bluuebunny/crossref_metadata_2025 huggingface dataset:
Pleasure junkies all around! Why it matters and why ‘the arts’ might be the answer: a biopsychological perspective
Authors: Christensen Julia F.
Published: May 2017

Today's society is pleasure seeking. We expect to obtain pleasurable experiences fast and easily. We are used to hyper-palatable foods and drinks, and we can get pornography, games and gadgets whenever we want them. The problem: with this type of pleasure-maximizing choice behaviour we may be turning ourselves into mindless pleasure junkies, handing over our free will for the next dopamine shoot. Pleasure-only activities are fun. In excess, however, such activities might have negative effects on our biopsychological health: they provoke a change in the neural mechanisms underlying choice behaviour. Choice behaviour becomes biased towards short-term pleasure-maximizing goals, just as in the addicted brain (modulated by the amygdala, posterior ventromedial prefrontal cortex' (VMPFC), striatum, nucleus accumbens; ‘A-system’) and away from long-term prosperity and general well-being maximizing objectives (normally ensured by the insula, anterior VMPFC, hippocampus, dorsolateral prefrontal cortex (DLPFC), anterior cingulate cortex (ACC); ‘I-system‘). This paper outlines, first, what ‘pleasure’ is and what ‘pleasure-only’ activities are (e.g. social media engagement, hyper-palatable eating). Second, an account is given of the type of action that might aid to maintain the neural systems underlying choice behaviour balanced. Finally, it is proposed that engagement with the arts might be an activity with the potential to foster healthy choice behaviour—and not be just for pleasure. The evidence in this rather new field of research is still piecemeal and inconclusive. This review aims to motivate targeted research in this domain.
Flightin maintains myofilament lattice organization required for optimal flight power and courtship song quality inDrosophila
Authors: Chakravorty Samya , Tanner Bertrand C. W. , Foelber Veronica Lee , Vu Hien , Rosenthal Matthew , Ruiz Teresa , Vigoreaux Jim O.
Published: May 2017

The indirect flight muscles (IFMs) ofDrosophilaand other insects with asynchronous flight muscles are characterized by a crystalline myofilament lattice structure. The high-order lattice regularity is considered an adaptation for enhanced power output, but supporting evidence for this claim is lacking. We show that IFMs from transgenic flies expressing flightin with a deletion of its poorly conserved N-terminal domain (flnΔN62) have reduced inter-thick filament spacing and a less regular lattice. This resulted in a decrease in flight ability by 33% and in skinned fibre oscillatory power output by 57%, but had no effect on wingbeat frequency or frequency of maximum power output, suggesting that the underlying actomyosin kinetics is not affected and that the flight impairment arises from deficits in force transmission. Moreover, we show thatflnΔN62males produced an abnormal courtship song characterized by a higher sine song frequency and a pulse song with longer pulses and longer inter-pulse intervals (IPIs), the latter implicated in male reproductive success. When presented with a choice, wild-type females chose control males over mutant males in 92% of the competition events. These results demonstrate that flightin N-terminal domain is required for optimal myofilament lattice regularity and IFM activity, enabling powered flight and courtship song production. As the courtship song is subject to female choice, we propose that the low amino acid sequence conservation of the N-terminal domain reflects its role in fine-tuning species-specific courtship songs.
Identification of a novel epitope in the C terminus of hepatitis C virus-E2 protein that induces potent and cross-reactive neutralizing antibodies
Authors: Das Soma , Mullick Ranajoy , Kumar Anuj , Tandon Himani , Bose Mihika , Gouthamchandra K , Chandra Madhavi , Ravishankar Bagepally , Khaja M. N , Srinivasan Narayanaswamy , Das Saumitra , Melkote Subbarao Shaila , Karande Anjali Anoop
Published: May 2017

Hepatitis C virus (HCV) is a leading cause of chronic viral hepatitis, but an effective vaccine is still not available to prevent infection. Use of neutralizing antibodies could be a potential therapeutic option. In this study, the presence of anti-HCV antibodies in HCV-infected patients was assessed from 50 patients and the presence of neutralizing antibodies was examined using ‘hepatitis C virus-like particles’. Antibodies from two samples exhibited significant inhibitory activity, suggesting that these may neutralize viral infection. Antigenic determinants generating the neutralizing antibodies from these two samples were delineated by epitope mapping using the core, E1 and E2 regions and a stretch of 45 amino acid peptide (E2C45) derived from the C-terminal region of HCV-E2 protein (aa 634–679) was designed. Results suggest that this hitherto uncharacterized region has the potential to generate neutralizing antibodies against HCV and thus be effective in preventing virus entry into liver cells. Computational analysis of the structure of the modelled peptide (E2C45) suggested high conformational entropy for this region. Furthermore, E2C45 peptide-generated antibodies could block virus entry and monoclonal antibodies generated against this peptide could also significantly reduce virus replication in a cell culture system. It is possible that the inhibition could be partly due to a conformational alteration of the CD81-binding region, preventing virus attachment to liver cells. In conclusion, this work focused on the discovery of a novel epitope at the C terminus of E2 that induces potent neutralizing antibodies in HCV-infected patients.
Extraction of saccades from eye movements triggered by reflex blinks
Authors: Jagadisan Uday K. , Gandhi Neeraj J.
Published: May 2017

