bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of the growth of Brahman and F1 Senepol × Brahman steers in an Indonesian feedlot
Authors: Schatz T. J.
Published: July 2016

This study compares the performance of F1 Senepol × Brahman steers (F1 SEN) to Brahman (BRAH) steers in an Indonesian feedlot. The focus was to address concerns that crossbred cattle are discriminated against by live export cattle buyers due to a perception that they do not perform as well as Brahmans in Indonesian feedlots. F1 SEN (n = 54) and BRAH (n = 32) steers that had grazed together since weaning at Douglas Daly Research Farm (Northern Territory) were exported to Indonesia and fed for 121 days in a feedlot near Lampung (Sumatra, Indonesia). The average daily gain of the F1 SEN steers over the feeding period was 0.17 kg/day higher (P < 0.001) than the BRAH steers (1.71 vs 1.54 kg/day). As a result the F1 SEN put on an average of 21.6 kg more over the 121-day feeding period and they did not have a higher mortality rate. Consequently, F1 SEN steers performed better than BRAH in an Indonesian feedlot and these results should encourage live export cattle buyers to purchase this type of cattle (Brahman crossed with a tropically adapted Bos taurus breed) with confidence that they can perform at least as well as Brahmans in Indonesian feedlots, although it should be noted that growth rates are usually higher in F1 crosses than in subsequent generations.
Shift in origin of plant nitrogen alters carbon and nitrogen assimilation during reproductive stages of soybean grown in a Mollisol
Authors: Li Y. S. , Liu X. B. , Wang G. H. , Yu Z. H. , Mathesius U. , Liu J. D. , Herbert S. J. , Jin J.
Published: July 2016

Excessive fertiliser has been commonly applied in the soybean (Glycine max (L.) Merr.) cropping system in fertile Mollisols in Northeast China. However, it is necessary to understand how reducing nitrogen (N) fertiliser application may affect plant N acquisition and remobilisation, which is associated with photosynthetic carbon (C) assimilation and seed yield. The aim of this study was to investigate the origin of plant N (i.e. derived from N2 fixation, fertiliser or soil) under two different levels of N application, and the subsequent influence on C assimilation. A pot experiment was conducted with soybean grown in a Mollisol supplied with 5 mg N kg–1 soil (N5) or 100 mg N kg–1 soil (N100). Nitrogen was applied as 19.83% of 15N atom-excess in urea before sowing, and 13CO2 labelling was performed at the R5 (initial seed-filling) stage. Plants were harvested at R5 and full maturity stages to determine the 15N and 13C abundance in plant tissues. Seed yield and N content were not affected by different N rates. Symbiotically fixed N accounted for 64% of seed N in treatment N5, whereas fertiliser-derived N dominated seed N in N100, resulting in 58% of seed N. The proportion of soil-derived N in shoot and seed showed no difference between the two N treatments. A similar trend was observed for whole-plant N. The enhanced N2 fixation in N5 significantly increased assimilation of N and C during the seed-filling period compared with N100. Nodule density (nodule number per unit root length) and amount of photosynthetically fixed 13C in roots in N5 were greater than in N100. These results indicate that a greater contribution of N2 fixation to N assimilation during the seed-filling period is likely to meet N demand for maintaining soybean yield when fertiliser N supply is reduced. Greater allocation of photosynthetic C to roots and enhanced nodulation would greatly contribute to the alteration of N acquisition pattern under such condition.
Structural and functional basis of protein phosphatase 5 substrate specificity
Authors: Oberoi Jasmeen , Dunn Diana M. , Woodford Mark R. , Mariotti Laura , Schulman Jacqualyn , Bourboulia Dimitra , Mollapour Mehdi , Vaughan Cara K.
Published: July 2016

Significance

The activity of many proteins is dependent on molecular chaperones and their accessory proteins, cochaperones. The ability of a cohort of kinases, many of which are oncogenic, to transduce signals is promoted by the heat shock protein 90 (Hsp90) chaperone and Cdc37 cochaperone, and requires the removal of a phosphate from Cdc37 by protein phosphatase 5 (PP5). We present the crystal structure of PP5 with Cdc37 trapped in the active site. The structure reveals how PP5 can associate with different substrates and previously unknown determinants of specificity. Our findings show kinase release from the chaperone complex is critically dependent on this dephosphorylation and that combined inhibition of both Hsp90 and PP5 could provide an effective therapeutic strategy for treating cancers addicted to these kinases.
Contiguity and the causal theory of memory
Authors: Robins Sarah K.
Published: July 2016

In Memory: A Philosophical Study, Bernecker argues for an account of contiguity. This Contiguity View is meant to solve relearning and prompting, wayward causation problems plaguing the causal theory of memory. I argue that Bernecker’s Contiguity View fails in this task. Contiguity is too weak to prevent relearning and too strong to allow prompting. These failures illustrate a problem inherent in accounts of memory causation. Relearning and prompting are both causal relations, wayward only with respect to our interest in specifying remembering’s requirements. Solving them requires saying more about remembering, not causation. I conclude by sketching such an account.
VE-cadherin interacts with cell polarity protein Pals1 to regulate vascular lumen formation
Authors: Brinkmann Benjamin F. , Steinbacher Tim , Hartmann Christian , Kummer Daniel , Pajonczyk Denise , Mirzapourshafiyi Fatemeh , Nakayama Masanori , Weide Thomas , Gerke Volker , Ebnet Klaus
Published: July 2016

