bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust weak antilocalization due to spin-orbital entanglement in Dirac material Sr3SnO
Authors: Nakamura H. , Huang D. , Merz J. , Khalaf E. , Ostrovsky P. , Yaresko A. , Samal D. , Takagi H. 
Published: March 2020

AbstractThe presence of both inversion (P) and time-reversal (T) symmetries in solids leads to a double degeneracy of the electronic bands (Kramers degeneracy). By lifting the degeneracy, spin textures manifest themselves in momentum space, as in topological insulators or in strong Rashba materials. The existence of spin textures with Kramers degeneracy, however, is difficult to observe directly. Here, we use quantum interference measurements to provide evidence for the existence of hidden entanglement between spin and momentum in the antiperovskite-type Dirac material Sr3SnO. We find robust weak antilocalization (WAL) independent of the position of EF. The observed WAL is fitted using a single interference channel at low doping, which implies that the different Dirac valleys are mixed by disorder. Notably, this mixing does not suppress WAL, suggesting contrasting interference physics compared to graphene. We identify scattering among axially spin-momentum locked states as a key process that leads to a spin-orbital entanglement.
Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons
Authors: Hodge Rebecca D. , Miller Jeremy A. , Novotny Mark , Kalmbach Brian E. , Ting Jonathan T. , Bakken Trygve E. , Aevermann Brian D. , Barkan Eliza R. , Berkowitz-Cerasano Madeline L. , Cobbs Charles , Diez-Fuertes Francisco , Ding Song-Lin , McCorrison Jamison , Schork Nicholas J. , Shehata Soraya I. , Smith Kimberly A. , Sunkin Susan M. , Tran Danny N. , Venepally Pratap , Yanny Anna Marie , Steemers Frank J. , Phillips John W. , Bernard Amy , Koch Christof , Lasken Roger S. , Scheuermann Richard H. , Lein Ed S. 
Published: March 2020

Abstractvon Economo neurons (VENs) are bipolar, spindle-shaped neurons restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear to be selectively vulnerable to neuropsychiatric and neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing of frontoinsula layer 5 identifies a transcriptomically-defined cell cluster that contained VENs, but also fork cells and a subset of pyramidal neurons. Cross-species alignment of this cell cluster with a well-annotated mouse classification shows strong homology to extratelencephalic (ET) excitatory neurons that project to subcerebral targets. This cluster also shows strong homology to a putative ET cluster in human temporal cortex, but with a strikingly specific regional signature. Together these results suggest that VENs are a regionally distinctive type of ET neuron. Additionally, we describe the first patch clamp recordings of VENs from neurosurgically-resected tissue that show distinctive intrinsic membrane properties relative to neighboring pyramidal neurons.
The mTOR pathway is necessary for survival of mice with short telomeres
Authors: Ferrara-Romeo Iole , Martinez Paula , Saraswati Sarita , Whittemore Kurt , Graña-Castro Osvaldo , Thelma Poluha Lydia , Serrano Rosa , Hernandez-Encinas Elena , Blanco-Aparicio Carmen , Maria Flores Juana , Blasco Maria A. 
Published: March 2020

AbstractTelomerase deficiency leads to age-related diseases and shorter lifespans. Inhibition of the mechanistic target of rapamycin (mTOR) delays aging and age-related pathologies. Here, we show that telomerase deficient mice with short telomeres (G2-Terc−/−) have an hyper-activated mTOR pathway with increased levels of phosphorylated ribosomal S6 protein in liver, skeletal muscle and heart, a target of mTORC1. Transcriptional profiling confirms mTOR activation in G2-Terc−/− livers. Treatment of G2-Terc−/− mice with rapamycin, an inhibitor of mTORC1, decreases survival, in contrast to lifespan extension in wild-type controls. Deletion of mTORC1 downstream S6 kinase 1 in G3-Terc−/− mice also decreases longevity, in contrast to lifespan extension in single S6K1−/− female mice. These findings demonstrate that mTOR is important for survival in the context of short telomeres, and that its inhibition is deleterious in this setting. These results are of clinical interest in the case of human syndromes characterized by critically short telomeres.
Molecular and cellular determinants of motor asymmetry in zebrafish
Authors: Horstick Eric J. , Bayleyen Yared , Burgess Harold A. 
Published: March 2020

