bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular targeting of Cisd2/Miner1 to the endoplasmic reticulum
Authors: Bian Claudie , Marchetti Anna , Hammel Philippe , Cosson Pierre 
Published: September 2021

Abstract
Background
Cisd1 and Cisd2 proteins share very similar structures with an N-terminal membrane-anchoring domain and a C-terminal cytosolic domain containing an iron-cluster binding domain and ending with a C-terminal KKxx sequence. Despite sharing a similar structure, Cisd1 and Cisd2 are anchored to different compartments: mitochondria for Cisd1 and endoplasmic reticulum for Cisd2. The aim of this study was to identify the protein motifs targeting Cisd2 to the ER and ensuring its retention in this compartment.

Results
We used new recombinant antibodies to localize Cisd1 and Cisd2 proteins, as well as various protein chimeras. Cisd2 is targeted to the ER by its N-terminal sequence. It is then retained in the ER by the combined action of a C-terminal COPI-binding KKxx ER retrieval motif, and of an ER-targeting transmembrane domain. As previously reported for Cisd1, Cisd2 can alter the morphology of the compartment in which it accumulates.

Conclusion
Although they share a very similar structure, Cisd1 and Cisd2 use largely different intracellular targeting motifs to reach their target compartment (mitochondria and endoplasmic reticulum, respectively).
Global identification of long non-coding RNAs involved in the induction of spinach flowering
Authors: Ghorbani Fatemeh , Abolghasemi Reza , Haghighi Maryam , Etemadi Nematollah , Wang Shui , Karimi Marzieh , Soorni Aboozar 
Published: September 2021

Abstract
Background
Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait.

Results
In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs.

Conclusions
This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.
Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution
Authors: Xiong Qian , Hu Yuxin , Lv Wenqi , Wang Qinghua , Liu Guoxiang , Hu Zhengyu 
Published: September 2021

AbstractBackgroundThe order Oedogoniales within the single family Oedogoniaceae comprised of three genera,Oedogonium,Oedocladium,andBulbochaetebased on traditional morphological criteria. While several molecular phylogenetic studies have suggested that bothOedogoniumandOedocladiummay not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes ofOedogoniumspecies and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales.ResultsThe fiveOedogoniumcp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that bothOedocladiumandOedogoniumare polyphyletic groups. A positively selected gene (psbA) was identified in the twoOedocladiumspecies and the terrestrialOedogoniumspecies, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats.ConclusionsOur results enrich the data on cp genomes of the genusOedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.
MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen
Authors: Shao Li , Liao Jie , Qian Jingyang , Chen Wenbin , Fan Xiaohui 
Published: September 2021

Abstract
Background
Microbiome big data from population-scale cohorts holds the key to unleash the power of microbiomes to overcome critical challenges in disease control, treatment and precision medicine. However, variations introduced during data generation and processing limit the comparisons among independent studies in respect of interpretability. Although multiple databases have been constructed as platforms for data reuse, they are of limited value since only raw sequencing files are considered.

Description
Here, we present MetaGeneBank, a standardized database that provides details on sample collection and sequencing, and abundances of genes, microbiota and molecular functions for 4470 raw sequencing files (over 12 TB) collected from 16 studies covering over 10 types of diseases and 14 countries using a unified data-processing pipeline. The incorporation of tools that enable browsing and searching with descriptive attributes, gene sequences, microbiota and functions makes the database user-friendly. We found that the source of specimen contributes more than sequencing centers or platforms to the variations of microbiota. Special attention should be paid when re-analyzing sequencing files from different countries.

Conclusions
Collectively, MetaGeneBank provides a gateway to utilize the untapped potential of gut metagenomic data in helping fighting against human diseases. With the continuous updating of the database in terms of data volume, data types and sample types, MetaGeneBank would undoubtedly be the benchmarking database in the future in respect of data reuse, and would be valuable in translational science.
Prevalence and determinants of frailty in older adult patients with chronic coronary syndrome: a cross-sectional study
Authors: Lyu Hong , Wang Chuanxia , Jiang Hong , Wang Ping , Cui Jingjing 
Published: September 2021

Abstract
Background
Frailty is an expression of vulnerability and decline of physical, mental, and social activities, more commonly found in older adults. It is also closely related to the occurrence and poor prognosis of coronary artery disease (CAD). Little investigation has been conducted on the prevalence and determinants of frailty in older adult patients with chronic coronary syndrome (CCS).

