bluuebunny/crossref_metadata_2025 huggingface dataset:
Codon based co-occurrence network motifs in human mitochondria
Authors: Shinde Pramod , Sarkar Camellia , Jalan Sarika
Published: December 2016

Human mitochondrial DNA (mtDNA) generates a highly divergent pool of alleles even within species that have dispersed and expanded in size. On top of that codon position bias plays a relative role in prompting population wide sequence based variations. Codon positions are immensely studied as independent evolutionary genetic markers, however co-evolution of codon positions are still largely unexplored. Using 18,411 genome samples, we analyze nucleotide co-occurrences over mitochondrial DNA of human sub-populations covering most of the mtDNA diversity on the earth. Our codon based network motif investigation reveals that codon position is one of the critical factor to form higher order motifs. It is interesting to report a different evolution of Asian genomes than those of the rest which is divulged by motifs in non-coding regions. Most notably, we demonstrate that there are preferences of codon position co-evolution with respect to codon position sensitivity implying the selective role of evolutionary processes on fundamental formation of genetic code in terms of codon bias evolution. These network based findings not only recapitulates the established facts regarding the importance of each codon position in providing codon bias but also highlight their preferential role in resulting correlated mutations. Moreover, codon based nucleotide co-occurrence provides framework to investigate important evolutionary insights into human mitochondrial evolutionary genomics.
Puckered in pioneer neurons coordinates the motor activity of theDrosophilaembryo
Authors: Karkali Katerina , Vernon Samuel W. , Baines Richard A. , Panayotou George , Martín-Blanco Enrique
Published: December 2016

Central Nervous System (CNS) organogenesis is a complex process that obeys precise architectural rules. The impact that nervous system architecture may have on its functionality remains, however, relatively unexplored. To clarify this problem, we analyzed the development of the Drosophila embryonic Ventral Nerve Cord (VNC). VNC morphogenesis requires the tight control of Jun kinase (JNK) signaling, exerted in part via a negative feedback loop mediated by the dual specificity phosphatase Puckered, in a subset of pioneer neurons. Here we show that the JNK pathway autonomously regulates neuronal electrophysiological properties without affecting synaptic vesicle transport. Manipulating, during early embryogenesis, JNK signaling activity in pioneer neurons, directly influences their function as ‘organizers’ of VNC architecture and, moreover, uncovers a role in the coordination of the embryonic motor circuitry that is required for hatching. Together, our data reveal critical links, mediated by the control of the JNK signaling cascade by Puckered, between the structural organization of the VNC and its functional optimization.
Recombinant DNA resources for the comparative genomics ofAncylostoma ceylanicum
Authors: Kapulkin Wadim J. , Magalska Adriana , Janecka Ewa , Ciesielski Arkadiusz , Lobocka Malgorzata , Behnke Jerzy M. , Wedrychowicz Halina
Published: December 2016

We describe the construction and initial characterization of genomic resources (a set of recombinant DNA libraries, representing in total over 90,000 independent plasmid clones), originating from the genome of a hamster adapted hookworm,Ancylostoma ceylanicum. First, with the improved methodology, we generated sets of SL1 (5‘-linker - GGTTAATTACCCAAGTTTGAG), and captured cDNAs from two different hookworm developmental stages: pre-infective L3 and parasitic adults. Second, we constructed a small insert (2-10kb) genomic library. Third, we generated a Bacterial Artificial Chromosome library (30-60kb). To evaluate the quality of our libraries we characterized sequence tags on randomly chosen clones and with first pass screening we generated almost a hundred novel hookworm sequence tags. The sequence tags detected two broad classes of genes: i. conserved nematode genes and ii. putative hookworm-specific proteins. Importantly, some of the identified genes encode proteins of general interest including potential targets for hookworm control. Additionally, we identified a syntenic region in the mitochondrial genome, where the gene order is shared between the free-living nematodeC. elegansandA. ceylanicum. Our results validate the use of recombinant DNA resources for comparative genomics of nematodes, including the free-living genetic model organismC. elegansand closely related parasitic species. We discuss the potential and relevance ofAncylostoma ceylanicumdata and resources generated by the recombinant DNA approach.
In vivo magnetic recording of neuronal activity
Authors: Caruso Laure , Wunderle Thomas , Murphy Lewis Christopher , Valadeiro Joao , Trauchessec Vincent , Trejo Rosillo Josué , Pedro Amaral José , Ni Jianguang , Jendritza Patrick , Fermon Claude , Cardoso Susana , Peixeiro Freitas Paulo , Fries Pascal , Pannetier-Lecoeur Myriam
Published: December 2016

