bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endogenous circadian time genes expressions in the liver of mice under constant darkness
Authors: Li Huan , Zhang Shiyao , Zhang Wenxiang , Chen Siyu , Rabearivony Anjara , Shi Yujie , Liu Jie , Corton Christopher J. , Liu Chang 
Published: March 2020

Abstract
Background
The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6 weeks, and the liver samples were collected starting at 9:00 AM (CT1), and every 4 h in a 24-h cycle (CT5, CT9, CT13, CT17 and CT21). Total RNA was extracted and subjected to RNA-Seq data (deposited as GSE 133342, L-DD). To compare gene oscillation pattern under normal light-dark condition (LD, GSE114400) and short time (2 days) dark-dark condition (S-DD, GSE70497), these data were retried from GEO database, and the trimmed mean of M-values normalization was used to normalize the three RNA-seq data followed by MetaCycle analysis.

Results
Approximate 12.1% of the genes under L-DD exhibited significant rhythmically expression. The top 5 biological processes enriched in L-DD oscillation genes were mRNA processing, aromatic compound catabolic process, mitochondrion organization, heterocycle catabolic process and cellular nitrogen compound mitotic catabolic process. The endogenous circadian rhythms of clock genes, P450 genes and lipid metabolism genes under L-DD were further compared with LD and S-DD. The oscillation patterns were similar but the period and amplitude of those oscillation genes were slightly altered. RT-qPCR confirmed the selected RNA sequence findings.

Conclusions
This is the first study to profile oscillation gene expressions under L-DD. Our data indicate that clock genes, P450 genes and lipid metabolism genes expressed rhythmically under L-DD. Light was not the necessary factor for persisting circadian rhythm but influenced the period and amplitude of oscillation genes.
Effects of shell sand burial on seedling emergence, growth and stoichiometry of Periploca sepium Bunge
Authors: Li Tian , Sun Jingkuan , Yang Hongjun , Liu Jingtao , Xia Jiangbao , Shao Pengshuai 
Published: March 2020

AbstractBackgroundSand burial plays an irreplaceable and unique role in the growth and distribution of vegetation on the Shell Dike Island in the Yellow River Delta. There are still some unknown on the effects of sand burial on the morphology, biomass, and especially the stoichiometry ofPeriploca sepium, as well as the relationship between these factors.ResultsShell sand burial depth had a significant influence on seedling emergence, growth, and biomass ofP. sepium. Shallow sand burial shortened the emergence time and improved the emergence rate, morphological and biomass ofP. sepiumcompared to deep burial and the control. Burial depth significantly affected the nitrogen (N) and phosphorus (P) contents of the leaves. With deep burial, the carbon/nitrogen (C/N) and carbon/phosphorus (C/P) ratios decreased firstly and then increased with depth, while the nitrogen/phosphorus ratio (N/P) presented the contrary trend. Correlation analysis showed that the stoichiometry of N/P was positively correlated to morphology and biomass ofP. sepiumat different burial depths. Structural equation model analysis revealed that N was the largest contributor toP. sepiumbiomass.ConclusionsOptimal burial depth is beneficial to the seedling emergence, growth and nutritional accumulation ofP. sepium. Stoichiometry has an important influence on the morphological formation and biomass accumulation.
Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis
Authors: Duan Hui-Rong , Wang Li-Rong , Cui Guang-Xin , Zhou Xue-Hui , Duan Xiao-Rong , Yang Hong-Shan 
Published: March 2020

Abstract
Background
To understand the gene expression networks controlling flower color formation in alfalfa, flowers anthocyanins were identified using two materials with contrasting flower colors, namely Defu and Zhongtian No. 3, and transcriptome analyses of PacBio full-length sequencing combined with RNA sequencing were performed, across four flower developmental stages.

