bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
Authors: Vankan Mezzalina , Ho Simon Y W , Duchêne David A 
Published: July 2021

Abstract
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.]
Interleukin-1β and Interleukin-1 receptor antagonist gene polymorphism in pediatric patients with Helicobacter pylori-associated chronic gastritis
Authors: Barakat Sana Hosny , Meheissen Marwa Ahmed , El-Gendi Saba Mohamed , Fouad Ingy Ali , Mahfouz Aml Mohamed 
Published: July 2021

Background
The severity of Helicobacter pylori infection is determined by the interplay between bacterial virulence, host genetic and environmental factors. This study aimed to identify interleukin-1 beta (IL-1β) and interleukin receptor antagonist (IL-1RN) gene polymorphisms and their associations with H. pylori infection, and severity of chronic gastritis in Egyptian children.

Methods
A case control study was conducted on 100 children (50 H. pylori positive and 50 controls). Genotyping of IL-1β-31 gene was done by PCR-CTPP (confronting two-pair primers), of IL-1β-511 was performed using allele specific PCR, and investigation of the variable number tandem repeat polymorphism of the IL-1RN gene was done by PCR.

Results
The genotype C/T of IL1β-511 was the predominant genotype (36/50; 72%) among H. pylori positive cases (p ≤ 0.001). The presence of C/T genotype at position 511 of IL1β was associated with increased risk of infection with H. pylori (p ≤ 0.001, odds ratio = 6.612) and with more severe disease (p = 0.004, odds ratio = 8.333). No association of IL-1β-31 or IL-1RN gene polymorphisms with H. pylori infection or with risk of severe gastric diseases was found. Children who carry two polymorphisms are almost four times at risk for development of H. pylori infection (p = 0.026, odds ratio = 3.937).

Conclusions
Polymorphism at position -511 of IL1β gene is associated with increased risk of H. pylori infection as well as of severe corpus gastric disease in Egyptian children. This population should be considered a high-risk group, which needs regular gastric endoscopic surveillance, and should be target for H. pylori eradication.
Lay summary
The genotype C/T of IL1β-511 gene was the predominant genotype (36/50; 72%) among H. pylori positive children. Polymorphism at position -511 of IL1β gene is associated with increased risk of Helicobacter pylori infection as well as of severe corpus gastric disease in Egyptian children. No association of IL-1β-31 or IL-1RN gene polymorphisms with H. pylori infection or with risk of severe gastric diseases in Egyptian children.
Original Research: Well-Being and Resilience Among Health Care Workers During the COVID-19 Pandemic: A Cross-Sectional Study
Authors: Munn Lindsay Thompson , Liu Tsai-Ling , Swick Maureen , Rose Robert , Broyhill Britney , New Luci , Gibbs Michael 
Published: July 2021

ABSTRACT

Background:
Poor well-being among health care workers, often observed as professional burnout, is a well-documented phenomenon. The coronavirus disease 2019 (COVID-19) pandemic has further stressed the health care workforce, but its specific effects on this workforce remain unknown. This study examined well-being and resilience among health care workers during the COVID-19 pandemic.

Methods:
The study used a cross-sectional survey design. Data collection took place through anonymous surveys of nurses (LPNs and RNs), advanced practice providers (NPs, physician assistants, and certified nurse midwives), certified registered nurse anesthetists, respiratory therapists, health care technicians, and therapy service professionals (physical, occupational, and speech therapists). Of the 6,120 health care workers recruited to participate in the study, data from 2,459 participants were analyzed using logistic regression and linear regression.

Results:
The study found that several factors significantly increased the likelihood of at-risk well-being. These included having a lower level of resilience, using support resources, feeling the organization lacked understanding of the emotional support needs of health care workers during the pandemic, believing the workload had increased, believing there was insufficient personal protective equipment, believing there was inadequate staffing to safely care for patients, and having a lower degree of psychological safety. After controlling for health care workers' role and employment location, several factors were found to be significantly associated with higher levels of resilience. These included having positive perceptions about the organization's understanding of the emotional support needs of health care workers during the pandemic, believing sufficient educational resources were available regarding the care of COVID-19 patients, having positive perceptions of leadership support from direct managers, having positive perceptions of the redeployment policy, and having a higher degree of psychological safety.

