stress markers and a good correlation with protein carbonyls (PC) at all time points was observed. Moreover there was a significant correlation with static oxidation-reduction potential (sORP) at 24 h, and a negative correlation with capacity oxidation-reduction potential (cORP) at 24 and 48 h. In addition, an individual analysis of albumin dimers exhibited great inter-individual differences. This inter-individual variability in the oxidation of HSA may suggest different interventions (e.g. through diet) in order to confront the effects on athletes’ organism after a strenuous exercise. In conclusion, this study supported the importance of the assessment of albumin dimers as a predictive marker for exercise-induced oxidative stress.

Large datasets play a crucial role in the progression of surgical robotics, facilitating advancements in the fields of surgical task recognition and automation. Moreover, public datasets enable the comparative analysis of various algorithms and methodologies, thereby assessing their effectiveness and performance. The ROSMA (Robotics Surgical Maneuvers) dataset provides 206 trials of common surgical training tasks performed with the da Vinci Research Kit (dVRK). In this work, we extend ROSMA dataset with two annotated subsets: ROSMAT24, which contains bounding box annotations for instrument detection, and ROSMAG40, which contains high and low level gesture annotations. We propose an annotation method that provides independent labels for the right-handed tool and the left-handed tool. For instrument identification, we validate our proposal with a YOLOv4 model in two experimental scenarios. We demonstrate the generalization capabilities of the network to detect instruments in unseen scenarios. For gesture segmentation, we propose two label categories: high-level annotations that describe gestures at a maneuvers level, and low-level annotations that describe gestures at a fine-grain level. To validate this proposal, we have designed a recurrent neural network based on a bidirectional long-short term memory layer. We present results for four cross-validation experimental setups, reaching up to a 77.35% mAP.

The current study was designed to investigate the anti-inflammatory effect of salidroside (SDS) and the underlying mechanism by using lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages in vitro and a mouse model of binge drinking induced liver injury in vivo. SDS downregulated protein expression of toll-like receptor 4 (TLR4) and CD14. SDS inhibited LPS-triggered phosphorylation of LPS-activated kinase 1 (TAK1), p38, c-Jun terminal kinase (JNK), and extracellular signal-regulated kinase (ERK). Degradation of IκB-α and nuclear translocation of nuclear factor (NF)-κB were effectively blocked by SDS. SDS concentration-dependently suppressed LPS mediated inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein levels, as well as their downstream products, NO. SDS significantly inhibited protein secretion of interleukin (IL)-1β. Additionally C57BL/6 mice were orally administrated SDS for continuous 5 days, followed by three gavages of ethanol every 30 min. Alcohol binge drinking caused the increasing of hepatic lipid accumulation and serum transaminases levels. SDS pretreatment significantly alleviated liver inflammatory changes and serum transaminases levels. Further investigation indicated that SDS markedly decreased protein level of IL-1β in serum. Taken together, these data implied that SDS inhibits liver inflammation both in vitro and in vivo, and may be a promising candidate for the treatment of inflammatory liver injury.

Improper sitting positions are known as the primary reason for back pain and the emergence of musculoskeletal disorders (MSD) among individuals who spend prolonged time working with computer screens, keyboards, and mice. At the same time, it is well understood that automated technological tools can play an important role in the process of unhealthy habit alteration, so plenty of research efforts are focused on research and technology development (RTD) activities that aim to provide support to the prevention of back pain or the development of MSD. Here, we report on creating a new resource in support of RTD activities aiming at the automated detection of improper sitting positions. It consists of multimodal multisensory recordings of 100 persons made with a video recorder, camera, and wrist-attached sensors that capture physiological signals (PPG, EDA, Skin temperature), as well as motion sensors (three-axis accelerometer). Our multimodal multisensory dataset (MMD-MSD) opens new opportunities for modeling the body stance (sitting posture and movements), physiological state (stress level, attention, emotional arousal, valence), and performance (success rate on the Stroop test) of people working with a computer. Finally, we demonstrate two use cases: improper neck posture detection from pictures and cognitive load detection from physiological signals.

Spermatogenesis is critical for insect reproduction and is regulated by many different genes. In this study, we found that Forkhead transcription factor Fd59a functions as a key factor in spermatogenesis of Drosophila melanogaster. Fd59a contains a conversed Forkhead domain, and it is clustered to the FoxD subfamily with other FoxD members from some insect and vertebrate species. Mutation in Fd59a caused swelling in the apical region of the testis. More importantly, only a few mature sperm were present in the seminal vesicle of Fd59a mutant flies compared to the control flies, and the fertility of Fd59a2/2 mutant males was significantly lower than that of the control flies. Immunofluorescence staining showed that the homeostasis of testis stem cell niche in Fd59a2/2 mutant and Fd59a RNAi flies was disrupted, and apoptosis of sperm bundles was increased. Furthermore, results from RNA-sequencing and qRT-PCR suggest that Fd59a can regulate expression of genes related to reproductive process and cell death. Taken together, our results indicated that Fd59a plays a key role in the spermatogenesis of Drosophila.

Background: The control of energy metabolism is fundamental for cell growth and function, and anomalies are implicated in complex diseases and ageing. It is important for cells to carefully tune metabolic pathways to optimize their function in response to different nutrient or physiological conditions. Metabolism in yeast cells can be easily manipulated by supplying different carbon sources: on glucose yeast rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration. Results: We screened deletion libraries of fission yeast to identify over 200 genes required for respiratory growth. The growth medium and auxotrophic mutants strongly influenced respiratory metabolism. Most genes uncovered in the mutant screens have not been implicated in respiration in budding yeast. We applied gene expression profiling approaches to compare steady-state fermentative and respiratory growth and to analyse the dynamic adaptation to respiratory growth. The transcript levels of most genes functioning in key energy metabolism pathways were coherently tuned, reflecting anticipated differences in metabolic flows between fermenting and respiring cells. We show that the acetyl-CoA synthase, rather than the citrate lyase, is essential for acetyl-CoA synthesis in fission yeast. We also investigated the transcriptional response to mitochondrial damage by genetic or chemical perturbations, defining a retrograde response that involves the concerted regulation of distinct groups of nuclear genes that may avert harm from mitochondrial malfunction. Conclusions: These systematic and targeted analyses provide a rich framework of the genetic and regulatory basis of fundamental metabolic states to guide future studies on energy metabolism in fission yeast and beyond. Our study pinpoints weaknesses of commonly used auxotroph mutants for investigating energy metabolism. As a model for cellular energy regulation, fission yeast provides an attractive and complementary system to budding yeast.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.

Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for the beginners as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detections including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes the transposon classification and explains why the terms of ‘autonomous’ and ‘non-autonomous’ cannot be used to classify the superfamilies of transposons. Last, this review also discusses how to identify misannotated transposons and improve the quality of transposon database. This review provides helpful information about plant transposons and a beginner’s guide on annotating these repetitive sequences.

Background: Previous neuroimaging studies have identified brain regions related to respiratory motor control and perception. However, little is known about the resting-state functional connectivity (FC) associated with respiratory impairment. We aimed to determine the FC involved in mild respiratory impairment without changing the saturation of percutaneous oxygen. Methods: We obtained resting-state functional magnetic resonance imaging data from 36 healthy volunteers during normal respiration and mild respiratory impairment induced by resistive load (effort breathing). ROI-to-ROI and seed-to-voxel analyses were performed using Statistical Parametric Mapping 12 and the CONN toolbox. Results: Compared to normal respiration, effort breathing activated FCs within and between the sensory perceptive area of respiration (the postcentral gyrus, anterior insular cortex (AInsula), and anterior cingulate cortex) and visual cortex (the visual occipital, occipital pole (OP), and occipital fusiform gyrus). Graph theoretical analysis showed strong centrality in the visual cortex. A significant positive correlation was observed between the dyspnoea score (modified Borg scale) and FC between the left AInsula and right OP. Conclusions: These results suggested that the FCs within the respiratory sensory area via the network hub may be neural mechanisms underlying effort breathing and modified Borg scale scores.

The AREB/ABF (ABA response element binding) proteins in plants are vital for plant stress responses, but the understanding of AREB/ABFs in orchid species, an important traditional medicinal and ornamental plants, is limited. Here, twelve AREB/ABF genes were identified within three orchids’ complete genome and classified into three groups (groups I, II, and III) via a phylogenetic analysis, which was further supported by the analysis of their conserved motifs and gene structures. The cis-elements analysis showed that hormone response elements followed by light and stress responses were widely rich in AREB/ABFs. A prediction analysis of orchid ABRE/ABF-mediated regulatory network was further constructed through cis-regulatory elements (CREs) analysis of their promoter regions and revealed that several transcriptional factor (TF) gene family were abundant as the potential regulators for orchid AREB/ABFs. Expression profile analysis based on public transcriptomic data showed that most AREB/ABF genes have distinct tissue-specific expression patterns in orchid plants. Additionally, DcaABI5 as the homolog of ABA INSENSITIVE 5 (ABI5) from Arabidopsis was selected for further analysis. The results showed that Arabidopsis transgenic overexpressing DcaABI5 could rescue the ABA insensitive phenotype in the mutant abi5. Collectively, these findings will provide valuable information on AREB/ABF genes in orchids.

Aim: To evaluate the panmacular subthreshold micropulse laser treatment results among patients with central serous chorioretinopathy (CSC) and their correlation with functional and morphological parameters. Material and methods: The examined group included 10 non-treated and 41 treated patients with acute, recurrent, and chronic CSC (13 F, 38 M, mean age 44.11±6.5) and 14 healthy controls (6 F, 8 M, mean age 45±9.3). The BCVA examination, ophthalmoscopy, microp-erimetry, angio-OCT and OCT were performed. The medical history regarding chronic general disorders and known risk factors were recorded. Results: Complete resorption of SRF was obtained in 100% aCSC, 86.66% cCSC, and 63.63% r CSC. BCVA and RetSens significantly improved most of the patients treated in aCSC. The lowest BCVA and RetSens, but the largest pachyvessel and disease duration, were found in rCSC. A strong negative correlation between final BCVA and disease duration was found. No patient demonstrated laser lesions following treatment. Conclusions: The panmacular MPLT therapy leads to long-term enhancement of functional and morphological parameters in all CSC patients. The acute CSC patients showed the most significant improvement. The procedure is safe and could be considered a preferred treatment option for all active CSC cases. Timely treatment is crucial for beneficial outcomes.

