bluuebunny/crossref_metadata_2025 huggingface dataset:
Live cell monitoring of double strand breaks inS. cerevisiae
Authors: Waterman David P. , Lee Cheng-Sheng , Tsabar Michael , Zhou Felix , Eapen Vinay V. , Mazzella Allison , Haber James E.
Published: February 2018

We have used two different live-cell fluorescent protein markers to monitor the formation and localization of double-strand breaks (DSBs) in budding yeast. Using GFP derivatives of the Rad51 recombination protein or the Ddc2 checkpoint protein, we find that cells with three site-specific DSBs, on different chromosomes, usually display 2 or 3 foci that coalesce and dissociate. Rad51-GFP, by itself, is unable to repair DSBs by homologous recombination in mitotic cells, but is able to form foci and allow repair when heterozygous with a wild type Rad51 protein. The kinetics of disappearance of Rad51-GFP foci parallels the completion of DSB repair. However, in meiosis, Rad51-GFP is proficient when homozygous. Using Ddc2-GFP, we conclude that co-localization of foci following 3 DSBs does not represent formation of a homologous recombination "repair center," as the same distribution of Ddc2-GFP foci was found in the presence or absence of the Rad52 protein. The maintenance of separate DSB foci and much of their dynamics depend on functional microtubules, as addition of nocodazole resulted in a greater population of cells displaying a single focus.

Author Summary

Double strand breaks (DSBs) pose the greatest threat to the fidelity of an organism’s genome. While much work has been done on the mechanisms of DSB repair, the arrangement and interaction of multiple DSBs within a single cell remain unclear. Using two live-cell fluorescent DSB markers, we show that cells with 3 site-specific DSBs usually form 2 or 3 foci what can coalesce into fewer foci but also dissociate. The aggregation of DSBs into a single focus does not depend on the Rad52 recombination protein, suggesting that there is no “repair center” for homologous recombination. DSB foci are highly dynamic and their dynamic nature is dependent on microtubules.
Modeling brain dynamics in brain tumor patients using The Virtual Brain
Authors: Aerts Hannelore , Schirner Michael , Jeurissen Ben , Van Roost Dirk , Achten Rik , Ritter Petra , Marinazzo Daniele
Published: February 2018

Presurgical planning for brain tumor resection aims at delineating eloquent tissue in the vicinity of the lesion to spare during surgery. To this end, non-invasive neuroimaging techniques such as functional MRI and diffusion weighted imaging fiber tracking are currently employed. However, taking into account this information is often still insufficient, as the complex non-linear dynamics of the brain impede straightforward prediction of functional outcome after surgical intervention. Large-scale brain network modeling carries the potential to bridge this gap by integrating neuroimaging data with biophysically based models to predict collective brain dynamics.

As a first step in this direction, an appropriate computational model has to be selected, after which suitable model parameter values have to be determined. To this end, we simulated large-scale brain dynamics in 25 human brain tumor patients and 11 human control participants using The Virtual Brain, an open-source neuroinformatics platform. Local and global model parameters of the Reduced Wong-Wang model were individually optimized and compared between brain tumor patients and control subjects. In addition, the relationship between model parameters and structural network topology and cognitive performance was assessed.

Results showed (1) significantly improved prediction accuracy of individual functional connectivity when using individually optimized model parameters; (2) local model parameters can differentiate between regions directly affected by a tumor, regions distant from a tumor, and regions in a healthy brain; and (3) interesting associations between individually optimized model parameters and structural network topology and cognitive performance.
Distinct co-modulation rules of synaptic and voltage-gated currents coordinates interactions of multiple neuromodulators
Authors: Li Xinping , Bucher Dirk , Nadim Farzan
Published: February 2018

Different neuromodulators usually activate distinct receptors but can have overlapping targets. Consequently, circuit output depends on neuromodulator interactions at shared targets, a poorly understood process. We explored quantitative rules of co-modulation of two principal targets: voltage-gated and synaptic ionic currents. In the stomatogastric ganglion of the crab Cancer borealis, the neuropeptides proctolin and CCAP modulate synapses of the pyloric circuit, and activate a voltage-gated current (IMI) in multiple neurons. We examined the validity of a simple dose-dependent quantitative rule that co-modulation by proctolin and CCAP is predicted by the linear sum of the individual effects of each modulator, up to saturation. We found that this rule is valid for co-modulation of synapses, but not for the activation of IMI, where co-modulation was sublinear. Given the evolutionary conservation of neuromodulator receptors and signaling pathways, such distinct rules for co-modulation of different targets are likely to be common across neuronal circuits.
Protein pheromone MUP20/Darcin is a vector and target of indirect genetic effects in mice
Authors: Bachmann Sven O. , Cross Ellen , Kalbassi Shireene , Sarraf Matthew Alexandar ,   Michael Anthony Woodley of Menie, Baudouin Stéphane J.
Published: February 2018

