bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supporting and Empowering Nurses Undergoing Critical Care Certification
Authors: Beaudoin Geneviève , St-Louis Lyne , Alderson Marie 
Published: June 2016

Purpose:Nurses working in critical care settings face multiple sources of stress, such as complex clinical situations and the use of new advanced technologies, which can affect their psychological health. Literature suggests that the promotion of educational activities, such as a certification process within a specialty, can contribute to nurses’ empowerment, professional growth, and personal satisfaction. However, it is of utmost importance that the institutional organizations support nurses undergoing the certification process to optimize positive impacts of this educational activity on the nurses, on the patients, and within the institutions.Description of the Project:In the course of a graduate studies stage, an educational program aiming at supporting and creating an empowering environment for nurses undergoing a critical care certification process was developed and implemented, in a Canadian intensive care unit, over a 7-month period. The Humanist model was used as a theoretical framework and was complemented by the problem-based learning pedagogical approach.Outcomes:A postintervention qualitative questionnaire revealed that the program was tailored to nurses’ learning needs and that participants felt supported by their institution throughout the process.Conclusion:This program could help institutions support nurses in achieving higher professional and personal development levels through specialty certification.
Antibiotic Prophylaxis following Implant-Based Breast Reconstruction: What Is the Evidence?
Authors: Phillips Brett T. , Halvorson Eric G. 
Published: June 2016

Background:
Although data from other surgical disciplines do not support the use of prolonged postoperative prophylactic antibiotics, implant-based breast reconstruction is one area of plastic surgery where this may be warranted. The purpose of this study was to review the literature on antibiotic prophylaxis in prosthetic breast reconstruction, summarize findings, and provide recommendations.

Methods:
A literature review was performed to identify studies that compared different perioperative prophylactic antibiotic regimens with respect to infectious outcomes in prosthetic breast reconstruction.

Results:
Five studies and five systematic reviews were identified. One prospective randomized trial showed that a single preoperative dose was better than placebo, and another showed no difference between 24 hours versus until drain removal. Three studies were retrospective, one showing no difference between a single preoperative dose and prolonged antibiotic use, and two showing significant reduction in infectious complications with prolonged antibiotic use. One systematic review suggested an increased rate of infection with prolonged antibiotic use, and the other showed no difference between less than 24 hours and greater than 24 hours, but showed a reduction in infections compared to no treatment.

Conclusions:
The literature contains conflicting data regarding the optimal duration for perioperative antibiotic prophylaxis following prosthetic breast reconstruction. The authors’ opinion is that 24 hours of antibiotic prophylaxis is warranted. Further studies are needed. Patient-centered antibiotic prophylaxis based on a risk-assessment model may be a more effective alternative to the current indiscriminate model of surgical-site infection control.
Facial Aesthetic Outcomes of Cleft Surgery: Assessment of Discrete Lip and Nose Images Compared with Digital Symmetry Analysis
Authors: Deall Ciara E. , Kornmann Nirvana S. S. , Bella Husam , Wallis Katy L. , Hardwicke Joseph T. , Su Ting-Li , Richard Bruce M. 
Published: June 2016

Background:
High-quality aesthetic outcomes are of paramount importance to children growing up after cleft lip and palate surgery. Establishing a validated and reliable assessment tool for cleft professionals and families will facilitate cleft units, surgeons, techniques, and protocols to be audited and compared with greater confidence. This study used exemplar images across a five-point aesthetic scale, identified in a pilot project, to score lips and noses as separate units and compared these human scores with computer-based SymNose symmetry scores.

Methods:
Forty-five assessors (17 cleft surgeons nationally and 28 other cleft professionals from the UK South West Tri-centre units), scored 25 standardized photographs, uploaded randomly onto a Web-based platform, twice. Each photograph was shown in three forms: lip and nose together, and separately cropped images of nose only and lip only. The same images were analyzed using the SymNose software program.

Results:
Scoring lips gave the best intrarater and interrater reliabilities. Nose scores were more variable. Lip scoring associated most closely with the whole-image score. SymNose ranking of the lip images related highly to the same ranking by humans (p = 0.001). The exemplar images maintained their established previous ranking.