Mesial temporal lobe epilepsy (mTLE) is one of the most common and refractory focal epilepsy syndromes. The molecular mechanisms of TLE are not completely understood. The aim of this study was to investigate the expression and potential function of plasma exosomal miRNAs (miR-483-5p, miR-671-5p, and miR-150-3p) in a mouse mode and in temporal lobe epilepsy patients. It was found that exosomal miRNAs were differentially expressed in three phases of the mouse mode, and exosomal miRNAs were down-regulated in mTLE patients compared with healthy controls. A bioinformatics analysis showed that target genes of exosomal miRNAs were significantly involved in the apoptotic process, cell adhesion, nervous system development, neurotrophin signaling pathway, PI3K-Akt signaling pathway, and metabolic pathways. The areas under the curve of miR-483-5p and miR-150-3p were 0.8714 (sensitivity = 75.00%, specificity = 91.65%) and 0.8213 (sensitivity = 67.50%, specificity = 90.00%), respectively. More importantly, the exosomal miRNAs were significantly associated with clinical parameters. Exosomal miRNAs may have the potential to become diagnostic and therapeutic biomarkers.

Numerous image processing techniques (IPTs) have been employed to detect crack defects, offering an alternative to human-conducted onsite inspections. These IPTs manipulate images to extract defect features, particularly cracks in surfaces produced through Additive Manufacturing (AM). This article presents a vision-based approach that utilizes deep convolutional neural networks (CNNs) for crack detection in AM surfaces. Traditional image processing techniques face challenges with diverse real-world scenarios and varying crack types. To overcome these challenges, our proposed method leverages CNNs, eliminating the need for extensive feature extraction. Annotation for CNN training is facilitated by LabelImg without the requirement for additional IPTs. The trained CNN, enhanced by OpenCV preprocessing techniques, achieves an outstanding 99.54% accuracy on a dataset of 14,982 annotated images with resolutions of 1536 × 1103 pixels. Evaluation metrics exceeding 96% precision, 98% recall, and a 97% F1-score highlight the precision and effectiveness of the entire process.

In recent years, ontology plays an important role in facilitating the semantic description of images which consists of describing the image by a set of words to describe the scene which signifies the belonging of the image. This description specified in several archaeological fields such as cultural, religious objects and heritage objects of France. However, the description of archaeological images is not yet exploited because this field is very diverse. In this article, we present a panel of ontology construction methods as well as archaeological ontologies. Also, we show our own OntunAr ontology to describe Tunisian archaeological images. In addition, we integrate OnTunAr into the automatic annotation of Tunisian archaeological images.

In China, 65 types of venomous snakes exist, with the Chinese Cobra Naja atra being prominent and a major cause of snakebites in humans. Furthermore, N. atra is a protected animal in some areas, as it has been listed as vulnerable by the International Union for Conservation of Nature. Recently, due to the medical value of snake venoms, venomics has experienced growing research interest. In particular, genomic resources are crucial for understanding the molecular mechanisms of venom production. Here, we report a highly continuous genome assembly of N. atra, based on a snake sample from Huangshan, Anhui, China. The size of this genome is 1.67 Gb, while its repeat content constitutes 37.8% of the genome. A total of 26,432 functional genes were annotated. This data provides an essential resource for studying venom production in N. atra. It may also provide guidance for the protection of this species.

The Oriental ratsnake Ptyas mucosa is a common non-venomous snake of the colubrid family, with a wide geographic range spanning much of South and Southeast Asia. P. mucosa is widely cultivated dut to it used in traditional medicine, scientific research, and handicrafts. Therefore, genome resources could play an important role in the efficacy of traditional medicine and the analysis of the living environment of the species. We collected a snake sample in Hezhou, Guangxi, China, which was identified as P. mucosa by morphological identification. Here we present a highly continuous P. mucosa genome with a genome size of 1.74Gb. The scaffold N50 length is 9.57Mb and the maximal length of scaffold is 78.3Mb, the P. mucosa genome has a CG content of 37.9% and the integrity of the gene reached 86.6%.Assembled using long-reads, the total length of the repeat sequence in the genome reached 735 Mb, and its repeat content was as high as 42.19%. A total of 24,869 functional genes were annotated. This study will assist in the understanding of the P. mucosa, and also provide a basis for medicinal research.

Research on fall and movement detection with wearable devices has witnessed promising growth. However, there are few publicly available datasets, all recorded with smartphones, that prevent authors to evenly compare their new proposals. Here, we present a dataset of falls and activities of daily living (ADL) acquired with a self-developed device composed of two types of accelerometer and one gyroscope. It consists of 19 ADL and 15 fall types performed by 23 young adults, 15 ADL types performed by 14 healthy and independent participants over 62 years old, and data from one participant of 60 years old that performed all ADL and falls. These activities were selected based on a survey and a literature analysis. We test the dataset with widely used feature extraction and a simple to implement threshold based classification, achieving up to 96~\% of accuracy in fall detection. An individual activity analysis demonstrates that most errors coincide in a few number of activities where algorithms could be focused on. Finally, validation tests with elderly people significantly reduced the fall detection performance of the tested features. This validates findings of other authors and encourages to develop new strategies with this new dataset as benchmark.

This research presents a comprehensive framework for efficiently generating forest fire datasets from Google Earth Engine data sources. The primary contribution of this work lies in providing a methodology to swiftly extract forest fire factors without the need for permissions or access to private datasets, rendering the dataset openly accessible and shared without barriers. Furthermore, given that the remote sensing data used is a global dataset, it can be applied in any region without restrictions. In this study, Peninsular Malaysia is chosen as a case study to demonstrate the framework's effectiveness. The generated dataset includes essential variables including the climate and environment, landcover, topography, and anthropogenic factors facilitating the analysis of fire occurrences. The methodology empowers data scientists, enabling them to leverage their analytical skills on the extracted dataset without requiring specialized remote sensing knowledge. Additionally, this study also showcases the adoption of large language models, specifically GPT-4 with the Noteable plugin, as a tool for conducting preliminary analyses on the generated dataset. Sample analyses reveal that several key features, including the KBDI, LST, PDSI, climate water deficit, and precipitation, significantly impact forest fire occurrences in Peninsular Malaysia. Despite the successful application of the GPT-4 with Noteable plugin, certain limitations and challenges are identified, highlighting the necessity for further validation of the tool's applicability and limitations. This study encourages future research to (1) adopt the proposed framework in other regions, (2) explore more detailed analyses encompassing all variables, and (3) leverage machine learning for advanced forecasting.

We have carried out a systematic review of the scientific literature published on PM and, more specifically, on its presence in fish and seafood of interest to the population from Mediterranean area. Given its preference and wide acceptability in the scientific community, we followed the PRISMA. The potential functional and clinical toxicity in humans due to MP in fish must be considered by the chemical composition of the microplastics the presence of PM and its additives, associated contaminants and pathogens in fish and shellfish, as well as the possible effects on human health, requires improving legislation on evaluation and providing a basis for consumer protection.

Kinesiophobia (fear of movement) has been recognized as a significant barrier to recovery and rehabilitation in patients after total knee arthroplasty (TKA). Our goal was to identify predictors of kinesiophobia and examine its correlation with early functional outcomes in TKA recipients. On the first and fifth postoperative days (POD1 and POD5), we evaluated pain using the International Pain Outcomes Questionnaire (IPO-Q) and created multidimensional pain composite scores (PCS). Pain Composite Score-total (PCStotal) assesses the overall impact of pain, taking into account outcomes of pain intensity, pain-related interference with function, and emotions and side effects. Functional status on POD 5 was determined by the Barthel index, 6-minute walking test, and knee range of motion. Kinesiophobia was measured on POD5 using the Tampa Scale for Kinesiophobia (TSK) and multivariable logistic regression was used to assess factors associated with kinesiophobia. Among 75 TKA patients, 27% exhibited kinesiophobia. The final regression model highlighted PCStotal on POD5 (OR=6.2, CI=1.9-19.9), PCStotal (OR=2.1, CI=1.2-3.8) on POD1, and the intensity of chronic pain before surgery (OR=1.4, CI=1.1-2.1) as significant kinesiophobia predictors. On POD5, those with kinesiophobia showed increased dependency, slower gait, and poorer knee extension recovery. This study highlights the importance of identifying and addressing kinesiophobia in TKA patients to optimize functional outcomes and improve recovery. Also, it is important to assess not only pain intensity but also the physical and emotional interference caused by pain, which can contribute to the development of kinesiophobia.

Thorough and precise gene structure annotations are essential for maximizing the benefits of genomic data and unveiling valuable genetic insights. The cucumber genome was first released in 2009 and updated in 2019. To increase the accuracy of predicted gene models, 64 published RNA-seq data and 9 new strand-specific RNA-seq data from multiple tissues were used for manual comparison with the gene models. The updated annotation file (version 2.0) contains increased 24,145 predicted genes from previous version (24317 genes) with a higher BUSCO value of 96.9%. 6231 and 1490 transcripts were adjusted and newly added, respectively, accounting for 31.99% of the overall gene tally. These newly added and adjust genes were renamed (CsaV3.1_XGXXXXX), while genes remaining unaltered preserve their original des ignations. A random selection of 21 modified/added genes were validated using RT-PCR analyses. Additionally, tissue-specific patterns of gene expression were examined using newly obtained transcriptome data with the revised gene prediction model. This improved annotation of cucumber genome will provide essential and accurate resources for studies in cucumber.

With nearly 1,700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help in understanding the biological functions of these microorganisms, complete genome sequencing is used routinely. Nevertheless, the proper prediction of their gene catalogue is challenging due to taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small genes (&lt; 300bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot’s accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides accurate prediction of translation initiation sites, efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes including those under 300 bp. Thanks to its web interface (https://microannot.org), MicroAnnot is available to the community to ensure high quality annotation of microsporidian genomes.

Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still poses a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.