Social behavior in animals is an adaptive process influenced by environmental factors and direct and indirect genetic effects. Indirect genetic effects (IGEs) include mechanisms by which individuals of particular genotypes can influence the behavioral phenotypes and genotypes (via modulated patterns of gene expression) of other individuals with different genotypes. In groups of adult mice, IGEs can be unidirectional, from one genotype to the other, or bidirectional, resulting in a homogenization of the behavioral phenotypes within the group. Critically, it has been theorized that IGEs constitute a large fitness target on which deleterious mutations can have pleiotropic effects, meaning that individuals carrying certain behavior-altering mutations can impose the fitness costs of those mutations on others comprising the broader social genome. Experimental data involving a mouse model support the existence of these IGE-amplified fitness losses; however, the underlying biological mechanisms that facilitate these remain unknown. In a mouse model of IGEs, we demonstrate that the Major Urinary Protein 20 pheromone, also called Darcin, produced by mice lacking the adhesion protein Neuroligin-3 acts as a vector to deleteriously modify the social behavior of wild-type mice. Additionally, we showed that lack of social interest on the part of Neuroligin-3 knockout mice is independent of their environment. These findings reveal a new role for mammalian pheromones in mediating the externalization of social deficits from one individual to others comprising the population through IGEs.

Author Summary

Indirect genetic effects (IGEs) are mechanisms by which individuals of particular genotypes can influence the behavioral phenotype of individuals of different genotypes, sometimes disruptively, in instances where one member of the population carriers a deleterious behavior altering variant. Although disruptive IGEs have been demonstrated in mice, its underlying molecular and genetic mechanisms remain unknown. Using an IGEs mouse model, we demonstrated that the pheromone protein Major Urinary Protein 20, also named Darcin, is as a vector and target of social epistasis a specific type of IGEs. This finding reveals a new function for mammalian pheromones in mediating social epistasis to degrade group social behavior.
Epigenome-wide association study of placental DNA methylation and maternal exposure to night shift work in the Rhode Island Child Health Study
Authors: Clarkson-Townsend Danielle A. , Everson Todd M. , Deyssenroth Maya A. , Burt Amber A. , Hermetz Karen E. , Hao Ke , Chen Jia , Marsit Carmen J.
Published: February 2018

Objectives

Circadian disruption from environmental and occupational exposures can potentially impact health, including offspring health, through epigenetic alterations. Night shift workers experience circadian disruption, but little is known about how this exposure could influence the epigenome of the placenta, which is situated at the maternal-fetal interface. To investigate whether night shift work is associated with variations in DNA methylation patterns of placental tissue, we conducted an epigenome-wide association study (EWAS) of night shift work.

Methods

CpG specific methylation genome-wide of placental tissue (measured with the Illumina 450K array) from participants (n=237) in the Rhode Island Child Health Study (RICHS) who did (n=53) and did not (n=184) report working the night shift was compared using robust linear modeling, adjusting for maternal age, pre-pregnancy smoking, infant sex, maternal adversity, and putative cell mixture.

Results

Night shift work was associated with differential methylation in placental tissue, including CpG sites in the genes NAV1, SMPD1, TAPBP, CLEC16A, DIP2C, FAM172A, and PLEKHG6 (Bonferroni-adjusted p<0.05). CpG sites within NAV1, MXRA8, GABRG1, PRDM16, WNT5A, and FOXG1 exhibited the most hypomethylation, while CpG sites within TDO2, ADAMTSL3, DLX2, and SERPINA1 exhibited the most hypermethylation (BH q<0.10). PER1 was the only core circadian gene demonstrating differential methylation. Functional analysis indicated GO-terms associated with cell-cell adhesion.

Conclusions

Night shift work was associated with differential methylation of the placenta, which may have implications for fetal health and development. Additionally, neuron navigator 1 (NAV1) may play a role in the development of the human circadian system.

What is already known about this subject?

Night shift work and circadian disruption may play a role in the development and progression of many diseases. However, little is known about how circadian disruption impacts human fetal health and development.

What are the new findings?

Working the night shift is associated with altered placental methylation patterns, and particularly, neuron navigator 1 (NAV1) may play a role in the development of the human circadian system.

How might this impact on policy or clinical practice in the foreseeable future?

