bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship Between Liver Cancer Mortality and Racial Residential Segregation Across Wisconsin Metropolitan Areas
Authors: Bemanian Amin , Cassidy Laura D. , Fraser Raphael , Laud Purushottam W. , Saeian Kia , Beyer Kirsten M. M. 
Published: February 2020

AbstractPurposeThis cross-sectional study tested relationships between racial segregation and liver cancer across several different metropolitan areas in Wisconsin.MethodsTract level liver cancer mortality rates in Wisconsin were calculated using cases from 2003-2012. Hotspot analysis was conducted and segregation scores in high, low, and baseline mortality tracts were compared with ANOVA. Spatial regression analysis was done controlling for socioeconomic advantage and rurality.ResultsBlack isolation scores were significantly higher in high mortality tracts compared to baseline and low mortality tracts, but stratification by metropolitan areas found this relationship was driven by two of the five metropolitan areas. Hispanic isolation was predictive for higher mortality in regression analysis, but this effect was not found across all metropolitan areas.ConclusionsThis study showed associations between liver cancer mortality and racial segregation, but found this relationship was not generalizable to all metropolitan areas in the study area.
Evidence of accelerated epigenetic aging in patients diagnosed with coronary artery disease: Results of the LipidCardio study
Authors: Banszerus Verena Laura , Vetter Valentin Max , König Maximilian , Landmesser Ulf , Demuth Ilja 
Published: February 2020

AbstractDNA methylation (DNAm) age acceleration, defined as the deviation of chronological and epigenetic age determined by an epigenetic clock, has been proposed as a biomarker of biological aging. To address the above hypothesis in the context of cardiovascular disease, we evaluated whether patients (N=827, mean chronological age: 69.82±11.01 years, DNAm age: 71.91±16.11, residual DNAm age acceleration: 0.00±9.65 years), who were diagnosed with obstructive coronary artery disease (CAD) by coronary angiography were aged prematurely, i.e. had an increase in the DNAm age acceleration, in comparison with patients for whom obstructive CAD was ruled out (controls).Stratified analysis yielded a significant acceleration in DNAm age (determined by a seven cytosine-phosphate-guanine epigenetic clock) in patients diagnosed with obstructive CAD, defined by at least one >50% coronary stenosis (N=588, rDNA age acceleration=0.58±9.47, corrected p= 2.05⨯10−3) compared to control subjects (N=145, residual (r)DNAm age acceleration= -3.11±10.51 years). Moreover, rDNAm age acceleration was significantly associated with systolic blood pressure (ß=0.069, 95% CI 0.027 – 0.112, p= 1.44⨯10−3), sex (ß=-2.438, 95% CI -4.591 - -0.285, p= 2.65⨯10−2), estimated glomerular filtration rate (eGFR, ß=0.040, 95% CI 0.011 – 0.069, p= 6.87⨯10−9) and smoking status (ß=-8.538, 95% CI -10.772 - -6.303, p= 2,45⨯10−13).Across studies, assessing CAD and its risk factors in the context of epigenetic age acceleration findings are remarkably inconclusive. While the here employed seven-cytosine-phosphate-guanine epigenetic clock suggests premature biological aging in CAD patients, compared to controls without coronary stenosis, its association with cardiovascular risk factors was limited.
Clinical features and laboratory inspection of novel coronavirus pneumonia (COVID-19) in Xiangyang, Hubei
Authors: Cao Weiliang , Shi Li , Chen Lin , Xu Xuemei , Wu Zirong 
Published: February 2020