Conclusions:
This study identified several work environment factors that have significantly affected health care workers' well-being and resilience during the COVID-19 pandemic. This knowledge has practical relevance for health care leaders who aim to better understand and address the well-being and resilience of the health care workforce during this pandemic and beyond.
CE: Monitoring Adult Patients for Intolerance to Gastric Tube Feedings
Authors: Metheny Norma A. 
Published: July 2021

ABSTRACT:
Gastric tube feeding is a common and valuable intervention for patients in a variety of care settings. While tube feeding can save the lives of patients for whom oral feeding isn't possible, intolerance to tube feeding is a potential complication. This article discusses risk factors for feeding intolerance; the assessment of signs and symptoms of feeding intolerance; the various means of assessing gastric emptying, including the practice of monitoring gastric residual volume (GRV); the controversy surrounding GRV monitoring in assessing feeding tolerance; and the special considerations for monitoring feeding tolerance in acutely and critically ill adults with coronavirus disease 2019. The author, a nurse researcher with extensive experience in the area of enteral feeding, briefly summarizes recommendations and guidelines for enteral feeding published by national and international health care organizations between 2015 and 2020, and offers her perspective on best nursing practices for monitoring food tolerance in adults.
Inflammatory Biomarkers Are Associated With a Decline in Functional Status at Discharge in Children With Acute Respiratory Failure: An Exploratory Analysis
Authors: Carlton Erin F. , Weeks Heidi M. , Dahmer Mary K. , Quasney Michael W. , Sapru Anil , Curley Martha A.Q. , Flori Heidi R. 
Published: July 2021

OBJECTIVES:
To evaluate the link between early acute respiratory failure and functional morbidity in survivors using the plasma biomarkers interleukin-8, interleukin-1 receptor antagonist, thrombomodulin, and plasminogen activator inhibitor-1. We hypothesized that children with acute respiratory failure with higher levels of inflammation would have worse functional outcomes at discharge, as measured by Pediatric Overall Performance Category.

DESIGN:
Secondary analysis of the Genetic Variation and Biomarkers in Children with Acute Lung Injury (R01HL095410) study.

SETTING:
Twenty-two PICUs participating in the multisite clinical trial, Randomized Evaluation of Sedation Titration for Respiratory Failure (U01 HL086622) and the ancillary study (Biomarkers in Children with Acute Lung Injury).

SUBJECTS:
Children 2 weeks to 17 years requiring invasive mechanical ventilation for acute airways and/or parenchymal lung disease. Patients with an admission Pediatric Overall Performance Category greater than 3 (severe disability, coma, or brain death) were excluded.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Among survivors, 387 patients had no worsening of Pediatric Overall Performance Category at discharge while 40 had worsening functional status, defined as any increase in Pediatric Overall Performance Category from baseline. There was no significant relationship between worsening of Pediatric Overall Performance Category and interleukin-8 or plasminogen activator inhibitor-1 on any day. There was no significant relationship between interleukin-1 receptor antagonist, or thrombomodulin, and worsening Pediatric Overall Performance Category on day 1. Plasma interleukin-1 receptor antagonist and thrombomodulin were significantly elevated on days 2 and 3 in those with worse functional status at discharge compared with those without. In multivariable analysis, interleukin-1 receptor antagonist and thrombomodulin were associated with a decline in functional status on days 2 and 3 after adjustment for age and highest oxygenation index. However, after adjusting for age and cardiovascular failure, only day 2 thrombomodulin levels were associated with a worsening in Pediatric Overall Performance Category.

