bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)
Authors: Gaudino Maria , Chiapponi Chiara , Moreno Ana , Zohari Siamak , O’Donovan Tom , Quinless Emma , Sausy Aurélie , Oliva Justine , Salem Elias , Fusade-Boyer Maxime , Meyer Gilles , Hübschen Judith M , Saegerman Claude , Ducatez Mariette F , Snoeck Chantal J 
Published: August 2022

Abstract
Influenza D virus (IDV) is an emerging influenza virus that was isolated for the first time in 2011 in the USA from swine with respiratory illness. Since then, IDV has been detected worldwide in different animal species, and it was also reported in humans. Molecular epidemiological studies revealed the circulation of two major clades, named D/OK and D/660. Additional divergent clades have been described but have been limited to specific geographic areas (i.e. Japan and California). In Europe, IDV was detected for the first time in France in 2012 and subsequently also in Italy, Luxembourg, Ireland, the UK, Switzerland, and Denmark. To understand the time of introduction and the evolutionary dynamics of IDV on the continent, molecular screening of bovine and swine clinical samples was carried out in different European countries, and phylogenetic analyses were performed on all available and newly generated sequences. Until recently, D/OK was the only clade detected in this area. Starting from 2019, an increase in D/660 clade detections was observed, accompanied by an increase in the overall viral genetic diversity and genetic reassortments. The time to the most recent common ancestor (tMRCA) of all existing IDV sequences was estimated as 1995—16 years before its discovery, indicating that the virus could have started its global spread in this time frame. Despite the D/OK and D/660 clades having a similar mean tMRCA (2007), the mean tMRCA for European D/OK sequences was estimated as January 2013 compared to July 2014 for European D/660 sequences. This indicated that the two clades were likely introduced on the European continent at different time points, as confirmed by virological screening findings. The mean nucleotide substitution rate of the hemagglutinin-esterase-fusion (HEF) glycoprotein segment was estimated as 1.403 × 10−3 substitutions/site/year, which is significantly higher than the one of the HEF of human influenza C virus (P &lt; 0.0001). IDV genetic drift, the introduction of new clades on the continent, and multiple reassortment patterns shape the increasing viral diversity observed in the last years. Its elevated substitution rate, diffusion in various animal species, and the growing evidence pointing towards zoonotic potential justify continuous surveillance of this emerging influenza virus.
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data
Authors: Charon Justine , Buchmann Jan P , Sadiq Sabrina , Holmes Edward C 
Published: August 2022

Abstract
Despite a rapid expansion in the number of documented viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remain challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral ‘dusk matter’: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational resource—RdRp-scan—that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA-dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific hidden Markov models (HMMs) and structural comparisons, we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10 per cent to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motifs, as well as pre-built RdRp multiple sequence alignments. In parallel, our analysis of the sequence diversity detected by the RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some fell into potentially new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B, and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position that might provide new insights into the structure, function, and evolution of viral polymerases.
Food Insecurity and Substance Use Among Young Adult College Students in the United States
Authors: Oh Hans , Smith Lee , Jacob Louis , Du Jinyu , Shin Jae Il , Zhou Sasha , Koyanagi Ai 
Published: August 2022

Background
Food insecurity is prevalent among college students in the United States and has been associated with substance use. We sought to provide updated prevalence estimates and associations between food insecurity and a broad range of substances during the SARS-CoV-2 pandemic.

Methods
Using cross-sectional data from the Health Minds Study (N = 94,722; September 2020–June 2021), we used multivariable logistic regression to examine associations between food insecurity and several substances, adjusting for age, gender, race/ethnicity, hours worked, and residence. We then added a block of adjustments consisting of mental health factors (depression, anxiety, loneliness, financial stress).

Results
Food insecurity was associated with significantly greater odds of having used most individual substances, including greater odds of binge drinking (adjusted odds ratio [aOR], 1.21; 95% confidence interval [CI], 1.13–1.30), cigarette use (aOR, 1.91; 95% CI, 1.73–2.10), vaping (aOR, 1.74; 95% CI, 1.62–1.87), and a range of illicit or prescription drugs (using any illicit/prescription drug; aOR, 1.43; 95% CI, 1.32–1.55) These associations attenuated and many lost significance after adjusting for mental health factors.

Conclusions
This study found evidence to suggest that food insecurity is related to substance use in a large sample of young adult college students in the United States, calling for targeted interventions.
Impact of Family Presence on Delirium in Critically Ill Patients: A Retrospective Cohort Study*
Authors: Mohsen Samiha , Moss Stephana J. , Lucini Filipe , Krewulak Karla D. , Stelfox Henry T. , Niven Daniel J. , Sauro Khara M. , Fiest Kirsten M. 
Published: August 2022

OBJECTIVE:
To assess the effect of family presence on the prevalence and duration of delirium in adults admitted to an ICU.

