bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raised without antibiotics: impact on animal welfare and implications for food policy
Authors: Karavolias Joanna , Salois Matthew Jude , Baker Kristi T , Watkins Kevin 
Published: August 2018

Abstract
This study assesses the impact of broilers raised without antibiotics and the information gap that exists between consumer perception and production methods. Specifically looking at risk of eye burns, footpad lesions, and airsacculitis, key indicators of animal welfare, bird-level data are collected on the occurrence and severity of each disease state by the type of antibiotic program: no antibiotics ever, nonmedically important antibiotics, or medically important antibiotics. Odds ratios and marginal effects are calculated to understand how the occurrence and severity change with access to medicine. Broilers never given antibiotics had a higher likelihood of disease states investigated, and with greater severity. In some cases, access to nonmedically important ionophores mitigated the risk of occurrence and severity of the conditions. The finding indicates that the growing trend of raising broilers without antibiotics may negatively affect animal welfare. This stands in contrast to existing consumer research showing that consumers purchase poultry raised without antibiotics because they believe that it promotes healthier animals. Therefore, a significant consumer information gap exists which needs to be addressed. JEL Codes: Q130, Q160, Q180
Endothelin‐1 differentially directs lineage specification of adipose‐ and bone marrow–derived mesenchymal stem cells
Authors: Lee Ming-Song , Wang Jesse , Yuan Huihua , Jiao Hongli , Tsai Tsung-Lin , Squire Matthew W. , Li Wan-Ju 
Published: August 2018

ABSTRACTBlood vessels composed of endothelial cells (ECs) contact with mesenchymal stem cells (MSCs) in different tissues, suggesting possible interaction between these 2 types of cells. We hypothesized that endothelin‐1 (ET1), a secreted paracrine factor of ECs, can differentially direct the lineages of adipose‐derived stem cells (ASCs) and bone marrow–derived MSCs (BMSCs). Predifferentiated ASCs and BMSCs were treated with ET1 for 2 cell passages and then induced for multilineage differentiation. Our results showed that adipogenesis of ET1‐pretreated ASCs and osteogenesis of ET1‐pretreated BMSCs were increased compared to those of control cells. The effect of ET1 on enhancing adipogenesis of ASCs and osteogenesis of BMSCs was attenuated by blocking endothelin receptor type A (ETAR) and/or endothelin receptor type B (ETBR). Western blot analysis indicated that regulation by ET1 was mediated through activation of the protein kinase B and ERK1/2 signaling pathways. We analyzed subpopulations of ASCs and BMSCs with or without ETAR and/or ETBR, and we found that ETAR+/ETBR− and ETAR−/ETBR+ subpopulations of ASCs and those of BMSCs pretreated with ET1 were prone to turning into adipocytes and osteoblasts, respectively, after differentiation induction. Our findings provide insight into the differential regulation of MSC specification by ET1, which may help develop viable approaches for tissue regeneration.—Lee, M.‐S., Wang, J., Yuan, H., Jiao, H., Tsai, T.‐L., Squire, M. W., Li, W.‐J. Endothelin‐1 differentially directs lineage specification of adipose‐ and bone marrow–derived mesenchymal stem cells. FASEB J. 33, 996–1007 (2019). www.fasebj.org
Innovative PhD-DNP Faculty Collaboration to Advance Baccalaureate Student Population Health Competencies
Authors: Mauro Ann Marie P. , Tracey Debora L. , LoGrippo Maria Torchia , Brienza-Arcilla Diane , Williams-Gregory Mona , Shugg Suzanne , Bravo Angelica , Byrne Claire 
Published: August 2018

Abstract
Entry-level nurses require health promotion, chronic disease self-management, care coordination, data utilization, and evidence translation competencies to address complex population health needs. An innovative PhD-DNP faculty collaboration implemented a descriptive survey design to evaluate simulation-based strategies using an unfolding chronically ill adult case to address population health. Results showed the PhD-DNP faculty team was effective in developing clinically meaningful learning experiences to assist baccalaureate students to develop population health competencies. This project provides strong evidence supporting the value and positive impact of engaging faculty from research and practice for future educational research.
An Enhanced Actualized DNP Model to Improve DNP Project Placements, Rigor, and Completion
Authors: VanderKooi Marie E. , Conrad Dianne M. , Spoelstra Sandra L. 
Published: August 2018