Neuronal activity generates ionic flows and thereby both magnetic fields and electric potential differences, i.e. voltages. Voltage measurements are widely used, but suffer from isolating and smearing properties of tissue between source and sensor, are blind to ionic flow direction, and reflect the difference between two electrodes, complicating interpretation. Magnetic field measurements could overcome these limitations, but have been essentially limited to magnetoencephalography (MEG), using centimeter-sized, helium-cooled extracranial sensors. Here, we report on in vivo magnetic recordings of neuronal activity from visual cortex of cats withmagnetrodes, specially developed needle-shaped probes carrying micron-sized, non-cooled magnetic sensors based on spin electronics. Event-related magnetic fields inside the neuropil were on the order of several nanoteslas, informing MEG source models and efforts for magnetic field measurements through MRI. Though the signal-to-noise ratio is still inferior to electrophysiology, this proof of concept demonstrates the potential to exploit the fundamental advantages of magnetophysiology.

HIGHLIGHTS

Spin-electronics based probes achieve local magnetic recordings inside the neuropil

Magnetic field recordings were performed in vivo, in anesthetized cat visual cortex

Event-related fields (ERFs) to visual stimuli were up to several nanoteslas in size

ERFs could be detected after averaging less than 20 trials

IN BRIEF

Caruso et al. report in vivo, intra-cortical recordings of magnetic fields that reflect neuronal activity, using magnetrodes, i.e. micron size magnetic sensors based on spin electronics.
Fast and Stable Signal Deconvolution via Compressible State-Space Models
Authors: Kazemipour Abbas , Liu Ji , Solarana Krystyna , Nagode Daniel A. , Kanold Patrick O. , Wu Min , Babadi Behtash
Published: December 2016

Abstract–Objective:

Common biological measurements are in the form of noisy convolutions of signals of interest with possibly unknown and transient blurring kernels. Examples include EEG and calcium imaging data. Thus, signal deconvolution of these measurements is crucial in understanding the underlying biological processes. The objective of this paper is to develop fast and stable solutions for signal deconvolution from noisy, blurred and undersampled data, where the signals are in the form of discrete events distributed in time and space.Methods: We introduce compressible state-space models as a framework to model and estimate such discrete events. These state-space models admit abrupt changes in the states and have a convergent transition matrix, and are coupled with compressive linear measurements. We consider a dynamic compressive sensing optimization problem and develop a fast solution, using two nested Expectation Maximization algorithms, to jointly estimate the states as well as their transition matrices. Under suitable sparsity assumptions on the dynamics, we prove optimal stability guarantees for the recovery of the states and present a method for the identification of the underlying discrete events with precise confidence bounds.Results: We present simulation studies as well as application to calcium deconvolution and sleep spindle detection, which verify our theoretical results and show significant improvement over existing techniques.Conclusion: Our results show that by explicitly modeling the dynamics of the underlying signals, it is possible to construct signal deconvolution solutions that are scalable, statistically robust, and achieve high temporal resolution.Significance: Our proposed methodology provides a framework for modeling and deconvolution of noisy, blurred, and undersampled measurements in a fast and stable fashion, with potential application to a wide range of biological data.
The Dachsous/Fat/Four-jointed pathway implements axial long-range cell orientation
Authors: Mangione Federica , Martín-Blanco Enrique
Published: December 2016

Despite a cumulative body of knowledge describing short-range cell interactions in morphogenetic processes, relatively little is known on the mechanism involved in the long-range spatial and temporal coordination of cells to build functional and structurally organized tissues. In particular, the attainment of a functionally optimized epithelia must require directional cues to instruct cell movements and cell orientations throughout the tissue field. InDrosophila,the adult epidermis of the abdominal segments is createdde novoby the replacement of obsolete larval epidermal cells (LECs) by histoblasts (imaginal founder cells). As these proliferate, expand and fuse, they uniformly organize orienting on the surface along the antero-posterior axis. We found that the coordinated, axially oriented changes in shape of histoblasts respond to a dynamic, yet stereotyped redesign of the epithelial field mediated by the Dachsous/Fat/Four-jointed (Ds/Ft/Fj) pathway. The establishment and refinement of the expression gradients of the atypical cadherins Ds and Ft result in their axial polarization across cell interfaces and differential adhesiveness. We suggest that the role of Ds/Ft/Fj in long-range axially oriented planar cell alignment is a general function and that the regulation of the expression of its components would be crucial in the achievement of tissue uniformity in many other morphogenetic models or during tissue repair.
Local genetic correlation gives insights into the shared genetic architecture of complex traits
Authors: Shi Huwenbo , Mancuso Nicholas , Spendlove Sarah , Pasaniuc Bogdan
Published: December 2016

Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions contribute to the genome-wide genetic correlation is currently lacking. Here, we introduceρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach only requires GWAS summary data and makes no distributional assumption on the causal variant effects sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 35 complex traits, and identified 27 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 7 genomic regions that contribute to the genetic correlation of 12 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we leverage the distribution of local genetic correlations across the genome to assign putative direction of causality for 15 pairs of traits.
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance
Authors: Oda Toshiyuki , Lim Kyungtaek , Tomii Kentaro
Published: December 2016

PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate estimation of the weights of sequences in an MSA is crucially important for PSSM construction. PSI-BLAST divides a given MSA into multiple blocks, for which sequence weights are calculated. When the block width becomes very narrow, the sequence weight calculation can be difficult.