Pathogenicity is unknown for the majority of human gene variants. For prioritization of sequenced somatic and germline mutation variants, in silico approaches can be utilized. In this study, 84 million non-synonymous Single Nucleotide Variants (SNVs) in the human coding genome were annotated using consensus Variant Effect Prediction (cVEP) method. An algorithm, implemented as a stacked ensemble of supervised learners, performed combination of the 39 functional, conservation mutation impact scores from dbNSFP4.0. Adding gene indispensability score, accounting for differences in the pathogenicities of the variants in the essential and the mutation-tolerant genes, improved the predictions. For each SNV the consensus combination gives either a continuous-value pathogenicity score, or a categorical score in five classes: pathogenic, likely pathogenic, uncertain significance, likely benign, benign. The provided class database is aimed for direct use in clinical practice. The trained prediction models were 5-fold cross-validated on the evidence-based categorical annotations from the ClinVar database. The rankings of the scores based on their ability to predict pathogenicity were obtained. A two-step strategy using the rankings, scores and class annotations is suggested for filtering and prioritization of the human exome mutations in clinical and biological applications of NGS technology.

The digital format opens up new possibilities for interaction with monographic publications. In particular, annotation tools make it possible to broaden the discussion on the content of a book, to suggest new ideas, to report errors or inaccuracies, and to conduct open peer reviews. However, this requires the support of the users who might not yet be familiar with the annotation of digital documents. This paper will give concrete examples and recommendations for exploiting the potential of annotation in academic research and teaching. After presenting the annotation tool of Hypothesis, the article focuses on its use in the context of HIRMEOS (High Integration of Research Monographs in the European Open Science Infrastructure), a project aimed to improve the Open Access digital monograph. The general line and the aims of a post-peer review experiment with the annotation tool, as well as its usage in didactic activities concerning monographic publications are presented and proposed as potential best practices for similar annotation activities.

Pancreatic cancer (PC) has a poor prognosis and displays resistance to immunotherapy. A better understanding of tumor-derived extracellular vesicles (EVs) effects on immune responses might contribute to improved immunotherapy. EVs derived from Capan-2 and BxPC-3 PC cells isolated by ultracentrifugation were characterized by atomic force microscopy, western blot (WB), nanoparticle tracking analysis and label-free proteomics. Fresh PBMCs from healthy donors were treated with PC- or control-derived heterologous EVs followed by flow cytometry analysis of CD8+ and CD4+ lymphocytes. Proteomics of lymphocytes sorted from EV-treated, or -untreated PBMCs was performed and IFN-γ concentration was measured by ELISA. Notably, most of the proteins identified in Capan-2 and BxPC-3 EVs by proteomic analysis were connected in a single functional network (p=1x10-16) and were involved in “Immune System” (FDR: 1.10x10-24 and 3.69x10-19, respectively). Interestingly, treatment of healthy donor-derived PBMCs with Capan-2 EVs, but not with BxPC-3 EVs or heterologous control EVs induced early activation of CD8+ and CD4+ lymphocytes. Proteomics of lymphocytes sorted from EV-treated PBMCs was consistent with their activation by Capan-2 EVs, indicating IFN-γ among major upstream regulators, as confirmed by ELISA. Proteomic and functional analyses indicate that PC-EVs have pleiotropic effects, and some may activate early immune response, which might be relevant for the development of highly needed immunotherapeutic strategies in this immune-cold tumor.

Sea cucumber peptides are small molecular peptides with biological function obtained from fresh sea cucumber as feedstock, which were hydrolyzed by protease, separated ,and purified. As the main product of sea cucumber refinement, it more accurately expresses the nutritional effect of sea cucumber and has a wide range of potential applications. It has been demonstrated that sea cucumber has a certain value-added effect on bone mineral density regulation, but the differences in bone mineral density regulation of extracts from different parts of sea cucumber and the techniques contributing to the efficient isolation of bone sea cucumber peptides have not been reported. Firstly, the aim of this study was to reveal the differences in osteogenic activities of enzymatic peptides from three major parts of sea cucumber: the body wall, the egg protein, and the intestinal protein. Then, the bone-enhancing sea cucumber peptides were isolated based on the characteristics of the dif-ferences in molecular weight distribution, hydrophilicity, and ionisation degree of sea cucumber, and to explore the possible mechanisms of their action. The findings indicated that sea cucumber peptides extracted from three distinct sites exhibited a dose-dependent enhancement of osteoblast proliferation and differentiation. Upon evaluating the three methods of sea cucumber peptide separation based on molecular weight distribution, hydrophilicity, and ionization, it was observed that the fraction isolated by hydrophobicity and

Genetic testing allows for identification of germline DNA variations which are associated with a significant increase in risk of developing breast and ovarian cancer. Detection of a BRCA1 or BRCA2 pathogenic variant triggers several clinical management actions, which may include increased surveillance and prophylactic surgery for healthy carriers or treatment with PARP inhibitor therapy for carriers diagnosed with cancer. Thus, standardized validated criteria for annotation of BRCA1 and BRCA2 variants according to their pathogenicity are necessary to support clinical decision making and ensure improved outcomes. Upon detection, variants whose pathogenicity can be inferred by the genetic code are typically classified as pathogenic, likely pathogenic, likely benign, or benign. Variants whose impact on function cannot be directly inferred by the genetic code are labeled as Variants of Uncertain Clinical Significance (VUS) and are evaluated by multifactorial likelihood models that use personal and family history of cancer, segregation data, prediction tools, and co-occurrence with a pathogenic BRCA variant. Missense variants, coding alterations that replace a single amino acid residue with another, are a class of variants for which determination of clinical relevance is particularly challenging. Here, we discuss current issues in variant classification by following a typical life cycle of a BRCA1 missense variant through detection, annotation and information dissemination. Advances in massively parallel sequencing have led to a substantial increase in VUS findings. Although comprehensive assessment and classification of missense variants according to their pathogenicity remains the bottle neck, new developments in functional analysis, high throughput assays, data sharing, and statistical models are rapidly changing this scenario.

Sensory integration is an essential function of human life, and its decline causes difficulties in the quality of life, especially in older adults. In this study, we proposed an arm-reaching task based on a virtual reality head-mounted display (VR-HMD) system to assess sensory integration in daily life, and examined whether reaching task performance was associated with age and resting-state functional connectivity (rsFC) between the brain regions of interest involved in sensory integration. We hypothesized that performance during a reaching task with multiple cognitive loadings would be affected by aging. The gap angle between the reaching hand and target positions was compared between older and middle-aged adults as a measure of sensory integration function. In addition, rsFC, which was significantly correlated with the gap angles of individual participants in the older adult group, was identified using resting-state functional magnetic resonance imaging data. The mean gap angle was significantly larger in the older adults than in the middle-aged group and was also significantly correlated with connections between the left primary motor area and the left inferior temporal gyrus, temporo-occipital part. Because the connectivity between the areas is known to be related to visuomotor integration, the results suggest the involvement of visuomotor integration in the decline of sensory integration function in old age and the validity of the gap angle during the proposed VR-HMD task as an index for the decline in function.

This study focuses on enhancing controllable fibrin-based hydrogels for tissue engineering, addressing existing weaknesses. By integrating a novel copolymer, we improve the foundation for cell-based angiogenesis with adaptable structural features. Tissue engineering often faces challenges like waste disposal and nutrient supply beyond the 200 µm diffusion limit. Angiogenesis breaks through this limitation, allowing the construction of larger constructs. Our innovative scaffold combination significantly boosts angiogenesis, resulting in longer branches and more capillary network junctions. The copolymer attached to fibrin fibers enables precise adjustment of hydrogel mechanical-dynamic properties for specific applications. Our material proves effective for angiogenesis, even under suppression factors like suramin. In our study, we prepared fibrin-based hydrogels with and without the copolymer PVP12400-co-GMA10mol%. Using a co-culture system of human umbilical vein endothelial cells (HUVEC) and mesenchymal stem cells (MSC), we analyzed angiogenetic behavior on and within the modified hydrogels. Capillary-like structures were reproducibly formed on different surfaces, demonstrating the general feasibility of three-dimensional endothelial cell networks in fibrin-based hydrogels. This highlights the biomaterial's suitability for in vitro pre-vascularization of biohybrid implants.

Brown-Spotted Pit viper (Protobothrops mucrosquamatus), also known as the Chinese habu, is a widespread and highly venomous snake distributed from from northeastern India to eastern China. Genomics research can help provide much insight in understanding venom components and natural selection in vipers. Here, we collected, sequenced and assembled the genome of a male P. mucrosquamatus individual from China, producing a highly continuous reference genome, with the length of 1.53 Gb and 41.18% repeat element content. From this 24,799 genes were identified, and 97.97% genes could be annotated. Nuclear genome single-copy genes phylogenetic tree including 6 species verified the validity of our genome assembly and annotation process. This research will contribute to further study on Protobothrops biology and the genetic basis of the snake venom.

The BET family of proteins is characterized by the presence of two tandem bromodomains and an extra-terminal domain. The mammalian BET family of proteins comprises Brd2, Brd3, Brd4, and Brdt, which are encoded by paralogous genes that may have been generated by repeated duplication of an ancestral gene during evolution. Bromodomains that can specifically bind acetylated lysine residues in histones serve as chromatin-targeting modules that decipher the histone acetylation code. BET proteins play a crucial role in regulating gene transcription through epigenetic interactions between bromodomains and acetylated histones during cellular proliferation and differentiation processes. On the other hand, BET proteins have been reported to mediate latent viral infection in host cells and be involved in oncogenesis. Human BRD4 is involved in multiple processes of the DNA virus life cycle, including viral replication, genome maintenance, and gene transcription through interaction with viral proteins. Aberrant BRD4 expression contributes to carcinogenesis by mediating hyperacetylation of the chromatin containing the cell proliferation-promoting genes. BET bromodomain blockade using small-molecule inhibitors gives rise to selective repression of the transcriptional network driven by c-Myc. These inhibitors are expected to be potential therapeutic drugs for a wide range of cancers. This review presents an overview of the basic roles of BET proteins and highlights the pathological functions of BET and the recent developments in cancer therapy targeting BET proteins in animal models.