Abstract
Doctor of nursing practice (DNP) projects are summative evaluations of enactment of the DNP Essentials. However, information about structure, process, and outcomes of DNP projects is scarce. Guided by an enhanced actualized DNP model, this study tested the effect of a PhD-DNP-site mentor model to guide DNP projects. Time-to-complete assignments, defense, and graduation improved; high satisfaction for students, mentors, and faculty were found; and a strengthened academic-practice partnership occurred, leading to additional student placements. Broader testing of the enhanced model in various size and types of academic-practice settings is needed prior to use.
Constructive Feedback Teaching Strategy
Authors: Altmiller Gerry , Deal Belinda , Ebersole Nancy , Flexner Randi , Jordan Janet , Jowell Vicki , Norris Tommie , Risetter Mary Jo , Schuler Monika , Szymanski Kathleen , Vottero Beth , Walker Danielle 
Published: August 2018

Abstract

AIM
The study purpose was to describe students’ perceptions of feedback after participating in a teaching strategy designed to foster a view of feedback as an opportunity for improvement.

BACKGROUND
Although delivering and receiving constructive feedback are essential to the role of the professional nurse, feedback has been identified as a trigger for incivility in academia and practice.

METHOD
Twelve nurse educators from the Quality and Safety Education for Nurses Academic Task Force, located at nine schools of nursing across the nation, implemented a presentation about giving and receiving constructive feedback in junior and senior courses.

RESULTS
Five hundred twenty-three students submitted a total of 985 posts or essays in response to viewing the presentation; seven themes were identified.

CONCLUSION
Viewing this teaching strategy enabled nursing students to develop an awareness of the opportunity that constructive feedback presents for professional development, self-improvement, teamwork and collaboration, and patient safety.
Congenital Tuberculosis
Authors: Newberry Desi M. , Robertson Bell Tracey 
Published: August 2018

Background:
Congenital tuberculosis (TB) is rare in the United States. Recent immigration patterns to the United States have made the diagnosis of congenital TB an important public health issue.

Purpose:
To explore the epidemiology, pathophysiology, diagnostic evaluation, treatment, and prognosis for congenital TB. The implications for exposed healthcare professionals in the neonatal intensive care unit (NICU) setting are also explored.

Methods/Search Strategy:
Relevant articles were accessed via PubMed, CINAHL, and Google Scholar.

Findings/Results:
Until 1994, fewer than 400 cases of confirmed congenital TB had been reported in the literature worldwide. An additional 18 cases were reported from 2001 to 2005. Neonatal providers need to be aware of the potential for congenital TB infection as the immigrant population in the United States continues to increase, many of whom originate from TB endemic countries.

Implications for Practice:
The interpretation of TB-specific tests is problematic in newborns due to decreased sensitivity and specificity. Congenital TB should be ruled out in infants with signs and symptoms of sepsis or pneumonia and in whom broad-spectrum antibiotic therapy does not improve their clinical status.

Implications for Research:
The interpretation of TB-specific tests is problematic in newborns due to decreased sensitivity and specificity; more research is needed regarding best practice in diagnosis. Established protocols are needed to address the healthcare of TB-exposed providers in the NICU.
Case Fatality and Adverse Outcomes Are Reduced in Pregnant Women With Severe Sepsis or Septic Shock Compared With Age-Matched Comorbid-Matched Nonpregnant Women
Authors: Kidson Kristen M. , Henderson William R. , Hutcheon Jennifer A. 
Published: August 2018

Objectives:
Case fatality in pregnancy-associated severe sepsis or septic shock appears reduced compared with nonpregnant women with severe sepsis or septic shock. It remains unclear if this difference is due to pregnancy or better baseline health status, among others. Our study compared adverse outcomes of pregnancy-associated severe sepsis or septic shock with nonpregnant women with severe sepsis or septic shock while controlling for age and chronic comorbidities.

Design:
Retrospective cohort study.

Setting:
Nationwide Inpatient Sample, a stratified sample of 20% acute care hospital admissions in the United States. Each entry includes patient and hospital characteristics as well as International Classification of Diseases, 9th revision, Clinical Modification, diagnoses and procedures.