AbstractBackgroundSince December 2019, a novel coronavirus pneumonia (COVID-19) rapidly spread in China, reached multiple continents currently.We aimed to reveal the infectious characteristics of COVID-19 that provide more information for the research of novel coronavirus.MethodsWe performed a retrospective study on the clinical characteristics of 128 COVID-19 cases with laboratory-confirmed from Xiangyang No 1 Hospitalad during January 2020 to 16 February 2020.ResultsFemale patients account for 53.1%. The aged below 20 years that accounts for 1.6% of overall patients. The aged in 21∼50, 51∼65, over 66 years were accounts for 44.5%, 35.1%,18.8%, respectively. In the difference age spectrum, all severe groups compared with non-severe groups were difference significantly (P < 0.01). Fever (89.8%) and Cough (67.2%) were common clinical symptoms. The rate of patients with sore throats (14.1%) was rare. The rate of chest computed tomography scan showing ground glass opacity in overall, non-severe, severe groups were 63.3%, 60.7%, 76.2%, respectively. White blood cell counts in the normal range of overall patients, but severe group patients were increased significantly (P < 0.01). Lymphocytes of overall patients were decreased. Alanine transaminase (ALT) and aspartate transaminase (AST) in the normal range of overall patients, but its were elevated in the severe group. Creatinine (CR) and blood urea nitrogen (BUN) of overall patients in the normal range. C-reactive protein (CRP) level of all patients were increased markedly, but it in the severe group was significantly higher than that in the non-severe group (P < 0.01).ConclusionsOur data provide more information that advanced age, lower lymphocytes levels at the diagnosed COVID-19 patients may be a risk factor for unfavourable prognosis. The white blood cells and C-reactive protein level elevated in severe COVID-19 patients may be accompanying bacterial infection. 2019-nCov may be carries a risk factor of impaired liver and kidney function.
Successful Correction of ALD Patient-derived iPSCs Using CRISPR/Cas9
Authors: Jung Eul Sik , Quan Zhejiu , Chang Mi-Yoon , Hong Wonjun , Kim Ji Hun , Kim Seung Hyun , You Seungkwon , Kim Dae-Sung , Jang Jiho , Lee Sang-Hun , Kim Hyongbum (Henry) , Kang Hoon Chul 
Published: February 2020

AbstractX-linked adrenoleukodystrophy (ALD) caused by theABCD1mutation, is the most common inherited peroxisomal disease. It is characterized by three phenotypes: inflammatory cerebral demyelination, progressive myelopathy, and adrenal insufficiency, but there is no genotype-phenotype correlation. Hematopoietic stem cell transplantation can only be used in a few patients in the early phase of cerebral inflammation; therefore, most affected patients have no curative option. Previously, we reported the generation of an ALD patient-derived iPSC model and its differentiation to oligodendrocytes. In this study, we have performed the first genome editing of ALD patient-derived iPSCs using homology-directed repair (HDR). The mutation site, c.1534G>A [GenBank:NM_000033.4], was corrected by introducing ssODN and the CRISPR/Cas9 system. The cell line exhibited normal ALD protein expression following genome editing. We differentiated the intermediate oligodendrocytes from mutation-corrected iPSCs and the metabolic derangement of ALD tended to correct but was not statistically significant. Mutation-corrected iPSCs from ALD patient can be used in research into the pathophysiology of and therapeutics for ALD.
The virulence of theCryptococcus neoformansVNIa-5 lineage is highly plastic and associated with isolate background
Authors: Hai Trieu Phan , Tuan Thanh Lam , Van Anh Duong , Mai Trinh Nguyen , Phu Huong Lan Nguyen , Thwaites Guy E. , Johnson Errin , Van Vinh Chau Nguyen , Baker Stephen , Ashton Philip M. , Day Jeremy N. 
Published: February 2020

AbstractCryptococcus neoformansmost frequently causes disease in immunocompromised patients. However, in Vietnam and east Asia, disease is frequently reported in apparently immunocompetent patients. We have previously shown that almost all such disease is due to a specific lineage ofC. neoformans– VNIa-5. However, in HIV-infected patients, infections due to this lineage are not associated with worse outcomes. Here, we demonstrate that the VNIa-5 lineage presents different virulence phenotypes depending on its source. Isolates derived from immunocompetent patients are more virulent than those from HIV-infected patients or the environment. Moreover, the virulence phenotype is plastic – sterile culture filtrate from highly virulent VNIa-5 strains can induce increased virulence in less virulent VNIa-5 isolates, which in turn can then induce increased virulence in their low virulence states. We present evidence that this phenomenon is driven by secreted proteins associated with extra-cellular vesicles.
Genomic Prediction with Genotype by Environment Interaction Analysis for Kernel Zinc Concentration in Tropical Maize Germplasm
Authors: Mageto Edna K. , Crossa Jose , Pérez-Rodríguez Paulino , Dhliwayo Thanda , Palacios-Rojas Natalia , Lee Michael , Guo Rui , Vicente Félix San , Zhang Xuecai , Hindu Vemuri 
Published: February 2020

