bluuebunny/crossref_metadata_2025_split huggingface dataset:
Target-enhanced whole-genome sequencing (TE-WGS) shows clinical validity equivalent to commercially available targeted oncology panel
Authors: Lee Sangmoon , Roh Jin , Park Jun Sung , Tuncay Islam Oguz , Lee Wonchul , Kim Jung-Ah , Oh Brian Baek-Lok , Shin Jong-Yeon , Lee Jeong Seok , Ju Young Seok , Kim Ryul , Park Seongyeol , Koo Jaemo , Park Hansol , Lim Joonoh , Connolly-Strong Erin , Kim Tae-Hwan , Choi Yong Won , Ahn Mi Sun , Lee Hyun Woo , Kim Seokhwi , Kim Jang-Hee , Kwon Minsuk 
Published: December 2023

ABSTRACTCancer poses a significant global health challenge, with increasing incidence rates demanding precise genomic testing for individualized treatment strategies. Targeted-panel sequencing (TPS) has improved personalized oncology but often lacks comprehensive coverage of crucial cancer alterations. Whole-genome sequencing (WGS) addresses this gap, offering extensive genomic testing. This study demonstrates the potential medical application of WGS.MethodsThis study evaluates the power of target-enhanced WGS (TE-WGS), a clinical-grade WGS method sequencing both cancer and matched normal tissues. A cohort of forty-nine patients with various solid cancer types underwent both TE-WGS and TruSight Oncology 500 (TSO500), one of the mainstream TPS approaches currently used in the clinic.ResultsTE-WGS methods detected all the variants reported from TSO500 (100%, 498/498). A high correlation in the detection of variant allele fractions (VAF) was observed between the TE-WGS and TSO500 methodologies (r=0.977). Notably, within the pool of 498 variants commonly detected by both approaches, 223 variants (44.8%) were discerned within peripheral blood samples exclusively through the TE-WGS technique, suggesting their presence as constitutional variants inherent to the germline. Conversely, the remaining subset of 275 variants (55.2%) were not detected in peripheral blood using the TE-WGS method, signifying them as bona fide somatic variants. Further, TE-WGS provided accurate copy number profiles, fusion-genes, MSI- and homologous-recombination deficiency (HRD) scores, which were essential for clinical decision making.ConclusionTE-WGS proves to be a comprehensive approach in personalized oncology, matching the key biomarker detection capabilities of the established TSO500 panel. Additionally, TE-WGS uniquely identifies germline variants and genomic instability markers, offering additional clinical actions. Its adaptability and cost-effectiveness further underscore its clinical utility, making TE-WGS a valuable tool in personalized cancer treatment.
Anemia in Pregnant Women as a Cultural Phenomenon: A Literature Review
Authors: Aden Christine , Pandin Moses Glorino Rumambo , Nursalam Nursalam 
Published: December 2023

AbstractBackgroundExplores how restrictions on food intake during pregnancy, due to cultural taboos, can lead to anemia. The study aims to provide an overview of prohibited food types, the supportive environment, the impact on pregnancy, and interventions that can be implemented to overcome anemia.MethodThe authors conducted a literature review by searching for articles on five databases, namely Science Direct, Springer Link, Pubmed, Sage, and Scopus. They also searched for suitable articles from other references, mainly journal articles published in the last five years (2019-2023).ResultsIn total, there were 20 reviewed explaining the types of food prohibited during pregnancy and the reasons for this as well as support from family, religious figures, mothers, and in-laws. Overcoming anemia in pregnant women with a cultural approach resulted in meaningful results, with the intervention carried out for around three months. The use of picture books that are appropriate to the cultural context and local wisdom increases information about the importance of iron for pregnant women, increases the frequency of eating, the number of iron tablet intakes, the amount of food intake containing iron each day, and increases the baby’s birth weight.ConclusionAnemia caused by cultural taboos on certain foods during pregnancy can be prevented and treated with local wisdom intervention approaches.
Recent cross-sectional prevalence studies in sub-Saharan Africa for communicable, maternal, neonatal, and nutritional diseases and conditions: a scoping review
Authors: Dolley S , Miller C , Quach P , Norman T 
Published: December 2023

