bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants
Authors: Belkadi Aziz , Bolze Alexandre , Itan Yuval , Cobat Aurélie , Vincent Quentin B. , Antipenko Alexander , Shang Lei , Boisson Bertrand , Casanova Jean-Laurent , Abel Laurent 
Published: October 2014

AbstractWe compared whole-exome sequencing (WES) and whole-genome sequencing (WGS) in six unrelated individuals. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and 13,325, respectively, for WES, and 84,968 and 12,702, respectively, for WGS. For both SNVs and indels, the distributions of coverage depth, genotype quality, and minor read ratio were more uniform for WGS than for WES. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called by both platforms. A mean of 105 coding HQ SNVs and 32 indels were identified exclusively by WES, whereas 692 HQ SNVs and 105 indels were identified exclusively by WGS. We Sanger sequenced a random selection of these exclusive variants. For SNVs, the proportion of false-positive variants was higher for WES (78%) than for WGS (17%). The estimated mean number of real coding SNVs (656, ∼3% of all coding HQ SNVs) identified by WGS and missed by WES was greater than the number of SNVs identified by WES and missed by WGS (26). For indels, the proportions of false-positive variants were similar for WES (44%) and WGS (46%). Finally, WES was not reliable for the detection of copy number variations, almost all of which extended beyond the targeted regions. Although currently more expensive, WGS is more powerful than WES for detecting potential disease-causing mutations within WES regions, particularly those due to SNVs.SignificanceWhole-exome sequencing (WES) is gradually being optimized to identify mutations in increasing proportions of the protein-coding exome, but whole-genome sequencing (WGS) is becoming an attractive alternative. WGS is currently more expensive than WES, but its cost should decrease more rapidly than that of WES. We compared WES and WGS on six unrelated individuals. The distribution of quality parameters for single-nucleotide variants (SNVs) and insertions/deletions (indels) was more uniform for WGS than for WES. The vast majority of SNVs and indels were identified by both techniques, but an estimated 650 high-quality coding SNVs (∼3% of coding variants) were detected by WGS and missed by WES. WGS is therefore slightly more efficient than WES for detecting mutations in the targeted exome.
Mutation of the Inducible ARABIDOPSIS THALIANA CYTOCHROME P450 REDUCTASE2 Alters Lignin Composition and Improves Saccharification
Authors: Sundin Lisa , Vanholme Ruben , Geerinck Jan , Goeminne Geert , Höfer René , Kim Hoon , Ralph John , Boerjan Wout 
Published: October 2014

Abstract
ARABIDOPSIS THALIANA CYTOCHROME P450 REDUCTASE1 (ATR1) and ATR2 provide electrons from NADPH to a large number of CYTOCHROME P450 (CYP450) enzymes in Arabidopsis (Arabidopsis thaliana). Whereas ATR1 is constitutively expressed, the expression of ATR2 appears to be induced during lignin biosynthesis and upon stresses. Therefore, ATR2 was hypothesized to be preferentially involved in providing electrons to the three CYP450s involved in lignin biosynthesis: CINNAMATE 4-HYDROXYLASE (C4H), p-COUMARATE 3-HYDROXYLASE1 (C3H1), and FERULATE 5-HYDROXYLASE1 (F5H1). Here, we show that the atr2 mutation resulted in a 6% reduction in total lignin amount in the main inflorescence stem and a compositional shift of the remaining lignin to a 10-fold higher fraction of p-hydroxyphenyl units at the expense of syringyl units. Phenolic profiling revealed shifts in lignin-related phenolic metabolites, in particular with the substrates of C4H, C3H1 and F5H1 accumulating in atr2 mutants. Glucosinolate and flavonol glycoside biosynthesis, both of which also rely on CYP450 activities, appeared less affected. The cellulose in the atr2 inflorescence stems was more susceptible to enzymatic hydrolysis after alkaline pretreatment, making ATR2 a potential target for engineering plant cell walls for biofuel production.
The boundaryless career at 20: where do we stand, and where can we go?
Authors: B. Arthur Michael 
Published: October 2014