Modeling what makes an advertisement persuasive, i.e., eliciting the desired response from consumer, is critical to the study of propaganda, social psychology, and marketing. Despite its importance, computational modeling of per- suasion in computer vision is still in its infancy, primarily due to the lack of benchmark datasets that can provide persuasion-strategy labels associated with ads. Motivated by persuasion literature in social psychology and marketing, we introduce an extensive vocabulary of persuasion strategies and build the first ad image corpus annotated with persuasion strategies. We then formulate the task of persuasion strategy prediction with multi-modal learning, where we design a multi-task attention fusion model that can leverage other ad-understanding tasks to predict persuasion strategies. Further, we conduct a real-world case study on 1600 advertising campaigns of 30 Fortune-500 companies where we use our model’s predictions to analyze which strategies work with different demographics (age and gender). The dataset also provides image segmentation masks, which labels persuasion strategies in the corresponding ad images on the test split. We publicly release our code and dataset: https://midas-research.github.io/persuasion-advertisements/

In recent years many different deep neural networks were developed, but due to a large number of layers in deep networks, their training requires a long time and a large number of datasets. Today is popular to use trained deep neural networks for various tasks, even for simple ones in which such deep networks are not required. The well-known deep networks such as YoloV3, SSD, etc. are intended for tracking and monitoring various objects, therefore their weights are heavy and the overall accuracy for a specific task is low. Eye-tracking tasks need to detect only one object - an iris in a given area. Therefore, it is logical to use a neural network only for this task. But the problem is the lack of suitable datasets for training the model. In the manuscript, we presented a dataset that is suitable for training custom models of convolutional neural networks for eye-tracking tasks. Using data set data, each user can independently pre-train the convolutional neural network models for eye-tracking tasks. This dataset contains annotated 10,000 eye images in an extension of 416 by 416 pixels. The table with annotation information shows the coordinates and radius of the eye for each image. This manuscript can be considered as a guide for the preparation of datasets for eye-tracking devices.

The internet has changed the way people perceived fiction to a new level. For instance, online forums have given people the opportunity to write without revealing their real identities. Especially in the Saudi context, online users were using these forums to write web novels that reflect their culture, lives, concerns, hopes and dreams. In this paper, we describe a dataset that was collected from one of the online forums that was used for sharing web novels among its readers. The collected dataset contains 1,267 novels between 2003-2015. This data set is available to the research community to analyze to gain a better understanding of the social, economical, and behavioral mindset that was manifested in the community in that decade.

The COVID-19 pandemic spread of the coronavirus across the globe has affected our lives on many different levels. The world we knew before the spread of the virus has become another one. Every country has taken preventive measures, including social distancing, travel restrictions, and curfew, to control the spread of the disease. With these measures implemented, people have shifted to social media platforms in the online sphere, such as Twitter, to maintain connections. In this paper, we describe a coronavirus data set of Arabic tweets collected from January 1, 2020, primarily from hashtags populated from Saudi Arabia. This data set is available to the research community to glean a better understanding of the societal, economical, and political effects of the outbreak and to help policy makers make better decisions for fighting this epidemic.

Abstract: A. baumannii exhibits resilience in harsh environments and progressively develops resistance to diverse antibacterial agents over time. This adaptability poses a significant challenge in treating an infection caused by this bacterium within healthcare settings. The presence of peptidoglycan, a crucial precursor for cell wall synthesis, contributes to this challenge. Peptidoglycan serves not only as a structural support in bacterial cells but also provides protection against adverse environmental conditions. The synthesis of the peptidoglycan layer involves a group of substrates such as N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), within a three-partitioned process occurring in the membrane, periplasmic space, and cytoplasm of each bacterium. Initiated in the cytoplasm and extending to the inner cell membrane, this synthesis starts with the production of nucleotide precursors. The first step involves the synthesis of UDP-GlcNAc, orchestrated by Glm (GlmS, GlmM, and GlmU) enzymes using fructose-6-phosphate. Subsequently, enzymes from the Mur family, namely MurB, MurA, MurD, MurC, MurI, MurF, and MurE, synthesize UDP-N-acetylmuramyl-pentapeptide (UDP-Mpp) from UDP-GlcNAc. Concurrently, on the cytosolic side, the production of membrane-surrounded undecaprenyl phosphate occurs, involving membrane-side proteins MraY and MurG in the biosynthesis of peptidoglycan. This review emphasizes updated information on Mur family proteins, encompassing physicochemical properties, nature of binding site, number and type of binding site residues, functional domain details, three-dimensional structural aspects, and their functions within bacterial cells. Special attention is directed towards their enzymatic role in peptidoglycan biosynthesis due to the limited availability of precursors in the market. Additionally, the review provides a comprehensive summary of existing inhibitors and ongoing efforts in identifying new targeted inhibitors, recognizing these enzymes as potential candidates for antibacterial drug design and discovery.

Fractional flow reserve (FFR) is well recognized as a gold standard measure for the estimation of functional coronary stenosis. Technological progressions in image processing have empowered the reconstruction of three-dimensional models of the coronary arteries via both non-invasive imaging modalities, such as Coronary Computed Tomography Angiography (CCTA), and invasive coronary angiography or intravascular imaging. The application of computational fluid dynamics (CFD) techniques to coronary 3D anatomical models allows the virtual evaluation of the hemodynamic significance of a coronary lesion with high diagnostic accuracy in comparison to the invasive FFR using pressure wires. These opportunities providing hemodynamic information based on anatomy have given rise to a new era of functional angiography and coronary imaging. However, further validations are needed to overcome several scientific and computational challenges before these methods are applied in everyday clinical practice. This review aims to present all the data on the studies and methodologies that have been presented for the virtual estimation of FFR, and the diagnostic execution of the virtual tools for the hemodynamic assessment of coronary lesions compared to the invasive FFR.

Psoriasis is a lifelong, systemic, immune mediated inflammatory skin condition, affecting 1-3% of the world’s population, with an impact on quality of life similar to diseases like cancer or diabetes. Genetics are the single largest risk factor in psoriasis, with GWAS studies showing that many psoriasis risk genes lie along the IL23/Th17 axis. Potential psoriasis risk genes determined through GWAS can be annotated and characterised using functional genomics, allowing the identification of novel drug targets and the repurposing of existing drugs. The pathogenesis of psoriasis is complex and focusing on the IL23/Th17 axis can provide insight into key cell types, cytokines and intracellular signaling pathways involved. Examination of currently available biological treatments, time to relapse post drug withdrawal and rates of drug primary/secondary drug failure show the need for greater understanding of the underlying genetic mechanisms of psoriasis and how they can impact treatment. This could allow for patient stratification towards the treatment most likely reduce dis-ease burden for the longest period possible.

Introduction. Intra-abdominal cystic formations represent heterogeneous pathologies with varied localization and clinical manifestation. The first challenge of a giant intra-abdominal cystic lesion is identifying the organ of origin. The clinical presentation of intra-abdominal cystic lesions varies from acute manifestations to non-specific symptoms or accidental discovery. Case presentation: A 2-year-old girl presents to the emergency unit with a fever of 38.5 Celsius, loss of appetite, and apathy. The investigations showed a gigantic intra-abdominal mass whose organ belonging could not be specified. Postoperatively, a giant mesenteric lymphangioma was evident, which was completely excised. Discussions Giant cystic formations modify the anatomical reports and become space-replacing formations, and the starting point is even more challenging to assess preoperatively. Nevertheless, the careful evaluation of the characteristics of the formation, the effect on the adjacent organs, the age of the patient, and the clinical picture can provide elements of differential diagnosis.

Trimeresurus albolabris, also known as the white-lipped pit viper or white-lipped tree viper, is a highly venomous snake distributed across Southeast Asia and the cause of many snakebite cases. In this study, we report the first whole genome assembly of T. albolabris obtained with next-generation sequencing from a specimen collected in Mengzi, Yunnan, China. After genome sequencing and assembly, the genome of this male T. albolabris individual was 1.51 Gb in length and included 38.42% repeat-element content. Using this genome, 21,695 genes were identified, and 99.17% of genes could be annotated using gene functional databases. Our genome assembly and annotation process was validated using a phylogenetic tree, which included six species and focused on single-copy genes of nuclear genomes. This research will contribute to future studies on Trimeresurus biology and the genetic basis of snake venom.

Most natural language processing (NLP) tasks operate an input sentence as a sequence with token-level embeddings and features, despite its clausal structures. Taking Abstract Meaning Representation (AMR) parsing as an example, recent parsers are empowered by Transformers and pre-trained language models, but long-distance dependencies (LDDs) introduced by long sequences are still open problems. We argue that LDDs are not superficially blamed on the sequence length but are essentially related to the internal clause hierarchy. Typically, non-verb words in a clause cannot depend on words outside, and verbs from different but related clauses have much longer dependencies than those in the same clause. With this intuition, we introduce a type of clausal feature, hierarchical clause annotation (HCA), into AMR parsing and propose two HCA-based approaches, HCA-based self-attention (HCA-SA) and HCA-based curriculum learning (HCA-CL), to integrate HCA trees of complex sentences for addressing LDDs. We conduct extensive experiments on two in-distribution (ID) AMR datasets (AMR 2.0 and AMR 3.0) and three out-of-distribution (OOD) ones (TLP, New3, and Bio). Experimental results show that our HCA-based approaches achieve significant and explainable improvements against the baseline model and outperform the state-of-the-art (SOTA) model when encountering sentences with complex clausal structures that introduce most LDD cases.

Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments, and can be used for connecting biological molecules into regulatory computational models that represent biological systems. However, including a molecular causal interaction into a model requires assessing its relevance to that model, based on detailed knowledge about the biomolecules, interaction type, and biological context. In order to standardize the representation of this knowledge in ‘causal statements’, we recently developed the MI2CAST guidelines. Here we introduce causalBuilder: an intuitive web-based curation interface for the annotation of molecular causal interactions that comply with the MI2CAST standard. The causalBuilder prototype essentially embeds the MI2CAST curation guidelines in its interface, and makes its rules easy to follow by a curator. In addition, causalBuilder serves as an original application of the VSM general-purpose curation technology, and provides both curators and tool developers with an interface that can be fully configured to allow focusing on selected MI2CAST concepts to annotate. After information is entered, the causalBuilder prototype produces genuine causal statements that can be exported in different formats.