Results
Malvidin and petunidin glycoside derivatives were the major anthocyanins in the flowers of Defu, which were lacking in the flowers of Zhongtian No. 3. The two transcriptomic datasets provided a comprehensive and systems-level view on the dynamic gene expression networks underpinning alfalfa flower color formation. By weighted gene coexpression network analyses, we identified candidate genes and hub genes from the modules closely related to floral developmental stages. PAL, 4CL, CHS, CHR, F3’H, DFR, and UFGT were enriched in the important modules. Additionally, PAL6, PAL9, 4CL18, CHS2, 4 and 8 were identified as hub genes. Thus, a hypothesis explaining the lack of purple color in the flower of Zhongtian No. 3 was proposed.

Conclusions
These analyses identified a large number of potential key regulators controlling flower color pigmentation, thereby providing new insights into the molecular networks underlying alfalfa flower development.
Prasugrel or ticagrelor relative to clopidogrel in triple-antiplatelet treatment combined with glycoprotein IIb/IIIa inhibitor for patients with STEMI undergoing PCI: a meta-analysis
Authors: Wang Zhe , Zhou Da-Yan , Su Yong , Si Liang-Yi , Xu Qiang 
Published: March 2020

Abstract
Background
For patients with ST-segment elevation myocardial infarction (STEMI) undergoing percutaneous coronary intervention (PCI), the efficacy and safety of novel P2Y12 antagonists, including prasugrel or ticagrelor, has not been established relative to that of the clopidogrel-based triple-antiplatelet treatments (TAPTs; in combination with glycoprotein IIb/IIIa inhibitor). The present meta-analysis evaluated the efficacy and safety of prasugrel- or ticagrelor-based TAPTs relative to that of clopidogrel TAPTs in patients with STEMI undergoing PCI.

Methods
The databases PubMed, Embase, and Cochrane’s Library were systematically searched for relevant randomized controlled trials concerning prasugrel or ticagrelor (test) relative to clopidogrel (control). Depending on heterogeneity, studies were pooled with a random effects or a fixed effects model. Outcomes of blood flow after PCI were evaluated, including TIMI (thrombolysis in myocardial infarction), bleeding events, and major adverse cardiovascular events (MACEs).

Results
Seven studies comprising 11,874 patients conformed to the inclusion criteria. The pooled results with the fixed effects model indicated that after PCI patients in the prasugrel or ticagrelor groups were as likely as those treated with clopidogrel to achieve TIMI grade 3 flow or experience bleeding events. However, compared with the control, the test groups had significantly less risk of MACE (OR: 0.81, 95% CI: 0.70–0.94, P = 0.004), especially at the 1-year follow-up (OR: 0.79, 95% CI: 0.66–0.95, P = 0.01).

Conclusions
A prasugrel- or ticagrelor-based TAPT may reduce the rate of MACEs, without increasing bleeding in STEMI patients undergoing PCI. However, due to the limited RCT studies and variations in study weight, results of this meta-analysis should be confirmed in a large RCT with adequate sample size and follow-up duration.
Assessing left ventricular systolic function in children with a history of Kawasaki disease
Authors: Lin Zhou , Zheng Jingjing , Chen Weiling , Ding Tingting , Yu Wei , Xia Bei 
Published: March 2020

Abstract
Background
The incidence of Kawasaki disease (KD) is increasing. Indeed, KD has become the most common cause of acquired heart disease in children. Previous studies have well summarized the acute phase left ventricular (LV) systolic dysfunction using speckle tracking echocardiography (STE); however, changes in LV systolic function after long-term follow-up remain unclear.

Methods
One hundred children with a history of KD, but without coronary artery aneurysms, were enrolled. These children were divided into two subgroups based on the presence or absence of coronary artery dilatation (CAD). The duration of follow-up was > 7 years. The control group consisted of 51 healthy children. The LV myocardial strain were measured by two- and three-dimensional STE.

Results
Two-dimensional STE not only revealed that LV longitudinal strain decreased in part of segments in both KD groups, but also showed that global strain decreased in the KD group with CAD compared to the controls (P < 0.05). Global longitudinal strain (GLS), global circumferential strain (GCS), global radial strain (GRS), and global area strain (GAS) were obtained by 3D STE. Compared to the controls, GLS and GAS decreased in both KD groups (P < 0.05). GCS and GRS decreased in the KD group with CAD, but was unchanged in the KD group without CAD (P < 0.05).