Night shift work prior to or during pregnancy may alter the placental epigenome, which has implications for fetal health. Further studies are needed to evaluate night shift work as a possible risk factor for gestational diabetes and to evaluate the impact of circadian disruption on fetal health and development.
PET by MRI: Glucose Imaging by 13C-MRS without Dynamic Nuclear Polarization by Noise Suppression through Tensor Decomposition Rank Reduction
Authors: Brender Jeffrey R. , Kishimoto Shun , Merkle Hellmut , Reed Galen , Hurd Ralph E. , Chen Albert P. , Ardenkjaer-Larsen Jan Henrik , Munasinghe Jeeva , Saito Keita , Seki Tomohiro , Oshima Nobu , Yamamoto Kazu , Choyke Peter L. , Mitchell James , Krishna Murali C.
Published: February 2018

Metabolic reprogramming is one of the defining features of cancer and abnormal metabolism is associated with many other pathologies. Molecular imaging techniques capable of detecting such changes have become essential for cancer diagnosis, treatment planning, and surveillance. In particular, 18F-FDG (fluorodeoxyglucose) PET has emerged as an essential imaging modality for cancer because of its unique ability to detect a disturbed molecular pathway through measurements of glucose uptake. However, FDG-PET has limitations that restrict its usefulness in certain situations and the information gained is limited to glucose uptake only. 13C magnetic resonance spectroscopy theoretically has certain advantages over FDG-PET, but its inherent low sensitivity has restricted its use mostly to single voxel measurements. We show here a new method of imaging glucose metabolism in vivo that relies on a simple, but robust and efficient, post-processing procedure by the higher dimensional analog of singular value decomposition, tensor decomposition. Using this procedure, we achieve an order of magnitude increase in signal to noise in both dDNP and non-hyperpolarized non-localized experiments without sacrificing accuracy. In CSI experiments an approximately 30-fold increase was observed, enough that the glucose to lactate conversion indicative of the Warburg effect can be imaged without hyper-polarization with a time resolution of 12 s and an overall spatial resolution that compares favorably to 18F-FDG PET.
Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning
Authors: Zhou Naihui , Siegel Zachary D , Zarecor Scott , Lee Nigel , Campbell Darwin A , Andorf Carson M , Nettleton Dan , Lawrence-Dill Carolyn J , Ganapathysubramanian Baskar , Kelly Jonathan W , Friedberg Iddo
Published: February 2018

The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good quality. We explore an image analysis task involving the segmentation of corn tassels from images taken in a field setting. We investigate the accuracy, speed and other quality metrics when this task is performed by students for academic credit, Amazon MTurk workers, and Master Amazon MTurk workers. We conclude that the Amazon MTurk and Master Mturk workers perform significantly better than the for-credit students, but with no significant difference between the two MTurk worker types. Furthermore, the quality of the segmentation produced by Amazon MTurk workers rivals that of an expert worker. We provide best practices to assess the quality of ground truth data, and to compare data quality produced by different sources. We conclude that properly managed crowdsourcing can be used to establish large volumes of viable ground truth data at a low cost and high quality, especially in the context of high throughput plant phenotyping. We also provide several metrics for assessing the quality of the generated datasets.

Author Summary

Food security is a growing global concern. Farmers, plant breeders, and geneticists are hastening to address the challenges presented to agriculture by climate change, dwindling arable land, and population growth. Scientists in the field of plant phenomics are using satellite and drone images to understand how crops respond to a changing environment and to combine genetics and environmental measures to maximize crop growth efficiency. However, the terabytes of image data require new computational methods to extract useful information. Machine learning algorithms are effective in recognizing select parts of images, butthey require high quality data curated by people to train them, a process that can be laborious and costly. We examined how well crowdsourcing works in providing training data for plant phenomics, specifically, segmenting a corn tassel – the male flower of the corn plant – from the often-cluttered images of a cornfield. We provided images to students, and to Amazon MTurkers, the latter being an on-demand workforce brokered by Amazon.com and paid on a task-by-task basis. We report on best practices in crowdsourcing image labeling for phenomics, and compare the different groups on measures such as fatigue and accuracy over time. We find that crowdsourcing is a good way of generating quality labeled data, rivaling that of experts.
A Genomic Reference Panel forDrosophila serrata
Authors: Reddiex Adam R. , L. Allen Scott , Chenoweth Stephen F.
Published: February 2018

Here we describe a collection of re-sequenced inbred lines ofDrosophila serrata, sampled from a natural population situated deep within the species endemic distribution in Brisbane, Australia.D. serratais a member of the speciosemontiumgroup whose members inhabit much of south east Asia and has been well studied for aspects of climatic adaptation, sexual selection, sexual dimorphism, and mate recognition. We sequenced 110 lines that were inbred via 17-20 generations of full-sib mating at an average coverage of 23.5x with paired-end Illumina reads. 15,228,692 biallelic SNPs passed quality control after being called using the Joint Genotyper for Inbred Lines (JGIL). Inbreeding was highly effective and the average levels of residual heterozygosity (0.86%) were well below theoretical expectations. As expected, linkage disequilibrium decayed rapidly, with r2dropping below 0.1 within 100 base pairs. With the exception of four closely related pairs of lines which may have been due to technical errors, there was no statistical support for population substructure. Consistent with other endemic populations of otherDrosophilaspecies, preliminary population genetic analyses revealed high nucleotide diversity and, on average, negative Tajima’s D values. A preliminary GWAS was performed on a cuticular hydrocarbon trait, 2-MeC28revealing 4 SNPs passing Bonferroni significance residing in or near genes. One geneCht9may be involved in the transport of CHCs from the site of production (oenocytes) to the cuticle. Our panel will facilitate broader population genomic and quantitative genetic studies of this species and serve as an important complement to existingD. melanogasterpanels that can be used to test for the conservation of genetic architectures across theDrosophilagenus.
HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer
Authors: Kim Daehwan , Paggi Joseph , Salzberg Steven L.
Published: February 2018

Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses of human genomes. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT-genotype, for representing and searching an expanded model of the human reference genome, in which a comprehensive catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a very fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate HISAT-genotype’s accuracy for HLA typing, a critical task in human organ transplantation, and for the DNA fingerprinting tests widely used in forensics. In both applications, HISAT-genotype not only improves upon earlier computational methods, but matches or exceeds the accuracy of laboratory-based assays.

One Sentence Summary

HISAT-genotype is a software platform that has the ability to genotype all the genes in an individual’s genome within a few hours on a desktop computer.
Feature Specific Prediction Errors and Surprise across Macaque Fronto-Striatal Circuits during Attention and Learning
Authors: Oemisch Mariann , Westendorff Stephanie , Azimi Marzyeh , Hassani Seyed Ali , Ardid Salva , Tiesinga Paul , Womelsdorf Thilo
Published: February 2018

Prediction errors signal unexpected outcomes indicating that expectations need to be adjusted. For adjusting expectations efficiently prediction errors need to be associated with the precise features that gave rise to the unexpected outcome. For many visual tasks this credit assignment proceeds in a multidimensional feature space that makes it ambiguous which object defining features are relevant. Here, we report of a potential solution by showing that neurons in all areas of the medial and lateral fronto-striatal networks encode prediction errors that are specific to separate features of attended multidimensional stimuli, with the most ubiquitous prediction error occurring for the reward relevant features. These feature specific prediction error signals (1) are different from a non-specific prediction error signal, (2) arise earliest in the anterior cingulate cortex and later in lateral prefrontal cortex, caudate and ventral striatum, and (3) contribute to feature-based stimulus selection after learning. These findings provide strong evidence for a widely-distributed feature-based eligibility trace that can be used to update synaptic weights for improved feature-based attention.

Highlights

Neural reward prediction errors carry information for updating feature-based attention in all areas of the fronto-striatal network.

Feature specific neural prediction errors emerge earliest in anterior cingulate cortex and later in lateral prefrontal cortex.

Ventral striatum neurons encode feature specific surprise strongest for the goal-relevant feature.

Neurons encoding feature-specific prediction errors contribute to attentional selection after learning.
SNAP-tagged nanobodies enable reversible optical control of a G protein-coupled receptor via a remotely tethered photoswitchable ligand
Authors: Farrants Helen , Ruiz Amanda Acosta , Gutzeit Vanessa A. , Trauner Dirk , Johnsson Kai , Levitz Joshua , Broichhagen Johannes
Published: February 2018

G protein-coupled receptors (GPCRs) mediate the transduction of extracellular signals into complex intracellular responses. Despite their ubiquitous roles in physiological processes and as drug targets for a wide range of disorders, the precise mechanisms of GPCR function at the molecular, cellular, and systems levels remain partially understood. In order to dissect the function of individual receptors subtypes with high spatiotemporal precision, various optogenetic and photopharmacological approaches have been reported that use the power of light for receptor activation and deactivation. Here, we introduce a novel and, to date, most remote way of applying photoswitchable orthogonally remotely-tethered ligands (PORTLs) by using a SNAP-tag fused nanobody. Our nanobody-photoswitch conjugates (NPCs) can be used to target a GFP-fused metabotropic glutamate receptor by either gene-free application of purified complexes or co-expression of genetically encoded nanobodies to yield robust, reversible control of agonist binding and subsequent downstream activation. By harboring and combining the selectivity and flexibility of both nanobodies and self-labelling enzymes, we set the stage for targeting endogenous receptors in vivo.
Motor cortex is an input-driven dynamical system controlling dexterous movement
Authors: Sauerbrei Britton , Guo Jian-Zhong , Mischiati Matteo , Guo Wendy , Kabra Mayank , Verma Nakul , Branson Kristin , Hantman Adam
Published: February 2018