The trigeminal blink reflex can be evoked by delivering an air puff to the eye. If timed appropriately, e.g., during motor preparation, the small, loopy blink-related eye movement (BREM) associated with eyelid closure disinhibits the saccadic system and reduces the reaction time of planned eye movements. The BREM and intended eye movement overlap temporally, thus a mathematical formulation is required to objectively extract saccade features – onset time and velocity profile – from the combined movement. While it has been assumed that the interactions are nonlinear, we show that blink-triggered movements can be modeled as a linear combination of a typical BREM and a normal saccade, crucially, with an imposed delay between the two components. Saccades reconstructed with this approach are largely similar to control movements in their temporal and spatial profiles. Furthermore, activity profiles of saccade-related bursts in superior colliculus neurons for the recovered saccades closely match those for normal saccades. Thus, blink perturbations, if properly accounted for, offer a non-invasive tool to probe the behavioral and neural signatures of sensory-to-motor transformations.

New and noteworthy

The trigeminal blink reflex is a brief noninvasive perturbation that disinhibits the saccadic system and provides a behavioral readout of the latent motor preparation process. The saccade, however, is combined with a loopy blink related eye movement. Here, we provide a mathematical formulation to extract the saccade from the combined movement. Thus, blink perturbations, when properly accounted for, offer a non-invasive tool to probe the behavioral and neural signatures of sensory-to-motor transformations.
PaperBLAST: Text-mining papers for information about homologs
Authors: Price Morgan N. , Arkin Adam P.
Published: May 2017

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available athttp://papers.genomics.lbl.gov/.
LEAP: A Generalization of the Landau-Vishkin Algorithm with Custom Gap Penalties
Authors: Xin Hongyi , Kim Jeremie , Nahar Sunny , Alkan Can , Mutlu Onur
Published: May 2017

Motivation

Approximate String Matching is a pivotal problem in the field of computer science. It serves as an integral component for many string algorithms, most notably, DNA read mapping and alignment. The improved LV algorithm proposes an improved dynamic programming strategy over the banded Smith-Waterman algorithm but suffers from support of a limited selection of scoring schemes. In this paper, we propose the Leaping Toad problem, a generalization of the approximate string matching problem, as well as LEAP, a generalization of the Landau-Vishkin’s algorithm that solves the Leaping Toad problem under a broader selection of scoring schemes.

Results

We benchmarked LEAP against 3 state-of-the-art approximate string matching implementations. We show that when using a bit-vectorized de Bruijn sequence based optimization, LEAP is up to 7.4x faster than the state-of-the-art bit-vector Levenshtein distance implementation and up to 32x faster than the state-of-the-art affine-gap-penalty parallel Needleman Wunsch Implementation.

Availability

We provide an implementation of LEAP in C++ at github.com/CMU-SAFARI/LEAP.

Contact

hxin@cmu.edu,calkan@cs.bilkent.edu.troronur.mutlu@inf.ethz.ch
Higher levels ofgrp78and lower levels oftlr4anticipate a positive evolution of sepsis and patient survival
Authors: Stan Razvan C. , Bonin Camila P. , Porto Rose , Soriano Francisco G. , de Camargo Maristela M.
Published: May 2017

In sepsis caused by Gram-negative bacteria, modulation of Toll-like receptor 4 (TLR4) activity by modulators such as glucose-regulated protein 78 kDa (GRP78), is believed to shift the equilibrium between pro- and anti-inflammatory downstream signaling cascade. We measured daily mRNAtlr4andgrp78expression levels in peripheral blood of a cohort of septic patients, upon intensive care admission, and modeled these mRNA values based on a sine damping function. We obtained negative correlations betweentlr4andgrp78mRNA in the survivor group. In contrast, such relation is lost in the deceased patients. Loss of homeostasis predicted by our model within the initial 5 days of hospitalization was confirmed by death of those patients up to 28 days later. Measuring the correlation patterns of the expression of these two genes serves as a robust means to gauge sepsis progression, requiring only three points of measurement on the first day of hospitalization.
Advanced lesion symptom mapping analyses and implementation asBCBtoolkit
Authors: Foulon C , Cerliani L , Kinkingnéhun S , Levy R , Rosso C , Urbanski M , Volle E , Thiebaut de Schotten M
Published: May 2017

Background

Patients with brain lesions provide a unique opportunity to understand the functioning of the human mind. However, even when focal, brain lesions have local and remote effects that impact functionally and structurally connected circuits. Similarly, function emerges from the interaction between brain areas rather than their sole activity. For instance, category fluency requires the association between executive, semantic and language production functions.

