bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals
Authors: Crooks Kevin R. , Burdett Christopher L. , Theobald David M. , King Sarah R. B. , Di Marco Moreno , Rondinini Carlo , Boitani Luigi 
Published: July 2017

SignificanceDespite the critical threat of habitat fragmentation, global patterns of fragmentation and its relationship to extinction risk have not been quantified for any major taxon. We developed high-resolution models that provide a global assessment of the degree of habitat fragmentation impacting the world’s terrestrial mammals. Results demonstrate that mammals with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Quantification of habitat fragmentation will help guide strategic priorities for global mammal conservation.
Disruption of a horizontally transferred phytoene desaturase abolishes carotenoid accumulation and diapause inTetranychus urticae
Authors: Bryon Astrid , Kurlovs Andre H. , Dermauw Wannes , Greenhalgh Robert , Riga Maria , Grbić Miodrag , Tirry Luc , Osakabe Masahiro , Vontas John , Clark Richard M. , Van Leeuwen Thomas 
Published: July 2017

SignificanceIn animals, carotenoid pigments fulfill a number of essential roles in vision, protection from stresses, and signaling. Although carotenoids are synthesized primarily by plants and some bacteria and fungi, carotenoid biosynthetic genes have been acquired by horizontal gene transfer in some insects and mites. In the two-spotted spider mite,Tetranychus urticae, as well as in a related species, we show that a horizontally transferred carotenoid biosynthetic gene is required for normal pigmentation. Spider mites can therefore synthesize their own carotenoids. Further, in aT. urticaestrain, the gene is required for the induction of diapause, a key for overwintering of this widespread and important agricultural pest.
Fast and accurate HLA typing from short-read next-generation sequence data with xHLA
Authors: Xie Chao , Yeo Zhen Xuan , Wong Marie , Piper Jason , Long Tao , Kirkness Ewen F. , Biggs William H. , Bloom Ken , Spellman Stephen , Vierra-Green Cynthia , Brady Colleen , Scheuermann Richard H. , Telenti Amalio , Howard Sally , Brewerton Suzanne , Turpaz Yaron , Venter J. Craig 
Published: July 2017

Significance
Regulation of the human immune system is largely controlled by the HLA gene complex on chromosome 6 and is important in infectious disease immunity, graft rejection, autoimmunity, and cancer. HLA typing is traditionally performed by serotyping and/or targeted sequencing. However, the advent of precision medicine and cheaper personal genome sequencing has sprung an unmet need for a fast and accurate way of predicting HLA types from short-read sequencing data. Here, we present xHLA, an algorithm for HLA typing based on translated short reads, exhaustive multiple sequence alignment-based alignment expansion, and iterative solution set refinement that is also faster and more accurate than existing methods. Results are achievable within minutes and could greatly benefit individuals who have had their genome sequenced.
From the glass through the nose and the mouth
Authors: Caballero Rosario 
Published: July 2017

Motion verbs are often used to predicate entities such as roads, paths and the like as in “The road snakes tothe port of Shakespeare Baybefore climbing over the last hillto Picton” or “La carreteraserpenteaunos 30 kilómetros entre las montañas de la cordillera Nipe”. The verbs foreground thepathconfiguration and dynamic rendering of things that cannot move – a phenomenon known asfictive motion(Langacker 1987;Talmy 1996). However, motion verbs are also frequent components in specialized contexts such as wine discourse, where they communicate different sensory experience of wines as in “Exotic, exuding red berry aromas and flavors thatsneak upon you rather than hit you over the head”, “Bright and focused, offering delicious flavors thatglidesmoothlythroughthe silky finish”, or “En boca tiene una magnifica entrada, aunque en el pasosobresalenrasgos vegetales y seprecipitahacia un final en el que predominan notas tostadas y amargas”. Using two corpora of tasting notes written in English and in Spanish, I examine the motion expressions used to communicate the sensory experiences of the wines and explore the motivations for their use in descriptions of wines’ aromas, flavours and mouthfeel. Three questions are at the heart of this study. They are (i) what types of scenarios are described through motion expressions, (ii) what sensory perceptions do they describe, and (iii) what may the differences between English and Spanish be?
Escherichia coli yjjPB genes encode a succinate transporter important for succinate production
Authors: Fukui Keita , Nanatani Kei , Hara Yoshihiko , Yamakami Suguru , Yahagi Daiki , Chinen Akito , Tokura Mitsunori , Abe Keietsu 
Published: July 2017