We demonstrate that PSI-BLAST indeed generates a significant fraction of blocks having widths less than 5, thereby degrading the PSI-BLAST performance. We revised the code of PSI-BLAST to prevent the blocks from being narrower than a given minimum block width (MBW). We designate the modified application of PSI-BLAST as PSI-BLASTexB. When MBW is 25, PSI-BLASTexB notably outperforms PSI-BLAST consistently for three independent benchmark sets. The performance boost is even more drastic when an MSA, instead of a sequence, was used as a query.

Our results demonstrate that the generation of narrow-width blocks during the sequence weight calculation is a critically important factor that restricts the PSI-BLAST search performance. By preventing narrow blocks, PSI-BLASTexB remarkably upgrades the PSI-BLAST performance.
Genomic determinants of protein abundance variation in colorectal cancer cells
Authors: Roumeliotis Theodoros I. , Williams Steven Paul , Gonçalves Emanuel , Zamanzad Ghavidel Fatemeh , Aben Nanne , Michaut Magali , Schubert Michael , Wright James C. , Yang Mi , Alsinet Clara , Dienstmann Rodrigo , Guinney Justin , Beltrao Pedro , Brazma Alvis , Stegle Oliver , Adams David J. , Wessels Lodewyk , Saez-Rodriguez Julio , McDermott Ultan , Choudhary Jyoti S.
Published: December 2016

Assessing the extent to which genomic alterations compromise the integrity of the proteome is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labelling and tribrid mass spectrometry to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the relationships between genomic and proteomic variation. The robust quantification of 12,000 proteins and 27,000 phosphopeptides revealed how protein symbiosis translates to a co-variome which is subjected to a hierarchical order and exposes the collateral effects of somatic mutations on protein complexes. Targeted depletion of key chromatin modifiers confirmed the transmission of variation and the directionality as characteristics of protein interactions. Protein level variation was leveraged to build drug response predictive models towards a better understanding of pharmacoproteomic interactions in colorectal cancer. Overall, we provide a deep integrative view of the molecular structure underlying the variation of colorectal cancer cells.

Highlights

The cancer cell functional “co-variome” is a strong attribute of the proteome.

Mutations can have a direct impact on protein levels of chromatin modifiers.

Transmission of genomic variation is a characteristic of protein interactions.

Pharmacoproteomic models are strong predictors of response to DNA damaging agents.

Abbreviations

COREAD

Colorectal Adenocarcinoma

IMAC

Immobilized Metal ion Affinity Chromatography

ROC

Receiver Operating Characteristic

AUC

Area Under the Curve

WGCNA

Weighted Correlation Network Analysis

CNA

Copy Number Alteration

SOM

Self-Organizing Map

QTL

Quantitative Trait Loci

MSI

Microsatellite Instability

CPS

Colorectal Proteomic Subtypes
High-dimensional regression over disease subgroups
Authors: Dondelinger Frank , Mukherjee Sach ,   The Alzheimer’s Disease Neuroimaging Initiative
Published: December 2016

We consider high-dimensional regression over subgroups of observations. Our work is motivated by biomedical problems, where disease subtypes, for example, may differ with respect to underlying regression models, but sample sizes at the subgroup-level may be limited. We focus on the case in which subgroup-specific models may be expected to be similar but not necessarily identical. Our approach is to treat subgroups as related problem instances and jointly estimate subgroup-specific regression coefficients. This is done in a penalized framework, combining anℓ1term with an additional term that penalizes differences between subgroup-specific coefficients. This gives solutions that are globally sparse but that allow information-sharing between the subgroups. We present algorithms for estimation and empirical results on simulated data and using Alzheimer’s disease, amyotrophic lateral sclerosis and cancer datasets. These examples demonstrate the gains our approach can offer in terms of prediction and the ability to estimate subgroup-specific sparsity patterns.
The Evolution of Primate Body Size: Left-skewness, Maximum Size, and Cope’s Rule
Authors: Tillquist Richard C. , Shoemaker Lauren G. , Knight Kevin Bracy , Clauset Aaron
Published: December 2016