Findings

Here we provide, for the first time, a set of complementary solutions to measure the impact of a given lesion upon the neuronal circuits. Our methods, which were applied to 37 patients with a focal frontal brain lesion, revealed a large set of directly and indirectly disconnected brain regions that had significantly impacted category fluency performance. The directly disconnected regions corresponded to areas that are classically considered as functionally engaged in verbal fluency and categorization tasks. These regions were also organized into larger directly and indirectly disconnected functional networks, including the left ventral fronto-parietal network, whose cortical thickness correlated with performance on category fluency.

Conclusions

The combination of structural and functional connectivity together with cortical thickness estimates reveals the remote effects of brain lesions, provide for the identification of the affected networks and strengthen our understanding of their relationship with cognitive and behavioural measures. The methods presented are available and freely accessible in theBCBtoolkitas supplementary software [1].
Network dynamics in the healthy and epileptic developing brain
Authors: Rosch RE , Baldeweg T , Moeller F , Baier G
Published: May 2017

Electroencephalography (EEG) allows recording of cortical activity at high temporal resolution. EEG recordings can be summarised along different dimensions using network-level quantitative measures, e.g. channel-to-channel correlation, or band power distributions across channels. These reveal network patterns that unfold over a range of different time scales and can be tracked dynamically.

Here we describe the dynamics of network-state transitions in EEG recordings of spontaneous brain activity in normally developing infants and infants with severe early infantile epileptic encephalopathies (n=8, age: 1-8 months). We describe differences in measures of EEG dynamics derived from band power, and correlation-based summaries of network-wide brain activity.

We further show that EEGs from different patient groups and controls can be distinguished based on a small set of the novel quantitative measures introduced here, which describe dynamic network state switching. Quantitative measures related to the smoothness of switching from one correlation pattern to another show the largest differences between groups.

These findings reveal that the early epileptic encephalopathies are associated with characteristic dynamic features at the network level. Quantitative network-based analyses like the one presented here may in future inform the clinical use of quantitative EEG for diagnosis.
Arabidopsis thaliana Centromere Regions: Genetic Map Positions and Repetitive DNA Structure
Authors: Round Elaine K. , Flowers Susan K. , Richards Eric J.
Published: May 2017

The genetic positions of the five Arabidopsis thalianacentromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic behavior of the centromeric arrays suggests that recombination within the arrays is suppressed. These results indicate that the centromere regions ofA. thaliana resemble human centromeres in size and genomic organization.
A Simple Method for Automated Allele Binning in Microsatellite Markers
Authors: Idury Ramana M. , Cardon Lon R.
Published: May 2017

High-throughput fluorescent genotyping requires a considerable amount of automation for accurate and efficient processing of genetic markers. Automated DNA sequencers and corresponding software products are commercially available that contribute substantially to increased throughput rates for large-scale genotyping projects. However, some conceptually simple tasks still require time-consuming manual intervention that imposes bottlenecks on throughput capacity. One of these tasks is the conversion of imprecise DNA fragment sizes determined by commercial software programs to the underlying discrete alleles that the sizes represent. Here we describe a simple method for assigning allele sizes into their appropriate allele “bins” using least-squares minimization procedures. The method requires no special treatment of family data on plates, internal/external size standards, or electropherogram data manipulation. Tests of the method using the ABI 373A automated DNA sequencer and accompanying Genescan/Genotyper software resulted in accurate automatic classification of all alleles in >80% of 208 markers analyzed, with the remaining 20% being appropriately identified as requiring additional attention to laboratory conditions. Specific characteristics of different markers, including differences in PCR product size and inexact repeat lengths (e.g., 1.9 bp for a dinucleotide repeat), are accommodated by the method and their properties discussed.
A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus
Authors: Ruddy David A. , Kronmal Gregory S. , Lee Vincent K. , Mintier Gabriel A. , Quintana Leah , Domingo Rodolfo , Meyer Nicole C. , Irrinki Alivelu , McClelland Erin E. , Fullan Amy , Mapa Felipa A. , Moore Theodore , Thomas Winston , Loeb Deborah B. , Harmon Cyrus , Tsuchihashi Zenta , Wolff Roger K. , Schatzman Randall C. , Feder John N.
Published: May 2017

