bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Model Order Choice on the Results of Parallel Independent Component Analysis
Authors: Jensen D. M. , Zendehrouh E. , Liu J. , Calhoun V. D. , Turner J. A. 
Published: September 2020

AbstractParallel independent component analysis (pICA) is a data-driven method that identifies the maximally independent components of multiple imaging modalities while simultaneously investigating the strength of their correlations. Researchers using pICA are given the option to use the suggested model order calculated by the minimum descriptive length (MDL) algorithm, or they can choose their own model order. To date, there are no suggested guidelines for this choice. To test the sensitivity of pICA to the selection of model order, we applied it to a well-researched brain disorder, schizophrenia, looking at the correlations between patterns of grey matter volume (GM) volume and white matter integrity, measured using fractional anisotropy (FA). We varied model orders from low to high, and tested the sensitivity to disorder effects (cases vs controls), similarity of spatial maps identified across model orders, consolidation or distribution effects related to model order selection, and the performance of the minimum descriptive length (MDL) algorithm. The pICA results (multimodal analysis) were also compared to the ICA (unimodal analysis) for each imaging modality. Across model orders, there was consistent sensitivity to disorder effects, and clustered patterns of spatial maps for both the GM and FA reflecting those differences. The MDL-estimated model order captured the majority, but not all, of the spatial patterns present in the GM and FA. There was not the expected consolidation of spatial maps at lower model orders, nor the distribution of spatial maps at higher model orders. The spatial patterns identified in the ICA closely resemble those found in the pICA, although lacking the benefit of the optimization algorithm, were not as highly correlated. This offers some insight and guidance for researchers interested in using pICA with regard to selecting model order for their particular analysis of multiple imaging modalities.
Fully Automated Detection of Paramagnetic Rims in Multiple Sclerosis Lesions on 3T Susceptibility-Based MR Imaging
Authors: Lou Carolyn , Sati Pascal , Absinta Martina , Clark Kelly , Dworkin Jordan D. , Valcarcel Alessandra M. , Schindler Matthew K. , Reich Daniel S. , Sweeney Elizabeth M. , Shinohara Russell T. 
Published: September 2020

AbstractBackground and PurposeThe presence of a paramagnetic rim around a white matter lesion has recently been shown to be a hallmark of a particular pathological type of multiple sclerosis (MS) lesion. Increased prevalence of these paramagnetic rim lesions (PRLs) is associated with a more severe disease course in MS. The identification of these lesions is time-consuming to perform manually. We present a method to automatically detect PRLs on 3T T2*-phase images.MethodsT1-weighted, T2-FLAIR, and T2*-phase MRI of the brain were collected at 3T for 19 subjects with MS. The images were then processed with lesion segmentation, lesion center detection, lesion labelling, and lesion-level radiomic feature extraction. A total of 877 lesions were identified, 118 (13%) of which contained a paramagnetic rim. We divided our data into a training set (15 patients, 673 lesions) and a testing set (4 patients, 204 lesions). We fit a random forest classification model on the training set and assessed our ability to classify lesions as PRL on the test set.ResultsThe number of PRLs per subject identified via our automated lesion labelling method was highly correlated with the gold standard count of PRLs per subject, r = 0.91 (95% CI [0.79, 0.97]). The classification algorithm using radiomic features can classify a lesion as PRL or not with an area under the curve of 0.80 (95% CI [0.67, 0.86]).ConclusionThis study develops a fully automated technique for the detection of paramagnetic rim lesions using standard T1 and FLAIR sequences and a T2*phase sequence obtained on 3T MR images.HighlightsA fully automated method for both the identification and classification of paramagnetic rim lesions is proposed.Radiomic features in conjunction with machine learning algorithms can accurately classify paramagnetic rim lesions.Challenges for classification are largely driven by heterogeneity between lesions, including equivocal rim signatures and lesion location.
Defining the role of asymptomatic SARS-CoV-2 transmission – a living systematic review
Authors: Qiu Xueting , Nergiz Ali Ihsan , Maraolo Alberto Enrico , Bogoch Isaac I. , Low Nicola , Cevik Muge 
Published: September 2020