ABSTRACTZinc (Zn) deficiency is a major risk factor for human health, affecting about 30% of the world’s population. To study the potential of genomic selection (GS) for maize with increased Zn concentration, an association panel and two doubled haploid (DH) populations were evaluated in three environments. Three genomic prediction models, M (M1: Environment + Line, M2: Environment + Line + Genomic, and M3: Environment + Line + Genomic + Genomic x Environment) incorporating main effects (lines and genomic) and the interaction between genomic and environment (G x E) were assessed to estimate the prediction ability (rMP) for each model. Two distinct cross-validation (CV) schemes simulating two genomic prediction breeding scenarios were used. CV1 predicts the performance of newly developed lines, whereas CV2 predicts the performance of lines tested in sparse multi-location trials. Predictions for Zn in CV1 ranged from −0.01 to 0.56 for DH1, 0.04 to 0.50 for DH2 and −0.001 to 0.47 for the association panel. For CV2,rMPvalues ranged from 0.67 to 0.71 for DH1, 0.40 to 0.56 for DH2 and 0.64 to 0.72 for the association panel. The genomic prediction model which included G x E had the highest averagerMPfor both CV1 (0.39 and 0.44) and CV2 (0.71 and 0.51) for the association panel and DH2 population, respectively. These results suggest that GS has potential to accelerate breeding for enhanced kernel Zn concentration by facilitating selection of superior genotypes.
Expecting the unexpected: the paranoid style of belief updating across species
Authors: Reed Erin J. , Uddenberg Stefan , Mathys Christoph D. , Taylor Jane R. , Groman Stephanie M. , Corlett Philip R. 
Published: February 2020

AbstractParanoia is the belief that harm is intended by others. It may arise from selective pressures to infer and avoid social threats, particularly in ambiguous or changing circumstances. We propose that uncertainty may be sufficient to elicit learning differences in paranoid individuals, without social threat. We used reversal learning behaviour and computational modelling to estimate belief updating across individuals with and without mental illness, online participants, and rats exposed to chronic methamphetamine, an elicitor of paranoia in humans. Paranoia is associated with a strong but immutable prior on volatility, accompanied by elevated sensitivity to perceived changes in the task environment. Methamphetamine exposure in rats recapitulates this impaired uncertainty-driven belief updating and rigid anticipation of a volatile environment. Our work provides evidence of fundamental, domain-general learning differences in paranoid individuals. This paradigm enables further assessment of the interplay between uncertainty and belief-updating across individuals and species.
Convergent evolution of niche structure in Northeast Pacific kelp forests
Authors: Starko Samuel , Demes Kyle W. , Neufeld Christopher J. , Martone Patrick T. 
Published: February 2020

AbstractMuch of the morphological and ecological diversity present on earth is believed to have arisen through the process of adaptive radiation. Yet, this is seemingly at odds with substantial evidence that niches tend to be similar among closely related species (i.e., niche conservatism). Identifying the relative importance of these opposing processes in different circumstances is therefore essential to our understanding of the interaction between ecological and evolutionary phenomena.In this study, we make use of recent advances in our understanding of the phylogeny of kelps (Laminariales) to investigate niche evolution in one of the most important groups of benthic habitat-forming organisms on the planet. We quantify functional traits and use community sampling data from a kelp diversity hotspot to determine which traits are responsible for the habitat (β) niche of kelps and whether they are labile or conserved across the kelp phylogeny.We find that combinations of functional traits have evolved convergently across kelp subclades and that these traits are significant predictors of community structure. Specifically, traits associated with whole-kelp structural reinforcement and material properties were found to be significantly correlated with species distributions along a gradient of wave disturbance and thus predict the outcome of environmental filtering. However, kelp assemblages were made up of species that are more phylogenetically distinct than predicted from null models (i.e., phylogenetic overdispersion), suggesting that niche partitioning along this gradient of wave disturbance has been an important driver of divergence between close relatives.These results collectively demonstrate that environmental filtering by waves plays an essential role in determining the habitat niche of kelps across local communities and further suggest that this community-level process can drive phenotypic divergence between close relatives. We propose that parallel adaptive radiation of kelp subclades has shaped the diversity and species composition of kelp forests in the Northeast Pacific and we discuss how evidence from the literature on incipient or ongoing speciation events support this hypothesis.
Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Authors: Ardakany Abbas Roayaei , Gezer Halil Tuvan , Lonardi Stefano , Ay Ferhat 
Published: February 2020

