bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serbian primary care physicians’ perspectives on adolescents’ right to confidentiality in sexual and reproductive healthcare—a qualitative interview study
Authors: Jeremic Stojkovic Vida , Matejic Bojana , Turza Karel 
Published: June 2018

Abstract

Background
In prominent international documents and professional position papers, confidentiality was recognized as a necessary condition for effective reproductive healthcare of adolescents. Although legally guaranteed, it is questionable if the right to confidentiality of adolescents is respected in healthcare practice in Serbia.

Objectives
To assess primary care physicians’ perspectives on the legal right of minors to confidentiality in sexual and reproductive healthcare, as well as their experiences in practice.

Methods
Qualitative, semi-structured face-to-face interviews with 12 primary care pediatricians and gynecologists at several municipalities of the city of Belgrade were performed. Interview transcripts were analyzed using qualitative content analysis method.

Results
Most interviewees were aware of their legal obligations and support the general idea of granting adolescents the right to confidentiality. They recognized that the lack of confidentiality assurances prevents adolescents’ access to sensitive care. However, physicians expressed concerns regarding medical situations when parents should be notified, which was reflected in their inconsistent respect of said right in actual practice. Several organizational obstacles were emphasized by interviewees, including insufficient number of physicians, time constraints, poor access to gynecological services and vague definitions of legal provisions.

Conclusion
If the aim is for adolescents’ right to confidentiality to be consistently respected in practice, primary care physicians need to be systematically educated about legal provisions and given comprehensive clinical guidelines. The general positive attitude towards confidentiality expressed by the primary care physicians implies that a possibility exists to engage them as main advocates for improvements in access to the necessary health care.
A workflow for simplified analysis of ATAC-cap-seq data in R
Authors: Shrestha Ram Krishna , Ding Pingtao , Jones Jonathan D G , MacLean Dan 
Published: June 2018

Abstract

Background
Assay for Transposase-Accessible Chromatin (ATAC)-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragments. There are increased analytical difficulties arising from working with a set of regions of interest that may be small in number and biologically dependent. Common statistical pipelines for RNA sequencing might be assumed to apply but can give misleading results on ATAC-cap-seq data. A tool is needed to allow a nonspecialist user to quickly and easily summarize data and apply sensible and effective normalization and analysis.

Results
We developed atacR to allow a user to easily analyze their ATAC enrichment experiment. It provides comprehensive summary functions and diagnostic plots for studying enriched tag abundance. Application of between-sample normalization is made straightforward. Functions for normalizing based on user-defined control regions, whole library size, and regions selected from the least variable regions in a dataset are provided. Three methods for detecting differential abundance of tags from enriched methods are provided, including bootstrap t, Bayes factor, and a wrapped version of the standard exact test in the edgeR package. We compared the precision, recall, and F-score of each detection method on resampled datasets at varying replicate, significance threshold, and genes changed and found that the Bayes factor method had the greatest overall detection power, though edgeR was slightly stronger in simulations with lower numbers of genes changed.

Conclusions
Our package allows a nonspecialist user to easily and effectively apply methods appropriate to the analysis of ATAC-cap-seq in a reproducible manner. The package is implemented in pure R and is fully interoperable with common workflows in Bioconductor.
Adiabatic exponential midpoint rule for the dispersion-managed nonlinear Schrödinger equation
Authors: Jahnke T , Mikl M 
Published: June 2018

Abstract
Modeling long-haul data transmission through dispersion-managed optical fiber cables leads to a nonlinear Schrödinger equation where the linear part is multiplied by a large, discontinuous and rapidly changing coefficient function. Typical solutions oscillate with high frequency and have low regularity in time, such that traditional numerical methods suffer from severe step size restrictions and typically converge only with low order. We construct and analyse a norm-conserving, uniformly convergent time-integrator called the adiabatic exponential midpoint rule by extending techniques developed in Jahnke & Mikl (2018, Adiabatic midpoint rule for the dispersion-managed nonlinear Schrödinger equation. Numer. Math., 138, 975–1009). This method is several orders of magnitude more accurate than standard schemes for a relevant set of parameters. In particular, we prove that the accuracy of the method improves considerably if the step size is chosen in a special way.
Course Evaluation Summary: An Enlightening and Useful Documentation Tool for Assessing Learner Outcomes and Developing Plans for Nursing Course Improvement
Authors: Kern Jacqueline 
Published: June 2018