Blood vessel tubulogenesis requires the formation of stable cell-to-cell contacts and the establishment of apicobasal polarity of vascular endothelial cells. Cell polarity is regulated by highly conserved cell polarity protein complexes such as the Par3-aPKC-Par6 complex and the CRB3-Pals1-PATJ complex, which are expressed by many different cell types and regulate various aspects of cell polarity. Here we describe a functional interaction of VE-cadherin with the cell polarity protein Pals1. Pals1 directly interacts with VE-cadherin through a membrane-proximal motif in the cytoplasmic domain of VE-cadherin. VE-cadherin clusters Pals1 at cell–cell junctions. Mutating the Pals1-binding motif in VE-cadherin abrogates the ability of VE-cadherin to regulate apicobasal polarity and vascular lumen formation. In a similar way, deletion of the Par3-binding motif at the C-terminus of VE-cadherin impairs apicobasal polarity and vascular lumen formation. Our findings indicate that the biological activity of VE-cadherin in regulating endothelial polarity and vascular lumen formation is mediated through its interaction with the two cell polarity proteins Pals1 and Par3.
Introduction
Authors: Linafelt Tod
Published: July 2016

Toward the end of the twentieth century a genuine, sustained appreciation of the Bible’s literary art—regardless of its historical veracity or of its religious value—arose. The Introduction explains that focus of this VSI is on the two traditional literary genres found in the Bible, namely narrative and poetry. It asks what it means to read the Bible “as literature” and concludes that it is to pay attention to precisely those qualities that do more than communicate information, those qualities of linguistic imagining that may startle and provoke, or soothe and comfort, or perhaps just ask us to enjoy the play of language itself, because we can.
Indian Cinema
Authors: Rajadhyaksha Ashish
Published: July 2016

One film out of every five made anywhere comes from India. From its beginnings under colonial rule through to the heights of Bollywood, Indian cinema has challenged social injustices such as caste, the oppression of Indian women, religious intolerance, rural poverty, and the pressures of life in the burgeoning cities. Indian Cinema: A Very Short Introduction delves into the political, social, and economic factors which have shaped Indian cinema into a fascinating counterculture. Covering everything from silent cinema through to the digital era, it examines how the industry reflects the complexity and variety of Indian society through the dramatic changes of the 20th century, and into the beginnings of the 21st.
plasmidSPAdes: assembling plasmids from whole genome sequencing data
Authors: Antipov Dmitry , Hartwick Nolan , Shen Max , Raiko Mikhail , Lapidus Alla , Pevzner Pavel A.
Published: July 2016

Motivation: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell’s chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects.

Results: We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes.

Availability and Implementation:  plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/

Contact:  d.antipov@spbu.ru

Supplementary information:  Supplementary data are available at Bioinformatics online.
Gaps in globular cluster streams: giant molecular clouds can cause them too
Authors: Amorisco Nicola C. , Gómez Facundo A. , Vegetti Simona , White Simon D. M.
Published: July 2016

As a result of their internal dynamical coherence, thin stellar streams formed by disrupting globular clusters (GCs) can act as detectors of dark matter (DM) substructure in the Galactic halo. Perturbations induced by close flybys amplify into detectable density gaps, providing a probe both of the abundance and of the masses of DM subhaloes. Here, we use N-body simulations to show that the Galactic population of giant molecular clouds (GMCs) can also produce gaps (and clumps) in GC streams, and so may confuse the detection of DM subhaloes. We explore the cases of streams analogous to the observed Palomar 5 and GD1 systems, quantifying the expected incidence of structure caused by GMC perturbations. Deep observations should detect such disturbances regardless of the substructure content of the Milky Way's halo. Detailed modelling will be needed to demonstrate that any detected gaps or clumps were produced by DM subhaloes rather than by molecular clouds.
Raman Spectroscopy Differentiates Each Tissue from the Skin to the Spinal Cord
Authors: Anderson T. Anthony , Kang Jeon Woong , Gubin Tatyana , Dasari Ramachandra R. , So Peter T. C.
Published: July 2016

Background

Neuraxial anesthesia and epidural steroid injection techniques require precise anatomical targeting to ensure successful and safe analgesia. Previous studies suggest that only some of the tissues encountered during these procedures can be identified by spectroscopic methods, and no previous study has investigated the use of Raman, diffuse reflectance, and fluorescence spectroscopies. The authors hypothesized that real-time needle-tip spectroscopy may aid epidural needle placement and tested the ability of spectroscopy to distinguish each of the tissues in the path of neuraxial needles.