Abstract
Under anaerobic conditions, Escherichia coli produces succinate from glucose via the reductive tricarboxylic acid cycle. To date, however, no genes encoding succinate exporters have been established in E. coli. Therefore, we attempted to identify genes encoding succinate exporters by screening an E. coli MG1655 genome library. We identified the yjjPB genes as candidates encoding a succinate transporter, which enhanced succinate production in Pantoea ananatis under aerobic conditions. A complementation assay conducted in Corynebacterium glutamicum strain AJ110655ΔsucE1 demonstrated that both YjjP and YjjB are required for the restoration of succinate production. Furthermore, deletion of yjjPB decreased succinate production in E. coli by 70% under anaerobic conditions. Taken together, these results suggest that YjjPB constitutes a succinate transporter in E. coli and that the products of both genes are required for succinate export.
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments
Authors: Bansal Vikas 
Published: July 2017

Abstract

Motivation
The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention.

Results
We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25–30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets.

Availability and implementation
FragmentCut is available from https://bansal-lab.github.io/software/FragmentCut

Supplementary information
Supplementary data are available at Bioinformatics online.
Shifting the Curve: Fostering Academic Success in a Diverse Student Body
Authors: Elks Martha L. , Herbert-Carter Janice , Smith Marjorie , Klement Brenda , Knight Brandi Brandon , Anachebe Ngozi F. 
Published: July 2017

Problem
Diversity in the health care workforce is key to achieving health equity. Although U.S. medical schools have worked to increase the matriculation and academic success of underrepresented minority (URM) students (African Americans, Latinos, others), they have had only limited success. Lower standardized test scores, including on the Medical College Admission Test (MCAT), have been a barrier to matriculation for many URM applicants. Lower subsequent standardized exam scores, including on the United States Medical Licensing Exam Step 1, also have been an impediment to students’ progress, with mean scores for URM students lagging behind those for others.

Approach
Faculty at the Morehouse School of Medicine developed and implemented interventions to enhance the academic success of their URM students (about 75% are African American, and 5% are from other URM groups). To assess the outcomes of this work, the authors analyzed the MCAT scores and subsequent Step 1 scores of students in the graduating classes of 2009–2014. They also reviewed course evaluations, Graduation Questionnaires, and student and faculty interviews and focus groups.

Outcomes
Students’ Step 1 scores exceeded those expected based on their MCAT scores. This success was due to three key elements: (1) milieu and mentoring, (2) structure and content of the curriculum, and (3) monitoring.

Next Steps
A series of mixed-method studies are planned to better discern the core elements of faculty–student relationships that are key to students’ success. Lower test scores are not a fixed attribute; with the elements described, success is attainable for all students.
Reconstruction of parotidectomy and lateral skull base defects
Authors: Bertelsen Caitlin , Liu Changxing , Kokot Niels 
Published: July 2017

Purpose of reviewThe purpose of this review is to summarize the options for reconstruction of parotid and lateral skull base defects based on the size and functional requirements of the defect.Recent findingsFree grafts with dermal fat or acellular human dermis, superficial musculoaponeurotic system flaps, and sternocleidomastoid flaps have been successful in preventing Frey's syndrome and restoring facial contour defects after superficial and total parotidectomy. Lateral skull base resections often require reconstruction with pedicled or free flaps to restore extensive soft tissue and dural defects. Supraclavicular artery island flaps and submental flaps have been recently been gaining popularity for use for these purposes. Free tissue transfer remains the best reconstructive option for repair of large soft tissue and/or dural defects. The most reliable free flap for lateral skull base reconstruction is the anterolateral thigh flap, which is highly versatile because of its large skin paddle and potential for harvest with varying amounts of fascial and muscle tissue.SummaryHere we will summarize the most appropriate and widely used reconstructive options for parotid and lateral skull base defects of various sizes, discussing the most recent evidence pertaining to each technique along with advantages and limitations of each reconstructive strategy.
New Tool for Monitoring Molecular Response in Patients With Chronic Myeloid Leukemia
Authors: Badar Talha , Luthra Rajyalakshmi , Kantarjian Hagop , Jabbour Elias , Borthakur Gautam , Garcia-Manero Guillermo , Huang Xuelin , Singh Rajesh , Alvarez Brittany , Austermiller Bradley , Morrison Tom B. , Patel Keyur P. , Cortes Jorge 
Published: July 2017

Objective:
Chronic myeloid leukemia treatment monitoring using polymerase chain reaction-based peripheral blood testing of t
9;22
BCR-ABL1 provides improved test sensitivity over cytology but suffers from inadequate standardization in most laboratories due to variations inherent in the existing polymerase chain reaction methodologies. We performed the initial analytic performance evaluation of a novel competitive template-based peripheral blood b2a2/b3a2 transcript abundance method, called standardized nucleic acid quantification (SNAQ) test, with hypothesis that this will produced more consistent results with less frequent interlaboratory variations.