Body size is a key physiological, ecological, and evolutionary characteristic of species. Within most major clades, body size distributions follow a right-skewed pattern where most species are relatively small while a few are orders of magnitude larger than the median size. Using a novel database of 742 extant and extinct primate species’ sizes over the past 66 million years, we find that primates exhibit the opposite pattern: a left-skewed distribution. We investigate the long-term evolution of this distribution, first showing that the initial size radiation is consistent with plesiadapiformes (an extinct group with an uncertain ancestral relationship to primates) being ancestral to modern primates. We calculate the strength of Cope’s Rule, showing an initial tendency for descendants to increase in size relative to ancestors until the trend reverses 40 million years ago. We explore when the primate size distribution becomes left-skewed and study correlations between body size patterns and climactic trends, showing that across Old and New World radiations the body size distribution initially exhibits a right-skewed pattern. Left-skewness emerged early in Old World primates in a manner consistent with a previously unidentified possible maximum body size, which may be mechanistically related to primates’ encephalization and complex social groups.
Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate
Authors: Jasinska Anna J. , Zelaya Ivette , Service Susan K. , Peterson Christine B. , Cantor Rita M. , Choi Oi-Wa , DeYoung Joseph , Eskin Eleazar , Fairbanks Lynn A. , Fears Scott , Furterer Allison E. , Huang Yu S. , Ramensky Vasily , Schmitt Christopher A. , Svardal Hannes , Jorgensen Matthew J. , Kaplan Jay R. , Villar Diego , Aken Bronwen L. , Flicek Paul , Nag Rishi , Wong Emily S. , Blangero John , Dyer Thomas D. , Bogomolov Marina , Benjamini Yoav , Weinstock George M. , Dewar Ken , Sabatti Chiara , Wilson Richard K. , Jentsch J. David , Warren Wesley , Coppola Giovanni , Woods Roger P. , Freimer Nelson B.
Published: December 2016

By analyzing multi-tissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalogue of expression quantitative trait loci (eQTLs) in a non-human primate model. This catalogue contains more genome-wide significant eQTLs, per sample, than comparable human resources, and reveals sex and age-related expression patterns. Findings include a master regulatory locus that likely plays a role in immune function, and a locus regulating hippocampal long non-coding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.
Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data
Authors: Wymant Chris , Blanquart François , Gall Astrid , Bakker Margreet , Bezemer Daniela , Croucher Nicholas J. , Golubchik Tanya , Hall Matthew , Hillebregt Mariska , Ong Swee Hoe , Albert Jan , Bannert Norbert , Fellay Jacques , Fransen Katrien , Gourlay Annabelle , Grabowski M. Kate , Gunsenheimer-Bartmeyer Barbara , Günthard Huldrych F. , Kivelä Pia , Kouyos Roger , Laeyendecker Oliver , Liitsola Kirsi , Meyer Laurence , Porter Kholoud , Ristola Matti , van Sighem Ard , Vanham Guido , Berkhout Ben , Cornelissen Marion , Kellam Paul , Reiss Peter , Fraser Christophe ,   The BEEHIVE Collaboration
Published: December 2016

Next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of rapid between- and within-host evolution may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions.De novoassembly avoids this bias by effectively aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the toolshiverto preprocess reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We useshiverto reconstruct the consensus sequence and minority variant information from paired-end short-read data produced with the Illumina platform, for 65 existing publicly available samples and 50 new samples. We show the systematic superiority of mapping toshiver’s constructed reference over mapping the same reads to the standard reference HXB2: an average of 29 bases per sample are called differently, of which 98.5% are supported by higher coverage. We also provide a practical guide to working with imperfect contigs.
Random versus maximum entropy models of neural population activity
Authors: Ferrari Ulisse , Obuchi Tomoyuki , Mora Thierry
Published: December 2016

The principle of maximum entropy provides a useful method for inferring statistical mechanics models from observations in correlated systems, and is widely used in a variety of fields where accurate data are available. While the assumptions underlying maximum entropy are intuitive and appealing, its adequacy for describing complex empirical data has been little studied in comparison to alternative approaches. Here data from the collective spiking activity of retinal neurons is reanalysed. The accuracy of the maximum entropy distribution constrained by mean firing rates and pairwise correlations is compared to a random ensemble of distributions constrained by the same observables. In general, maximum entropy approximates the true distribution better than the typical or mean distribution from that ensemble. This advantage improves with population size, with groups as small as 8 being almost always better described by maximum entropy. Failure of maximum entropy to outperform random models is found to be associated with strong correlations in the population.
A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells
Authors: Imamachi Naoto , Salam Kazi Abdus , Suzuki Yutaka , Akimitsu Nobuyoshi
Published: December 2016

Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3′ untranslated region (UTR) of target mRNAs via as-yet-unknown sequence features. Herein, we aimed to identify characteristic sequence features of UPF1 targets. We identified 246 UPF1 targets by measuring RNA stabilization upon UPF1 depletion and by identifying mRNAs that associate with UPF1. By analyzing RNA footprint data of phosphorylated UPF1 and two CLIP-seq data of UPF1, we found that 3′ UTR but not 5′ UTRs or open reading frames of UPF1 targets have GC-rich motifs embedded in high GC-content regions. Reporter gene experiments revealed that GC-rich motifs in UPF1 targets were indispensable for UPF1-mediated mRNA decay. These findings highlight the important features of UPF1 target 3′ UTRs.
Crystal structures of (E)-4-[1-(2-carbamothioylhydrazinylidene)ethyl]phenyl acetate and (E)-4-[1-(2-carbamothioylhydrazinylidene)ethyl]phenyl benzoate
Authors: Viswanathan Vijayan , Ananth Mani Karthik , Narasimhan S. , Velmurugan Devadasan
Published: December 2016

In the title compounds, C11H13N3O2S, (I), and C16H15N3O2S, (II), the thiosemicarbazone group adopts an extended conformation. The acetate ester (I) crystallizes with two independent molecules in the asymmetric unit. In the benzoate ester (II), the planes of the two aryl rings are inclined to one another by 46.70 (7)°. In both compounds, there is a short intramolecular N—H...N contact present, forming anS(5) ring motif. In the crystals of both compounds, molecules are linkedviapairs of N—H...S hydrogen bonds, forming dimers withR22(8) ring motifs. The dimers are linked by N—H...S and N—H...O hydrogen bonds, forming slabs parallel to (01-1). In (I), there are N—H...π and C—H...π interactions present within the slabs, while in (II), there are only N—H...π interactions present.
Crystal structure of {(S)-1-phenyl-N,N-bis[(pyridin-2-yl)methyl]ethanamine-κ3N,N′,N′′}bis(thiocyanato-κN)zinc from synchrotron data
Authors: Lee Dong Won , Shin Jong Won
Published: December 2016

The title ZnIIcomplex, [Zn(NCS)2(C20H21N3)], has been characterized by synchrotron single-crystal diffraction and FT–IR spectroscopy. The central ZnIIion has a distorted square-pyramidal coordination geometry, with three N atoms of the chiral (S) 1-phenyl-N,N-bis[(pyridin-2-yl)methyl]ethanamine (S-ppme) ligand and one N atom of a thiocyanate anion in the equatorial plane, and one N atom of another thiocyanate anion at the apical position. The average Zn—NS-ppmeand Zn—NNCSbond lengths are 2.183 (2) and 1.986 (2) Å, respectively. In the crystal, intermolecular C—H...S hydrogen bonds and a face-to-face π–π interaction [centroid–centroid distance = 3.482 (1) Å] link the molecules and give rise to a supramolecular sheet structure parallel to theacplane.
Crystal structure of (perchlorato-κO)(1,4,7,10-tetraazacyclododecane-κ4N)copper(II) perchlorate
Authors: Gray Jessica L. , Gerlach Deidra L. , Papish Elizabeth T.
Published: December 2016

The crystal structure of the title salt, [Cu(ClO4)(C8H20N4)]ClO4, is reported. The CuIIion exhibits a square-pyramidal geometry and is coordinated by the four N atoms of the neutral 1,4,7,10-tetraazacyclododecane (cyclen) ligand and an O atom from one perchlorate anion, with the second perchlorate ion hydrogen-bonded to one of the amine N atoms of the cyclen ligand. Additional N—H...O hydrogen bonds between the amine H atoms and the coordinating and non-coordinating perchlorate groups create a three-dimensional network structure. Crystals were grown from a concentrated methanol solution at ambient temperature, resulting in no co-crystallization of solvent.
Dimethyl 4,4′-(dimethylsilanediyl)dibenzoate
Authors: Zhang Lingling , Xia Yan , Li Dongfeng , Hou Ruibin
Published: December 2016

The complete molecule of the title compound, C18H20O4Si, is generated by crystallographic twofold symmetry, with the Si atom lying on the rotation axis. The molecule adopts a V-shape: the dihedral angle between the benzene ring and it attached methyl formate unit is 9.3 (2)°, and the dihedral angle between the benzene rings is 68.8 (1)°. In the crystal, weak C—H...O hydrogen bonds link the molecules into [101] chains.
Ethyl 4-(furan-2-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate: a triclinic polymorph
Authors: Novina J. J. , Vasuki G. , Suresh M. , Viswanathan Vijayan , Velmurugan Devadasan
Published: December 2016