Methods

For comparison of detection methods, the spectra of individual, dissected ex vivo paravertebral and neuraxial porcine tissues were collected using Raman spectroscopy (RS), diffuse reflectance spectroscopy, and fluorescence spectroscopy. Real-time spectral guidance was tested using a 2-mm inner-diameter fiber-optic probe-in-needle device. Raman spectra were collected during the needle’s passage through intact paravertebral and neuraxial porcine tissue and analyzed afterward. The RS tissue signatures were verified as mapping to individual tissue layers using histochemical staining and widefield microscopy.

Results

RS revealed a unique spectrum for all ex vivo paravertebral and neuraxial tissue layers; diffuse reflectance spectroscopy and fluorescence spectroscopy were not distinct for all tissues. Moreover, when accounting for the expected order of tissues, real-time Raman spectra recorded during needle insertion also permitted identification of each paravertebral and neuraxial porcine tissue.

Conclusions

This study demonstrates that RS can distinguish the tissues encountered during epidural needle insertion. This technology may prove useful during needle placement by providing evidence of its anatomical localization.
Total Hip Arthroplasty for Femoral Neck Fractures: Improved Outcomes With Higher Hospital Volumes
Authors: Maceroli Michael , Nikkel Lucas E. , Mahmood Bilal , Ketz John P. , Qiu Xing , Ciminelli Joseph , Messing Susan , Elfar John C.
Published: July 2016

Objectives:

To determine if hospital arthroplasty volume affects patient outcomes after undergoing total hip arthroplasty (THA) for displaced femoral neck fractures.

Methods:

The Statewide Planning and Research Cooperative System database from the New York State Department of Health was used to group hospitals into quartiles based on overall THA volume from 2000 to 2010. The database was then queried to identify all patients undergoing THA specifically for femoral neck fracture during this time period. The data were analyzed to investigate outcomes between the 4 volume quartiles in 30-day and 1-year mortality, 1-year revision rate, and 90-day complication rate (readmission for dislocation, deep vein thrombosis, pulmonary embolism, prosthetic joint infection, or other complications related to arthroplasty in the treatment of femoral neck fractures with THA).

Results:

Patients undergoing THA for femoral neck fracture at hospitals in the top volume quartile had significantly lower 30-day (0.9%) and 1-year (7.51%) mortality than all other volume quartiles. There were no significant differences on pairwise comparisons between the second, third, and fourth quartiles with regard to postoperative mortality. There was no significant difference in revision arthroplasty at 1 year between any of the volume quartiles. On Cox regression analysis, THA for fracture at the lowest volume (fourth) quartile [hazard ratio (HR), 1.91; P = 0.016, 95% confidence interval (CI), (1.13–3.25)], second lowest volume (third) quartile (HR, 2.01; P = 0.013, 95% CI, 1.16–3.5) and third lowest volume (second) quartile (HR, 2.13; P = 0.005, 95% CI, 1.26–3.62) were associated with increased risk for a 1-year postoperative mortality event. Hospital volume quartile was also a significant risk factor for increased 90-day complication (pulmonary embolism/deep vein thrombosis, acute dislocation, prosthetic joint infection) following THA for femoral neck fracture. Having surgery in the fourth quartile (HR, 2.71; P < 0.001, 95% CI, 1.7–4.31), third quartile (HR, 2.61; P < 0.001, 95% CI, 1.61–4.23), and second quartile (HR, 2.41; P < 0.001, 95% CI, 1.51–3.84), all were significant risk factors for increased 90-day complication risk.

Conclusions:

The results of this population-based study indicate that THA for femoral neck fractures at high-volume arthroplasty centers is associated with lower mortality and 90-day complication rates but does not influence 1-year revision rate. THA for femoral neck fractures at top arthroplasty volume quartile hospitals are performed on healthier patients more quickly. Patient health is a critical factor that influences mortality outcomes following THA for femoral neck fractures.

Level of Evidence:

Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.
Layered Plating for Complex Fractures
Authors: Nazir Omar F. , Mirarchi Adam
Published: July 2016

Complex fractures provide a unique challenge to the musculoskeletal surgeon. Traditional fracture reduction techniques are not always feasible, and often difficult depending on the anatomic area involved. We describe a novel technique, called layered plating, which can ease anatomic reduction and fixation of complex fractures. The aim of this paper was to describe 3 applications for layered plating, including provisional reduction, stability enhancement, and endosteal plating. All of the patients in which this technique was used went on to clinical and radiographic healing.
Costs of Keratinocyte Carcinoma (Nonmelanoma Skin Cancer) and Actinic Keratosis Treatment in the Veterans Health Administration
Authors: Yoon Jean , Phibbs Ciaran S. , Chow Adam , Pomerantz Hyemin , Weinstock Martin A.
Published: July 2016

BACKGROUND

The Veterans Health Administration (VHA) provides health care to large numbers of veterans afflicted with keratinocyte carcinoma (KC).

OBJECTIVE

To estimate the number of veterans treated for KCs and the related diagnosis, actinic keratosis (AK) and the costs of treating these conditions over a 1-year period.

