bluuebunny/crossref_metadata_2025_split huggingface dataset:
Older age at infection and nulliparity are associated with long-term non-progression in female sex workers infected with non-subtype B HIV-1
Authors: Mochache Vernon , Richardson Barbra A , Masese Linnet N , Graham Susan M , Mandaliya Kishorchandra , Kinuthia John , Jaoko Walter , Overbaugh Julie , McClelland R Scott 
Published: April 2020

Studies have reported on HIV-infected, antiretroviral therapy (ART)-naïve individuals who show minimal disease progression despite prolonged infection. The characteristics of these long-term non-progressors (LTNPs) are not well-characterized in populations predominantly infected with non-subtype B HIV-1. Female sex workers in Mombasa, Kenya who acquired HIV-1 were studied to ascertain immunologic disease progression. Long-term non-progression was defined as an ART-naïve duration of infection ≥7 years and a majority of CD4+ cell counts ≥600 cells/µl with a non-declining CD4+ trend. Correlates of long-term non-progression were determined using multivariable logistic regression. Between February 1993 and March 2014, 332 women acquired HIV-1. Of these, 77 (23%) had ≥7 years of follow-up and 13 (17%) were categorized as LTNPs. Factors associated with long-term non-progression included age >30 years at infection (aOR = 9.41, 95% CI: 1.48–59.86, P = 0.005) and nulliparity (aOR = 20.19, 95% CI: 1.36–299.90, P = 0.03). Each log10 copies/ml increase in viral load (VL) set point was associated with a lower likelihood of being a LTNP (aOR = 0.31, 95% CI: 0.12–0.79, P = 0.01). These findings suggest that age and parity may influence the likelihood of long-term non-progression through mechanisms that are not mediated by the effects of these variables on VL. Future studies should seek to determine whether the associations presented are reproducible.
Relationship between hemodialysis patients’ educational level and arteriovenous fistula patency
Authors: Yolgösteren Atıf 
Published: April 2020

Objectives Vascular access is a lifeline for the patients who are in need of long-term hemodialysis. Native arteriovenous fistula is the most intensively preferred vascular access method owing to its longevity and convenience of use. Therefore, in this study, we aimed to determine whether there might be a relationship between hemodialysis patients’ educational levels and arteriovenous fistula patency. Methods A total of 349 patients who were attending in a chronic hemodialysis program between June 2018 and September 2018 at Bursa Uludağ University, Faculty of Medicine Dialysis Unit and in a private dialysis center in İstanbul were included in this study. The patients were grouped into two: those who have had arteriovenous fistula primary failure at least once and those who have never had arteriovenous fistula primary failure. Educational levels of the patients were classified according to Turkish National Education system (illiterate, primary school graduate, secondary school graduate, high school graduate, and university graduate). Mann–Whitney U and Chi-square tests were performed for statistical analyses. Risk factors were determined by applying backward binary logistic regression analysis. Results A total of 349 patients, 161 (46.1%) females and 188 (53.9%) males, were examined retrospectively. The median age of the patients was 64 years (range: 18–90 years). Educational level comparison revealed statistically significant difference in terms of fistula patency ( p = 0.016). In particular, fistula patency was significantly lower in illiterate, primary, secondary, and high school graduates in comparison with university graduates ( p = 0.001, p = 0.015, p = 0.003, and p = 0.018, respectively). When each group of educational level was analyzed separately in terms of fistula patency, it was observed that the higher the educational level was, the lower arteriovenous fistula primary failure rates were. Conclusions In this study, we observed a lower rate of fistula patency in patients with a low level of education. Hence, we are of the opinion that the trainings delivered on arteriovenous fistula care in dialysis centers are required to be shaped in accordance with educational levels of patients.
Bayesian methods for pilot studies
Authors: Willan Andrew R , Thabane Lehana 
Published: April 2020