AbstractBackgroundReports suggest that asymptomatic individuals (those with no symptoms at all throughout the infection) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are infectious, but the extent of asymptomatic transmission requires further understanding.PurposeThis living review aims to critically appraise available data about secondary attack rates from people with asymptomatic and pre-symptomatic SARS-CoV-2 infection.Data sourcesMedline, EMBASE, China Academic Journals full-text database (CNKI), and preprint servers were searched from 30 December 2019 to 3 July 2020 using relevant MESH terms.Study selectionStudies that report on contact tracing of index cases with asymptomatic or pre-symptomatic SARS-CoV-2 infection, in either English or Chinese were included.Data extractionTwo authors independently extracted data and assessed study quality and risk of bias. We calculated the secondary attack rate as the number of contacts with SARS-CoV-2, divided by the number of contacts tested.Data synthesisOf 928 studies identified, 19 were included. Secondary attack rates from asymptomatic index cases ranged from 0% to 2.8% (9 studies). Pre-symptomatic secondary attack rates ranged from 0.7% to 31.8% (10 studies). The highest secondary attack rates were found in contacts who lived in the same household as the index case. Other activities associated with transmission were group activities such as sharing meals or playing board games with the index case.LimitationsWe excluded some studies because the index case or number of contacts were unclear. Owing to the anticipated heterogeneity, we did not produce a summary estimate of the included studies.ConclusionAsymptomatic patients can transmit SARS-CoV-2 to others, but our findings indicate that such individuals are responsible for fewer secondary infections than people with symptoms in the same studies.Systematic review registrationPROSPERO CRD42020188168FundingNo funding was received
Point Sensitivity of the Multi-target Stool DNA Test for Colorectal Cancer Screening in Individuals Ages 45-49 Years
Authors: Domanico Michael , Statz Sandra , Weiser Emily , Berger Barry M , Limburg Paul 
Published: September 2020

AbstractBackgroundMost colorectal cancer (CRC) screening tests have not been rigorously studied in younger age groups.AimsTo estimate sensitivity of the multi-target stool DNA (mt-sDNA) test in patients ages 45-49 years.MethodsWe identified archived stool samples (Exact Sciences; Madison, WI) from individuals ages 45-49 years who had completed an index colonoscopy and had confirmed diagnoses of CRC or advanced precancerous lesions (APL; defined as high-grade dysplasia, >25% villous morphology, or ≥1 cm in size [conventional adenoma or serrated lesion]). Data annotation referent to potential CRC risk factors, other than age, was limited. Stool samples were collected at least 7 days after the index colonoscopy, prior to lesion excision or treatment. Stool samples were processed and analyzed per established laboratory protocols for the mt-sDNA assay. Mt-sDNA test sensitivity for CRC, APL, and CRC+APL was estimated from the available sample set. Samples were collected from 2010-2013 (NCT01260168) and 2014-2017 (NCT02503631), with sample testing and analysis in 2019.ResultsStool samples were analyzed from 19 eligible subjects, 13 with CRC and 6 with APL. Estimated mt-sDNA test sensitivity for CRC, APL, and CRC+APL were 92%, 83%, and 89%, respectively.ConclusionsIn this small pilot study using existing archived stool samples from subjects ages 45-49 years, mt-sDNA test sensitivity was similar to previously reported estimates for individuals ages ≥50 years. These results support the application of mt-sDNA screening to 76 average-risk patients beginning at age 45 years. Larger studies are needed to confirm and extend these findings.
Cross-reactive antibody responses against SARS-CoV-2 and seasonal common cold coronaviruses
Authors: Klompus Shelley , Leviatan Sigal , Vogl Thomas , Kalka Iris N. , Godneva Anastasia , Shinar Eilat , Weinberger Adina , Segal Eran 
Published: September 2020