Purpose– The purpose of this paper is to reflect on a broad body of work that responds to the boundaryless career concept, first introduced in 1993, and to anticipate new theory-building and research.Design/methodology/approach– Covers the origination of the concept, its meaning and definition, the underlying influence of an earlier group of careers scholars from Massachusetts Institute of Technology (MIT), and the importance of an interdisciplinary perspective.Findings– Identifies three categories of activity – involving internal debates, fresh theoretical contributions, and new collaborative opportunities – that have occurred citing boundaryless career scholarship.Research limitations/implications– Suggests how scholars can build on the legacy of both organizational and boundaryless careers research in their future work.Originality/value– Links between foundational MIT work on careers, boundaryless careers and current debates to suggests future research directions.
Boundarylessness as a dynamic construct: the case of Chinese early career expatriates
Authors: Yao Christian , Thorn Kaye , Doherty Noeleen 
Published: October 2014

Purpose– The purpose of this paper is to explore the dynamic nature of boundaryless careers of Chinese early career corporate expatriates. It also investigates the demographic and contextual factors influencing individual perceived career mobility.Design/methodology/approach– Qualitative, semi-structured interviews with 31 Chinese corporate expatriates were conducted and a template analysis approach was used to analyze the data.Findings– Results suggest that Chinese early career corporate expatriates’ perceptions of boundaries as facilitating or limiting career mobility change over time. Changing boundary properties are found to be linked to the salience of Chinese cultural values, demographics and career/life stages. Based on expatriates’ narratives, this study highlights how these demographic and contextual factors shape domains of career boundarylessness.Originality/value– Using an under-researched sample of Chinese corporate expatriates, this paper contributes to the conceptualization of boundaryless careers identifying the changing nature of the boundaries that facilitate or restrict mobility over time. The study calls for the use of combined, multi-dimensional approaches incorporating individual agency, organizational and cultural factors to understand individual career development.
Organizational boundaries and beyond
Authors: Gubler Martin , Arnold John , Coombs Crispin 
Published: October 2014

Purpose– The purpose of this paper is to develop a new conceptualization of the boundaryless career – a widely acknowledged contemporary career concept – that reflects its original description more fully than previous literature has done, and to apply this conceptualization in an empirical investigation of career behavior and intentions of a large sample of European information technology (IT) professionals.Design/methodology/approach– As part of a large study of IT professionals in Europe (N=1,350), the paper had three research objectives. First, the paper developed and empirically tested a new operationalization of a person’s boundaryless career orientation (BCO) that reflects the originally proposed boundaryless career meanings more closely than existing approaches. Second, the paper used this to identify in a holistic manner different patterns of BCO. Third, the paper examined the nature and extent of links between BCO and self-reported career behavior and intentions.Findings– The paper identified five BCO factors that differentiate individuals into three distinct clusters. Although organizational boundaries appeared to be salient for most individuals, they did not differentiate the clusters. Instead, geographical mobility preference and rejection of career opportunities emerged as highly differentiating but hitherto rarely examined types of career boundaries.Practical implications– The findings can help HR managers to gain a better understanding of different mobility preferences among different groups of employees, which could lead to the development and implementation of more refined reward schemes and career development practices in organizations.Originality/value– This study provides a new operationalization of the BCO that is grounded in its original definition and offers a new empirically tested 15-item BCO measure. It contributes to career research with scarce empirical findings regarding the components of the BCO, their salience for individuals, and the connections between BCO and behavior.
Management communication, unionization, FDI and company performance in a developing country
Authors: Croucher Richard , Rizov Marian , Goolaup Ram 
Published: October 2014

Purpose
– The purpose of this paper is to examine the associations between management direct communication to employees, unionization, foreign direct investment (FDI) and company performance in Mauritius, Africa's most successful economy.

Design/methodology/approach
– The authors use firm data from a survey conducted in Mauritius in late 2011. The authors conduct regression analysis to study the relationship between direct communication, unionization and performance conditional on ownership type.