Skillful control of movement is central to our ability to sense and manipulate the world. A large body of work in nonhuman primates has demonstrated that motor cortex provides flexible, time-varying activity patterns that control the arm during reaching and grasping. Previous studies have suggested that these patterns are generated by strong local recurrent dynamics operating autonomously from inputs during movement execution. An alternative possibility is that motor cortex requires coordination with upstream brain regions throughout the entire movement in order to yield these patterns. Here, we developed an experimental preparation in the mouse to directly test these possibilities using optogenetics and electrophysiology during a skilled reach-to-grab-to-eat task. To validate this preparation, we first established that a specific, time-varying pattern of motor cortical activity was required to produce coordinated movement. Next, in order to disentangle the contribution of local recurrent motor cortical dynamics from external input, we optogenetically held the recurrent contribution constant, then observed how motor cortical activity recovered following the end of this perturbation. Both the neural responses and hand trajectory varied from trial to trial, and this variability reflected variability in external inputs. To directly probe the role of these inputs, we used optogenetics to perturb activity in the thalamus. Thalamic perturbation at the start of the trial prevented movement initiation, and perturbation at any stage of the movement prevented progression of the hand to the target; this demonstrates that input is required throughout the movement. By comparing motor cortical activity with and without thalamic perturbation, we were able to estimate the effects of external inputs on motor cortical population activity. Thus, unlike pattern-generating circuits that are local and autonomous, such as those in the spinal cord that generate left-right alternation during locomotion, the pattern generator for reaching and grasping is distributed across multiple, strongly-interacting brain regions.
Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration
Authors: Tomaz David , Pereira Pedro Matos , Guerra Nadia , Dyson Julian , Gould Keith , Henriques Ricardo
Published: February 2018

NK cell responses depend on the balance of signals from inhibitory and activating receptors. However, how the integration of antagonistic signals occurs upon NK cell-target cell interaction is not fully understood. Here, we provide evidence that NK cell inhibition via the inhibitory receptor Ly49A is dependent on its relative colocalization at the nanometer scale with the activating receptor NKG2D upon immune synapse (IS) formation. NKG2D and Ly49A signal integration and colocalization was studied using NKG2D-GFP and Ly49A-RFP-expressing primary NK cells, forming ISs with NIH3T3 target cells, with or without expression of single chain trimer (SCT) H2-Ddand an extended form of SCT H2-Dd-CD4 MHC-I molecules. Nanoscale colocalization was assessed by Förster resonance energy transfer (FRET) between NKG2D-GFP and Ly49A-RFP and measured for each synapse. In the presence of their respective cognate ligands, NKG2D and Ly49A colocalize at a nanometer scale leading to NK cell inhibition. However, increasing the size of the Ly49A ligand reduced the nanoscale colocalization with NKG2D consequently impairing Ly49A-mediated inhibition. Thus, our data shows NK cell signal integration is critically dependent on the dimensions of NK cell ligand-receptor pairs by affecting their relative nanometer-scale colocalization at the IS. Together, our results suggest the balance of NK cell signals, and NK cell responses, are determined by the relative nanoscale colocalization of activating and inhibitory receptors in the immune synapse.
GeneQC: A quality control tool for gene expression estimation based on RNA-sequencing reads mapping
Authors: McDermaid Adam , Chen Xin , Zhang Yiran , Xie Juan , Wang Cankun , Ma Qin
Published: February 2018

Motivation

One of the main benefits of using modern RNA-sequencing (RNA-Seq) technology is the more accurate gene expression estimations compared with previous generations of expression data, such as the microarray. However, numerous issues can result in the possibility that an RNA-Seq read can be mapped to multiple locations on the reference genome with the same alignment scores, which occurs in plant, animal, and metagenome samples. Such a read is so-called a multiple-mapping read (MMR). The impact of these MMRs is reflected in gene expression estimation and all downstream analyses, including differential gene expression, functional enrichment, etc. Current analysis pipelines lack the tools to effectively test the reliability of gene expression estimations, thus are incapable of ensuring the validity of all downstream analyses.

Results

Our investigation into 95 RNA-Seq datasets from seven species (totaling 1,951GB) indicates an average of roughly 22% of all reads are MMRs for plant and animal species. Here we present a tool called GeneQC (Gene expression Quality Control), which can accurately estimate the reliability of each gene’s expression level. The underlying algorithm is designed based on extracted genomic and transcriptomic features, which are then combined using elastic-net regularization and mixture model fitting to provide a clearer picture of mapping uncertainty for each gene. GeneQC allows researchers to determine reliable expression estimations and conduct further analysis on the gene expression that is of sufficient quality. This tool also enables researchers to investigate continued re-alignment methods to determine more accurate gene expression estimates for those with low reliability.

Availability

GeneQC is freely available at http://bmbl.sdstate.edu/GeneQC/home.html.

Contact

qin.ma@sdstate.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
The Constriction Ring of Amniotic Band Syndrome Reveals Idiosyncrasies of Wound Repair in Infancy
Authors: Bhattacharyya Surjya N. , Ilyashov Isaac M. , Chu Alice
Published: February 2018

We hypothesized that the constriction rings in Amniotic Band Syndrome (ABS) are the sequelae of localized mechanical injury. Typical scarring pattern was examined in skin tissue of ABS origin, containing an amniotic band constriction, for collagen and elastin distribution, and the ratio of collagen I to collagen III (CI:CIII). A skin sample from an extra finger was the control. In the ABS specimens, sub-epidermal structures were intact and present throughout, and collagen I exhibited a normal basket-weave pattern. At the site of constriction in both ABS samples, reticular dermis elastin fibers were fragmented and papillary dermis elastin fibers were absent. In the control tissue, the reticular dermis contained relatively thick, branching fibers of elastin, and papillary dermis elastin was present.