In the process of positionally cloning a candidate gene responsible for hereditary hemochromatosis (HH), we constructed a 1.1-Mb transcript map of the region of human chromosome 6p that lies 4.5 Mb telomeric toHLA-A. A combination of three gene-finding techniques, direct cDNA selection, exon trapping, and sample sequencing, were used initially for a saturation screening of the 1.1-Mb region for expressed sequence fragments. As genetic analysis further narrowed the HH candidate locus, we sequenced completely 0.25 Mb of genomic DNA as a final measure to identify all genes. Besides the novel MHC class 1-like HH candidate geneHLA-H, we identified a family of five butyrophilin-related sequences, two genes with structural similarity to a type 1 sodium phosphate transporter, 12 novel histone genes, and a gene we namedRoRetbased on its strong similarity to the 52-kDRo/SSAlupus and Sjogren’s syndrome auto-antigen and theRETfinger protein. Several members of the butyrophilin family and theRoRetgene share an exon of common evolutionary origin called B30-2. The B30-2 exon was originally isolated from the HLA class 1 region, yet has apparently “shuffled” into several genes along the chromosome telomeric to the MHC. The conservation of the B30-2 exon in several novel genes and the previously described amino acid homology ofHLA-Hto MHC class 1 molecules provide further support that this gene-rich region of 6p21.3 is related to the MHC. Finally, we performed an analysis of the four approaches for gene finding and conclude that direct selection provides the most effective probes for cDNA screening, and that as much as 30% of ESTs in this 1.1-Mb region may be derived from noncoding genomic DNA.

[The sequence data described in this paper have been submitted to GenBank under accession nos.U90543–U90548,U90550–U90552, andU91328.]
The Complex Mutation Pattern of a Microsatellite
Authors: Macaubas Claudia , Jin Li , Hallmayer Joachim , Kimura Akinori , Mignot Emmanuel
Published: May 2017

DQCARis a (CA)nmicrosatellite located in the HLA class II region and tightly linked toHLA–DQB1. Previous studies showed a strikingly low level of size variation inDQCARalleles within an extensive subfamily ofHLA–DQsubtypes (DQ1).DQCARalleles in non-DQ1subtypes showed a higher degree of size polymorphism. In this study sequence analysis demonstrates thatDQ1- associatedDQCARalleles have a single C → A nucleotide substitution interupting the CA repeat array. Frequent CA → GA mutations are also observed inDQ1-associated microsatellites with identical allele sizes. In contrast,DQCARalleles associated with non-DQ1haplotypes display a perfect CA repeat sequence and the variation in allele size is attributable only to differences in the number of CA repeats. Our results imply that several mutational mechanisms are involved in the generation of allelic diversity within the same microsatellite locus. The possibility of different mutation rates in the same locus should to be taken into account when using these markers in evolutionary and disease studies.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.U96944–U96962andS87165.]
A Locus for Autosomal Recessive Pseudoxanthoma Elasticum, with Penetrance of Vascular Symptoms in Carriers, Maps to Chromosome 16p13.1
Authors: van Soest Simone , Swart Jaap , Tijmes Nel , Sandkuijl Lodewijk A. , Rommers Jago , Bergen Arthur A.B.
Published: May 2017

Pseudoxanthoma elasticum (PXE) is a heritable systemic disorder characterized by calcification of the elastic fibers of the connective tissue. Symptoms are predominantly noted in the eye, the skin, and the cardiovascular system, resulting in visual loss, skin lesions, and life-threatening vascular disease. In this study we combined homozygosity mapping and genome scanning with 374 markers in affected individuals from a PXE family from a genetically isolated population in The Netherlands. Initial homozygosity in two or three patients was found with up to 20 markers, among which D16S292 located in 16p13.1. Upon refined and more extensive family screening of the latter region, close linkage without recombination was found with the marker D16S764 (Zmax = 6.27). Despite clear autosomal recessive inheritance of the ocular symptoms in PXE, vascular symptoms appear in 40%–50% of the heterozygotes.
Gene Discovery by EST Sequencing inToxoplasma gondiiReveals Sequences Restricted to the Apicomplexa
Authors: Ajioka James W. , Boothroyd John C. , Brunk Brian P. , Hehl Adrian , Hillier Ledeana , Manger Ian D. , Marra Marco , Overton G. Christian , Roos David S. , Wan Kiew-Lian , Waterston Robert , Sibley L. David
Published: May 2017

To accelerate gene discovery and facilitate genetic mapping in the protozoan parasiteToxoplasma gondii,we have generated >7000 new ESTs from the 5′ ends of randomly selected tachyzoite cDNAs. Comparison of the ESTs with the existing gene databases identified possible functions for more than 500 newT. gondiigenes by virtue of sequence motifs shared with conserved protein families, including factors involved in transcription, translation, protein secretion, signal transduction, cytoskeleton organization, and metabolism. Despite this success in identifying new genes, more than 50% of the ESTs correspond to genes of unknown function, reflecting the divergent evolutionary status of this parasite. A newly recognized class of genes was identified based on its similarity to sequences known only from other members of the same phylum, therefore identifying sequences that are apparently restricted to the Apicomplexa. Such genes may underlie pathways common to this group of medically important parasites, therefore identifying potential targets for intervention.
A Gene Map of the Best’s Vitelliform Macular Dystrophy Region in Chromosome 11q12–q13.1
Authors: Stöhr Heidi , Marquardt Andreas , Rivera Andrea , Cooper Paul R. , Nowak Norma J. , Shows Thomas B. , Gerhard Daniela S. , Weber Bernhard H.F.
Published: May 2017

