bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tongue as a Wire? Glossokinetic Artifact and Insights From Intracranial EEG
Authors: Bayram Ayşe Kaçar , Spencer Dennis D. , Alkawadri Rafeed 
Published: February 2021

Background:
Glossokinetic artifact (GKA) is a well-known scalp EEG artifact characterized by deflections within the delta to low-theta frequency bands and dynamic polarity typically attributed to the direction of tongue movement. This study aims to investigate intracranial EEG correlations of scalp-GKA. If the tongue is a dipole, per the conventional view, then volume-conducted deflections are expected in the nearest frontal intracranial EEG contacts.

Materials and Methods:
Simultaneous scalp and intracranial EEG recordings were evaluated in five consecutive medically resistant epilepsy patients at Yale Epilepsy Center in 2017 and 2018, who had classic GKA deflections on scalp EEG. The EEG was sampled at 2,048 to 4,096 Hz and analyzed visually, using a reference placed in the diploic space or over the convexity, and confirmed quantitatively by a statistical framework. Ten GKA deflections were analyzed per case.

Results:
The medians of age at the time of recording, contacts per case, and amplitude of scalp GKA deflections were 35 years (range: 20–41 years), 171 contacts (range: 165–241 contacts), and 56 μV (range: 51–72 μV), respectively. There were no slow discharges in the frontal intracranial EEG contacts synchronized with the scalp GKA, either in the delta (1–3 Hz) or in the sub-delta (0.1–1 Hz) bands. However, the expected physiologic attenuation of alpha and beta rhythms and the emergence of high-gamma activity were observed over the peri-Rolandic regions in the invasive recordings.

Conclusions:
The traditional view of the tongue as a dipole generator of scalp GKA is simplistic and does not account for the findings reported herein. The tongue most probably shunts other scalp and soft-tissue currents. Knowledge of tongue potentials is of interest in the education and the design of tongue–computer interfaces.
Neurophysiological Findings in Critical COVID-19 Patients With Peripheral Nervous System Manifestations
Authors: Santiago-Pérez Susana , Espinosa-García Sandra , Martínez-Pérez Almudena , Herráez-Sánchez Erika , Rizea Cristian , Ruiz-Ávila Lilia Alejandrina 
Published: February 2021

Introduction:
Coronavirus disease 2019 patients hospitalized in intensive care units develop neuromuscular manifestations. However, to our knowledge, a study describing the neurophysiological findings in these patients has not been reported. The objective of this study was to diagnose the cause of neuromuscular deficit in severe coronavirus disease 2019 patients, through neurophysiological examination.

Methods:
This is a retrospective, observational case series. Data were collected from April 13, 2020, to May 31, 2020. Twenty-two coronavirus disease 2019 patients with generalized neuromuscular deficit during intensive care unit hospitalization were studied. Neurophysiological examinations included motor and sensory peripheral nerve conductions, needle electromyography, F waves, and repetitive nerve stimulation.

Results:
The subjects were 14 men (63.6%) and eight women, ranged from 35 to 74 years old (58.0, interquartile ranges 50.7–66.2). Intensive care unit hospitalization time ranged from 14 to 82 days (median 37.5, interquartile ranges 22.7–55.0). Through neurophysiological examination, myopathy was diagnosed in 17 patients (77.3%) and polyneuropathy in four (18.2%). Focal neuropathies were diagnosed in 12 patients (54.6%), with a total of 19 affected nerves. Common peroneal nerve lesions at the fibular head (68.4%) and ulnar nerve lesions at the elbow level (21.1%) were the most frequent locations. No significant differences were established between neurophysiological findings and clinical or analytical data.

Conclusions:
In critical coronavirus disease 2019 patients with neuromuscular complaints, neurophysiological examination provides an accurate diagnosis—useful to select treatment measures and establish the prognosis of recovery. Neurophysiological findings are similar to those described for critical illness neuromuscular disease, with myopathy being the most frequent diagnosis.
The relationship between rheumatoid arthritis and diabetes mellitus: a systematic review and meta-analysis
Authors: Tian Zixing , Mclaughlin John , Verma Arpana , Chinoy Hector , Heald Adrian H. 
Published: February 2021

Objective
This systematic review/meta-analysis was conducted to investigate the relationship between rheumatoid arthritis and the incidence of diabetes mellitus.

