bluuebunny/crossref_metadata_2025_split huggingface dataset:
The DUB family in Populus: identification, characterization, evolution and expression patterns
Authors: Zheng Wenqing , Du Liang 
Published: July 2021

Abstract
Background
The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants.

Results
In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus.

Conclusions
The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.
Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang)
Authors: Qi Tong , Li Jinping , Wang Huifang , Han Xiaofan , Li Junrong , Du Jinzhe 
Published: July 2021

Abstract
Background
Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic and eukaryotic cells, including in plants. The Chinese herb rhubarb (Dahuang) is one of the most widely used traditional Chinese medicines in clinical applications. To better understand the physiological activities and mechanism of treating diseases with the herb, it is necessary to conduct intensive research on rhubarb. However, Khib modification has not been reported thus far in rhubarb.

Results
In this study, we performed the first global analysis of Khib-modified proteins in rhubarb by using sensitive affinity enrichment combined with high-accuracy HPLC-MS/MS tandem spectrometry. A total of 4333 overlapping Khib modification peptides matched on 1525 Khib-containing proteins were identified in three independent tests. Bioinformatics analysis showed that these Khib-containing proteins are involved in a wide range of cellular processes, particularly in protein biosynthesis and central carbon metabolism and are distributed mainly in chloroplasts, cytoplasm, nucleus and mitochondria. In addition, the amino acid sequence motif analysis showed that a negatively charged side chain residue (E), a positively charged residue (K), and an uncharged residue with the smallest side chain (G) were strongly preferred around the Khib site, and a total of 13 Khib modification motifs were identified. These identified motifs can be classified into three motif patterns, and some motif patterns are unique to rhubarb and have not been identified in other plants to date.

Conclusions
A total of 4333 Khib-modified peptides on 1525 proteins were identified. The Khib-modified proteins are mainly distributed in the chloroplast, cytoplasm, nucleus and mitochondria, and involved in a wide range of cellular processes. Moreover, three types of amino acid sequence motif patterns, including EKhib/KhibE, GKhib and k.kkk….Khib….kkkkk, were extracted from a total of 13 Khib-modified peptides. This study provides comprehensive Khib-proteome resource of rhubarb. The findings from the study contribute to a better understanding of the physiological roles of Khib modification, and the Khib proteome data will facilitate further investigations of the roles and mechanisms of Khib modification in rhubarb.
Benzylpenicillin-producing Trichophyton erinacei and methicillin resistant Staphylococcus aureus carrying the mecC gene on European hedgehogs – A pilot-study
Authors: Dube Faruk , Söderlund Robert , Lampinen Salomonsson Matilda , Troell Karin , Börjesson Stefan 
Published: July 2021

Abstract
Background
A high carriage rate of methicillin-resistant Staphylococcus aureus with the mecC gene (mecC-MRSA) has been described among Wild European hedgehogs (Europeaus erineaus). Due to this frequent occurrence, it has been suggested that hedgehogs could be a natural reservoir for mecC-MRSA. However, the reason why hedgehogs carry mecC-MRSA remains unknown, but it has been hypothesized that mecC-MRSA could have evolved on the skin of hedgehogs due to the co-occurrence with antibiotic producing dermatophytes. The aim of this pilot-study was therefore to investigate if hedgehogs in Sweden carry Trichophyton spp. and to provide evidence that these dermatophytes are able to produce penicillin or similar substances. In addition, the study aimed to identify if dermatophytes co-occurred with mecC-MRSA.

Methods
Samples were collected from hedgehogs (Europeaus erineaus) that were euthanized or died of natural causes. All samples were screened for dermatophytes and mecC-MRSA using selective cultivation methods. Suspected isolates were characterized using PCR-based methods, genome sequencing and bioinformatic analyses. Identification of penicillin was performed by ultra-high-performance liquid chromatography-tandem mass spectrometry.

Results
In total 23 hedgehogs were investigated, and it was shown that two carried Trichophyton erinacei producing benzyl-penicillin, and that these hedgehogs also carried mecC-MRSA. The study also showed that 60% of the hedgehogs carried mecC-MRSA.

Conclusion
The pilot-study demonstrated that Trichophyton erinacei, isolated from Swedish hedgehogs, can produce benzylpenicillin and that these benzylpenicillin-producing T. erinacei co-occurred with mecC-MRSA. The study also reconfirmed the high occurrence of mecC-MRSA among hedgehogs.
Normal values for high-resolution anorectal manometry in healthy young adults: evidence from Vietnam
Authors: Cuong Le Manh , Van Quyet Ha , Hung Tran Manh , Anh Nguyen Ngoc , Ha Tran Thu , Van Du Vu , Van Loi Do , Khai Ha Huu Hoang , Kien Vu Duy 
Published: July 2021

Abstract
Background
High-resolution anorectal manometry (HRAM) has been developed to improve measurement of anorectal functions. This study aims to identify normal HRAM values in healthy young Vietnamese adults.

