bluuebunny/crossref_metadata_2025_split huggingface dataset:
The application of Hybrid deep learning Approach to evaluate chest ray images for the diagnosis of pneumonia in children
Authors: Abbasa Mohammad Ali , Bukhari Syed Usama Khalid , Arssalan Bokhari Syed Khuzaima , niazi manal 
Published: December 2020

AbstractBackgroundPneumonia is a leading cause of morbidity and mortality worldwide, particularly among the developing nations. Pneumonia is the most common cause of death in children due to infectious etiology. Early and accurate Pneumonia diagnosis could play a vital role in reducing morbidity and mortality associated with this ailment. In this regard, the application of a new hybrid machine learning vision-based model may be a useful adjunct tool that can predict Pneumonia from chest X-ray (CXR) images.Aim & Objectivewe aimed to assess the diagnostic accuracy of hybrid machine learning vision-based model for the diagnosis of Pneumonia by evaluating chest X-ray (CXR) imagesMaterials & MethodsA total of five thousand eight hundred and fifty-six digital X-ray images of children from ages one to five were obtained from the Chest X-Ray Pneumonia dataset using the Kaggle site. The dataset contains fifteen hundred and eighty-three digital X-ray images categorized as normal, where four thousand two hundred and seventy-three digital X-ray images are categorized as Pneumonia by an expert clinician. In this research project, a new hybrid machine learning vision-based model has been evaluated that can predict Pneumonia from chest X-ray (CXR) images. The proposed model is a hybrid of convolutional neural network and tree base algorithms (random forest and light gradient boosting machine). In this study, a hybrid architecture with four variations and two variations of ResNet architecture are employed, and a comparison is made between them.ResultsIn the present study, the analysis of digital X-ray images by four variations of hybrid architecture RN-18 RF, RN-18 LGBM, RN-34 RF, and RN-34 LGBM, along with two variations of ResNet architecture, ResNet-18 and ResNet-30 have revealed the diagnostic accuracy of 97.78%, 96.42%, 97.1%,96.59%, 95.05%, and 95.05%, respectively.DiscussionThe analysis of the present study results revealed more than 95% diagnostic accuracy for the diagnosis of Pneumonia by evaluating chest x-ray images of children with the help of four variations of hybrid architectures and two variations of ResNet architectures. Our findings are in accordance with the other published study in which the author used the deep learning algorithm Chex-Net with 121 layers.ConclusionThe hybrid machine learning vision-based model is a useful tool for the assessment of chest x rays of children for the diagnosis of Pneumonia.
A holistic approach for suppression of COVID-19 spread in workplaces and universities
Authors: Poole Sarah F. , Gronsbell Jessica , Winter Dale , Nickels Stefanie , Levy Roie , Fu Bin , Burq Maximilien , Saeb Sohrab , Edwards Matthew D. , Behr Michael K. , Kumaresan Vignesh , Macalalad Alexander R. , Shah Sneh , Prevost Michelle , Snoad Nigel , Brenner Michael P. , Myers Lance J. , Varghese Paul , Califf Robert M. , Washington Vindell , Lee Vivian S. , Fromer Menachem 
Published: December 2020

AbstractAs society has moved past the initial phase of the COVID-19 crisis that relied on broad-spectrum shutdowns as a stopgap method, industries and institutions have faced the daunting question of how to return to a stabilized state of activities and more fully reopen the economy. A core problem is how to return people to their workplaces and educational institutions in a manner that is safe, ethical, grounded in science, and takes into account the unique factors and needs of each organization and community. In this paper, we introduce an epidemiological model (the “Community-Workplace” model) that accounts for SARS-CoV-2 transmission within the workplace, within the surrounding community, and between them. We use this multi-group deterministic compartmental model to consider various testing strategies that, together with symptom screening, exposure tracking, and nonpharmaceutical interventions (NPI) such as mask wearing and social distancing, aim to reduce disease spread in the workplace. Our framework is designed to be adaptable to a variety of specific workplace environments to support planning efforts as reopenings continue.Using this model, we consider a number of case studies, including an office workplace, a factory floor, and a university campus. Analysis of these cases illustrates that continuous testing can help a workplace avoid an outbreak by reducing undetected infectiousness even in high-contact environments. We find that a university setting, where individuals spend more time on campus and have a higher contact load, requires more testing to remain safe, compared to a factory or office setting. Under the modeling assumptions, we find that maintaining a prevalence below 3% can be achieved in an office setting by testing its workforce every two weeks, whereas achieving this same goal for a university could require as much as fourfold more testing (i.e., testing the entire campus population twice a week). Our model also simulates the dynamics of reduced spread that result from the introduction of mitigation measures when test results reveal the early stages of a workplace outbreak. We use this to show that a vigilant university that has the ability to quickly react to outbreaks can be justified in implementing testing at the same rate as a lower-risk office workplace. Finally, we quantify the devastating impact that an outbreak in a small-town college could have on the surrounding community, which supports the notion that communities can be better protected by supporting their local places of business in preventing onsite spread of disease.
Multi-tissue transcriptome-wide association study identifies genetic mechanisms underlying endometrial cancer susceptibility
Authors: Kho Pik-Fang , Partida Gabriel Cuellar , Dörk Thilo , Goode Ellen L. , Lambrechts Diether , Scott Rodney J. ,   Endometrial Cancer Association Consortium, Spurdle Amanda B. , O’Mara Tracy A. , Glubb Dylan M. 
Published: December 2020

