bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)
Authors: Li Pingbo , Zhou Hao , Yang Hanyuan , Xia Duo , Liu Rongjia , Sun Ping , Wang Quanxiu , Gao Guanjun , Zhang Qinglu , Wang Gongwei , He Yuqing 
Published: February 2020

Abstract
Background
Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations.

Results
In this study, two F1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6.

Conclusions
Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.
Role of Tamsulosin with or without Deflazacort to facilitate stone clearance after ESWL: a single-center randomized controlled study
Authors: Jain Saurabh , Singh Mahendra , Khanna Sudhir , Rasool Shahnawaz , Gupta Manu , Kathuria Sachin , Pathak Amrendra , Pandey Himanshu 
Published: February 2020

Abstract
Background
Extracorporeal shock wave lithotripsy (ESWL) is the treatment of choice for upper tract calculi of moderate size. After ESWL, various factors affect the passage of small fragments through ureter like fragment’s size and location. To facilitate fragment passage, a lot of medications have been tried and few have stood the test of the time. In this prospective study, we evaluated the role of Tamsulosin with or without Deflazacort versus no treatment after ESWL for ureteric and renal stones in terms of requirement of the number of ESWL sessions, stone clearance rate, stone expulsion time and analgesia requirements.

Results
Patients presenting between age-groups of 18–70 years with solitary renal/ureteric calculus of size between 6 and 15 mm in major axis with Hounsfield unit less than 1000 were recruited in one of the three groups (A, B and C) randomly. Patients in Group A were prescribed Tamsulosin (0.4 mg once daily) with Deflazacort (30 mg once daily), Group B were given Tamsulosin (0.4 mg once daily), and Group C received no treatment (analgesics SOS and hydration therapy) after undergoing ESWL. Two hundred and twenty-five patients were recruited in Group A, and 240 patients were recruited in Group B and Group C each. There was an insignificant difference for required mean ESWL sessions and stone clearance rate between three groups. There was an early clearance of stone fragments in Group A than in Groups B and C, and it was statistically significant between Group A and Group C, specifically in the subgroup of stone size 10.1–15 mm. The requirement of mean analgesic tablets difference was significant between Groups A and C.

Conclusions
Tamsulosin with Deflazacort decreases the number of required ESWL sessions and improves complete stone clearance, but the difference is not significant. There were significant improvement in facilitating early stone clearance and decrease in requirement of mean analgesic tablets after ESWL with Tamsulosin and Deflazacort. Thus, Tamsulosin with Deflazacort can be used safely to facilitate stone clearance without increased complication rate.
The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity
Authors: Zhou Yan , Liang Yuan , Yan Qing , Zhang Liang , Chen Dianbao , Ruan Lingwei , Kong Yuan , Shi Hong , Chen Mingliang , Chen Jianming 
Published: February 2020

AbstractBackgroundHorseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against invading microbes are still unclear.ResultsHere, we describe the 2.06 Gbp genome assembly ofTachypleus tridentatuswith 24,222 predicted protein-coding genes. Comparative genomics shows thatT. tridentatusand the Atlantic horseshoe crabLimulus polyphemushave the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. Divergence time dating results show that the last common ancestor of Asian horseshoe crabs (includingT. tridentatusandC. rotundicauda) andL. polyphemusappeared approximately 130 Mya (121–141), and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57–69). Hox gene analysis suggests two clusters in both horseshoe crab assemblies. Surprisingly, selective analysis of immune-related gene families revealed the high expansion of conserved pattern recognition receptors. Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. Intact coagulation cascade-related genes were present in theT. tridentatusgenome with a higher number of coagulation factor genes. Moreover, most reported antibacterial peptides have been identified inT. tridentatuswith their potentially effective antimicrobial sites.ConclusionsThe draft genome ofT. tridentatuswould provide important evidence for further clarifying the taxonomy and evolutionary relationship of Chelicerata. The expansion of conserved immune signalling pathway genes, coagulation factors and intact antimicrobial peptides inT. tridentatusconstitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments.
STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency
Authors: Islam Mazharul , Sarker Kowshika , Das Trisha , Reaz Rezwana , Bayzid Md. Shamsuzzoha 
Published: February 2020

Abstract
Background
Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence resulting from incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent process. Maximum likelihood and Bayesian MCMC methods can potentially result in accurate trees, but they do not scale well to large datasets.