MATERIALS AND METHODS

The authors conducted a cross-sectional analysis of veterans diagnosed with KC or AK during fiscal year 2012 using administrative data on outpatient encounters and prescription drugs provided or paid by VHA. Marginal costs of each condition were estimated from a regression model. The authors estimated counts of outpatient encounters, procedures, and costs related to KC and AK care.

RESULTS

In 2012, there were 49,229 veterans with basal cell carcinoma, 26,310 veterans with squamous cell carcinoma, and 8,050 veterans with unspecified invasive KC. There were also 197,041 veterans with AK and 6,388 veterans with KC-related diagnoses. The VHA spent $356 million on KC and AK outpatient treatment for procedures, prescription drugs, and other dermatologic care during FY2012.

CONCLUSION

There was high prevalence of KC and AK and considerable spending to treat these conditions in VHA. Treatment costs are not generalizable to care provided by non-VHA providers where a facility fee was not incurred.
A Clinical Review of Laser and Light Therapy for Nail Psoriasis and Onychomycosis
Authors: Wiznia Lauren E. , Quatrano Nicola A. , Mu Euphemia W. , Rieder Evan A.
Published: July 2016

BACKGROUND

There are considerable emerging data in the use of lasers and lights to treat onychomycosis and psoriasis of the nail subunit.

OBJECTIVE

We aimed to review all of the medical literature on laser therapy of nail psoriasis and onychomycosis published since 1992.

METHODS AND MATERIALS

We performed a PubMed literature search using the search terms “nail,” “laser therapy,” “laser surgery,” “light,” with search terms “psoriasis” and “onychomycosis.” In addition, we performed extensive MeSH and bibliographic searches as delineated in the manuscript. Because of the poor quality of evidence, we were not able to complete a quantitative review and thus present our findings qualitatively.

RESULTS

Although the trials are small, PDL (595 nm) and IPL with a 550-nm filter demonstrate compelling data in treating nail psoriasis. Laser studies of onychomycosis fall short on many levels. Q-switched Nd:YAG lasers with very short pulse durations and fractionated CO2 demonstrate the most promise for the treatment of onychomycosis.

CONCLUSION

The data for treating nail psoriasis and onychomycosis with laser and light therapy are rapidly emerging. With increased subject data, improved study methodology, and more precise output parameters, lasers may become an important modality in the treatment of nail psoriasis and onychomycosis.
Interprofessional Collaboration in Perinatal Care
Authors: Smith Denise C.
Published: July 2016

Healthcare delivered by teams is becoming more common, and an estimated 50% of obstetricians in the United States (US) work with or employ nurse practitioners or nurse-midwives. The number of midwife-attended births in the United States is also growing. Interprofessional collaboration between midwives and physicians can increase access to safe, quality maternity care for women in the United States. A review of the literature indicates that successful collaborative practice includes effective communication, trust, and respect between providers. A review of concepts and theoretical frameworks offers a foundation for scholarly inquiry, suggests a research agenda for future study, and provides suggestions for organizational leaders to translate current knowledge into the clinical setting. Midwifery, through increasing collaborative practices, has the potential to change care delivery in the years to come.
Challenges and Creative Strategies in Undergraduate Nursing Education in Maternal-Child Health
Authors: Drake Emily
Published: July 2016

Maternal-child health (MCH) is an integral part of most nursing undergraduate curricula. However, there are variations in implementation related to classroom and clinical experiences. The purpose of this article is to describe recent trends in MCH education, explore potential challenges, and highlight creative solutions for MCH nursing education. Perinatal nursing requires a solid skill base and sound knowledge base in many subjects, including health promotion and behavior change theory. Educators need to provide students with a firm educational foundation to meet both workforce demands and the needs of childbearing women, infants, and families.
Academic-Practice Partnerships
Authors: Bakewell-Sachs Susan
Published: July 2016

The 3 recognized missions of academic nursing—education, practice, and research—are not new. Yet, the continued separation of nursing education and service, with a lack of integration between schools of nursing and clinical practice, continues to be discussed as contributing to academic programs that produce graduates unready for clinical practice, research that does not adequately support clinical care needs, and isolation of both the nurse faculty from the clinical enterprise and clinicians from the education and research missions. Recently, academic-practice partnerships have been reemphasized as a concept and mechanism for supporting changes in nursing education and improving clinical care. This article highlights some of the driving forces behind the focus on academic-practice partnerships and summarizes 3 changes in education.
Supporting Neonatal Intensive Care Unit Parents Through Social Media
Authors: Dzubaty Dolores R.
Published: July 2016

Parents of infants in the neonatal intensive care unit may often find themselves seeking healthcare information from online and social media sources. Social media applications are available to healthcare consumers and their families, as well as healthcare providers, in a variety of formats. Information that parents gather on their own, and information that is explained by providers, is then used when parents make healthcare decisions regarding their infants. Parents also seek support from peers and family while making healthcare decisions. The combination of knowledge obtained and social support given may empower the parent to feel more confident in their decision making. Healthcare professionals can guide parents to credible resources. The exchange of information between providers and parents can occur using a variety of communication methods. Misperceptions can be corrected, support given, open sharing of information occurs, and parent empowerment may result.
Trends in Family-Centered Care in Neonatal Intensive Care
Authors: Maree Carin , Downes Fiona
Published: July 2016