Methods

We conducted a cross-sectional study at the National Hospital of Traditional Medicine (Hanoi, Vietnam) from July through December 2014. Healthy young adults were invited to participate in the study. All anorectal measurement values were performed using the ISOLAB high-resolution manometry system. Differences between groups were analyzed using Student’s t-tests.

Results
Thirty healthy young adults, including 15 males and 15 females aged 19–26 years, were recruited. Mean functional anal canal length was 3.4 ± 0.5 cm (range: 2.4–4.8 mm). Mean maximum resting pressure, mean maximum squeezing pressure, mean maximum coughing pressure, and mean maximum strain pressure were 65.5, 168.0, 125.9, and 84.2 mm Hg, respectively. All anal pressure values were significantly different between males and females. For rectal sensation measurements, only the volume at first sensation was significantly higher in males than in females.

Conclusions
This study provides normal HRAM value for healthy young adults in Vietnam. Sex may influence anal pressure and first rectal sensation values in this cohort. Further studies should be conducted in order to improve the quality of HRAM normal values and to confirm the effects of sex.
The effect of ventilator-associated pneumonia on the prognosis of intensive care unit patients within 90 days and 180 days
Authors: Luo Wenjuan , Xing Rui , Wang Canmin 
Published: July 2021

Abstract
Background
Mechanical ventilation (MV) is often applied in critically ill patients in intensive care unit (ICU) to protect the airway from aspiration, and supplement more oxygen. MV may result in ventilator-associated pneumonia (VAP) in ICU patients. This study was to estimate the 90-day and 180-day mortalities of ICU patients with VAP, and to explore the influence of VAP on the outcomes of ICU patients.

Methods
Totally, 8182 patients who aged ≥18 years and received mechanical ventilation (MV) in ICU from Medical Information Mart for Intensive Care III (MIMIC III) database were involved in this study. All subjects were divided into the VAP group (n = 537) and the non-VAP group (n = 7626) based on the occurrence of VAP. Clinical data of all participants were collected. The effect of VAP on the prognosis of ICU patients was explored by binary logistic regression analysis.

Results
The results delineated that the 90-day mortality of VAP patients in ICU was 33.33% and 180-day mortality was 37.62%. The 90-day and 180-day mortality rates were higher in the VAP group than in the non-VAP group. After adjusting the confounders including age, ethnicity, heart failure, septicemia, simplified acute physiology score II (SAPSII) score, sequential organ failure assessment (SOFA) score, serum lactate, white blood cell (WBC), length of ICU stay, length of hospital stay, length of ventilation, antibiotic treatment, Pseudomonas aeruginosa (P.aeruginosa), methicillin-resistant Staphylococcus aureus (MRSA), other pathogens, the risk of 90-day and 180-day mortalities in VAP patients were 1.465 times (OR = 1.465, 95%CI: 1.188–1.807, P < 0.001) and 1.635 times (OR = 1.635, 95%CI: 1.333–2.005, P < 0.001) higher than those in non-VAP patients, respectively.

Conclusions
Our study revealed that ICU patients with VAP had poorer prognosis than those without VAP. The results of this study might offer a deeper insight into preventing the occurrence of VAP.
Associations of education and work status with alcohol use and cessation among pregnant women in Japan: the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study
Authors: Murakami Keiko , Obara Taku , Ishikuro Mami , Ueno Fumihiko , Noda Aoi , Kuriyama Shinichi 
Published: July 2021

Abstract
Background
There is inconsistent evidence on the associations of education and work status with alcohol use during pregnancy. Our aim was to examine the associations of education and work status with alcohol use and alcohol cessation during pregnancy in Japan.

Methods
Data were analyzed from 11,839 pregnant women who participated in the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study from 2013 to 2017 in Japan. Women were dichotomized as current drinkers or non-drinkers in both early and middle pregnancy. Alcohol cessation was defined as alcohol use in early pregnancy, but not in middle pregnancy. Multivariable log-binomial regression analyses were conducted to examine associations of education and work status with alcohol use in early and middle pregnancy and alcohol cessation, adjusted for age and income. The prevalence ratios (PRs) and 95% confidence intervals (CIs) were calculated by work status and education.

Results
The prevalence of alcohol use in early and middle pregnancy was 20.9 and 6.4%, respectively. Higher education was associated with alcohol use in early pregnancy both among working and non-working women; the PRs of university education or higher compared with high school education or lower were 1.62 (95% CI, 1.34–1.96) and 1.29 (95% CI, 1.16–1.45), respectively. Higher education was associated with alcohol cessation during pregnancy among working women; the corresponding PR was 1.09 (95% CI, 1.01–1.17). Working was associated with alcohol use in early and middle pregnancy. Working was associated with a decreased probability of alcohol cessation among women with lower education but with an increased probability of alcohol cessation among women with higher education; the PRs of working compared with not working were 0.91 (95% CI, 0.82–1.00) and 1.10 (95% CI, 1.00–1.20), respectively.

