bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reoxygenation with 100% Oxygen Following Hypoxia in Mice Causes Apoptosis
Authors: Nishimura Yoshiro , Ueki Masaaki , Imanishi Masaki , Tomita Shuhei , Ueno Masaki , Morishita Jun , Nishiyama Takashi 
Published: May 2017

ABSTRACT
After hypoxia, reoxygenation with air is the consensus treatment for full-term neonates; however, the effect of hyperoxic reoxygenation of adults is unknown. The present study was designed to investigate the effects of reoxygenation with 100% oxygen after hypoxia on inflammation and apoptosis in mice. Eight-week-old mice were either subjected to hypoxia in 8% oxygen for 30 min or air served as controls. Following hypoxia, mice underwent reoxygenation for 30 min with 21% or 100% oxygen. Tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), caspase-3 and brain derived neurotrophic factor (BDNF) mRNA study and histopathological study were performed. Reoxygenation with 100% oxygen significantly increased TNF-α (2.5 h after hypoxia), IL-1β (5 h after hypoxia), caspase-3 (8 h after hypoxia) mRNA levels in the whole brain compared with 21% oxygen, and significantly decreased erythropoietin mRNA expression compared with 21% oxygen 9 h after reoxygenation. However, reoxygenation with 100% oxygen and 21% oxygen significantly decreased BDNF mRNA levels compared with control air group. There were no clear abnormal findings showing neuronal death among the three groups. Reoxygenation with 100% oxygen after hypoxia induced inflammation and apoptosis in adult mice. Therefore, these results suggest that the reoxygenation with 100% oxygen after hypoxia has harmful effects on adult brain as well as on neonatal brain.
Pharmacological Stimulation of Neuronal Plasticity in Acquired Brain Injury
Authors: Carrillo-Mora Paul , Alcantar-Shramm Juan Manuel , Almaguer-Benavides Kievka M. , Macías-Gallardo Julio José , Fuentes-Bello Alim , Rodríguez-Barragán Marlene A. 
Published: May 2017

Introduction
Brain injuries are one of the leading causes of disability worldwide. It is estimated that nearly half of patients who develop severe sequelae will continue with a chronic severe disability despite having received an appropriate rehabilitation program. For more than 3 decades, there has been a worldwide effort to investigate the possibility of pharmacologically stimulating the neuroplasticity process for enhancing the recovery of these patients.

Objective
The objective of this article is to make a critical and updated review of the available evidence that supports the positive effect of different drugs on the recovery from brain injury.

Method
To date, there have been several clinical trials that tested different drugs that act on different neurotransmitter systems: catecholaminergic, cholinergic, serotonergic, and glutamatergic. There is both basic and clinical evidence that may support some positive effect of these drugs on motor, cognitive, and language skills; however, only few of the available studies are of sufficient methodological quality (placebo controlled, randomized, blinded, multicenter, etc) to make solid conclusions about their beneficial effects.

Conclusions
Currently, the pharmacological stimulation of neuroplasticity still does not have enough scientific evidence to make a systematic therapeutic recommendation for all patients, but it certainly is a feasible and very promising field for future research.
A unified internal model theory to resolve the paradox of active versus passive self-motion sensation
Authors: Laurens Jean , Angelaki Dora 
Published: May 2017

AbstractBrainstem and cerebellar neurons implement an internal model to accurately estimate self-motion during externally-generated (‘passive’) movements. However, these neurons show reduced responses during self-generated (‘active’) movements, indicating that the brain computes the predicted sensory consequences of motor commands in order to cancel sensory signals. Remarkably, the computational processes underlying sensory prediction during active motion and their relationship to internal model computations established during passive movements remain unknown. Here we construct a Kalman filter that incorporates motor commands into a previously-established model of optimal passive self-motion estimation. We find that the simulated sensory error and feedback signals match experimentally measured neuronal response during active and passive head and trunk rotations and translations. We conclude that a single internal model of head motion can process motor commands and sensory afferent signals optimally, and we describe how previously identified neural responses in the brainstem and cerebellum may represent distinct nodes in these computations.
Metagenomic binning through low density hashing
Authors: Luo Yunan , William Yu Y. , Zeng Jianyang , Berger Bonnie , Peng Jian 
Published: May 2017

