bluuebunny/crossref_metadata_2025_split huggingface dataset:
A neural signature of automatic lexical access in bilinguals
Authors: Aristei Sabrina , Lochy Aliette , Rossion Bruno , Schiltz Christine 
Published: July 2021

AbstractBilingualism is often associated with beneficial effects on cognitive control and top-down processes. The present study aimed at bypassing these processes to assess automatic visual word recognition in bilinguals. Using fast periodic visual stimulation, we recorded frequency-tagged word-selective EEG responses in French monolinguals and late bilinguals (German native, French as second language). Words were presented centrally within rapid (10 Hz) sequences of letter strings varying in word-likeness, i.e., consonant strings, non-words, pseudo-words, while participants performed an orthogonal task. Automatic word-selective brain responses in the occipito-temporal cortex arose almost exclusively for the languages mastered by participants: two in bilinguals vs. one in monolinguals. Importantly, the amplitude of bilinguals’ responses to words within consonant strings were unaffected by the native vs. late-learnt status of the language. Furthermore, for all and only known languages, word-selective responses were reduced by embedding them in pseudo-words relative to non-words, both derived from the same language as the words. This word-likeness effect highlights the lexical nature of the recorded brain visual responses. A cross-language word-likeness effect was observed only in bilinguals and only with pseudo-words derived from the native language, indicating an experience-based tuning to language. Taken together these findings indicate that the amount of exposure to a language determines the engagement of neural resources devoted to word processing in the occipito-temporal visual cortex. We conclude that automatic lexical coding occurs at early visual processing in bilinguals and monolinguals alike, and that language exposure determines the competition strength of a language.Significance StatementBilingualism and its possible impact on automatic processes have rarely attracted interest, contrary to bilingualism and its mutual relation with the executive functions. We assessed automatic visual word recognition in bi- and monolingual individuals while purposively bypassing executive functions. Visual brain potentials frequency tagged to words, that were flashed in rapid trains of strings with varying word-likeness degrees, exposed the automatic encoding of word-form as well as language identity at early stages of visual word processing within the occipito-temporal visual cortex. The mechanisms involved in both encoding processes reflect experience-based activity as the one characterizing tight-tuned neurons in the VWFA. Our findings provide a novel framework to understand the mechanisms behind the incredible efficiency of bilinguals in handling multiple languages.
Escaping the Fate of Sisyphus: Assessing Resistome Hybridization Baits for Antimicrobial Resistance Gene Capture
Authors: Beaudry Megan S. , Thomas Jesse C. , Baptista Rodrigo , Sullivan Amanda , Norfolk William , Devault Alison , Enk Jacob , Kieran Troy J. , Rhodes Olin , Perry Allison , Rose Laura , Bayona-Vásquez Natalia J. , Oladeinde Ade , Lipp Erin , Sanchez Susan , Glenn Travis C. 
Published: July 2021

SummaryFinding, characterizing, and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive, and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19,933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3,565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.Originality-Significance StatementThis work is applicable to a wide range of research. It helps to define conditions under which hybridization capture is useful regarding not only antimicrobial resistance specifically, but also more generally how to assess the ongoing utility of existing bait sets - giving objective criteria for when and by what strategies baits should be updated. We also provide a method for quantifying and comparing antimicrobial resistance genes (ARGs) similar to what is used for RNAseq experiments. This approach improves comparison of ARGs across environments. Thus, the work provides an improved foundation for ARG future studies, while cutting across traditional areas of microbiology and extending beyond.
cLoops2: a full-stack comprehensive analytical tool for chromatin interactions
Authors: Cao Yaqiang , Liu Shuai , Ren Gang , Tang Qingsong , Zhao Keji 
Published: July 2021

AbstractInvestigating chromatin interactions between regulatory regions such as enhancer and promoter elements is vital for a deeper understanding of gene expression regulation. The emerging 3D mapping technologies focusing on enriched signals such as Hi-TrAC/TrAC-looping, compared to Hi-C and variants, reduce the sequencing cost and provide higher interaction resolution forcis-regulatory elements. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of the 3D chromatin interaction data. cLoops2 consists of core modules for peak-calling, loop-calling, differentially enriched loops calling and loops annotation. Additionally, it also contains multiple modules to carry out interaction resolution estimation, data similarity estimation, features quantification and aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub:https://github.com/YaqiangCao/cLoops2.
Priority effects among amphibian microbes lead to varying levels of Bd infection
Authors: Barnes Elle M. , Lewis J.D. 
Published: July 2021

