bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation
Authors: Percher Avital , Ramakrishnan Srinivasan , Thinon Emmanuelle , Yuan Xiaoqiu , Yount Jacob S. , Hang Howard C. 
Published: April 2016

Significance
Cysteine fatty acylation (S-fatty acylation) regulates the stability, trafficking, and activity of proteins in eukaryotes. Current methods to study S-fatty acylation rely on the metabolic incorporation of fatty acid analogs or selective chemical labeling and affinity purification, which limits the detection of endogenous S-fatty acylated protein isoforms and levels. Here we demonstrate that the biochemical exchange of acyl groups on cysteines with defined mass-tags enables the direct visualization of endogenous S-fatty acylated protein levels. The application of this mass-tag labeling method revealed that site-specific S-fatty acylation of interferon-induced transmembrane protein 3 controls the antiviral activity of this IFN-induced effector.
Dr.seq: a quality control and analysis pipeline for droplet sequencing
Authors: Huo Xiao , Hu Sheng’en , Zhao Chengchen , Zhang Yong 
Published: April 2016

Abstract
Motivation: Drop-seq has recently emerged as a powerful technology to analyze gene expression from thousands of individual cells simultaneously. Currently, Drop-seq technology requires refinement and quality control (QC) steps are critical for such data analysis. There is a strong need for a convenient and comprehensive approach to obtain dedicated QC and to determine the relationships between cells for ultra-high-dimensional datasets.
Results: We developed Dr.seq, a QC and analysis pipeline for Drop-seq data. By applying this pipeline, Dr.seq provides four groups of QC measurements for given Drop-seq data, including reads level, bulk-cell level, individual-cell level and cell-clustering level QC. We assessed Dr.seq on simulated and published Drop-seq data. Both assessments exhibit reliable results. Overall, Dr.seq is a comprehensive QC and analysis pipeline designed for Drop-seq data that is easily extended to other droplet-based data types.
Availability and Implementation: Dr.seq is freely available at: http://www.tongji.edu.cn/∼zhanglab/drseq and https://bitbucket.org/tarela/drseq
Contact: yzhang@tongji.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Sea lice (Lepeophtheirus salmonis and Caligus elongatus) infestation levels on sea trout (Salmo trutta L.) around the Irish Sea, an area without salmon aquaculture
Authors: Gargan Patrick , Karlsbakk Egil , Coyne John , Davies Carys , Roche William 
Published: April 2016

AbstractSea trout are parasitized by two species of caligid copepod sea lice, Lepeophtheirus salmonis and Caligus elongatus. Generally, levels of lice infestation are low and few adverse effects on the host have been reported. However, with the advent of marine salmon farming since the 1980s, there have been many published accounts of L. salmonis sea lice epizootics on salmonids in aquaculture areas. Few large-scale studies are available on levels of sea lice infestation of sea trout in areas without salmon farms or before their development. Understanding natural background lice levels on sea trout is important to interpret lice levels on trout in aquaculture areas. The Celtic Sea Trout Project, an INTERREG IVA Ireland Wales EU funded project, examined the status, distribution, genetics, and ecology of sea trout around the Irish Sea and provided an opportunity to assess levels of lice on sea trout spatially and temporally in an area without marine salmon farming. The prevalence of L. salmonis remained constant over the 3 years (63–69%), whereas the prevalence of C. elongatus was lower (20–40%). The mean abundance of L. salmonis ranged from 3.6 to 3.8 and that of C. elongatus ranged from 0.6 to 4.3 (n = 850). There was a significant variation in L. salmonis abundance between marine areas. However, the relative stability in the prevalence and mean intensity of both lice species observed and the low mean abundances and very small proportion of juvenile life stages of L. salmonis reported here are similar to those reported from other studies in areas without salmon farming and likely represent natural background salmon lice levels on sea trout. This 3-year study, conducted over a wide geographic area, represents one of the largest studies of sea lice infestation patterns on sea trout in an area distant from finfish aquaculture influences.
Cytosine Variant Calling with High-throughput Nanopore Sequencing
Authors: Rand Arthur C. , Jain Miten , Eizenga Jordan , Musselman-Brown Audrey , Olsen Hugh E. , Akeson Mark , Paten Benedict 
Published: April 2016