Abstract
The Course Evaluation Summary (CES) is a data collection and analysis tool designed to assess the extent to which course learning outcomes are met by students within a course. Course assignments and assessments are linked to outcomes, allowing for the comparison of target and actual outcomes and the identification of strengths and areas of concern. The CES allows faculty to develop an action plan for course improvement as needed and to document implemented course changes and student concerns. Used every semester, the CES provides a history of continuous course evaluation and course improvement.
Clinical Nurses’ Perceptions of a Senior Capstone Dedicated Educational Unit
Authors: Glynn Donna M. , Wendt Judith , Russell Bonnie , Conley Grace , Hill Patrick 
Published: June 2018

Abstract
Clinical nurses’ perceptions of a senior capstone dedicated educational unit (DEU) model to transition to practice was evaluated in a pilot study. Nursing students were placed in the traditional capstone and the DEU senior capstone unit with clinical nurses. Staff nurses completed an online survey to compare and contrast satisfaction and effectiveness of the models. The results of the study revealed no perceived differences in the outcomes of a DEU experience as compared to the traditional preceptor model. However, nursing management reported an improved sense of leadership and teamwork on the unit with the DEU model.
Peace, Love, Field Day: An Innovative Approach to Cultivating Healthy Academic Communities
Authors: Kaylor Sara K. , Johnson Paige T. 
Published: June 2018

Abstract
The American Nurses Association declared 2017 the Year of the Healthy Nurse. In an effort to promote a healthy academic environment, faculty and staff in institutions of higher learning should serve as role models for healthy living for their students. This article describes an innovative approach to cultivating a healthy academic environment. Details about planning and implementation are provided along with recommendations for future implementation.
Surviving Sepsis Campaign: Research Priorities for Sepsis and Septic Shock
Authors: Coopersmith Craig M. , De Backer Daniel , Deutschman Clifford S. , Ferrer Ricard , Lat Ishaq , Machado Flavia R. , Martin Greg S. , Martin-Loeches Ignacio , Nunnally Mark E. , Antonelli Massimo , Evans Laura E. , Hellman Judith , Jog Sameer , Kesecioglu Jozef , Levy Mitchell M. , Rhodes Andrew 
Published: June 2018

Objective:
To identify research priorities in the management, epidemiology, outcome and underlying causes of sepsis and septic shock.

Design:
A consensus committee of 16 international experts representing the European Society of Intensive Care Medicine and Society of Critical Care Medicine was convened at the annual meetings of both societies. Subgroups had teleconference and electronic-based discussion. The entire committee iteratively developed the entire document and recommendations.

Methods:
Each committee member independently gave their top five priorities for sepsis research. A total of 88 suggestions (Supplemental Table 1, Supplemental Digital Content 2, http://links.lww.com/CCM/D636) were grouped into categories by the committee co-chairs, leading to the formation of seven subgroups: infection, fluids and vasoactive agents, adjunctive therapy, administration/epidemiology, scoring/identification, post-intensive care unit, and basic/translational science. Each subgroup had teleconferences to go over each priority followed by formal voting within each subgroup. The entire committee also voted on top priorities across all subgroups except for basic/translational science.

Results:
The Surviving Sepsis Research Committee provides 26 priorities for sepsis and septic shock. Of these, the top six clinical priorities were identified and include the following questions: 1) can targeted/personalized/precision medicine approaches determine which therapies will work for which patients at which times?; 2) what are ideal endpoints for volume resuscitation and how should volume resuscitation be titrated?; 3) should rapid diagnostic tests be implemented in clinical practice?; 4) should empiric antibiotic combination therapy be used in sepsis or septic shock?; 5) what are the predictors of sepsis long-term morbidity and mortality?; and 6) what information identifies organ dysfunction?