Best’s vitelliform macular dystrophy is an autosomal dominant disorder of unknown causes. To identify the underlying gene defect the disease locus has been mapped to an ∼1.4-Mb region on chromosome 11q12–q13.1. As a prerequisite for its positional cloning we have assembled a high coverage PAC contig of the candidate region. Here, we report the construction of a primary transcript map that places a total of 19 genes within the Best’s disease region. This includes 14 transcripts of as yet unknown function obtained by EST mapping and/or cDNA selection and five genes mapped previously to the interval (CD5, PGA, DDB1, FEN1, and FTH1). Northern blot analyses were performed to determine the expression profiles in various human tissues. At least three genes appear to be good candidates for Best’s disease based on their abundant expression in retina or retinal pigment epithelium. Additional information on the functional properties of these genes, as well as mutation analyses in Best’s disease patients, have to await their further characterization.

[The GenBank/EMBL accession numbers and details of the isolation, localization, and characterization of ESTs and selected cDNAs are available as online supplements in Online Tables 1–3 at http://www.genome.org.]
CeRep25B Forms Chromosome-Specific Minisatellite Arrays in Caenorhabditis elegans
Authors: Pilgrim Dave
Published: May 2017

With the completion of the Genome Sequencing Project, it is now possible to rapidly and accurately determine the frequency and position of a particular repeat sequence in the Caenorhabditis elegansgenome. Several repeat sequences with a variety of characteristics have been examined and with few exceptions they show a near-random distribution throughout the genome. We characterized several genes near the left end of Chromosome III in the C. elegans genome, and found a 24-bp minisatellite repeat sequence present in the introns of two unrelated genes. This prompted a search of the databank for other occurrences of this sequence. Multiple copy arrays of this repeat are all located on the same autosome and fall in two clusters: one near the left end, and one in the central region separated by ∼10 Mb. There are >200 copies of this repeat on the chromosome. This euchromatic repeat sequence seems unrelated to gene expression, is absent from homologous sites in a related species, is unstable in Escherichia coli, and is polymorphic between different wild isolates of C. elegans. Most CeRep25B units in the array match the consensus sequence very well, suggesting that either this repeat originated quite recently or its sequence is functionally constrained. Although chromosome-specific repeat sequences have been reported previously in many organisms, such sequences are usually structural and heterochromatic (e.g., centromeric α-satellite) or on the mammalian sex chromosomes. This report describes the first confirmed instance from a whole genome sequencing project of an autosomal euchromatic chromosome-specific minisatellite repeat.
Models of Molecular Evolution and Phylogeny: Table 1.
Authors: Liò Pietro , Goldman Nick
Published: May 2017

Phylogenetic reconstruction is a fast-growing field that is enriched by different statistical approaches and by findings and applications in a broad range of biological areas. Fundamental to these are the mathematical models used to describe the patterns of DNA base substitution and amino acid replacement. These may become some of the basic models for comparative genome research. We discuss these models, including the analysis of observed DNA base and amino acid mutation patterns, the concept of site heterogeneity, and the incorporation of structural biology data, all of which have become particularly important in recent years. We also describe the use of such models in phylogenetic reconstruction and statistical methods for the comparison of different models.
Allele Frequency Distributions in Pooled DNA Samples: Applications to Mapping Complex Disease Genes
Authors: Shaw Sarah H. , Carrasquillo Minerva M. , Kashuk Carl , Puffenberger Erik G. , Chakravarti Aravinda
Published: May 2017

Genetic studies of complex hereditary disorders require for their mapping the determination of genotypes at several hundred polymorphic loci in several hundred families. Because only a minority of markers are expected to show linkage and association in family data, a simple screen of genetic markers to identify those showing linkage in pooled DNA samples can greatly facilitate gene identification. All studies involving pooled DNA samples require the comparison of allele frequencies in appropriate family samples and subsamples. We have tested the accuracy of allele frequency estimates, in various DNA samples, by pooling DNA from multiple individuals prior to PCR amplification. We have used the ABI 377 automated DNA sequencer and GENESCAN software for quantifying total amplification using a 5′ fluorescently labeled forward PCR primer and relative peak heights to estimate allele frequencies in pooled DNA samples. In these studies, we have genotyped 11 microsatellite markers in two separate DNA pools, and an additional four markers in a third DNA pool, and compared the estimated allele frequencies with those determined by direct genotyping. In addition, we have evaluated whether pooled DNA samples can be used to accurately assess allele frequencies on transmitted and untransmitted chromosomes, in a collection of families for fine-structure gene mapping using allelic association. Our studies show that accurate, quantitative data on allele frequencies, suitable for identifying markers for complex disorders, can be identified from pooled DNA samples. This approach, being independent of the number of samples comprising a pool, promises to drastically reduce the labor and cost of genotyping in the initial identification of disease loci. Additional applications of DNA pooling are discussed. These developments suggest that new statistical methods for analyzing pooled DNA data are required.
Characterization and Comparison of the Human and MouseGLC1A Glaucoma Genes
Authors: Fingert John H. , Ying Lihua , Swiderski Ruth E. , Nystuen Arne M. , Arbour Nancy C. , Alward Wallace L.M. , Sheffield Val C. , Stone Edwin M.
Published: May 2017

