bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-length transcriptome sequencing reveals a low-temperature-tolerance mechanism in Medicago falcata roots
Authors: Cui Guowen , Chai Hua , Yin Hang , Yang Mei , Hu Guofu , Guo Mingying , Yi Rugeletu , Zhang Pan 
Published: August 2019

Abstract
Background

Low temperature is one of the main environmental factors that limits crop growth, development and production. Medicago falcata is an economically and ecologically important legume that is closely related to alfalfa and exhibits better tolerance to low temperature than alfalfa. Understanding the low-temperature-tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa.

Results

In this study, we explored the transcriptomic changes in low-temperature-treated M. falcata roots by combining SMRT and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs and 4,189 LncRNAs were predicted. A total of 111,587 genes from SMRT were annotated, and 11,369 DEGs were identified in this paper that are involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was WRKY, followed by ERF, MYB, bHLH and NAC. A total of 134 genes were differentially coexpressed at all five temperature points, including 101 upregulated genes and 33 downregulated genes. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. The WGCNA results showed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and corroborated that electrolyte leakage can be used as direct stress markers to reflect cell membrane damage from low-temperature stress in physiological assays. The consistency between the qRT-PCR results and RNA-Seq analyses confirm the validity of the RNA-Seq data and the analysis of the regulation of low-temperature stress in the transcriptome.

Conclusions

The full-length transcripts generated in this study provided a full characterization of the gene transcription of M. falcata and are useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings facilitate the understanding of low-temperature-tolerance mechanisms in M. falcata.
Pathogenic fungi-induced susceptibility is mitigated by mutual Lactobacillus plantarum in the Drosophila melanogaster model
Authors: Liu Wei , Su Wanzhen , Liu Jialin , Bai Peng , Ma Baocang 
Published: August 2019

Abstract
Background
Animals frequently encounter a variety of harmful fungi in the wild, but their ability to develop sophisticated anti-fungal strategies allows them to flourish across the globe. Extensive studies have highlighted significant involvement of indigenous microbial communities in host health, but the daunting complexity of microflora has hampered our understanding of the intricate relationships among them. In this work, we sought to develop a bacterium-fungus-Drosophila model that offered a model to systematically evaluate the anti-fungal effects of commensal bacteria.
Results
We isolated a pathogenic fungal strain, Diaporthe FY, that was detrimental to the survival and development of Drosophila upon infection. Using Drosophila as a model system, Drosophila-associated Lactobacillus plantarum functioned as a probiotics, and protected flies from mortality induced by Diaporthe FY. Our results shown that L. plantarum hindered the growth of Diaporthe FY in vitro, and decreased the mortality rate of Diaporthe FY-infected flies in vivo, therefore consequently mitigating the toxicity of Diaporthe FY to hosts. In addition, L. plantarum overrode the avoidance of oviposition on Diaporthe FY-associated substrates.
Conclusions
Diaporthe FY was identified as a potential pathogen to Drosophila. Commensal L. plantarum mitigated the pathogenic fungi-induced susceptibility in Drosophila, providing an insight into the natural interplays between commensal and pathogenic microbial communities that contribute to animal health and pathogenesis.
Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers
Authors: Egu Alemneh Mideksa , Dagne Kifle , Tesfaye Kassahun , Hu Xuebo 
Published: August 2019

Abstract
Background

Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand to its natural epoxidised oil, which can be used for the manufacturing of polyvinyl chloride, adhesives, and petrochemicals, cosmetic and pharmaceutical products. This study is initiated for the systematic and intensive assessment of V. galamensis accessions genetic diversity through SSR molecular markers to minimize the existing research gaps, and provide a clue for germplasm conservation and further research.