Conclusions:
While the Surviving Sepsis Campaign guidelines give multiple recommendations on the treatment of sepsis, significant knowledge gaps remain, both in bedside issues directly applicable to clinicians, as well as understanding the fundamental mechanisms underlying the development and progression of sepsis. The priorities identified represent a roadmap for research in sepsis and septic shock.
Increasing Evidence-Based Interventions in Patients with Acute Infections in a Resource-Limited Setting: A Before-and-After Feasibility Trial in Gitwe, Rwanda
Authors: Urayeneza Olivier , Mujyarugamba Pierre , Rukemba Zacharie , Nyiringabo Vincent , Ntihinyurwa Polyphile , Baelani John I. , Kwizera Arthur , Bagenda Danstan , Mer Mervyn , Musa Ndidiamaka , Hoffman Julia T. , Mudgapalli Ashok , Porter Austin M. , Kissoon Niranjan , Ulmer Hanno , Harmon Lori A. , Farmer Joseph C. , Dünser Martin W. , Patterson Andrew J. 
Published: June 2018

Objective:
To evaluate whether a focused education program and implementation of a treatment bundle increases the rate of early evidence-based interventions in patients with acute infections.

Design:
Single-center, prospective, before-and-after feasibility trial.

Setting:
Emergency department of a sub-Saharan African district hospital.

Patients:
Patients > 28 days of life admitted to the study hospital for an acute infection.

Interventions:
The trial had three phases (each of four months). Interventions took place during the second (educational program followed by implementation of the treatment bundle) and third (provision of resources to implement treatment bundle) phases.

Measurements and Main Results:
Demographic, clinical, and laboratory data were collected at study enrollment; 24, 48, and 72 hours after hospital admission; and at discharge. A total of 1,594 patients were enrolled (pre-intervention, n = 661; intervention I, n = 531; intervention II, n = 402). The rate of early evidence-based interventions per patient during Intervention Phase I was greater than during the pre-intervention phase (74 ± 17 vs. 79 ± 15%, p < 0.001). No difference was detected when data were compared between Intervention Phases I and II (79 ± 15 vs. 80 ± 15%, p = 0.58). No differences in the incidence of blood transfusion (pre-intervention, 6%; intervention I, 7%; intervention II, 7%) or severe adverse events in the first 24 hours (allergic reactions: pre-intervention, 0.2%; intervention I, 0%; intervention II, 0%; respiratory failure: pre-intervention, 2%; intervention I, 2%; intervention II, 2%; acute renal failure: pre-intervention, 2%; intervention I, 2%; intervention II, 1%) were observed.

Conclusions:
Our results indicate that a focused education program and implementation of an infection treatment bundle in clinical practice increased the rate of early evidence-based interventions in patients with acute infections (mostly malaria) admitted to a sub-Saharan African district hospital. Provision of material resources did not further increase this rate. While no safety issues were detected, this could be related to the very low disease severity of the enrolled patient population (www.clinicaltrials.gov: NCT02697513).
Survival of Patients With Vancomycin-Resistant Enterococcus faecium Bacteremia Treated With Conventional or High Doses of Daptomycin or Linezolid Is Associated With the Rate of Bacterial Clearance*
Authors: Chuang Yu-Chung , Lin Hsin-Yi , Chen Pao-Yu , Lin Chi-Ying , Chen Yee-Chun , Wang Jann-Tay , Chang Shan-Chwen 
Published: June 2018

Objectives:
Vancomycin-resistant enterococci are important pathogens for healthcare-associated infections. Although linezolid is bacteriostatic and daptomycin is rapidly bactericidal against vancomycin-resistant enterococci in vitro, it is not clear whether they differ in their effect on bacterial clearance in patients with vancomycin-resistant enterococci bloodstream infections.

Design:
Prospective observational study.

Setting:
Two university hospitals and research laboratory.

Patients:
Patients with vancomycin-resistant enterococci bloodstream infection proven by blood cultures were prospectively enrolled from January 2010 to July 2015.

Interventions:
Sequential blood samples were collected. Real-time quantitative polymerase chain reaction was used to monitor bacterial loads.