The GLC1A gene (which encodes the protein myocilin) has been associated with the development of primary open angle glaucoma. Bacterial artificial chromosomes containing the human GLC1Agene and its mouse ortholog were subcloned and sequenced to reveal the genomic structure of the genes. Comparison of the coding sequences of the human and mouse GLC1A genes revealed a high degree of amino acid homology (82%) and the presence of several conserved motifs in the predicted GLC1A proteins. The expression of GLC1A was examined by Northern blot analysis of RNA from adult human tissues.GLC1A expression was observed in 17 of 23 tissues tested, suggesting a wider range of expression than was recognized previously. The comparison of the human and mouse GLC1A genes suggests that the mouse may be a useful model organism in studying the molecular pathophysiology of glaucoma.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF049791–AF049796.]
Simultaneous Genotyping and Species Identification Using Hybridization Pattern Recognition Analysis of Generic Mycobacterium DNA Arrays
Authors: Gingeras Thomas R. , Ghandour Ghassan , Wang Eugene , Berno Anthony , Small Peter M. , Drobniewski Francis , Alland David , Desmond Edward , Holodniy Mark , Drenkow Jorg
Published: May 2017

High-density oligonucleotide arrays can be used to rapidly examine large amounts of DNA sequence in a high throughput manner. An array designed to determine the specific nucleotide sequence of 705 bp of therpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis. The nucleotide sequence diversity in 121 Mycobacterial isolates (comprised of 10 species) was examined by both conventional dideoxynucleotide sequencing of the rpoB and 16S genes and by analysis of the rpoB oligonucleotide array hybridization patterns. Species identification for each of the isolates was similar irrespective of whether 16S sequence, rpoBsequence, or the pattern of rpoB hybridization was used. However, for several species, the number of alleles in the 16S andrpoB gene sequences provided discordant estimates of the genetic diversity within a species. In addition to confirming the array’s intended utility for sequencing the region of M. tuberculosis that confers rifampin resistance, this work demonstrates that this array can identify the species of nontuberculous Mycobacteria. This demonstrates the general point that DNA microarrays that sequence important genomic regions (such as drug resistance or pathogenicity islands) can simultaneously identify species and provide some insight into the organism’s population structure.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AF09766–AF059853 and AF060279–AF060367.]
Chicken Microchromosomes Are Hyperacetylated, Early Replicating, and Gene Rich
Authors: McQueen Heather A. , Siriaco Giorgia , Bird Adrian P.
Published: May 2017

The chicken karyotype consists of 39 chromosomes of which 33 are classed as microchromosomes (MICs). MICs contain about one third of genomic DNA. The majority of mapped chicken genes are assigned to macrochromosomes (MACs), but a recent study indicated that CpG islands (CGIs), which are associated with most vertebrate genes, map predominantly to MICs. The present work establishes that chicken genes are concentrated on MICs by several criteria. Acetylated (lysine 5) histone H4, which is strongly correlated with the presence of genes, is highly enriched on MICs by immunocytochemistry. In addition, detailed analysis of chicken cosmids shows that CGI-like fragments are approximately six times denser on MICs than on MACs. Published mapping of randomly chosen genes by fluorescent in situ hybridization (FISH) also shows a significant excess of microchromosomal assignments. Finally, the finding that MICs replicate during the first half of S phase is also compatible with the suggestion that MICs represent gene-rich DNA. We use the cosmid data to predict that ∼75% of chicken genes are located on microchromosomes.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AJ001643 and AJ001644.]
Physical Map of Human 6p21.2–6p21.3: Region Flanking the Centromeric End of the Major Histocompatibility Complex
Authors: Tripodis Nicos , Mason Ruth , Humphray Sean J. , Davies Angela F. , Herberg Jethro A. , Trowsdale John , Nizetic Dean , Senger Gabriele , Ragoussis Jiannis
Published: May 2017

We have physically mapped and cloned a 2.5-Mb chromosomal segment flanking the centromeric end of the major histocompatibility complex (MHC). We characterized in detail 27 YACs, 144 cosmids, 51 PACs, and 5 BACs, which will facilitate the complete genomic sequencing of this region of chromosome 6. The contig contains the genes encoding CSBP, p21, HSU09564 serine kinase, ZNF76,TCP-11,RPS10, HMGI(Y), BAK, and the human homolog of Tctex-7 (HSET). TheGLO1gene was mapped further centromeric in the 6p21.2–6p21.1 region towardTCTE-1.The gene order of theGLO1–HMGI(Y)segment in respect to the centromere is similar to the gene order in the mouset-chromosome distal inversion, indicating that there is conservation in gene content but not gene order between humans and mice in this region. The close linkage of theBAKandCSBPgenes to the MHC is of interest because of their possible involvement in autoimmune disease.
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
Authors: Florea Liliana , Hartzell George , Zhang Zheng , Rubin Gerald M. , Miller Webb
Published: May 2017