Results

A total of 150 V. galamensis accessions were analyzed using 20 SSR markers. The markers detected a total of 79 with an average of 3.9 alleles per locus. The mean number of effective alleles was 3.06 and, the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The marker also showed the highest percent of polymorphism that ranged from 0.50 to 0.96 with an average of 0.76. The analysis of molecular variance showed only 11% variation was among populations, 22% among individuals within populations and 67% within individuals. The largest number of migrants per generation was occurred between Derashie and Wollo (Nm=7.37) whereas the lowest values was between East Harerghe and West Harerghe (Nm =1.42). A factor analysis including dendrogram clusters and principal coordinates classified the 150 accessions into 4 groups. However, the Bayesian model based clustering (STRUCTURE) grouped into 3 (K = 3) major gene pools. These analyses showed accessions collected from the same region of origin did not often grouped entirely together within a given major groups.

Conclusions

Molecular genetic diversity analysis, using SSR markers was the first report in V. galamensis. All the markers used were polymorphic in the population studied. The markers detected the larger number of alleles, higher expected heterozygosity than observed heterozygosity. The markers applied to ten populations, in which East Showa and West Harerghe revealed higher genetic diversity, and can be considered as the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content and population clusters are an important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.
Angiotensin-converting enzyme gene insertion/deletion polymorphism and susceptibility to psoriasis: A systematic review and meta-analysis
Authors: Ramezani Mazaher , Zavattaro Elisa , Sadeghi Masoud 
Published: August 2019

Abstract
Background: Psoriasis is a multifactorial disorder, impacted by both genetic and environmental factors. Herein, a meta-analysis assessed the association of angiotensin-converting enzyme gene insertion/deletion (ACE I/D) polymorphism and psoriasis susceptibility. Methods: A systematic search was used in databases of PubMed/Medline, Scopus, Web of Science, and Cochrane Library up to January 2019 without language restriction. A dichotomous analysis was carried out by RevMan 5.3 using crude odds ratio (OR) and 95% confidence interval (CI) to investigate the association between ACE I/D polymorphisms and the risk of psoriasis. A funnel plot analysis was used by CMA 2.0 to estimate a significant existence of publication bias. Results: Out of 61 studies retrieved from the databases, 16 studies were included in the meta-analysis. The pooled ORs for models of D vs. I, DD vs. II, ID vs. II, ID + DD vs. II, and DD vs. II + ID genotypes were 0.96 [95%CI: 0.82, 1.12; P=0.58], 0.99 [95%CI: 0.73, 1.36; P=0.96], 0.78 [95%CI: 0.62, 0.91; P=0.0003], 0.91 [95%CI: 0.73, 1.13; P=0.40], and 1.05 [95%CI: 0.85, 1.30; P=0.68], respectively. A significant difference between ACE polymorphisms in patients with/without family history for the disease [OR=1.44; 95%CI: 1.24, 1.67; P<0.001] and also in patients mild/severe psoriasis [OR=0.70; 95%CI: 0.55, 0.88; P=0.002] was identified. Conclusion: The results of the meta-analysis showed that ACE I/D polymorphism may be associated with psoriasis susceptibility, while ID genotype seemed to have a protective role in Caucasian patients affected by psoriatic arthritis and in studies with hospital-based controls.
The Analysis of Risk Factors Associated with Transcatheter Arterial Embolization for Percutaneous Nephrolithotomy
Authors: Miao Hongfei , Chen Yong , Ye Peng , Zeng Qingle , Pang Huajin 
Published: August 2019

Abstract
Abstract Background: This study aimed to evaluate the risk factors of transcatheter arterial embolization (TAE) in managing haemorrhage associated with percutaneous nephrolithotomy (PCNL) to improve the surgical effect. Methods: From May 2007 to June 2018, 112 patients (31–60 years) who underwent TAE treatment for haemorrhage after PCNL were retrospectively analyzed. All patient data and embolization details were retrieved from medical records. Univariate analysis was used to identify the risk factors related to clinical outcomes. Results: Technical and clinical success rates were 100% and 93%, respectively. On angiography, we observed injury to the main artery in 1 patient, to secondary branch in 22, to tertiary branch in 58, and to both secondary and tertiary branches in 31. Embolic agents were coils (n =31), gelatin sponge (n=15), and gelatin sponge with coils/microcoils (n =66). Bleeding control failed in 8 patients. Eight patients opted for a second operation, 6 by repeat TAE and 2 by surgery. Bleeding was eventually controlled in all patients. Univariate analysis indicated that extent of transfusion, embolic material used, and injured branches were significantly associated with clinical failure. Conclusions: TAE is effective and safe in treating postoperative bleeding after PCNL. Massive transfusion, embolic material used, and injured branches were related to failure of bleeding control.
A modified single-armed microsurgical vasoepididymostomy for epididymal obstructive azoospermia: intraoperative choice and postoperative consideration
Authors: Liu Nachuan , Li Peng , Zhi Erlei , Yao Chencheng , Yang Chao , Zhao Liangyu , Tian Ruhui , Chen Huixing , Huang Yuhua , Yu Yuexin , Li Zheng 
Published: August 2019