Background/aims: The use of pilot studies to help inform the design of randomized controlled trials has increased significantly over the last couple of decades. A pilot study can provide estimates of feasibility parameters, such as the recruitment, compliance and follow-up probabilities. The use of frequentist confidence intervals of these estimates fails to provide a meaningful measure of the uncertainty as it pertains to the design of the associated randomized controlled trial. The objective of this article is to introduce Bayesian methods for the analysis of pilot studies for determining the feasibility of an associated randomized controlled trial. Methods: An example from the literature is used to illustrate the advantages of a Bayesian approach for accounting for the uncertainty in pilot study results when assessing the feasibility of an associated randomized controlled trial. Vague beta distribution priors for the feasibility parameters are used. Based on the results from a feasibility study, simulation methods are used to determine the expected power of specified recruitment strategies for an associated randomized controlled trial. Results: The vague priors used for the feasibility parameters are demonstrated to be considerably robust. Beta distribution posteriors for the feasibility parameters lead to beta-binomial predictive distributions for an associated randomized controlled trial regarding the number of patients randomized, the number of patients who are compliant and the number of patients who complete follow-up. Ignoring the uncertainty in pilot study results can lead to inadequate power for an associated randomized controlled trial. Conclusion: Applying Bayesian methods to pilot studies’ results provides direct inference about the feasibility parameters and quantifies the uncertainty regarding the feasibility of an associated randomized controlled trial in an intuitive and meaningful way. Furthermore, Bayesian methods can identify recruitment strategies that yield the desired power for an associated randomized controlled trial.
A Proof-of-Concept Investigation of an Energy Management Education Program to Improve Fatigue and Life Participation in Adults on Chronic Dialysis
Authors: Farragher Janine F. , Polatajko Helene J. , McEwen Sara , Jassal Sarbjit V. 
Published: April 2020

Background: Fatigue and its negative impact on life participation are top research priorities of people on chronic dialysis therapy. Energy management education (EME) is a fatigue management approach that teaches people to use practical strategies (eg, prioritizing, using efficient body postures, organizing home environments) to manage their energy expenditure during everyday life. Objective: The aim of this study is to explore whether EME is associated with improvements in fatigue and life participation in adults on chronic dialysis. Design: Five single-case interrupted time-series AB studies, and follow-up qualitative interviews. Setting: The hemodialysis and peritoneal dialysis units at an academic hospital in Toronto, Canada. Patients: In total, 5 patients on chronic dialysis therapy were purposively selected to represent diversity in age, gender, and modality. Measurements: Brief questionnaires assessing fatigue and life participation were administered weekly during the baseline and intervention periods. Additional validated questionnaires (the Fatigue Impact Scale, 36-Item Short-Form Health Survey [SF-36] Vitality Scale, and Canadian Occupational Performance Measure) were also administered at baseline and post-intervention. Methods: All participants underwent “The PEP Program,” a personalized, web-supported EME program designed to meet the needs of people on dialysis. During the program, participants complete 2 brief web modules about energy management, and then use energy management principles and a problem-solving framework to work on 3 life participation goals during sessions with a trained program administrator. Data were analyzed using visual analysis and the Tau- U statistic for the weekly time-series data, and thematic analysis for the qualitative interviews. Results: Three of 5 participants displayed a consistently positive response to the Personal Energy Planning (PEP) program across multiple measures of fatigue and life participation. Tau- U effect size estimates ranged from small to moderate, according to the time-series data. All 5 participants expressed that the program had benefited them in qualitative follow-up interviews, with the most common reported benefit being that the program made day-to-day activities easier. The format of the program was also said to be feasible and convenient. Limitations: An exploratory, proof-of-concept study that used a small set of participants and lacked an active control comparison. Conclusions: The PEP program might have potential for improving fatigue-related outcomes in people on chronic dialysis. Larger, controlled studies of the program are warranted.
How to think like an emergency care provider: a conceptual mental model for decision making in emergency care
Authors: Al-Azri Nasser Hammad 
Published: April 2020

Abstract
Background
General medicine commonly adopts a strategy based on the analytic approach utilizing the hypothetico-deductive method. Medical emergency care and education have been following similarly the same approach. However, the unique milieu and task complexity in emergency care settings pose a challenge to the analytic approach, particularly when confronted with a critically ill patient who requires immediate action. Despite having discussions in the literature addressing the unique characteristics of medical emergency care settings, there has been hardly any alternative structured mental model proposed to overcome those challenges.

Methods
This paper attempts to address a conceptual mental model for emergency care that combines both analytic as well as non-analytic methods in decision making.

Results
The proposed model is organized in an alphabetical mnemonic, A–H. The proposed model includes eight steps for approaching emergency cases, viz., awareness, basic supportive measures, control of potential threats, diagnostics, emergency care, follow-up, groups of particular interest, and highlights. These steps might be utilized to organize and prioritize the management of emergency patients.

Discussion
Metacognition is very important to develop practicable mental models in practice. The proposed model is flexible and takes into consideration the dynamicity of emergency cases. It also combines both analytic and non-analytic skills in medical education and practice.