AbstractAsymmetries in motor behavior, such as human hand preference, are observed throughout bilateria. However, neural substrates and developmental signaling pathways that impose underlying functional lateralization on a broadly symmetric nervous system are unknown. Here we report that in the absence of over-riding visual information, zebrafish larvae show intrinsic lateralized motor behavior that is mediated by a cluster of 60 posterior tuberculum (PT) neurons in the forebrain. PT neurons impose motor bias via a projection through the habenular commissure. Acquisition of left/right identity is disrupted by heterozygous mutations in mosaic eyes and mindbomb, genes that regulate Notch signaling. These results define the neuronal substrate for motor asymmetry in a vertebrate and support the idea that haploinsufficiency for genes in a core developmental pathway destabilizes left/right identity.
Embracing the dropouts in single-cell RNA-seq analysis
Authors: Qiu Peng 
Published: March 2020

AbstractOne primary reason that makes single-cell RNA-seq analysis challenging is dropouts, where the data only captures a small fraction of the transcriptome of each cell. Almost all computational algorithms developed for single-cell RNA-seq adopted gene selection, dimension reduction or imputation to address the dropouts. Here, an opposite view is explored. Instead of treating dropouts as a problem to be fixed, we embrace it as a useful signal. We represent the dropout pattern by binarizing single-cell RNA-seq count data, and present a co-occurrence clustering algorithm to cluster cells based on the dropout pattern. We demonstrate in multiple published datasets that the binary dropout pattern is as informative as the quantitative expression of highly variable genes for the purpose of identifying cell types. We expect that recognizing the utility of dropouts provides an alternative direction for developing computational algorithms for single-cell RNA-seq analysis.
Comparison of Fever-reducing Effects in Self-reported Data from the Mobile App: Antipyretic Drugs in Pediatric Patients
Authors: Choi Jiyun , Chang Seyun , Ahn Jong Gyun 
Published: March 2020

AbstractWe compared the fever-reducing efficacy of acetaminophen (AA), ibuprofen (IBU), and dexibuprofen (DEX) using data collected from the mobile healthcare application FeverCoach, which provides parents with guidelines for determining their child’s health condition, according to body temperature. Its dataset includes 4.4 million body temperature measurement records and 1.6 million antipyretics treatment records. Changes in body temperature over time were compared after taking one of three different antipyretics (AA, IBU, and DEX), using a one-way ANOVA followed by a post-hoc analysis. A multivariate linear model was used to further analyze the average body temperature differences, calibrating for the influences of age, weight, and sex. Children administered IBU had average body temperatures that were 0.18 °C (0.17–0.19 °C), 0.25 °C (0.24–0.26 °C), and 0.18 °C (0.17–0.20 °C) lower than those of children administered AA, at time intervals of 1–2 hours, 2–3 hours, and 3–4 hours, respectively. Similarly, children administered DEX had average body temperatures that were 0.24 °C (0.24–0.25 °C), 0.28 °C (0.27–0.29 °C), and 0.12 °C (0.10–0.13 °C) lower than those of children administered AA, at time intervals of 1–2, 2–3, and 3–4 hours, respectively. Although the data were collected from the application by non-professional parents, the analysis showed that IBU and DEX were more effective in reducing body temperature than AA was.
Economic Diversification Supported the Growth of Mongolia’s Nomadic Empires
Authors: Wilkin Shevan , Ventresca Miller Alicia , Miller Bryan K. , Spengler Robert N. , Taylor William T. T. , Fernandes Ricardo , Hagan Richard W. , Bleasdale Madeleine , Zech Jana , Ulziibayar S. , Myagmar Erdene , Boivin Nicole , Roberts Patrick 
Published: March 2020