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.
Automated Sequence Preprocessing in a Large-Scale Sequencing Environment
Authors: Wendl Michael C. , Dear Simon , Hodgson Dave , Hillier LaDeana
Published: May 2017

A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing of all trace data, including shotgun and finishing reads, regardless of clone origin. Design considerations are discussed in detail, as are programming implementation and graphic tools. The importance of input validation, record tracking, and use of base quality values is emphasized. Several quality analysis metrics are proposed and applied to sample results from recently sequenced clones. Such quantities prove to be a valuable aid in evaluating modifications of sequencing protocol. The system is in full production use at both the Genome Sequencing Center and the Sanger Centre, for which combined weekly production is ∼100,000 sequencing reads per week.
Understanding users’ switching intentions and switching behavior on social networking sites
Authors: Lin Chun-Nan , Wang Hsiu-Yu
Published: May 2017

Purpose

The purpose of this paper is to explore the relationship between social networking sites (SNSs) users’ switching intentions and switching behavior. With regard to the former, the authors focus on three factors (perceived value, trust, and perceived risk), and investigate whether and to what extent habit moderates the relationship between SNS-switching intention and actual switching behavior.

Design/methodology/approach

Data collection for this study was carried out using an anonymous survey. The questionnaire was devised based on the literature review. It consisted of a total of 34 items, all of which used the seven-point Likert scale, and was divided into nine sections. Data collection lasted for approximately three months from March to May 2015. Data analysis used SPSS and SmartPLS statistical software packages. First, the descriptive statistics were computed. Next, reliability as a measure of internal consistency was calculated. Then, the relations between all factors were explored.

Findings

Before they switch, users usually evaluate the perceived values and risks of the SNSs they might join, as well as establish the degrees of trust with respect to those networks. Hence, this study is potentially useful to SNS providers planning their business strategies, and/or seeking to optimize their services based on a detailed understanding of the concerns of users and potential users.

Originality/value

This study is of considerable importance to the future development of research on switching intention behavior theory and practice, adding to the body of work on specific frameworks that explain the SNS-switching intention and behavior. The main theoretical implication is that the epistemic value component of the perceived value may not significantly affect switching intentions, at least in the SNS context. In addition, the results regarding the moderating effects of habits are a useful confirmation, in the SNS context, of the findings of a small but important body of prior studies.
Discovery of repost patterns by topic analysis in enterprise social networking
Authors: Luo Jianhong , Pan Xuwei , Zhu Xiyong
Published: May 2017

Purpose

An increasing number of users are inspired by enterprises to repost social media messages, which greatly contributes to the dissemination of such messages in an online social network. The purpose of this paper is to discover the repost patterns of users regarding enterprise social media messages to help enterprises improve information management abilities for social media.

Design/methodology/approach

This paper proposes a novel method to discover the repost patterns of users in enterprise social networking (ESN) at the macro-level through topic analysis. Speciﬁcally, it proposes the message-diversity metric to measure the latent topic diversity degree of the social media messages. Through this technique, the paper analyzes the message-diversity characteristics of the enterprise social media messages and then explores the repost patterns of users.

Findings

The experimental results show that a high repost rate is more prominent for the messages with diverse latent topics, where message-diversity is as high as 0.5.

Practical implications

The findings have great potential in several management areas, such as employing social media marketing, predicting popular messages, helping enterprises strengthen their online presence, and gathering more potential customers.

Originality/value

This study explores how the repost patterns of users in ESN can be determined through general macro-level behavior of users instead of their micro-level processes. The patterns can also lead to a deeper understanding of which contents can drive people to diffuse information. This study gives an important insight into the information behavior of social media users for enterprise management researchers.
Cultural modernization and work-related values and attitudes
Authors: Yeganeh Hamid
Published: May 2017

Purpose

The purpose of this study is to rely on the modernization theory to analyze and explain the cross-national differences in work-related values and attitudes (WVA).

Design/methodology/approach

First, the modernization theory and WVA are conceptualized, their relations are discussed and the hypotheses are formulated. Next, the data, measures, variables and empirical tests are presented. Finally, the theoretical and managerial implications are discussed, an integrative model is proposed and avenues for future research are suggested.

Findings

The empirical results confirm the explanatory strength of the modernization theory and provide valuable insights into the patterns of WVA across the world. It is found that the countries involved in the first phase of human development emphasize work centrality, extrinsic aspects of a job and material rewards and are likely to show noticeable discrimination against women and foreign workers. In contrast, post-industrial societies that are involved in the second phase of human development prefer emancipative WVA, such as low work centrality, tolerance of foreign workers, gender equality and hedonism at the workplace.

Research limitations/implications

Despite the remarkable acceptance of the modernization theory, some of Inglehart’s propositions have been subject to criticism. Furthermore, human development, modernization and the subsequent cultural shifts are “path-dependent” as they are affected by the national, religious and civilization heritage of a country.

