bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental effects on pattern visual evoked potentials characterized by principal component analysis
Authors: Gentile Carlyn Patterson , Joshi Nabin R. , Ciuffreda Kenneth J. , Arbogast Kristy B. , Master Christina , Aguirre Geoffrey K. 
Published: December 2020

ABSTRACTPurposePeak amplitude and peak latency in the pattern reversal visual evoked potential (prVEP) vary with maturation. We considered that principal component analysis (PCA) may be used to describe age-related variation over the entire prVEP time course and provide a means of modeling and removing variation due to developmental age.MethodsprVEP was recorded from 155 healthy subjects ages 11-19 years at two timepoints. We created a model of the prVEP by identifying principal components (PCs) that explained >95% of the variance in a “training” dataset of 40 subjects. We examined the ability of the PCs to explain variance in an age- and sex-matched “validation” dataset (n=40) and calculated the intra-subject reliability of the PC coefficients between the two timepoints. We explored the effect of subject age and sex upon the PC coefficients.ResultsSeven PCs accounted for 96.0% of the variability of the training dataset and 90.5% of the variability in the validation dataset with good within-subject reliability across timepoints (R>0.7 for all PCs). The PCA model revealed narrowing and amplitude reduction of the P100 peak with maturation, and a broader and smaller P100 peak in males compared to females.ConclusionsPCA is a generalizable, reliable, and unbiased method of analyzing prVEP. The PCA model revealed changes across maturation and biological sex not fully described by standard peak analysis.Translational relevanceWe describe a novel application of PCA to characterize developmental changes of prVEP in youth that can be used to compare healthy and pathologic pediatric cohorts.
Analysis of the area and the number of pulmonary alveoli through the normal aging process in CD1 mouse
Authors: Ortega-Martínez Marta , Gutiérrez-Arenas Esthefania , Gutiérrez-Dávila Vanessa , Niderhauser-García Alberto , Cerda-Flores Ricardo M. , Jaramillo-Rangel Gilberto 
Published: December 2020

AbstractDuring the aging process, the lung exhibits structural changes accompanied by a decline in its function. The related information currently available is still scarce and contradictory. In addition, changes in some pulmonary parameters through aging process are species- and strain-dependent. The aim of this study was the assessment of the area and the number of pulmonary alveoli through the normal aging process in CD1 mouse. Paraffin-embedded sections of lungs from CD1 mice at age of 2, 6, 12, 18, or 24 months were stained with hematoxylin and eosin and examined using a light microscope. Images were captured using a camera linked to an image analysis software to measure areas and count alveoli. There was a significant difference in the alveolar area among the ages analyzed (F=87.53, Sig.=0.000). The alveolar area of the 6-, 12-, 18-, and 24-month-old mice was significantly greater (allpvalues < 0.001) than in mice at 2 months of age. Also, the alveolar number was significantly different among the ages tested (F=3.21, Sig.=0.023). The number of alveoli in mice at 2 months of age was greater than in mice at all other age groups, reaching statistical significance when compared with the 6-, 12-, and 18-month-old mice (pvalues of 0.044, 0.014, and 0.002, respectively). Thus, we observed an increase in alveolar area and a decrease in alveolar number through the aging process. This information might be useful to understand pathologic changes underlying susceptibility of elderly individuals to chronic lower respiratory tract diseases.
Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals
Authors: Doddapaneni Harsha , Cregeen Sara Javornik , Sucgang Richard , Meng Qingchang , Qin Xiang , Avadhanula Vasanthi , Chao Hsu , Menon Vipin , Nicholson Erin , Henke David , Piedra Felipe-Andres , Rajan Anubama , Momin Zeineen , Kottapalli Kavya , Hoffman Kristi L. , Sedlazeck Fritz J. , Metcalf Ginger , Piedra Pedro A. , Muzny Donna M. , Petrosino Joseph F. , Gibbs Richard A. 
Published: December 2020

AbstractThe newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed
Authors: Lanman Richard B. , Hylkema Linda , Boone Cristie M. , Allée Brian , Castillo Roger O. , Moreno Stephanie A. , Flores Mary Faith , DeSilva Upuli , Bingham Brittany , Kemp Brian M. 
Published: December 2020

AbstractUnderstanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.One Sentence SummaryFirst application of ancient DNA to extend a species’ historic range finds Chinook salmon native to San Jose, California.
Multithreaded variant calling in elPrep 5
Authors: Herzeel Charlotte , Costanza Pascal , Decap Dries , Fostier Jan , Wuyts Roel , Verachtert Wilfried 
Published: December 2020

AbstractWe present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps. Our benchmarks show that elPrep 5 speeds up the runtime of the variant calling pipeline by a factor 8-16x on both whole-exome and whole-genome data while using the same hardware resources as GATK 4. This makes elPrep 5 a suitable drop-in replacement for GATK 4 when faster execution times are needed.
Real-time Synthesis of Imagined Speech Processes from Minimally Invasive Recordings of Neural Activity
Authors: Angrick Miguel , Ottenhoff Maarten , Diener Lorenz , Ivucic Darius , Ivucic Gabriel , Goulis Sofoklis , Saal Jeremy , Colon Albert J. , Wagner Louis , Krusienski Dean J. , Kubben Pieter L. , Schultz Tanja , Herff Christian 
Published: December 2020

ABSTRACTSpeech neuroprosthetics aim to provide a natural communication channel to individuals who are unable to speak due to physical or neurological impairments. Real-time synthesis of acoustic speech directly from measured neural activity could enable natural conversations and significantly improve quality of life, particularly for individuals who have severely limited means of communication. Recent advances in decoding approaches have led to high quality reconstructions of acoustic speech from invasively measured neural activity. However, most prior research utilizes data collected during open-loop experiments of articulated speech, which neglects the critical human-in-the-loop aspect of a practical speech neuroprosthetic.Here we present an approach that synthesizes audible speech in real-time for both imagined and whispered speech conditions. Using a participant implanted with stereotactic depth electrodes, we were able to reliably generate audible speech in real-time. The decoding models rely predominately on frontal activity suggesting that speech processes have similar representations when vocalized, whispered, or imagined. Our real-time synthesis approach represents an essential step towards investigating how patients will learn to operate a closed-loop speech neuroprosthesis, as well as the development of techniques that incorporate co-adaptation of the user and system for optimized performance.
Physiological and pathological changes in the enteric nervous system of rotenone-exposed mice as early biomarkers for Parkinson’s disease
Authors: Schaffernicht Gabriela , Shang Qi , Stievenard Alicia , Bötzel Kai , Dening Yanina , Kempe Romy , Toussaint Magali , Gündel Daniel , Kranz Mathias , Reichmann Heinz , Vanbesien-Mailliot Christel , Brust Peter , Dieterich Marianne , Funk Richard H.W. , Ravens Ursula , Pan-Montojo Francisco 
Published: December 2020

AbstractParkinson’s disease (PD) is known to involve the peripheral nervous system (PNS) and the enteric nervous system (ENS). Functional changes in PNS and ENS appear early in the course of the disease and are responsible for some of the non-motor symptoms observed in PD patients like constipation, that can precede the appearance of motor symptoms by years. We have shown that environmental toxins can trigger the disease by acting on the ENS and on the autonomic nervous system. Oral exposure to the pesticide rotenone, a mitochondrial Complex I inhibitor, leads to decreased stool depositions in mice. Here we analyzed the effect of rotenone on the function and structure of the ENS by measuring intestinal contractility in a tissue bath and by analyzing related protein expression. Our results show that rotenone changes the normal physiological response of the intestine to carbachol, dopamine and electric field stimulation. The magnitude and direction of these alterations varies between intestinal regions and exposure times and is associated with an early up-regulation of dopaminergic, cholinergic and adrenergic receptors and an irregular reduction in the amount of enteric neurons in rotenone-exposed mice. The early appearance of these alterations makes them ideal candidates to be used as biomarkers for the detection of Parkinson’s disease in its early stages.
CEDAR, an online resource for the reporting and exploration of complexome profiling data
Authors: van Strien Joeri , Haupt Alexander , Schulte Uwe , Braun Hans-Peter , Cabrera-Orefice Alfredo , Choudhary Jyoti S. , Evers Felix , Fernandez-Vizarra Erika , Guerrero-Castillo Sergio , Kooij Taco W.A. , Páleníková Petra , Pardo Mercedes , Ugalde Cristina , Wittig Ilka , Wöhlbrand Lars , Brandt Ulrich , Arnold Susanne , Huynen Martijn A. 
Published: December 2020