AbstractPopulations in Mongolia from the late second millennium B.C.E. through the Mongol Empire are traditionally assumed, by archaeologists and historians, to have maintained a highly specialized horse-facilitated form of mobile pastoralism. Until recently, a dearth of direct evidence for prehistoric human diet and subsistence economies in Mongolia has rendered systematic testing of this view impossible. Here, we present stable carbon and nitrogen isotope measurements of human bone collagen, and stable carbon isotope analysis of human enamel bioapatite, from 137 well-dated ancient Mongolian individuals spanning the period c. 4400 B.C.E. to 1300 C.E. Our results demonstrate an increase in consumption of C4plants beginning at c. 800 B.C.E., almost certainly indicative of millet consumption, an interpretation supported by archaeological evidence. The escalating scale of millet consumption on the eastern Eurasian steppe over time, and an expansion of isotopic niche widths, indicate that historic Mongolian empires were supported by a diversification of economic strategies rather than uniform, specialized pastoralism.
Generation of a conditional Flpo/FRT mouse model expressing constitutively active TGFβ in fibroblasts
Authors: Cardot-Ruffino Victoire , Chauvet Véronique , Caligaris Cassandre , Bertrand-Chapel Adrien , Chuvin Nicolas , Pommier Roxane M. , Valcourt Ulrich , Vincent David F. , Martel Sylvie , Aires Sophie , Kaniewski Bastien , Dubus Pierre , Cassier Philippe , Sentis Stéphanie , Bartholin Laurent 
Published: March 2020

AbstractTransforming growth factor (TGFβ) is a secreted factor, which accumulates in tissues during many physio- and pathological processes such as embryonic development, wound healing, fibrosis and cancer. In order to analyze the effects of increased microenvironmental TGFβ concentration in vivo, we developed a conditional transgenic mouse model (Flpo/Frt system) expressing bioactive TGFβ in fibroblasts, a cell population present in the microenvironment of almost all tissues. To achieve this, we created the genetically-engineered [Fsp1-Flpo; FSFTGFβCA] mouse model. The Fsp1-Flpo allele consists in the Flpo recombinase under the control of the Fsp1 (fibroblast-specific promoter 1) promoter. The FSFTGFβCA allele consists in a transgene encoding a constitutively active mutant form of TGFβ (TGFβCA) under the control of a Frt-STOP-Frt (FSF) cassette. The FSFTGFβCA allele was created to generate this model, and functionally validated by in vitro, ex vivo and in vivo techniques. [Fsp1-Flpo; FSFTGFβCA] animals do not present any obvious phenotype despite the correct expression of TGFβCA transgene in fibroblasts. This [Fsp1-Flpo; FSFTGFβCA] model is highly pertinent for future studies on the effect of increased microenvironmental bioactive TGFβ concentrations in mice bearing Cre-dependent genetic alterations in other compartments (epithelial or immune compartments for instance). These dual recombinase system (DRS) approaches will enable scientists to study uncoupled spatiotemporal regulation of different genetic alterations within the same mouse, thus better replicating the complexity of human diseases.
Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives
Authors: Jo Hye-Yeong , Han Hyo-Won , Jung Inuk , Ju Ji Hyeon , Park Soon-Jung , Moon Sunghwan , Geum Dongho , Kim Hyemin , Park Han-Jin , Kim Sun , Stacey Glyn N. , Koo Soo Kyung , Park Mi-Hyun , Kim Jung-Hyun 
Published: March 2020

AbstractAlthough human induced pluripotent stem cell (hiPSC) lines are karyotypically normal, they retain the potential for mutation in the genome. Accordingly, intensive and relevant quality controls for clinical-grade hiPSCs remain imperative. As a conceptual approach, we performed RNA-seq-based broad-range genetic quality tests on GMP-compliant human leucocyte antigen (HLA)-homozygous hiPSCs and their derivatives under postdistribution conditions to investigate whether sequencing data could provide a basis for future quality control. We found differences in the degree of single-nucleotide polymorphism (SNP) occurring in cells cultured at three collaborating institutes. However, the cells cultured at each centre showed similar trends, in which more SNPs occurred in late-passage hiPSCs than in early-passage hiPSCs after differentiation. In eSNP karyotyping analysis, none of the predicted copy number variations (CNVs) were identified, which confirmed the results of SNP chip-based CNV analysis. HLA genotyping analysis revealed that each cell line was homozygous for HLA-A, HLA-B, and DRB1 and heterozygous for HLA-DPB type. Gene expression profiling showed a similar differentiation ability of early- and late-passage hiPSCs into cardiomyocyte-like, hepatic-like, and neuronal cell types. However, time-course analysis identified five clusters showing different patterns of gene expression, which were mainly related to the immune response. In conclusion, RNA-seq analysis appears to offer an informative genetic quality testing approach for such cell types and allows the early screening of candidate hiPSC seed stocks for clinical use by facilitating safety and potential risk evaluation.
Microarray analyses reveal strain-specific antibody responses to Plasmodium falciparum apical membrane antigen 1 variants following natural infection and vaccination
Authors: Bailey Jason A. , Berry Andrea A. , Travassos Mark A. , Ouattara Amed , Boudova Sarah , Dotsey Emmanuel Y. , Pike Andrew , Jacob Christopher G. , Adams Matthew , Tan John C. , Bannen Ryan M. , Patel Jigar J. , Pablo Jozelyn , Nakajima Rie , Jasinskas Algis , Dutta Sheetij , Takala-Harrison Shannon , Lyke Kirsten E. , Laurens Matthew B. , Niangaly Amadou , Coulibaly Drissa , Kouriba Bourema , Doumbo Ogobara K. , Thera Mahamadou A. , Felgner Philip L. , Plowe Christopher V. 
Published: March 2020