AbstractPriority effects in host-associated microbiomes can influence not only community composition and structure, but also community functions, such as disease resistance. However, evidence for these priority effects remains scarce. Past studies suggest that amphibian protection from chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis (Bd), is related to antifungal bacterial composition on host skin. Priority effects in these bacterial communities may influence susceptibility to Bd, but this possibility has not been tested. Using in vitro microcosms, we demonstrated that priority effects can influence interactions among amphibian-associated microbes. We observed strong priority effects irrespective of high antifungal ability such that the Bd-inhibitory potential of two strongly inhibitory bacterial species did not always produce higher levels of Bd-inhibition. This result suggests that interactions may be more complex than previously thought. Additionally, our results suggest that priority effects between commensal and pathogenic taxa can be either facilitatory or inhibitory, with the strength and direction of this effect dependent on the composition of the community. Thus, changes in assembly may lead to varying levels of Bd infection, influencing how we might augment amphibian-associated microbiomes to conserve taxa currently at risk of extinction.
Uncertainty modulates visual maps during non-instrumental information demand
Authors: Li Yvonne , Daddaoua Nabil , Horan Mattias , Gottlieb Jacqueline 
Published: July 2021

AbstractAnimals are intrinsically motivated to resolve uncertainty and predict future events. This motivation is encoded in cortical and subcortical structures, but a key open question is how it generates concrete policies for attending to informative stimuli. We examined this question using neural recordings in the monkey lateral intraparietal area (LIP), a visual area implicated in attention and gaze, during non-instrumental information demand. We show that the uncertainty that was resolved by a visual cue enhanced visuo-spatial responses of LIP cells independently of reward probability. This enhancement was independent of immediate saccade plans but correlated with the sensitivity to uncertainty in eye movement behavior on longer time scales (across sessions/days). The findings suggest that topographic visual maps receive motivational signals of uncertainty, which enhance the priority of informative stimuli and the likelihood that animals will orient to the stimuli to reduce uncertainty.
The gut microbiome is associated with cocaine behavior and predicts addiction vulnerability in adult male rats
Authors: Suess Gregory J , Kasiah Jennysue , Simpson Sierra , Brennan Molly , Conlisk Dana , Maturin Lisa , George Olivier L , Chassaing Benoit , Frantz Kyle J 
Published: July 2021

AbstractThe gut-brain axis is a bi-directional communication system through which microbial communities in the gut interact with the nervous system, perhaps influencing neuropsychiatric disorders such as drug abuse. This study used behavioral data and biological samples from the Cocaine Biobank to test the hypothesis that the gut microbiota can predict and reflect susceptibility to cocaine reinforcement. Adult male heterogenous rats were catheterized and allowed to self-administer cocaine in short-access sessions (2 hr/day, 10 days, 0.5 mg/kg per intravenous infusion), followed by progressive ratio (PR) tests, long-access sessions (6 hr/day, 14 days), and alternating blocks of PR, long-access, and footshock testing. Fecal samples were collected at three time points and bacterial 16s rRNA genes were sequenced to profile the microbiota. As expected, cocaine-related behavior varied among subjects, such that a quartile split identified low and high responders on each measure, as well as an overall addiction index. Although beta diversity in the microbiota at baseline and after short access did not predict membership in high or low addiction quartiles, linear discriminant analysis (LDA) identified taxa that were more robustly represented in low or high responders. Beta diversity after long access was different among quartiles, as were several specific taxa. Investigation of baseline differences revealed that high relative abundance of Akkermansia muciniphila predicted future low response rates, whereas Ruminococcaceae predicted high response. This study is the first to report that microbiota variability reflects levels of cocaine intake and that microbial profiles might facilitate diagnosis and identify risk factors predictive of drug vulnerability.Significance StatementMicrobial organisms inhabiting the gut of animals appear to influence organismal function through various signaling pathways, ultimately affecting behavior and disease vulnerability. This experiment investigates links between gut bacteria and vulnerability to addiction-related behaviors in adult male rats. Not only did gut bacterial profiles change as a result of cocaine intake but also gut bacterial profiles before any exposure to cocaine predicted which animals would be high or low addiction-prone individuals. These results suggest that microbial profiles might facilitate diagnosis and identify risk factors predictive of drug addiction.
Abundance of Nef and p-Tau217 in brains of individuals diagnosed with HIV-associated neurocognitive disorders correlate with disease severance
Authors: Pushkarsky Tatiana , Ward Adam , Sviridov Dmitri , Bukrinsky Michael I 
Published: July 2021