Methods
A comprehensive search was conducted up to 10 March 2020 in Medline (via Ovid), Embase (via Ovid) and Web of Science core collection to identify cohort studies comparing the risk of diabetes mellitus incidence in people with rheumatoid arthritis with the general population. The I2 statistic was used to test heterogeneity. Pooled relative risks were calculated using random-effects models. Publication bias was assessed using Egger’s test and Begg’s test.

Results
The initial search provided 3669 articles. Of those, five journal articles/two conference abstracts comprising 1 629 854 participants were included in this study. The funnel plot showed potential publication bias, proven by Egger’s test (−3.15, P < 0.01), but not Begg’s test (−0.05, P = 1.00). Heterogeneity was observed in I2 test (I2 = 96%, P < 0.01). We found that rheumatoid arthritis was associated with a higher risk of diabetes mellitus incidence (pooled relative risk, 1.23; 95% confidence interval, 1.07–1.40). Exploration of potential sources of heterogeneity found significant heterogeneity in different countries/regions (P = 0.002), but heterogeneity was NS in different study designs (P = 0.30). Sensitivity analyses confirmed that the association between rheumatoid arthritis and diabetes mellitus incidence was robust.

Conclusion
Rheumatoid arthritis is associated with an increased risk of diabetes mellitus incidence. This finding supports the notion that inflammatory pathways are involved in the pathogenesis of diabetes. More intensive interventions targeting diabetes risk factors should be considered in people with rheumatoid arthritis.
Trends for Electroconvulsive Therapy Utilization in Children and Adolescents in the United States From 2002 to 2017
Authors: Trivedi Chintan , Motiwala Fatima , Mainali Pranita , Mansuri Zeeshan , Jain Shailesh 
Published: February 2021

Objectives
Electroconvulsive therapy (ECT) is controversial in children and adolescents (C/A). The primary objective of this study was to evaluate baseline characteristics of C/A in the utilization of ECT compared with the non-ECT group with the same primary indication. The secondary objective was to assess the trends in ECT utilization over 16 years and explore the predictors of length of stay.

Methods
Using the Nationwide Inpatient Sample database from the years 2002 to 2017, we identified patients (age ≤18 years) undergoing ECT in the United States using International Classification of Diseases, Ninth Revision and Tenth Revision, Clinical Modification/Procedure Coding System codes and compared with non-ECT C/A patients with the same primary diagnosis. Baseline clinical characteristics were assessed using descriptive analysis methods. Multilevel regression analysis and trend analysis were performed.

Results
Children and adolescent patients (n = 159,158) receiving (ECT: n = 1870) were more likely to be men (43.3% vs 36.7%) and of White race (58% vs 49%) (P < 0.001). The hospital stay was longer (19 days vs 6 days, P < 0.001) for the ECT group than controls. ECT receiving C/A patients were more likely to have private insurance (72% vs 42%, P < 0.001). African American patients undergoing ECT treatment increased in number over the course of years (2002 to 2017), whereas the privately insured C/A patients receiving ECT decreased over the same period (P < 0.001). There was an upward trend in ECT utilization for small bed size hospitals (P < 0.001). Length of stay for C/A receiving ECT was longer for males (P < 0.001) and patients with nonprivate insurance (p: 0.003).

Conclusions
Electroconvulsive therapy is not optimally used in C/A; therefore, formulated treatment guidelines are required.
A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria
Authors: Seef Sofiene , Herrou Julien , de Boissier Paul , My Laetitia , Brasseur Gael , Robert Donovan , Jain Rikesh , Mercier Romain , Cascales Eric , Habermann Bianca , Mignot Tâm 
Published: February 2021