DESIGN:
Retrospective cohort study.

SETTING:
Medical-surgical ICUs in Alberta, AB, Canada.

PATIENTS:
A population of 25,537 unique patients admitted at least once to an Alberta ICU.

METHODS:
We obtained electronic health records of consecutive adults (≥ 18 yr) admitted to one of 14 medical-surgical ICU in Alberta, Canada, from January 1, 2014, to December 30, 2018. Family presence was quantified using a validated algorithm and categorized as: 1) physical presence in ICU, 2) telephone call only, and 3) no presence (reference group). Delirium was measured using the Intensive Care Delirium Screening Checklist (ICDSC) and defined as an ICDSC greater than or equal to 4. Multivariable mixed-effects logistic and linear regression were used to evaluate the association between family presence and prevalence (binary) and duration (d) of delirium, respectively.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
The association between family presence and delirium prevalence differed according to admission type and admission Glasgow Coma Scale (GCS). Among medical and emergency surgical patients irrespective of admission GCS, physical presence of family was not significantly associated with the prevalence of delirium. In elective surgical patients, physical presence of family was associated with decreased prevalence of delirium in patients with intact Glasgow Coma Scale (GCS = 15; adjusted odds ratio, 0.60; 95% CI, 0.39–0.97; p = 0.02). Physical presence of family (adjusted mean difference [AMD] –1.87 d; 95% CI, –2.01 to –1.81; p < 0.001) and telephone calls (AMD –1.41 d; 95% CI, –1.52 to –1.31; p < 0.001) were associated with decreased duration of delirium in all patients.

CONCLUSIONS:
The effects of family presence on delirium are complex and dependent on type of visitation, reason for ICU admission, and brain function on ICU admission.
The Use of IV Vasoactive Intestinal Peptide (Aviptadil) in Patients With Critical COVID-19 Respiratory Failure: Results of a 60-Day Randomized Controlled Trial*
Authors: Youssef Jihad Georges , Lavin Philip , Schoenfeld David A. , Lee Richard A. , Lenhardt Rainer , Park David J. , Fernandez Javier Perez , Morganroth Melvin L. , Javitt Jonathan C. , Jayaweera Dushyantha 
Published: August 2022

OBJECTIVES:
Respiratory failure is a lethal complication of COVID-19 that has remained resistant to drug therapy. Vasoactive intestinal peptide (VIP) is shown in nonclinical studies to upregulate surfactant production, inhibit cytokine synthesis, prevent cytopathy, and block replication of the severe acute respiratory syndrome coronavirus 2 virus in pulmonary cells. The study aims to determine whether Aviptadil (synthetic VIP) can improve survival and recovery in patients with COVID-19 respiratory failure compared with placebo and demonstrate biological effects in such patients.

DESIGN:
A multicenter, placebo-controlled trial.

SETTING:
Ten U.S. hospitals: six tertiary-care hospitals and four community hospitals.

PATIENTS:
A total of 196 patients with COVID-19 respiratory failure.

INTERVENTIONS:
Participants were randomized 2:1 to receive 3 days of IV Aviptadil or placebo.

MEASUREMENTS AND MAIN RESULTS:
The primary end point (alive and free from respiratory failure at day 60) did not reach statistical significance (odds ratio [OR], 1.6; 95% CI, 0.86–3.11) for patients treated with Aviptadil when controlling for baseline ventilation status as prespecified in the protocol. There was, however, a statistically significant two-fold odds of improved survival (OR, 2.0; 95% CI, 1.1–3.9) at 60 days (p = 0.035). There was significant improvement in respiratory distress ratio and reduced interleukin 6 cytokine release (p = 0.02) by day 3.
Subgroup analysis identified a statistically significant likelihood of achieving primary end point among those treated with high-flow nasal oxygen at baseline (p = 0.039). Subjects on mechanical ventilation also experienced a 10-fold increased odds of survival with drug versus placebo (p = 0.031).

CONCLUSIONS:
The primary end point did not reach statistical significance, indicating that there was no difference between Aviptadil versus placebo. However, Aviptadil improves the likelihood of survival from respiratory failure at day 60 in critical COVID-19 across all sites of care. Given the absence of drug-related serious adverse events and acceptable safety profile, we believe the benefit versus risk for the use of Aviptadil is favorable for patient treatment.
Flexible Coping in Cancer Care
Authors: Eto Miwako , Yamamoto Sena , Arao Harue 
Published: August 2022

Background:
A cancer diagnosis, its associated symptoms, treatment, and side effects place a significant burden on patients. Therefore, the organization of various definitions and perceptions of flexibility in nursing care are crucial to support the development of coping strategies in adult patients in treatment for cancer.