Methods
A cross-sectional study was conducted, simple random sampling was used in this study. 218 older adults (age ≥ 60 years) with CCS with an inpatient admission number ending in 6 were randomly selected who hospitalized in Department of Geriatric Cardiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, China, between January and December 2018. For measurement and assessment, we used the 5-item FRAIL scale (fatigue, resistance, ambulation, illnesses, and loss of weight), demographic characteristics, Barthel Index(BI), Mini-Mental State Examination (MMSE), Geriatric Depression Scale (GDS-15), Mini Nutrition Assessment Shor-Form (MNA-SF), Morse Fall Scale (MFS), Caprini risk assessment, polypharmacy, and Numerical Rating Scale (NRS). Multivariate logistic regression analysis was used to confirme determinants.

Results
The FRAIL scale showed 30.3% of the subjects suffered from frailty. Determinants were aging (OR1.12; 95% CI 1.04 ~ 1.62), out-of-pocket (OR18.93; 95% CI 1.11 ~ 324.07), hearing dysfunction (OR9.43; 95% CI 1.61 ~ 55.21), MNA-SF score (OR0.71; CI 0.57 ~ 0.89), GDS-15 score (OR1.35; 95% CI 1.11 ~ 1.64), and Caprini score (OR1.34; 95% CI 1.06 ~ 1.70).

Conclusions
The FRAIL scale confirmed that the prevalence of frailty in patients with CCS was slightly lower than CAD. Aging, malnutrition, hearing dysfunction, depression, and VTE risk were significantly associated with frail for older adult patients with CCS. A comprehensive assessment of high-risk patients can help identify determinants for frailty progression. In the context of CCS, efforts to identify frailty are needed, as are interventions to limit or reverse frailty status in older CCS patients.
Association between tuberculosis in men and social network structure in Kampala, Uganda
Authors: Miller Paige B. , Zalwango Sarah , Galiwango Ronald , Kakaire Robert , Sekandi Juliet , Steinbaum Lauren , Drake John M. , Whalen Christopher C. , Kiwanuka Noah 
Published: September 2021

Abstract
Background
Globally, tuberculosis disease (TB) is more common among males than females. Recent research proposes that differences in social mixing by sex could alter infection patterns in TB. We examine evidence for two mechanisms by which social-mixing could increase men’s contact rates with TB cases. First, men could be positioned in social networks such that they contact more people or social groups. Second, preferential mixing by sex could prime men to have more exposure to TB cases.

Methods
We compared the networks of male and female TB cases and healthy matched controls living in Kampala, Uganda. Specifically, we estimated their positions in social networks (network distance to TB cases, degree, betweenness, and closeness) and assortativity patterns (mixing with adult men, women, and children inside and outside the household).

Results
The observed network consisted of 11,840 individuals. There were few differences in estimates of node position by sex. We found distinct mixing patterns by sex and TB disease status including that TB cases have proportionally more adult male contacts and fewer contacts with children.

Conclusions
This analysis used a network approach to study how social mixing patterns are associated with TB disease. Understanding these mechanisms may have implications for designing targeted intervention strategies in high-burden populations.
The prevalence of human immunodeficiency and of hepatitis B viral infections is not increased in patients with sickle cell disease in Tanzania
Authors: Shayo Grace , Makundi Irene , Luzzatto Lucio 
Published: September 2021

Abstract
Background
Tanzania ranks as the fourth country in the world with respect to the number of sickle cell disease (SCD) births; it is also endemic to the human immunodeficiency virus (HIV) and the hepatitis B virus (HBV). This study was done to determine the prevalence of HIV and HBV infections among SCD patients in Dar es Salaam, Tanzania.