AbstractGenome-wide association studies (GWAS) of endometrial cancer have identified 16 genetic susceptibility loci. To identify candidate endometrial cancer susceptibility genes, we have performed the first transcriptome-wide association study (TWAS) of endometrial cancer. For this analysis, we have used the largest endometrial cancer GWAS and gene expression from 48 tissues to maximise statistical power. We used colocalisation analysis to prioritise seven candidate susceptibility genes, including CYP19A1, which wes previously established as an endometrial cancer susceptibility gene. Notably, one of the candidate susceptibility genes was located at 17q24.2, a potentially novel risk locus for endometrial cancer. Using phenome-wide association analysis, candidate susceptibility genes were found to associate with traits related to endometrial cancer risk factors, in addition to other clinical phenotypes that may provide novel risk factors. TWAS data were also used to perform drug repurposing analysis and identified 14 compounds; two of these are tubulin inhibitors, a drug class used to treat advanced endometrial cancer. In summary, this study has revealed biologically relevant endometrial cancer susceptibility genes, providing insights into endometrial cancer aetiology and avenues for the development of new treatments.
A-to-I mRNA editing in a ferric siderophore receptor improves competition for iron inXanthomonas oryzae
Authors: Nie Wenhan , Wang Sai , Huang Jin , Xu Qin , Wang Peihong , Wu Yan , Yiming Ayizekeranmu , Ahmad Iftikhar , Zhu Bo , Chen Gongyou 
Published: December 2020

ABSTRACTAdenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by the adenosine deaminase RNA-specific family of enzymes, is a frequent post-transcriptional modification in metazoans. Research on A-to-I editing in bacteria is limited, and the importance is underestimated. In this study, we show that bacteria may use A-to-I editing as an alternative strategy to promote uptake of metabolic iron. The T408A editing event ofxfeAinXanthomonas oryzaepv.oryzicola(Xoc) senses extracytoplasmic iron and changes the hydrogen bonding network of ligand channel domains. The frequency of A-to-I RNA editing during iron-deficient conditions increased by 76.87%, which facilitated the passage of iron through the XfeA outer membrane channel. When bacteria were subjected to high iron concentrations, the percentage of A-to-I editing inxfeAdecreased, which reduced iron transport via XfeA. Furthermore, A-to-I RNA editing increased expression of multiple genes in the chemotaxis pathway, including methyl-accepting chemotaxis proteins (MCPs) that sense concentrations of exogenous ferric enterobactin (Fe-Ent) at the cytoplasmic membrane. A-to-I RNA editing helpsXocmove towards an iron-rich environment and supports our contention that editing inxfeAfacilitates entry of a ferric siderophore. Overall, our results reveal a new signaling mechanism that bacteria use to facilitate iron uptake and improve their competitiveness.
Neuroanatomical correlates of social intelligence measured by the Guilford test
Authors: Myznikov A , Zheltyakova M , Korotkov A , Kireev M , Masharipov R , Jagmurov O.Dz. , Habel U , Votinov M 
Published: December 2020

