bluuebunny/crossref_metadata_2025_split huggingface dataset:
The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide
Authors:   BICCN Data Ecosystem Collaboration, Hawrylycz Michael J , Martone Maryann E , Hof Patrick R , Lein Ed S , Regev Aviv , Ascoli Giorgio A. A , Bjaalie Jan G , Dong Hong-Wei , Ghosh Satrajit S , Gillis Jesse , Hertzano Ronna , Haynor David R , Kim Yongsoo , Liu Yufeng , Miller Jeremy A , Mitra Partha P , Mukamel Eran , Osumi-Sutherland David , Peng Hanchuan , Ray Patrick L , Sanchez Raymond , Ropelewski Alex , Scheuermann Richard H , Tan Shawn Z K , Tickle Timothy , Tilgner Hagen , Varghese Merina , Wester Brock , White Owen , Aevermann Brian , Allemang David , Ament Seth , Athey Thomas L , Baker Pamela M , Baker Cody , Baker Katherine S , Bandrowski Anita , Bishwakarma Prajal , Carr Ambrose , Chen Min , Choudhury Roni , Cool Jonah , Creasy Heather , D'Orazi Florence , Degatano Kylee , Dichter Benjamin , Ding Song-Lin , Dolbeare Tim , Ecker Joseph R , Fang Rongxin , Fillion-Robin Jean-Christophe , Fliss Timothy P , Gee James , Gillespie Tom , Gouwens Nathan , Halchenko Yaroslav O , Harris Nomi , Herb Brian R , Hintiryan Houri , Hood Gregory , Horvath Sam , Jarecka Dorota , Jiang Shengdian , Khajouei Farzaneh , Kiernan Elizabeth A , Kir Huseyin , Kruse Lauren , Lee Changkyu , Lelieveldt Boudewijn , Li Yang , Liu Hanqing , Markuhar Anup , Mathews James , Mathews Kaylee L , Miller Michael I , Mollenkopf Tyler , Mufti Shoaib , Mungall Christopher J , Ng Lydia , Orvis Joshua , Puchades Maja A , Qu Lei , Receveur Joseph P , Ren Bing , Sjoquist Nathan , Staats Brian , Thompson Carol L , Tward Daniel , van Velthoven Cindy T J , Wang Quanxin , Xie Fangming , Xu Hua , Yao Zizhen , Yun Zhixi , Zeng Hongkui , Zhang Guo-Qiang , Zhang Yun R , Zheng Jim W , Zingg Brian 
Published: October 2022

AbstractCharacterizing cellular diversity at different levels of biological organization across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also required to manipulate cell types in controlled ways, and to understand their variation and vulnerability in brain disorders. TheBRAIN Initiative Cell Census Network (BICCN)is an integrated network of data generating centers, data archives and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain and demonstration of prototypes for human and non-human primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed, and to accessing and using the BICCN data and its extensive resources, including theBRAIN Cell Data Center (BCDC)which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted by the BICCN toward FAIR (Wilkinson et al. 2016a) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
Influence of Poor Sleep on Cardiovascular Disease-Free Life Expectancy: A Multi-Resource-Based Population Cohort Study
Authors: Huang Bo-Huei , del Pozo Cruz Borja , Teixeira-Pinto Armando , Cistulli Peter A. , Stamatakis Emmanuel 
Published: October 2022