Materials and Methods:
Thirty-six chronic myeloid leukemia patients treated at our institution were enrolled. We compared SNAQ test with 2 laboratory developed test at the MD Anderson molecular diagnostic laboratory and Cancer Genetics Institute for analyzing BCR-ABL1 from peripheral blood samples. Each test result (n=36) was ranked against all the other samples tested by the same method.

Results:
The Pearson correlation between SNAQ and laboratory developed test done at 2 labs was met by correlations of 0.97, 0.96, 0.96, and 0.94. Analysis of variance of log %BCR-ABL1 interlaboratory results indicated no significant difference (P=0.98). Post hoc analysis of method agreement showed the SNAQ method had a 95% limit of agreement of ±3-fold between laboratories.

Conclusions:
In this pilot study, SNAQ methodology performed consistent with half-log accuracy. Additional studies from a larger sample size and correlation with clinical outcomes are required to confirm this observation.
Efficacy of Rapid Fluid Administration Using Various Setups and Devices
Authors: Balaban Onur , Walia Hina , Tumin Dmitry , Bhalla Tarun , Tobias Joseph D. 
Published: July 2017

Objectives
In clinical practice, there are various methods that can be used for the rapid administration of fluid in infants and children. The current study prospectively evaluates gravity, pressure-assisted, and hand-pump methods for the rapid administration of fluid using an in vitro model.

Methods
Thirty participants were asked to deliver 500 mL of fluid using 1 of 6 setups: (1) standard blood tubing with gravity administration, (2) standard blood tubing with pressure bag maintained at 300 mm Hg, (3) standard blood tubing with pressure bag inflated to 300 mm Hg and left to flow, (4) blood tubing with in-line bulb pump, (5) blood tubing with in-line bulb pump and pressure bag, and (6) standard blood tubing with 20-mL syringe attached to the stopcock for a push-and-pull technique using a 20-mL syringe.

Results
The blood tubing with an in-line bulb pump to allow manual acceleration of the administration of fluid along with a pressure bag on the intravenous fluid bag achieved the fastest flow rate, requiring an average of 98 seconds to deliver 500 mL of fluid.

Conclusions
When considering factors that affect fluid administration, Poiseuille’s law dictates that the most important variable is the radius of the intravenous cannula, whereas the length of the cannula and the viscosity of the fluid administered are of secondary importance. With these limitations in mind, other factors may be used to speed fluid administration. Our study demonstrates the advantage of using blood tubing with the in-line bulb pump combined with a pressure bag.
Authentic leadership as a contemporary leadership model applied in Nigeria
Authors: Emuwa Amara , Fields Dail 
Published: July 2017

PurposeThe purpose of this paper is to examine the extent to which each dimension of authentic leadership (AL) is related with employee organizational commitment (OC) and assessment of leadership effectiveness for employees in Nigeria and to investigate the moderating effects of contingent reward leadership behaviors on these relationships. By testing the dimensions of AL with employee outcomes, this study provides further validity and empirical evidence to the theoretical structure of AL theory across cultures.Design/methodology/approachThis empirical study used cross-sectional survey data collected from a sample of 212 Nigerian employees from 16 organizations across various sectors.FindingsThe results of hierarchical regression analysis of this study showed a positive relationship between AL behaviors and the outcome variables of OC and perceived leader effectiveness (LE) among Nigerian employees. The moderation result shows that the leader’s contingent reward behaviors reduce the effects of the internal moral perspective dimension of AL. As authentic leaders interact with followers and followers experience high levels of moral and ethical behaviors, contingent rewards become less important to followers.Practical implicationsLeadership effectiveness and OC are desirable organizational outcomes across cultures. From a practical standpoint, the results indicate several authentic dimensions are related to OC and leadership effectiveness among Nigerian employees. This extends the applicability of AL into the African countries. Particularly, it provides additional insight into a contemporary leadership model that can positively impact the leadership development in Nigeria. While the interactive effects of contingent reward were limited, they do suggest that some combinations of behaviors should be considered to effectively meet situational needs.Originality/valueThis is the first study that examines the relationship of the components that constitute AL with OC and perceived LE in the context of Nigeria, a major African nation.
Relational impact of authentic and transactional leadership styles on employee creativity
Authors: Sanda Aminu , Arthur Nana Ama Dodua 
Published: July 2017