Results
We present STELAR (Species Tree Estimation by maximizing tripLet AgReement), a new fast and highly accurate statistically consistent coalescent-based method for estimating species trees from a collection of gene trees. We formalized the constrained triplet consensus (CTC) problem and showed that the solution to the CTC problem is a statistically consistent estimate of the species tree under the multi-species coalescent (MSC) model. STELAR is an efficient dynamic programming based solution to the CTC problem which is highly accurate and scalable. We evaluated the accuracy of STELAR in comparison with SuperTriplets, which is an alternate fast and highly accurate triplet-based supertree method, and with MP-EST and ASTRAL – two of the most popular and accurate coalescent-based methods. Experimental results suggest that STELAR matches the accuracy of ASTRAL and improves on MP-EST and SuperTriplets.

Conclusions
Theoretical and empirical results (on both simulated and real biological datasets) suggest that STELAR is a valuable technique for species tree estimation from gene tree distributions.
From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor
Authors: Bhowal Bidisha , Singla-Pareek Sneh L. , Sopory Sudhir K. , Kaur Charanpreet 
Published: February 2020

Abstract
Background
The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), to convert MG into D-lactate, which is further metabolized to pyruvate by D-lactate dehydrogenases (D-LDH). Since D-lactate formation occurs solely by the action of glyoxalase enzymes, its metabolism may be considered as the ultimate step of MG detoxification. By maintaining steady state levels of MG and other reactive dicarbonyl compounds, the glyoxalase pathway serves as an important line of defence against glycation and oxidative stress in living organisms. Therefore, considering the general role of glyoxalases in stress adaptation and the ability of Sorghum bicolor to withstand prolonged drought, the sorghum glyoxalase pathway warrants an in-depth investigation with regard to the presence, regulation and distribution of glyoxalase and D-LDH genes.

Result
Through this study, we have identified 15 GLYI and 6 GLYII genes in sorghum. In addition, 4 D-LDH genes were also identified, forming the first ever report on genome-wide identification of any plant D-LDH family. Our in silico analysis indicates homology of putatively active SbGLYI, SbGLYII and SbDLDH proteins to several functionally characterised glyoxalases and D-LDHs from Arabidopsis and rice. Further, these three gene families exhibit development and tissue-specific variations in their expression patterns. Importantly, we could predict the distribution of putatively active SbGLYI, SbGLYII and SbDLDH proteins in at least four different sub-cellular compartments namely, cytoplasm, chloroplast, nucleus and mitochondria. Most of the members of the sorghum glyoxalase and D-LDH gene families are indeed found to be highly stress responsive.

Conclusion
This study emphasizes the role of glyoxalases as well as that of D-LDH in the complete detoxification of MG in sorghum. In particular, we propose that D-LDH which metabolizes the specific end product of glyoxalases pathway is essential for complete MG detoxification. By proposing a cellular model for detoxification of MG via glyoxalase pathway in sorghum, we suggest that different sub-cellular organelles are actively involved in MG metabolism in plants.
Non-alcoholic fatty liver disease among patients with sleep disorders: a Nationwide study of Taiwan
Authors: Wei Yu-Ting , Lee Peng-Yi , Lin Cheng-Yu , Chen Hsuan-Ju , Lin Che-Chen , Wu Jin-Shang , Chang Yin-Fan , Wu Chen-Long , Guo How-Ran 
Published: February 2020

Abstract
Background
Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases. Studies have shown that sleep apnea is associated with NAFLD. However, studies on the association between sleep disorders in general and NAFLD are limited. We conducted a nationwide population-based longitudinal study to evaluate this potential association.

Methods
We identified patients diagnosed with sleep disorders in the years 2000 through 2005 in Taiwan using the National Health Insurance Research Database and selected an equal number of patients without sleep disorders from the same database as the comparison cohort. The patients were followed from the index date to the diagnosis of NAFLD or the end of 2013. We used Cox proportional hazards models to estimate the risk of NAFLD associated with sleep disorders.