AbstractVaccines based on Plasmodium falciparum apical membrane antigen 1 (AMA1) have failed due to extensive polymorphism in AMA1. To assess the strain-specificity of antibody responses to malaria infection and AMA1 vaccination, we designed protein and peptide microarrays representing hundreds of unique AMA1 variants. Following clinical malaria episodes, children had short-lived, sequence-independent increases in average whole-protein seroreactivity, as well as strain-specific responses to peptides representing diverse epitopes. Vaccination resulted in dramatically increased seroreactivity to all 263 AMA1 whole-protein variants. High-density peptide analysis revealed that vaccinated children had increases in seroreactivity to four distinct epitopes that exceeded responses to natural infection. A single amino acid change was critical to seroreactivity to peptides in a region of AMA1 associated with strain-specific vaccine efficacy. Antibody measurements using whole antigens may be biased towards conserved, immunodominant epitopes. Peptide microarrays may help to identify immunogenic epitopes, define correlates of vaccine protection, and measure strain-specific vaccine-induced antibodies.
Deep learning applied to hyperspectral endoscopy for online spectral classification
Authors: Grigoroiu Alexandru , Yoon Jonghee , Bohndiek Sarah E. 
Published: March 2020

AbstractHyperspectral imaging (HSI) is being explored in endoscopy as a tool to extract biochemical information that may improve contrast for early cancer detection in the gastrointestinal tract. Motion artefacts during medical endoscopy have traditionally limited HSI application, however, recent developments in the field have led to real-time HSI deployments. Unfortunately, traditional HSI analysis methods remain unable to rapidly process the volume of hyperspectral data in order to provide real-time feedback to the operator. Here, a convolutional neural network (CNN) is proposed to enable online classification of data obtained during HSI endoscopy. A five-layered CNN was trained and fine-tuned on a dataset of 300 hyperspectral endoscopy images acquired from a planar Macbeth ColorChecker chart and was able to distinguish between its 18 constituent colors with an average accuracy of 94.3% achieved at 8.8 fps. Performance was then tested on a set of images simulating an endoscopy environment, consisting of color charts warped inside a rigid tube mimicking a lumen. The algorithm proved robust to such variations, with classification accuracies over 90% being obtained despite the variations, with an average drop in accuracy of 2.4% being registered at the points of longest working distance and most inclination. For further validation of the color-based classification system, ex vivo videos of a methylene blue dyed pig esophagus and images of different disease stages in the human esophagus were analyzed, showing spatially distinct color classifications. These results suggest that the CNN has potential to provide color-based classification during real-time HSI in endoscopy.
Evolutionary Traits that Enable Scleractinian Corals to Survive Mass Extinction Events
Authors: Dishon Gal , Grossowicz Michal , Krom Michael , Guy Gilad , Gruber David F. , Tchernov Dan 
Published: March 2020