AbstractBackgroundThe complexity of sleep hinders the formulation of sleep guidelines. Recent studies suggest that different unhealthy sleep characteristics jointly increase the risks for cardiovascular disease (CVD). This study aimed to estimate the differences in CVD-free life expectancy between people with different sleep profiles.MethodsWe included 308683 middle-aged adults from the UK Biobank among whom 140181 had primary care data linkage. We used an established composite sleep score comprising self-reported chronotype, duration, insomnia complaints, snoring, and daytime sleepiness to derive three sleep categories: poor, intermediate, and healthy. We also identified three clinical sleep disorders captured by primary care and inpatient records within two years before enrollment in the cohort: insomnia, sleep-related breathing disorders, and other sleep disorders. We estimated sex-specific CVD-free life expectancy with three-state Markov models conditioning on survival at age 40 across different sleep profiles and clinical disorders.ResultsWe observed a gradual loss in CVD-free life expectancy toward poor sleep such as, compared with healthy sleepers, poor sleepers lost 1·80 [95% CI 0·96-2·75] and 2·31 [1·46-3·29] CVD-free years in females and males, respectively, while intermediate sleepers lost 0·48 [0·41-0·55] and 0·55 [0·49-0·61] years. Among men, those with clinical insomnia or sleep-related breathing disorders lost CVD-free life by 3·84 [0·61-8·59] or 6·73 [5·31-8·48] years, respectively. Among women, sleep-related breathing disorders or other sleep disorders were associated with 7·32 [5·33-10·34] or 1·43 [0·20-3·29] years lost, respectively.ConclusionsBoth self-reported and doctor-diagnosed poor sleep are negatively associated with CVD-free life, especially pronounced in participants with sleep-related breathing disorders.
Activity-regulated growth of motoneurons at the neuromuscular junction is mediated by NADPH oxidases
Authors: Sobrido-Cameán Daniel , Oswald Matthew C. W. , Bailey David M. D. , Mukherjee Amrita , Landgraf Matthias 
Published: October 2022

AbstractNeurons respond to changes in the levels of activity they experience in a variety of ways, including structural changes at pre- and postsynaptic terminals. An essential plasticity signal required for such activity-regulated structural adjustments are reactive oxygen species (ROS). To identify sources of activity-regulated ROS required for structural plasticityin vivowe used theDrosophilalarval neuromuscular junction as a highly tractable experimental model system. For adjustments of presynaptic motor terminals, we found a requirement for both NADPH oxidases, Nox and Dual Oxidase (Duox), that are encoded in theDrosophilagenome. This contrasts with the postsynaptic dendrites from which Nox is excluded. NADPH oxidases generate ROS to the extracellular space. Here, we show that two aquaporins, Bib and Drip, are necessary ROS conduits in the presynaptic motoneuron for activity regulated, NADPH oxidase dependent changes in presynaptic motoneuron terminal growth. Our data further suggest that different aspects of neuronal activity-regulated structural changes might be regulated by different ROS sources: changes in bouton number require both NADPH oxidases, while activity-regulated changes in the number of active zones might be modulated by other sources of ROS. Overall, our results show NADPH oxidases as important enzymes for mediating activity-regulated plasticity adjustments in neurons.
Real-time Emotion Detection by Quantitative Facial Motion Analysis
Authors: Saadon Jordan R. , Yang Fan , Burgert Ryan , Mohammad Selma , Gammel Theresa , Sepe Michael , Rafailovich Miriam , Mikell Charles B. , Polak Pawel , Mofakham Sima 
Published: October 2022

AbstractBackgroundResearch into mood and emotion has often depended on slow and subjective self-report, highlighting a need for rapid, accurate, and objective assessment tools.MethodsTo address this gap, we developed a method using digital image speckle correlation (DISC), which tracks subtle changes in facial expressions invisible to the naked eye, to assess emotions in real-time. We presented ten participants with visual stimuli triggering neutral, happy, and sad emotions and quantified their associated facial responses via detailed DISC analysis.ResultsWe identified key alterations in facial expression (facial maps) that reliably signal changes in mood state across all individuals based on these data. Furthermore, principal component analysis of these facial maps identified regions associated with happy and sad emotions. Compared with commercial deep learning solutions that use individual images to detect facial expressions and classify emotions, such as Amazon Rekognition, our DISC-based classifiers utilize frame-to-frame changes. Our data show that DISC-based classifiers deliver substantially better predictions, and they are inherently free of racial or gender bias.LimitationsOur sample size was limited, and participants were aware their faces were recorded on video. Despite this, our results remained consistent across individuals.ConclusionsWe demonstrate that DISC-based facial analysis can be used to reliably identify an individual’s emotion and may provide a robust and economic modality for real-time, noninvasive clinical monitoring in the future.HighlightsWe detected the emotional state of participants in the absence of visible changes in facial expressionsWe identified distinct facial movement maps for happy and sad emotionsWe developed a highly sensitive, noninvasive, noncontact emotional state assessment tool
Corticospinal Responses Following Gait-Specific Training in Stroke Survivors: A Systematic Review
Authors: Cherni Yosra , Tremblay Alexia , Simon Margaux , Bretheau Floriane , K. Blanchette Andréanne , Mercier Catherine 
Published: October 2022

