bluuebunny/crossref_metadata_2025_split huggingface dataset:
UbE3-APA: a bioinformatic strategy to elucidate ubiquitin E3 ligase activities in quantitative proteomics study
Authors: Gong Yao , Chen Yue 
Published: February 2022

Abstract

Motivation
Ubiquitination is widely involved in protein homeostasis and cell signaling. Ubiquitin E3 ligases are critical regulators of ubiquitination that recognize and recruit specific ubiquitination targets for the final rate-limiting step of ubiquitin transfer reactions. Understanding the ubiquitin E3 ligase activities will provide knowledge in the upstream regulator of the ubiquitination pathway and reveal potential mechanisms in biological processes and disease progression. Recent advances in mass spectrometry-based proteomics have enabled deep profiling of ubiquitylome in a quantitative manner. Yet, functional analysis of ubiquitylome dynamics and pathway activity remains challenging.

Results
Here, we developed a UbE3-APA, a computational algorithm and stand-alone python-based software for Ub E3 ligase Activity Profiling Analysis. Combining an integrated annotation database with statistical analysis, UbE3-APA identifies significantly activated or suppressed E3 ligases based on quantitative ubiquitylome proteomics datasets. Benchmarking the software with published quantitative ubiquitylome analysis confirms the genetic manipulation of SPOP enzyme activity through overexpression and mutation. Application of the algorithm in the re-analysis of a large cohort of ubiquitination proteomics study revealed the activation of PARKIN and the co-activation of other E3 ligases in mitochondria depolarization-induced mitophagy process. We further demonstrated the application of the algorithm in the DIA (data-independent acquisition)-based quantitative ubiquitylome analysis.

Availability and implementation
Source code and binaries are freely available for download at URL: https://github.com/Chenlab-UMN/Ub-E3-ligase-Activity-Profiling-Analysis, implemented in python and supported on Linux and MS Windows.

Supplementary information
Supplementary data are available at Bioinformatics online.
Equity in a sea of debt: how better understanding of small-scale fisheries can help reel in sustainable seafood
Authors: Phelan Anna (Anya) , Ross Helen , Adhuri Dedi S , Richards Russell 
Published: February 2022

Abstract
Small-scale fisheries are globally important to food security, nutrition, culture, ecosystem health, and livelihoods for millions of people. They also face considerable ecological, and economic pressures, including climate change, privatization, and top-down decision-making. Historically, processes of exclusion (e.g. industrialization, market forces, and settler colonialism) have persisted in the global food system. To mitigate against such processes and protect the livelihoods and human rights of small-scale fishers, the socially responsible seafood movement has emerged. This paper examines the local relationships in a seafood value chain in Indonesia, which extends from village fishers to international export markets. We present a case study from Sumbawa Indonesia, where a foreign direct seafood exporter is focused on sourcing socially responsible seafood from waters worked by small-scale fishers. Applying a systems lens, we analyse how a system driven by market forces and underpinned by western values can integrate with a system driven by traditional customs, social ties, and trust. The findings demonstrate that social connections and feedbacks within the value chain play a key role. Systems thinking reveals pathways to help synergize the two systems. This research shows that to deliver on the promise of socially responsible seafood, better understanding is needed of the interconnected social, cultural, and economic ties of small-scale fishers.
Comparison of Commercial Test Kits for Detection of Salmonella and E. coli O157:H7 in Alfalfa Spent Sprout Irrigation Water
Authors: Fu Tong-Jen , Maks Nicole , Shazer Arlette G , Chrysogelos Christina 
Published: February 2022

Abstract

Background
Sprout growers in the United States are required to test spent sprout irrigation water (SSIW) or in-process sprouts for Escherichia coli O157:H7 and Salmonella species. Pathogen screening kits are commercially available; however, few have been validated for analysis of sprouts or SSIW.

Objective
This study evaluated AOAC-certified test kits (lateral flow devices [LFDs], enzyme immunoassays [EIAs], and molecular assays) in comparison with culture methods described in the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) for detection of Salmonella and E. coli O157:H7 in alfalfa SSIW.

Method
Twenty-five milliliter aliquots of alfalfa SSIW, either uninoculated or inoculated with Salmonella or E. coli O157:H7 at a low (∼0.5–0.7 CFU/25 mL) or high level (∼10–20 CFU/25 mL), were subjected to the enrichment and assay protocols recommended by each test. Pathogen presence was confirmed following FDA BAM procedures and, if applicable, test kit manufacturer protocols.