Conclusions
Women with higher education were more likely to consume alcohol in early pregnancy and to cease alcohol use between early and middle pregnancy, especially working women. Working women were more likely to consume alcohol throughout pregnancy. Working women with lower education were less likely to cease alcohol use, whereas working women with higher education were more likely to cease alcohol use between early and middle pregnancy.
The 3 levels of HIV stigma in the United States military: perspectives from service members living with HIV
Authors: Yabes Joseph M. , Schnarrs Phillip W. , Foster Leroy B. , Scott Paul T. , Okulicz Jason F. , Hakre Shilpa 
Published: July 2021

Abstract
Background
Epidemiological surveillance data indicate that a majority of HIV-infected in the United States (U.S.) military are African-Americans and men who have sex with men. There is limited research about barriers to HIV prevention among military service members and the unique factors that contribute to HIV stigma.

Methods
A convenience sample of 30 U.S. service members were recruited from an infectious disease clinic. In depth interviews were conducted and data analyzed using a thematic coding process.

Results
Two broad categories were identified: 1) Outcomes of HIV Stigma: Fear of Rejection, Shame, and Embarrassment; and 2) Strategies for combating stigma which include increasing HIV education and prevention resources. Military policies and institutional culture regarding sexuality were found to contribute to stigma.

Conclusions
Participants identified a need for HIV education and suggested individuals living with HIV serve as mentors. A peer-to-peer intervention for delivering HIV prevention education may address these needs and reduce HIV stigma.
Health authorities’ health risk communication with the public during pandemics: a rapid scoping review
Authors: Berg Siv Hilde , O’Hara Jane K. , Shortt Marie Therese , Thune Henriette , Brønnick Kolbjørn Kallesten , Lungu Daniel Adrian , Røislien Jo , Wiig Siri 
Published: July 2021

Abstract
Background
Responses from the H1N1 swine flu pandemic and the recent COVID-19 coronavirus pandemic provide an opportunity for insight into the role of health authorities’ ways of communicating health risk information to the public. We aimed to synthesise the existing evidence regarding different modes of communication used by health authorities in health risk communication with the public during a pandemic.

Methods
We conducted a rapid scoping review. MEDLINE and EMBASE were searched for publications in English from January 2009 through October 2020, covering both the full H1N1 pandemic and the response phase during the COVID-19 pandemic. The search resulted in 1440 records, of which 48 studies met our eligibility criteria.

Results
The present review identified studies across a broad interdisciplinary field of health risk communication. The majority focused on the H1N1 pandemic and the COVID-19 pandemic. A content analysis of the studies identified three categories for modes of communication: i) communication channels, ii) source credibility and iii) how the message is communicated. The identified studies on social media focused mainly on content and engagement, while studies on the effect of the use of social media and self-protective behaviour were lacking. Studies on the modes of communication that take the diversity of receivers in the field into account are lacking. A limited number of studies of health authorities’ use of graphic and audio-visual means were identified, yet these did not consider/evaluate creative communication choices.

Conclusion
Experimental studies that investigate the effect of health authorities’ videos and messages on social media platforms and self-protective behaviour are needed. More studies are needed across the fields of health risk communication and media studies, including visual communication, web design, video and digital marketing, at a time when online digital communication is central to reaching the public.
Evolution of knowledge on meniscal biomechanics: a 40 year perspective
Authors: Mohamadi Amin , Momenzadeh Kaveh , Masoudi Aidin , Walley Kempland C. , Ierardi Kenny , Ramappa Arun , DeAngelis Joseph P. , Nazarian Ara 
Published: July 2021