CONCLUSIONS:
Higher levels of interleukin-1 receptor antagonist or thrombomodulin following intubation were associated with worse Pediatric Overall Performance Category scores at hospital discharge in children who survive acute respiratory failure. These data suggest that persistent inflammation may be related to functional decline.
Performance Analysis of the National Early Warning Score and Modified Early Warning Score in the Adaptive COVID-19 Treatment Trial Cohort
Authors: Colombo Christopher J. , Colombo Rhonda E. , Maves Ryan C. , Branche Angela R. , Cohen Stuart H. , Elie Marie-Carmelle , George Sarah L. , Jang Hannah J. , Kalil Andre C. , Lindholm David A. , Mularski Richard A. , Ortiz Justin R. , Tapson Victor , Liang C. Jason 
Published: July 2021

OBJECTIVES:
We sought to validate prognostic scores in coronavirus disease 2019 including National Early Warning Score, Modified Early Warning Score, and age-based modifications, and define their performance characteristics.

DESIGN:
We analyzed prospectively collected data from the Adaptive COVID-19 Treatment Trial. National Early Warning Score was collected daily during the trial, Modified Early Warning Score was calculated, and age applied to both scores. We assessed prognostic value for the end points of recovery, mechanical ventilation, and death for score at enrollment, average, and slope of score over the first 48 hours.

SETTING:
A multisite international inpatient trial.

PATIENTS:
A total of 1,062 adult nonpregnant inpatients with severe coronavirus disease 2019 pneumonia.

INTERVENTIONS:
Adaptive COVID-19 Treatment Trial 1 randomized participants to receive remdesivir or placebo. The prognostic value of predictive scores was evaluated in both groups separately to assess for differential performance in the setting of remdesivir treatment.

MEASUREMENTS AND MAIN RESULTS:
For mortality, baseline National Early Warning Score and Modified Early Warning Score were weakly to moderately prognostic (c-index, 0.60–0.68), and improved with addition of age (c-index, 0.66–0.74). For recovery, baseline National Early Warning Score and Modified Early Warning Score demonstrated somewhat better prognostic ability (c-index, 0.65–0.69); however, National Early Warning Score+age and Modified Early Warning Score+age further improved performance (c-index, 0.68–0.71). For deterioration, baseline National Early Warning Score and Modified Early Warning Score were weakly to moderately prognostic (c-index, 0.59–0.69) and improved with addition of age (c-index, 0.63–0.70). All prognostic performance improvements due to addition of age were significant (p < 0.05).

CONCLUSIONS:
In the Adaptive COVID-19 Treatment Trial 1 cohort, National Early Warning Score and Modified Early Warning Score demonstrated moderate prognostic performance in patients with severe coronavirus disease 2019, with improvement in predictive ability for National Early Warning Score+age and Modified Early Warning Score+age. Area under receiver operating curve for National Early Warning Score and Modified Early Warning Score improved in patients receiving remdesivir versus placebo early in the pandemic for recovery and mortality. Although these scores are simple and readily obtainable in myriad settings, in our data set, they were insufficiently predictive to completely replace clinical judgment in coronavirus disease 2019 and may serve best as an adjunct to triage, disposition, and resourcing decisions.
Clostridioides difficile-Associated Atypical Hemolytic-Uremic Syndrome Successfully Treated With Eculizumab: A Case Report and Literature Review
Authors: Moulton Michael N. , Kay Carl L. , Romain Joshua T. , Morrow Benjamin D. , Bobele Gilda M. 
Published: July 2021

BACKGROUND:

Clostridioides difficile infection is a rare precipitant for patients to develop atypical hemolytic-uremic syndrome, of which the pathogenesis remains unclear. Previous reports suggest activation of cytokine storm from binding of cyotoxins A and B to colonic wall membranes.

CASE SUMMARY:
We present a case of a previously healthy 21-year-old woman who developed fulminant C. difficile colitis and atypical hemolytic-uremic syndrome requiring abdominal surgery and renal replacement therapy. She was ultimately treated with eculizumab without the use of plasmapheresis and remains in remission with full renal recovery.