AbstractBackgroundCross-sectional prevalence studies provide benefits to policymakers, epidemiologists, trialists, and the future health of target and general populations. Too few of these studies are performed in hotspots of traditional global health disease burden. This results in a lack of recent, local, accurate prevalence estimates to inform policy, epidemiology, and the design of interventional randomized controlled trials that may be conducted in these regions.ObjectiveThis scoping review aims to establish a novel dataset usable as an observational baseline. The topic being analyzed is the set of characteristics describing recently published prospective cross-sectional prevalence studies in sub-Saharan Africa for humans affected with communicable, maternal, neonatal, and nutritional diseases and conditions.MethodsThis scoping review conducted a systematic literature search of PubMed. The search identified publications in the last four years describing completed cross-sectional prevalence studies in sub-Saharan Africa. Title and abstract screening was completed. Data extraction was performed on a random sample of the final dataset.ResultsThis scoping review identified 868 titles and abstracts through our systematic search. Through our screening process, 394 of these were candidates eligible for inclusion in our dataset. Ultimately, 363 were in the final dataset. Of the 38 studies in the random sample, this scoping review found a large portion of the studies completed with no funding. Malaria was the predominant disease studied, followed by parasitic intestinal infection and malnutrition. Studies with funding were slower, from data collection to submission to a journal, than studies with no funding. Studies that use a national ethical review process tend to take longer than those using hospital or university institutional review boards.ConclusionsCross-sectional prevalence studies are happening in sub-Saharan Africa for many communicable, maternal, neonatal, and nutritional diseases and conditions. This healthy research ecosystem is filled with variety. A variety of data collection methods, sources of funding, types of study sites, and target populations exist. Many studies are self-funded by the principal investigator. These studies are rarely conducted for the explicit purpose of informing the designs of future randomized trials. Some trends might be observable in the data that point to causal factors for study speed or sample size.
Pathogenesis of Multiple Sclerosis: Genetic, Environmental, and Random Mechanisms
Authors: Goodin Douglas S. 
Published: December 2023

AbstractBACKGROUNDMS-pathogenesis requires both genetic factors and environmental events. The question remains, however, whether these factors and eventscompletelydescribe the MS disease-process. This question was addressed using the Canadian MS-data, which includes 29,478 individuals, representing 65-83% of all Canadian MS-patients.METHODSThe “genetically-susceptible” subset of the population, (G), includeseveryonewho hasany non-zerolife-time chance of developing MS, undersomeenvironmental-conditions. A “sufficient” environmental-exposure, forany“genetically-susceptible” individual, includeseveryset of environmental conditions, each of which issufficient, by itself, tocauseMS in that person. This analysis incorporates several differentepidemiologic-parameters, involved in MS-pathogenesis, only some of which are directly-observable, and establishes “plausible-value-ranges”for each parameter. Thoseparameter-valuecombinations (solutions) that fall within theseplausible-rangesare then determined.RESULTSOnly a fraction of the population can possibly be “genetically-susceptible”. Thus, many individuals haveno possibilityof developing MS underanyenvironmental conditions. Moreover,some“genetically-susceptible” individuals, despite their experiencing a “sufficient” environmental-exposure,will neverdevelop disease.CONCLUSIONSThis analysisexplicitly includesall of those genetic factors and environmental events (including interactions), which are necessary for MS-pathogenesis, regardless of whether these are known, suspected, or as yet unrecognized. Nevertheless, in addition, “true” randomness seems to play a critical role in disease-pathogenesis. This observation provides empirical evidence that undermines the widely-held deterministic view of nature. Moreover, both sexes seem to have a similar genetic and environmental disease-basis. If so, this indicates that this random element is primarily responsible for the currently-observed differences in disease-expression betweensusceptible-womenandsusceptible-men.
Characterization and Mitigation of a Simultaneous Multi-Slice fMRI Artifact: Multiband Artifact Regression in Simultaneous Slices
Authors: Tubiolo Philip N. , Williams John C. , Van Snellenberg Jared X. 
Published: December 2023