AbstractScleractinian “stony” corals are major habitat engineers, whose skeletons form the framework for the highly diverse, yet increasingly threatened, coral reef ecosystem. Fossil coral skeletons also present a rich record that enables paleontological analysis of coral origins, tracing them back to the Triassic (~241 Myr). While numerous invertebrate lineages were eradicated at the last major mass extinction boundary, the Cretaceous-Tertiary/K-T (66 Myr), a number of Scleractinian corals survived. We review this history and assess traits correlated with K-T mass extinction survival. Disaster-related “survival” traits that emerged from our analysis are: (1) deep water residing (>100 m); (2) cosmopolitan distributions, (3) non-symbiotic, (4) solitary or small colonies and (5) bleaching-resistant. We then compared these traits to the traits of modern Scleractinian corals, using to IUCN Red List data, and report that corals with these same survival traits have relatively stable populations, while those lacking them are presently decreasing in abundance and diversity. This shows corals exhibiting a similar dynamic survival response as seen at the last major extinction, the K-T. While these results could be seen as promising, that some corals may survive the Anthropocene extinction, they also highlight how our relatively-fragile Primate order does not possess analogous “survival” characteristics, nor have a record of mass extinction survival as some corals are capable.
TASH: Toolbox for the Automated Segmentation of Heschl’s gyrus
Authors: Dalboni da Rocha Josué Luiz , Schneider Peter , Benner Jan , Santoro Roberta , Atanasova Tanja , Van De Ville Dimitri , Golestani Narly 
Published: March 2020

AbstractAuditory cortex volume and shape differences have been observed in the context of phonetic learning, musicianship and dyslexia. Heschl’s gyrus, which includes primary auditory cortex, displays large anatomical variability across individuals and hemispheres. Given this variability, manual labelling is the gold standard for segmenting HG, but is time consuming and error prone. Our novel toolbox, called ‘Toolbox for the Automated Segmentation of HG’ or TASH, automatically segments HG in brain structural MRI data, and extracts measures including its volume, surface area and cortical thickness. TASH builds upon FreeSurfer, which provides an initial segmentation of auditory regions, and implements further steps to perform finer auditory cortex delineation. We validate TASH by showing significant relationships between HG volumes obtained using manual labelling and using TASH, in three independent datasets acquired on different scanners and field strengths, and by showing good qualitative segmentation. We also present two applications of TASH, demonstrating replication and extension of previously published findings of relationships between HG volumes and (a) phonetic learning, and (b) musicianship. In sum, TASH effectively segments HG in a fully automated and reproducible manner, opening up a wide range of applications in the domains of expertise, disease, genetics and brain plasticity.
Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: A Pilot Study Incorporating Microscopy and Sequencing
Authors: van de Wijgert Janneke H. H. M. , Verwijs Marijn C. , Agaba Stephen K. , Bronowski Christina , Mwambarangwe Lambert , Uwineza Mireille , Lievens Elke , Nivoliez Adrien , Ravel Jacques , Darby Alistair C. 
Published: March 2020

AbstractBacterial vaginosis (BV) is associated with HIV acquisition and adverse pregnancy outcomes. Recurrence after metronidazole treatment is high. HIV-negative, non-pregnant Rwandan BV patients were randomized to four groups (n = 17/group) after seven-day oral metronidazole treatment: behavioral counseling only (control), or counseling plus intermittent use of oral metronidazole, Ecologic Femi+ vaginal capsule (containing multiple Lactobacillus and one Bifidobacterium species), or Gynophilus LP vaginal tablet (L. rhamnosus 35) for two months. Vaginal microbiota assessments at all visits included Gram stain Nugent scoring and 16S rRNA gene qPCR and HiSeq sequencing. All interventions were safe. BV (Nugent 7–10) incidence was 10.18 per person-year at risk in the control group, and lower in the metronidazole (1.41/person-year; p = 0.004), Ecologic Femi+ (3.58/person-year; p = 0.043), and Gynophilus LP groups (5.36/person-year; p = 0.220). In mixed effects models adjusted for hormonal contraception/pregnancy, sexual risk-taking, and age, metronidazole and Ecologic Femi+ users, each compared to controls, had higher Lactobacillus and lower BV-anaerobes estimated concentrations and/or relative abundances, and were less likely to have a dysbiotic vaginal microbiota type by sequencing. Inter-individual variability was high and effects disappeared soon after intervention cessation. Lactobacilli-based vaginal probiotics warrant further evaluation because, in contrast to antibiotics, they are not expected to negatively affect gut microbiota or cause antimicrobial resistance.