Evidence suggests that COVID-19 infection can cause lasting health consequences. Multidiscipli-nary rehabilitation services have been recommended to reduce the sequalae. However, the effec-tiveness of physical exercise interventions remains insufficiently documented. The aim of this study was to develop and implement a specific and well tolerated protocol-based, intervention to reduce muscle weakness in older adults impacted by COVID-19. Forty six older adults random-ized into Intervention and Control Groups. Isometric and isokinetic strength assessments were conducted for selected muscle groups using JBA Staniak® torquemeter and Biodex System 3 dy-namometer. Functional abilities were evaluated with the Time Up and Go test and Chair Stand Tests. Men in intervention group demonstrated a significant improvement in static conditions for knee flexors (KF), trunk extensors (TE) and trunk flexors (TF) and in dynamic conditions for knee extensors (KE). Women in intervention group showed significant improvement in static condition for EF, KF, TE and TF and in dynamic for a KE and for a KF. The interaction GROUP x TESTING SESSION was significant for Chair test (s) and Chair test (n). Our results demonstrate the effec-tiveness of a well-tolerated, protocol-based approach that can be used to diminish long lasting functional deficits in post-covid survivors.

Jaundice is a common condition for newborns, and its complications can be severe and cause permanent damage to the patient’s brain if no action is taken at its early stages. Current methods for jaundice detection are invasive, which include collecting blood samples from the patient, which can be painful and stressful and may cause some complications. Alternatively, a non-invasive approach can be used to diagnose jaundice through image-processing and artificial intelligence (AI) techniques, requiring a database of infant images to achieve a high-accuracy diagnosis. This data article provides a collection of newborn images, called NJN, with various birthweight and skin tones, with ages ranging from 2 to 8 days, and an excel sheet file in CSV format for the values of RGB and YCrCb channels and the status for each raw which is freely accessible at (https://sites.google.com/view/neonataljaundice). It also provides Python code for data testing using different AI techniques. Thus, this article offers a unique resource for all AI researchers to train their AI system and develop algorithms to help neonatal intensive care unit (NICU) healthcare specialists monitor neonates and provide fast, real-time, non-invasive, and accurate jaundice diagnosis.

The rapid evolution of Next Generation Sequencing in clinical settings and the resulting challenge of variants interpretation in the light of constantly updated information, requires robust data management systems and organized approaches to variant reinterpretation. In this paper, we present iVar: a freely available and highly customizable tool provided with a user-friendly web interface. It represents a platform for the unified management of variants identified by different sequencing technologies. iVar accepts, as input, VCF files and text annotation files and elaborates them, optimizing data organization and avoiding redundancies. Updated annotations can be periodically re-uploaded and associated to variants as historicize attributes. Data can be visualized through variant-centered and sample-centered interfaces. A customizable search functionality can be exploited to periodically check if pathogenicity related data of a variant are changed over time. Patient recontacting ensuing from variant reinterpretation is made easier by iVar through the effective identification of all patients present in the database and carrying a specific variant. We tested iVar by uploading 4171 VCF files and 1463 annotation files, obtaining a database of 4166 samples and 22569 unique variants. iVar has proven to be a useful tool with good performances for collecting and managing data from medium-throughput

The promised dataset was obtained from the daily Turkish words and phrases pronounced by various people in the videos posted on YouTube. The purpose of collecting the dataset is to provide detection of the spoken word by recognizing patterns or classifying lip movements with supervised, unsupervised, semi-supervised learning and machine learning algorithms. Most of the datasets related with lip reading consist of people recorded on camera with fixed backgrounds and the same conditions, but the dataset presented here consists of images compatible with machine learning models developed for real-life challenges. It contains a total of 2335 instances taken from TV series, movies, vlogs, and song clips on YouTube. The images in the dataset vary due to factors such as the way people say words, accent, speaking rate, gender and age. Furthermore, the instances in the dataset consist of videos with different angles, shadows, resolution, and brightness that are not created manually. The most important feature of our lip reading dataset is that we contribute to the non-synthetic Turkish dataset pool, which does not have wide dataset varieties. Machine learning studies can be carried out in many areas, such as the defense industry and social life, with this dataset.

This article describes techniques employed in the production of a synthetic dataset of driver telematics emulated from a similar real insurance dataset. The synthetic dataset generated has 100,000 policies that included observations about driver’s claims experience together with associated classical risk variables and telematics-related variables. This work is aimed to produce a resource that can be used to advance models to assess risks for usage-based insurance. It follows a three-stage process using machine learning algorithms. The first stage is simulating values for the number of claims as multiple binary classifications applying feedforward neural networks. The second stage is simulating values for aggregated amount of claims as regression using feedforward neural networks, with number of claims included in the set of feature variables. In the final stage, a synthetic portfolio of the space of feature variables is generated applying an extended SMOTE algorithm. The resulting dataset is evaluated by comparing the synthetic and real datasets when Poisson and gamma regression models are fitted to the respective data. Other visualization and data summarization produce remarkable similar statistics between the two datasets. We hope that researchers interested in obtaining telematics datasets to calibrate models or learning algorithms will find our work valuable.

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.

Next-generation sequencing is now a mature technology, allowing partial animal genomes to be produced for many clades. Though many software exist for genome assembly and annotation, a simple pipeline that allows researchers to input raw sequencing reads in fastq format and allow the retrieval of a completely assembled and annotated mitochondrial genome is still missing. mitoMaker 1.0 is a pipeline developed in python that implements (i) recursive de novo assembly of mitochondrial genomes using a set of increasing k-mers; (ii) search for the best matching result to a target mitogenome and; (iii) performs iterative reference-based strategies to optimize the assembly. After (iv) checking for circularization and (v) positioning tRNA-Phe at the beginning, (vi) geneChecker.py module performs a complete annotation of the mitochondrial genome and provides a GenBank formatted file as output.

Functional connectivity (FC) is a potential candidate that can increase the performance of brain-computer interfaces (BCIs) in the elderly because of its compensatory role in neural circuits. However, it is difficult to decode FC by current machine learning techniques because of a lack of its physiological understanding. To investigate the suitability of FC in BCI for the elderly, we propose the decoding of lower- and higher-order FCs using a convolutional neural network (CNN) in six cognitive-motor tasks. The layer-wise relevance propagation (LRP) method describes how age-related changes in FCs impact BCI applications for the elderly compared to younger adults. Seventeen younger (24.5±2.7 years) and twelve older (72.5±3.2 years) adults were recruited to perform tasks related to hand-force control with or without mental calculation. CNN yielded a six-class classification accuracy of 75.3% in the elderly, exceeding the 70.7% accuracy for the younger adults. In the elderly, the proposed method increases the classification accuracy by 88.3% compared to the filter-bank common spatial pattern (FBCSP). LRP results revealed that both lower- and higher-order FCs were dominantly overactivated in the prefrontal lobe depending on task type. These findings suggest a promising application of multi-order FC with deep learning on BCI systems for the elderly.

The beneficial effects of Lanthanide incorporation into 0.94Na0.5Bi0.5TiO3-0.06BaTiO3 (BNT-BT) matrix on its functional properties were investigated. The conventional solid-state method was used for synthesizing samples. The structural refinement revealed that all samples crystallized in R3c rhombohedral symmetry. Raman spectroscopy study was carried out using green laser excitation and revealed that no clear perceptible variation in frequency is observed. Dielectric measurements unveiled that the introduction of rare earth obstructed the depolarization temperature promoted in BNT-BT with decreasing the diffusive phase transition with increasing the lanthanide size. Only Dysprosium addition showed comparable diffusion constant and dielectric behavior as the unmodified composition. Further, the comparison of the obtained ferroelectric hysteresis and strain-electric field loops revealed that only Dy-phase exhibited interesting properties comparing parent composition. In addition, the incorporation of lanthanides Ln3+ into the BNT-BT matrix led to the development of luminescence characteristics in the visible and near infrared regions, depending on the excitation wavelengths. The simultaneous occurrence of photoluminescence and ferroelectric/piezoelectric properties opens up possibilities for BNT-BT-Ln to exhibit multifunctionality in a wide range of applications.Keywords: Sodium Bismuth Titanate; structural refinement; dielectric properties; ferroelectric properties; piezoelectric properties; Photoluminescence.

Structured extraction of emergency event information can effectively enhance the ability to re-spond to emergency events. This article focuses on the extraction of Chinese document-level emergency events, which mainly faces two key issues in this field: first, related datasets; Secondly, existing DEE (document-level event extraction) studies mostly use sequence annotation to extract candidate entities in the subtask of candidate entity extraction without considering the problem of role overlapping between candidate entities. On the one hand, this article constructs a Chinese document-level emergency extraction dataset, CDEEE, which first annotates the issues of argu-ment scattering, multiple events, and role overlapping. On the other hand, this article proposes a model RODEE for the problem of role overlapping in DEE tasks. This model first uses two in-dependent modules to represent the head and tail positions of candidate entities, then uses a multiplication attention mechanism to interact with the two to obtain a scoring matrix. Finally, role-overlapping candidate entities are predicted to assist in completing DEE tasks. Experiments were conducted on our manually annotated dataset, CDEEE, and the results showed that RODEE can effectively solve the problem of role overlapping in candidate entities and improve the performance of the DEE model.

The predatory mirids Macrolophus pygmaeus Ramber and Nesidiocoris tenuis Reuter (Heteroptera: Miridae) are used for the biological control of Tuta absoluta Meyrick (Lep.: Gelechiidae) and other pests in tomato greenhouses. The functional response of 1 (young) and 10 (old) days old adult females and males of M. pygmaeus and N. tenuis on eggs of T. absoluta, was determined on tomato at two temperatures (20° and 25°C) and LD 16:8 and found to be Type II. M. pygmaeus females exhibited higher predation efficiency, than males at both tested temperatures. Young M. pygmaeus females had a higher efficiency than old ones, whereas males had a low efficiency irrespective of age. The predation efficiency of N. tenuis was high (but lower than M. pygmaeus) in both young females and males, although old females had a higher efficiency than the respective males. Our results show that the two predatory species have different functional response characteristics to their prey depending mainly on sex and age which may affect their role as biological control agents.