Objective:
To render an operational definition of flexible coping for cancer patients under diverse and variable stressful situations.

Interventions/Methods:
Walker and Avant’s analytical method was used to analyze the underlying attributes and internal structure of flexible coping and clarify its nature.

Results:
Based on its attributes, flexible coping was defined as “a dynamic process that involves appraising controllability amidst a long-term, unpredictable, and changing situation; selecting a strategy for coping with a difficult situation from a diverse repertoire; evaluating the overall process; discontinuing any ineffective strategies; devising valid alternatives; and moving toward adaptation”.

Conclusions:
This concept analysis revealed the characteristic attributes of flexible coping, and provides important suggestions for nursing practice aimed at assisting cancer patients to cope with stressful situations.

Implications for Practice:
These attributes are useful for assessing coping patterns in adult oncology patients. Nurses may discuss and evaluate the coping process with a patient in order to facilitate effective coping, support efforts to readjust goals, and identify appropriate coping strategies.

Foundational:
Flexible coping refers to the ability to evaluate one’s own coping strategies, abandon ineffective strategies, and create and implement effective alternatives. The use of this concept to provide individualized support to adult patients in treatment for cancer may improve their coping ability and mental health.
The Impact of COVID-19 on Adolescent and Young Adult Cancer Services
Authors: Hughes Luke , Peters Marlies , Ellis Isabelle , Mcmonagle Lisa 
Published: August 2022

Background:
The COVID-19 pandemic led to systemic change within healthcare settings. Policies were enacted in order to protect vulnerable cancer patients, meaning the landscape of service provision was significantly altered.

Objective:
To evaluate the experiences of young cancer patients and their caregivers during the first wave of the pandemic, to inform future service provision.

Method:
Semistructured interviews were conducted via video software with a cohort of teenage and young adult (AYA) patients (n = 8), as well as caregivers (n = 4). Interviews were analyzed using Framework Analysis.

Results:
AYA patients and caregivers highlighted areas of care which remained unchanged throughout the pandemic (treatment, communication, safety, and kindness) and areas impacted by the pandemic (visitation, inconsistent rules, lack of resources, and staff conduct).

Conclusions:
The pandemic was challenging for patients and caregivers. Issues such as extended periods of isolation and inconsistent rules have heavily impacted the wellbeing of AYA patients and their caregivers, and may possibly have further impacts on them.

Implications for Practice:
Patients and caregivers who received care during the pandemic may need further support. Isolation of patients should be avoided where possible, and rules should be consistent for all AYA patients. Staff should be reminded of the impact their conduct can have on patients and caregivers, both positively and negatively.

Foundational:
There is little currently known about the long term impact of having cancer during COVID-19 for the AYA cohort. This report makes suggestions on areas which will need attention.
Quality of Life Profiles of Colorectal Cancer Patients After Treatments in Oman
Authors: Chan Moon Fai , Al-Shandudi Maryam , Al-Moundhri Mansour , Al-Balushi Muna , Al-Azri Mohammed 
Published: August 2022

Background:
Persons treated for colorectal cancer (CRC) continue to suffer from physical, psychological, emotional, and social problems after post-treatment completion.

Objective:
To explore whether different profiles exist in a cohort of patients treated for CRC regarding their sociodemographic characteristics, medical, and quality of life outcomes.

Methods:
A cross-sectional study screened 124 patients, with 118 participating in the study (response rate of 95.2%). Data were collected from August 2020 to February 2021 using convenience sampling. Instruments included sociodemographic characteristics, medical history, and the EORTC QLQ-CR29 questionnaire. Cluster analysis, t-test, chi-square, Fisher’s exact tests were used for data analysis.

Results:
Cluster 1 (n = 44) was characterized as a “poor-to-moderate functional and severe symptom” group. Cluster 2 (n = 74) was characterized as a “good functional and less symptom” group.

Conclusions:
There are substantial differences in age, gender, marital status, employment status, symptoms, and functional deficiencies between the two clusters. A customized, individualized care plan and a specifically tailored approach are needed for those in cluster 1.

Implications for Practice:
It is essential that oncology nurses recognize that a one-sizefits-all policy is not adequate to address the needs of two distinct groups of adult survivors of CRC in Oman.

What is Foundational:
Despite knowledge gaps on the need of survivors of CRC, findings from this research can be used to enhance oncology nurses’ understanding of the need and support from different symptom and function groups.
Association of preconception mixtures of phenol and phthalate metabolites with birthweight among subfertile couples
Authors: Zhang Yu , Mustieles Vicente , Williams Paige L. , Souter Irene , Calafat Antonia M. , Demokritou Melina , Lee Alexandria , Vagios Stylianos , Hauser Russ , Messerlian Carmen 
Published: August 2022

Background:
Although parental preconception exposure to some phenols and phthalates have been associated with reduced birthweight, few studies have examined these chemicals as complex mixtures.