Abstract
Background：To evaluate the clinical outcomes and the time of sperm returning to the ejaculate after a modified single-armed 2-suture longitudinal intussusception vasoepididymostomy (SA-LIVE).
Methods：From March 2015 to December 2018, 134 patients with epididymal obstruction azoospermia underwent the modified single-armed vasoepididymostomy at Shanghai General Hospital. The outcomes and clinical findings were documented and evaluated.
Results: The mean follow-up period was 17 months (range 3-36 months). Patency was assessed by the return of sperm in the ejaculate. The overall patency rate is 55.2 %, and the patency rates were 58.9%, 40.7%, 36.4%, and 58.9% for bilateral surgery, unilateral surgery, proximal anastomosis and distal anastomosis, respectively. The average time it took to achieve patency is 4.11±2.74 months. And in the first six months, 87.8% (65/74) patency patients were reported to found sperm in the ejaculate. The overall pregnancy rate was 40.9 % (29/66) at the follow-up of 3 to 36 months, and the natural pregnancy rate was 30.3 % (20/66). The natural pregnancy rate was 32.1% for bilateral surgery, 33.3% for the site of distal anastomosis，but surprisingly, it was 0% for the site of proximal anastomosis.
Conclusion: Modified SA-LIVE is safe and may achieve favorable patency and pregnancy rates. When double-armed sutures are not accessible, single-armed ones may be a good choice. The expecting patency time is about within one year. Assisting with intraoperative sperm cryopreservation, patients can achieve better pregnancy outcomes. Moreover, the low natural pregnancy rate for the proximal anastomosis suggested that we should reconsider the indications of SA-LIVE for EOA patients.

Key words: obstructive azoospermia; male infertility; vasoepididymostomy; patency; pregnancy
Assessing physical activity in people with mental illness: 23-country reliability and validity of the Simple Physical Activity Questionnaire (SIMPAQ)
Authors: Rosenbaum Simon , Morell Rachel , Abdel-Baki Amal , Ahmadpanah Mohammad , Anilkumar Thekkethayyil Viswananthan , Baie Lara , Bauman Adrian , Bender Stefan , Han Justin Boyan , Brand Serge , Bratland-Sanda Solfrid , Bueno-Antequera Javier , Deslandes Andrea Camaz , Carneiro Lara , Carraro Attilio , Castaneda Carmen Paz , Monteiro Fernanda Castro , Chapman Justin , Chau Josephine , Chen Li-Jung , Chvatalova Barbara , Chwastiak Lydia , Corretti Giogio , Dillon Maurice , Douglas Christie , Egger Stephan , Gaughran Fiona , Gerber Markus , Gobbi Erica , Gould Kirrily , Hatzinger Martin , Holsboer-Tracksler Edith , Hoodbhoy Zara , Imboden Christian , Indu Pillaveetil Sathyadas , Iqbal Romaina , de Jesus-Moraleida Fabianna Resende , Kondo Shinsuke , Ku Po-Wen , Lederman Oscar , Lee Edwin Ho Ming , Malchow Berend , Matthews Evan , Mazur Peter , Meneghelli Anna , Mian Ayesha , Morseth Bente , Munguia-Izquierdo Diego , Nyboe Lene , O'Donoghue Brian , Perram Amy , Richards Justin , Romain Ahmed J , Romaniuk Madeline , Sadeghi-Bahmani Dena , Sarno Mariella , Schuch Felipe , Schweinfurth Nina , Stubbs Brendon , Uwakwe Richard , Damme Tine Van , Stouwe Elisabeth Van Der , Vancampfort Davy , Vetter Stefan , Waterreus Anna , Ward Philip B 
Published: August 2019