Results
Twelve of the 13 Salmonella test kits evaluated (except VIDAS UP) performed well and detected Salmonella in 100% of SSIW samples contaminated at 0.61 CFU/mL. Performance varied among E. coli O157:H7 test kits, with four (Reveal, MicroSEQ, GDS, MDA) of 12 kits designed for next-day detection, and four (Reveal, VIP Gold, MicroSEQ, GDS) of seven kits designed for same-day detection capable of detecting the pathogen in 100% samples contaminated at 0.90 CFU/mL.

Conclusions
Enrichment conditions play a key role in determining the performance of test kits and the success of confirmation.

Highlights
This study is the first to compare a wide range of commercial test kits for detection of Salmonella and E. coli O157:H7 in SSIW.
The Clinical and Economic Impact of Measles-Mumps-Rubella Vaccinations to Prevent Measles Importations From US Pediatric Travelers Returning From Abroad
Authors: Bangs Audrey C , Gastañaduy Paul , Neilan Anne M , Fiebelkorn Amy Parker , Walker Allison Taylor , Rao Sowmya R , Ryan Edward T , LaRocque Regina C , Walensky Rochelle P , Hyle Emily P 
Published: February 2022

Abstract

Background
Pediatric international travelers account for nearly half of measles importations in the United States. Over one third of pediatric international travelers depart the United States without the recommended measles-mumps-rubella (MMR) vaccinations: 2 doses for travelers ≥12 months and 1 dose for travelers 6 to &lt;12 months.

Methods
We developed a model to compare 2 strategies among a simulated cohort of international travelers (6 months to &lt;6 years): (1) No pretravel health encounter (PHE): travelers depart with baseline MMR vaccination status; (2) PHE: MMR-eligible travelers are offered vaccination. All pediatric travelers experience a destination-specific risk of measles exposure (mean, 30 exposures/million travelers). If exposed to measles, travelers’ age and MMR vaccination status determine the risk of infection (range, 3%-90%). We included costs of medical care, contact tracing, and lost wages from the societal perspective. We varied inputs in sensitivity analyses. Model outcomes included projected measles cases, costs, and incremental cost-effectiveness ratios ($/quality-adjusted life year [QALY], cost-effectiveness threshold ≤$100 000/QALY).

Results
Compared with no PHE, PHE would avert 57 measles cases at $9.2 million/QALY among infant travelers and 7 measles cases at $15.0 million/QALY among preschool-aged travelers. Clinical benefits of PHE would be greatest for infants but cost-effective only for travelers to destinations with higher risk for measles exposure (ie, ≥160 exposures/million travelers) or if more US-acquired cases resulted from an infected traveler, such as in communities with limited MMR coverage.

Conclusions
Pretravel MMR vaccination provides the greatest clinical benefit for infant travelers and can be cost-effective before travel to destinations with high risk for measles exposure or from communities with low MMR vaccination coverage.
We Are All Police—Abu Dhabi Police Community Engagement Initiative
Authors: Al Manhali Al Haye , Al Kaabi Faisal , Al Hanaee Mohamed 
Published: February 2022

Abstract
Globally, the concept of community policing while applied in a myriad of customized strategies to meet the needs of individual environments is underpinned by common objectives, which include engaging the community to complement a core business of policing, community safety. In parallel, police agencies of all sizes and nationalities have developed a range of targeted campaigns to support and enhance community engagement with police to contribute to building safe communities. The combination of ‘soft power’ or ‘soft’ policing strategies with community policing campaigns is a central tenant of the Abu Dhabi Police, We Are All Police initiative. This article presents the journey of the We Are All Police initiative and the outcome for more than 200 nationalities combining in a 1.48 million population of Abu Dhabi residents. Aligning the vision, aims, purpose, acceptance, and impact of the Abu Dhabi Police community-based strategy contributes to informing deliberations of policy and practice in the policing of a modern society.
Psychologic Distress and Quality of Life After ICU Treatment for Coronavirus Disease 2019: A Multicenter, Observational Cohort Study
Authors: Vlake Johan H. , Van Bommel Jasper , Hellemons Merel E. , Wils Evert-Jan , Bienvenu O. Joseph , Schut Anna F. C. , Klijn Eva , Van Bavel Marten P. , Gommers Diederik , Van Genderen Michel E. 
Published: February 2022

OBJECTIVES:
To quantify short- and long-term psychologic distress, that is, symptoms of posttraumatic stress disorder, anxiety, and depression, and the health-related quality of life in coronavirus disease 2019 ICU survivors.