AbstractComplexome profiling is an emerging ‘omics approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR,www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the “minimum information required for a complexome profiling experiment” (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.
NPRL3: Direct Effects on Human Phenotypic Variability, mTOR Signaling, Subcellular mTOR Localization, Cortical Lamination, and Seizure Susceptibility
Authors: Iffland Philip H. , Everett Mariah E. , Cobb-Pitstick Katherine M. , Bowser Lauren E. , Barnes Allan E. , Babus Janice K. , Romanowski Andrea , Baybis Marianna , Puffenberger Erik G. , Gonzaga-Jauregui Claudia , Poulopoulos Alexandros , Carson Vincent J. , Crino Peter B. 
Published: December 2020

AbstractNitrogen Permease Regulator Like 3(NPRL3)variants are associated with malformations of cortical development (MCD) and epilepsy. We report a large (n=133) founderNPRL3(c.349delG, p.Glu117LysFS) pedigree dating to 1727, with heterogeneous epilepsy and MCD phenotypes. Whole exome analysis in individuals with and without seizures in this cohort did not identify a genetic modifier to explain the variability in seizure phenotype. Then as a strategy to investigate the developmental effects of NPRL3 loss in human brain, we show that CRISPR/Cas9Nprl3knockout (KO) in Neuro2a cells (N2aC)in vitrocauses mechanistic target of rapamycin (mTOR) pathway hyperactivation, cell soma enlargement, and excessive cellular aggregation. Amino acid starvation caused mTOR inhibition and cytoplasmic mTOR localization in wildtype cells, whereas followingNprl3KO, mTOR remained inappropriately localized on the lysosome and activated, evidenced by persistent ribosomal S6 and 4E-BP1 phosphorylation, demonstrating thatNprl3loss decouples mTOR activation from metabolic state.Nprl3KO byin uteroelectroporation in fetal (E14) mouse cortex resulted in mTOR-dependent cortical dyslamination with ectopic neurons in subcortical white matter. EEG recordings of these mice showed hyperexcitability in the electroporated hemisphere.NPRL3variants are linked to a highly variable clinical phenotype likely as a consequence of mTOR-dependent effects on cell structure, cortical development, and network organization.
Distinct protocerebral neuropils associated with attractive and aversive female-produced odorants in the male moth brain
Authors: Kymre Jonas Hansen , Liu XiaoLan , Ian Elena , Berge Christoffer Nerland , Zhao XinCheng , Wang GuiRong , Berg Bente G. , Chu Xi 
Published: December 2020

AbstractThe pheromone system of heliothine moths is an optimal model for studying principles underlying higher-order olfactory processing. InHelicoverpa armigera, three male-specific glomeruli receive input about three female-produced signals, the primary pheromone component, serving as an attractant, and two minor constituents, serving a dual function, i.e. attraction versus inhibition of attraction. From the antennal-lobe glomeruli, the information is conveyed to higher olfactory centers, including the lateral protocerebrum, via three main paths – of which the medial tract is the most prominent. In this study, we traced physiologically identified medial-tract projection neurons from each of the three male-specific glomeruli with the aim of mapping their terminal branches in the lateral protocerebrum. Our data suggest that the neurons’ wide-spread projections are organized according to behavioral significance, including a spatial separation of signals representing attraction versus inhibition – however, with a unique capacity of switching behavioral consequence based on the amount of the minor components.
Introducingselfisher: open source software for statistical analyses of fishing gear selectivity
Authors: Brooks Mollie E , Melli Valentina , Savina Esther , Santos Juan , Millar Russell , O’Neill Finbarr Gerard , Veiga-Malta Tiago , Krag Ludvig Ahm , Feekings Jordan Paul 
Published: December 2020