The title compound, C12H14N2O4, crystallizes in the triclinic space groupP-1. The previously reported polymorph occurs in the monoclinic space groupP21/c, and has two independent molecules in the asymmetric unit [Wang (2010).Acta Cryst.E66, o2822]. The dihydropyrimidine ring adopts a screw-boat conformation. The furan ring is positioned axially and makes a dihedral angle of 85.94 (7)° with the mean plane through the pyrimidine ring. In the crystal, molecules are linkedviapairs of N—H...O hydrogen bonds, forming inversion dimers with anR22(8) ring motif. The dimers are linked by N—H...O and C—H...O hydrogen bonds, forming chains propagating along thea-axis direction.
Integration of social protection and climate change adaptation in Brazil
Authors: S. Mesquita Patricia , Bursztyn Marcel
Published: December 2016

Purpose

Social protection (SP) and climate change adaptation (CCA) are two subjects highly debated when discussing social vulnerabilities and food insecurity in rural areas of developing countries. Both fields address matters related to socioeconomic vulnerabilities and thus present opportunities for integration. However, many studies have stated the lack of interaction within the study areas. When dealing with CCA and SP in Brazil, the two offer an opportunity for integration since some SP programmes (such as food-based safety nets) can both affect adaptation and be impacted by expected changes in climate. Impacts from CC are projected to be extreme in the Brazilian semi-arid Northeast, a region where social programmes of assistance and aid are historically crucial during periods of drought. Thus, the purpose of this paper is to address the interaction of CCA and SP in a conceptual level on policies and programmes in Brazil.

Design/methodology/approach

A desk review of government documents (policies, plans, decrees) related to food security, food-based programmes and CC.

Findings

Based on the results the authors highlight the limited integration between CC and SP in Brazil and the potential for interaction in many of the programmes already in place.

Originality/value

The authors attribute findings to the segmented governmental structure and the weak interaction between sectors, and the only recent discussion of linkages between CC and poverty, development and food insecurity. Discussion on the challenges and benefits of this interaction are provided in a context of CC in Brazil, still not very debated in the academic literature.
Building psychological contract: the role of leader member exchanges
Authors: Kasekende Francis , Munene John C. , Ntayi Joseph M. , Ahiauzu Augustine
Published: December 2016

Purpose

The purpose of this paper is to address the building blocks for psychological contract among public institutions in Uganda by investigating the mediation effect of leader-member exchanges (LMX) in the relationship between perceived environmental dynamism and psychological contract.

Design/methodology/approach

The authors use structural equation modelling (AMOS) to investigate the hypotheses.

Findings

LMX is a significant mediator in the association between generational work values and psychological contract and technological advancement and psychological contract among employees in public institutions in Uganda.

Practical implications

At commissions and agencies level, generational work values and technological advancement seem to create better effects on employee-employer unwritten expectations and obligations when they go through LMX. This has important implications for the investment in and outcomes of these LMX endeavours from both the employer and the employee.

Originality/value

The study is one of the pioneers to demonstrate that the presence of LMX reflected in the form of a dyadic relationship helps to extend the positive effects generational work values and technological advancement have on psychological contract.
E-books usage by agricultural, engineering and social science students in selected universities of Pakistan
Authors: Khan Amjid , Bhatti Rubina , Khan Asad
Published: December 2016

Purpose

The purpose of this paper is to compare the usage patterns of e-books among the students of social, agricultural, and engineering sciences; demonstrate how e-books are used by students for various purposes; explore the main reasons for using e-books; and uncover the major issues being encountered by students while using e-books in Pakistani Universities.

Design/methodology/approach

During May to July 2014, a convenient sample technique was adopted, and a close-ended questionnaire was used as a survey tool for 300 graduates (BSc honor) and postgraduate (masters and MS) students in the age group of 21-60 years. In this study, the respondents’ gender, age, educational level and major disciplines were individual contextual variables. The data collection process was successfully completed with a 100 per cent response rate. SPSS-19 was utilized for testing the reliability of the instrument, as well as descriptive and inferential statistics (Chi-square test).

Findings

The results show that the adoption of e-books has reached a level where they have become an integral component of academic library services. The results of this study verify the previous findings that the students are relying on e-book adoption for various academic and research purposes. Comparatively, male students, postgraduate students and those between the ages of 21 and 40 years are more frequently e-book users. In addition, the percentage of e-book readership among engineering students on a “daily basis” is greater than the students of agricultural and social sciences. They prefer reading e-books because of the following reasons: to support research endeavors and improve academic performance; and the e-format is quick to read and easy to manage. Insufficient e-contents, lack of personal computers and the variety of e-book formats are the major constraints in the effective utilization of e-books for learning, education and research needs. The study has concluded that e-books have a key role in the set-up of academic libraries and information resources in Pakistan, though further development of e-book readership capabilities and building of e-book collections are required to support users’ needs, and a parallel investigation into their most effective usage is also required.