Practical implications

The findings of this study can help international mangers adopt the appropriate strategies for a wide range of issues, such as staffing, planning, job description and compensation policies.

Originality/value

The modernization theory is a suitable alternative to national cultural dimensions. This approach relies on the premise that socioeconomic development creates consistent patterns of values, beliefs and behaviors that ultimately shape WVA around the globe.
Twin-objective supply chain collaboration to cope with rare but high impact disruptions whilst improving performance
Authors: Zhu Quan , Krikke Harold , Caniëls Marjolein C.J. , Wang Yacan
Published: May 2017

Purpose

Rare but high impact (R-HI) disruptions, which are caused by legal changes, socio-technical accidents, or natural disasters, are becoming more frequent and have strong short-term and long-term impacts on performance. Meanwhile, the short-term perspective of managers leads to adoption of mitigation strategies with lower investments and immediate performance improvement. The purpose of this paper is to provide insights on supply chain collaboration (SCC) to establish so-called twin-objective strategy to help both risk mitigation (through moderation effects) and performance improvement (through a direct positive impact). Moreover, power position will be considered as the control variable.

Design/methodology/approach

A cross-sectional approach was adopted with primary data collected through a survey in China. Data were analyzed using structural equation modeling with partial least squares estimations. A sub-group model analysis was applied to test the effect of the control variable.

Findings

The findings verify that SCC has both a direct positive impact on performance and moderation effects on the relationships between sources of R-HI disruptions and performance. The results of sub-group model analysis illustrate that both powerful and weak focal firms benefit from SCC, but in different ways.

Originality/value

The study shows that the allocation of gains from collaborative advantage should be added to the theory-building of relational view. Meanwhile, the research extends the focal firm’s context to its supply chain’s context so that classic contingency theory can be extended to adequately explain supply chain management phenomena.
An information sharing theory perspective on willingness to share information in supply chains
Authors: Zaheer Nadia , Trkman Peter
Published: May 2017

Purpose

The quality of information sharing is of the utmost importance for supply chains (SCs). The purpose of this paper is to improve understanding of the human attitude: willingness to share, its antecedents and its role in improving information sharing quality.

Design/methodology/approach

Based on information sharing theory, a theoretical model and research hypotheses are developed. Data from 387 respondents were collected to test the hypotheses and model fit using structural equation modelling and mediation analysis. The impact of social-psychological factors and information technology (IT) infrastructure capability on willingness to share information and, consequently, its effect on information sharing quality were analysed using IBM SPSS Statistics, PROCESS and AMOS.

Findings

The statistical analysis showed a good model fit. Trust is the most important antecedent for willingness to share, while the impacts of commitment and reciprocity are also significant. Interestingly, power is not a significant antecedent of willingness. Life satisfaction is a significant precursor to willingness to share information, whereas surprisingly overall job satisfaction does not play a significant role.

Research limitations/implications

Cross-sectional data were used and the scope was limited to SCs.

Practical implications

Managers should be aware that trust, commitment and reciprocity with their SC partners influence the willingness to share information with varying effects. Access to proper IT capabilities increases willingness as does the life satisfaction. SC individuals who are happy with life are more willing. Interestingly, high power might get the sharer to share information albeit unwillingly.

Originality/value

The model provides a social-psychological understanding of the antecedents of human willingness to share information, which is crucial to sharing quality information. Overall, the social-psychological and IT factors model based on information sharing theory is statistically valid for the SC context.
The influence of supply chain integration on operational performance
Authors: Yuen Kum Fai , Thai Vinh Van
Published: May 2017

Purpose

An implicit assumption of current supply chain integration (SCI) research is that the results obtained from product supply chains can be directly extrapolated to service supply chains. The purpose of this paper is to question this assumption of equivalence by proposing that the effects of internal integration (II) and external integration (EI) on operational performance (OP) are contingent on whether a firm operates in a product and service supply chain.

Design/methodology/approach

Drawing on the contingency theory, a model that specifies and contrasts the interrelationships between II, EI, and OP in product and service supply chains was proposed. Subsequently, measures were developed and survey data were collected from 138 product and 174 service companies in Singapore. The data were then analysed using multi-sampling analysis.

Findings

The effects of II and EI on OP varied significantly between product and service supply chains. In addition, the relationship between II and OP was found to be partially mediated by EI in product supply chains whereas a fully mediated relationship was observed in service supply chains.

Research limitations/implications

Within the context of SCI, different mediation patterns exist in product and service supply chains. The results suggest adopting a contingency rather than a universalistic approach in the management of firms’ internal and external integrative capabilities to maximise OP. Specifically, managers should adjust their II and EI efforts to achieve congruency with the type of supply chain they serve.

Originality/value

This paper tests the assumption of equivalence and extends the current scope of SCI contingency research by cross-examining the effects of II and EI on OP in both product and service supply chains simultaneously.