AbstractWe present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in a multi-scale representation of chromatin contact maps parametrized by the size of the smoothing kernel. When applied to high-resolution Hi-C and Micro-C data, Mustache detects loops at a wide range of genomic distances, identifying potential structural and regulatory interactions that are supported by independent conformation capture experiments as well as by known correlates of loop formation such as CTCF binding, enhancers and promoters. Unlike the commonly used HiCCUPS tool, Mustache runs on general-purpose CPUs and it is very time efficient with a runtime of only a few minutes per chromosome for 5kb-resolution human genome contact maps. Extensive experimental results show that Mustache reports two to three times the number of HiCCUPS loops, which are reproducible across replicates. It also recovers a larger proportion of published ChIA-PET and HiChIP loops than HiCCUPS. A comparative analysis of Mustache’s experimental results on Hi-C and Micro-C data confirms strong agreement between the two datasets with Micro-C providing better power for loop detection. Overall, our experimental results show that Mustache enables a more efficient and comprehensive analysis of the chromatin looping from high-resolution Hi-C and Micro-C datasets. Mustache is freely available at https://github.com/ay-lab/mustache.
Predicting TUG score from gait characteristics with video analysis and machine learning
Authors: Jian MA 
Published: February 2020

AbstractFall is a leading cause of death which suffers the elderly and society. Timed Up and Go (TUG) test is a common tool for fall risk assessment. In this paper, we propose a method for predicting TUG score from gait characteristics extracted from video with computer vision and machine learning technologies. First, 3D pose is estimated from video captured with 2D and 3D cameras during human motion and then a group of gait characteristics are computed from 3D pose series. After that, copula entropy is used to select those characteristics which are mostly associated with TUG score. Finally, the selected characteristics are fed into the predictive models to predict TUG score. Experiments on real world data demonstrated the effectiveness of the proposed method. As a byproduct, the associations between TUG score and several gait characteristics are discovered, which laid the scientific foundation of the proposed method and make the predictive models such built interpretable to clinical users.
Intracranial-EEG evidence for medial temporal pole driving amygdala activity induced by multi-modal emotional stimuli
Authors: Sonkusare Saurabh , Nguyen Vinh Thai , Moran Rosalyn , van der Meer Johan , Ren Yudan , Koussis Nikitas , Dionisio Sasha , Breakspear Michael , Guo Christine 
Published: February 2020

AbstractThe temporal pole (TP) is an associative cortical region required for complex cognitive functions such as social and emotional cognition. However, functional mapping of the TP with functional magnetic resonance imaging is technically challenging and thus understanding of its interaction with other key emotional circuitry, such as the amygdala, remain elusive. We exploited the unique advantages of stereo-electroencephalography (SEEG) to assess the responses of the TP and the amygdala during the perception of emotionally salient stimuli of pictures, music and movies. These stimuli consistently elicited high gamma responses (70-140 Hz) in both the TP and the amygdala, accompanied by functional connectivity in the low frequency range (2-12 Hz). Computational analyses suggested the TP driving this effect in the theta-alpha frequency range and which was modulated by the emotional salience of the stimuli. Of note, cross-frequency analysis indicated the phase of theta-alpha oscillations in the TP modulated the amplitude of high gamma activity in the amygdala. These results were reproducible with three types of stimuli including naturalistic stimuli suggesting a hierarchical influence of the TP over the amygdala in non-threatening stimuli.
Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change
Authors: Cooke Ira , Ying Hua , Forêt Sylvain , Bongaerts Pim , Strugnell Jan , Simakov Oleg , Zhang Jia , Field Matt A. , Rodriguez-Lanetty Mauricio , Bell Sara C. , Bourne David G. , van Oppen Madeleine JH , Ragan Mark A. , Miller David J. 
Published: February 2020