Abstract
Background:
Physical inactivity is a key contributor to the global burden of disease and disproportionately impacts the wellbeing of people experiencing mental illness. Increases in physical activity are associated with improvements in symptoms of mental illness and reduction in cardiometabolic risk. Reliable and valid clinical tools that assess physical activity would improve evaluation of intervention studies that aim to increase physical activity and reduce sedentary behaviour in people living with mental illness.
Methods:
The five-item Simple Physical Activity Questionnaire (SIMPAQ) was developed by a multidisciplinary, international working group as a clinical tool to assess physical activity and sedentary behaviour in people living with mental illness. Investigators from 43 centres in 23 countries collected reliability and validity data on the SIMPAQ from patients with DSM or ICD mental illness diagnoses. Test-retest repeatability was assessed one-week apart.
Results:
Criterion SIMPAQ validity was assessed against accelerometer-derived measures of physical activity. Data were obtained from 1,010 participants. The SIMPAQ had good test-retest reliability (Spearman rho approximately 0.70). Criterion validity for moderate-vigorous physical activity was comparable to studies conducted in general population samples. Criterion validity of the sedentary behaviour item was poor. An alternative method to calculate sedentary behaviour had greater criterion validity. This alternative method is recommended for use in future studies employing the SIMPAQ.
Conclusions:
The SIMPAQ is a brief measure of physical activity and sedentary behaviour that can be reliably and validly administered by health professionals.
Abnormal Functional and Structural networks in Rectal Cancer with Depressive symptoms: A Graph Theory Analysis
Authors: Zhang Wenwen , Zou Ying , Li Yuan , Fu Yu , Shi Jie , Huang Gang , Yao Zhijun , Hu Bin 
Published: August 2019

Abstract
Background: Surgery and chemotherapy can cause emotional disorders in patients with rectal cancer (RC). However, few comprehensive studies are conducted on RC patients associated alterations in the topological organization of structural and functional networks.
Methods: Resting-state functional MRI and Diffusion tensor imaging data were collected from 36 RC patients with surgery and chemotherapy and 32 healthy controls (HC). Functional network (FN) was constructed from extracting average time courses for 246 regions of interest (ROI) and structural network (SN) was established by deterministic tractography. Graph theoretical analysis was used to calculate small-worldness property, clustering coefficients, shortest path length and network efficiency. Additionally, we assess network resilient on FN and SN.
Results: Abnormal small-worldness property of FN and SN were found in RC patients. The FN and SN exhibited increased local efficiency and global efficiency respectively in RC patients.The increased nodal efficiency in RC patients were mainly found in the frontal lobe, parietal lobe and limbic lobe for FN and SN, while the decreased nodal efficiency were distributed in subcortical nuclei, parietal lobe and limbic lobe only for SN. In network resilient analysis, the RC patients showed less resilient to targeted or random node deletion in both networks compared with HC. Moreover, FN is more robust than SN for all participants.
Conclusions: This study revealed that topological organizations of the FN and SN may be disrupted in RC patients. Brain network reorganization is a compensation mechanism for brain impairment after surgery and chemotherapy.
The psychometrics and diagnostic properties of the Montreal Cognitive Assessment 5-min protocol in screening for Mild Cognitive Impairment and dementia among older adults in Tanzania: A validation study
Authors: Masika Golden Mwakibo , Yu Doris S.F. , Li Polly W.C. , Wong Adrian , Lin Rose S.Y. 
Published: August 2019

Abstract
Introduction

The prevalence of dementia in Tanzania, as in other developing countries is progressively increasing. Yet international screening instruments for mild cognitive impairment are lacking. The aim of this study was to determine the psychometrics and the diagnostic ability of the Montreal Cognitive Assessment 5 minutes protocol (MoCA-5-min) among older adult in the rural Tanzania.