Findings
– Mauritian labour unions, in common with their counterparts from mainland Africa, are strongest in the public sector. They have been characterized as weak and lacking in influence on management. Yet the authors find a strong association between unionization and management communication in the private sector. The authors also find a positive association between direct communication and company performance which the authors argue is likely to be an indirect consequence of unionization. FDI shows no particular effects.

Research limitations/implications
– It appears that the consequences of union presence transcend pay and conditions. The effects are unexpectedly marked, particularly when the stress by some authors on union weakness in the private sector is taken into account.

Originality/value
– It may be that local unions’ strong focus on the enterprise – a form of representation favoured by US-based multinational companies, constitutes a strength in stimulating management communication to employees by focusing union activities at that level. Whilst the authors have suggested that this is unlikely to be primarily a result of conscious union strategy, the enterprise focus may serve to buttress existing employee attitudes. In any event, unionization is certainly closely associated in this African country with a practice that is linked to positive economic effects at the enterprise level.
The recovery-orientation of three mental health units
Authors: Bass Hollie , Tickle Anna , Lewis Nicholas 
Published: October 2014

Purpose– The purpose of this paper is to measure service user and staff views of the recovery orientation of three mental health rehabilitation units; two “open” and one “locked”. It identified elements of recovery that were important to service users. It measured the units’ performance on domains of recovery, attending to differences between staff members’ and service users’ perceptions and between the locked and open units.Design/methodology/approach– A cross-sectional design was used. Staff and service users completed the “Developing Recovery Enhancing Environment Measure (DREEM)”.Findings– Findings revealed some differences between staff and service user views. Service users in the locked unit reported the organisational climate to be more recovery oriented on some domains than those in the open units. Service users’ responses highlighted potential areas for service improvement.Research limitations/implications– The sample was small but reflected the applied setting. Some service users were not invited to participate because of significant communication or cognitive difficulties and it is recognised that they may have had alternative views that remain unrepresented.Practical implications– The DREEM provided valuable information about current practice and potential for service development. Both locked and open units can provide recovery-oriented environments. Services should be aware of discrepant views between staff and service users.Originality/value– To the knowledge, this is the first study to use the DREEM to evaluate the recovery orientation of a locked recovery unit and to compare locked and unlocked units.
Offender Personality Disorder Pathway: Evaluation of Team Consultation
Authors: McMullan Elaine , Ramsden Jo , Lowton Mark 
Published: October 2014

Purpose– The purpose of this paper is to highlight the findings of a service evaluation project assessing the impact of team consultation to criminal justice staff working with personality disordered offenders.Design/methodology/approach– A qualitative design using content analysis of focus groups and individual semi-structured interviews.Findings– Criminal justice staff report increased awareness and understanding, use of a person-centred approach, development of formulation skills and defensible practice following team consultation.Practical implications– This paper will be of interest to practitioners who offer and/or receive consultation for work with offenders with personality disorder. Suggested changes to team consultation formats may be of interest to services involved with the Offender Personality Disorder Pathway.Originality/value– This paper contributes towards the emerging literature on the role of consultation and formulation on workforce development for individuals with personality disorder. It also contributes to the evaluation of the services offered by this specialist team as they support probation Trusts across Yorkshire/Humber to support the community specification of the national Offender Personality Disorder Pathway.
Population pharmacokinetic–pharmacodynamic modelling to describe the effects of paracetamol and N‐acetylcysteine on the international normalized ratio
Authors: Owens Katie H , Medlicott Natalie J , Zacharias Mathew , Whyte Ian M , Buckley Nicholas A , Reith David M 
Published: October 2014