AbstractBackgroundCorticospinal excitability is subject to alterations after stroke. While the reversal of these alterations has been proposed as an underlying mechanism for improvement walking capacity after gait-specific training, this has not yet been clearly demonstrated. Therefore, the objective of this review is to evaluate the effect of gait-specific training on corticospinal excitability in stroke survivors.DesignSystematic review of the literatureMethodsWe conducted an electronic database search in four databases (i.e., Medline, Embase, CINAHL and Web of Science) in June 2022. Two authors independently screened and selected all studies that investigated the effect of gait-specific training in post-stroke individuals on variables such as motor-evoked potential amplitude, motor threshold, map size, latency, and corticospinal silent period.ResultsNineteen studies investigating the effect of gait-specific training on corticospinal excitability were included. Some studies showed an increased MEP amplitude (7/16 studies), a decreased latency (5/7studies), a decreased motor threshold (4/8 studies), an increased map size (2/3 studies) and a decreased cortical silent period (1/2 study) after gait-specific training. No change has been reported in term of short interval intracortical inhibition after training. Five studies did not report any significant effect after gait-specific training on corticospinal excitability.ConclusionThe results of this systematic review suggest that gait-specific training modalities can drive neuroplastic adaptation among stroke survivors. However, given the methodological disparity of the included studies, further clinical trials with better methodological quality are needed to draw conclusions. Hence, the findings from this review can serve as a rationale for future studies and continued efforts in investigating the effects of gait-specific training on the central nervous system.
Machine learning models for predicting severe COVID-19 outcomes in hospitals
Authors: Wendland Philipp , Schmitt Vanessa , Zimmermann Jörg , Häger Lukas , Göpel Siri , Schenkel-Häger Christof , Kschischo Maik 
Published: October 2022

AbstractThe aim of this observational retrospective study is to improve early risk stratification of hospitalized Covid-19 patients by predicting in-hospital mortality, transfer to intensive care unit (ICU) and mechanical ventilation from electronic health record data of the first 24 hours after admission. Our machine learning model predicts in-hospital mortality (AUC=0.918), transfer to ICU (AUC=0.821) and the need for mechanical ventilation (AUC=0.654) from a few laboratory data of the first 24 hours after admission. Models based on dichotomous features indicating whether a laboratory value exceeds or falls below a threshold perform nearly as good as models based on numerical features. We devise completely data-driven and interpretable machine-learning models for the prediction of in-hospital mortality, transfer to ICU and mechanical ventilation for hospitalized Covid-19 patients within 24 hours after admission. Numerical values of CRP and blood sugar and dichotomous indicators for increased partial thromboplastin time (PTT) and glutamic oxaloacetic transaminase (GOT) are amongst the best predictors.
Identifying trends in SARS-CoV-2 RNA in wastewater to infer changing COVID-19 incidence: Effect of sampling frequency
Authors: Chan Elana M. G. , Kennedy Lauren C. , Wolfe Marlene K. , Boehm Alexandria B. 
Published: October 2022

AbstractSARS-CoV-2 RNA concentrations in wastewater solids and liquids are correlated with reported incident COVID-19 cases. Reporting of incident COVID-19 cases has changed dramatically with the availability of at-home antigen tests. Wastewater monitoring therefore represents an objective tool for continued monitoring of COVID-19 occurrence. One important use case for wastewater data is identifying when there are sustained changes or trends in SARS-CoV-2 RNA concentrations. Such information can be used to inform public health messaging, testing, and vaccine resources. However, there is limited research on best approaches for identifying trends in wastewater monitoring data. To fill this knowledge gap, we applied three trend analysis methods (relative strength index (RSI), percent change (PC), Mann-Kendall (MK) trend test) to daily measurements of SARS-CoV-2 RNA in wastewater solids from a wastewater treatment plant to characterize trends. Because daily measurements are not common for wastewater monitoring programs, we also conducted a downsampling analysis to determine the minimum sampling frequency necessary to capture the trends identified using the “gold standard” daily data. The PC and MK trend test appear to perform similarly and better than the RSI in terms of early warning signaling for increasing and decreasing trends, so we only considered the PC and MK trend test methods in the downsampling analysis. Using an acceptable sensitivity and specificity cutoff of 0.5, we found that a minimum of 4 samples/week and 5 samples/week is necessary to detect trends identified by daily sampling using the PC and MK trend test method, respectively. If a higher sensitivity and specificity is needed, then more samples per week would be needed. Public health officials can adopt these trend analysis approaches and sampling frequency recommendations to wastewater monitoring programs aimed at providing information on how incident COVID-19 cases are changing in the contributing communities.
Poorer Sleep Health is Associated With Altered Brain Activation During Cognitive Control Processing in Healthy Adults
Authors: Smevik Hanne , Habli Sarah , Saksvik Simen Berg , Kliem Elisabeth , Evensmoen Hallvard Røe , Conde Virginia , Petroni Agustin , Asarnow Robert F. , Dennis Emily L. , Eikenes Live , Kallestad Håvard , Sand Trond , Thompson Paul M. , Saksvik-Lehouillier Ingvild , Håberg Asta Kristine , Olsen Alexander 
Published: October 2022