Conclusions
LV systolic dysfunction in children with KD and CAD was more severe than KD children without CAD compared to healthy children. This dysfunction can be assessed by LV regional and global myocardial strain using two- and three-dimensional STE.
Physical activity intervention for non-diabetic patients with non-alcoholic fatty liver disease: a meta-analysis of randomized controlled trials
Authors: Wang Shu-ting , Zheng Jing , Peng He-wei , Cai Xiao-lin , Pan Xin-ting , Li Hui-quan , Hong Qi-zhu , Peng Xian-E 
Published: March 2020

Abstract
Background
Non-alcoholic fatty liver disease (NAFLD) is currently the most common cause of chronic liver disease nowadays. Changes in diet and lifestyle have led to a dramatic increase in the prevalence of NAFLD around the world. This meta-analysis is to investigate the efficacy of physical activity intervention on liver-specific endpoints in the population with NAFLD, including hepatic enzyme, serum lipid, glucose metabolism and intra-hepatic lipid.

Methods
PubMed and China National Knowledge Infrastructure (CNKI) databases were searched for randomized clinical trials of physical activity intervention on NAFLD patients through April 20th, 2019. Effect sizes were reported as standardized mean difference (SMD) and 95% confidence intervals (CI). Quality of included studies was assessed according to the Cochrane risk of bias tool. Meta-analyses were conducted using random-effect or fixed-effect models depending on the significance of heterogeneity. Subgroup analyses according to types and duration of physical activity were conducted to investigate clinical variability.

Results
Nine studies with a cumulative total of 951 participants met selection criteria. Physical activity was found associated with small reductions in hepatic enzyme parameters: ALT (SMD -0.17, 95% CI:-0.30 to − 0.05), AST (SMD -0.25, 95% CI: − 0.38, − 0.13) and GGT (SMD -0.22, 95% CI: − 0.36, − 0.08). Significant small improvements were also found in serum lipid parameters including TC (SMD = − 0.22, 95% CI: − 0.34, − 0.09), TG (SMD = − 0.18, 95% CI: − 0.31 to − 0.06) and LDL-C (SMD = − 0.26, 95% CI: − 0.39 to − 0.13). Significant improvement was also found in intra-hepatic lipid content (SMD = − 0.21, 95% CI: − 0.36 to − 0.06) There was no difference between physical intervention group and control group in HDL and three glucose metabolism parameters. Subgroup analysis suggested both aerobic exercise alone and resistance exercise alone can improve most liver function and longer period of exercise generally had better improvement effect.

Conclusions
Our findings suggest that physical activity alone can only slightly improve hepatic enzyme levels, most serum lipid levels and intra-hepatic lipid content in non-diabetic patients with NAFLD.
Long-term outcomes and quality of life of patients with Hirschsprung disease: a systematic review and meta-analysis
Authors: Dai Ying , Deng Yongfang , Lin Yan , Ouyang Runxian , Li Le 
Published: March 2020

Abstract
Background
Advances in surgical techniques and perioperative care have improved the short- and mid-term postoperative outcomes of patients with Hirschsprung disease (HD). However, the long-term outcomes of these patients (older than 10 years) have not been fully investigated. The aim of this systematic review is to clarify the prevalence of long-term outcomes and the quality of life of these patients.

Methods
PubMed, AMED, Cochrane Library, CINAHL and PsycINFO databases were searched from inception to October 2018, following the Meta-analysis of Observational Studies in Epidemiology (MOOSE) guideline. Original studies reporting the outcomes of patients older than ten years with HD were selected and reviewed. The overall prevalence of fecal incontinence, constipation, bowel function score, bladder dysfunction symptoms, and patients’ quality of life were extracted from the included studies and pooled through the random-effects meta-analysis model. The heterogeneity and variation in the pooled estimations were evaluated by Cochrane’s Q test and the I2 test. The sensitivity analysis was conducted by the sequential omission of individual studies. Publication bias was evaluated by Egger’s linear regression test. The whole procedure was conducted with Stata (version 14).