Methods

The MoCA-5-min and the IDEA cognitive screening were concurrently administered through face to face to 202 community-dwelling older adults in Chamwino district. Exploratory factor analysis (EFA) using principal component method and oblique rotation was performed to determine the underlying factor structure of the scale. The concurrent, construct as well as predictive validities of the MoCA-5-min were examined by comparing its score with IDEA cognitive screening and psychiatrist’s diagnosis using DSM-V criteria respectively.

Results

The EFA found that all the MoCA-5-min items highly loaded into one component, with factor loading ranging from 0.550 to 0.879. The intraclass correlation coefficient for 6 weeks test-retest reliability was 0.85. Its strong significant correlation with the IDEA screening (Pearson's r = 0.614, p < 0.001) demonstrated a good concurrent validity. Using the psychiatrist’s rating as the gold standard, MoCA-5-min demonstrated the optimal cut-off score for MCI at 22, which yielded the sensitivity of 80% and specificity of 74%; and dementia at score of 16 giving a sensitivity of 90% and specificity of 80%. Upon stratifying the sample into different age groups, the optimal cut-off scores tended to decrease with the increase in age.

Conclusion

The MoCA-5-min is reliable and provides a valid and accurate measure of cognitive decline among older population in the rural settings of Tanzania. The use of varying cut-off scores across age groups may ensure more precise discriminatory power of the MoCA-5-min.
Systemic Erythropoietin Concentration and its Correlation with Stage of Diabetic Retinopathy
Authors: Davidović Sofija , Nikola Babić , Sandra Jovanović , Sava Barišić , Desanka Grković , Aleksandar Miljković 
Published: August 2019

Abstract
Summary:
Background: Erythropoietin (Epo) is one of systemic angiogenic factors, and its role in ocular angiogenesis and in diabetic retinopathy (DR) is not yet fully understood. Latest research data reveal possible correlation of higher EPO concentrations of erythropoietin in blood and in the eye, with more severe of stages of DR.
The main aim of this work was to examine the possible influence of serum concentrations of erythropoietin on the development and stages of diabetic retinopathy in patients with diabetes mellitus type 2.
Methods: The research involved 90 patients examined at University Eye Clinic in Clinical Center of Vojvodina in Novi Sad, Serbia. First group comprised of 60 patients with diabetes mellitus lasting 10 years or more, with diabetic retinopathy. Second, control group, consisted of 30 healthy individuals. In the first group of 60 diabetic patients, 30 of them had non-proliferative diabetic retinopathy (NPDR), and 30 had proliferative diabetic retinopathy (PDR). Laboratory EPO serum levels were determined, and they were correlated to the stage of DR. Concentration of EPO was assessed by ELISA method at the end of the study.
Results: The highest average concentration of EPO in serum (9.95 mIU/ml) was determined in group of diabetics with PDR. The lowest average concentration of EPO in serum (6.90 mIU/ml) was found in control group. The average concentration of Epo in serum in group of diabetics with NPDR was 7.00 mIU/ml. EPO concentration in serum was elevated in group of PDR, and it was directly proportional to the level of clinical stadium of PDR, being significantly higher in moderate and severe subgroup of PDR comparing to control healthy subjects, NPDR and mild PDR (h=9.858, p=0.007).
Conclusions: Significantly elevated serum concentration of EPO in advanced stages of DR, and positive correlation between EPO serum concentration and clinical stadium of PDR, suggest that erythropoietin presents one of the important growth factors from blood, which plays role in retinal ischemia and angiogenesis in diabetic retinopathy, especially in the proliferative stage of this disease.
Keywords: diabetic retinopathy; erythropoietin; glycated hemoglobin; non-proliferative diabetic retinopathy; proliferative diabetic retinopathy.