AbstractHIV-associated neurological disorders (HAND) is a term used to describe a variety of neurological impairments observed in HIV-infected individuals. The pathogenic mechanisms of HAND and its connection to HIV infection remain unknown. The brain samples from HIV-infected individuals, both with and without HAND, were characterized by increased abundance of p-Tau217 peptide, which correlated with the abundance of flotillin 1, a marker of lipid rafts. HIV-1 Nef was detected in some, but not all, samples from HAND-affected individuals. Samples positive for Nef had lower abundance of cholesterol transporter ABCA1, higher abundance of flotillin 1 and p-Tau217, and were obtained from individuals with higher severity of HAND relative to Nef-negative samples. These results highlight the contribution of Nef and Nef-dependent effects on cholesterol metabolism and lipid rafts to the pathogenesis of HAND and support a connection between pathogenesis of HAND and Alzheimer’s disease.
Blood Unit Segments Accurately Represent the Biophysical Properties of Red Blood Cells in Blood Bags but Not Hemolysis
Authors: Islamzada Emel , Matthews Kerryn , Lamoureux Erik , Duffy Simon P. , Scott Mark D. , Ma Hongshen 
Published: July 2021

ABSTRACTBACKGROUNDThe biophysical properties of red blood cells (RBCs) provide potential biomarkers for the quality of donated blood. Blood unit segments provide a simple and nondestructive way to sample RBCs in clinical studies of transfusion efficacy, but it is not known whether RBCs sampled from segments accurately represent the biophysical properties of RBCs in blood bags.STUDY DESIGN AND METHODSRBCs were sampled from blood bags and segments every two weeks during 8 weeks of storage at 4 °C. RBC deformability was measured by deformabilitybased sorting using the microfluidic ratchet device in order to derive a rigidity score. Standard hematological parameters, including mean corpuscular volume (MCV), red cell distribution width (RDW), mean cell hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and hemolysis were measured at the same time points.RESULTSDeformability of RBCs stored in blood bags was retained over 4 weeks storage but a progressive loss of deformability was observed at weeks 6 and 8. This trend was mirrored in blood unit segments with a strong correlation to the blood bag data. Strong correlations were also observed between blood bag and segment for MCV, MCHC and MCH, but not for hemolysis.CONCLUSIONRBCs sampled from blood unit segments accurately represents the biophysical properties of RBCs in blood bags, but not hemolysis. Blood unit segments provide a simple and non-destructive sample for measuring RBC biophysical properties in clinical studies.
The impact of rheotaxis and flow on the aggregation of organisms
Authors: Painter Kevin J. 
Published: July 2021

AbstractDispersed populations often need to organise into groups. Chemical attractants provide one means of directing individuals into an aggregate, but whether these structures emerge can depend on various factors, such as there being a sufficiently large population or the response to the attractant being sufficiently sensitive. In an aquatic environment, fluid flow may heavily impact on population distribution and many aquatic organisms adopt a rheotaxis response when exposed to a current, orienting and swimming according to the flow field. Consequently, flow-induced transport could be substantially different for the population members and any aggregating signal they secrete. With the aim of investigating how flows and rheotaxis responses impact on an aquatic population’s ability to form and maintain an aggregated profile, we develop and analyse a mathematical model that incorporates these factors. Through a systematic analysis into the effect of introducing rheotactic behaviour under various forms of environmental flow, we demonstrate that each of flow and rheotaxis can act beneficially or detrimentally on the ability to form and maintain a cluster. Synthesising these findings, we test a hypothesis that density-dependent rheotaxis may be optimal for group formation and maintenance, in which individuals increase their rheotactic effort as they approach an aggregated state.
Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes
Authors: Mordant Angie , Kleiner Manuel 
Published: July 2021