AbstractChemical modifications to DNA regulate cellular state and function. The Oxford Nanopore MinION is a portable single-molecule DNA sequencer that can sequence long fragments of genomic DNA. Here we show that the MinION can be used to detect and map two chemical modifications cytosine, 5-methylcytosine and 5-hydroxymethylcytosine. We present a probabilistic method that enables expansion of the nucleotide alphabet to include bases containing chemical modifications. Our results on synthetic DNA show that individual cytosine base modifications can be classified with accuracy up to 95% in a three-way comparison and 98% in a two-way comparison.Statement of SignificanceNanopore-based sequencing technology can produce long reads from unamplified genomic DNA, potentially allowing the characterization of chemical modifications and non-canonical DNA nucleotides as they occur in the cell. As the throughput of nanopore sequencers improves, simultaneous detection of multiple epigenetic modifications to cytosines will become an important capability of these devices. Here we present a statistical model that allows the Oxford Nanopore Technologies MinION to be used for detecting chemical modifications to cytosine using standard DNA preparation and sequencing techniques. Our method is based on modeling the ionic current due to DNA k-mers with a variable-order hidden Markov model where the emissions are distributed according to a hierarchical Dirichlet process mixture of normal distributions. This method provides a principled way to expand the nucleotide alphabet to allow for variant calling of modified bases.
Network competence in Finnish SMEs: implications for growth
Authors: Torkkeli Lasse , Kuivalainen Olli , Saarenketo Sami , Puumalainen Kaisu 
Published: April 2016

Purpose– The purpose of this paper is to examine how network competence is related to the growth of domestic and international SMEs originating from the Nordic region. Business networks have been found to drive internationalization of SMEs in the Nordic context, but the impact of network-related organizational competencies on them has not been considered.Design/methodology/approach– The authors apply regression analysis on a sample of 298 Finnish SMEs across five industry sectors, gathered via an online survey in 2008, and with the data having been updated for its financial indicators up to 2010.Findings– The authors find that cross-relational network competence is a significant predictor of growth in internationally operating SMEs. This result is robust across measures among the firms. In comparison, the network competence of domestically operating SMEs is not related to their growth, and relationship-specific competence does not influence growth.Research limitations/implications– The study does not account for longitudinal aspect of competence development. Growth is measured by the growth in sales and assets, and there are other ways to measure organizational growth. A single-country context also extends some restrictions on the generalizability of the results, although they could be expected to hold across small, open economies similar to Finland and the Nordic area.Practical implications– The results imply that the strategic aims of SMEs determine their need for network competence, those SMEs seeking internationalization and growth through geographic expansion come to benefit from developing certain types of network competence.Social implications– Policy implications arise where governments in Finland and in the Nordic area may aid SMEs’ internationalization efforts by enabling the growth-seeking firms with increased resources for competence development.Originality/value– This is the first study to examine how the organizational competencies to develop and manage business networks, in particular dyadic and network-level competencies, come to determine realized growth outcomes in domestic and international SMEs. It contributes to the theory of SME internationalization and international entrepreneurship from the business network point of view, while providing further knowledge on internationalization of SMEs originating from the Nordic area.
The role of coworker and supervisor support on job burnout and job satisfaction
Authors: Charoensukmongkol Peerayuth , Moqbel Murad , Gutierrez-Wirsching Sandra 
Published: April 2016

Purpose
This study investigates the role of coworker and supervisor support on three aspects of burnout (emotional exhaustion, depersonalization, perceived lack of personal accomplishment) and job satisfaction. The authors argue that different sources of social support at work can influence these three aspects of burnout differently.