Conclusion
Combining various clinical reasoning provides better opportunity, particularly for trainees and novices, to develop their experience and learn new skills. This mental model could be also of help for seasoned practitioners in their teaching, audits, and review of emergency cases.
Manual ventilation quality is improved with a real-time visual feedback system during simulated resuscitation
Authors: Gould Jeffrey R. , Campana Lisa , Rabickow Danielle , Raymond Richard , Partridge Robert 
Published: April 2020

Abstract
Introduction
Manual ventilations during cardiac arrest are frequently performed outside of recommended guidelines. Real-time feedback has been shown to improve chest compression quality, but the use of feedback to guide ventilation volume and rate has not been studied. The purpose of this study was to determine whether the use of a real-time visual feedback system for ventilation volume and rate improves manual ventilation quality during simulated cardiac arrest.

Methods
Teams of 2 emergency medical technicians (EMTs) performed two 8-min rounds of cardiopulmonary resuscitation (CPR) on a manikin during a simulated cardiac arrest scenario with one EMT performing ventilations while the other performed compressions. The EMTs switched roles every 2 min. During the first round of CPR, ventilation and chest compression feedback was disabled on a monitor/defibrillator. Following a 20-min rest period and a brief session to familiarize the EMTs with the feedback technology, the trial was repeated with feedback enabled. The primary outcome variables for the study were ventilations and chest compressions within target. Ventilation rate (target, 8–10 breaths/minute) and tidal volume (target, 425–575 ml) were measured using a novel differential pressure-based flow sensor. Data were analyzed using paired t tests.

Results
Ten teams of 2 EMTs completed the study. Mean percentages of ventilations performed in target for rate (41% vs. 71%, p < 0.01), for volume (31% vs. 79%, p < 0.01), and for rate and volume together (10% vs. 63%, p < 0.01) were significantly greater with feedback.

Conclusion
The use of a novel visual feedback system for ventilation quality increased the percentage of ventilations in target for rate and volume during simulated CPR. Real-time feedback to perform ventilations within recommended guidelines during cardiac arrest should be further investigated in human resuscitation.
Host-parasite interactions in non-native invasive species are dependent on the levels of standing genetic variation at the immune locus
Authors: Biedrzycka Aleksandra , Popiołek Marcin , Zalewski Andrzej 
Published: April 2020

Abstract
Background
Parasites may mediate the success of biological invasions through their effect on host fitness and thus, on host population growth and stability. However, a release from the pressure of parasites is strongly related to the genetic differentiation of the host. In invasive host populations, the number of available genetic variants, allowing them to ‘fight’ the infection, are likely to be influenced by founder events and genetic drift. The level standing genetic variation of invasive populations may be crucial in successfully adapting to new environments and resisting diseases. We studied invasive populations of raccoon that experienced a random reduction in genetic diversity during the establishment and evaluated the relationship between host immune genetic diversity and intestinal parasites infection.

Results
We distinguished two different genetic clusters that are characterized by different sets of functionally relevant MHC-DRB alleles. Both clusters were characterized by considerably different allele-parasite associations and different levels of parasite infection. The specific resistance MHC-DRB alleles explained the lower prevalence of Digenea parasites. An increased infection intensity was related to the presence of two MHC-DRB alleles. One of these alleles significantly decreased in frequency over time, causing a decrease of Digenea abundance in raccoons in consecutive years.

Conclusions
Our findings suggest that intestinal parasites can exert selective pressure on an invasive host with lowered levels of immune genetic diversity and contribute to promoting local adaptation over time. The random genetic drift that created the two different genetic clusters in the invasive raccoon range imposed completely different MHC-parasite associations, strongly associated with the infection status of populations. Our findings underline the role of standing genetic variation in shaping host-parasite relationships and provide empirical support that functional genetic variation may be, at least partly, responsible for differences in the success of invasive populations.
Unblended disjoint tree merging using GTM improves species tree estimation
Authors: Smirnov Vladimir , Warnow Tandy 
Published: April 2020

Abstract
Background
Phylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods.

Results
We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods. Yet, despite the potential limitation, our study shows that GTM has excellent accuracy, generally matching or improving on two previous DTMs, and is much faster than both.