AbstractBackgroundKnowledge regarding the biomechanics of the meniscus has grown exponentially throughout the last four decades. Numerous studies have helped develop this knowledge, but these studies have varied widely in their approach to analyzing the meniscus. As one of the subcategories of mechanical phenomena Medical Subject Headings (MeSH) terms, mechanical stress was introduced in 1973. This study aims to provide an up-to-date chronological overview and highlights the evolutionary comprehension and understanding of meniscus biomechanics over the past forty years.MethodsA literature review was conducted in April 2021 through PubMed. As a result, fifty-seven papers were chosen for this narrative review and divided into categories; Cadaveric, Finite element (FE) modeling, and Kinematic studies.ResultsInvestigations in the 1970s and 1980s focused primarily on cadaveric biomechanics. These studies have generated the fundamental knowledge basis for the emergence of FE model studies in the 1990s. As FE model studies started to show comparable results to the gold standard cadaveric models in the 2000s, the need for understanding changes in tissue stress during various movements triggered the start of cadaveric and FE model studies on kinematics.ConclusionThis study focuses on a chronological examination of studies on meniscus biomechanics in order to introduce concepts, theories, methods, and developments achieved over the past 40 years and also to identify the likely direction for future research. The biomechanics of intact meniscus and various types of meniscal tears has been broadly studied. Nevertheless, the biomechanics of meniscal tears, meniscectomy, or repairs in the knee with other concurrent problems such as torn cruciate ligaments or genu-valgum or genu-varum have not been extensively studied.
Reporting ethical approval in health and social science articles: an audit of adherence to GDPR and national legislation
Authors: Asplund Kjell , Hulter Åsberg Kerstin 
Published: July 2021

Abstract
Background
Previous studies have indicated that failure to report ethical approval is common in health science articles. In social sciences, the occurrence is unknown. The Swedish Ethics Review Act requests that sensitive personal data, in accordance with the EU General Data Protection Regulation (GDPR), should undergo independent ethical review, irrespective of academic discipline. We have explored the adherence to this regulation.

Methods
Using the Web of Science databases, we reviewed 600 consecutive articles from three domains (health sciences with and without somatic focus and social sciences) based on identifiable personal data published in 2020.

Results
Information on ethical review was lacking in 12 of 200 health science articles with somatic focus (6%), 21 of 200 health science articles with non-somatic focus (11%), and in 54 of 200 social science articles (27%; p < 0.001 vs. both groups of health science articles). Failure to report on ethical approval was more common in (a) observational than in interventional studies (p < 0.01), (b) articles with only 1–2 authors (p < 0.001) and (c) health science articles from universities without a medical school (p < 0.001). There was no significant association between journal impact factor and failure to report ethical approval.

Conclusions
We conclude that reporting of research ethics approval is reasonably good, but not strict, in health science articles. Failure to report ethical approval is about three times more frequent in social sciences compared to health sciences. Improved adherence seems needed particularly in observational studies, in articles with few authors and in social science research.
Short leukocyte telomeres predict 25-year Alzheimer's disease incidence in non-APOE ε4-carriers
Authors: Hackenhaar Fernanda Schäfer , Josefsson Maria , Adolfsson Annelie Nordin , Landfors Mattias , Kauppi Karolina , Hultdin Magnus , Adolfsson Rolf , Degerman Sofie , Pudas Sara 
Published: July 2021

Abstract
Background
Leukocyte telomere length (LTL) has been shown to predict Alzheimer’s disease (AD), albeit inconsistently. Failing to account for the competing risks between AD, other dementia types, and mortality, can be an explanation for the inconsistent findings in previous time-to-event analyses. Furthermore, previous studies indicate that the association between LTL and AD is non-linear and may differ depending on apolipoprotein E (APOE) ε4 allele carriage, the strongest genetic AD predictor.

Methods
We analyzed whether baseline LTL in interaction with APOE ε4 predicts AD, by following 1306 initially non-demented subjects for 25 years. Gender residualized LTL (rLTL) was categorized into tertiles of short, medium, and long rLTLs. Two complementary time-to-event models that account for competing risks were used; the Fine-Gray model to estimate the association between the rLTL tertiles and the cumulative incidence of AD, and the cause-specific hazard model to assess whether the cause-specific risk of AD differed between the rLTL groups. Vascular dementia and death were considered competing risk events. Models were adjusted for baseline lifestyle-related risk factors, gender, age, and non-proportional hazards.

Results
After follow-up, 149 were diagnosed with AD, 96 were diagnosed with vascular dementia, 465 died without dementia, and 596 remained healthy. Baseline rLTL and other covariates were assessed on average 8 years before AD onset (range 1–24). APOE ε4-carriers had significantly increased incidence of AD, as well as increased cause-specific AD risk. A significant rLTL-APOE interaction indicated that short rLTL at baseline was significantly associated with an increased incidence of AD among non-APOE ε4-carriers (subdistribution hazard ratio = 3.24, CI 1.404–7.462, P = 0.005), as well as borderline associated with increased cause-specific risk of AD (cause-specific hazard ratio = 1.67, CI 0.947–2.964, P = 0.07). Among APOE ε4-carriers, short or long rLTLs were not significantly associated with AD incidence, nor with the cause-specific risk of AD.

Conclusions
Our findings from two complementary competing risk time-to-event models indicate that short rLTL may be a valuable predictor of the AD incidence in non-APOE ε4-carriers, on average 8 years before AD onset. More generally, the findings highlight the importance of accounting for competing risks, as well as the APOE status of participants in AD biomarker research.