AbstractThis study investigated how proactive and reactive cognitive control processing in the brain was associated with habitual sleep health. BOLD fMRI data was acquired from 81 healthy adults with normal sleep (41 females, age 20.96 - 39.58 years) during a test of cognitive control (Not-X CPT). Sleep health was assessed in the week before MRI scanning, using both objective (actigraphy) and self-report measures. Multiple measures indicating poorer sleep health - including later/more variable sleep timing, later chronotype preference, more insomnia symptoms and lower sleep efficiency - were associated with stronger and more widespread BOLD activations in fronto-parietal and subcortical brain regions during cognitive control processing (adjusted for age, sex, education, and fMRI task performance). Most associations were found forreactivecognitive control activation, indicating that poorer sleep health is linked to a ‘hyper-reactive’ brain state. Analysis of time-on-task effects showed that, with longer time on task, poorer sleep health was predominantly associated with increasedproactivecognitive control activation, indicating recruitment of additional neural resources over time. Finally, shorter objective sleep duration was associated with lower BOLD activation with time on task and poorer task performance. In conclusion, even in ‘normal sleepers’, relatively poorer sleep health is associated with altered cognitive control processing, possibly reflecting compensatory mechanisms and / or inefficient neural processing.
Protein kinase A gene knockout inCoprinopsis cinereaby CRISPR/Cas9 RNP complex system
Authors: Chan Po Lam , Kwan Hoi Shan , Chang JinHui 
Published: October 2022

AbstractCoprinopsis cinereais a model mushroom for studying the developmental processes of homobasidiomycetous fungi. The development ofC. cinereadepends on the sensing of environmental conditions, such as light, temperature, humidity and nutrients. The signal transduction pathway from the environmental condition sensors to the regulators and reproduction is an important research topic as the knowledge on it is still fragmentary. Protein kinases not only are crucial to the signal transduction, but also can be master switches of development. However, information on their role in basidiomycetous fungi is still limited. Using the effective gene-targeting of the current gene modification, a system of CRISPR/ Cas9 RNP with double strain template donor that contained a selective mark hygromycin cassette was developed in this study. In this system,CcPka1gene knockout was successfully generated through homologues repair together with Cas9 RNP complexes. This was the first report to use CRISPR/ Cas9 RNP approach with C. cinerea. ΔCcPka1mutants showed slow mycelial growth and rapid fruiting body induction compared to the wild type even when under high glucose condition. In addition, ΔCcPka1mutants had significantly increased intracellular glucose level and decreased glycogen level. Moreover, ΔCcPka1mutants regulated the gene expression of components in cAMP-PKA pathway. All these results demonstrated that PKA played an important role in the nutrient signal transduction and negatively regulated the fruiting body formation. This study also confirmed that GSK3 could be the downstream target of PKA, but their interaction requires further investigation.
Nonhuman primates exploit the prior assumption that the visual world is vertical
Authors: Khazali Mohammad Farhan , Daddaoua Nabil , Thier Peter 
Published: October 2022