AbstractClimate change at the Pleistocene/Holocene boundary reshaped many coastal landscapes, and provides an opportunity to study recent adaptive processes in marine species and ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea level rise flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. To investigate how the coral holobiont has adapted to these conditions we first generated a highly contiguous genome assembly forAcropora tenuisbased on long-read sequencing, and then used shallow whole-genome resequencing of 148Acropora tenuiscolonies from five inshore locations to model demographic history, identify signatures of selection and profile symbiont communities. We show that corals from Magnetic Island, located in the central inshore region of the GBR, are genetically distinct from those 50-500km further north, reflecting a Pleistocene (250-600Kya) split, whereas photosymbiont genotypes differ between reefs in a pattern more likely to reflect contemporary (Holocene) conditions. We also identified loci in the coral host genome with signatures of positive selection in the northern population and used coalescent simulations to show that these are unlikely to be accounted for by demographic history. Genes at these loci have roles in a diverse range of processes that includes heterotrophic nutrition, osmotic regulation, skeletal development and the establishment and maintenance of symbiosis. Our results show that, in the case ofA. tenuisholobionts from the inshore GBR, the genomes of both the coral host and the primary photosymbiont of have been significantly shaped by their environment and illustrate the complexity of adaptations that have occurred in response to past climate change.
The C-terminal helix of BubR1 is essential for CENP-E-dependent chromosome alignment
Authors: Legal Thibault , Hayward Daniel , Gluszek-Kustusz Agata , Blackburn Elizabeth A. , Spanos Christos , Rappsilber Juri , Gruneberg Ulrike , Welburn Julie P.I. 
Published: February 2020

AbstractDuring cell division, misaligned chromosomes are captured and aligned by motors before their segregation. The CENP-E motor is recruited to polar unattached kinetochores, to facilitate chromosome alignment. The spindle checkpoint protein BubR1 has been reported as a CENP-E interacting partner, but to what extent, if at all, BubR1 contributes to CENP-E localization at kinetochores, has remained controversial. Here we define the molecular determinants that specify the interaction between BubR1 and CENP-E. The basic C-terminal helix of BubR1 is necessary but not sufficient for CENP-E interaction, while a minimal key acidic patch on the kinetochore-targeting domain of CENP-E, is also essential. We then demonstrate that BubR1 is required for the recruitment of CENP-E to kinetochores to facilitate chromosome alignment. This BubR1-CENP-E axis is critical to align chromosomes that have failed to congress through other pathways and recapitulates the major known function of CENP-E. Overall, our studies define the molecular basis and the function for CENP-E recruitment to BubR1 at kinetochores during mammalian mitosis.
Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases
Authors: De Feo Riccardo , Shatillo Artem , Sierra Alejandra , Valverde Juan Miguel , Gröhn Olli , Giove Federico , Tohka Jussi 
Published: February 2020

AbstractSkull-stripping and region segmentation are fundamental steps in preclinical magnetic resonance imaging (MRI) studies, and these common procedures are usually performed manually. We present Multi-task U-Net (MU-Net), a convolutional neural network designed to accomplish both tasks simultaneously. MU-Net achieved higher segmentation accuracy than state-of-the-art multi-atlas segmentation methods with an inference time of 0.35 seconds and no pre-processing requirements. We evaluated the performance of our network in the presence of skip connections and recently proposed framing connections, finding the simplest network to be the most effective. We tested MU-Net with an unusually large dataset combining several independent studies consisting of 1,782 mouse brain MRI volumes of both healthy and Huntington animals, and measured average Dice scores of 0.906 (striati), 0.937 (cortex), and 0.978 (brain mask). These high evaluation scores demonstrate that MU-Net is a powerful tool for segmentation and skull-stripping, decreasing inter and intra-rater variability of manual segmentation. The MU-Net code and the trained model are publicly available athttps://github.com/Hierakonpolis/MU-Net.