Results
In total, 3406 articles were identified from the literature search, among which twelve studies, including 625 patients, were included for analysis. The pooled prevalences of fecal incontinence, constipation, and bladder dysfunction symptoms and good to excellent bowel function scores were 0.20 (95% CI 0.13–0.28), 0.14 (95% CI 0.06–0.25), 0.07 (95% CI 0.04–0.12), and 0.95 (95% CI: 0.91–0.97), respectively; the pooled mean score of gastrointestinal-related quality of life was 118 (95% CI: 112.56–123.44).

Conclusions
HD patients older than ten years old have an overall high prevalence of fecal incontinence and a low quality of life. Targeted and evidence-based follow-up procedures and transitional care are essential to meet these patients’ long-term care needs. Prospective and multicenter research that focuses on the attributes and predictors of the long-term prognosis of patients with HD are necessary.
An internal hernia caused by Meckel’s diverticulum: a case report
Authors: Zhang Yang , Guo Yuchen , Sun Yuanlin , Xu Yuechao 
Published: March 2020

Abstract
Background
Meckel’s diverticulum is a remnant of the omphalomesenteric duct. It can lead to intestinal perforation, obstruction and gastrointestinal bleeding. While the internal hernia caused by Meckel’s diverticulum is rarely reported.

Case presentation
We report a case of a 45-year old female patient who presented with intestinal obstruction and on laparotomy was found to have Meckel’s diverticulum with internal hernia causing intestinal gangrene. Segmental bowel resection was performed and the patient had uneventful recovery.

Conclusions
In patients with acute intestinal obstruction without previous abdominal surgery, Meckel’s diverticulum and its complications should be suspected.
A cluster randomised trial of the program to enhance adjustment to residential living (PEARL): a novel psychological intervention to reduce depression in newly admitted aged care residents
Authors: Davison Tanya E. , McCabe Marita P. , Busija Lucy , O’Connor Daniel W. , Costa Vera Camões , Byers Jessica 
Published: March 2020

Abstract
Background
Depression rates are high in residential aged care (RAC) facilities, with newly admitted residents at particular risk. New approaches to address depression in this population are urgently required, particularly psychological interventions suitable for widespread use across the RAC sector. The Program to Enhance Adjustment to Residential Living (PEARL) is a brief intervention, designed to provide individually tailored care approaches to meet the psychological needs of newly admitted residents, delivered in collaboration with facility staff.

Methods
PEARL will be evaluated using a cluster randomised controlled design, comparing outcomes for residents who participate in the intervention with those residing in care as usual control facilities. Participants are RAC residents aged 60 years or above, with normal cognition or mild-moderate cognitive impairment, who relocated to the facility within the previous 4 weeks. The primary outcomes are depressive symptoms and disorders, with secondary outcomes including anxiety, stress, quality of life, adjustment to RAC, and functional dependence, analysed on an intention to treat basis using multilevel modelling.

Discussion
PEARL is an intervention based on self-determination theory, designed to reduce depression in newly admitted residents by tailoring day to day care to meet their psychological needs. This simple psychological approach offers an alternative care model to the current over-reliance of antidepressant medications.

Trial registration
ACTRN12616001726448; Registered 16 December 2016 with the Australian New Zealand Clinical Trials Registry.
Comparison of predictive models for hepatitis C co-infection among HIV patients in Cambodia
Authors: Buyze Jozefien , Weggheleire Anja De , van Griensven Johan , Lynen Lutgarde 
Published: March 2020

Abstract
Background
Hepatitis C virus (HCV) infection is a major global health problem. WHO guidelines recommend screening all people living with HIV for hepatitis C. Considering the limited resources for health in low and middle income countries, targeted HCV screening is potentially a more feasible screening strategy for many HIV cohorts. Hence there is an interest in developing clinician-friendly tools for selecting subgroups of HIV patients for whom HCV testing should be prioritized. Several statistical methods have been developed to predict a binary outcome. Multiple studies have compared the performance of different predictive models, but results were inconsistent.