Design/methodology/approach
Questionnaires were delivered to supervisors of each campus department at two state universities in South Texas asking them to encourage their employees to complete the survey. The sample consisted of 174 personnel.

Findings
The results show that coworker support was negatively associated with emotional exhaustion and depersonalization but not with perceived lack of personal accomplishment while supervisor support was negatively associated with all aspects of burnout. The analysis also confirmed the direct and indirect effects of coworker and supervisor support on job satisfaction.

Practical implications
Due to the detrimental consequences of burnout to employee satisfaction, organizations need to make sure that employees receive sufficient support from their coworkers and supervisors to avoid this burnout problem.

Originality/value
Even though the role of social support on job burnout has been previously investigated, existing studies tended to combine three dimensions of burnout into a single measure. Using an aggregated measure of burnout as an outcome variable can limit our understanding about the role that social support plays on each individual dimension of burnout. By employing burnout as a multidimensional construct, the present study can determine whether coworker support and supervisor support can have a different impact on each of the three dimensions of burnout.
Job insecurity and compensation evaluations: the role of overall justice
Authors: Haynie Jeffrey J. , Svyantek Daniel J. , Mazzei Matthew J. , Varma Virajanand 
Published: April 2016

Purpose
– The purpose of this paper is to examine the relations of job insecurity with pay and incentive satisfaction and the role of overall justice in these relationships.

Design/methodology/approach
– The authors surveyed employees of an industrial equipment sales firm located in the Southeastern USA. Surveys were completed by 151 employees using instruments assessing job insecurity, overall justice, pay satisfaction, and incentive satisfaction.

Findings
– The study results indicated job insecurity is negatively related to both pay and incentive satisfaction. Further, the study found that overall justice mediated the job insecurity to pay satisfaction relationship, but not the job insecurity to incentive satisfaction relationship.

Research limitations/implications
– Because overall justice only explained the job insecurity-pay satisfaction relationship, future research should examine other potential mediators to better understand these disparate effects when compared with incentive satisfaction. Future research should also examine the model with a larger sample using a time-lagged design to further mitigate the limitations of the study.

Practical implications
– The results of this study suggest that employees who contain a strong fear of job loss tend to experience reduced pay and incentive satisfaction levels. Managers should do what they can to limit the impact of job insecurity on these attitudes and provide additional training to employees in coping strategies so that they might better deal with the job insecurity stressor.

Originality/value
– Integrating the literatures on stress appraisal and organizational justice, the empirical model provides understanding of how job stressors and perceptions of organizational justice influence pay and incentive satisfaction.
Ethical research involving children: facilitating reflexive engagement
Authors: Powell Mary Ann , Graham Anne , Truscott Julia 
Published: April 2016

Purpose
Qualitative researchers working with children are increasingly sharing accounts of their research journeys, including the inherent ethical tensions they navigate. Within such accounts, reflexivity is consistently signalled as an important feature of ethical practice. The purpose of this paper is to explore how reflexive engagement can be stimulated within ethical decision-making processes, with the aim of generating professional dialogue and improved practice in qualitative research involving children.

Design/methodology/approach
The paper draws on the authors’ work in the Ethical Research Involving Children (ERIC) project, an international initiative that synthesised literature, research evidence and the views and experiences of almost 400 researchers and other key stakeholders internationally, to consider the key philosophical and practical components that underpin reflexivity in the context of research involving children.

Findings
A conceptual approach linking ‘Three Rs’ - reflexivity, rights and relationship - was found to be a useful framework for enacting universal ethical principles while provoking the kind of critical engagement required for navigating the ethical tensions that characterise decision-making in research involving children.