AbstractBacterial microbiomes of incredible complexity are found throughout the world, from exotic marine locations to the soil in our yards to within our very guts. With recent advances in Next-Generation Sequencing (NGS) technologies, we have vastly greater quantities of microbial genome data, but the nature of environmental samples is such that DNA from different species are mixed together. Here, we present Opal for metagenomic binning, the task of identifying the origin species of DNA sequencing reads. Our Opal method introduces low-density, even-coverage hashing to bioinformatics applications, enabling quick and accurate metagenomic binning. Our tool is up to two orders of magnitude faster than leading alignment-based methods at similar or improved accuracy, allowing computational tractability on large metagenomic datasets. Moreover, on public benchmarks, Opal is substantially more accurate than both alignment-based and alignment-free methods (e.g. on SimHC20.500, Opal achieves 95% F1-score while Kraken and CLARK achieve just 91% and 88%, respectively); this improvement is likely due to the fact that the latter methods cannot handle computationally-costly long-range dependencies, which our even-coverage, low-density fingerprints resolve. Notably, capturing these long-range dependencies drastically improves Opal’s ability to detect unknown species that share a genus or phylum with known bacteria. Additionally, the family of hash functions Opal uses can be generalized to other sequence analysis tasks that rely on k-mer based methods to encode long-range dependencies.
Deep Sequencing: Intra-terrestrial metagenomics illustrates the potential of off-grid Nanopore DNA sequencing
Authors: Edwards Arwyn , Soares André , Rassner Sara M.E. , Green Paul , Félix João , Mitchell Andrew C. 
Published: May 2017

AbstractGenetic and genomic analysis of nucleic acids from environmental samples has helped transform our perception of the Earth’s subsurface as a major reservoir of microbial novelty. Many of the microbial taxa living in the subsurface are under-represented in culture-dependent investigations. In this regard, metagenomic analyses of subsurface environments exemplify both the utility of metagenomics and its power to explore microbial life in some of the most extreme and inaccessible environments on Earth. Hitherto, the transfer of microbial samples to home laboratories for DNA sequencing and bioinformatics is the standard operating procedure for exploring microbial diversity. This approach incurs logistical challenges and delays the characterization of microbial biodiversity. For selected applications, increased portability and agility in metagenomic analysis is therefore desirable. Here, we describe the implementation of sample extraction, metagenomic library preparation, nanopore DNA sequencing and taxonomic classification using a portable, battery-powered, suite of off-the-shelf tools (the “MetageNomad”) to sequence ochreous sediment microbiota while within the South Wales Coalfield. While our analyses were frustrated by short read lengths and a limited yield of DNA, within the assignable reads, Proteobacterial (α-, β-, γ-Proteobacteria) taxa dominated, followed by members ofActinobacteria, FirmicutesandBacteroidetes, all of which have previously been identified in coals. Further to this, the fungal genusCandidawas detected, as well as a methanogenic archaeal taxon. To the best of our knowledge, this application of the MetageNomad represents an initial effort to conduct metagenomics within the subsurface, and stimulates further developments to take metagenomics off the beaten track.
Interpreting a Sequenced Genome: Toward a Cosmid Transgenic Library ofCaenorhabditis elegans
Authors: Janke Diana L. , Schein Jacqueline E. , Ha Thê , Franz Norman W. , O’Neil Nigel J. , Vatcher Greg P. , Stewart Helen I. , Kuervers Lynnette M. , Baillie David L. , Rose Ann M. 
Published: May 2017

We have generated a library of transgenic Caenorhabditis elegans strains that carry sequenced cosmids from the genome of the nematode. Each strain carries an extrachromosomal array containing a single cosmid, sequenced by the C. elegans Genome Sequencing Consortium, and a dominate Rol-6 marker. More than 500 transgenic strains representing 250 cosmids have been constructed. Collectively, these strains contain approximately 8 Mb of sequence data, or ∼8% of the C. elegans genome. The transgenic strains are being used to rescue mutant phenotypes, resulting in a high-resolution map alignment of the genetic, physical, and DNA sequence maps of the nematode. We have chosen the region of chromosome III deleted bysDf127 and not covered by the duplicationsDp8(III;I) as a starting point for a systematic correlation of mutant phenotypes with nucleotide sequence. In this defined region, we have identified 10 new essential genes whose mutant phenotypes range from developmental arrest at early larva, to maternal effect lethal. To date, 8 of these 10 essential genes have been rescued. In this region, these rescues represent ∼10% of the genes predicted by GENEFINDER and considerably enhance the map alignment. Furthermore, this alignment facilitates future efforts to physically position and clone other genes in the region.[Updated information about the Transgenic Library is available via the Internet at http://darwin.mbb.sfu.ca/imbb/dbaillie/cosmid.html.]
The Organization of the γ-Glutamyl Transferase Genes and Other Low Copy Repeats in Human Chromosome 22q11
Authors: Collins John E. , Mungall Andrew J. , Badcock Karen L. , Fay Joanne M. , Dunham Ian 
Published: May 2017