Methods
A cross-sectional HCV diagnostic study was conducted in the HIV cohort of Sihanouk Hospital Center of Hope in Phnom Penh, Cambodia. We compared the performance of logistic regression, Spiegelhalter-Knill-Jones and CART to predict Hepatitis C co-infection in this cohort. We estimated the number of HCV co-infections that would be missed. To correct for over-optimism, the leave-one-out bootstrap estimator was used for estimating this quantity.

Results
Logistic regression misses the fewest HCV co-infections (8%), but would still refer 98% of HIV patients for HCV testing. Spiegelhalter-Knill-Jones (SKJ) and CART respectively miss 12% and 29% of HCV co-infections but would only refer about 30% for HCV testing.

Conclusions
In our dataset, logistic regression has the highest log-likelihood and smallest proportions of HCV co-infections missed but Spiegelhalter-Knill-Jones has the highest area under the ROC curve. The likelihood ratios estimated by Spiegelhalter-Knill-Jones might be easier to interpret for clinicians than odds ratios estimated by logistic regression or the decision tree from CART. CART is the most flexible method, and no model has to be specified regarding presence of interactions and form of the relationship between outcome and predictor variables.
Pulmonary endarteritis and endocarditis complicated with septic embolism: a case report and review of the literature
Authors: Khosravi Arezoo , Rostami Zohreh , Javanbakht Mohammad , Jafari Nematollah Jonaidi , Ghahroudi Mohsen Sadeghi , Kalantar-Motamed Mohammad Hassan , Jafari Ramezan , Einollahi Behzad 
Published: March 2020

Abstract
Background
Pulmonary endarteritis is a rare clinical phenomenon with congenital heart that can potentially lead to major complications.

Case presentation
We report a 47-year-old man with pulmonary endarteritis. This patient presented with hypertension, chest pain and a previous history of pulmonary valve disease during childhood. Also, eight-months prior, he was hospitalized with dyspnea (Functional Class III), cough, phlegm, and night sweats without fever. Echocardiographic diagnosis in the first transtransthoracic echocardiography (TTE) was intense pulmonary valve stenosis (PVS) an, thus, the pulmonary valve vegetation and PVS, established by transesophageal echocardiography (TEE). He was referred for surgery after 1 weeks of intravenous antibiotic therapy for removal of the vegetation.

Conclusions
Finally he was asymptomatic at 3-months of follow-up and was clinically in good condition. Therefore, the detection of infective endocarditis of the lung valve must not lengthy be prolonged.
Rubella IgM epidemiology in the pre-rubella vaccination era in Uganda
Authors: Bagenda Fred , Mulogo Edgar Mugema , Apecu Richard Onyuthi , Kisakye Anette , Opar Benard Toliva 
Published: March 2020

Abstract
Background
Control of Rubella and Congenital Rubella Syndrome using vaccination has shown great success in the America’s. Uganda is due to introduce the Rubella vaccine however the magnitude of transmission is not well documented. Therefore this study was done to determine IgM sero-prevalance for Rubella in order to help monitor vaccine effectiveness post introduction of the vaccine in routine vaccination programme.

Methods
A retrospective review of suspected measles cases data for the reporting period January 2007 to December 2016 in Uganda was Done. rubella IgM testing was done on 15,296 of the cases and the data was analyzed using STATA version 13.

Results
In total 15,296 cases were tested and 4255 (27.8%) tested positive and among females aged 15-49 years 88 out of 322 (27%) tested positive. The age distribution range was 0–80 years, rubella IgM positivity was reported in all the 15 regions of Uganda and throughout the ten year period in every month. Age group 5–15 years had OR 2.5 p-value < 0.001 of being rubella IgM positive compared to age < 5 years and testing measles IgM negative OR 6.3 p-value < 0.001.

Conclusion
Rubella is endemic in Uganda and although rubella IgM positivity is highest in the age 5-15 years even the younger, older and women of reprodutive age are affected. This means the risk of Congenital Rubella Syndrome is high hence the need to introduce the rubella vaccine for infants and pregnant mothers and continued surveillance to enhance its control.