Family-centered care in neonatal intensive care changed over the last decades. Initially, parents and infants were separated and parents were even being blamed for cau-sing infections in their infants. The importance, though, of the parents being the constant in the infant's life emerged and with that the importance of early bonding and attachment for the parents to take on their role and responsibi-lities as primary caregivers. Facilitation of family-centered care includes involving the parents in daily care activities, kangaroo care, developmental care, interaction and communication with the infant, as well as involving grandparents and siblings. Implementation of family-centered care requires appropriate policies, facilities and resources, education of all involved, and a positive attitude.
Interprofessional Education in Neonatal Care
Authors: Kenner Carole
Published: July 2016

Interprofessional education is not a new concept. Yet, the operationalization of interprofessional education with related competencies for collaborative team-based practice in neonatal units is often difficult. Changes in healthcare with an emphasis on patient-focused care and the concern for patient safety and quality care are accelerating the need for more interprofessional education. This article briefly outlines the evolution of interprofessional education to support collaborative team-based practice and how that facilitates safety and quality care in neonatal units.
Construct and Predictive Validity of a Cystoscopic Checklist to Evaluate Surgical Competency in the Operating Room
Authors: Swift Steven , Edenfield Autumn L. , Clark Dyanna
Published: July 2016

Purpose

The aim of this study was to demonstrate the construct and predictive validity of a task-specific checklist for cystoscopy in the operating room.

Methods

This study is a prospective observational study evaluating the validity of a task-specific checklist for cystoscopic proficiency on residents performing cystoscopy in the operating room over a 4-year period. Residents were scored on 2 task-specific checklists: (1) assembly and (2) performance of a diagnostic cystoscopy. Construct validity was evaluated by comparing absolute checklist scores based on resident year with a Kruskal-Wallis and χ2 test, respectively. Paired analysis was performed with Wilcoxon sign rank and McNemar tests to assess differences between initial and final observations. Predictive validity was evaluated by determining the percent of competently performed task-specific checklists subsequent to 1 competent task-specific checklist completion.

Results

One hundred fifty-three evaluations were performed on 30 residents from all 4 levels of training. The median task-specific checklist scores for both (1) assembly and (2) performance of a diagnostic cystoscopy demonstrated construct validity with statistically significant trends demonstrating improved scores as resident year increased from intern to chief, P values of <0.001 and <0.0001, respectively. Once competency was obtained for 1 cystoscope assembly checklist, 92% of future assembly checklists were competently competent. For diagnostic cystoscopy once checklist competency was obtained, 69% of future checklists were completed competently. All scores and competencies were significantly improved from the initial to the final observation.

Discussion

The task-specific checklists for (1) assembly and (2) performance of a diagnostic cystoscopy demonstrated construct validity. Predicative validity for assembly of a cystoscope is high but less so for performance of a diagnostic cystoscope.
Recurrent Urinary Tract Infection After Midurethral Sling: A Retrospective Study
Authors: Hammett Jessica , Lukman Revana , Oakes Megan , Whitcomb Emily L.
Published: July 2016

Objectives

Our primary objective was to estimate the proportion of patients with culture-proven urinary tract infection (UTI) and recurrent UTI after midurethral sling (MUS), as well as to evaluate their risk factors. Our secondary objective was to characterize the difference in the proportion of patients with recurrent UTI before and after MUS.

Methods

We conducted a retrospective study of patients who underwent MUS from 2009 to 2012 within a large health maintenance organization and subsequently had documentation of at least 1 positive urine culture (>100 K CFU/mL) within 1 year. Validated procedural and diagnostic codes were used to identify patients undergoing MUS and the diagnosis of UTI, respectively.

Results

Of the 7461 MUS performed, 883 (12%) patients had at least 1 culture-proven UTI and 258 (3.5%) patients met the definition of recurrent UTI postoperatively. Of those 883 patients, 89 (10%) patients met the definition of recurrent UTI before, and 258 (29%) patients after, MUS. McNemar χ2 test revealed that patients were more likely to have recurrent UTI after MUS compared with before (P < 0.0001). In multivariate logistic regression, Caucasian (odds ratio [OR], 1.60, 95% confidence interval [95% CI], 1.12–2.29; P = 0.01) and African-American (OR, 3.42; 95% CI, 1.42–8.29; P = 0.01) ethnicity, older age (OR, 1.02; 95% CI, 1.00–1.04; P = 0.03), and a history of recurrent UTI (OR 3.79, 95% CI 1.88–7.93, P = 0.0003) were risk factors for postoperative recurrent UTI.