Subjects:
Women of childbearing age (15–44 yr) with severe sepsis or septic shock–related hospitalizations during 1998–2012 identified using International Classification of Diseases, 9th revision, Clinical Modification, codes.

Outcomes:
Case fatality, hospital length of stay, length of stay until death, number of organ failures, rates of mechanical ventilation, and hemodialysis were compared in women according to pregnancy status, controlling for age, and chronic comorbidities.

Measurements and Main Results:
We identified 5,968 pregnancy-associated severe sepsis or septic shock and 85,240 nonpregnant women with severe sepsis or septic shock hospitalizations. Crude case fatality of pregnancy-associated severe sepsis or septic shock (9.6%) was lower than nonpregnant women with severe sepsis or septic shock (16.8%). The rate ratio for case fatality adjusted for socioeconomic status and race was 0.57 (95% CI, 0.52–0.62) while sequential adjustments for age and chronic comorbidities did not eliminate the association (rate ratio, 0.62 [95% CI, 0.57–0.68]) and 0.63 [95% CI, 0.57–0.68], respectively). Pregnancy-associated severe sepsis or septic shock was associated with shorter hospital length of stay (–0.83 d [95% CI, –1.32 to –0.34 d]), longer length of stay until death (2.61 d; [95% CI, 1.28–3.94 d]), and fewer organ failures (rate ratio, 0.95 [95% CI, 0.94–0.97]).

Conclusions:
Case fatality and adverse outcomes are reduced in women with pregnancy-associated severe sepsis or septic shock compared with nonpregnant women with severe sepsis or septic shock, and this is not explained by differences in age or chronic comorbidities alone. A less severe presentation of sepsis or protective effect of pregnancy may account for the difference observed with pregnancy-associated severe sepsis or septic shock.
Increased Fibrinolysis as a Specific Marker of Poor Outcome After Cardiac Arrest
Authors: Buchtele Nina , Schörgenhofer Christian , Spiel Alexander O. , Jilma Bernd , Schwameis Michael 
Published: August 2018

Objectives:
Recent data suggest that early increased fibrinolysis may be associated with unfavorable prognosis in cardiac arrest. The current study aimed to assess whether there is an optimal fibrinolysis cutoff value as determined by thrombelastometry at hospital admission to predict poor outcome in a cohort of adult patients with out-of-hospital cardiac arrest.

Design:
Prospective observational cohort study.

Setting:
Emergency department of a 2.100-bed tertiary care facility in Vienna, Austria, Europe.

Patients:
Patients with out-of-hospital cardiac arrest of presumed cardiac origin, subjected to targeted temperature management, who had achieved return of spontaneous circulation at admission were analyzed.

Interventions:
None.

Measurements and Main Results:
Fibrinolysis was assessed by thrombelastometry at the bedside immediately after hospital admission and is given as maximum lysis (%). The outcome measure was the optimal cutoff for maximum lysis at hospital admission to predict poor outcome (a composite of Cerebral Performance Category 3–5 or death) at day 30, assessed by receiver operating characteristic curve analysis. Seventy-eight patients (61% male, median 59 yr) were included in the study from March 2014 to March 2017. Forty-two patients (54%) had a poor 30-day outcome including 23 nonsurvivors (30%). The maximum lysis cutoff at admission predicting poor 30-day outcome with 100% specificity (95% CI, 90–100%) was greater than or equal to 20%. Tissue-type plasminogen activator antigen levels were likewise elevated in patients with poor neurologic outcome or death 52 ng/mL (interquartile range, 26–79 ng/mL) versus 29 ng/mL (interquartile range, 17–49 ng/mL; p = 0.036).

Conclusions:
Increased fibrinolysis at admission assessed by thrombelastometry specifically predicts poor outcome in cardiac arrest with presumed cardiac etiology.
Which Early Childhood Experiences and Skills Predict Kindergarten Working Memory?
Authors: Wang Aubrey H. , Fitzpatrick Caroline 
Published: August 2018

ABSTRACT:

Objective:
We examined how empirically and theoretically important predictors help explain the development of kindergarten working memory, an understudied predictor of school readiness and adjustment to schooling in early childhood. Our specific aim was to examine the extent to which antecedents, opportunity, and propensity variables directly and indirectly predict working memory development.