Conclusions
The proposed GTM approach to the DTM problem is a useful new tool for large-scale phylogenomic analysis, and shows the surprising potential for unblended DTM methods.
Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
Authors: Rubert Diego P. , Martinez Fábio V. , Stoye Jens , Doerr Daniel 
Published: April 2020

Abstract
Background
Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants.

Results
Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process. Instead of using gene annotations for inferring the genome content of the ancestral sequence, we identify genomic markers through a process called genome segmentation. This enables us to reconstruct the ancestral genome from hundreds of thousands of markers rather than the tens of thousands of annotated genes. We also introduce the concept of local genome rearrangement, through which we refine syntenic blocks before they are used in the reconstruction of contiguous ancestral regions. With the enhanced workflow at hand, we reconstruct the ancestral genome of eudicots, a major sub-clade of flowering plants, using whole genome sequences of five modern plants.

Conclusions
Our reconstructed genome is highly detailed, yet its layout agrees well with that reported in Badouin et al. (2017). Using local genome rearrangement, not only the marker-based, but also the gene-based reconstruction of the eudicot ancestor exhibited increased genome content, evidencing the power of this novel concept.
High-throughput sequencing study of the effect of transabdominal hysterectomy on intestinal flora in patients with uterine fibroids
Authors: Wang Wantong , Li Yibing , Wu Qijun , Pan Xin , He Xinhui , Ma Xiaoxin 
Published: April 2020

Abstract
Background
To investigate the effect of transabdominal hysterectomy on the diversity of the intestinal flora in patients with uterine fibroids. Patients with uterine fibroids were selected from September 2018 to December 2018, in the Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, and stool specimens were collected from patients before and after surgery.

Results
High-throughput sequencing of the 16S rRNA gene was used to detect the changes in microbial community structure and diversity, and the effects of total hysterectomy on the intestinal flora were further analyzed. Estrogen levels decreased after trans-abdominal hysterectomy. High-throughput sequencing showed that after abdominal hysterectomy, the abundance and diversity of the intestinal flora decreased. The abundance changes were mainly due to Proteobacteria, where their abundance increased.

Conclusions
Trans-abdominal hysterectomy changes the intestinal flora of the body by lowering the level of estrogen in the body, which reduces the diversity and abundance of the intestinal flora.
Predictive value of circulating plasma mitochondrial DNA for Sepsis in the emergency department: observational study based on the Sepsis-3 definition
Authors: Wang Lifeng , Zhou Wei , Wang Kaiwen , He Shuangjun , Chen Yi 
Published: April 2020

Abstract
Background
The definition of sepsis is regularly updated; however, there is no standard diagnostic test. To improve diagnosis and prognostic prediction, the aim of this study was to determine the predictive value of circulating plasma mitochondrial DNA (mtDNA) levels in patients admitted to the emergency department (ED) with sepsis.

Methods
A total of 107 patients hospitalized from June 2018 to January 2019 were divided into the sepsis (n = 72) and septic shock (n = 35) groups based on the sepsis-3 definition. Clinical and laboratory data were measured within 24 h of admission. The mtDNA concentrations in clarified plasma were estimated by quantitative polymerase chain reaction. Binary logistic regression analysis and the receiver operating characteristic (ROC) curve were used to determine predictive value of mtDNA and other markers for sepsis outcome (28-day mortality).

Results
The median plasma mtDNA levels on admission were significantly higher in the septic shock patients than in the sepsis patients (134,252(IQR 70215–203,184) vs. 59,945(IQR 13274–95,319) copies/μL, P < 0.01), and were also higher in non-survivors than in survivors within 28 days (165,291(IQR 89919–272,228)vs. 63,025(IQR 17031–98,401)copies/μL, P < 0.01). Binary logistic regression showed that plasma lactate and mtDNA levels were independent risk factors for 28-day mortality [odds ratio (OR) 1.341, 95% confidence interval (CI) 1.035–1.736, P = 0.026 and OR 13.299, 95%CI 2.765–63.956, P = 0.001, respectively). The area under the ROC curve values for plasma mtDNA levels, lactate concentration, and their combined were 0.781 (p < 0.001, 95%CI 0.671–0.891), 0.733 (p < 0.001, 95%CI 0.635–0.832), and 0.799 (p < 0.001, 95%CI 0.698–0.901), respectively. The calibration test for the combined variable showed X2 of 2.559 and P = 0.923.

Conclusion
A higher plasma mtDNA level was associated with a poor prognosis of sepsis in the emergency room, and could serve as a predictor of sepsis for 28-day mortality.