Conclusions:
Images illustrating the aesthetic outcome grades are confirmed. The lip score is reliable and seems to dominate in the whole-image score. Noses are much harder to score reliably. It appears that SymNose can score lip images very effectively by symmetry. Further use of SymNose will be investigated, and families of children with cleft will trial the scoring system.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)
Authors: Glenn Travis C. , Nilsen Roger A. , Kieran Troy J. , Sanders Jon G. , Bayona-Vásquez Natalia J. , Finger John W. , Pierson Todd W. , Bentley Kerin E. , Hoffberg Sandra L. , Louha Swarnali , García-De León Francisco J. , Del Río-Portilla Miguel Angel , Reed Kurt D. , Anderson Jennifer L. , Meece Jennifer K. , Aggrey Samuel E. , Rekaya Romdhane , Alabady Magdy , Bélanger Myriam , Winker Kevin , Faircloth Brant C. 
Published: June 2016

AbstractNext-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing NGS for the first time); 2) buy-in (i.e., getting the smallest possible amount of data from a run); and 3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 × 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: 1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and 2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequentAdapteramapapers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms.
Estimating the efficacy of transcranial magnetic stimulation in small animals
Authors: Koponen Lari M. , Nieminen Jaakko O. , Ilmoniemi Risto J. 
Published: June 2016

AbstractThe efficacy of transcranial magnetic stimulation (TMS) is determined by the magnitude and direction of the induced electric field in the cortex. The electric field distribution is influenced by the conductivity structure, in particular, the size of the head and the shapes of conductivity boundaries. We show that neglecting the head size can result in overestimating the stimulus intensity by a factor of 5–8 in the case of the rat brain. In the current modelling literature, the TMS-induced electric field is estimated with detailed computational simulations; however, in many experimental studies, less attention is paid on modelling. We attempt to bridge this gap by suggesting the use of simple simulations, for example with the spherical head model, when studying bioelectromagnetic phenomena.
Exploring the genetic architecture of inflammatory bowel disease by whole genome sequencing identifies association atADCY7
Authors: Luo Yang , de Lange Katrina M. , Jostins Luke , Moutsianas Loukas , Randall Joshua , Kennedy Nicholas A. , Lamb Christopher A. , McCarthy Shane , Ahmad Tariq , Edwards Cathryn , Serra Eva Goncalves , Hart Ailsa , Hawkey Chris , Mansfield John C. , Mowat Craig , Newman William G. , Nichols Sam , Pollard Martin , Satsangi Jack , Simmons Alison , Tremelling Mark , Uhlig Holm , Wilson David C. , Lee James C. , Prescott Natalie J. , Lees Charlie W. , Mathew Christopher G. , Parkes Miles , Barrett Jeffrey C. , Anderson Carl A. 
Published: June 2016

AbstractIn order to further resolve the genetic architecture of the inflammatory bowel diseases, ulcerative colitis and Crohn’s disease, we sequenced the whole genomes of 4,280 patients at low coverage, and compared them to 3,652 previously sequenced population controls across 73.5 million variants. To increase power we imputed from these sequences into new and existing GWAS cohorts, and tested for association at ~12 million variants in a total of 16,432 cases and 18,843 controls. We discovered a 0.6% frequency missense variant inADCY7that doubles risk of ulcerative colitis, and offers insight into a new aspect of disease biology. Despite good statistical power, we did not identify any other new low-frequency risk variants, and found that such variants as a class explained little heritability. We did detect a burden of very rare, damaging missense variants in known Crohn’s disease risk genes, suggesting that more comprehensive sequencing studies will continue to improve our understanding of the biology of complex diseases.
An ancient fecundability-associated polymorphism switches a repressor into an enhancer of endometrialTAP2Expression
Authors: Mika Katelyn M. , Lynch Vincent J. 
Published: June 2016