SummaryMyxococcus xanthus, a soil bacterium, predates collectively using motility to invade prey colonies. Prey lysis is mostly thought to rely on secreted factors, cocktails of antibiotics and enzymes, and direct contac withMyxococcuscells. In this study, we show that on surfaces the coupling of A-motility and contact-dependent killing is the central predatory mechanism driving effective prey colony invasion and consumption. At the molecular level, contact-dependent killing involves a newly discovered type IV filament-like machinery (Kil) that both promotes motility arrest and prey cell plasmolysis. In this process, Kil proteins assemble at the predator-prey contact site, suggesting that they allow tight contact with prey cells for their intoxication. Kil-like systems form a new class of Tad-like machineries in predatory bacteria, suggesting a conserved function in predator-prey interactions. This study further reveals a novel cell-cell interaction function for bacterial pili-like assemblages.
Chronic wireless neural population recordings with common marmosets
Authors: Walker Jeffrey D. , Pirschel Friederice , Sundiang Marina , Niekrasz Marek , MacLean Jason N. , Hatsopoulos Nicholas G. 
Published: February 2021

SUMMARYMarmosets are an increasingly important model system for neuroscience in part due to genetic tractability and enhanced cortical accessibility, due to a lissencephalic neocortex. However, many of the techniques generally employed to record neural activity in primates inhibit the expression of natural behaviors in marmosets precluding neurophysiological insights. To address this challenge, we developed methods for recording neural population activity in unrestrained marmosets across multiple ethological behaviors, multiple brain states, and over multiple years. Notably, our flexible methodological design allows for replacing electrode arrays and removal of implants providing alternative experimental endpoints. We validate the method by recording sensorimotor cortical population activity in freely moving marmosets across their natural behavioral repertoire and during sleep.HIGHLIGHTS– Simultaneous and chronic wireless neural population recordings in multiple freely moving marmosets– Neural recording approach enables studies of natural repertoire of behaviors and sleep– Methyl-methacrylate free surgical approach designed to promote biocompatibility and longitudinal success of the implant– Modular headstage configuration requires minimal daily animal handling for daily neural recordings– Alternative experimental endpoints: implant removal, healing, and electrode array replacement
A public broadly neutralizing antibody class targets a membrane-proximal anchor epitope of influenza virus hemagglutinin
Authors: Guthmiller Jenna J. , Han Julianna , Utset Henry A. , Li Lei , Lan Linda Yu-Ling , Henry Carole , Stamper Christopher T. , Stovicek Olivia , Gentles Lauren , Dugan Haley L. , Zheng Nai-Ying , Richey Sara T. , Tepora Micah E. , Bitar Dalia J. , Changrob Siriruk , Strohmeier Shirin , Huang Min , García-Sastre Adolfo , Nachbagauer Raffael , Palese Peter , Bloom Jesse D. , Krammer Florian , Coughlan Lynda , Ward Andrew B. , Wilson Patrick C. 
Published: February 2021

SummaryBroadly neutralizing antibodies against influenza virus hemagglutinin (HA) have the potential to provide universal protection against influenza virus infections. Here, we report a distinct class of broadly neutralizing antibodies targeting an epitope toward the bottom of the HA stalk domain where HA is “anchored” to the viral membrane. Antibodies targeting this membrane-proximal anchor epitope utilized a highly restricted repertoire, which encode for two conserved motifs responsible for HA binding. Anchor targeting B cells were common in the human memory B cell repertoire across subjects, indicating pre-existing immunity against this epitope. Antibodies against the anchor epitope at both the serological and monoclonal antibody levels were potently induced in humans by a chimeric HA vaccine, a potential universal influenza virus vaccine. Altogether, this study reveals an underappreciated class of broadly neutralizing antibodies against H1-expressing viruses that can be robustly recalled by a candidate universal influenza virus vaccine.
GUIdEStaR (G-quadruplex, uORF, IRES, Epigenetics, Small RNA, Repeats), the integrated metadatabase in conjunction with neural network methods
Authors: Kang Jee Eun 
Published: February 2021