AbstractA critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for approaches that measure gene expression, such as metaproteomics, which is used to identify and quantify proteins in microbiomes. Intestinal microbiome samples are typically stored by flash freezing and storage at −80°C, but some experimental set-ups do not allow for immediate freezing of samples. In this study, we evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash freezing is not possible. We collected fecal samples from C57BL/6 mice and stored them for 1 and 4 weeks using the following methods: flash-freezing in liquid nitrogen, immersion in RNAlater™, immersion in 95% ethanol, immersion in a RNAlater-like buffer, and combinations of these methods. After storage we extracted protein and prepared peptides for LC-MS/MS analysis to identify and quantify peptides and proteins. All samples produced highly similar metaproteomes, except for ethanol-preserved samples that were distinct from all other samples in terms of protein identifications and protein abundance profiles. Flash-freezing and RNAlater™ (or RNAlater-like treatments) produced metaproteomes that differed only slightly, with less than 0.7% of identified proteins differing in abundance. In contrast, ethanol preservation resulted in an average of 9.5% of the identified proteins differing in abundance between ethanol and the other treatments. Our results suggest that preservation at room temperature in RNAlater™, or an RNAlater-like solution, performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses.ImportanceMetaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members. A critical step for metaproteomic workflows is preserving samples before analysis because protein profiles are susceptible to fast change in response to changes in environmental conditions (air exposure, temperature changes, etc.). This study evaluated the effects of different preservation treatments on the metaproteomes of intestinal microbiome samples.
MIXTURE of human expertise and deep learning—Developing an explainable model for predicting pathological diagnosis and survival in patients with interstitial lung disease
Authors: Uegami Wataru , Bychkov Andrey , Ozasa Mutsumi , Uehara Kazuki , Kataoka Kensuke , Johkoh Takeshi , Kondo Yasuhiro , Sakanashi Hidenori , Fukuoka Junya 
Published: July 2021

AbstractInterstitial pneumonia is a heterogeneous disease with a progressive course and poor prognosis, at times even worse than those in the main cancer types. Histopathological examination is crucial for its diagnosis and estimation of prognosis. However, the evaluation strongly depends on the experience of pathologists, and the reproducibility of diagnosis is low.Herein, we propose MIXTURE (huMan-In-the-loop eXplainable artificial intelligence Through the Use of REcurrent training), a method to develop deep learning models for extracting pathologically significant findings based on an expert pathologist’s perspective with a small annotation effort. The procedure of MIXTURE consists of three steps as follows. First, we created feature extractors for tiles from whole slide images using self-supervised learning. The similar looking tiles were clustered based on the output features and then pathologists integrated the pathologically synonymous clusters. Using the integrated clusters as labeled data, deep learning models to classify the tiles into pathological findings were created by transfer-learning the feature extractors. We developed three models for different magnifications.Using these extracted findings, our model was able to predict the diagnosis of usual interstitial pneumonia, a finding suggestive of progressive disease, with high accuracy (AUC 0.90). This high accuracy could not be achieved without the integration of findings by pathologists. The patients predicted as UIP had significantly poorer prognosis (five-year overall survival [OS]: 55.4%) than those predicted as non-UIP (OS: 95.2%). The Cox proportional hazards model for each microscopic finding and prognosis pointed out dense fibrosis, fibroblastic foci, elastosis, and lymphocyte aggregation as independent risk factors. We suggest that MIXTURE may serve as a model approach to different diseases evaluated by medical imaging, including pathology and radiology, and be the prototype for artificial intelligence that can collaborate with humans.
Single-cell transcriptomic resolution of stem cells and their developmental trajectories in the hippocampus reveals epigenetic control of cell state perseverance
Authors: Salas-Bastos Adrián , Treppner Martin , Herman Josip S. , Koutsogiannis Dimitrios , Binder Harald , Stadler Michael B. , Grün Dominic , Vogel Tanja 
Published: July 2021

AbstractDespite conceptual research on hippocampus development and the application of single-cell-resolved technologies, the nature and maturation of its diverse progenitor populations are unexplored. The chromatin modifier DOT1L balances progenitor proliferation and differentiation, and conditional loss-of-function mice featured impaired hippocampus development. We applied single-cell RNA sequencing on DOT1L-mutant mice and explored cell trajectories in the E16.5 hippocampus. We resolved in our data five distinct neural stem cell populations with the developmental repertoire to specifically generate the cornu ammonis (CA) 1 field and the dentate gyrus (DG). Within the two developing CA1- and CA3-fields, we identified two distinct maturation states and we thus propose CA1- and CA3-differentiation along the radial axis. In the developing hippocampus, DOT1L is primarily involved in the proper development of CA3 and the DG, and it serves as a state-preserving epigenetic factor that orchestrates the expression of several important transcription factors that impact neuronal differentiation and maturation.Graphical AbstractThe developing hippocampus contains distinct and spatially separated NSC populations that differ in expression of a specific set of firstly described marker genes.CA pyramidal neurons mature along the radial axis and pass through distinct maturation states.DOT1L preserves the dentate granule cell lineage in the developing hippocampus and limits maturation in the CA1- and CA3-fields development.DOT1L gates cell maturation as upstream regulator of transcription factor expression that confer instrumental roles in hippocampus development.