Methods:
We conducted structural equation modeling on a nationally representative and longitudinal sample of 14,000 kindergarten students. Predictors of end-of-kindergarten working memory include parent reports of antecedent variables such as socioeconomic status, mother's marital status, breastfeeding, child's age, and perception of child learning skills; teacher reports of opportunity variables including the frequency children read aloud and counted in their kindergarten class and classroom climate; and direct assessments of child propensity variables including earlier working memory, cognitive fluidity, teacher reports of child self-regulation, and math and reading knowledge.

Results:
Together, childhood antecedents, opportunity, and propensity latent factors contributed to 41% of the variance of kindergarten working memory. Child propensity had a significant direct effect on child working memory, whereas antecedent and opportunity factors had significant indirect effects on working memory through child propensity.

Conclusion:
In this study, we identify several modifiable variables that directly and indirectly predict child working memory skills using a large population-based sample. Better understanding of how child-, family-, and school-level variables contribute to the development of working memory in young children can be seen as an important step in the creation of preventive interventions designed to improve these important skills.
Enhancing and Advancing Shared Governance Through a Targeted Decision-Making Redesign
Authors: Dechairo-Marino Ann E. , Collins Raggi Mara E. , Mendelson Sherri Garber , Highfield Martha E.F. , Hess Robert G. 
Published: August 2018

OBJECTIVE
The study aim was to determine if a targeted redesign of shared decision making improved shared governance (SG).

BACKGROUND
Nursing SG is collaborative decision making between nurses at every level; it improves quality of care, empowers nurses, and enhances nurse satisfaction.

METHODS
Using a quasi-experimental, pretest/posttest design, researchers electronically distributed the Index of Professional Nursing Governance (IPNG) to an inclusive, convenience sample of RNs in a Magnet®-designated 377-bed community medical center. Preintervention scores were used to tailor a redesign of shared decision making, and postintervention data were collected within 1 year to measure outcomes.

RESULTS
IPNG overall score and 5 of 6 subscale scores significantly increased after the redesign.

CONCLUSIONS
Changes to an SG structure can take 2 to 5 years to be realized. Our findings corroborate that the IPNG is a valuable tool in promoting setting-specific SG.
Target-specific precision of CRISPR-mediated genome editing
Authors: Chakrabarti Anob M. , Henser-Brownhill Tristan , Monserrat Josep , Poetsch Anna R. , Luscombe Nicholas M. , Scaffidi Paola 
Published: August 2018

ABSTRACTThe CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict editing accuracy, efficacy and outcome at specific sites is limited by an incomplete understanding of how the bacterial system interacts with eukaryotic genomes and DNA repair machineries. Here, we performed the largest comparison of indel profiles to date, examining over one thousand sites in the genome of human cells, and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing varies considerably among sites, with some targets showing one highly-preferred indel and others displaying a wide range of infrequent indels. Editing precision correlates with editing efficiency, homology-associated end-joining for both insertions and deletions, and a preference for single-nucleotide insertions. Precise targets and the identity of their preferred indel can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the PAM sequence. Regardless of precision, site-specific indel profiles are highly robust and depend on both DNA sequence and chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal general patterns of broken end-joining that can inform us on DNA repair mechanisms in human cells.
The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation
Authors: Anselmi Massimiliano , Hub Jochen S. 
Published: August 2018