AbstractSimultaneous multi-slice (multiband) acceleration in fMRI has become widespread, but may be affected by novel forms of signal artifact. Here, we demonstrate a previously unreported artifact manifesting as a shared signal between simultaneously acquired slices in all resting-state and task-based multiband fMRI datasets we investigated, including publicly available consortium data from the Human Connectome Project (HCP) and Adolescent Brain Cognitive Development (ABCD) Study. We propose Multiband Artifact Regression in Simultaneous Slices (MARSS), a regression-based detection and correction technique that successfully mitigates this shared signal in unprocessed data. We demonstrate that the signal isolated by MARSS correction is likely non-neural, appearing stronger in neurovasculature than grey matter. Additionally, we evaluate MARSS both against and in tandem with sICA+FIX denoising, which is implemented in HCP resting-state data, to show that MARSS mitigates residual artifact signal that is not modeled by sICA+FIX. MARSS correction leads to study-wide increases in signal-to-noise ratio, decreases in cortical coefficient of variation, and mitigation of systematic artefactual spatial patterns in participant-level task betas. Finally, MARSS correction has substantive effects on second-level t-statistics in analyses of task-evoked activation. We recommend that investigators apply MARSS to multiband fMRI datasets with moderate or higher acceleration factors, in combination with established denoising methods.
Effects of Probiotics, Glucose Oxidase and its Combination on Immune Function, Antioxidant Status, Serum Biochemical Incides and Toxin Residue in Sheep when Challenged with Aflatoxin B1
Authors: Zhang Yu , Lu Henan , Erdene-Khas  , Zhang Caixia , Wang Hairong 
Published: December 2023

AbstractThe objective of this study was to investigate the ability of a mixed mycotoxins detoxification agent (probiotics, Glucose oxidase (GOD) and its combination) to alleviate the toxicity of aflatoxin B1 (AFB1) by assessing growth performance, serum toxin residue, immune function, antioxidant status and serum biochemical indices of sheep. Twenty 8-month-old Mongolian sheep were randomly assigned to 1-5 diet treatment groups: 1) the control (CON) group: basal diet; 2) the AFB1 (A) group: CON + 0.2 mg/kg AFB1; 3) the AFB1 and probiotics (AP) group: A + 0.5% probiotics; 4) the AFB1 and GOD (AG) group: A + 0.5% GOD; 5) the AFB1, probiotics, and GOD (APG) group: A + 0.5% probiotics + 0.5% GOD. Results showed that treatment A adversely affected the health and performance of sheep. However, the treatments AP, AG, or APG exerted a positive effect on health, performance and other indications. In conclusion, probiotics, GOD, and its combination induced injury of Mongolian sheep by alleviating the negative effects of AFB1 on the production performance, immune indexes, antioxidant indexes, and serum biochemical indexes and effectively reducing serum toxin residue.Key ContributionThe study investigated the effects of probiotics, Glucose oxidase and its combination on serum detoxification of AFB1 by assessing growth performance, serum toxin residue, immune function, antioxidant status and blood biochemical indices of sheep. AFB1 - contaminated diets supplemented with probiotics and GOD were effective in improving growth performance, immunity, antioxidant function, liver function, and decreasing serum AFB1 residue of sheep.
Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images
Authors: Zhang Bohan , Li Mei , Kang Qiang , Deng Zhonghan , Qin Hua , Su Kui , Feng Xiuwen , Chen Lichuan , Liu Huanlin , Fang Shuangsang , Zhang Yong , Li Yuxiang , Brix Susanne , Xu Xun 
Published: December 2023