Conclusions

In this population, preoperative recurrent UTI was the only modifiable risk factor associated with an increased risk of postoperative recurrent UTI.
Clonal heterogeneity influences the fate of new adaptive mutations
Authors: Vázquez-García Ignacio , Salinas Francisco , Li Jing , Fischer Andrej , Barré Benjamin , Hallin Johan , Bergström Anders , Alonso-Perez Elisa , Warringer Jonas , Mustonen Ville , Liti Gianni
Published: July 2016

In Brief

Vázquez-García et al. examine the role of clonal heterogeneity in the acquisition of antimicrobial resistance. They report that pre-existing andde novogenetic variation jointly contribute to clonal evolution. By building a library of adaptive mutations in multiple genetic backgrounds, they resolve the fitness effects of mutations in a clonal lineage.

Highlights

Clonal heterogeneity influences the acquisition of antimicrobial resistance

Joint role of pre-existing andde novogenetic variation in clonal evolution

Clonal dynamics are shaped by background-dependent fitness effects of mutations

Loss of clonal heterogeneity is balanced by genomic instability and diversification

The joint contribution of pre-existing andde novogenetic variation to clonal adaptation is poorly understood, but essential to design successful antimicrobial or cancer therapies. To address this, we evolve genetically diverse populations of budding yeast,S. cerevisiae, consisting of diploid cells with unique haplotype combinations. We study the asexual evolution of these populations under selective inhibition with chemotherapeutic drugs by time-resolved whole-genome sequencing and phenotyping. All populations undergo clonal expansions driven byde novomutations, but remain genetically and phenotypically diverse. The clones exhibit widespread genomic instability, rendering recessivede novomutations homozygous and refining pre-existing variation. Finally, we decompose the fitness contributions of pre-existing andde novomutations by creating a large recombinant library of adaptive mutations in an ensemble of genetic backgrounds. Both pre-existing andde novomutations substantially contribute to fitness, and the relative fitness of pre-existing variants sets a selective threshold for new adaptive mutations.
Genetic Regulation of Phenotypic Plasticity and Canalisation in Yeast Growth
Authors: Yadav Anupama , Dhole Kaustubh , Sinha Himanshu
Published: July 2016

The ability of a genotype to show diverse phenotypes in different environments is called phenotypic plasticity. Phenotypic plasticity helps populations to evade extinctions in novel environments, facilitates adaptation and fuels evolution. However, most studies focus on understanding the genetic basis of phenotypic regulation in specific environments. As a result, while it’s evolutionary relevance is well established, genetic mechanisms regulating phenotypic plasticity and their overlap with the environment specific regulators is not well understood.Saccharomyces cerevisiaeis highly sensitive to the environment, which acts as not just external stimulus but also as signalling cue for this unicellular, sessile organism. We used a previously published dataset of a biparental yeast population grown in 34 diverse environments and mapped genetic loci regulating variation in phenotypic plasticity, plasticity QTL, and compared them with environment-specific QTL. Plasticity QTL is one whose one allele exhibits high plasticity whereas the other shows a relatively canalised behaviour. We mapped phenotypic plasticity using two parameters – environmental variance, an environmental order-independent parameter and reaction norm (slope), an environmental order-dependent parameter. Our results show a partial overlap between pleiotropic QTL and plasticity QTL such that while some plasticity QTL are also pleiotropic, others have a significant effect on phenotypic plasticity without being significant in any environment independently. Furthermore, while some plasticity QTL are revealed only in specific environmental orders, we identify large effect plasticity QTL, which are order-independent such that whatever the order of the environments, one allele is always plastic and the other is canalised. Finally, we show that the environments can be divided into two categories based on the phenotypic diversity of the population within them and the two categories have differential regulators of phenotypic plasticity. Our results highlight the importance of identifying genetic regulators of phenotypic plasticity to comprehensively understand the genotype-phenotype map.
Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on evidence from mtDNA analysis, MC1R, and Y-chromosome haplotypes
Authors: Osei-Amponsah R. , Skinner B.M. , Adjei O.D , Bauer J , Larson G , Affara N.A , Sargent C.A
Published: July 2016

The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA,MC1Rand Y-chromosome sequence polymorphisms, as well as genome-wide SNP genotyping.

The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with dominant blackMC1Ralleles of both Asian and European origin contributing. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, such as the Large White.

The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences.. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.
fMRI Dependent Components Analysis Reveals Dynamic Relations Between Functional Large Scale Cortical Networks
Authors: Hertz Uri , Zoran Daniel , Weiss Yair , Amedi Amir
Published: July 2016