SummaryParacetamol is one of the most common pharmaceutical agents taken in self‐poisonings, and can increase the prothrombin time (PT) through liver injury, and in overdose without hepatic injury by reducing functional factor VII. PT is a measure of hepatic injury used to predict and monitor hepatotoxicity, reported as the international normalized ratio (INR). The antidote for paracetamol poisoning, N‐acetylcysteine (NAC), has been reported to have an effect on the PT. This analysis included patients from a retrospective case series, a prospective inception cohort of paracetamol and psychotropic (control) overdoses, and a cross‐over clinical trial. A population pharmacokinetic–pharmacodynamic model describing the pharmacodynamic effects of paracetamol and NAC on the INR was developed in Phoenix NLME. The dataset included 172 patients; the median age was 22 years (range 13–71 years). A one‐compartment model with first‐order input and linear disposition best described paracetamol pharmacokinetics. The population mean estimate of the concentration that induced a response halfway between the baseline and maximal pharmacological effect of paracetamol was 1302 μmol/L (242), the maximum effect of paracetamol was 0.534 (202; from baseline) and the maximum effect of NAC was 0.325 (9.03; from baseline). Both paracetamol and NAC contributed a pharmacological effect to the elevation of INR. The estimated paracetamol concentration that induced a response halfway between the baseline and maximal pharmacological effect was within the range of plasma paracetamol values studied, fivefold greater than the maximum therapeutic concentration, suggesting that an elevated INR would not be expected within the therapeutic range. Simulated 24 and 48 g paracetamol overdoses with NAC administration produced INR values (50th percentile) that reached the upper limit of, or exceeded, the reference range.
Twelve‐month outcomes following midurethral sling procedures for stress incontinence: impact of obesity
Authors: Brennand EA , Tang S , Williamson T , Birch C , Murphy M , Robert M , Ross S ,   the Calgary Women's Pelvic Health Research Group
Published: October 2014

ObjectiveTo evaluate impact of body mass index (BMI) ≥30 on objective and subjective cure rates 12 months after midurethral sling surgery.DesignSecondary analysis.SettingThree hospitals in Calgary, Canada, 2005–07.PopulationA total of 182 women enrolled in a randomised control trial of tension‐free vaginal tape versus transobturator tape.MethodsWomen were classified as obese or nonobese from height and weight on day of surgery. Women underwent postoperative standardised pad tests, self‐reporting of urinary incontinence, and quality of life scores. Categorical data compared with chi‐square or Fisher's exact, continuous data compared with Mann–Whitney U test.Main outcome measuresPrimary outcome was objective cure, defined as <1 g urine loss on postoperative 1‐hour pad test. Secondary outcomes were subjective cure of incontinence (no stress incontinence in previous 7 days), presence of urinary urgency in previous 7 days, Urogenital Distress Inventory (UDI‐6) scores, Incontinence Impact Questionnaire (IIQ‐7) scores, and surgical complication rates.ResultsObjective cure differed, with 85.6% of nonobese women leaking <1 g on 1‐hour pad test, versus 67.8% of obese women (P = 0.006, risk difference [RD] 17.8%, 95% confidence interval [95% CI] 4.2–31.4%). Subjective cure was 85.8% for nonobese women versus 70.7% for obese women (P = 0.016, RD 15.1%, 95% CI 1.9–28.4%). For both groups, improvement was seen for postoperative UDI‐6 (median −33.3 [−44.4 to −22.2] and −27.2 [−44.4 to −16.7]) and IIQ‐7 scores (median −26.2 [−45.2 to −14.3] and −23.8 [−42.9 to −14.3]). No differences existed in rates of operative complications between the two groups.ConclusionTwelve months after midurethral sling surgery, obese women experience lower rates of cure than those who are nonobese.
Stereo and Scanning Electron Microscopy of In‐Shell Brazil Nut (Bertholletia excelsa H.B.K.): Part Two—Surface Sound Nut Fungi Spoilage Susceptibility
Authors: Scussel Vildes M. , Manfio Daniel , Savi Geovana D. , Moecke Elisa H.S. 
Published: October 2014