Metabolomics is a powerful set of methods that uses analytical techniques to identify and quantify metabolites in biological samples, providing a snapshot of the metabolic state of a biological system. In medicine, metabolomics can help diagnose diseases, reveal molecular basis of a disease, and monitor treatment responses, while in agriculture, it can improve crop yields and plant breeding. However, animal metabolomics faces several challenges due to the complexity and diversity of animal metabolomes, the lack of standardized protocols, and the difficulty in interpreting metabolomic data. The current dataset includes quantitative metabolomic profiles of eye lens tissues from 26 bird species (111 specimens) that can aid researchers in developing new experiments, mathematical models, and integrations with other omics data. The dataset includes raw 1H NMR spectra, protocols for sample preparation, and data preprocessing with the final table containing information on 89 reliably identified and quantified metabolites. The dataset is quantitative, making it relevant for supplementing with new specimens or comparison groups, followed by data mining and expected new interpretations. It was obtained from bird specimens collected in compliance with ethical standards and reveals potential differences in metabolic pathways due to phylogenetic difference or environmental exposure.

When analyzing user geospatial information through deep learning methods, it is typically necessary to annotate existing geospatial data. Currently, manual annotation methods are commonly employed, suffering from issues related to low efficiency and accuracy. This design is based on the TensorFlow deep learning framework and first realizes the BiLSTM+CRF+AGG deep learning model. Among the models, AGG is the aggregation layer, which is introduced to solve the problem of solid particle size equilibrium. Secondly, based on the characteristics of original data and professional data, an automatic labeling algorithm is proposed. The algorithm first preprocesses the acquired original data set and professional data set, The most valuable unlabeled data set which can make the training model converge quickly is selected from the original data set as the target data set. Sort the target data set based on preset rules and set annotation parameters for the sorted target data set. Based on the set annotation parameters, the corpus is synthesized and used as the annotation result. Thirdly, based on the active learning strategy, a manual annotation auxiliary scheme is proposed, and an Excel generation module that is convenient for manual annotation correction is designed and developed to further improve the efficiency and quality of annotation through iterative processing. The combination of the BiLSTM+CRF+AGG deep learning model and high-quality annotation can accurately identify non-standard, incomplete, or even incorrect geographical information entities. This annotation method has found successful practical application within the context of the research project and has been granted an invention patent.

Background: Transposable elements (TEs) constitute the vast majority of all eukaryotic DNA, and display extreme diversity, with thousands of families. Given their abundance and diversity, TEs discovery and annotation becomes challengeable. At present, tools and databases have built libraries to mask TEs in genomes based on de novo- and homology-based identification strategies, but no consensus criteria about which tools should be used have been proposed. Results: In the de novo-based strategy, we compared performances of TE libraries developed by four commonly used tools, including RepeatModeler, LTR_FINDER, LTRharvest, and MITE_Hunter, by using a simulated genome as a standard control. The results showed that the performance of RepeatModeler decreased as it was combined with either LTR_FINDER or LTRharvest. Combination of RepeatModeler and MITE_Hunter showed better performance than RepeatModeler and MITE_Hunter alone. In the homology-based strategy, we evaluated different sources from a taxonomic point of view to build an accurate TE library. When we selected a library from databases to identify TEs for Arabidopsis thaliana genome, the library from a genus genetically closer to Arabidopsis achieved better performance than other genera with further genetic distance. Without the Arabidopsis, combination of top three genera closer to Arabidopsis showed better performance than combination of all genera. Conclusion: This study proposes a series of recommendations to perform an accurate TE annotation: 1) For de novo-based strategy, RepeatModeler and MITE_Hunter are suggested to build a TE library; 2) For homology-based strategy, it is recommended to use library of genus genetically close to the species rather than use combined library from all genera.

Despite the growing capabilities of large language models, concerns exist about the biases they develop. In this paper, we propose a novel, automated mechanism for debiasing through specified dataset augmentation in the lens of bias producers that can be useful in a variety of industries, especially ones that are “restricted” and have limited data. We consider that bias can occur due to intrinsic model architecture and dataset quality. The two aspects are evaluated using two different metrics we created. We show that our dataset augmentation algorithm reduces bias as measured by our metrics.

Sunn pest is one of the most crucial noxious species in agriculture. As the sunn pest penetrates and makes damage to the grains, they can no longer be utilized to make bakery goods like bread, pasta, and other baked foods since they become unusable. Therefore, analysis and detection of damaged wheat grains are necessary for production to continue. We recommend that the dataset could be used for analysis and segmentation of the wheat grains, detection of the sunn pest damage condition, and classification of the 6 species of which the dataset consists. As mentioned, in our dataset, there are 6 different species of wheat, including Bezostaja, Müfitbey, Nacibey, Sönmez-2001, Tosunbey, and Ekiz, which are the species that were made in Türkiye. Our dataset differs from the others due to its various species and the condition, whether it is healthy or sunn pest damaged or broken wheat grain, and because the dataset is a multiclass one, it can be used for the classification of the varieties. On the other hand, when the sunn pest damage condition is taken into account, the dataset is suitable for the detection of the sunn pest damage. In addition to that, the dataset includes grains that touch each other which makes it more applicable to problems that arise in real-life. The dataset consists of 83 sunn pest damaged and 87 healthy wheat images. In addition, there are 170 images that contain 3565 wheat grains. As can be observed, the dataset contains a variety of wheat species with sunn pest affected which displays that the promised dataset is suitable for numerous machine learning problems such as classification, segmentation, and detection.

The development of autonomous vehicles is becoming increasingly popular and gathering real world data is considered a valuable task. Many datasets have been published recently in the autonomous vehicle sector, with synthetic datasets gaining particular interest due to availability and cost. For a real implementation and correct evaluation of vehicles at higher levels of autonomy it is also necessary to consider human interaction, which is precisely something that lacks in existing datasets. In this article the UPCT dataset is presented, a public dataset containing high quality, multimodal data obtained using state of the art sensors and equipment installed onboard the UPCT’s CICar autonomous vehicle. The dataset includes data from a variety of perception sensors including 3D LiDAR, cameras, IMU, GPS, encoders, as well as driver biometric data and driver behaviour questionnaires. In addition to the dataset, the software developed for data synchronisation and processing has been made available. The quality of the dataset was validated using an end-to-end neural network model with multiple inputs to obtain speed and steering wheel angle and obtained very promising results.

We describe a dataset that contains job description published on a popular online website in the information and technology sector. As the website focus mainly on United Kingdom based jobs, the data have a specific focus on this country. It contains 11.501 job vacancies and 13 related meta data information. The dataset is suitable for HR analysis using machine learning techniques such as natural language processing and neural networks.

The analysis of curated genomic, metagenomic, and proteomic data are of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw form in free international repositories, its access requires plenty of computing, storage, and processing capacities for the domestic user. The purpose of the study is to offer a comprehensive set of genomic and proteomic reference data, in an accessible and easy-to-use form to the scientific community. A representative type material set of genomes, proteomes and metagenomes were directly downloaded from the site: https://www.ncbi.nlm.nih.gov/assembly/ and from Genome Taxonomy Database, associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy raw reduced representations, by using Mash software. Our dataset contains near to 100 GB of space disk reduced to 585.78 MB and represents 87,476 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with computational resources. Potential uses of this dataset include but are not limited to, microbial species delimitation, estimation of genomic distances, genomic novelties, paired comparisons between proteomes, genomes, and metagenomes.

Cancer cells require substantial amounts of energy and substrates for their metabolic hyperactivity, enabling the synthesis of new cells at the expense of healthy ones. Preliminary in vitro data suggest that a mix of free essential amino acids (EAA-mix) can promote cancer cell apoptosis by enhancing autophagy. This study aimed to confirm, both in vitro and in vivo, whether EAA intake could influence the development of colon cancer in mice. We investigated changes in cancer proliferation in CT26 cells treated with EAA-mix, and in mice fed with EAA rich modified diets (EAARD) as compared to those on a standard laboratory diet (StD). CT26 cells were injected subcutaneously (s.c.) or intraperitoneally (i.p.). After 21 days, tumors were removed and measured. In vitro data corroborated that EAA-mix impairs cancer growth by inducing autophagy and apoptosis. In vivo data revealed that mice on StD developed significantly larger (s.c.) and more numerous (i.p.) cancers than those on EAARD. EAA administration appears to influence cancer cell survival with notable anti-proliferative properties.

Most natural language processing (NLP) tasks suffer performance degradation when encountering long complex sentences, such as semantic parsing, syntactic parsing, machine translation, and text summarization. Previous works address the issue with an intuition of decomposing complex sentences and linking simple ones, such as RST-style discourse parsing, split-and-rephrase (SPRP), text simplification (TS), simple-sentence-decomposition (SSD), etc. However, these works are not applicable for semantic parsing like abstract meaning representation (AMR) parsing and semantic dependency parsing due to misalignments to semantic relations and unavailabilities to preserve original semantics. Following the same intuition and avoiding deficiencies of previous works, we propose a novel framework, hierarchical clause annotation (HCA), based on the linguistic research of clause hierarchy. With the HCA framework, we annotate a large HCA corpus to explore the potentialities of integrating HCA structural features into semantic parsing with complex sentences. Moreover, we decompose HCA into two subtasks, i.e., clause segmentation and clause parsing, and provide neural baseline models for more silver annotations.