AbstractSocial interactions are a crucial aspect of human behaviour. Numerous neurophysiological studies have focused on socio-cognitive processes associated with the so-called theory of mind – the ability to attribute mental states to oneself and others. Theory of mind is closely related to social intelligence defined as a set of abilities that facilitate effective social interactions. Social intelligence encompasses multiple theory of mind components and can be measured by the Four Factor Test of Social Intelligence (the Guilford-Sullivan test). However, it is unclear whether the differences in social intelligence are reflected in structural brain differences. During the experiment, 48 healthy right-handed individuals completed the Guilford-Sullivan test. T1-weighted structural MRI images were obtained for all participants. Voxel-based morphometry analysis was performed to reveal grey matter volume differences between the two groups (24 subjects in each) – with high social intelligence scores and with low social intelligence scores, respectively. Participants with high social intelligence scores had larger grey matter volumes of the bilateral caudate, left insula, left inferior parietal lobule, inferior temporal gyrus, and middle occipital gyrus. Only the cluster in the caudate nuclei survived a cluster-level FWE correction for multiple comparisons. The obtained results suggest caudate nucleus involvement in the neural system of socio-cognitive processes, reflected by its structural characteristics.
Tolerance of an acute warming challenge declines with body mass in Nile tilapia: evidence of a link to capacity for oxygen uptake
Authors: Blasco F.R. , Taylor E.W. , Leite C.A.C. , Monteiro D.A. , Rantin F.T. , McKenzie D.J. 
Published: December 2020

AbstractIt is proposed that larger individuals within fish species may be more sensitive to global warming, due to limitations in their capacity to provide oxygen for aerobic metabolic activities. This could affect size distributions of populations in a warmer world but evidence is lacking. In Nile tilapiaOreochromis niloticus(n=18, mass range 21-313g), capacity to provide oxygen for aerobic activities (aerobic scope) was independent of mass at acclimation temperature (26°C). Tolerance of acute warming, however, declined significantly with mass when evaluated as critical temperature for fatigue from aerobic swimming (CTswim). The CTswimprotocol challenges a fish to meet the oxygen demands of constant intense aerobic exercise while their demands for basal metabolism are accelerated by incremental warming, culminating in fatigue. CTswimelicited pronounced increases in oxygen uptake but maximum rates achieved prior to fatigue declined very significantly with mass. Mass-related variation in CTswimand maximum oxygen uptake rates were positively correlated, which may indicate a causal relationship. When faced with acute thermal stress, larger fishes within populations may become constrained in their ability to swim at lower temperatures than smaller con-specifics. This could affect survival and fitness of larger fish in a world with more frequent and extreme heatwaves, with consequences for population productivity.
A thermodynamic scaling law for electrically perturbed lipid membranes: validation with the steepest-entropy-ascent framework
Authors: Goswami I. , Bielitz R. , Verbridge S.S. , von Spakovsky M.R. 
Published: December 2020

AbstractExperimental evidence has demonstrated the potential of transient pulses of electric fields to alter mammalian cell phenotypes. Strategies with these pulsed electric fields (PEFs) have been developed for clinical applications in cancer therapeutics, in-vivo decellularization, and tissue regeneration. Successful implementation of these strategies involves understanding how PEFs impact the cellular structures and, hence, cell behavior. The caveat, however, is that the PEF parameter space comprised of different pulse widths, amplitudes, and the number of pulses is very large, and design of experiments to explore all possible combinations of PEF parameters is prohibitive from a cost and time standpoint. In this study, a scaling law based on the Ising model is introduced to understand the impact of PEFs on the outer cell lipid membrane so that an understanding developed in one PEF pulse regime may be extended to another. Experimental study is used to argue for the scaling model. Next, the validity of this scaling model to predict the behavior of both thermally quenched and electrically perturbed lipid membranes is demonstrated via computational predictions made by the steepest-entropy-ascent quantum thermodynamic (SEAQT) framework. Based on the simulation results, a form of scaled PEF parameters is thus proposed for lipid membrane.
EccDNA formation is dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA double-strand break
Authors: Paulsen Teressa , Malapati Pumoli , Eki Rebeka , Abbas Tarek , Dutta Anindya 
Published: December 2020