The elastin fragmentation at the constriction ring indicates localized elastin remodeling in response to injury. The absence of elastin in the papillary dermis of the constriction likely indicates a localized disruption in elastin formation. The formation and deposition of collagen and the presence of sub-epidermal structures favor a non-scarring phenotype, while the organization of elastin favors that of localized scarring.

Summary Statement

A rare, fetal model of healing after constrictive injury of skin, in which elastin fragmentation at the constriction injury indicates remodeling explained by the differential expression of elastin during gestation.
X-ray reflectivity from curved liquid interfaces
Authors: Festersen Sven , Hrkac Stjepan B. , Koops Christian T. , Runge Benjamin , Dane Thomas , Murphy Bridget M. , Magnussen Olaf M.
Published: February 2018

X-ray reflectivity studies of the structure of liquid–vapour and liquid–liquid interfaces at modern sources, such as free-electron lasers, are currently impeded by the lack of dedicated liquid surface diffractometers. It is shown that this obstacle can be overcome by an alternative experimental approach that uses the natural curvature of a liquid drop for variation of the angle of incidence. Two modes of operation are shown: (i) sequential reflectivity measurements by a nanometre beam and (ii) parallel acquisition of large ranges of a reflectivity curve by micrometre beams. The feasibility of the two methods is demonstrated by studies of the Hg/vapour, H2O/vapour and Hg/0.1 MNaF interface. The obtained reflectivity curves match the data obtained by conventional techniques up to 5αcin micro-beam mode and up to 35αcin nano-beam mode, allowing observation of the Hg layering peak.
Small-angle scattering of polychromatic X-rays: effects of bandwidth, spectral shape and high harmonics
Authors: Chen Sen , Luo Sheng-Nian
Published: February 2018

Polychromatic X-ray sources can be useful for photon-starved small-angle X-ray scattering given their high spectral fluxes. Their bandwidths, however, are 10–100 times larger than those using monochromators. To explore the feasibility, ideal scattering curves of homogeneous spherical particles for polychromatic X-rays are calculated and analyzed using the Guinier approach, maximum entropy and regularization methods. Monodisperse and polydisperse systems are explored. The influence of bandwidth and asymmetric spectra shape are exploredviaGaussian and half-Gaussian spectra. Synchrotron undulator spectra represented by two undulator sources of the Advanced Photon Source are examined as an example, as regards the influence of asymmetric harmonic shape, fundamental harmonic bandwidth and high harmonics. The effects of bandwidth, spectral shape and high harmonics on particle size determination are evaluated quantitatively.
Board independence and managerial authority
Authors: Dah Mustafa , Jizi Mohammad , Sbeity Sadim
Published: February 2018

Purpose

The imposition of the Sarbanes Oxley (SOX) Act and the NYSE/NASDAQ regulations boosted the proportion of independent directors serving on corporate boards. For certain firms, increasing the number of independent directors may impose costs that exceed the benefits. The purpose of this paper is to examine the implications of increased independence following SOX, relative to the pre-SOX board independence benchmark, on managerial authority and entrenchment within the firm.

Design/methodology/approach

Data are collected from COMPUSTAT, ExecuComp, and RiskMetrics. Data are divided into two periods, pre-SOX (1996-2001) and post-SOX (2002-2006). The focus is on the sub-group of firms who were not complying with the board independence requirement prior to SOX and became compliant afterwards. Various regressions are employed to assess the implications of increased independence following SOX on managerial authority and entrenchment.

Findings

The appreciation in board independence post-SOX significantly inflates both managerial compensation and the likelihood of CEO duality. Also, there is a positive association between board independence and managerial entrenchment during both the pre- and post-SOX periods. Imposed board composition requirements diminished board monitoring efficiency and boosted the CEO dominance and control over the firm.

Originality/value

This research adds to the extant literature investigating the implications of SOX on internal monitoring and governance. The results are based on an off-equilibrium phenomenon in which companies were obliged to alter their endogenously determined board structure. Thus, regulations to improve governance could backfire as the CEO might abuse them to extract private benefits.
Innovative sustainable methodology for managing in-house software development in SMEs
Authors: Tarhini Abbas , Yunis Manal , El-Kassar Abdul-Nasser
Published: February 2018

Purpose

The purpose of this paper is to present an innovative agile methodology that proposes fundamental changes in managing the development of in-house information systems in small- and medium-sized enterprises (SMEs) and benchmarks it with one of two database technologies enabling these systems to be both efficient and competitive.

Design/methodology/approach

The objectives are achieved by presenting an elaborated design of the agile methodology that manages the system development process by addressing three basic components: roles played by system players, process needed to fulfill the system development, and artifacts to document the project. A case study is conducted as a proof of the effectiveness of the proposed methodology and measures whether the selection of the database technology affects the effectiveness of the system development process.