PurposeThe purpose of this paper is to explore how authentic leadership and transactional leadership styles in Ghanaian telecom firms influence employees’ creativity, and the effect that climate for innovation and work-related flow have on such influencing relationship.Design/methodology/approachGuided by the implicit theory of leadership, and using questionnaires, data were collected from 335 employees in five mining firms and analyzed descriptively and inferentially.FindingsIt was found that managers in the telecom firms use transactional leadership styles and authentic leadership styles to enhance employees’ creativity. The work climate fostered employees’ creativity and encouraged their innovation. The prevalence of work-related flow enhanced employees’ job performances. The innovative climate mediated the effect of authentic leadership on employees’ creativity, but moderated the effect of transactional leadership on the employees’ creativity. Work-related flow also moderated the effects of both authentic and transactional leadership styles on employee creativity. It is concluded that managers in telecom firms influence their followers’ creativity by altering their leadership styles in accordance with the given situation to achieve organizational goals.Research limitations/implicationsThe study sample was drawn from a single sub-sector of the Ghanaian economy. This represents a limitation, for which the findings cannot be generalized. Replications and extensions of the study in different industrial sectors will help test the robustness and generalizability of the findings.Originality/valueThis study has shown that managers of telecom firms in Ghana can cultivate and nurture the creativities of their employees toward increased performances by creating conducive psychosocial work climate that supports innovativeness, and use the requisite authentic and transactional leadership skills in the conduct of their managerial functions.
The recontextualisation of values in the multilingual workplace
Authors: Bjørge Anne Kari , Sandvik Alexander Madsen , Whittaker Sunniva 
Published: July 2017

PurposeThe purpose of this paper is to explore how corporate values are interpreted by local and international employees in a multilingual organisation that has opted for the local language, not English, as its corporate language.Design/methodology/approachThis is a research paper exploring how the recontextualisation and resemiotisation of value terms impact on how corporate values are interpreted, employing triangulation of questionnaire and interview results.FindingsWhen values are recontextualised in employee discourse, proficiency in the corporate language and cultural background was found to have an impact on their interpretation. Internationals were found to have a broader and not exclusively professional interpretation compared to the locals. Internationals with a low level of proficiency in the local language were more sceptical than the locals as to whether there was a shared understanding of the values.Research limitations/implicationsThe questionnaire yielded fewer respondents than the authors expected, which should be taken into account when interpreting the results.Practical implicationsThe paper suggests best practices for communicating corporate values to a multilingual workforce.Social implicationsThis paper contributes to the understanding of linguistic challenges in the multilingual work contexts.Originality/valueTo the authors’ knowledge, there is little prior in-depth research on how language impacts on employees’ interpretation of corporate values. As values are cohesive devices in organisations, the language used to convey them is worth addressing as the present paper aims to demonstrate.
Introducing knowledge management pattern at national level applying grounded theory method and fuzzy dematel
Authors: Akhavan Peyman , Nabizadeh Masoumeh , Rajabion Lila 
Published: July 2017

Purpose
Although there are some studies about knowledge management at national level, no integrated attempts have been reported in the direction of introducing knowledge management pattern at national level based on real experiences. Numerous researches have been conducted in the domain of knowledge management at micro level. But at macro/national level, some concepts and components have been investigated briefly. The purpose of this paper is to deal with this gap.

Design/methodology/approach
This research uses the hybrid method. The technique of qualitative case study of grounded theory method has been selected in this research for gathering and analyzing data. Data have been categorized and analyzed from case studies (at countries level) using the steps of this method. The degree of correlation and causality and the importance of each concept existing in the pattern have been computed by applying decision-making trial and evaluation (dematel) technique. The obtained concepts and pattern could be applied as a guide for accepting and implementing knowledge management at national level.

Findings
Total positive findings have been obtained from case studies, and the authors attained 14 concepts and one pattern. These findings provide the steps of designing and are useful in implementing projects and programs of knowledge management at national level. The degree of correlation between the components of the pattern is the other finding of this study.

Practical implications
The obtained concepts and patterns can be used as a guide in countries and governments which decide to implement knowledge management at national level. These can be a basis for countries which are in the process of implementing the projects of knowledge management at national level.

Originality/value
This research is the first study that aims to provide the pattern of knowledge management at national level and can provide useful information for countries and governments and can be used as a reference to guide them for the implementation. So these countries will be able to design and implement their programs of knowledge management purposefully.