Results
A total of 33,045 patients with sleep disorders were identified. The incidence of NAFLD was 14.0 per 10,000 person-year in patients with sleep disorders and 6.2 per 10,000 person-year in the comparison cohort. The adjusted hazard ratio (AHR) of NAFLD associated with sleep disorders was 1.78 (95% confidence interval [95%CI]: 1.46–2.16), and other independent risk factors included male sex (AHR = 1.31, 95%CI: 1.12–1.54), age 40–59 years (AHR = 1.49, 95%CI: 1.21–1.82), and dyslipidemia (AHR = 2.51, 95%CI: 2.08–3.04). In the subgroup analyses, both patients with (AHR = 2.24, 95%CI: 1.05–4.77) and without (AHR = 1.77, 95%CI: 1.46–2.15) sleep apnea had an increased risk of NAFLD.

Conclusions
Sleep disorders are associated with NAFLD, even in patients without sleep apnea. Further studies are warranted to explore the mechanisms of the association.
Correction to: Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection
Authors: Dobbins G. Clement , Patki Amit , Chen Dongquan , Tiwari Hemant K. , Hendrickson Curtis , Britt William J. , Fowler Karen , Chen Jake Y. , Boppana Suresh B. , Ross Shannon A. 
Published: February 2020

After publication of the original article [1], we were notified that Fig. 3 has “Fig. 1” posted on the top of it and Figs. 4 and 5 have “Genomic Position” in a different spot.
Epidemiological and clinical characteristics of healthcare-associated infection in elderly patients in a large Chinese tertiary hospital: a 3-year surveillance study
Authors: Zhao Xia , Wang Lihong , Wei Nan , Zhang Jingli , Ma Wenhui , Zhao Huijie , Han Xu 
Published: February 2020

Abstract
Background
We analyzed the results of a 3-year surveillance study on the epidemiological and clinical characteristics of healthcare associated-infections (HAIs) in elderly inpatients in a large tertiary hospital in China.

Methods
Real-time surveillance was performed from January 1, 2015 to December 31, 2017. All HAIs were identified by infection control practitioners and doctors. Inpatient data were collected with an automatic surveillance system.

Results
A total of 134,637 inpatients including 60,332 (44.8%) elderly ≥60 years were included. The overall incidence of HAI was 2.0%. The incidence of HAI in elderly patients was significantly higher than that in non-elderly patients (2.6% vs. 1.5%, χ2 = 202.421, P < 0.01) and increased with age. The top five sites of HAIs in the elderly were the lower respiratory tract, urinary tract, blood stream, antibiotic-associated diarrhea, and surgical site. The five most common pathogens detected in elderly HAI patients were Candida albicans, Klebsiella pneumonia, Acinetobacter baumannii, Escherichia coli, and Pseudomonas aeruginosa. The incidence of ventilator-associated pneumonia in the elderly was lower than in the non-elderly, catheter-associated urinary tract infections were more common in elderly patients, and the rate of central line-associated bloodstream infection was similar between groups. The numbers of male patients and patients with comorbidities and special medical procedures (e.g., intensive care unit admission, cerebrovascular disease, brain neoplasms, hypertension, hyperlipidemia, diabetes mellitus, coronary artery disease, chronic obstructive pulmonary disease, malignant tumor, malignant hematonosis, and osteoarthropathy) were significantly higher in the elderly group, but the number of patients who underwent surgery was lower.

Conclusion
We observed a significantly higher overall incidence of HAI in elderly inpatients ≥60 compared to non-elderly inpatients < 60 years, but the trend was different for device-associated HAIs, which was attributed to the higher rates of comorbidities and special medical procedures in the elderly group. The main HAI sites in elderly inpatients were the lower respiratory tract, urinary tract, and bloodstream, and the main pathogens were gram-negative bacilli and Candida albicans.
Healthy pregnancies and essential fats: focus group discussions with Zambian women on dietary need and acceptability of a novel RUSF containing fish oil DHA
Authors: Chunda-Liyoka Catherine , Lubeya Mwansa Ketty , Imakando Mercy , Kisling Sophia , Majid Sonoor , Willis Mary S. , Wood Charles , Kankasa Chipepo , DiRusso Concetta C. 
Published: February 2020

Abstract
Background
Nut butter-based Ready to Use Supplemental Foods (RUSF) are an effective way to add nutrients and calories to diets of malnourished and food insecure populations. The RUSF formulations have been further modified to add micronutrients including iron and folic acid needed during pregnancy and lactation. Because docosahexaenoic acid (DHA, C22:6 n-3) enhances fetal development and birth outcomes, it has been suggested that perhaps RUSF formulations for pregnancy should also include this Omega 3 fatty acid. The goal of the present study was to gain an understanding of Zambian women’s knowledge of nutritional needs in pregnancy through structured focus group discussions, and to formulate and determine the acceptability of a RUSF with DHA.