AbstractThis work reports the in‐shell Brazil nut spoilage susceptible morpho‐histological characteristics and fungi infection (shell, edible part, and brown skin) through stereo and scanning electron microscopies (SEM). The following characteristics related to shell (a) morphology—that allow fungi and insects’ entrance to inner nut, and (b) histology—that allow humidity absorption, improving environment conditions for living organisms development, were identified. (a.1) locule in testae—the nut navel, which is a cavity formed during nut detaching from pods (located at 1.0 to 2.0/4th of the shell B&C nut faces linkage). It allows the nut brown skin (between shell and edible part) first contact to the external environment, through the (a.2) nut channel—the locule prolongation path, which has the water/nutrients cambium function for their transport and distribution to the inner seed (while still on the tree/pod). Both, locule followed by the channel, are the main natural entrance of living organisms (fungi and insects), including moisture to the inner seed structures. In addition, the (a.3) nut shell surface—which has a crinkled and uneven surface morphology—allows water absorption, thus adding to the deterioration processes too. The main shell histological characteristic, which also allows water absorption (thus improving environment conditions for fungi proliferation), is the (b.1) cell wall porosity—the multilayered wall and porous rich cells that compose the shell faces double tissue layers and the (b.2) soft tissue—the mix of tissues 2 faces corner/linkage. This work also shows in details the SEM nut spoilage susceptible features highly fungi infected with hyphae and reproductive structures distribution.
Investigation of Ice‐Assisted Sonication on the Microstructure and Chemical Quality of Ganoderma lucidum Spores
Authors: Zhao Ding , Chang Ming‐Wei , Li Jing‐Song , Suen William , Huang Jie 
Published: October 2014

AbstractGanoderma lucidum spores (GLS) are well known for disease treatment and vitality enhancement, and have been shown to contain a variety of bioactive components, such as polysaccharides and triterpenes. However, the resilient bilayer sporoderm structure of GLS restricts the release of bioactive components and limits its complete pharmacological effects. The current study was aimed to improve the quality of GLS by means of a customized sonication technique, particularly, the effect of sonication processing parameters on GLS‐breaking efficiencies was investigated. Significant morphological changes, such as cracked, fractured, and disintegrated GLS were observed using scanning electron microscopy (SEM) after sonication treatment. The performance for breaking GLS sporoderm was obtained at ultrasonic power density of 23.7 W/cm2, duty cycle 100%, and 90‐min processing time. Through the combination of sonication in an ice bath, sporoderm breaking efficiency can be further increased from 45% to almost 75%. FTIR analysis revealed an increase in bioactive components of polysaccharide, protein, and fatty acid from the sonication processed GLS when compared to ground spores available commercially. The current results indicated that the ice bath combined sonication method is more effective in delivering GLS ingredients and could be an economic technique for the production of high‐quality broken sporoderm GLS.
Low‐Fat Beef Patties with Augmented Omega‐3 Fatty Acid and CLA Levels and Influence of Grape Seed Extract
Authors: Gómez Inmaculada , Beriain María J. , Sarriés María V. , Insausti Kizkitza , Mendizabal José A. 
Published: October 2014

AbstractThe effects of raising the omega‐3 fatty acid (FA), conjugated linoleic acid (CLA), or omega‐3 FA plus CLA levels on beef by means of dietary supplementation and of adding grape seed extract (250 mg/kg meat product) in beef patties stored at 2 ± 1 °C in aerobic packaging under simulated retail display conditions for 6 d was evaluated by measuring the thiobarbituric acid reactive substances (TBARS), pH, and instrumental color measurement values and by means of sensory analysis. The pH, instrumental color measurements, and sensory attribute values for patties made from beef with augmented omega‐3 FA and/or CLA contents were similar to the values for the control patties made from beef from animals fed a conventional diet. Adding GSE lowered oxidation levels on day 6 (P < 0.001) and did not affect the instrumental color or sensory analysis results during the display period. This suggests that omega‐3 FA and CLA‐augmented beef could be used to make low‐fat beef patties having characteristics similar to those of conventional beef patties while being more in keeping with currently recommended nutritional guidelines.