ABSTRACTStereo-seq is a cutting-edge technique for spatially resolved transcriptomics that combines subcellular resolution with centimeter-level field-of-view, serving as a technical foundation for analyzing large tissues at the single-cell level. Our previous work presents the first one-stop software that utilizes cell nuclei staining images and statistical methods to generate high-confidence single-cell spatial gene expression profiles for Stereo-seq data. With recent advancements in Stereo-seq technology, it is possible to acquire cell boundary information, such as cell membrane/wall staining images. To take advantage of this progress, we update our software to a new version, named STCellbin, which utilizes the cell nuclei staining images as a bridge to align cell membrane/wall staining images with spatial gene expression maps. By employing an advanced cell segmentation technique, accurate cell boundaries can be obtained, leading to more reliable single-cell spatial gene expression profiles. Experimental results verify that STCellbin can be applied on the mouse liver (cell membranes) andArabidopsisseed (cell walls) datasets and outperforms other competitive methods. The improved capability of capturing single cell gene expression profiles by this update results in a deeper understanding of the contribution of single cell phenotypes to tissue biology.Availability & ImplementationThe source code of STCellbin is available athttps://github.com/STOmics/STCellbin.
Portable Multi-focal Visual Evoked Potential Diagnostics for Multiple Sclerosis/Optic Neuritis patients
Authors: Banijamali S. Mohammad Ali , Versek Craig , Babinski Kristen , Kamarthi Sagar , Green-LaRoche Deborah , Sridhar Srinivas 
Published: December 2023

AbstractPurposeMultiple Sclerosis (MS) is a neuro-inflammatory disease of the Central Nervous System (CNS) in which the body’s immune system attacks and destroys myelin sheath that protects nerve fibers and causes disruption in axonal signal transmission. Demyelinating Optic Neuritis (ON) is often a manifestation of MS and involves inflammation of the optic nerve. ON can cause vision loss, pain and discomfort in the eyes, and difficulties in color perception.In this study, we developed NeuroVEP, a portable, wireless diagnostic system that delivers visual stimuli through a smartphone in a headset and measures evoked potentials at the visual cortex from near the O1, Oz, O2, O9 and O10 locations on the scalp (extended 10-20 system) using custom electroencephalography (EEG) electrodes.MethodsEach test session is constituted by a short 2.5-minute full-field visual evoked potentials (ffVEP) test, followed by a 12.5-minute multifocal VEP (mfVEP) test. The ffVEP test evaluates the integrity of the visual pathway by analyzing the P1 (also known as P100) component of responses from each eye, while the mfVEP test evaluates 36 individual regions of the visual field for abnormalities. Extensive signal processing, feature extraction methods, and machine learning algorithms were explored for analyzing the mfVEP responses. The results of the ffVEP test for patients were evaluated against normative data collected from a group of subjects with normal vision. Custom visual stimuli with simulated defects were used to validate the mfVEP results which yielded 91% accuracy of classification.Results20 subjects, 10 controls and 10 with MS and/or ON were tested with the NeuroVEP device and a standard-of-care (SOC) VEP testing device which delivers only ffVEP stimuli. In 91% of the cases, the ffVEP results agreed between NeuroVEP and SOC device. Where available, the NeuroVEP mfVEP results were in good agreement with Humphrey Automated Perimetry visual field analysis. The lesion locations deduced from the mfVEP data were consistent with Magnetic Resonance Imaging (MRI) and Optical Coherence Tomography (OCT) findings.ConclusionThis pilot study indicates that NeuroVEP has the potential to be a reliable, portable, and objective diagnostic device for electrophysiology and visual field analysis for neuro-visual disorders.
Optimal distance metrics for single-cell RNA-seq populations
Authors: Ji Yuge , Green Tessa D. , Peidli Stefan , Bahrami Mojtaba , Liu Meiqi , Zappia Luke , Hrovatin Karin , Sander Chris , Theis Fabian J. 
Published: December 2023