AbstractBeyond SARS-CoV-2, six more coronaviruses infect humans (hCoVs), four of which cause only mild symptoms (seasonal/common cold hCoVs) 12. Previous exposures to seasonal hCoVs may elicit immunological memory that could benefit the course of SARS-CoV-2 infections 3. While cross-reactive T cells epitopes of SARS-CoV-2 and seasonal hCoVs have been reported in individuals unexposed to SARS-CoV-2 4-6, potential antibody-based cross-reactivity is incompletely understood.Here, we have probed for high resolution antibody binding against all hCoVs represented as 1,539 peptides with a phage-displayed 7 antigen library. We detected broad serum antibody responses against peptides of seasonal hCoVs in up to 75% of individuals. Recovered COVID-19 patients exhibited distinct antibody repertoires targeting variable SARS-CoV-2 epitopes, and could be accurately classified from unexposed individuals (AUC=0.96). Up to 50% of recovered patients also mounted antibody responses against unique epitopes of seasonal hCoV-OC43, that were not detectable in unexposed individuals.These results indicate substantial interindividual variability and antibody cross-reactivity between hCoVs from the direction of SARS-CoV-2 infections towards seasonal hCoVs. Our accurate high throughput assay allows profiling preexisting antibody responses against seasonal hCoVs cost-effectively and could inform on their protective nature against SARS-CoV-2.
Effects of Public Health Interventions on the Epidemiological Spread During the First Wave of the COVID-19 Outbreak in Thailand
Authors: Triukose Sipat , Nitinawarat Sirin , Satian Ponlapat , Somboonsavatdee Anupap , Chotikarn Ponlachart , Thammasanya Thunchanok , Wanlapakorn Nasamon , Sudhinaraset Natthinee , Boonyamalik Pitakpol , Kakhong Bancha , Poovorawan Yong 
Published: September 2020

AbstractA novel infectious respiratory disease was recognized in Wuhan (Hubei Province, China) in December 2019. In February 2020, the disease was named “coronavirus disease 2019” (COVID-19). COVID-19 became a pandemic in March 2020, and, since then, different countries have implemented a broad spectrum of policies. Thailand is considered to be among the top countries in handling its first wave of the outbreak -- 12 January to 31 July 2020. Here, we illustrate how Thailand tackled the COVID-19 outbreak, particularly the effects of public health interventions on the epidemiologic spread. This study shows how the available data from the outbreak can be analyzed and visualized to quantify the severity of the outbreak, the effectiveness of the interventions, and the level of risk of allowed activities during an easing of a “lockdown.” This study shows how a well-organized governmental apparatus can overcome the havoc caused by a pandemic.
SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence
Authors: Neault Nafisa , Baig Aiman Tariq , Graber Tyson E. , D’Aoust Patrick M. , Mercier Elisabeth , Alexandrov Ilya , Crosby Daniel , Baird Stephen , Mayne Janice , Pounds Thomas , MacKenzie Malcolm , Figeys Daniel , MacKenzie Alex , Delatolla Robert 
Published: September 2020

ABSTRACTThe COVID-19 pandemic has given rise to diverse approaches to track infections. The causative agent, SARS-CoV-2, is a fecally-shed RNA virus, and many groups have assayed wastewater for viral RNA fragments by quantitative reverse transcription polymerase chain reaction (qRT-PCR) as a proxy for COVID-19 prevalence in the community. Most groups report low levels of viral RNA that often skirt the method’s theoretical limits of detection and quantitation. Here, we demonstrate the presence of SARS-CoV-2 structural proteins in wastewater using traditional immunoblotting and quantitate them from wastewater solids using an immuno-linked PCR method called Multiplex Paired-antibody Amplified Detection (MPAD). MPAD demonstrated facile detection of SARS-CoV-2 proteins compared with SARS-CoV-2 RNA via qRT-PCR in wastewater. In this longitudinal study, we corrected for stochastic variability inherent to wastewater-based epidemiology using multiple fecal content protein biomarkers. These normalized SARS-CoV-2 protein data correlated well with public health metrics. Our method of assaying SARS-CoV-2 protein from wastewater represents a promising and sensitive epidemiological tool to assess prevalence of fecally-shed pathogens in the community.
Mechanical Loading Recovers Bone but not Muscle Lost During Unloading
Authors: Krause Andrew R. , Speacht Toni A. , Steiner Jennifer L. , Lang Charles H. , Donahue Henry J. 
Published: September 2020