Findings

Results show that, compared with traditional methodologies, the proposed methodology reduced the cost of system development and testing by 30 percent and enhanced the IT – business alliance. Further, this work found that the selection of a suitable database technology is strongly related to the complexity and interrelationships between the data used.

Originality/value

Such research did not receive the needed attention (Hunter, 2004) even in the past decade. Successful adoption of IT by companies could be in the form of customized IS which could be expensive for SMEs to adopt due to a lack in technical expertise and financial resources. The proposed methodology has the potential to promote sustainable development through helping SMEs in reducing the time and cost of IT project development.
Sustainability strategies in the Indian leather industry: an empirical analysis
Authors: Gupta Sandeep , Gupta Shivam , Dhamija Pavitra , Bag Surajit
Published: February 2018

Purpose

Burgeoning challenges of climate change and poverty alleviation across many parts of the world have enforced the policy makers and researchers to develop an alternate system for performance assessment of an individual, a country, and a corporate. The purpose of this paper is to analyze the sustainability strategies of three leading states in the Indian leather industry – Tamil Nadu (TN), West Bengal (WB) and Uttar Pradesh (UP) – to gain insights into their efforts and progress in generating economic, social, and environmental values.

Design/methodology/approach

This study used case study approach for investigative analysis, and triangulation method – interviews and field visits, for data verification. The study examines the various sustainability strategies by applying economic value creation (evaluation of growth in total turnover, evaluation of the growth in profitability, evaluation of leverage), social value creation (evaluation of the growth in wages, evaluation of the growth in employee welfare expenses), and environmental value creation (conservation in raw material consumption, conservation in energy consumption, evaluation of waste management practices).

Findings

The findings reveal that the three states differ significantly from each other both in terms of efforts made and progress achieved during the period of study, 1998-2013. UP seems to be making the most consistent progress in achieving economic value, while WB shows the most progress in creating social value, and TN leads the pack in terms of creating environmental value. Thus, the three leading states in the Indian leather industry have been allowing trade-offs to get competitive advantage over others.

Research limitations/implications

The opaqueness with which the Indian leather Industry conducts social and environmental practices clearly limits the sources of accurate and reliable data, and the ability of researchers to precisely identify the problems and suggest solutions.

Practical implications

The opaqueness with which the Indian leather Industry conducts social and environmental practices clearly impacts the policy makers, practitioners, and researchers to continue such initiatives and improve the lives of people in India for whom continuing this profession is a big challenge and a hurdle to accomplish their livelihood.

Originality/value

The paper gives a theoretical explanation of the sustainability in the leather industry with respect to its strategies in terms of economic value, social value, and environmental value.
Same, same but different? Women’s experiences with gender inequality in Brazil
Authors: Santos Clarice , Hilal Adriana V. Garibaldi de
Published: February 2018

Purpose

The purpose of this paper is to examine gender issues in Brazil from the perceptions, experiences, and discourses of professional women in Rio de Janeiro and São Paulo.

Design/methodology/approach

The study is based on 26 in-depth interviews with female professionals. The methodology consists of an exploratory approach through content analysis.

Findings

Despite the fact that Brazil demonstrates an idealized national ethos that promotes equality, gender roles are still very traditional. Participants recognized gender issues at work, including covert discrimination, though most did not acknowledge experiencing them personally.

Originality/value

There is dissonance between global trends and the actual experience of female professionals in Brazil. Although participants rejected the idea of personally experiencing inequality, they acknowledge its existence in human resources (HR) practices. This leads to a self-fulfilling prophecy where gender inequality is perpetuated and organizations and HR departments do not seem to have a proactive role as change agents.
Knowledge about sport and exercise science
Authors: Leal Acácia Gonçalves Ferreira , Vancini Rodrigo Luiz , Gentil Paulo , Benedito-Silva Ana Amélia , da Silva Antonio Carlos , Campos Mário Hebling , Andrade Marilia Santos , de Lira Claudio Andre Barbosa
Published: February 2018

Purpose

The purpose of this paper was to assess the knowledge on sport and exercise science held by a sample of Brazilian physiotherapists, nutritionists and physical educators.

Design/methodology/approach

A cross-sectional research design was used. The answers given by 1,147 professionals (300 physiotherapists, 705 physical educators and 142 nutritionists) who participated in a qualifying process for a specialization course on exercise physiology were analyzed. Questions were analyzed on maximal oxygen uptake (four questions), physical fitness assessment (three questions), physical training (two questions), bioenergetics (one question) and exercise in extreme environments (one question).

Findings

The results revealed misconceptions held by Brazilian health professionals on a number of concepts related to sport and exercise science, such as maximal oxygen uptake.

Practical implications

These results reinforce the need for continuing education programs to maximize the quality of the service provided by sport and exercise science professionals in Brazil. Improvements in the undergraduate courses curriculum are also recommended.