One of the major advantages of whole brain fMRI is the detection of large scale cortical networks. Dependent Components Analysis (DCA) is a novel approach designed to extract both cortical networks and their dependency structure. DCA is fundamentally different from prevalent data driven approaches, i.e. spatial ICA, in that instead of maximizing the independence of components it optimizes their dependency (in a tree graph structure, tDCA) depicting cortical areas as part of multiple cortical networks. Here tDCA was shown to reliably detect large scale functional networks in single subjects and in group analysis, by clustering non-noisy components on one branch of the tree structure. We used tDCA in three fMRI experiments in which identical auditory and visual stimuli were presented, but novelty information and task relevance were modified. tDCA components tended to include two anticorrelated networks, which were detected in two separate ICA components, or belonged in one component in seed functional connectivity. Although sensory components remained the same across experiments, other components changed as a function of the experimental conditions. These changes were either within component, where it encompassed other cortical areas, or between components, where the pattern of anticorrelated networks and their statistical dependency changed. Thus tDCA may prove to be a useful, robust tool that provides a rich description of the statistical structure underlying brain activity and its relationships to changes in experimental conditions. This tool may prove effective in detection and description of mental states, neural disorders and their dynamics.
Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
Authors: Wang Su , Zang Chongzhi , Xiao Tengfei , Fan Jingyu , Mei Shenglin , Qin Qian , Wu Qiu , Li Xujuan , Xu Kexin , He Housheng Hansen , Brown Myles , Meyer Clifford A. , Liu X. Shirley
Published: July 2016

Model-based analysis of regulation of gene expression (MARGE) is a framework for interpreting the relationship between the H3K27ac chromatin environment and differentially expressed gene sets. The framework has three main functions: MARGE-potential, MARGE-express, and MARGE-cistrome. MARGE-potential defines a regulatory potential (RP) for each gene as the sum of H3K27ac ChIP-seq signals weighted by a function of genomic distance from the transcription start site. The MARGE framework includes a compendium of RPs derived from 365 human and 267 mouse H3K27ac ChIP-seq data sets. Relative RPs, scaled using this compendium, are superior to superenhancers in predicting BET (bromodomain and extraterminal domain) -inhibitor repressed genes. MARGE-express, which uses logistic regression to retrieve relevant H3K27ac profiles from the compendium to accurately model a query set of differentially expressed genes, was tested on 671 diverse gene sets from MSigDB. MARGE-cistrome adopts a novel semisupervised learning approach to identify cis-regulatory elements regulating a gene set. MARGE-cistrome exploits information from H3K27ac signal at DNase I hypersensitive sites identified from published human and mouse DNase-seq data. We tested the framework on newly generated RNA-seq and H3K27ac ChIP-seq profiles upon siRNA silencing of multiple transcriptional and epigenetic regulators in a prostate cancer cell line, LNCaP-abl. MARGE-cistrome can predict the binding sites of silenced transcription factors without matched H3K27ac ChIP-seq data. Even when the matching H3K27ac ChIP-seq profiles are available, MARGE leverages public H3K27ac profiles to enhance these data. This study demonstrates the advantage of integrating a large compendium of historical epigenetic data for genomic studies of transcriptional regulation.
Human resource management (HRM) and public service motivation (PSM)
Authors: Homberg Fabian , Vogel Rick
Published: July 2016

Purpose

– The purpose of this paper is to provide an introduction to the special issue on public service motivation (PSM) and human resource management (HRM). The authors analyse and review how the literatures on HRM and PSM relate to each other.

Design/methodology/approach

– The paper combines two complementary studies: a bibliometric analysis of the interrelationships between the two literatures and a meta-analysis of the impact of HR practices on PSM.

Findings

– Although HRM is among the core subject categories to which the literature on PSM refers, the pre-eminence of HR topics self-reported by PSM researchers indicates large room for further transfer. Intrinsic HR practices show positive and significant effects on PSM, while no such association was found for extrinsic HR practices.

Originality/value

– The editorial is a complement to a recent bibliometric review of PSM research, focusing more particularly on the interrelationships with HRM and applying hitherto unused techniques. It is also the first meta-analysis of the association between HR practices and PSM.
Negative association of pretreatment cigarette use with smoking‐induced striatal dopamine release in smokers receiving bupropion treatment
Authors: Weinstein Aviv Malkiel , Freedman Nanette , Greif Joel , Yemini Zipi , Mishani Eyal , London Edythe , Chisin Roland , Bocher Moshe
Published: July 2016

Background and Objectives

In an effort to help identify factors that maintain heavy smoking, this study tested the association of pretreatment cigarette use (cigarettes per day) with striatal dopamine release during smoking‐cessation treatment.

Methods

Thirteen regular smokers (≥10 cigarettes per day) were evaluated on parameters of smoking behavior, and they entered a smoking cessation treatment protocol, including bupropion administration and individual counseling for 2 months. On week 7 of treatment, 10 of the participants underwent brain scans using [11C]raclopride with positron emission tomography to assess smoking‐induced dopamine release in the caudate nucleus and putamen, inferred from changes in dopamine D2‐type receptor availability.

Results

Receptor availability, measured as binding potential referred to non‐displaceable uptake (BPND) in both striatal regions re‐demonstrated a significant decrease after smoking a cigarette; and pre‐treatment cigarette use significantly negatively correlated with smoking‐induced dopamine release in the caudate.