AbstractVariation in female reproductive traits such as fertility, fecundity, and fecundability are heritable in humans, but identifying and functionally characterizing genetic variants associated with these traits has been challenging. Here we explore the functional significance and evolutionary history of a C/T polymorphism of SNP rs2071473, which we have previously shown is an eQTL forTAP2and significantly associated with fecundability (time to pregnancy). We replicated the association between rs2071473 genotype andTAP2expression using GTEx data and demonstrate thatTAP2is expressed by decidual stromal cells at the maternal-fetal interface. Next, we show that rs2071473 is located within a progesterone responsive cis-regulatory element that functions as a repressor with the T allele and an enhancer with the C allele. Remarkably, we found this polymorphism arose before the divergence of modern and archaic humans, is segregating at intermediate to high frequencies across human populations, and has genetic signatures of long-term balancing selection. This variant has also previously been identified in GWA studies of immune related disease, suggesting both alleles are maintained due to antagonistic pleiotropy.Author SummaryFemale reproductive traits such as fertility and the time it takes to become pregnant are heritable. Many factors, including widespread contraceptive use and environmental influences, make identifying the genetic differences between individuals that are responsible for fertility differences between women difficult. We previously identified a common single nucleotide polymorphism that affects the expression of the geneTAP2and is significantly associated with how long it takes woman to become pregnant. Here we show thatTAP2is expressed at the maternal-fetal interface in the uterus during pregnancy. We then show that the T version of the polymorphism functions to repressTAP2expression whereas the C form enhancesTAP2expression. Remarkably, the C variant arose before the divergence of Neanderthals and modern humans and has become common in all human populations. This derived variant has previously associated with immune related diseases, suggesting the ancestral T and derived C variants are being maintained because they affect multiple traits.
ANFIS-based fuzzy systems for searching dna-protein binding sites
Authors: Wang Dianhui , Alhamdoosh Monther , Pedrycz Witold 
Published: June 2016

AbstractTranscriptional regulation mainly controls how genes are expressed and how cells behave based on the transcription factor (TF) proteins that bind upstream of the transcription start sites (TSSs) of genes. These TF DNA binding sites (TFBSs) are usually short (5-15 base pairs) and degenerate (some positions can have multiple possible alternatives). Traditionally, computational methods scan DNA sequences using the position weight matrix (PWM) of a given TF, calculate binding scores for each K-mer against the PWM, and finally classify a K-mer as to whether it is a putative TFBS or a background sequence based on a cut-off threshold. The FSCAN system, which is proposed in this paper, employs machine learning techniques to build a learner model that is able to identify TFBSs in a set of bound sequences without the need for a cut-off threshold. Our proposed method utilizes fuzzy inference techniques along with a distribution-based filtering algorithm to predict the binding sites of a TF given its PWM model and phastCons scores for the input DNA sequences. Data imbalance reduction techniques are also used to ease the learning of the adaptive-neuro fuzzy inference system (ANFIS) algorithm. The proposed system is tested on 22 ChIP-chip sequence-sets from the Saccharomyces Cerevisiae genome. Our results show that FSCAN outperforms other approaches like MatInspector and MATCH and is quite robust. As more transcriptional data becomes available, our proposed framework encourages the use of fuzzy logic techniques in the prediction of TFBSs.
Programmed cell death can increase the efficacy of microbial bet-hedging
Authors: Libby Eric , Driscoll William W. , Ratcliff William C. 
Published: June 2016

AbstractProgrammed cell death (PCD) occurs in both unicellular and multicellular organisms. While PCD plays a key role in the development and maintenance of multicellular organisms, explaining why single-celled organisms would evolve to actively commit suicide has been far more challenging. Here, we explore the potential for PCD to act as an accessory to microbial bet-hedging strategies that utilize stochastic phenotype switching. We consider organisms that face unpredictable and recurring disasters, in which fitness depends on effective phenotypic diversification. We show that when reproductive opportunities are limited by carrying capacity, PCD drives population turnover, providing increased opportunities for phenotypic diversification through stochastic phenotype switching. The main cost of PCD, providing resources for growth to a PCD(-) competitor, is ameliorated by genetic assortment driven by population spatial structure. Using three dimensional agent based simulations, we explore how basic demographic factors, namely cell death and clonal reproduction, can create populations with sufficient spatial structure to favor the evolution of high PCD rates.
Population Structure Analysis of Globally Diverse Bull Genomes
Authors: Chung Neo Christopher , Szyda Joanna , Fra̧szczak Magdalena ,   the 1000 Bull Genomes Project
Published: June 2016

AbstractSince domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics ofBos taurus. In turn, characterization of population structure among globally diverse bull genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the global bull population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. We identified a highly complex population structure that defies the conventional hypothesis based on discrete membership and contributes to pervasive genetic differentiation in bull genomes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our comprehensive analysis of bull population structure can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth.
3D-Printed Autonomous Capillaric Circuits†
Authors: Olanrewaju A. O. , Robillard A. , Dagher M. , Juncker D. 
Published: June 2016