Methods
A multicenter hospital-based descriptive cross sectional study was carried out among participants aged ≥ 16 years with a proven diagnosis of SCD. Socio-demographic and clinical data were recorded. Blood samples were drawn for HIV and HBV diagnosis. All categorical variables were summarized into frequencies.

Results
There were 185/325 (56.9 %) females. The mean age (SD) was 23.0 ± 7.5 years. The prevalence of HIV was 1.8 %; the prevalence of HBV was 1.2 %.

Conclusions
The prevalence of both HIV and HBV in SCD patients is no greater than in the general population of Dar es Salaam or Tanzania. For associations, a large study would be needed. From a detailed blood transfusion history of SCD patients we found no evidence that HIV or HBV infection was transmitted through blood transfusion.
Relationship between renal function and blood pressure dipping status in renal transplant recipients: a longitudinal study
Authors: Jaques David A. , Saudan Patrick , Martinez Chantal , Andres Axel , Martin Pierre-Yves , Pechere-Bertschi Antoinette , Ponte Belen 
Published: September 2021

AbstractBackgroundHypertension (HT) is associated with adverse outcomes in kidney transplant (KTX) recipients. Blunting of physiological decrease in nighttime compared to daytime blood pressure (non-dipping status) is frequent in this setting. However, weather non-dipping is independently associated with renal function decline in KTX patients is unknown.MethodsWe retrospectively screened KTX outpatients attending for a routine ambulatory blood pressure monitoring (ABPM) (T1) at a single tertiary hospital. Patients had two successive follow-up visits, 1 (T2) and 2 (T3) years later respectively. Routine clinical and laboratory data were collected at each visit. Mixed linear regression models were used with estimated glomerular filtration rate (eGFR) as the dependent variable.ResultsA total of 123 patients were included with a mean follow-up of 2.12 ± 0.45 years after ABPM. Mean age and eGFR at T1 were 56.0 ± 15.1 and 54.9 ± 20.0 mL/min/1.73m2respectively. 61 patients (50.4%) had sustained HT and 81 (65.8%) were non-dippers. In multivariate analysis, systolic dipping status was positively associated with eGFR (p = 0.009) and compared to non-dippers, dippers had a 10.4 mL/min/1.73m2higher eGFR. HT was negatively associated with eGFR (p = 0.003).ConclusionsWe confirm a high prevalence of non-dippers in KTX recipients. We suggest that preserved systolic dipping is associated with improved renal function in this setting independently of potential confounders, including HT and proteinuria. Whether modification of dipping status by chronotherapy would preserve renal function remains to be tested in clinical trials.
Electronic media use and sleep in children and adolescents in western countries: a systematic review
Authors: Lund Lisbeth , Sølvhøj Ida Nielsen , Danielsen Dina , Andersen Susan 
Published: September 2021

Abstract
Background
Sleep is essential for child and adolescent health and well-being. There is an increasing interest in whether electronic media use affects children and young adolescents’ sleep. Prior reviews have focused on a school-aged population. Moreover, it is crucial that research continuously addresses the processes of technology and media use and the implication on sleep. This systematic review examines the evidence of electronic media use related to sleep among 0–15-year-olds.

Methods
Searches were carried out in four databases (CINAHL, Web of Science, EMBASE, and Medline). Inclusion criteria included age ≤ 15 years, and intervention, cohort, or cross-sectional studies from western countries. Methodological quality was rated using the Quality Assessment Tool for Quantitative Studies by two independent reviewers. Data was extracted using a standardized data extraction form. Synthesis was done by summarizing results across studies by age groups of 0–5, 6–12, and 13–15 years within four sleep domains: Bedtime and sleep onset; Sleep quality; Sleep duration; Daytime tiredness.