AbstractSpace travel and prolonged bed rest are examples of mechanical unloading that induce significant muscle and bone loss. To explore interactions between skeletal bone and muscle during reloading, we hypothesized that acute external mechanical loading of bone in combination with re-ambulation facilitates proportional recovery of bone and muscle lost during hind limb suspension (HLS) unloading. Adult male C57Bl/6J mice were assigned to a HLS or time-matched ground control (GC) group. After 2-weeks of HLS, separate groups of mice were studied at day 14 (no re-ambulation), day 28 (14 days re-ambulation) and day 56 (42 days re-ambulation); throughout the re-ambulation period, one limb received mechanical loading and the contralateral limb served as an internal control. HLS induced loss of trabecular bone volume (BV/TV; -51%±2%) and muscle weight (-15%±2%) compared to GC at day 14. At day 28, the left tibia (re-ambulation only) of HLS mice had recovered 20% of BV/TV lost during HLS, while the right tibia (re-ambulation and acute external mechanical loading) recovered to GC values of BV/TV (∼100% recovery). At day 56, the right tibia continued to recover bone for some outcomes (trabecular BV/TV, trabecular thickness), while the left limb did not. Cortical bone displayed a delayed response to HLS, with a 10% greater decrease in BV/TV at day 28 compared to day 14. In contrast to bone, acute external mechanical loading during the re-ambulation period did not significantly increase muscle mass or protein synthesis in the gastrocnemius, compared to re-ambulation alone.
Butyribacter intestinigen. nov., sp. nov., a butyric acid-producing bacterium of the familyLachnospiraceaeisolated from the human faeces, and reclassification ofAcetivibrio ethanolgignensasAcetanaerobacter ethanolgignensgen. nov., comb. nov
Authors: Xue Wenbin , Lin Xiaoqian , Lv Mei , Luo Guangwen , Dai Ying , Sun Haipeng , Xiao Liang , Zou Yuanqiang 
Published: September 2020

AbstractA novel, non-motile, Gram-stain-positive, non-spore-forming, obligate anaerobic bacterium, designated strain TF01-11T, was isolated from human faeces. The isolate was characterized by phylogenetic and phenotypic properties, as well as by determination of its whole genome sequence. The growth temperature and pH ranges were 30–42 °C and 6.0–8.5, respectively. The end products of glucose fermentation were butyric acid and a small amount of acetic acid. The genome was estimated to be 3.61Mbp with G+C content of 36.79 mol%. Genes related to biosynthesis of diaminopimelic acid, polar lipids, polyamines, teichoic and lipoteichoic acids were present. The predominant fatty acids were C16:0(37.9 %), C14:0(16.4 %), C13:0OH/iso-C15:1H (11.1 %) and C18:1ω9c(10.6 %). Phylogenetic analyses based on 16S rRNA gene sequences, the isolate was a member of familyLachnospiraceae, with the highest sequence similarity to the type strain ofRoseburia intestinalisDSM 14610Tat 92.18 % followed byAcetivibrio ethanolgignensATCC 33324Tat 91.99 %. The average nucleotide identity (ANI) calculated for the genomes between strain TF01-11Tand these closest relatives were 70.5 % and 68.1 %. Based on results of phenotypic characteristics and genotypic properties presented in this study, strain TF01-11Trepresent a novel species in a new genus, for which the nameButyribacter intestinigen. nov., sp. nov. is proposed. The type strain of the type species is TF01-11T(CGMCC 1.5203T= CGMCC 10984T= DSM 105140T). In addition,Acetivibrio ethanolgignensis proposed to be reclassified asAcetanaerobacter ethanolgignensgen. nov., comb. nov.
Genome-wide maps of enhancer regulation connect risk variants to disease genes
Authors: Nasser Joseph , Bergman Drew T. , Fulco Charles P. , Guckelberger Philine , Doughty Benjamin R. , Patwardhan Tejal A. , Jones Thouis R. , Nguyen Tung H. , Ulirsch Jacob C. , Natri Heini M. , Weeks Elle M. , Munson Glen , Kane Michael , Kang Helen Y. , Cui Ang , Ray John P. , Eisenhaure Tom M. , Mualim Kristy , Collins Ryan L. , Dey Kushal , Price Alkes L. , Epstein Charles B. , Kundaje Anshul , Xavier Ramnik J. , Daly Mark J. , Huang Hailiang , Finucane Hilary K. , Hacohen Nir , Lander Eric S. , Engreitz Jesse M. 
Published: September 2020