Measurements and Main Results:
One hundred eight patients with vancomycin-resistant enterococci bloodstream infection were enrolled. Quantitative polymerase chain reaction assays were performed on 465 blood isolates. We found this method to be closely correlated with colony-forming units and more sensitive than culture. Sixty-three patients (58.3%) received “conventional dose” daptomycin (6–9 mg/kg), 15 (13.9%) received high-dose daptomycin (≥ 9 mg/kg), and 30 (27.8%) were treated with linezolid (600 mg every 12 hr) as sole agents. The initial mean bacterial load was 1.03 log10 copies/mL and unrelated to survival. Survivors had a more rapid early bacterial clearance than nonsurvivors (Δ log10 copies/mL/d; –0.16 vs 0.31; p = 0.02). Multivariable logistic regression showed that a slower early bacterial clearance independently predicted increased mortality (odds ratio, 3.21; 95% CI, 1.03–10.02; p = 0.045). Conventional dose daptomycin was associated with a significantly slower rate of bacterial clearance than high-dose daptomycin (Δ log10 copies/mL/d; –0.04 vs –0.41; p < 0.001) and linezolid (–0.04 vs –0.56; p = 0.043).

Conclusions:
We found that survivors of vancomycin-resistant enterococci bloodstream infection had a significantly more rapid early bacterial clearance by quantitative polymerase chain reaction than nonsurvivors. High-dose daptomycin and linezolid were associated with more rapid bacterial clearance than conventional dose daptomycin. These results support recommendations that conventional dose daptomycin not be used for the treatment of patients with vancomycin-resistant enterococci bloodstream infection.
Microcirculatory Impairment Is Associated With Multiple Organ Dysfunction Following Traumatic Hemorrhagic Shock: The MICROSHOCK Study
Authors: Hutchings Sam D. , Naumann David N. , Hopkins Philip , Mellis Clare , Riozzi Paul , Sartini Stefano , Mamuza Jasna , Harris Tim , Midwinter Mark J. , Wendon Julia 
Published: June 2018

Objectives:
To assess the relationship between microcirculatory perfusion and multiple organ dysfunction syndrome in patients following traumatic hemorrhagic shock.

Design:
Multicenter prospective longitudinal observational study.

Setting:
Three U.K. major trauma centers.

Patients:
Fifty-eight intubated and ventilated patients with traumatic hemorrhagic shock.

Interventions:
Sublingual incident dark field microscopy was performed within 12 hours of ICU admission (D0) and repeated 24 and 48 hours later. Cardiac output was assessed using oesophageal Doppler. Multiple organ dysfunction syndrome was defined as Serial Organ Failure Assessment score greater than or equal to 6 at day 7 post injury.

Measurements and Main Results:
Data from 58 patients were analyzed. Patients had a mean age of 43 ± 19 years, Injury Severity Score of 29 ± 14, and initial lactate of 7.3 ± 6.1 mmol/L and received 6 U (interquartile range, 4–11 U) of packed RBCs during initial resuscitation. Compared with patients without multiple organ dysfunction syndrome at day 7, patients with multiple organ dysfunction syndrome had lower D0 perfused vessel density (11.2 ± 1.8 and 8.6 ± 1.8 mm/mm2; p < 0.01) and microcirculatory flow index (2.8 [2.6–2.9] and 2.6 [2.2–2.8]; p < 0.01) but similar cardiac index (2.5 [± 0.6] and 2.1 [± 0.7] L/min//m2; p = 0.11). Perfused vessel density demonstrated the best discrimination for predicting subsequent multiple organ dysfunction syndrome (area under curve 0.87 [0.76–0.99]) compared with highest recorded lactate (area under curve 0.69 [0.53–0.84]), cardiac index (area under curve 0.66 [0.49–0.83]) and lowest recorded systolic blood pressure (area under curve 0.54 [0.39–0.70]).

Conclusions:
Microcirculatory hypoperfusion immediately following traumatic hemorrhagic shock and resuscitation is associated with increased multiple organ dysfunction syndrome. Microcirculatory variables are better prognostic indicators for the development of multiple organ dysfunction syndrome than more traditional indices. Microcirculatory perfusion is a potential endpoint of resuscitation following traumatic hemorrhagic shock.
Evaluation of Effect of Probiotics on Cytokine Levels in Critically Ill Children With Severe Sepsis: A Double-Blind, Placebo-Controlled Trial*
Authors: Angurana Suresh K. , Bansal Arun , Singhi Sunit , Aggarwal Ritu , Jayashree Muralidharan , Salaria Manila , Mangat Navdeep K. 
Published: June 2018

Objectives:
To evaluate the effect of probiotics on cytokines in children with severe sepsis.

Design:
Randomized, double-blind, placebo-controlled trial.