The Src homology-2 domain containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as the key “allosteric switch” driving SHP2 activation. To test the putative coupling between binding cleft opening and SHP2 activation as assumed by the “allosteric switch” model, we critically reviewed structural data of SHP2 and we used extensive molecular dynamics (MD) simulation and free energy calculations of isolated N-SH2 in solution, SHP2 in solution, and SHP2 in a crystal environment. Our results demonstrate that the binding cleft in N-SH2 is constitutively flexible and open in solution, and that a closed cleft found in certain structures is a consequence of crystal contacts. The degree of opening of the binding cleft has only a negligible effect on the free energy of SHP2 activation. Instead, SHP2 activation is greatly favored by the opening of the central β- sheet of N-SH2. We conclude that opening of the N-SH2 binding cleft is not the key allosteric switch triggering SHP2 activation.Significance StatementSHP2 is a multi-domain protein, playing an important role in up-regulating cellular processes such as cell survival, proliferation, and programmed cell death. SHP2 mutations cause developmental disorders and were found in many cancer types, including neuroblastoma, breast cancer, and leukemia. In healthy cells, SHP2 mainly takes an autoinhibited, inactive form, and SHP2 is activated upon binding of phosphopeptides to the N-SH2 domain. For the past two decades, the widening of the binding cleft upon peptide binding has been considered as the key event driving SHP2 activation. Here, by analyzing crystallographic data and molecular simulations, we demonstrate that the binding cleft in N-SH2 is, instead, already open and accessible in solution, and its degree of opening does not influence SHP2 activation.
deGSM: memory scalable construction of large scale de Bruijn Graph
Authors: Guo Hongzhe , Fu Yilei , Gao Yan , Li Junyi , Wang Yadong , Liu Bo 
Published: August 2018

AbstractMotivationDe Bruijn graph, a fundamental data structure to represent and organize genome sequence, plays important roles in various kinds of sequence analysis tasks such as de novo assembly, high-throughput sequencing (HTS) read alignment, pan-genome analysis, metagenomics analysis, HTS read correction, etc. With the rapid development of HTS data and ever-increasing number of assembled genomes, there is a high demand to construct de Bruijn graph for sequences up to Tera-base-pair level. It is non-trivial since the size of the graph to be constructed could be very large and each graph consists of hundreds of billions of vertices and edges. Current existing approaches may have unaffordable memory footprints to handle such a large de Bruijn graph. Moreover, it also requires the construction approach to handle very large dataset efficiently, even if in a relatively small RAM space.ResultsWe propose a lightweight parallel de Bruijn graph construction approach, de Bruijn Graph Constructor in Scalable Memory (deGSM). The main idea of deGSM is to efficiently construct the Bur-rows-Wheeler Transformation (BWT) of the unipaths of de Bruijn graph in constant RAM space and transform the BWT into the original unitigs. It is mainly implemented by a fast parallel external sorting of k-mers, which allows only a part of k-mers kept in RAM by a novel organization of the k-mers. The experimental results demonstrate that, just with a commonly used machine, deGSM is able to handle very large genome sequence(s), e.g., the contigs (305 Gbp) and scaffolds (1.1 Tbp) recorded in Gen-Bank database and Picea abies HTS dataset (9.7 Tbp). Moreover, deGSM also has faster or comparable construction speed compared with state-of-the-art approaches. With its high scalability and efficiency, deGSM has enormous potentials in many large scale genomics studies.Availabilityhttps://github.com/hitbc/deGSM.Contactydwang@hit.edu.cn(YW) andbo.liu@hit.edu.cn(BL)Supplementary informationSupplementary data are available online.
PCH-2TRIP13regulates spindle checkpoint strength
Authors: Défachelles Lénaïg , Russo Anna E. , Nelson Christian R. , Bhalla Needhi 
Published: August 2018

ABSTRACTSpindle checkpoint strength is dictated by three criteria: the number of unattached kinetochores, cell volume and cell fate. We show that the conserved AAA-ATPase, PCH-2/TRIP13, which remodels the checkpoint effector Mad2 from an active conformation to an inactive one, controls checkpoint strength inC. elegans. When we manipulate embryos to decrease cell volume, PCH-2 is no longer required for the spindle checkpoint or recruitment of Mad2 at unattached kinetochores. This role in checkpoint strength is not limited to large cells: the stronger checkpoint in germline precursor cells also depends on PCH-2. PCH-2 is enriched in germline precursor cells and this enrichment relies on conserved factors that induce asymmetry in the early embryo. Finally, the stronger checkpoint in germline precursor cells is regulated by CMT-1, the ortholog of p31comet, which is required for both PCH-2’s localization to unattached kinetochores and its enrichment in germline precursor cells. Thus, PCH-2, likely by regulating the availability of inactive Mad2 at and near unattached kinetochores, governs checkpoint strength. This role may be specifically relevant in scenarios where maintaining genomic stability is particularly challenging, such as in oocytes and early embryos enlarged for developmental competence and germline cells that maintain immortality.