bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Density Adaptive Ten Ten: Proposal for Electrode Nomenclature for High-Density EEG
Authors: Heine Walter , Dobrota Mary-Ann , Schomer Donald , Wigton Rebekah , Herman Susan 
Published: September 2019

Purpose:
High-density EEG (HD-EEG) systems and electrical source imaging techniques have revolutionized our ability to assess the potential sources of epileptiform activity and other EEG features. Nonetheless, clinical use of HD-EEG is hampered by the lack of a standardized electrode nomenclature system and the inherent difficulties encountered in visually reviewing recordings. Inefficient visual review of HD-EEG remains a major barrier to incorporating these techniques into routine clinical care.

Methods:
Extension of the 10-10 is first defined by the addition of 2 reference curves: the −10% and −20% axial reference curves. Electrode positions over the face are named based on facial bony structures (N = nasion, Z = zygomatic prominence, M = mandible) and over the back of the head on posterior landmarks (I = inion, S = subinion, B = Base). Then, following the 10% incremental distance rule, we define additional electrode positions. Electrodes with nonstandard positions are clustered around the closest 10-10 electrode, deemed their cardinal point.

Results:
The 256-electrode Geodesic Sensor Net mapped to 96 of the 120 extended 10-10 cardinal electrodes.

Conclusions:
Electrode position nomenclature that builds upon the international standard 10-10 system allows electroencephalographers to identify spatial areas of interest in HD-EEG relative to positions in routine use. A standard viewing montage for HD-EEG and its application with electrical source imaging boost efficiency when reviewing data and improve accuracy in recognizing epileptiform discharges. Additionally, our proposed system is not limited to a specific HD-EEG system, electrode count, or electrode layout.
Determinants of first aid knowledge and basic practice among elementary school teachers in Debre Tabor City, Northwest Ethiopia
Authors: Taklual Wubet , Mekie Maru , Yenew Chalachew 
Published: September 2019

AbstractBackgroundUnpremeditated injuries are the leading causes of morbidity and mortality in pediatrics population, especially in low and middle-income countries. Giving immediate help for an injured child is a crucial step for saving the child from further disability and/or death. This study aimed to assess the determinant factors of first aid knowledge and basic practice among elementary school teachers in Debre Tabor, Ethiopia.MethodInstitution based cross-sectional study was employed in Debre Tabor City. Single population proportion formula was used for sample size calculation and a total of 216 elementary school teachers were included in study. Simple random sampling technique with proportional allocation was applied for selections of the study participant. Data entry was done by Epi data version 3.1 and the data was exported to SPSS version 21 for analysis. Binary and multivariable logistic regression analysis were performed to identify determinants of knowledge on first aid. Crude and adjusted odds ratios were used to determine the significance and strength of association at 95% confidence interval.ResultOur study revealed that 45.8% of the subjects were knowledgeable on first aid. More than 75% of study participant reported that they have encountered a child who need first aid. Among this 64% of them provide first aid. The multivariable analysis revealed that service year (AOR=3.51, 95%CI: (1.06, 11.59)), educational status (AOR=12.15, 95%CI: (3.17, 46.67)), previous first aid training (AOR=0.43, 95%CI: (0.21, 0.87)) and information about first aid (AOR=0.12, 95%CI ;(0.03, 0.48)) were found to be significantly associated with having knowledge on first aid.ConclusionSchool teachers have low knowledge on first aid. Educational status, service year, previous first aid training and information on first aid were the predictor of first aid knowledge. Introducing essential first aid training in the curriculum during teachers’ training shall be considered.
Input dose differentiation by NF-κB
Authors: Son Minjun , Wang Andrew , Tu Hsiung-Lin , Metzig Marie O , Patel Parthiv , Husain Kabir , Lin Jing , Murugan Arvind , Hoffmann Alexander , Tay Savaş 
Published: September 2019

AbstractCells receive a wide range of dynamic signaling inputs during immune regulation, but how gene regulatory networks measure and interpret such dynamic inputs is not understood. Here, we used microfluidic live-cell analysis and mathematical modeling to study how NF-κB pathway in single-cells responds to time-varying immune inputs such as increasing, decreasing or fluctuating cytokine signals. Surprisingly, we found that NF-κB acts as a differentiator, responding strictly to the absolute difference in cytokine concentration, and not to the concentration itself. Our analyses revealed that negative feedbacks by the regulatory proteins A20 and IκBα enable dose differentiation by providing short-term memory of prior cytokine level and continuously resetting kinase cycling and receptor levels. Investigation of NF-κB target gene expression showed that cells create unique transcriptional responses under different dynamic cytokine profiles. Our results demonstrate how cells use simple network motifs and transcription factor dynamics to efficiently extract information from complex signaling environments.
Distinguishing pedigree relationships using multi-way identical by descent sharing and sex-specific genetic maps
Authors: Qiao Ying , Sannerud Jens , Basu-Roy Sayantani , Hayward Caroline , Williams Amy L. 
Published: September 2019