Originality/value

This empirical research is a first and unique study that systematically and quantitatively compares the relationship between respondents’ e-books usage with their individual contextual variables in the perspective of academic libraries in Pakistan.
Heuristic production line balancing problem solution with MATLAB software programming
Authors: Türkmen Aysun , Yesil Yalcin , Kayar Mahmut
Published: December 2016

Purpose

The purpose of this paper is to find the most efficient assembly line balancing solution across many heuristic line balancing methods, in assistance with a developed computer program.

Design/methodology/approach

In this paper, assembly line balancing problem was analyzed using t-shirt and knitted pants data. A computer program using MATLAB software for the solution of assembly line balancing problems has been developed. In this study, following heuristic assembly line balancing methods were applied: Hoffman method; position weight method; COMSOAL method; and Kilbridge and Wester method. A MATLAB program has been developed by taking into account of theoretical solution of all these methods. Later the program is developed further by analyzing solutions made manually and is made to verify the developed program.

Findings

Pre-studies which were conducted in order to decide which programming language would be the best choice for line balancing methods’ application came out with the result that MATLAB, from between C, C++, C# and Java, would be the best software choice. The main reason for this choice is that MATLAB is a powerful matrix operation software with a powerful user interface designing tool and has the tools to make development program to be used universally in every computer.

Originality/value

When the researches were investigated, it is clearly seen that, this study is the first research on using computer program for solving assembly line balancing problem.
Adopting Agile software development: the project manager experience
Authors: Taylor Katie Jane
Published: December 2016

Purpose

Early research into Agile approaches explored particular practices or quantified improvements in code production. Less well researched is how Agile teams are managed. The project manager (PM) role is traditionally one of “command and control” but Agile methods require a more facilitative approach. How this changing role plays out in practice is not yet clearly understood. The purpose of this paper is to provide insight into how adopting Agile techniques shape the working practices of PMs and critically reflect on some of the tensions that arise.

Design/methodology/approach

An ethnographic approach was used to surface a richer understanding of the issues and tensions faced by PMs as Agile methods are introduced. Ethnographic fiction conveys the story to a wider audience.

Findings

Agile approaches shift responsibility and spread expert knowledge seeming to undermine the traditional PM function. However, the findings here show various scenarios that allow PMs to wrest control and become more of a “gate-keeper”. Ethnographic fiction communicates a sense of the PMs frustration with the conflict between the need to control and the desire for teams to take more responsibility.

Originality/value

Stories provide insight and communicate the experiential feel behind issues faced by PMs adopting Agile to surface useful knowledge. The objective is not how to measure knowledge, but how to recognize it. These reflections are valuable to fellow researchers as well as practitioners and contribute to the growing literature on Agile project management.
Health beliefs and the valence framework in health information seeking behaviors
Authors: Mou Jian , Shin Dong-Hee , Cohen Jason
Published: December 2016

Purpose

The purpose of this paper is to help understand consumer acceptance of online health information services by integrating the health belief model and extended valence framework.

Design/methodology/approach

A laboratory-based, experimental-scenarios research design is used to collect data, and the structural equation modeling technique is used to test the research model.

Findings

The model explains 47.6 percent of the variance in intentions to use online health information services. Trust appeared to have the strongest effect on acceptance. Perceived risk also had a significant impact on acceptance. Furthermore, health belief variables are confirmed as important factors for consumer acceptance. Self-efficacy was found to moderate the effect of perceived severity on acceptance.

Research limitations/implications

This study helped identify the relative salience of the health belief model and extended valence framework in consumer acceptance of online health information services.

Practical implications

This study can help practitioners better understand the development of trust and the profiles of consumers who may browse their sites. When online health service providers promote their information to encourage potential online health information seekers, they should use countermeasures against risk perceptions.

Originality/value

This study attempted to extend the valence framework to the non-commercial service context. Moreover, health beliefs and the valence framework are two fundamental aspects that health information seekers consider when making decisions about online health services.
How user personality and social value orientation influence avatar-mediated friendship
Authors: Chesney Thomas , Chuah Swee-Hoon , Hoffmann Robert , Hui Wendy , Larner Jeremy
Published: December 2016

Purpose

The purpose of this paper is to study the influence of user personality and vlaues on the number of connections users make, the number of requests for connections that users give out, and the number of connections invitations users receive.

Design/methodology/approach

This is a field study of 179 participants interacting in a novel virtual world. The world’s server logs are used to capture sociometrics about the users and their interaction.

Findings

Findings suggest that personality and values influence the number of friends users make and the number of friendship requests users give out, but not the number of friendship invitations users receive. Only one personality trait – conscientiousness – exhibits homophily.