DESIGN:
A prospective, observational cohort study.

SETTING:
Postcoronavirus disease 2019 clinics of three hospitals in Rotterdam, the Netherlands.

PATIENTS:
Adult patients admitted for coronavirus disease 2019 to the ICU, who visited the postcoronavirus disease 2019 follow-up clinic.

MEASURES AND MAIN RESULTS:
The primary outcomes were psychologic distress and overall and mental health-related quality of life, assessed using the Impact of Event Scale-Revised, Hospital Anxiety and Depression Scale, Short-Form 36, and European Quality of Life 5D, 6 weeks, 3 months, and 6 months post hospital discharge. Second, we compared 3-month psychologic and mental health-related quality of life outcomes with a historical critical illness survivor cohort and overall and mental health-related quality of life with the Dutch population. We included 118 patients with a median age of 61 years (95% range, 36–77 yr) of whom 79 (68%) were male. At 6 weeks, 13 patients (23%) reported psychologic distress, copresence of probable psychiatric disorders was common, and no decline in psychologic distress was observed throughout follow-up. Coronavirus disease 2019 patients tend to suffer less from posttraumatic stress disorder and reported less severe symptoms of anxiety (Hospital Anxiety and Depression Scale Anxiety Score: 3 [0–17] vs 5 [0–16]; estimated mean difference 2.3 [95% CI, 0.0–4.7]; p = 0.05) and depression (Hospital Anxiety and Depression Scale Depression Score: 3 [0–15] vs 5 [0–16]; estimated mean difference 2.4 [95% CI, 0.1–2.4]; p = 0.04) than the historical critical illness cohort. Overall and mental health-related quality of life increased over time. Coronavirus disease 2019 ICU survivors reported better mental health-related quality of life than our historical cohort, but overall and mental health-related quality of life was still poorer than the Dutch population.

CONCLUSIONS:
Psychologic distress was common in coronavirus disease 2019 ICU survivors and remained similar until 6 months after hospital discharge. Health-related quality of life increased over time and was higher than in a historical cohort, but was lower than in the Dutch population. Our findings highlight that coronavirus disease 2019 ICU survivors should be monitored after ICU treatment to detect possible psychologic distress.
Improved oral health knowledge in a primary care pediatric nurse practitioner program
Authors: Pike Nancy A. , Kinsler Janni J. , Peterson Jennifer K. , Verzemnieks Inese , Lauridsen Lauren , Love-Bibbero Laurie , Ramos-Gomez Francisco 
Published: February 2022

ABSTRACT
Pediatric nurse practitioners (PNPs) are a significant workforce in primary care and are uniquely positioned to improve oral health in children through ongoing surveillance in the well-child visit. The purpose of this study was to evaluate PNP student satisfaction and knowledge gained with the integration of the Strategic Partnership for Interprofessional Collaborative Education in Pediatric Dentistry (SPICE-PD) oral health education program into the first-year primary care curriculum. A descriptive, comparative design examined dental test scores across the pre-SPICE-PD (2013–2014; n = 26) and post-SPICE-PD (2015–2020; n = 55) cohorts. An electronic survey was completed (n = 47; 67%), and focus group (n = 12) audio-recordings were analyzed using Atlas.ti 8.0. Chi-square test and independent samples t-test were used to assess differences between groups. The SPICE-PD students reported improved knowledge and skill in clinical practice. Focus group themes were oral health education was beneficial, impact of coronavirus disease 2019, and suggestions for improvement. Mean dental test scores improved pre- and post-SPICE-PD (83 vs. 93; p < .001). The SPICE-PD oral health education improved knowledge and was highly satisfying for students. Pediatric nurse practitioners are ideally positioned to integrate oral health into primary care services, thereby improving access to care and ultimately reducing or mitigating early childhood caries. Evaluation of PNP postgraduation practices in the primary care setting is needed to assess whether improved knowledge results in practice change.
Ex-vivo lung perfusion therapies: do they add value to organ donation?
Authors: Lyengar Amit , Schiazza Alexis , Cantu Edward 
Published: February 2022

Purpose of review
Significant limitations in organ availability and postoperative graft dysfunction plague lung transplantation and there is continual need for innovation. Ex-vivo lung perfusion (EVLP) has emerged over the last decade as an alternative and/or complementary allograft storage and assessment tool, however logistical hurdles have limited its widespread dissemination. As such, the overall current and potential value of EVLP on modern-day lung transplantation should be considered as innovation moves forward.