Originality/value
This paper introduces a framework to help bridge the gap between espoused ethical principles and the real world dilemmas that emerge in research practice. In doing so, the paper invites a deeper engagement with the ways in which children are constructed in and through research, while offering a shared language for shifting professional dialogue and academic discourse from the aspirational to the operational of ethical reflexivity.
Utilization of Partially Methylolated Poly acrylamide Guar Gum in Pigment Printing
Authors: Zahran M.K. , Mahmoud R.I. , El Rafie M.H. 
Published: April 2016

Polyacrylamid-guar gum composite has been prepared via graft copolymerization of acrylamide onto guar gum using the KBrO3/ thiourea redox system. The amide groups (40%) in the composite are converted to reactive groups through methylolation with formaldehyde, with a view to obtaining reactive composite. The composite and the reactive composite were used as pastes for printing cotton fabrics with pigment dyes. The prints were assessed for color strength (K/S) and overall fastness properties.
Printing was carried out under different conditions, including the amount of composite used as a substitute for kerosene emulsion, the amount of binder incorporated into the printing paste and the types of catalysts. The printed samples were evaluated by monitoring the color strength (K/S) and fastness properties such as washing, rubbing and light. Based on the results obtained, it is concluded that a partial substitution ratio of 20/75 (composite/kerosene emulsion), 8gm binder/100gm printing paste and 1% of catalyst (NH4Cl, DAP, Citric acid or [NH4]2SO4) represent the proper formulation for gaining good dye fixation and excellent fastness properties. The results indicate that the reactive composite prepared is the most suitable thickener for printing cellulosic fabrics with pigment dyes.
Study on the Dyed Cotton Fibers Damage in Spinning Processes and its Effect on the Cotton Mélange Yarn Properties
Authors: Moghassem A.R. 
Published: April 2016

Grey cotton fibers with a mean fiber length and fineness of 29 mm and 4.2 micronair was pretreated, scoured and dyed. Three ring yarns were spun separately from 100% grey cotton (R.R.Y.), 50% dyed and 50% grey cotton blend (M.R.Y.) and 100% dyed cotton (D.R.Y.). The extent of fiber damage was assessed by measuring the length and the mechanical characteristics of cotton fibers after passing the fibers through the lap machine and the draw frame II. Properties of R.R.Y., M.R.Y. and D.R.Y. samples were examined. In terms of tenacity and elongation at break, grey and dyed cotton fibers, which were selected after being processed by the lap machine and the draw frame II, were very similar. The fiber length by number and weight of grey cotton was longer than that of dyed cotton, while the amount of fiber nep and short fiber content of dyed cotton were more than those of grey cotton.
The three yarn samples were the same in terms of elongation at break. The tenacity of R.R.Y. was the highest but the yarn sample was the lowest in terms of coefficients of mass variation (Cv%), imperfection and hairiness in comparison with the M.R.Y. and D.R.Y. samples.
Effect of Tannic Acid on the Dyeing Process of Nylon 6 Fabric with Cationic Dye
Authors: El-Gabry L.K. , El-Zawahry M.M. 
Published: April 2016

Nylon 6 fabric is pretreated with tannic acid and subsequently dyed with a cationic dye, Rhodamine B, from an aqueous dye solution and emulsion phase. The emulsion phase of n-hexadecane is emulsified by isopropyl alcohol and stabilized by Rhodamine B/tannic acid complex. Different factors affecting pretreatment and dyeing process have been studied. Changes of moisture regain, tensile strength, elongation and binding stiffness of the pretreated fabric are investigated.
The FTIR spectra of tannic acid pretreatment of nylon are also examined. The pretreated fabric with 10% owf tannic acid shows a slight increase in the tensile strength and elongation percentage. A higher moisture regain and binding stiffness are observed with increases in the amount of tannic acid. The results also indicate that the pretreatment for cationic dyed nylon 6 fabrics with tannic acid promote a higher dye uptake and cationic dye-based emulsion system with better fastness properties relative to those of the dye solution based system. A further improvement in wet fastness is secured by an aftertreatment of all dyed fabrics with a commercial anionic fluorescent whitening agent, Uvitex® RSB 150%.
Development of a Safety Vest for Hospital Patients
Authors: Yick K.L. , Lai K.Y. , Yim C.M. , Tsui H.M. , Chiu L.T. 
Published: April 2016