Results
The search identified 10,719 unique studies, of which 109 fulfilled inclusion and exclusion criteria and were assessed for methodological quality. In total, 49 studies were included in the review. The study designs were randomized controlled trials (n = 3), quasi-experimental studies (n = 2), prospective cohort studies (n = 15), and cross-sectional studies (n = 29). Evidence for an association between electronic media use and sleep duration was identified, with stronger evidence for 6–15-years-olds than 0–5-year-olds. The evidence for a relationship between electronic media use and other sleep outcomes was more inconclusive. However, for 6–12-year-old children, there was evidence for associations of electronic media use with delayed bedtime and poor sleep quality. For 13–15-year-olds, there was evidence for associations between screen time and problems falling asleep, and between social media use and poor sleep quality.

Conclusions
Overall, electronic media use was generally associated with shorter sleep duration in children and adolescents. Studies with stronger research design and of higher quality are needed to draw solid conclusions about electronic media’s impact on other sleep outcomes. Public awareness and interventions could be promoted about the potential negative impact on children’s sleep of electronic media devices that are used excessively and close to bedtime.
Evaluation of the University of California Diabetes Prevention Program (UC DPP) Initiative
Authors: Gholami Maryam , Jackson Nicholas J. , Chung Un Young Rebecca , Duru O. Kenrik , Shedd Kelly , Soetenga Samantha , Loeb Tamara , Elashoff David , Hamilton Alison B. , Mangione Carol M. , Slusser Wendelin , Moin Tannaz 
Published: September 2021

Abstract
Background
Type 2 diabetes can negatively impact long term health outcomes, healthcare costs and quality of life. However, intensive lifestyle interventions, including the Diabetes Prevention Program (DPP), can significantly lower risk of incident type 2 diabetes among overweight adults with prediabetes. Unfortunately, the majority of adults in the US who are at risk of developing diabetes do not engage in DPP-based lifestyle change programs. Increased adoption of evidence-based obesity and diabetes prevention interventions, such as the DPP, may help large employers reduce health risks and improve health outcomes among employees. In 2018, the University of California Office of thePresident (UCOP) implemented the UC DPP Initiative, a novel, multi-component program to address diabetes and obesity prevention across the UC system.

Methods
The goal of our study is to conduct a multifaceted evaluation of the UC DPP Initiative using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework. Our evaluation will integrate unique and diverse UC data sources, including electronic health record (EHR) data, administrative claims, campus-based DPP cohort data, qualitative interviews and site visits. Our primary outcome of interest is the mean percent weight change among three groups of overweight/obese UC beneficiaries at risk for diabetes at 12-month follow-up. Secondary outcomes include mean percent weight change at 24-month follow-up, barriers and facilitators associated with implementatio, as well as the degree of program adoption and maintenance.

Discussion
Our study will help inform diabetes and obesity prevention efforts across the UC system. Findings from this evaluation will also be highly applicable to universities and large employers, as well as community organizers, healthcare organizations and insurers implementing the DPP and/or other health promotion interventions.
The susceptibility of SERPINE1 rs1799889 SNP in diabetic vascular complications: a meta-analysis of fifty-one case-control studies
Authors: Chen JingYi , Zhai ChuanNan , Wang ZhiQian , Li Rui , Wu WenJing , Hou Kai , Alzogool Mohammad , Wang Yan , Cong HongLiang 
Published: September 2021

Abstract
Background
The serine protease inhibitor-1 (SERPINE1) rs1799889 single nucleotide polymorphism (SNP) has been constantly associated with diabetes mellitus (DM) and its vascular complications. The aim of this meta-analysis was to evaluate this association with combined evidences.

Methods
The systematic search was performed for studies published up to March 2021 which assess the associations between SERPINE1 rs1799889 SNP and the risks of DM, diabetic retinopathy (DR), diabetic cardiovascular disease (CVD) and diabetic nephropathy (DN). Only case-control studies were identified, and the linkage between SERPINE1 rs1799889 polymorphism and diabetic vascular risks were evaluated using genetic models.