ABSTRACTExtrachromosomal circular DNAs (eccDNA) are widespread in normal and cancer cells and are known to amplify oncogenic genes. However, the mechanisms that form eccDNA have never been fully elucidated due to the complex interactions of DNA repair pathways and lack of a method to quantify eccDNA abundance. Through the development of a sensitive and quantitative assay for eccDNA we show that the formation of eccDNA is through resection dependent repair of double-strand DNA breaks, especially micro-homology mediated end joining, and through mismatch repair. The most significant decreases in eccDNA levels occurred in cells lacking PARP1, POLQ, NBS1, RAD54, and FAN1. Further, a significant increase in eccDNA occurred in cells lacking c-NHEJ proteins DNA-PKcs, XRCC4, XLF, LIG4 and 53BP1. This suggests that when alt-NHEJ pathways are utilized to repair DNA breaks by necessity, the formation of eccDNA is increased. Induced and site-directed double-strand DNA breaks increase eccDNA formation, even from a single break. Additionally, we find that eccDNA levels accumulate as cells undergo replication in S-phase and that levels of eccDNA are decreased if DNA synthesis is prevented. Together, these results show that the bulk of eccDNA form by resection based alt-NHEJ pathways, especially during DNA replication and the repair of double-strand breaks.
Inhibition of HIV infection by structural proteins of the inner nuclear membrane is associated with reduced chromatin dynamics
Authors: Bhargava Anvita , Maurin Mathieu , Davidson Patricia M. , Jouve Mabel , Lahaye Xavier , Manel Nicolas 
Published: December 2020

AbstractThe Human Immunodeficiency Virus (HIV) enters the nucleus to establish infection. HIV interacts with nuclear pore components to cross the nuclear envelope. In contrast, the role of other proteins of the nuclear envelope in HIV infection is not yet understood. The inner nuclear transmembrane proteins SUN1 and SUN2 connect lamins in the interior of the nucleus to the cytoskeleton in the cytoplasm. Increased levels of SUN1 or SUN2 potently restrict HIV infection through an unresolved mechanism. Here, we find that SUN1 and SUN2 exhibit a differential and viral strain-specific antiviral activity HIV-1 and HIV-2. In macrophages and HeLa cells, HIV-1 and HIV-2 are respectively preferentially inhibited by SUN1 and SUN2. This specificity maps to the nucleoplasmic domain of SUN proteins, which associates with Lamin A/C and participates to the DNA damage response. We find that etoposide, a DNA-damaging drug, stimulates infection. Inhibition of the DNA damage signaling kinase ATR, which induces a DNA damage response, also enhances HIV-1 infection. The proviral effect of ATR inhibition on infection requires the HIV-1 Vpr gene. Depletion of endogenous Lamin A/C, which sensitizes cells to DNA damage, also enhances HIV-1 infection in HeLa cells. SUN1 overexpression neutralizes these proviral effects, while the antiviral effect of SUN2 is rescued by etoposide treatment. Finally, we show that inhibition of HIV-1 infection by overexpressed SUN proteins and endogenous Lamin A/C is associated with reduced internal movements of chromatin and reduced rotations of the nucleus. Altogether, these results highlight distinct antiviral activities of SUN1 and SUN2 and reveal an emerging role of nuclear movements and the DNA damage response in the control of HIV infection by structural components of the nuclear envelope.
Evolution of the Codling Moth Pheromone Through the Member of an Ancient Desaturase Expansion
Authors: Lassance Jean-Marc , Ding Bao-Jian , Löfstedt Christer 
Published: December 2020