Conclusions and Significance

The negative association of cigarette use with dopamine release suggests tolerance or down‐regulation of the dopamine system by chronic smoking, or a pre‐existing condition that promotes more frequent smoking. This association should be regarded as preliminary evidence that warrants verification. (Am J Addict 2016;25:486–492)
Diagnostic laparoscopy in pre‐surgical planning for higher stage endometriosis: Is it still relevant?
Authors: Menakaya Uche A. , Rombauts Luk , Johnson Neil P.
Published: July 2016

It has become necessary to re ‐ examine the relevance of diagnostic laparoscopy in the two‐stage approach to surgical management of symptomatic women with higher stage endometriosis following emerging evidence demonstrating acceptable diagnostic performance of alternative less invasive and less expensive imaging modalities. We highlight the relative merits of these presurgical diagnostic imaging modalities and propose strategies that address the challenge of transitioning to a new diagnostic paradigm in the management of symptomatic women with higher stage endometriosis.
An index with improved diagnostic accuracy for the diagnosis of Crohn's disease derived from the Lennard‐Jones criteria
Authors: Reinisch S. , Schweiger K. , Pablik E. , Collet‐Fenetrier B. , Peyrin‐Biroulet L. , Alfaro I. , Panés J. , Moayyedi P. , Reinisch W.
Published: July 2016

Background

The Lennard‐Jones criteria are considered the gold standard for diagnosing Crohn's disease (CD) and include the items granuloma, macroscopic discontinuity, transmural inflammation, fibrosis, lymphoid aggregates and discontinuous inflammation on histology. The criteria have never been subjected to a formal validation process.

Aim

To develop a validated and improved diagnostic index based on the items of Lennard‐Jones criteria.

Methods

Included were 328 adult patients with long‐standing CD (median disease duration 10 years) from three centres and classified as ‘established’, ‘probable’ or ‘non‐CD’ by Lennard‐Jones criteria at time of diagnosis. Controls were patients with ulcerative colitis (n = 170). The performance of each of the six diagnostic items of Lennard‐Jones criteria was modelled by logistic regression and a new index based on stepwise backward selection and cut‐offs was developed. The diagnostic value of the new index was analysed by comparing sensitivity, specificity and accuracy vs. Lennard‐Jones criteria.

Results

By Lennard‐Jones criteria 49% (n = 162) of CD patients would have been diagnosed as ‘non‐CD’ at time of diagnosis (sensitivity/specificity/accuracy, ‘established’ CD: 0.34/0.99/0.67; ‘probable’ CD: 0.51/0.95/0.73). A new index was derived from granuloma, fibrosis, transmural inflammation and macroscopic discontinuity, but excluded lymphoid aggregates and discontinuous inflammation on histology. Our index provided improved diagnostic accuracy for ‘established’ and ‘probable’ CD (sensitivity/specificity/accuracy, ‘established’ CD: 0.45/1/0.72; ‘probable’ CD: 0.8/0.85/0.82), including the subgroup isolated colonic CD (‘probable’ CD, new index: 0.73/0.85/0.79; Lennard‐Jones criteria: 0.43/0.95/0.69).

Conclusion

We developed an index based on items of Lennard‐Jones criteria providing improved diagnostic accuracy for the differential diagnosis between CD and UC.
Randomised clinical trial: a Lactobacillus GG and micronutrient‐containing mixture is effective in reducing nosocomial infections in children, vs. placebo
Authors: Bruzzese E. , Fedele M. C. , Bruzzese D. , Viscovo S. , Giannattasio A. , Mandato C. , Siani P. , Guarino A.
Published: July 2016

Background

Nosocomial infections are a major public health issue and preventative strategies using probiotics and micronutrients are being evaluated.

Aim

To investigate the efficacy of a mixture of Lactobacillus GG and micronutrients in preventing nosocomial infections in children.

Methods

A randomised, double‐blind, placebo‐controlled trial was conducted in hospitalised children. Children (6 months to 5 years of age) received Lactobacillus GG (6 × 109 CFU/day) together with vitamins B and C and zinc or placebo, for 15 days, starting on the first day of hospitalisation. The incidence of gastrointestinal and respiratory nosocomial infections after discharge was determined by follow‐up telephone call at 7 days. After 3 months, another telephone call estimated the incidence of further infections during follow‐up.

Results

Ninety children completed the follow‐up. Of 19/90 children with a nosocomial infection (20%), 4/45 children (9%) were in the treatment group and 15/45 (33%) in the placebo group (P = 0.016). Specifically, 2/45 (4%) children in the treatment group vs. 11/45 (24%) children in the placebo group (P = 0.007) presented with diarrhoea. The duration of hospitalisation was significantly shorter in the treatment group (3.9 days ± 1.7 vs. 4.9 ± 1.2; P = 0.003). At the follow‐up, a total of 11/45 (24.4%) children in the treatment group had at least one episode of infection compared to 22/45 (48.9%) in the placebo group (P = 0.016).

Conclusion

A mixture containing Lactobacillus GG and micronutrients may reduce the incidence of nosocomial infections, supporting the hypothesis that this may represent a valid strategy to prevent nosocomial infections.