A clone map consisting of YACs, cosmids, and fosmids has been constructed covering low copy repeat regions of human chromosome 22q11. A combination of clone restriction digest analysis, single-copy landmark content analysis, HindIII–Sau3AI fingerprinting, and sequencing of PCR products derived from clones was required to resolve the map in this region. Seven repeat-containing contigs were placed in 22q11, five containing γ-glutamyl transferase (GGT) sequences described previously. In one case, a single interval at the resolution of the YAC map was shown to contain at least three GGT sequences after higher resolution mapping. The sequence information was used to design a rapid PCR/restriction digest technique that distinguishes the GGT loci placed in the YAC map. This approach has allowed us to resolve the previous cDNA and mapping information relating to GGT and link it to the physical map of 22q11.[The sequence data described in this paper have been submitted to EMBL under accession nos. Z93342 (gene 11; EMBL identification no. HSGGT11), Z93343 (gene 12; EMBL no. HSGGT12), Z93344(gene 1; EMBL no. HSGGT1A), Z93345 (gene 2; EMBL no. HSGGT2A), Z93346(gene 3; EMBL no. HSGGT3A), Z93347 (gene 3-like; EMBL no. HSGGT3L), andZ93348 (gene 6; EMBL no. HSGGT6).]
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes
Authors: Devine Scott E. , Chissoe Stephanie L. , Eby Yolanda , Wilson Richard K. , Boeke Jef D. 
Published: May 2017

Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3–140 copies per genome. Copies of IR-1, IR-2, IR-4, and IR-5 are located on all (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-5 element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http://www.welch.jhu.edu/~devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set of tools may be used to sequence, track, and study repetitive DNA in model organisms and humans.[The sequences reported in this paper have been deposited in GenBank under accession nos. U53139 and U86946–U86951.]
High-Resolution Mapping and Transcript Identification at the Progressive Epilepsy with Mental Retardation Locus on Chromosome 8p
Authors: Ranta Susanna , Lehesjoki Anna-Elina , Bonaldo Maria de Fatima , Knowles James A. , Hirvasniemi Aune , Ross Barbara , de Jong Pieter J. , Soares Marcelo Bento , de la Chapelle Albert , Gilliam T. Conrad 
Published: May 2017

Progressive epilepsy with mental retardation (EPMR) is an autosomal recessive central nervous system disorder characterized by childhood onset epilepsy and subsequent mental retardation. The locus for EPMR has been mapped to human chromosome 8p23. We recently reported the construction of a YAC contig across the 4 centimorgan minimum genetic region that harbors the disease locus. We now report further delineation of the critical region to <700 kb. Our mapping strategy relied on the identification of nine novel microsatellite markers and the construction of a complete BAC contig across the critical region. Several partial gene sequences have been identified from the region and are being analyzed as candidate genes for EPMR.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF009188–AF009214.]
Two Large Families of Chemoreceptor Genes in the NematodesCaenorhabditis elegans and Caenorhabditis briggsae Reveal Extensive Gene Duplication, Diversification, Movement, and Intron Loss
Authors: Robertson Hugh M. 
Published: May 2017

The str family of genes encoding seven-transmembrane G-protein-coupled or serpentine receptors related to the ODR-10 diacetyl chemoreceptor is very large, with at least 197 members in theCaenorhabditis elegans genome. The closely relatedstl family has 43 genes, and both families are distantly related to the srd family with 55 genes. Analysis of the structures of these genes indicates that a third of them are clearly or likely pseudogenes. Preliminary surveys of other candidate chemoreceptor families indicates that as many as 800 genes and pseudogenes or 6% of the genome might encode 550 functional chemoreceptors constituting 4% of the C. elegans protein complement. Phylogenetic analyses of the str and stlfamilies, and comparisons with a few orthologs in Caenorhabditis briggsae, reveal ongoing processes of gene duplication, diversification, and movement. The reconstructed ancestral gene structures for these two families have eight introns each, four of which are homologous. Mapping of intron distributions on the phylogenetic tree reveals that each intron has been lost many times independently. Most of these introns were lost individually, which might best be explained by precise in-frame deletions involving nonhomologous recombination between short direct repeats at their termini.[Alignment of the putatively functional proteins in the str and stl families is available from Pfam (http://genome.wustl.edu/Pfam); alignments of all translations are available at http://cshl.org/gr; alignments of the genes are available from the author at hughrobe@uiuc.edu]
Ribonuclease k6: Chromosomal Mapping and Divergent Rates of Evolution within the RNase A Gene Superfamily
Authors: Deming Madeleine S. , Dyer Kimberly D. , Bankier Alan T. , Piper Michael B. , Dear Paul H. , Rosenberg Helene F. 
Published: May 2017