AbstractIn single-cell data workflows and modeling, distance metrics are commonly used in loss functions, model evaluation, and subpopulation analysis. However, these metrics behave differently depending on the source of variation, conditions and subpopulations in single-cell expression profiles due to data sparsity and high dimensionality. Thus, the metrics used for downstream tasks in this domain should be carefully selected. We establish a set of benchmarks with three evaluation measures, capturing desirable facets of absolute and relative distance behavior. Based on seven datasets using perturbation as ground truth, we evaluated 16 distance metrics applied to scRNA-seq data and demonstrated their application to three use cases. We find that linear metrics such as mean squared error (MSE) performed best across our three evaluation criteria. Therefore, we recommend the use of MSE for comparing single-cell RNA-seq populations and evaluating gene expression prediction models.
Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
Authors: Kudo Takamasa , Meireles Ana M. , Moncada Reuben , Chen Yushu , Wu Ping , Gould Joshua , Hu Xiaoyu , Kornfeld Opher , Jesudason Rajiv , Foo Conrad , Höckendorf Burkhard , Bravo Hector Corrada , Town Jason P. , Wei Runmin , Rios Antonio , Chandrasekar Vineethkrishna , Heinlein Melanie , Cai Shuangyi , Lu Cherry Sakura , Celen Cemre , Kljavin Noelyn , Jiang Jian , Hleap Jose Sergio , Kayagaki Nobuhiko , de Sousa e Melo Felipe , McGinnis Lisa , Li Bo , Singh Avtar , Garraway Levi , Rozenblatt-Rosen Orit , Regev Aviv , Lubeck Eric 
Published: December 2023

ABSTRACTOptical pooled screening (OPS) is a highly scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture, due to limitations associated within situsequencing (ISS) of perturbation barcodes. Here, we developed PerturbView, an OPS technology that leveragesin vitrotranscription (IVT) to amplify barcodes prior to ISS, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in iPSC-derived neurons, primary immune cells, and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NFκB signaling. Furthermore, we combined PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way toin vivoscreens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.
The Anti-inflammatory Drug Leflunomide Inhibits NS2B3 Cluster Formation During Dengue Viral Infection as Revealed by Single Molecule Imaging
Authors: Varghese Jiby Mary , Aravinth S , Pant Neeraj , Mondal Partha Pratim 
Published: December 2023

A prerequisite for Dengue viral infection is the clustering of NS2B3 viral protein in the infected cell. This calls for drugs capable of reversing the biological processes leading to the declustering of NS2B3 viral complex. In this work, we report a new drug (leflunomide) that shows reversal of NS2B3 clustering, post 24 hours of cell transfection with a recombinant probe (Dendra2-NS2B3) containing the viral complex of interest (NS2B3). To study, we constructed a photoactivable recombinant plasmid for visualizing the activity of the target protein-of-interest (Dendra2-NS2B3). This enabled a better understanding of the underlying biological processes involved in Dengue and the role of NS2B3. The study was performed in a cellular system by transfecting the cell (NIH3T3 -mouse fibroblast cell line), followed by drug treatment studies. A range of physiologically relevant concentrations (250nM −10μM) of the FDA-approved drug (leflunomide) was used. The single molecule super-resolution microscopy (scanSM LM) study showed declustering of NS2B3 clusters for concentrations>250nMand near complete disappearance of clusters at concentrations>5μM. Moreover, the associated critical biophysical parameters suggest a substantial decrease in clustered molecules (from 53.2±1.77% for control to 14.89±4.80% at 250nM, and further reduction to 10.55±2.91% at 500nM). Moreover, the number of clusters reduced from 46±15 to 13±4, and the number of molecules per cluster decreased from 133±29 to 62±3, with a depletion in large clusters (from 24 to 12). The parameters collectively indicate the clustering nature of NS2B3 viral protein during the infection process at a cellular level and the effect of leflunomide in declustering. The results supported by statistical analysis suggest strong declustering promoted by leflunomide, which holds the promise to contain/treat dengue viral infection.Statement of SignificanceThe fact that there is no approved antiviral approach for Dengue makes it life-threatening and calls for ways to tackle viral infection. Hence, understanding Dengue biology at a single molecule level plays a vital role. In the present super-resolution study, we noted the formation of key viral protein (NS2B3) clusters post 24 hours of transfection in a cellular system. We identified a repurposed FDA-approved drug (Leflunomide) that inhibits the clustering process and promotes declustering at higher drug concentrations. This may become the basis of future studies, which may have therapeutic potential against Dengue.