Methods:
We included 384 mothers and 211 fathers (203 couples) who gave birth to 384 singletons from a prospective cohort of couples seeking fertility evaluation. Urinary concentrations of bisphenol A (BPA), parabens, and 11 phthalate metabolites including those of di(2-ethylhexyl) phthalate (DEHP) were examined. Birthweight was abstracted from delivery records. We used principal component analysis and Bayesian Kernel Machine Regression (BKMR) to examine maternal and paternal preconception mixtures in relation to singleton birthweight. We also fit couple-based BKMR with hierarchical variable selection to assess couples’ joint mixtures in relation to birthweight.

Results:
PC scores of maternal and paternal preconception low molecular weight phthalates factor, and paternal preconception DEHP-BPA factor were associated with reduced birthweight. In BKMR models, we found that maternal preconception monoethyl phthalate and BPA concentrations, and paternal preconception mono-n-butyl phthalate concentrations were inversely associated with birthweight when the remaining mixture components were held at their median concentrations. In couple-based BKMR models, paternal preconception biomarkers contributed more to couples’ joint effect on birthweight compared with maternal preconception biomarkers. A decreasing trend of birthweight was observed across quantiles of maternal, paternal, and couples’ total preconception mixture concentrations, respectively.

Conclusions:
Results from this preconception cohort of subfertile couples suggest a complex interplay between paternal and maternal preconception exposure to mixtures of nonpersistent chemicals, with both parental windows of exposure jointly contributing to reduced birthweight.
Legislations Mandating Insurance Coverage Are Highly Effective in Delivering Surgical Care of Transgender Patients
Authors: Faletsky Adam , Jonczyk Michael M. , Guo Lifei 
Published: August 2022

Background:
Although gender-affirming surgery is increasingly performed, few studies have examined any temporal correlation between legislations mandating transgender care and the actuation of such surgical care.

Methods:
We assembled a retrospective cohort utilizing the National Inpatient Sample database from 2000 to 2018. We stratified utility trends of gender-affirming surgery based on insurance payer types and regions in a crisscrossing effort to detect any temporal or cause-effect relationship between legislations and outcomes. All regions according to the latest National Inpatient Sample categorization were examined based on the nature of their member state’s legislations relating to gender-affirming care coverage. Diametrically, opposite regions were selected for further comparisons. Interrupted time series analyses were used to demonstrate any significant uptrend since implementation of relevant legislations.

Results:
In states with explicit inclusion of gender-affirming care, our interrupted time series analyses showed a significant increase in the number of patients on state-dependent insurance (Medicaid and private insurance) receiving gender-affirming surgery around the time during which state legislations began mandating care (P < 0.01) and thereafter (P < 0.01). This significance was not seen in the same regions among patients under nonstate-dependent payers (Medicare and self-pay), nor was it seen in either payer group in states without explicit inclusion of gender-affirming care. At the federal level, statistical significance was noted among Medicare recipients across all states around the time federal legislations took effect and thereafter.

Conclusion:
Legislations mandating coverage seem highly effective in actuating surgical care of transgender patients in corresponding jurisdictions, which may provide a roadmap for further care expansion.
An Exploration of Organizational Characteristics and Training Adoption in Irish Community Drug Treatment Services
Authors: Kelly Peter , Hegarty Josephine , Dyer Kyle R. , Donovan Aine O. 
Published: August 2022

Abstract

Background
Changes in patterns of drug use and population needs necessitate the adoption of new technologies. Despite high failure rates in adopting new technologies acquired in training, little is known about the process that can support successful change. This study explores the impact that staff and service characteristics have on the process of training adoption in Irish opiate substitution therapy services, with a specific focus on the concept of organizational readiness to change.

Methods
A cross-sectional survey was conducted on a convenience sample of 132 staff members across 12 services in Ireland. The relationship between staff demographics, their perceptions of organizational readiness to change, burnout, and a four-stage process of training adoption were considered.

Results
Discipline, job tenure, and educational levels are important predictors of engagement in the adoption process. Staff in services with higher institutional needs, greater pressures for change, and poorer resources were less likely to be exposed to, or adopt, training. Having lower levels of stress and more influence with peers was associated with better adoption of training.

Conclusions
Planners and service managers need to carefully consider the composition or dynamics of services when initiating change. Organizational readiness to change and staff characteristics as measured by instruments used in this study are important determinants of the process of innovation or training adoption and provide a good basis for developing further understanding of how treatment services work. This article expands on results from previous studies conducted in the United States to a European context.