AbstractWhen human subjects tilt their heads in dark surroundings, the noisiness of vestibular information impedes precise reports on objects’ orientation with respect to earth’s vertical axis. This difficulty is mitigated if a vertical visual background is available. Tilted visual backgrounds induce feelings of head tilt in subjects who are in fact upright. This is often explained as a result of the brain resorting to the prior assumption that natural visual backgrounds are vertical. Here, we tested whether monkeys show comparable perceptual mechanisms. To this end we trained two monkeys to align a visual arrow to a vertical reference line that had variable luminance across trials, while including a large, clearly visible background square whose orientation changed from trial to trial. On around 20% of all trials, the vertical reference line was left out to measure the subjective visual vertical (SVV). When the frame was upright, the monkeys’SVVwas aligned with the gravitational vertical. In accordance with the perceptual reports of humans, however, when the frame was tilted, it induced an illusion of head tilt as indicated by a bias inSVVtowards the frame orientation. Thus all primates exploit the prior assumption that the visual world is vertical.
Neural mechanisms underlying uninstructed orofacial movements during reward-based learning behaviors
Authors: Li Wanru , Nakano Takashi , Mizutani Kohta , Matsubara Takanori , Kawatani Masahiro , Mukai Yasutaka , Danjo Teruko , Ito Hikaru , Aizawa Hidenori , Yamanaka Akihiro , Petersen Carl C. H. , Yoshimoto Junichiro , Yamashita Takayuki 
Published: October 2022

ABSTRACTDuring reward-based learning tasks, animals make orofacial movements that globally influence brain activity at the timings of reward expectation and acquisition. These orofacial movements are not explicitly instructed and typically appear along with goal-directed behaviors. Here we show that reinforcing optogenetic stimulation of midbrain dopamine neurons (oDAS) in mice is sufficient to induce orofacial movements in the whiskers and nose without accompanying goal-directed behaviors. Pavlovian conditioning with a sensory cue and oDAS elicited cue-locked and oDAS aligned orofacial movements, which were distinguishable by a machine learning model. Inhibition or knock-out of dopamine D1 receptors in the nucleus accumbens inhibited oDAS-induced motion but spared cue-locked motion, suggesting differential neural regulation of these two types of orofacial motions. In contrast, inactivation of the whisker primary motor cortex (wM1) abolished both types of orofacial movements. We found specific neuronal populations in wM1 representing either oDAS-aligned or cue-locked whisker movements. Notably, optogenetic stimulation of wM1 neurons successfully replicated these two types of movements. Our results thus suggest that accumbal D1 receptor-dependent and -independent neuronal signals converge in the wM1 for facilitating uninstructed orofacial movements during a reward-based learning task.
Structure of the Calvin-Benson-Bassham sedoheptulose-1,7-bisphosphatase from the model microalgaChlamydomonas reinhardtii
Authors: Le Moigne Théo , Santoni Martina , Jomat Lucile , Lemaire Stéphane D. , Zaffagnini Mirko , Chéron Nicolas , Henri Julien 
Published: October 2022

AbstractThe Calvin-Benson-Bassham cycle (CBBC) performs carbon fixation in photosynthetic organisms. Among the eleven enzymes that participate in the pathway, sedoheptulose-1,7-bisphosphatase (SBPase) is expressed in photo-autotrophs and catalyzes the hydrolysis of sedoheptulose-1,7- bisphosphate (SBP) to sedoheptulose-7-phosphate (S7P). SBPase, along with nine other enzymes in the CBBC, contributes to the regeneration of ribulose-1,5-bisphosphate, the carbon-fixing co- substrate used by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The metabolic role of SBPase is restricted to the CBBC, and a recent study revealed that the three-dimensional structure of SBPase from the mossPhyscomitrium patenswas found to be similar to that of fructose-1,6- bisphosphatase (FBPase), an enzyme involved in both CBBC and neoglucogenesis. In this study we report the first structure of an SBPase from a chlorophyte, the model unicellular green microalgaChlamydomonas reinhardtii. By combining experimental and computational structural analyses, we describe the topology, conformations and quaternary structure ofChlamydomonas reinhardtiiSBPase (CrSBPase). We identify active site residues and locate sites of redox- and phospho-post- translational modifications that contribute to enzymatic functions. Finally, we observe thatCrSBPase adopts distinct oligomeric states that may dynamically contribute to the control of its activity.