AbstractThe proportion of samples with one or more close relatives in a genetic dataset increases rapidly with sample size, necessitating relatedness modeling and enabling pedigree-based analyses. Despite this, relatives are generally unreported and current inference methods typically detect only the degree of relatedness of sample pairs and not pedigree relationships. We developed CREST, an accurate and fast method that identifies the pedigree relationships of close relatives. CREST utilizes identical by descent (IBD) segments shared between a pair of samples and their mutual relatives, leveraging the fact that sharing rates among these individuals differ across pedigree configurations. Furthermore, CREST exploits the profound differences in sex-specific genetic maps to classify pairs as maternally or paternally related—e.g., paternal half-siblings—using the locations of autosomal IBD segments shared between the pair. In simulated data, CREST correctly classifies 91.5-99.5% of grandparent-grandchild (GP) pairs, 70.5-97.0% of avuncular (AV) pairs, and 79.0-98.0% of half-siblings (HS) pairs compared to PADRE’s rates of 38.5-76.0% of GP, 60.5-92.0% of AV, 73.0-95.0% of HS pairs. Turning to the real 20,032 sample Generation Scotland (GS) dataset, CREST correctly determines the relationship of 99.0% of GP, 85.7% of AV, and 95.0% of HS pairs that have sufficient mutual relative data, completing this analysis in 10.1 CPU hours including IBD detection. CREST’s maternal and paternal relationship inference is also accurate, as it flagged five pairs as incorrectly labeled in the GS pedigrees— three of which we confirmed as mistakes, and two with an uncertain relationship—yielding 99.7% of HS and 93.5% of GP pairs correctly classified.
Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes
Authors: Ashwood Christopher , Waas Matthew , Weerasekera Ranjuna , Gundry Rebekah L. 
Published: September 2019

AbstractCell surface glycoproteins play critical roles in maintaining cardiac structure and function in health and disease and the glycan-moiety attached to the protein is critical for proper protein folding, stability and signaling. However, despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. In the current study, we used porous graphitized carbon liquid chromatography interfaced with mass spectrometry (PGC-LC-MS) to generate glycan structure libraries for primary human heart tissue homogenate, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM). Altogether, we established the first reference structure libraries of the cardiac glycome containing 265N-andO-glycans. Comparing theN-glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, 21 structures significantly differed, and the high mannose class is increased in enriched CM. Moreover, by comparing primary CM to hiPSC-CM collected during 20-100 days of differentiation, dynamic changes in the glycan profile throughoutin vitrodifferentiation were observed and differences between primary and hiPSC-CM were revealed. Namely, >30% of theN-glycome significantly changed across these time-points of differentiation and only 23% of theN-glycan structures were shared between hiPSC-CM and primary CM. These observations are an important complement to current genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. Finally, these data are expected to support future regenerative medicine efforts by informing targets for evaluating the immunogenic potential of hiPSC-CM and harnessing differences between immature, proliferative hiPSC-CM and adult primary CM.
Meta-16S rRNA gene phylogenetic reconstruction reveals astonishing diversity of the cosmopolitan myxobacteria
Authors: Liu Yang , Yao Qing , Zhu Hong-Hui 
Published: September 2019

ABSTRACTNumerous ecological studies for myxobacteria have been conducted well, but their true diversity hidden in plain sight remains to be explored. To bridge this gap, we here implemented a comprehensive survey of diversity and distribution of myxobacteria by using 4997 publicly available 16S rRNA gene sequences (≥1200 bp) collected from several hundreds of sites across multiple countries and regions. In the study, the meta-16S rRNA gene phylogenetic reconstruction clearly revealed that these sequences were classified to 998 species, 445 genera, 58 families, and 20 suborders, highlighting a considerable taxonomic diversity of myxobacteria, the great majority of which belonged to new taxa. Most cultured myxobacteria including the well-described type strains were strongly inclined to locate on the shallow branches of the phylogenetic tree; on the contrary, the majority of uncultured myxobacteria the deep branches. The geographical analysis of sequences based on their environmental categories clearly demonstrated that myxobacteria showed a nearly cosmopolitan distribution, despite the presence of some habitat-specific taxa, especially at genus and species levels. Among all abundant suborders, members of Suborder_4, Suborder_15, and Suborder_17 were more widely distributed in marine environments, the remaining suborders preferred to reside in terrestrial ecosystems, particularly in soils, indicating a potential selectivity of geographical distribution. In conclusion, this study profiles a clear framework of diversity and distribution of the cosmopolitan myxobacteria and sheds light on the isolation of the uncultured myxobacteria.IMPORTANCEMyxobacteria are an attractive bacterial group ubiquitous in soil and aquatic environments. However, the biodiversity and ecological preferences of myxobacteria remain poorly understood across heterogeneous environments. We analyzed thousands of publicly available and high-quality 16S rRNA gene sequences of myxobacteria by using the phylogenetic reconstruction. The study presented an astonishing diversity than that expected from the previous studies. This study further demonstrated that the culturability of myxobacteria was perfectly comparable to its phylogeny in the phylogenetic tree. The geographical analysis clearly indicated that myxobacteria showed a nearly cosmopolitan distribution, while some taxa exhibited obvious preferences for specific environmental conditions. Together, our study provides novel insights into the diversity, distributions, and ecological preferences of of myxobacteria from diverse environments and lays the foundation for innovation of isolation techniques and the discovery of new secondary metabolites.
Potential of genomic selection for improvement of resistance to Ostreid Herpes virus in Pacific oyster (Crassostrea gigas)
Authors: Gutierrez Alejandro P. , Symonds Jane , King Nick , Steiner Konstanze , Bean Tim P. , Houston Ross D. 
Published: September 2019