Recent findings
Since inception, EVLP has made important safety strides in conclusively showing noninferiority to cold storage in several trials. Recent advances have highlighted potential mechanisms by which EVLP in its current form may reduce the pathogenic origins of primary graft dysfunction. Exciting work on organ reconditioning with EVLP via reduction in intermediaries of acute inflammation and oxidative stress have been performed in animal models. In addition, cross-circulation during EVLP has emerged as a method to achieve more prolonged ex situ storage. The impending translation of these to clinical use will markedly improve the overall value of EVLP.

Summary
This review will highlight the current status of EVLP as it pertains to overall value in lung transplantation, focusing on historical and recent preclinical work and how innovation therein will improve lung transplantation as a field.
Association between temporal summation and conditioned pain modulation in chronic low back pain: baseline results from 2 clinical trials
Authors: Kong Jiang-Ti , You Dokyong Sophia , Law Christine Sze Wan , Darnall Beth D. , Gross James J. , Manber Rachel , Mackey Sean 
Published: February 2022

Abstract

Introduction:
Temporal summation (TS) and conditioned pain modulation (CPM) represent different aspects of central pain processing. Their relationship and differential performance within distinct body locations are not well understood.

Objectives:
To examine the association between TS and CPM in chronic low back pain and the influence of testing location on this relationship.

Methods:
We analyzed baseline data from 2 clinical trials on participants with chronic low back pain (n = 264; 47.3% female; mean age = 41 years, SD = 12; mean pain = 5.3/10, SD = 1.4). Measures used included questionnaires assessing pain and negative affect, phasic thermal TS at the hand (thenar) and the lower back (lumbar), followed by CPM that included a thermal testing stimulus (Heat-6, the temperature where pain rating is 6/10) and a cold-pressor conditioning stimulus. Nonparametric, proportional odds logistic regression was used to model thenar, and separately, lumbar TS, using CPM, Heat-6, negative affect, and demographics.

Results:
Our models revealed a small association (βs = 0.17, P = 0.01) between reduced CPM and heightened TS at both testing sites, regardless of demographics or negative affect.

Conclusion:
Results suggest a modest association between TS and CPM, irrespective of anatomical testing location, demographics, and negative affect. These findings will help improve the methodology and interpretation of TS and CPM measurement in clinical pain populations.
Creating a Biological Breast Implant with an Omental Fat-Augmented Free Flap
Authors: Nguyen Dung H. , Ma Irene T. , Choi Youna K. , Zak Yulia , Dua Monica M. , Wapnir Irene L. 
Published: February 2022

Summary:
Women with inadequate myocutaneous or fasciocutaneous soft-tissue donor sites for breast reconstruction after mastectomy are mostly limited to implants. Alternative substitutes are needed for those who do not want—or in whom there are contraindications for—implant-based reconstruction. The authors report a novel technique using an omental fat-augmented free flap to create an autologous breast mound that has comparable shape and projection to a breast implant. Three patients with breast cancer who desired unilateral reconstruction were identified in the period 2019 to 2020. All had insufficient traditional autologous sites and were averse to the use of implants. A nipple-sparing mastectomy was performed, and the omentum was laparoscopically harvested and fat-grafted ex vivo and then encased in acellular dermal matrix for microvascular anastomoses. The body mass indexes of the three patients were 17.6, 25, and 28.3 kg/m2. Each individual’s mastectomy specimens and corresponding omentum plus fat-grafting weights were 113.7/228, 271/293, and 270/360 g. No postoperative complications occurred. The reconstructed breast remains soft, with stable breast volume at 6 months and without evidence of fat necrosis. This novel use of fat grafting into an omental flap enveloped in acellular dermal matrix, the omental fat-augmented free flap, provides a viable and successful autologous alternative for patients who are not candidates for traditional autologous breast reconstruction options because of body habitus or personal preference.
Postoperative Sedation Duration as an Independent Risk Factor for Postoperative Pneumonia in Head and Neck Cancer Patients Undergoing Free Flap Reconstruction
Authors: Chuang Chih-Chao , Chen Mei-Chun , Perng Cherng-Kang , Liao Wen-Chieh , Wang Tien-Shiang , Wu Szu-Hsien , Shih Yu-Chung , Lin Chih-Hsun , Hsiao Fu-Yin , Feng Chin-Jung , Ma Hsu 
Published: February 2022