CONCLUSIONS:
Our patient’s significant response to terminal complement inhibitor, without the use of plasmapheresis, suggests that the underlying pathology is significantly driven by the alternative complement pathway. We propose that C. difficile-associated atypical hemolytic-uremic syndrome be defined as primary atypical hemolytic-uremic syndrome and strongly consider eculizumab as first-line therapy.
Pharmacotherapy in Coronavirus Disease 2019 and Risk of Secondary Infections: A Single-Center Case Series and Narrative Review
Authors: Behal Michael , Barlow Brooke , Mefford Breanne , Thompson Bastin Melissa L. , Donaldson J. Chris , Laine Melanie , Bissell Brittany D. 
Published: July 2021

OBJECTIVES:
Since the onset of the coronavirus disease 2019 pandemic, immune modulators have been considered front-line candidates for the management of patients presenting with clinical symptoms secondary to severe acute respiratory syndrome coronavirus 2 infection. Although heavy emphasis has been placed on early clinical efficacy, we sought to evaluate the impact of pharmacologic approach to coronavirus disease 2019 within the ICU on secondary infections and clinical outcomes.

DATA SOURCES:
PubMed (inception to March 2021) database search and manual selection of bibliographies from selected articles.

STUDY SELECTION AND DATA EXTRACTION:
Articles relevant to coronavirus disease 2019, management of severe acute respiratory syndrome coronavirus 2–associated respiratory failure, and prevalence of secondary infections with pharmacotherapies were selected. The MeSH terms “COVID-19,” “secondary infection,” “SARS-CoV-2,” “tocilizumab,” and “corticosteroids” were used for article identification. Articles were narratively synthesized for this review.

DATA SYNTHESIS:
Current data surrounding the use of tocilizumab and/or corticosteroids for coronavirus disease 2019 management are limited given the short follow-up period and conflicting results between studies. Further complicating the understanding of immune modulator role is the lack of definitive understanding of clinical impact of the immune response in coronavirus disease 2019.

CONCLUSIONS:
Based on the current available literature, we suggest prolonged trials and follow-up intervals for those patients managed with immune modulating agents for the management of coronavirus disease 2019.
Posture-induced Changes in Intraocular Pressure After Trabeculectomy in Patients With Primary Open-angle Glaucoma
Authors: Kang Yeon Soo , Helong Piao , Sung Mi Sun , Park Sang Woo 
Published: July 2021

Précis:
Trabeculectomy can effectively reduce posture-induced changes in intraocular pressure (IOP) in patients with primary open-angle glaucoma (POAG).

Purpose:
The purpose of this study was to investigate posture-induced changes in IOP after trabeculectomy in patients with medically uncontrolled POAG.

Design:
This was a prospective, consecutive study.

Methods:
Thirty-seven eyes of 37 patients with POAG were included. IOP was measured before trabeculectomy and 1, 2, 3, and 6 months postoperatively with patients in the sitting position, supine position, and lateral decubitus position (LDP) sequentially using iCare IC200 rebound tonometry. In the LDP, the eye scheduled for trabeculectomy was in the dependent position, the contralateral unoperated eye was a control eye. The central corneal thickness, axial length, and anterior chamber depth were measured using partial coherence interferometry.

Results:
In the sitting, supine, and LDP, the IOP was significantly reduced at every time point during the follow-up. Although the posture-induced changes in IOP persisted during the follow-up, the range of IOP changes in the sitting and supine positions, sitting and LDP, and the supine and LDP were significantly reduced after than before trabeculectomy. The central corneal thickness did not change significantly after trabeculectomy.

Conclusion:
Trabeculectomy can effectively reduce posture-induced changes in IOP in patients with POAG.
Transient infection with SARS-CoV-2 without induction of systemic immunity
Authors: Gärtner Barbara C. , Klemis Verena , Schmidt Tina , Sester Martina , Meyer Tim 
Published: July 2021