AbstractIn genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values (gEBVs) for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the “summer mortality syndrome”. This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the Ostreid herpesvirus (OsHV-1-μvar). In the current study, we evaluated the potential of genomic selection for host resistance OsHV in Pacific oysters, and compared it to pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for seven days. 768 samples were genotyped using the medium density SNP array for oysters. GWAS was performed for the survival trait using a GBLUP approach in BLUPF90 software. Heritability ranged from 0.25±0.05 to 0.37±0.05 (mean±s.e) based on pedigree and genomic information, respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below ∼500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programs and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate gEBVs, thus potentially making the implementation of GS more cost effective.
Streptococcus pyogenes Cas9 displays biased one-dimensional diffusion on dsDNA to search for a target
Authors: Yang Mengyi , Zhang Lijingyao , Sun Ruirui , Zhong Weixiong , Yang Yuzhuo , Chen Chunlai 
Published: September 2019

AbstractThe RNA-guided Streptococcus pyogenes Cas9 (spCas9) is a sequence-specific DNA endonuclease that works as one of the most powerful genetic editing tools. However, how the Cas9 locates its target among huge amounts of dsDNAs remains controversial. Here, combining biochemical and single-molecule assays, we revealed that Cas9 uses both three-dimensional and one-dimensional diffusion to find its target. We further observed a surprising biased one-dimensional diffusion of Cas9 from 3’ to 5’ end of the non-target strand under physiological salt condition, whereas low ionic concentration or mutations on PAM recognition residues induce unbiased one-dimensional diffusion of Cas9 along dsDNA. We quantified the diffusion length of 27 bp, which accelerates the target search efficiency of Cas9 by ∼ 10 folds. Our results reveal a unique searching mechanism of Cas9 at physiological salt conditions, and provide important guidance for both in-vitro and in-vivo applications of Cas9.
Predicting Alzheimer’s disease progression using deep recurrent neural networks
Authors: Nguyen Minh , He Tong , An Lijun , Alexander Daniel C. , Feng Jiashi , Yeo B.T. Thomas ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: September 2019

AbstractEarly identification of individuals at risk of developing Alzheimer’s disease (AD) dementia is important for developing disease-modifying therapies. In this study, given multimodal AD markers and clinical diagnosis of an individual from one or more timepoints, we seek to predict the clinical diagnosis, cognition and ventricular volume of the individual for every month (indefinitely) into the future. We proposed and applied a minimal recurrent neural network (minimalRNN) model to data from The Alzheimer’s Disease Prediction Of Longitudinal Evolution (TADPOLE) challenge, comprising longitudinal data of 1677 participants (Marinescu et al. 2018) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). We compared the performance of the minimalRNN model and four baseline algorithms up to 6 years into the future. Most previous work on predicting AD progression ignore the issue of missing data, which is a prevalent issue in longitudinal data. Here, we explored three different strategies to handle missing data. Two of the strategies treated the missing data as a “preprocessing” issue, by imputing the missing data using the previous timepoint (“forward filling”) or linear interpolation (“linear filling). The third strategy utilized the minimalRNN model itself to fill in the missing data both during training and testing (“model filling”). Our analyses suggest that the minimalRNN with “model filling” compared favorably with baseline algorithms, including support vector machine/regression, linear state space (LSS) model, and long short-term memory (LSTM) model. Importantly, although the training procedure utilized longitudinal data, we found that the trained minimalRNN model exhibited similar performance, when using only 1 input timepoint or 4 input timepoints, suggesting that our approach might work well with just cross-sectional data. An earlier version of our approach was ranked 5th (out of 53 entries) in the TADPOLE challenge in 2019. The current approach is ranked 2nd out of 63 entries as of June 3rd, 2020.
No division of labour, and subfertile foundresses, in a phyllode-gluing Acacia thrips
Authors: Gilbert James D. J. 
Published: September 2019