A new design of safety vests was developed for patients with uncontrollable behaviour or altered conscious level in this study. A comprehensive approach for designing functional textile and apparel products was adopted. The design request and exploration of the design situation and problem were identified. The settings in the general and psychiatric wards and the traditional ways of the use of safety vests on patients were examined. Problems of the traditional safety vests were identified, such as loose fitting design and large armholes, tight neckline which may result in unexpected accidents such as strangulation, difficulty of wearing, limited mobility, and obsolete functional design.
A new set of design criteria and specifications were then developed. An interaction matrix of design specification for safety vests was formulated since some of the design specifications are in conflict with each other. For instance, a tight fit design could optimize the level of restraint, but it may result in patients' psychological and physiological discomfort due to limited mobility. Supported by the evaluation of fabric materials and fastening systems, a new design of safety vests was then developed and evaluated.
Dyeing Of Cotton Fabric Using UV Irradiated Turmeric (Curcuma longa L.) as Natural Dye
Authors: Adeel Shahid , Bhatti Ijaz A. , EL-Nagar K. , Mohboob Alam M. , Ali Nagia 
Published: April 2016

The rhizomes of Curcuma longa L. which contains curcumin, the main coloring component that imparts a yellow color onto cotton fabric, has been selected for study in this paper. The extracts are obtained by using different concentrations of irradiated turmeric powder. In order to improve colour fastness properties, pre and post- mordanting are applied by using alum and iron as mordants. The dyed samples are subjected to a CIE Lab system with a spectra flash spectrophotometer for the evaluation of L* (lighter/darker), a* (redder/greener) and b* (yellower/bluer) values.
Finally, ISO standard methods are employed to study colour fastness to light, washing and rubbing (dry and wet) in order to observe the influence of UV radiation on the dyeing behaviour of turmeric. It is observed that UV radiation not only enhances the color strength of dye on irradiated cotton fabric using low concentrations of dye, but also improves the color fastness properties of pre-irradiated cotton fabric by using pre-irradiated turmeric powder with a low concentration of mordant.
The challenges of the first migration: movement and behaviour of juvenile vs. adult white storks with insights regarding juvenile mortality
Authors: Rotics Shay , Kaatz Michael , Resheff Yehezkel S. , Turjeman Sondra Feldman , Zurell Damaris , Sapir Nir , Eggers Ute , Flack Andrea , Fiedler Wolfgang , Jeltsch Florian , Wikelski Martin , Nathan Ran 
Published: April 2016

Summary

Migration conveys an immense challenge, especially for juvenile birds coping with enduring and risky journeys shortly after fledging. Accordingly, juveniles exhibit considerably lower survival rates compared to adults, particularly during migration. Juvenile white storks (Ciconia ciconia), which are known to rely on adults during their first fall migration presumably for navigational purposes, also display much lower annual survival than adults.

Using detailed GPS and body acceleration data, we examined the patterns and potential causes of age‐related differences in fall migration properties of white storks by comparing first‐year juveniles and adults. We compared juvenile and adult parameters of movement, behaviour and energy expenditure (estimated from overall dynamic body acceleration) and placed this in the context of the juveniles’ lower survival rate.

Juveniles used flapping flight vs. soaring flight 23% more than adults and were estimated to expend 14% more energy during flight. Juveniles did not compensate for their higher flight costs by increased refuelling or resting during migration. When juveniles and adults migrated together in the same flock, the juvenile flew mostly behind the adult and was left behind when they separated. Juveniles showed greater improvement in flight efficiency throughout migration compared to adults which appears crucial because juveniles exhibiting higher flight costs suffered increased mortality.

Our findings demonstrate the conflict between the juveniles’ inferior flight skills and their urge to keep up with mixed adult–juvenile flocks. We suggest that increased flight costs are an important proximate cause of juvenile mortality in white storks and likely in other soaring migrants and that natural selection is operating on juvenile variation in flight efficiency.