We have localized the gene encoding human RNase k6 to within ∼120 kb on the long (q) arm of chromosome 14 by HAPPY mapping. With this information, the relative positions of the six human RNase A ribonucleases that have been mapped to this locus can be inferred. To further our understanding of the individual lineages comprising the RNase A superfamily, we have isolated and characterized 10 novel genes orthologous to that encoding human RNase k6 from Great Ape, Old World, and New World monkey genomes. Each gene encodes a complete ORF with no less than 86% amino acid sequence identity to human RNase k6 with the eight cysteines and catalytic histidines (H15 and H123) and lysine (K38) typically observed among members of the RNase A superfamily. Interesting trends include an unusually low number of synonymous substitutions (Ks) observed among the New World monkey RNase k6 genes. When considering nonsilent mutations, RNase k6 is a relatively stable lineage, with a nonsynonymous substitution rate of 0.40 × 10−9 nonsynonymous substitutions/nonsynonymous site/year (ns/ns/yr). These results stand in contrast to those determined for the primate orthologs of the two closely related ribonucleases, the eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), which have incorporated nonsilent mutations at very rapid rates (1.9 × 10−9and 2.0 × 10−9 ns/ns/yr, respectively). The uneventful trends observed for RNase k6 serve to spotlight the unique nature of EDN and ECP and the unusual evolutionary constraints to which these two ribonuclease genes must be responding.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF037081–AF037090.]
Mouse Palmitoyl Protein Thioesterase: Gene Structure and Expression of cDNA
Authors: Salonen Tarja , Hellsten Elina , Horelli-Kuitunen Nina , Peltonen Leena , Jalanko Anu 
Published: May 2017

Palmitoyl protein thioesterase (PPT) is the defective enzyme in infantile neuronal ceroid lipofuscinosis (INCL), which is a recessively inherited, progressive neurodegenerative disorder. We present here the cloning, chromosomal mapping, genomic structure, and the expression of the cDNA of mouse PPT. The mouse PPT gene spans >21 kb of genomic DNA and contains nine exons with a coding sequence of 918 bp. Fluorescence in situ hybridization to metaphase chromosomes localized the mouse PPT gene to the chromosome 4 conserved syntenic region with human chromosome 1p32 where the human PPTis located. PPT is expressed widely in a variety of mouse tissues. The mouse PPT cDNA is conserved highly with the human and rat PPT both at the nucleotide and amino acid sequence level. Transient expression of mouse PPT in COS-1 cells yielded a 38/36-kD differentially glycosylated polypeptide that was also secreted into culture media. Immunofluorescence analysis of transiently transfected HeLa cells indicated lysosomal localization of mouse PPT. Based on the high conservation of the gene and polypeptide structure as well as similar processing and intracellular localization, the function of PPT in mouse and human are likely to be very similar.[The sequence data described in this paper have been submitted to GenBank under accession no. AF071O25.]
Overlapping Genomic Sequences: A Treasure Trove of Single-Nucleotide Polymorphisms
Authors: Taillon-Miller Patricia , Gu Zhijie , Li Qun , Hillier LaDeana , Kwok Pui-Yan 
Published: May 2017

An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21–7q22, and 13q12–13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AC003015 (for GS113423),AC002380 (GS330J10), AC000066 (RG293F11), AC003086 (RG104F04), AC002525(257C22A), and U73331 (96A18A).]
Comparative Gene Mapping: A Fine-Scale Survey of Chromosome Rearrangements between Ruminants and Humans
Authors: Schibler Laurent , Vaiman Daniel , Oustry Anne , Giraud-Delville Corinne , Cribiu Edmond P. 
Published: May 2017

A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perform a genome-wide comparison between three mammalian orders. Twice as many rearrangements as revealed by ZOO-FISH were observed. The average size of conserved fragments could be estimated at 27 and 8 cm with humans and mice, respectively. The position of evolutionary breakpoints often correspond with human chromosome sites known to be vulnerable to rearrangement in neoplasia. Furthermore, 75 microsatellite markers, 30 of which were isolated from gene-containing bacterial artificial chromosomes (BACs), were added to the previous goat genetic map, achieving 88% genome coverage. Finally, 124 microsatellites were cytogenetically mapped, which made it possible to physically anchor and orient all the linkage groups. We believe that this comprehensive map will speed up positional cloning projects in domestic ruminants and clarify some aspects of mammalian chromosomal evolution.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. G40978–G41020,AF083170–AF083184, AF088286, AF08287, AF083401–AF083406, AF082884, and AF082885.]