ABSTRACTBehavioural variation is a hallmark of animal societies, which commonly contain breeders and nonbreeders, and helpers and nonhelpers. In some cases labour is divided with nonbreeders “helping” – gaining indirectly, via genetic benefits, or directly, e.g. by augmenting group size. Conversely, they may benefit by not helping, conserving energy for breeding later. However, subordinate behaviour after inheriting a breeding position is rarely evaluated.In the Australian interior, Acacia thripsDunatothrips aneurae(Thysanoptera) glueAcaciaphyllodes together into “domiciles”. Foundresses, usually sisters, build domiciles singly or communally. Some co-foundresses are nonreproductive, and their role is currently unknown. I experimentally rejected the idea that they substantially “help” by contributing to domicile repair. Nonreproductives were less likely to repair damage than reproductives. Alternatively, they may be waiting to inherit the domicile, or simply of too poor quality to reproduce or help. To test these alternatives, in the field, I allowed repairer or nonrepairer females to “inherit” a domicile by removing their nestmate(s). Thus isolated, “nonrepairer” females took much longer to repair domiciles than “repairers”, control singletons or pairs. Although ovarian condition was equivalent across groups, after 21 days nonrepairers actually laid fewer eggs compared to other groups.Thus, labour was not divided: instead reproduction and helping covaried, probably depending on female quality and the outcome of intra-domicile competition. Nonreproductive nonhelpers were not waiting to breed. Their role, and their net effect on colony productivity, remains to be shown. They are likely subfertile, and may make the “best of a bad job” by gaining indirect benefits to the best of their limited ability.
Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP
Authors: Crozat Estelle , Tardin Catherine , Salhi Maya , Rousseau Philippe , Lablaine Armand , Bertoni Tommaso , Holcman David , Sclavi Bianca , Cicuta Pietro , Cornet François 
Published: September 2019

AbstractThe ter region of the bacterial chromosome, where replication terminates, is the last to be segregated before cell division in Escherichia coli. Delayed segregation is controlled by the MatP protein, which binds to specific sites (matS) within ter, and interacts with other proteins such as ZapB. Here, we investigate the role of MatP by combining short-time mobility analyses of the ter locus with biochemical approaches. We find that ter mobility is similar to that of a non-ter locus, except when sister ter loci are paired after replication. This effect depends on MatP, the persistence of catenanes, and ZapB. We characterise MatP/DNA complexes and conclude that MatP binds DNA as a tetramer, but bridging matS sites in a DNA-rich environment remains infrequent. We propose that tetramerisation of MatP links matS sites with ZapB and/or with non-specific DNA to promote optimal pairing of sister ter regions until cell division.
Analysis of genes within the schizophrenia-linked 22q11.2 deletion identifies interaction of night owl/LZTR1 and NF1 in GABAergic sleep control
Authors: Maurer Gianna W. , Malita Alina , Nagy Stanislav , Koyama Takashi , Werge Thomas M. , Halberg Kenneth A. , Texada Michael J. , Rewitz Kim 
Published: September 2019

AbstractThe human 22q11.2 chromosomal deletion is one of the strongest identified genetic risk factors for schizophrenia. Although the deletion spans a number of genes, the contribution of each of these to the 22q11.2 deletion syndrome (DS) is not known. To investigate the effect of individual genes within this interval on the pathophysiology associated with the deletion, we analyzed their role in sleep, a behavior affected in virtually all psychiatric disorders, including the 22q11.2 DS. We identified the gene LZTR1 (night owl, nowl) as a regulator of sleep in Drosophila. Neuronal loss of nowl causes short and fragmented sleep, especially during the night. In humans, LZTR1 has been associated with Ras-dependent neurological diseases also caused by Neurofibromin-1 (Nf1) deficiency. We show that Nf1 loss leads to a night-time sleep phenotype nearly identical to that of nowl loss, and that nowl negatively regulates Ras and interacts with Nf1 in sleep regulation. We also show that nowl is required for metabolic homeostasis, suggesting that LZTR1 may contribute to the genetic susceptibility to obesity associated with the 22q11.2 DS. Furthermore, knockdown of nowl or Nf1 in GABA-responsive sleep-promoting neurons elicits the sleep-fragmentation phenotype, and this defect can be rescued by increased GABAA receptor signaling, indicating that Nowl promotes sleep by decreasing the excitability of GABA-responsive wake-driving neurons. Our results suggest that nowl/LZTR1 may be a conserved regulator of GABA signaling and sleep that contributes to the 22q11.2 DS.