AbstractFishing gear is constantly being improved to select certain sizes and species while excluding others. Experiments are conducted to quantify the selectivity and the resulting data needs to be analyzed using specialized statistical methods in many cases. Here, we present a new estimation tool for analyzing this type of data: an R package namedselfisher. It can be used for both active and passive gears, and can handle different trial designs. It allows fitting models containing multiple fixed effects (e.g. length, total catch weight, mesh size, water turbidity) and random effects (e.g. haul). A bootstrapping procedure is provided to account for between and within haul variability and overdispersion. We demonstrate its use via four case studies including (1) covered codend analyses of four gears, (2) a paired gear study with numerous potential covariates, (3) a catch comparison study of unpaired hauls of gillnets and (4) a catch comparison study of paired hauls using polynomials and splines. This free and open source software will make it easier to model fishing gear selectivity, teach the statistical methods, and make analyses more repeatable.
Cell type-specific isolation and transcriptomic profiling informs glial pathology in human temporal lobe epilepsy
Authors: Tome-Garcia Jessica , Nudelman German , Mussa Zarmeen , Caballero Elodia , Jiang Yan , Beaumont Kristin G. , Wang Ying-Chih , Sebra Robert , Akbarian Schahram , Pinto Dalila , Zaslavsky Elena , Tsankova Nadejda M. 
Published: December 2020

SUMMARYThe pathophysiology of epilepsy underlies complex network dysfunction, the cell-type-specific contributions of which remain poorly defined in human disease. In this study, we developed a strategy that simultaneously isolates neuronal, astrocyte and oligodendroglial progenitor (OPC)-enriched nuclei from human fresh-frozen neocortex and applied it to characterize the distinct transcriptome of each cell type in temporal lobe epilepsy (TLE) surgical samples. Differential RNA-seq analysis revealed several dysregulated pathways in neurons, OPCs, and astrocytes, and disclosed an immature phenotype switch in TLE astrocytes. An independent single cell RNA-seq TLE dataset uncovered a hybrid population of cells aberrantly co-expressing canonical astrocyte and OPC-like progenitor markers (GFAP+OLIG2+ glia), which we corroborated in-situ in human TLE samples, and further demonstrated their emergence after chronic seizure injury in a mouse model of status epilepticus. In line with their immature signature, a subset of human TLE glia were also abnormally proliferative, both in-vivo and in-vitro. Generally, this analysis validates the utility of the proposed cell type-specific isolation strategy to study glia-specific changes ex vivo using fresh-frozen human samples, and specifically, it delineates an aberrant glial phenotype in human TLE specimens.
The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria
Authors: Ansorge Rebecca , Romano Stefano , Sayavedra Lizbeth , Rubin-Blum Maxim , Gruber-Vodicka Harald , Scilipoti Stefano , Molari Massimiliano , Dubilier Nicole , Petersen Jillian 
Published: December 2020

AbstractSulfur-oxidizingThioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generatedThioglobaceaegenomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within mostThioglobaceaepopulations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.
Four-dimensional tractography animates neural propagations via distinct interhemispheric pathways
Authors: Mitsuhashi Takumi , Sonoda Masaki , Jeong Jeong-won , Silverstein Brian H. , Iwaki Hirotaka , Luat Aimee F. , Sood Sandeep , Asano Eishi 
Published: December 2020

AbstractObjectiveTo visualize and validate the dynamics of interhemispheric neural propagations induced by single-pulse electrical stimulation (SPES).MethodsThis methodological study included three patients with drug-resistant focal epilepsy who underwent measurement of cortico-cortical spectral responses (CCSRs) during bilateral stereo-electroencephalography recording. We delivered SPES to 83 electrode pairs and analyzed CCSRs recorded at 268 nonepileptic electrode sites. Diffusion-weighted imaging (DWI) tractography localized the interhemispheric white matter pathways as streamlines directly connecting two electrode sites. We localized and visualized the putative SPES-related fiber activation, at each 1-ms time window, based on the propagation velocity defined as the DWI-based streamline length divided by the early CCSR peak latency.ResultsThe resulting movie, herein referred to as four-dimensional tractography, delineated the spatiotemporal dynamics of fiber activation via the corpus callosum and anterior commissure. Longer streamline length was associated with delayed peak latency and smaller amplitude of CCSRs. The cortical regions adjacent to each fiber activation site indeed exhibited CCSRs at the same time window.ConclusionsOur four-dimensional tractography successfully animated neural propagations via distinct interhemispheric pathways.SignificanceOur novel animation method has the potential to help investigators in addressing the mechanistic significance of the interhemispheric network dynamics supporting physiological function.