Originality/value

Perosnality and social value orientation have rarely been studied together in information systems (IS) research, despite research showing the two have an impact on IS relevant constructs. The use of server logs for data capture is novel. Avatar friendship is an under-researched concept in IS.
Healthcare resource allocation decisions affecting uninsured services
Authors: Harrison Krista Lyn , Taylor Holly A.
Published: December 2016

Purpose

Using the example of community access programs (CAPs), the purpose of this paper is to describe resource allocation and policy decisions related to providing health services for the uninsured in the USA and the organizational values affecting these decisions.

Design/methodology/approach

The study used comparative case study methodology at two geographically diverse sites. Researchers collected data from program documents, meeting observations, and interviews with program stakeholders.

Findings

Five resource allocation or policy decisions relevant to providing healthcare services were described at each site across three categories: designing the health plan, reacting to funding changes, and revising policies. Organizational values of access to care and stewardship most frequently affected resource allocation and policy decisions, while economic and political pressures affect the relative prioritization of values.

Research limitations/implications

Small sample size, the potential for social desirability or recall bias, and the exclusion of provider, member or community perspectives beyond those represented among participating board members.

Practical implications

Program directors or researchers can use this study to assess the extent to which resource allocation and policy decisions align with organizational values and mission statements.

Social implications

The description of how healthcare decisions are actually made can be matched with literature that describes how healthcare resource decisions ought to be made, in order to provide a normative grounding for future decisions.

Originality/value

This study addresses a gap in literature regarding how CAPs actually make resource allocation decisions that affect access to healthcare services.
To downsize or not to downsize – what does the empirical evidence suggest?
Authors: Carriger Michael
Published: December 2016

Purpose

There has been much written about the effects of downsizing on the financial health and the valuation of companies that engage in this practice. But this literature is fragmented, focusing on various aspects of companies, various reasons for downsizing, and various financial and market outcome measures. The purpose of this paper is to try and address some of this fragmentation by comparing those companies that downsized in 2008, whether financially healthy or not, with those companies that did not downsize.

Design/methodology/approach

The impact of the downsizing event was assessed by using various financial measures as well as a measure of company valuation over the short term (2009-2011) and long term (2009-2014).

Findings

Findings indicate that across all financial measures, except return on equity, downsizing makes no difference to the financial health of a company either in the short term (up to three years after the downsizing) or in the long term (up to six years after the downsizing). And with regards to return on equity, downsizing companies did more poorly immediately after the downsizing in efficiently using their equity.

Originality/value

The hope is that this work will better inform, not only scholars, but also senior leaders faced with a decision to downsize or not to downsize.
Using Primo for undergraduate research: a usability study
Authors: Kliewer Greta , Monroe-Gulick Amalia , Gamble Stephanie , Radio Erik
Published: December 2016

Purpose

The purpose of this paper is to observe how undergraduate students approach open-ended searching for a research assignment, specifically as it affected their use of the discovery interface Primo.

Design/methodology/approach

In total, 30 undergraduate students were provided with a sample research assignment and instructed to find resources for it using web tools of their choice, followed by the Primo discovery tool. Students were observed for 30 minutes. A survey was provided at the end to solicit additional feedback. Sources students found were evaluated for relevance and utility.

Findings

Students expressed a high level of satisfaction with Primo despite some difficulty navigating through more complicated tasks. Despite their interest in the tool and previous exposure to it, it was usually not the first discovery tool students used when given the research assignment. Students approached the open-ended search environment much like they would with a commercial search engine.

Originality/value

This paper focused on an open-ended search environment as opposed to a known-item scenario in order to assess students’ preferences for web search tools and how a library discovery layer such as Primo was a part of that situation. Evaluation of the resources students found relevant were also analyzed to determine to what degree the students understood the level of quality they exhibited and from which tool they were obtained.
The application of social media in outreach of academic libraries’ resources and services
Authors: Zhu Qiandong
Published: December 2016

Purpose

The purpose of this paper is to introduce the implementation of the official WeChat account, the most popular mobile social media site in China, to share Jinan University Library collections and services to students, faculty and staff. The implementation, experience and issues have implications for academic libraries and other institutions to run and improve social media tools.

Design/methodology/approach

This paper is a case study, which elaborates on the implementation process of the official WeChat account, including project group establishment, account application and management, users’ needs analysis, WeChat secondary development and model of development.

Findings

The official WeChat account has already engaged a population of followers who are able to directly access library resources and service via their mobile device. The social media tool is an effective approach to promote library services and to enhance relationships between the library and its users. The issues appear during the process of WeChat implementation and promotion, which requires WeChat’s provider, third-party application vendors and the library to work together to solve.

Originality/value

The implementation of official WeChat account has practical implications for academic libraries and other institutions to conduct it and similar social media tools, such as Sina Weibo, Facebook and Line. In particular, it is beneficial for academic libraries outside China which desire to use WeChat to engage Chinese international students. Additionally, it provides insight into the future effort on social media promotion, secondary development and cooperation within the social networking industry.