Objective
Patients who had reconstruction for head and neck cancer usually have long duration of postoperative sedation and intensive care. This is due to the complex nature of large-area soft tissue defect surgeries and upper respiratory tract infections associated with them. Postoperative pulmonary complications are common in these patients. In this study, we analyzed the risk factors and the relationship between postoperative complications and the duration of sedation to improve the patients' recovery process after free flap reconstruction for head and neck surgery.

Materials and Methods
This was a retrospective study that included 188 patients who had head and neck surgery with free flap reconstruction in 2011 (traditional recovery group) and 2018 (early recovery group). Postoperative recovery events were compared between the 2 groups. Complications such as pneumonia, wound infection, vascular thrombosis, and bleeding were also analyzed.

Results
The results showed that the early recovery group had a shorter duration of sedation (P < 0.001), shorter duration of intensive care unit stay (P = 0.05), more rapid ventilator weaning (P < 0.001), and fewer pneumonia events (8.8% vs 39.1%) than the traditional recovery group. Wound- and vessel-related complications were not affected by the duration of sedation.

Conclusions
Our study demonstrated that shortening the duration of postoperative sedation can effectively decrease the length of intensive care unit stay and reduce postoperative incidence of pneumonia without increasing wound- and vessel-related complications.
An integrative analysis of clinical and epigenetic biomarkers of mortality
Authors: Huan Tianxiao , Nguyen Steve , Colicino Elena , Ochoa-Rosales Carolina , David Hill W. , Brody Jennifer A. , Soerensen Mette , Zhang Yan , Baldassari Antoine , Elhadad Mohamed Ahmed , Toshiko Tanaka , Zheng Yinan , Domingo-Relloso Arce , Lee Dong Heon , Ma Jiantao , Yao Chen , Liu Chunyu , Hwang Shih-Jen , Joehanes Roby , Fornage Myriam , Bressler Jan , van Meurs Joyce BJ , Debrabant Birgit , Mengel-From Jonas , Hjelmborg Jacob , Christensen Kaare , Vokonas Pantel , Schwartz Joel , Gahrib Sina A. , Sotoodehnia Nona , Sitlani Colleen M. , Kunze Sonja , Gieger Christian , Peters Annette , Waldenberger Melanie , Deary Ian J. , Ferrucci Luigi , Qu Yishu , Greenland Philip , Lloyd-Jones Donald M , Hou Lifang , Bandinelli Stefania , Voortman Trudy , Hermann Brenner , Baccarelli Andrea , Whitsel Eric , Pankow James S. , Levy Daniel 
Published: February 2022

AbstractDNA methylation (DNAm) has been reported to be associated with many diseases and mortality. We hypothesized that the integration of DNAm with clinical risk factors would improve mortality prediction.We performed an epigenome-wide association study of whole blood DNAm in relation to mortality in 15 cohorts (n=15,013). During a mean follow-up of 10 years, there were 4314 deaths from all-causes including 1235 cardiovascular disease (CVD) deaths and 868 cancer deaths. Ancestry-stratified meta-analysis of all-cause mortality identified 163 CpGs in European ancestry (EA) and 17 in African ancestry (AA) participants at P<1x10-7, of which 41 (EA) and 16 (AA) were also associated with CVD death, and 15 (EA) and 9 (AA) with cancer death. We built DNAm-based prediction models for all-cause mortality that predicted mortality risk independent of clinical risk factors. The mortality prediction model trained by integrating DNAm with clinical risk factors showed a substantial improvement in prediction of cancer death with 11% and 5% increase in the C-index in internal and external replications, compared with the model trained by clinical risk factors alone. Mendelian randomization identified 15 CpGs in relation to longevity, CVD, or cancer risk. For example, cg06885782 (in KCNQ4) was positively associated with risk for prostate cancer (Beta=1.2, PMR=4.1x10-4), and negatively associated with longevity (Beta=-1.9, PMR=0.02). Pathway analysis revealed that genes associated with mortality-related CpGs are enriched for immune and cancer related pathways. We identified replicable DNAm signatures of mortality and demonstrated the potential utility of CpGs as informative biomarkers for prediction of mortality risk.