AbstractGenome-wide association studies have now identified tens of thousands of noncoding loci associated with human diseases and complex traits, each of which could reveal insights into biological mechanisms of disease. Many of the underlying causal variants are thought to affect enhancers, but we have lacked genome-wide maps of enhancer-gene regulation to interpret such variants. We previously developed the Activity-by-Contact (ABC) Model to predict enhancer-gene connections and demonstrated that it can accurately predict the results of CRISPR perturbations across several cell types. Here, we apply this ABC Model to create enhancer-gene maps in 131 cell types and tissues, and use these maps to interpret the functions of fine-mapped GWAS variants. For inflammatory bowel disease (IBD), causal variants are >20-fold enriched in enhancers in particular cell types, and ABC outperforms other regulatory methods at connecting noncoding variants to target genes. Across 72 diseases and complex traits, ABC links 5,036 GWAS signals to 2,249 unique genes, including a class of 577 genes that appear to influence multiple phenotypes via variants in enhancers that act in different cell types. Guided by these variant-to-function maps, we show that an enhancer containing an IBD risk variant regulates the expression ofPPIFto tune mitochondrial membrane potential. Together, our study reveals insights into principles of genome regulation, illuminates mechanisms that influence IBD, and demonstrates a generalizable strategy to connect common disease risk variants to their molecular and cellular functions.
PhenoImage: an open-source GUI for plant image analysis
Authors: Zhu Feiyu , Saluja Manny , Singh Jaspinder , Paul Puneet , Sattler Scott E. , Staswick Paul , Walia Harkamal , Yu Hongfeng 
Published: September 2020

AbstractHigh-throughput genotyping coupled with molecular breeding approaches has dramatically accelerated crop improvement programs. More recently, improved plant phenotyping methods have led to a shift from manual measurements to automated platforms with increased scalability and resolution. Considerable effort has also gone into the development of large-scale downstream processing of the imaging datasets derived from high-throughput phenotyping (HTP) platforms. However, most available tools require some programing skills. We developedPhenoImage– an open-source GUI based cross-platform solution for HTP image processing with the aim to make image analysis accessible to users with either little or no programming skills. The open-source nature provides the possibility to extend its usability to meet user-specific requirements. The availability of multiple functions and filtering parameters provides flexibility to analyze images from a wide variety of plant species and platforms.PhenoImagecan be run on a personal computer as well as on high-performance computing clusters. To test the efficacy of the application, we analyzed the LemnaTec Imaging system derived RGB and fluorescence shoot images from two plant species: sorghum and wheat differing in their physical attributes. In the study, we discuss the development, implementation, and working of thePhenoImage.HighlightPhenoImageis an open-source application designed for analyzing images derived from high-throughput phenotyping.
Whole-brain functional connectivity neuromarkers uncover the cognitive recovery scheme for overt hepatic encephalopathy after liver transplantation
Authors: Cheng Yue , Shen Wen , Xu Junhai , Amey Rachel C. , Huang Li-Xiang , Zhang Xiao-Dong , Li Jing-Li , Akhavan Cameron , Duffy Ben A. , Jiang Wenjuan , Liu Mengting , Kim Hosung 
Published: September 2020

AbstractNeurocognitive impairment is present in cirrhosis and may be more severe in cirrhosis with the overt hepatic encephalopathy (OHE). Liver transplantation (LT) may reverse the impaired brain function. MRI of resting-state functional connectivity can help unravel the underlying mechanisms that lead to these cognitive deficits and recovery. Sixty-four cirrhotic patients (28 with OHE; 36 without) and 32 healthy controls were recruited for resting-state fMRI. The patients were scanned before and after LT. We evaluated pre- and postsurgical neurocognitive performance in cirrhotic patients using psychomotor tests, i.e. number connection test (NCT) and digit symbol test (DST). Network-based statistics found significant disrupted connectivity in both groups of cirrhosis with OHE and without compared to controls. However, the presurgical connectivity disruption in patients with OHE was included in a greater number of connections than those without (65 vs. 17). The decrease in FC for both OHE and non-OHE patient groups was reversed to the level of controls after LT. An additional hyperconnected network (i.e., higher than controls) was observed in OHE patients after LT (p=0.009). Regarding the neural-behavior relationship, the functional network that predicted cognitive performance in healthy individuals, showed no correlation in presurgical cirrhotic patients. Such an impaired neural-behavior relationship was re-established after LT for non-OHE patients but not for OHE. OHE patients displayed abnormal hyperconnectivity and persistently impaired neural-behavior relationship after LT. Our results suggest that patients with OHE may undergo a different trajectory of postsurgical neurofunctional recovery in comparison to those without, which needs further clarification in the future study.