Setting:
ICU of a tertiary care teaching hospital in North India.

Patients:
Children 3 months to 12 years old with severe sepsis.

Interventions:
Enrolled children were randomized to probiotic (n = 50) and placebo (n = 50) groups. Probiotic group received VSL#3 (Danisco-Dupont USA, Madison, WI) (Lactobacillus paracasei, L. plantarum, L. acidophilus, L. delbrueckii, Bifidobacterium longum, B. infantis, B. breve, Streptococcus salivarius; maltose and silicon dioxide), and placebo group received maltose and silicon dioxide. Dose was 1 sachet twice daily for 7 days. Blood was collected on days 1 and 7 for estimation of interleukin-6, interleukin-12p70, interleukin-17, tumor necrosis factor-α, interleukin-10, and transforming growth factor -β1. “Primary outcome”: Change in cytokine levels in probiotic and placebo groups from day 1 to 7. “Secondary outcomes”: Sequential Organ Failure Assessment score, healthcare-associated infections, ICU stay, and mortality.

Measurements and Main Results:
On day 7, probiotic group had significantly lower levels of proinflammatory cytokines (interleukin-6 [80 vs 186 pg/mL, p = 0.001]; interleukin-12p70 [44 vs 79 pg/mL, p = 0.001]; interleukin-17 [217 vs 293 pg/mL, p = 0.01]; and tumor necrosis factor-α [192 vs 348 pg/mL, p = 0.01]) and higher levels of antiinflammatory cytokines (interleukin-10 [320 vs 240 pg/mL, p = 0.02] and transforming growth factor-β1 [311 vs 221 ng/mL, p = 0.01]) than placebo group. From day 1 to 7, probiotic group showed significant decrease in proinflammatory cytokines (interleukin-6 [196–80 pg/mL, p = 0.001]; interleukin-12p70 [71–44 pg/mL, p = 0.01]; interleukin-17 [258–217 pg/mL, p = 0.01]; and tumor necrosis factor-α [347–192 pg/mL, p = 0.001]) and increase in antiinflammatory cytokines (interleukin-10 [198–320 pg/mL, p = 0.001] and transforming growth factor-β1 [216–311 ng/mL, p = 0.001]) as compared to placebo group. Sequential Organ Failure Assessment score on day 7 was significantly less in probiotic group (1 vs 3). There was a nonsignificant trend toward lower incidence of healthcare-associated infections (14% vs 20%) and duration of ICU stay (6.5 vs 9 d) in probiotic group. Mortality was similar in two groups.

Conclusions:
Probiotics supplementation for 7 days resulted in significant decrease in proinflammatory and increase in antiinflammatory cytokines in children with severe sepsis.
Liquid Biopsies to Monitor Solid Organ Transplant Function: A Review of New Biomarkers
Authors: Verhoeven Jeroen G. H. P. , Boer Karin , Van Schaik Ron H. N. , Manintveld Olivier C. , Huibers Manon M. H. , Baan Carla C. , Hesselink Dennis A. 
Published: June 2018

Abstract:
Despite modern immunosuppressive therapy, allograft rejection remains a major cause of solid organ transplant dysfunction. For clinical care, organ transplant function is routinely monitored by measuring biomarkers that, depending on the organ transplanted, include serum creatinine, N-terminal pro-hormone of brain natriuretic peptide (NT-proBNP), and aspartate aminotransferase. All can be measured easily in clinical chemistry laboratories. The main problem with these biomarkers is that they have a low sensitivity for the detection of allograft damage and are nonspecific for the detection of allograft rejection. To diagnose rejection, histologic examination of grafted tissue is necessary, which requires an invasive biopsy procedure. There is thus an unmet need in transplantation medicine for biomarkers that are specific for rejection, identify graft injury at an early stage, and may eventually overcome the need for a transplant biopsy. Recently, tremendous progress in the field of biomarkers has been made. In this narrative review, the potential of donor-derived cell-free DNA (ddcfDNA), cell-free nucleosomes, and extracellular vesicles to act as next-generation biomarkers for solid organ transplant is discussed. Based on the fact that cell content is released during rejection, these markers could serve as very specific biomarkers for allograft injury and rejection. These markers have the potential to improve rejection monitoring, evaluate the response to antirejection therapy, and may decrease the need for invasive procedures.