AbstractCapillaric circuits (CCs) are advanced capillary microfluidic devices that move liquids in complex pre-programmed sequences without external pumps and valves-relying instead on microfluidic control elements powered by capillary forces. CCs were thought to require high-precision micro-scale features manufactured by photolithography in a cleanroom, which is slow and expensive. Here we present rapidly and inexpensively 3D-printed autonomous CCs. Molds for CCs were fabricated with a benchtop 3D-printer, Poly(dimethylsiloxane) replicas were made, and fluidic functionality was verified with aqueous solutions. We established design rules for 3D-printed CCs by a combination of modelling and experimentation. The functionality and reliability of 3D-printed trigger valves-an essential fluidic element that stops one liquid until flow is triggered by a second liquid-was tested for different geometries and different solutions. Trigger valves with geometries up to 80-fold larger than cleanroom-fabricated ones were found to function reliably. We designed 3D-printed retention burst valves that encode sequential liquid drainage and delivery using capillary pressure differences encoded by varying valve height and width. Using an electrical circuit analogue of the CC, we established circuit design rules for ensuring strictly sequential liquid delivery. We realized a 3D-printed CC with reservoir volumes 60 times larger than cleanroom-fabricated circuits and autonomously delivered eight liquids in a pre-determined sequence in < 7 min, exceeding the number of sequentially-encoded, self-regulated fluidic delivery events apreviously reported. Taken together, our results demonstrate that 3D-printing enables rapid prototyping of reliable CCs with improved functionality and potential applications in diagnostics, research and education.
The Evolutionary Trade-off between Stem Cell Niche Size, Aging, and Tumorigenesis
Authors: Cannataro Vincent L. , McKinley Scott A. , St. Mary Colette M. 
Published: June 2016

AbstractMany epithelial tissues within large multicellular organisms are continually replenished by small independent populations of stem cells. These stem cells divide within their niches and differentiate into the constituent cell types of the tissue, and are largely responsible for maintaining tissue homeostasis. Mutations can accumulate in stem cell niches and change the rate of stem cell division and differentiation, contributing to both aging and tumorigenesis. Here, we create a mathematical model of the intestinal stem cell niche, crypt system, and epithelium. We calculate the expected effect of fixed mutations in stem cell niches and their expected effect on tissue homeostasis throughout the intestinal epithelium over the lifetime of an organism. We find that, due to the small population size of stem cell niches, fixed mutations are expected to accumulate via genetic drift and decrease stem cell fitness, leading to niche and tissue attrition, and contributing to organismal aging. We also explore mutation accumulation at various stem cell niche sizes, and demonstrate that an evolutionary trade-off exists between niche size, tissue aging, and the risk of tumorigenesis; where niches exist at a size that minimizes the probability of tumorigenesis, at the expense of accumulating deleterious mutations due to genetic drift. Finally, we show that the probability of tumorigenesis and the extent of aging trade-off differently depending on whether mutational effects confer a selective advantage, or not, in the stem cell niche.
The relationship between dynamic capabilities and firm competitive advantage
Authors: Jurksiene Lolita , Pundziene Asta 
Published: June 2016

PurposeDynamic capabilities and organizational ambidexterity are closely related concepts. Unfortunately, there is still a lack of understanding about the relation between the two. This paper aims to offer a theoretical explanation of the relationship between dynamic capabilities, organizational ambidexterity and firm competitive advantage. The authors find that organizational ambidexterity may be considered as a mediator in the relationship between dynamic capabilities and firm competitive advantage. Therefore, this paper contributes theoretically to the authors’ understanding of the relationship between organizational ambidexterity and dynamic capabilities with regard to firm competitive advantage.Design/methodology/approachIn this conceptual paper, the review of research literature on dynamic capabilities and organizational ambidexterity is presented. Theoretical analysis is followed by theoretical prepositions that should be subsequently tested empirically.FindingsBy considering dynamic capabilities and organizational ambidexterity related to competitive advantage, this paper provides a new perspective on concepts’ relationship. The theoretical findings described in this paper suggest that organizational ambidexterity plays a mediating role in the relationship between dynamic capabilities and firm competitive advantage.Research limitations/implicationsFurther research are required to develop organizational ambidexterity and dynamic capabilities theories, focusing more on the relation to competitive advantage. Additional testing is necessary to empirically validate the propositions given in this paper.Originality/valueBased on theoretical findings, this paper clarifies the relationship between dynamic capabilities and organizational ambidexterity concepts. Theoretical findings described in this paper also determine the guidelines for further theoretical and empirical research within the fields.