AbstractGUIdEStaR integrates existing databases of various types of G-quadruplex, upstream Open Reading Frame (uORF), Internal Ribosome Entry Site (IRES), methylation to RNA and histone protein, small RNA, and repeats. GUIdEStaR consists of approx. 40,000 genes and 320,000 transcripts. An mRNA transcript is divided into 5 regions (5’UTR, 3’UTR, exon, intron, and biological region) where each region contains presence-absence data of 169 different types of elements. Recently, artificial intelligence (AI) based analysis of sequencing data has been gaining popularity in the area of bioinformatics. GUIdEStaR generates datasets that can be used as inputs to AI methods. At the GUIdEStaR homepage, users submit gene symbols by clicking a “Send” button, and shortly result files in CSV format are available for download at the result website. Users have an option to send the result files to their email addresses. Additionally, the entire database and the example Java codes are also freely available for download. Here, we demonstrate the database usage with three neural network classification studies-1) small RNA study for classifying transcription factor (TF) genes into either one of TF mediated by small RNA originated from SARS-CoV-2 or by human microRNA (miRNA), 2) cell membrane receptor study for classifying receptor genes as either with virus interaction or without one, and 3) nonsense mediated mRNA decay (NMD) study for classifying cell membrane and nuclear receptors as either NMD target or non-target. GUIdEStaR is available for access to the easy-to-use web-based database atwww.guidestar.krand for download athttps://sourceforge.net/projects/guidestar.
AMBIENT: Accelerated Convolutional Neural Network Architecture Search for Regulatory Genomics
Authors: Zhang Zijun , Cofer Evan M. , Troyanskaya Olga G. 
Published: February 2021

AbstractConvolutional neural networks (CNN) have become a standard approach for modeling genomic sequences. CNNs can be effectively built by Neural Architecture Search (NAS) by trading computing power for accurate neural architectures. Yet, the consumption of immense computing power is a major practical, financial, and environmental issue for deep learning. Here, we present a novel NAS framework, AMBIENT, that generates highly accurate CNN architectures for biological sequences of diverse functions, while substantially reducing the computing cost of conventional NAS.
Calprotectin-mediated zinc chelation inhibitsPseudomonas aeruginosaprotease activity in cystic fibrosis sputum
Authors: Vermilyea Danielle M. , Crocker Alex W. , Gifford Alex H. , Hogan Deborah A. 
Published: February 2021

AbstractPseudomonas aeruginosainduces pathways indicative of low zinc availability in the cystic fibrosis (CF) lung environment. To learn more aboutP. aeruginosazinc access in CF, we grewP. aeruginosastrain PAO1 directly in expectorated CF sputum. TheP. aeruginosaZur transcriptional repressor controls the response to low intracellular zinc, and we used the NanoString methodology to monitor levels of Zur-regulated transcripts including those encoding a zincophore system, a zinc importer, and paralogs of zinc containing proteins that do not require zinc for activity. Zur-controlled transcripts were induced in sputum-grownP. aeruginosacompared to control cultures, but not if the sputum was amended with zinc. Amendment of sputum with ferrous iron did not reduce expression of Zur-regulated genes. A reporter fusion to a Zur-regulated promoter had variable activity inP. aeruginosagrown in sputum from different donors, and this variation inversely correlated with sputum zinc concentrations. Recombinant human calprotectin (CP), a divalent-metal binding protein released by neutrophils, was sufficient to induce a zinc-starvation response inP. aeruginosagrown in laboratory medium or zinc-amended CF sputum indicating that CP is functional in the sputum environment. Zinc metalloproteases comprise a large fraction of secreted zinc-bindingP. aeruginosaproteins. Here we show that recombinant CP inhibited both LasB-mediated casein degradation and LasA-mediated lysis ofStaphylococcus aureus, which was reversible with added zinc. These studies reveal the potential for CP-mediated zinc chelation to post-translationally inhibit zinc metalloprotease activity and thereby impact the protease-dependent physiology and/or virulence ofP. aeruginosain the CF lung environment.ImportanceThe factors that contribute to worse outcomes in individuals with cystic fibrosis (CF) with chronicPseudomonas aeruginosainfections are not well understood. Therefore, there is a need to understand environmental factors within the CF airway that contribute toP. aeruginosacolonization and infection. We demonstrate that growing bacteria in CF sputum induces a zinc-starvation response that inversely correlates with sputum zinc levels. Additionally, both calprotectin and a chemical zinc chelator inhibit the proteolytic activities of LasA and LasB proteases suggesting that extracellular zinc chelators can influence proteolytic activity and thusP. aeruginosavirulence and nutrient acquisitionin vivo.
Functional characterization of ovine dorsal root ganglion neurons reveals peripheral sensitization after osteochondral defect
Authors: Chakrabarti Sampurna , Ai Minji , Katherine Wong Wai Ying , Newell Karin , Henson Frances M.D. , John Smith Ewan St. 
Published: February 2021