Smokeless tobacco (ST) products vary significantly in their oral carcinogenicity. Much is known about the differences in chemical, but not bacterial, constituents of these products. In this study, we explore the composition and function of the bacteriome in ST products from 4 countries using q-PCR and 16S rRNA-based next generation sequencing. The bacterial load (16S rRNA copies/gram) was lowest in Swedish snus (3.4E+6) and highest in Yemeni shammah (6.6E+11). A total of 491 species-level taxa, many of which are potentially novel, belonging to 178 genera and 11 phyla were identified. Species richness and diversity were highest for Swedish snus and lowest for Yemeni shammah. Bacillus, Paenibacillus, and Oceanobacillus spp. were the most abundant in American snuff; species of Pseudomonas, Massilia, Propionibacterium, Puniceispirillum and Gloeothece predominated in Swedish snus. In Sudanese toombak, Facklamia, Desemzia, Atopostipes and Lysinibacillus spp. accounted for the majority of the bacteriome. Yemeni shammah exclusively contained Bacillus spp. PICRUSt functional prediction showed that genes encoding cadmium/zinc and nickel transport systems were enriched in the presumptively “high carcinogenicity” products. The bacteriome of ST products thus differed qualitatively, quantitatively and functionally. The relevance of these differences, particularly with respect to nickel and cadmium, to oral carcinogenesis warrants further investigation.

Pulsed thermography is a vital technique in the nondestructive evaluation field. However, its data analysis can be complex and requires skilled experts. Advances in deep learning have yielded exceptional results, including image segmentation. Therefore, many efforts have been made to apply deep learning methods to data processing for nondestructive evaluation. Despite this, there is currently no public Pulsed thermographic dataset available for evaluating various spatial-temporal deep methods of segmenting pulsed thermographic data. This article aims to provide such a dataset and assess the performance of commonly used deep learning-based instance segmentation models on it. Additionally, the impact of the number of frames and data transformations on model performance is examined. The findings suggest that suitable preprocessing methods can effectively reduce the data size without compromising the deep models’ performance.

Spectral unmixing represents both an application per se and a pre-processing step for several applications involving data acquired by imaging spectrometers. However, there is still a lack of publicly available reference data sets suitable for the validation and comparison of different spectral unmixing methods. In this paper we introduce the DLR HyperSpectral Unmixing (DLR HySU) benchmark dataset, acquired over German Aerospace Center (DLR) premises in Oberpfaffenhofen. The dataset includes airborne hyperspectral and RGB imagery of targets of different materials and sizes, complemented by simultaneous ground-based reflectance measurements. The DLR HySU benchmark allows a separate assessment of all spectral unmixing main steps: dimensionality estimation, endmember extraction (with and without pure pixe assumption), and abundance estimation. Results obtained with traditional algorithms for each of these steps are reported. To the best of our knowledge, this is the first time that real imaging spectrometer data with accurately measured targets are made available for hyperspectral unmixing experiments. The DLR HySU benchmark dataset is openly available online and the community is welcome to use it for spectral unmixing and other applications.

The Dph1•Dph2 heterodimer from yeast is a radical SAM (RS) enzyme that generates the 3-amino-3-carboxy-propyl (ACP) precursor for diphthamide, a clinically relevant modification on eukaryotic elongation factor 2 (eEF2). ACP formation requires SAM cleavage and atypical Cys-bound Fe-S clusters in each Dph1 and Dph2 subunit. Intriguingly, the first Cys residue in each motif locates next to another, ill-defined cysteine that we show in-here is conserved across eukaryotes. As judged from structural modeling, the orientation of these tandem cysteine motifs (TCM) suggests a candidate Fe-S cluster ligand role. Hence, we generated by site-directed DPH1 and DPH2 mutagenesis, Dph1•Dph2 variants with cysteines from each TCM replaced individually or in combination by serines. Assays diagnostic for diphthamide formation in vivo reveal that while single substitutions in the TCM of Dph2 cause mild defects, double mutations almost entirely inactivate the RS enzyme. Based on enhanced Dph1 and Dph2 subunit instability in response to cycloheximide chases, the variants with Cys substitutions in their cofactor motifs are particularly prone to protein degradation. In sum, we identify a fourth functionally cooperative Cys residue within the Fe-S motif of Dph2 and show that the Cys-based cofactor binding motifs in Dph1 and Dph2 are critical for the structural integrity of the dimeric RS enzyme in vivo.

This study examines the performance of the Indian Monsoon Data Assimilation and Analy-sis (IMDAA) in predicting five extremely severe cyclonic storms (ESCS) over the Bay of Bengal. The Advanced Research version of the WRF (ARW) model is utilized for this analysis over the last two decades. The initial and lateral boundary conditions are derived from the IMDAA datasets with a horizontal resolution of 0.12° × 0.12°. Five ESCSs from the past two decades are considered: Sidr 2007, Phailin 2013, Hudhud 2014, Fani 2019, and Amphan 2020. The model is integrated up to 96 hours using double nested domains of 12 km and 4 km. Model performance is evaluated using the 4 km results, compared with available observational datasets, including the best-fit data from the India Meteorological Department (IMD), The Tropical Rainfall Measuring Mission (TRMM) satellite, and Doppler Weather Radar (DWR). The results indicate that IMDAA provides accurate forecasts for ESCSs Fani, Hudhud, and Sidr in terms of track, intensity, and mean sea level pressure, aligning well with IMD observational datasets. However, Sidr's track deviates more from the observations. The calculated mean absolute maximum sustained wind speed errors range from 8.4 m/s to 10.6 m/s from day-1 to day-4, while mean track errors range from 114 km to 496 km during the same period. Statistical analysis, including bias, mean error, and standard deviation, underscores the significance of ESCS prediction. The discussion also covers rainfall prediction, maximum reflectivity, and the associated structure of the storms.

Shoulder tendinopathies produce pain and reduce functionality. The aim of this randomized clinical trial was to analyze the effects of Percutaneous electrolysis (PE), Percutaneous peripheral Nerve Stimulation (PNS) and eccentric exercise (EE), on pain (NPRS), strength, electromyographic activity, ultrasound characteristics of the tendon (echogenicity, thickness and hypervascularization) and functionality (DASH and SPADI) on individuals with supraspinatus tendinopathy. Participants (n=50) were divided into two groups, they received 4 treatment sessions, one per week, of PE and PNS (n=25) or 10 treatment sessions of TENS and US (n=25). Both groups performed EE program consisted of 3 sets of 10 repetitions of each of the 3 exercises, twice a day, during the 4 weeks. Follow-up was carried out at 4, 12 and 24 weeks after the start of the intervention. There are statistically significant differences in the analysis between groups (p&lt;0.001) in the post-treatment and follow-up measurements favorable to the PE+PNS+EE treatment on pain (NPRS), strength, supraspinatus electromyographic amplitude, ultrasound characteristics of the tendon (echogenicity, thickness and hypervascularization) and DASH and SPADI questionnaires. The combined treatment PE, PNS and EE is an effective option in the clinical management of tendinopathies, with positive results in the short and long term on the variables studied.

Text annotation is an essential element of the natural language processing approaches. The manual annotation process performed by humans has several drawbacks, such as subjectivity, slowness, fatigue, and possibly carelessness. In addition, annotators may annotate ambiguous data. So, we developed the concept of automated annotation to get the best annotations using several machine-learning approaches. The proposed approach is based on an ensemble algorithm of meta-learners and meta-vectorizer techniques. The approach employs a semi-supervised learning technique for automated annotation, aimed at detecting hate speech. This involves leveraging various machine learning algorithms, including Support Vector Machine (SVM), Decision Tree (DT), K-Nearest Neighbors (KNN), and Naive Bayes (NB), in conjunction with Word2Vec and TF-IDF text extraction methods. The annotation process is performed using 13,169 Indonesian YouTube comments data. The proposed model used a Stemming approach using data from Sastrawi and also new data of 2,245 words. Semi-supervised learning uses 5%, 10%, and 20% of labeled data as compared to performing labeling based on 80% of the datasets. In semi-supervised learning, the model learns from the labeled data, which provides explicit information, and the unlabeled data, which offers implicit insights. This hybrid approach enables the model to generalize and make informed predictions even when limited labeled data is available, ultimately enhancing its ability to handle real-world scenarios with scarce annotated information. In addition, the proposed method uses a variety of thresholds for matching words labeled with hate speech ranging from 0.6, 0.7, 0.8, and 0.9. The experiment showed that the KNN-Word2ec model has the best accuracy value of 96.9% with a scenario of 5%:80%:0.9. However, several other methods have also accuracy above 90%, such as SVM and DT based on both text extraction methods in several test scenarios.

The study of the currently known >3,000 species of snakes can provide valuable insights into the evolution of their genomes. Deinagkistrodon acutus, also known as Sharp-nosed Pit Viper, one hundred-pacer viper or five-pacer viper, is a venomous snake with significant economic, medicinal and scientific importance. Widely distributed in southeastern China and South-East Asia, D. acutus has been primarily studied for its venom. Here, we employed next-generation sequencing to assemble and annotate a highly continuous genome of D. acutus. The genome size is 1.46 Gb; its scaffold N50 length is 6.21 Mb, the repeat content is 42.81%, and 24,402 functional genes were annotated. This study helps to further understand and utilize D. acutus and its venom at the genetic level.

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions have been reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation has been improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regards, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

Intellecta dataset emerges as an innovative synthetic dataset, engineered to enhance the cognitive processing capabilities of contemporary language models. With a composition of 11.53 billion tokens, integrating 8.01 billion tokens of synthetic data with 3.52 billion tokens of rich textbook data, Intellecta is crafted to foster advanced reasoning and comprehensive educational narrative generation. Leveraging the Mixtral-8x7B-Instruct-v0.1 model, the dataset facilitates the generation of complex thought processes and detailed, textbook-style explanations, thus enabling language models to engage in both critical thinking and profound educational discourse. This hybrid dataset stands as a testament to the potential of synthetic data in pushing the boundaries of AI, offering a repository that is not only vast and varied but also refined to align with ethical standards and intellectual rigor.

Characters are one of the most important elements in composing digital animation. The appear-ance and voice of a character should be designed to express the personality and values of the character. However, it is not easy for animation producers to harmoniously match the appear-ance and voice of a character. Advances in deep learning technology have made it possible to overcome this limitation. To achieve this, firstly, an audio-visual dataset of characters is required. In this study, we construct and verify a Korean audio-visual dataset consisting of frontal face im-ages of various characters and short voice clips. We developed an application that can automati-cally extract the frontal face image and a short voice clip of a character by collecting videos up-loaded to YouTube. Through this, a dataset consisting of a total of 1,522 face images and a total of 7,999 seconds of voice clips was built based on 490 characters. Furthermore, we automatically la-bel characters by gender and age to validate the dataset. The dataset built in this study is expected to be used in various deep learning fields, such as classification, generative adversarial networks, and speech synthesis.