Originality/value

This is the first study to assess misconceptions about sport and exercise science among Brazilian health professionals.
Food consumers’ views of essential food knowledge and skills for all consumers
Authors: Burton Melissa , Riddell Lynn , Worsley Anthony
Published: February 2018

Purpose

Food education in secondary schools can provide adolescents with essential food knowledge and skills required for healthy, independent living. The purpose of this paper is to identify food-related knowledge and skills that Australian consumers believe are required for all consumers, and to identify their demographic and psychographic associations based on two studies.

Design/methodology/approach

Two online surveys were conducted in 2012 and 2014 in different samples of Australian consumers (n=2,146 and 770, respectively), both drawn from a commercial research panel. Respondents rated their views on the importance of food knowledge and skills items as “essential” or “not essential” in the 2012 survey, or by rating their importance in the 2014 using five-point scales. Principal components analysis, confirmatory factor analysis and stepwise multiple regression analysis were used to group the different types of food knowledge and skills and identify their associations.

Findings

In both surveys, “the effects of food on people’s health” and “how to prepare food safely” were viewed as the most important knowledge and skills, and food production, food system and environmental items were the least important. Food knowledge and equality values were positively associated with the importance of Nutrition Knowledge and Practical Skills in both surveys. In addition, food mavenism was a positive predictor of Nutrition and Health Knowledge and The Food System in 2012 and female sex was positively associated with Practical Food Skills.

Research limitations/implications

Most respondents believed that nutrition and health knowledge and practical food skills were more important than knowledge of food production, the food system or the environment. The findings suggest that psychological factors such as personal values, food knowledge and food mavenism may be more important influences over these perceptions than respondents’ demographic characteristics.

Originality/value

This research is novel as it explores consumers’ views about the food knowledge and skills that all consumers need to be healthy and independent, and has important implications for food education, particularly in secondary schools. In addition, it assessed consumers’ views at two different time points, two years apart and, thus, provides evidence for stability of these views.
Gender differences in self-employment in Spain
Authors: Rico Paz , Cabrer-Borrás Bernardí
Published: February 2018

Purpose

The purpose of this paper is to analyse the gender differences of self-employment in Spain.

Design/methodology/approach

A binary choice model is specified and estimated, using information from the Continuous Working Life Sample drawn from the registers of the Spanish Social Security. Moreover, the differences in self-employment between men and women are also analysed, through the decomposition proposed by Yun (2004).

Findings

The results indicate that the differences between both groups in the probability of being entrepreneurs stem from unobservable factors. The difference explained by the unobservable component is 84.12 per cent, whereas the rest, 15.88 per cent, is explained by the characteristics component. The explanatory factors of being an entrepreneur affect men and women in the same way, but to a different extent, explained mainly by factors related to gender.

Originality/value

This paper sets out to identify whether there are gender differences in the probability of becoming self-employed and, if there are, to quantify what part of the difference in entrepreneurship between men and women is explained by the characteristics of each gender group and what part is because of unobservable factors. From the perspective of the public authority, knowing the determinants that explain why the entrepreneurial activity is different depending on gender is fundamental in being able to reduce the entrepreneurial gap between men and women.
Structural production factors’ impact on the financial performance of agribusiness cooperatives in Brazil
Authors: Martins Fellipe Silva , Lucato Wagner Cezar
Published: February 2018

Purpose

Studies on the performance of agribusiness cooperatives in Brazil focus on economic and financial aspects. The purpose of this paper is to further delve into such studies by investigating which commonly measurable structural production factors (horizontal, vertical and lateral diversification; operating area; number of associates; and time in operation) have greater impacts on the financial performance of such cooperatives.

Design/methodology/approach

To achieve such a goal, a survey was conducted with a sampling pool divided by size (annual net revenues of US$ 50 million or higher), and the questionnaire was employed as a method of data collection. The sample was concentrated in the southern, south-eastern and mid-western regions of Brazil; classified by size; and deemed adequate after several adequacy tests.

Findings

The results were analysed using Spearman’s correlation, which showed that there were no significant correlations between the structural production factors considered in this study and the economic-financial performance of agricultural cooperatives, which leads to questions about the effectiveness of employing diversification strategies with a conjoint approach. Nonetheless, it was possible to identify several relationships not mentioned in the original hypotheses that might be addressed further in future studies.

Research limitations/implications

The data obtained should be interpreted with caution because heteroscedasticity was detected. Although the cause could not be clearly identified, the presence of heteroscedasticity could mean that smaller and similar cooperatives present similar variation in their diversification and production base strategies.

Originality/value

This work sought to generate knowledge regarding operations management, which was achieved by demonstrating that production diversification in a dynamic and relevant economic sector, that is, agricultural cooperatives, is limited in terms of financial return when performed in an isolated mode. Hence, cooperatives’ production managers should take into account the totality of structural production factors during their planning activities.