AbstractSARS-CoV-2 testing using PCR is currently used as screening test to guide isolation and contact tracing. Among 1,700 players and staff of the German Bundesliga and Bundesliga 2 who were regularly tested twice weekly, 98 individuals had a positive PCR. Among those, 11 asymptomatic cases were identified who only had a transient single positive PCR of low viral load. As only one out of 11 individuals developed SARS-CoV-2 specific cellular and humoral immunity, this indicates that transient colonization with SARS-CoV-2 may frequently occur without systemic induction of specific adaptive immunity. This knowledge may have implications for management of isolation and contact tracing, which may not be justified in these cases.
Metaphors that shape parents’ perceptions of effective communication with healthcare practitioners following child death: a qualitative UK study
Authors: Turner Sarah , Littlemore Jeannette , Topping Annie , Parr Eloise , Taylor Julie 
Published: July 2021

AbstractObjectivesTo offer an interpretation of bereaved parents’ evaluations of communication with healthcare practitioners surrounding the death of a child.DesignInterpretative qualitative study employing thematic and linguistic analyses of metaphor embedded in interview data.SettingEngland and Scotland.Participants24 bereaved parents (21 women, 3 men)MethodsParticipants were recruited through the True Colours Trust website and mailing list, similar UK charities, and word of mouth. Following interviews in person or via video-conferencing platforms (Skype/Zoom), transcripts first underwent thematic and subsequently linguistic analyses supported by Nvivo. A focused analysis of metaphors used by the parents was undertaken allow in-depth interpretation of how they conceptualised their experiences.ResultsThe findings illuminate the ways parents experienced communication with healthcare practitioners surrounding the death of a child. They show how their evaluations of effective care relate to the experience of the bereavement itself, as expressed through metaphor. We identified three broad themes: (1) Identity (2) Emotional and Physical Response(s) and (3) Time. Successful communication from healthcare practitioners takes account of parents’ experiences related to these themes.ConclusionsThis study suggests that healthcare practitioners when communicating with bereaved parents need to recognise, and seek to comprehend, the ways in which the loss impacts upon an individual’s identity as a parent, the ‘physical’ nature of the emotions that can be unleashed, and the ways in which the death of a child can alter their metaphorical conceptions of time.Strengths and limitations of the studyThis interpretative qualitative study contributes to the growing literature on the experience of parental bereavement through its focus on the use of metaphor in parents’ accounts of child loss.The metaphor analysis afforded a focus not only on the content of the interviews, but also on the language that was used to express this content, providing more depth and nuance to the interpretation of the findings.Participants were all UK-based and self-selecting which could limit transferability.
Direct detection of humoral marker corelates of COVID-19, glycated HSA and hyperglycosylated IgG3, by MALDI-ToF mass spectrometry
Authors: Iles Ray K , IIes Jason K , Zmuidinaite Raminta , Gardiner Anna , Lacey Jonathan , Harding Stephen , Heeney Jonathan , Baxendale Helen 
Published: July 2021

AbstractThe prefusion Spike protein of SARS-CoV2 binds advanced glycation end product (AGE) glycated human serum albumin (HSA) and a higher mass, hyperglycosylated/glycated, IgG3, as determined by matrix assisted laser desorption mass spectrometry (MALDI-ToF MS). We set out to investigate if the total blood plasma of patients who had recovered from acute respiratory distress as a result of COVID-19, contained more glycated HSA and higher mass (glycosylated/glycated) IgG3 than those with only clinically mild or asymptomatic infections. A direct dilution and disulphide bond reduction method was development and applied to plasma samples from SARS-CoV2 seronegative (N = 30) and seropositive (N = 31) healthcare workers and 38 convalescent plasma samples from patients who had been admitted with acute respiratory distress syndrome (ARDS) associated with COVID-19.Patients recovering from COVID-19 ARDS had significantly higher mass, AGE-glycated HSA and higher mass IgG3 levels. This would indicate that increased levels and/or ratios of hyper-glycosylation (probably terminal sialic acid) IgG3 and AGE glycated HSA may be predisposition markers for development of ARDS as a result of COVID-19 infection. Furthermore, rapid direct analysis of plasma samples by MALDI-ToF MS for such humoral immune correlates of COVID-19 presents a feasible screening technology for the most at risk; regardless of age or known health conditions.Abstract Figure