The dataset reports a collection of earnings call transcripts, the related stock prices, and the related sector index. It contains a total of 188 transcripts, 11970 stock prices, and 1196 sector index values. Furthermore, all of these data originated in the period 2016-2020 and are related to the NASDAQ stock market. The data have been collected using Yahoo Finance and Thomson Reuters Eikon. Specifically, Yahoo Finance offered daily stock prices and traded volume. At the same time, Thomson Reuters Eikon has been used as source for the earnings call transcripts. The dataset can be used as a benchmark for the evaluation of several NLP techniques as well as machine learning algorithms for understanding their potential for financial applications. Moreover, it is also possible to expand the dataset by extending the period in which the data originated following a similar procedure.

Managing Water, Energy, and Food (WEF) resources within socio-environmental systems demands innovative strategies that provide decision-makers with actionable insights. This article explores the challenges and potential solutions of employing Focus Maps and choremes as a novel approach for assessing anthropogenic impacts and enhancing the visualization of the WEF Nexus in specific geographic areas. By integrating geospatial data, multi-criteria analysis, and involving stakeholders, our research aims to develop Choreomatic Focus Maps (CFMs) that offer a comprehensive spatial representation of the WEF Nexus, facilitating better-informed decision-making at the community level. Our current work outlines visualization of WEF Nexus, as an initial stages of creating CFMs through a detailed step-by-step process. This includes identifying the main drivers for WEF nexus, such as anthropogenic activities and their distribution, evaluating environmental factors, linking anthropogenic impact with environmental indicators over time, and conducting on-site validation. Our focus is on advancing through these crucial steps, particularly emphasizing field validation within the Local Decision-Makers Tools, visualized here by using Focus Maps. This phase is vital for ensuring our approach is grounded in reality and meets the needs of the communities within the Danube Delta region. By doing so, we aim to provide a visual summary of the WEF Nexus that not only captures the complexity of this fragile ecosystem but also incorporates local insights and priorities, identifying key areas where human activities have significant impacts.

Boundary behavior of a given important function or its limit values are essential in the whole spectrum of mathematics and science. We consider some tractable cases of limit values in which either a difference of two ingredients or a difference equation is used coupled with the relevant functional equations to give rise to unexpected results. This involves the expression for the Laurent coefficients including the residue, the Kronecker limit formulas and higher order coefficients as well as the difference formed to cancel the inaccessible part, typically the Clausen functions. We also state Abelian results which yield asymptotic formulas for weighted summatory function from that for the original summatory function

Website defacement is an illegal electronic act of changing a website. In this paper, robust machine learning classifiers’ capabilities were exploited to select the best input feature set for evaluating a website’s defacement risk. Zone-H, a private organization, offered us a defacement mining dataset. A sample of 93644 datapoints was concisely pre-processed and used for modelling purposes. Considering multidimensional features as input, reason and hackmode variables were chosen as outputs. Massive machine learning models were examined; however, decision tree (DT), k-nearest neighbour (k-NN), and random forest (RF) were the most powerful algorithms used to predict the target model. The input variables 'domain', 'system', 'web_server','redefacement', 'type', 'def_grade', and 'reason/hackmode' were tested and used to shape the final model. Using the cross-validation (CV) technique, the model’s key performance factors were calculated and reported. After calculating the average scores for the hyperbolic metrics (i.e., max-depth, min-sample-leaf, weight, max-features, and CV), both targets were evaluated, and the learning algorithms were ranked as RF, DT, and k-NN. The reason and hackmode variables were thoroughly analysed. The average score accuracies for the reason and hackmode targets were 0.85 and 0.585, respectively. The results showed a significant development in terms of modelling and optimizing website defacement risk. The study also successfully addresses the main cybersecurity concerns, in particular website defacement.

The mutton sheep breeding industry has transformed significantly in recent years, from traditional grassland free-range farming to a more intelligent approach. As a result, automated sheep face recognition systems have become vital to modern breeding practices and have gradually replaced ear tagging and other manual tracking techniques. Although sheep face datasets have been introduced in previous studies, they have often involved pose or background restrictions (e.g., fixing of the subject’s head, cleaning of the face), which restrict data collection and have limited the size of available sample sets. As a result, a comprehensive benchmark designed exclusively for the evaluation of individual sheep recognition algorithms is lacking. To address this issue, this study develops a large-scale benchmark dataset, Sheepface-107, comprised of 5,350 images acquired from 107 different subjects. Images were collected from each sheep at multiple angles, including front and back views, in a diverse collection that provides a more comprehensive representation of facial features. In addition to the dataset, an assessment protocol is developed by applying multiple evaluation metrics to the results produced by three different deep learning models: VGG16, GoogLeNet, and ResNet50, which achieved F1-scores of 83.79%, 89.11%, and 93.44%, respectively. A statistical analysis of each algorithm suggested that accuracy and the number of parameters were the most informative metrics for use in evaluating recognition performance.

In Mexico, the incorporation of deaf people into education has been lacking since only 14% of the deaf population in the age group between 3 and 29 years access education with the support of a hearing aid. Additionally, those who have been incorporated frequently face inappropriate educational strategies which poorly develop the use of Mexican Sign Language (MSL) and therefore academical success and opportunities for insertion in the workplace are difficult. This research explores a novel mexican sign language lexicon video dataset containing the dynamical gestures most frequently used by MSL. Each gesture consists of a set of different versions of videos under uncontrolled conditions. MX-ITESO-100 data set is composed of a lexicon of 100 gestures and 5,000 videos from three participants with different grammatical elements. Additionally, the data set is evaluated in a two-step neural network model with an accuracy greater than 99%. and thus serves as a benchmark for future training of machine learning models in computer vision systems. Finally, this research provides an inclusive environment within society and organizations in particular for people with hearing impairment.

Vehicle identification is an important task in traffic monitoring because it allows for efficient inference and provides a cause for action. Vehicle classification via deep learning and other approaches such as segmentation is a critical tool for re-identification. In this paper, instance segmentation is used to identify vehicle makes with license plate detection, allowing for better unique vehicle recognition for re-identification. A dataset is annotated and modified, for example, by segmenting it with polygonal bounding boxes that capture the vehicle's unique frontal features. In addition, license plate localization is performed. The results showed improved classification as well as a high mAP for the dataset when compared to previous approaches based on CNN and deformed CNN. Furthermore, a deep residual network and fully connected layer-based classification were utilized as the backbone for feature representation. Instance segmentation detects objects by segmenting and classifying regions of interest. The imbalance in the dataset is resolved using a mosaic-tiled approach, which produces greater precision than other approaches.

This study describes the development of an image-based insect trap diverging from the plug-in camera insect trap paradigm. In short, a) it does not require manual annotation of images to learn how to count targeted pests and, b) it self-disposes the captured insects, and therefore is suitable for long-term deployment. The device consists of an imaging sensor integrated with Raspberry Pi microcontroller units with embedded deep learning algorithms that count agricultural pests inside a pheromone-based funnel trap. The device also receives commands from the server which configures its operation while an embedded servomotor can automatically rotate the detached bottom of the bucket to dispose of hydrated insects as they begin to pile up. Therefore, it completely overcomes a major limitation of camera-based insect traps: the inevitable overlap and occlusion caused by the decay and layering of insects during long-term operation, thus extending the autonomous operational capability. We study cases that are underrepresented in literature such as counting in situations of congestion and significant debris using crowd counting algorithms encountered in human surveillance. Finally, we perform comparative analysis of the results from different deep-learning approaches (YOLO7/8, crowd counting, deep learning regression) and we open-source the code and a large database of Lepidopteran plant pests.

This study used established biomarkers of death due to ischemic stroke (IS) and performed network, enrichment, and annotation analysis. Protein-protein interaction (PPI) network analysis revealed that the backbone of the highly connective network of IS death consisted of IL6, ALB, TNF, SERPINE1, VWF, VCAM1, TGFB1, and SELE. Cluster analysis revealed immune and hemostasis subnetworks, which were strongly interconnected through the major switches ALB and VWF. Enrichment analysis revealed that the PPI immune subnetwork of death due to IS was highly associated with TLR2/4, TNF, JAK-STAT, NOD, IL10, IL13, IL4, and TGF-β1/SMAD pathways. The top biological and molecular functions and pathways enriched in the hemostasis network of death due IS were platelet degranulation and activation, the intrinsic pathway of fibrin clot formation, the urokinase-type plasminogen activator pathway, post-translational protein phosphorylation, integrin cell surface interactions, and the proteoglycan-integrin-extra cellular matrix complex (ECM). Regulation Explorer analysis of transcriptional factors shows: a) that NFKB1, RELA and SP1 were the major regulating actors of the PPI network; and b) hsa-mir-26-5p and hsa-16-5p were the major regulating microRNA actors. In conclusion, prevention of death due to IS should consider that current IS treatments may be improved by targeting VWF, VEGFA, proteoglycan-integrin-ECM complex, NFKB/RELA and SP1.

In this paper, comprehensive datasets are presented to advance research on information security breaches. The datasets include data on disclosed information security breaches affecting S&P500 companies between 2020 and 2023, collected through manual search of the Internet. Overall, the datasets include 504 companies, with detailed information security breach and financial data available for 97 firms that experienced a disclosed information security breach. This document will describe the datasets in detail, explain the data collection procedure and shows the initial versions of the datasets.

Several studies in computer vision have examined specular removal, which is crucial for object detection and recognition. This research has traditionally been divided into two tasks: specular highlight removal, which focuses on removing specular highlights on object surfaces, and reflection removal, which deals with specular reflections occurring on glass surfaces. In reality, however, both types of specular effects often coexist, making it a fundamental challenge that has not been adequately addressed. Recognizing the necessity of integrating specular components handled in both tasks, we constructed a Specular-Light (S-Light) DB for training single-image-based deep learning models. Moreover, considering the absence of benchmark datasets for quantitative evaluation, the Multi-Scale Normalized Cross Correlation (MS-NCC) metric, which considers the correlation between specular and diffuse components, was introduced to assess the learning outcomes.