AbstractObjectiveKnee joint trauma can cause an osteochondral defect (OD), a risk factor for osteoarthritis and cause of debilitating pain in patients. Modelling OD in rodents is difficult due to their smaller joint size. This study proposes sheep as a translationally relevant model to understand the neuronal basis of OD pain.MethodsUnilateral 6 mm deep OD was induced in adult sheep, 2-6 weeks after which dorsal root ganglion neurons (DRG neurons) were cultured from the control and OD side. Functional assessment of neuronal excitability and activity of the pain-related ion channels, TRPV1 and P2X3, was carried out using electrophysiology and Ca2+-imaging. Immunohistochemistry was utilized to verify expression of pain-related proteins.ResultsAn increased proportion of OD DRG neurons (sheep, n = 3, Ctrl neurons, n =15, OD neurons, n = 16) showed spontaneous electrical excitability (p = 0.009, unpaired t-test) and hyperexcitability upon TRPV1 agonist (capsaicin) application (p = 0.04, chi-sq test). Capsaicin also produced Ca2+influx in an increased proportion of OD DRG neurons isolated (p = 0.001, chi-sq test). By contrast, neither protein expression, nor functionality of the P2X3 ion channel were altered in OD neurons.ConclusionsWe provide evidence of increased excitability of DRG neurons (which is an important neural correlate of pain) and TRPV1 function in an OD sheep model. Our data show that functional assessment of sheep DRG neurons can provide important insights into the neural basis of OD pain and thus potentially prevent its progression into arthritic pain.
Genomic analyses of the extinct Sardinian dhole (Cynotherium sardous) reveal its evolutionary history
Authors: Ciucani Marta Maria , Jensen Julie Kragmose , Sinding Mikkel-Holger S. , Smith Oliver , Lucenti Saverio Bartolini , Rosengren Erika , Rook Lorenzo , Tuveri Caterinella , Area Marisa , Cappellini Enrico , Galaverni Marco , Randi Ettore , Guojie Chunxue , Zhang Guojie , Sicheritz-Pontén Thomas , Dalén Love , Gilbert M. Thomas P. , Gopalakrishnan Shyam 
Published: February 2021

SummaryThe Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene2–5. Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor 3,6–9. Morphometric analyses3,6,8–12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian and Asian dhole lineages diverged ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the landbridge between Sardinia and mainland Italy was broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.
A Regression Framework for Brain Network Distance Metrics
Authors: Tomlinson Chal E. , Laurienti Paul J. , Lyday Robert G. , Simpson Sean L. 
Published: February 2021

AbstractAnalyzing brain networks has long been a prominent research topic in neuroimaging. However, statistical methods to detect differences between these networks and relate them to phenotypic traits are still sorely needed. Our previous work developed a novel permutation testing framework to detect differences between two groups. Here we advance that work to allow both assessing differences by continuous phenotypes and controlling for confounding variables. To achieve this, we propose an innovative regression framework to relate distances between brain network features to functions of absolute differences in continuous covariates and indicators of difference for categorical variables. We explore several similarity metrics for comparing distances between connection matrices, and adapt several standard methods for estimation and inference within our framework: Standard F-test, F-test with individual level effects (ILE), Feasible Generalized Least Squares (FGLS), and Permutation. Via simulation studies, we assess all approaches for estimation and inference while comparing them with existing Multivariate Distance Matrix Regression (MDMR) methods. We then illustrate the utility of our framework by analyzing the relationship between fluid intelligence and brain network distances in Human Connectome Project (HCP) data.HighlightsRelated distances between connection matrices to differences in covariates.Adapted methods for estimation and inference in this framework.Assessment of methods and distance metrics via simulation.Compared our methods to existing MDMR methods via simulation.Analysis of the HCP data with the best approach for each distance metric.