AbstractDefining the origin of genetic novelty is central to our understanding of the evolution of novel traits. Diversification among fatty acid desaturase (FAD) genes has played a fundamental role in the introduction of structural variation in fatty acyl derivatives. Because of its central role in generating diversity in insect semiochemicals, the FAD gene family has become a model to study how gene family expansions can contribute to the evolution of lineage-specific innovations. Here we used the codling moth (Cydia pomonella) as a study system to decipher the proximate mechanism underlying the production of the Δ8Δ10 signature structure of Olethreutine moths. Biosynthesis of the codling moth sex pheromone, (E8,E10)-dodecadienol (codlemone), involves two consecutive desaturation steps, the first of which is unusual in that it generates anE9 unsaturation. The second step is also atypical: it generates a conjugated diene system from theE9 monoene C12intermediate via 1,4-desaturation. Here we describe the characterization of the FAD gene acting in codlemone biosynthesis. We identify 27 FAD genes corresponding to the various functional classes identified in Insects and Lepidoptera. These genes are distributed across theC. pomonellagenome in tandem arrays or isolated genes, indicating that the FAD repertoire consists of both ancient and recent duplications and expansions. Using transcriptomics, we show large divergence in expression domains: some genes appear ubiquitously expressed across tissue and developmental stages; others appear more restricted in their expression pattern. Functional assays using heterologous expression systems reveal that one gene, Cpo_CPRQ, which is prominently and exclusively expressed in the female pheromone gland, encodes an FAD that possesses bothE9 and Δ8Δ10-desaturation activities. Phylogenetically, Cpo_CPRQ clusters within the Lepidoptera-specific Δ10/Δ11 clade of FADs, a classic reservoir of unusual desaturase activities in moths. Our integrative approach shows that the evolution of the signature pheromone structure of Olethreutine moths relied on a gene belonging to an ancient gene expansion. Members of other expanded FAD subfamilies do not appear to play a role in chemical communication. This advises for caution when postulating the consequences of lineage-specific expansions based on genomics alone.
Integration of Magnetic Tweezers and Traction Force Microscopy for the Exploration of Matrix Rheology and Keratinocyte Mechanobiology: Model Force- and Displacement-Controlled Experiments
Authors: Moghram Waddah I. , Singh Pratibha , VandeLune Christian A. , Sander Edward A. , Selby John C. 
Published: December 2020

ABSTRACTIn this work we demonstrate the integration of magnetic tweezers (MT) with substrate deformation tracking microscopy (DTM) and traction force microscopy (TFM) for the investigation of extracellular matrix rheology and human epidermal keratinocyte mechanobiology in the context of human blistering skin diseases. Two model bead-on-gel experiments are described in which an MT device is used to apply a prescribed force or displacement waveform to a fibronectin-coated superparamagnetic bead attached to a type I collagen gel containing a layer of covalently attached red-fluorescent microspheres. Serial fast time-lapse DIC and epifluorescence image acquisitions are used to capture displacements of the bead and microspheres, respectively, in response to the applied force or displacement. Due to the large number of acquired images and the dynamic behavior of substrate microspheres observed during the experiment, new quantitative methods are developed for the tracking and filtering of microsphere displacement data, the selection of L2 regularization parameters used for TFM analysis, and the identification of time intervals within the overall image set that can be approximated as being subject to elastostatic conditions. Two major proof-of-concept applications are described in which integrated MT-DTM/TFM experiments are used to (i) estimate the elastic properties of a fibrillar type I collagen gel substrate and (ii) demonstrate how a force applied to a focal adhesion contact on the apical surface of a living keratinocyte is directly transmitted to basal cell-matrix anchoring junctions as observed by substrate deformations and incremental traction stresses that develop within the collagen subjacent to the cell.
Differential impact of maternal overnutrition and undernutrition on offspring glucose homeostasis
Authors: Adekunbi Praise B. , Ogunsola Abimbola O. , Adekunbi Daniel A. 
Published: December 2020

AbstractTo test the hypothesis that maternal undernutrition exerts a greater effect on offspring metabolic function compared to maternal overnutrition, female rats (n=10 per group) were subjected to a high calorie diet or 50 % global nutrient restriction relative to control rats on standard rat chow, for 8 weeks prior to pregnancy and during pregnancy. Birth weight was determined on the day dams were found with pups. At 3 months of age, offspring’s fasting blood glucose, serum insulin and triglyceride levels as well as glucose tolerance and insulin sensitivity were determined. A 50 % calorie restriction caused a significant weight loss in the under-nourished dams but those on high calorie diet had similar body weight as control rats. Maternal overnutrition and undernutrition significantly lowered birth weight, indicating intra-uterine growth restriction in these animals. Fasting blood glucose was significantly higher in female offspring of over-nourished dams, but neither maternal overnutrition nor undernutrition affected offspring’s glucose tolerance. Male offspring of dams exposed to maternal overnutrition or undernutrition had a significantly higher insulin level compared to control, whereas female offspring were unaffected. The development of hyperinsulinaemia in male offspring of undernourished dams was accompanied by reduced insulin sensitivity. This study demonstrates that early-life exposure to two extreme ends of the nutritional plane is associated with similar birth weight outcome but different metabolic phenotype in adulthood. Evidence of insulin resistance only in male offspring of under-nourished dams indicates differences in sex-specific metabolic effect of maternal undernutrition compared to overnutrition.