Results
51 comparisons were enrolled. The results revealed a significant association with diabetes risk in overall population (allelic: OR = 1.34, 95 % CI = 1.14–1.57, homozygous: OR = 1.66, 95 % CI = 1.23–2.14, heterozygous: OR = 1.35, 95 % CI = 1.08–1.69, dominant: OR = 1.49, 95 % CI = 1.18–1.88, recessive: OR = 1.30, 95 % CI = 1.06–1.59) as well as in Asian descents (allelic: OR = 1.45, 95 % CI = 1.16–1.82, homozygous: OR = 1.88, 95 % CI = 1.29–2.75, heterozygous: OR = 1.47, 95 % CI = 1.08-2.00, dominant: OR = 1.64, 95 % CI = 1.21–2.24, recessive: OR = 1.46, 95 % CI = 1.09–1.96). A significant association was observed with DR risk (homozygous: OR = 1.25, 95 % CI = 1.01–1.56, recessive: OR = 1.20, 95 % CI = 1.01–1.43) for overall population, as for the European subgroup (homozygous: OR = 1.32, 95 % CI = 1.02–1.72, recessive: OR = 1.38, 95 % CI = 1.11–1.71). A significant association were shown with DN risk for overall population (allelic: OR = 1.48, 95 % CI = 1.15–1.90, homozygous: OR = 1.92, 95 % CI = 1.26–2.95, dominant: OR = 1.41, 95 % CI = 1.01–1.97, recessive: OR = 1.78, 95 % CI = 1.27–2.51) and for Asian subgroup (allelic: OR = 1.70, 95 % CI = 1.17–2.47, homozygous: OR = 2.46, 95 % CI = 1.30–4.66, recessive: OR = 2.24, 95 % CI = 1.40–3.59) after ethnicity stratification. No obvious association was implied with overall diabetic CVD risk in any genetic models, or after ethnicity stratification.

Conclusions
SERPINE1 rs1799889 4G polymorphism may outstand for serving as a genetic synergistic factor in overall DM and DN populations, positively for individuals with Asian descent. The association of SERPINE1 rs1799889 SNP and DR or diabetic CVD risks was not revealed.
Long-term follow-up of portal vein thrombosis in an American Cocker Spaniel with lobular dissecting hepatitis: a case report
Authors: Sakamoto Yumi , Sato Keita , Ishikawa Chieko , Kagawa Yumiko , Nakayama Tomohiro , Sakai Manabu 
Published: September 2021

Abstract
Background
Lobular dissecting hepatitis (LDH) is a rare form of canine liver cirrhosis that may be accompanied by portal hypertension in American Cocker Spaniels. In human patients with liver cirrhosis, portal vein thrombosis (PVT) is a common complication. However, PVT has not been reported in dogs with LDH. Herein, we describe the long-term follow-up of PVT in an American Cocker Spaniel with LDH.

Case presentation
An 8-year-old neutered male American Cocker Spaniel presented with a 1-month history of severe abdominal effusion. The dog was histopathologically diagnosed with LDH and treated with low-dose prednisolone on day 14. On day 115, computed tomography angiography (CTA) confirmed the presence of a thrombus in the portal vein. Therefore, the dog was subcutaneously administered with the anticoagulant dalteparin, and low-dose prednisolone was continued. As a follow-up for PVT, CTA examinations were performed on days 207, 515, 886, and 1168, and the dog’s antithrombin and D-dimer levels were measured. Following anticoagulant therapy, the dog was confirmed to have gradually increased antithrombin activity and decreased D-dimer concentrations. In addition, although the thrombus was confirmed to be in the same area of the portal vein system by CTA, atrophy and increased CT values due to organization were observed during the follow-up period. The dog’s condition remained stable without clinical signs until day 1112 when it developed hepatic encephalopathy. The dog died on day 1208. On postmortem examination, histopathologically, the liver showed marked bile duct hyperplasia and fibrosis with chronic thrombus in the portal vein.

Conclusions
This case demonstrated that low-dose glucocorticoid combined with dalteparin allowed long-term follow-up of PVT in an American Cocker Spaniel with LDH.