Methods
Structured focus group sessions were conducted among women attending an antenatal clinic at the University Teaching Hospitals in Lusaka, Zambia. Dietary and nutrition knowledge was surveyed through structured dialogue that was recorded by audio and transcribed verbatim. An RUSF containing 400 mg DHA from fish oil in 50 g RUSF was designed and assessed for fatty acid content and product stability. Participants then sampled the RUSF-DHA, provided feedback on taste, and were surveyed about willingness to consume the novel formula using a standardized hedonic instrument.

Results
The participants’ knowledge of foods recommended for use in pregnancy included fruits, vegetables, meat, and fish. Most women reported eating fish at least once per week, although the specific type of fish varied. Most did not have prior knowledge of the importance of consuming fish during pregnancy or that some fish types were more nutritional than others as they included omega 3 fatty acids. The participants were uniformly accepting of the RUSF-DHA for the purpose of enhancing birth and developmental outcomes, but were critical of the aroma in hedonic testing.

Conclusions
Women were committed to consuming a healthy diet that would impact the outcome of pregnancy, and were receptive to advice on the importance of consuming foods such as fish as a source of DHA. The RUSF-DHA formulation was acceptable due to the potential benefits for the developing infant, however, the fishy odor may be limiting for long-term daily use.
Young-onset colorectal cancer in the North East of Scotland: survival, clinico-pathological features and genetics
Authors: Perrott Sarah , Laurie Kirsten , Laws Kirsten , Johnes Annie , Miedzybrodzka Zosia , Samuel Leslie 
Published: February 2020

Abstract
Background
Colorectal cancer (CRC) in patients aged under 55 years is on the rise, constituting approximately 10% of cases. Our aim was to determine the survival and clinico-pathological details of young-onset CRC (yCRC), as well as audit the referral rate to genetic services and thus establish the incidence of inherited cancer syndromes.

Methods
A retrospective case note review was conducted for patients aged under 55 years who were diagnosed with CRC between 2005 and 2015 in the North East of Scotland. Cases were identified by pathology records and data was obtained from patient notes. Analysis was performed using SPSS version 25 (IBM, New York, USA) to produce Kaplan-Meier survival estimates, descriptive statistics and markers predictive for genetic referral.

Results
Data from 345 patients (age range 22–54 years) were identified. The one year, five year and overall survival rates were found to be 89, 63 and 55%, respectively. Most patients (61%) presented with advanced disease. Of 201 patients that met criteria for genetic referral, only 93 (46%) were referred to genetic services. Microsatellite instability (MSI) was identified in 14% of those referred.

Conclusion
Survival in yCRC was found to be better than that in later onset disease, despite higher rates of advanced disease. Patients were under-referred to genetic services, where a significant proportion were found to be MSI positive and investigated for Lynch syndrome.
Persistent depressive disorder across the adult lifespan: results from clinical and population-based surveys in Germany
Authors: Nübel Julia , Guhn Anne , Müllender Susanne , Le Hong Duyen , Cohrdes Caroline , Köhler Stephan 
Published: February 2020

Abstract
Background
Although the individual and economic disease burden of depression is particularly high for long-term symptoms, little is known of the lifetime course of chronic depression. Most evidence derives from clinical samples, and the diagnostic distinction between persistent depressive disorder (PDD) and non-chronic major depression (NCMDD) is still debated. Thus, we examined characteristics of PDD among clinical vs. non-clinical cases, and the associated disease burden at a population level.

Methods
Data were drawn from the mental health module of the German Health Interview and Examination Survey for Adults (DEGS1-MH, 2009–2012, n = 4483) and a clinical sample of PDD inpatients at Charité – Universitätsmedizin Berlin (2018–2019, n = 45). The DSM-5 definition of PDD was operationalized a priori to the study using interview-based DSM-IV diagnoses of dysthymia and major depression lasting at least 2 years in both surveys. Additional depression characteristics (depression onset, self-classified course, suicidality, comorbid mental disorders, treatment history and current depressive symptoms [Patient Health Questionnaire-9]) were assessed. In the DEGS1-MH, health-related quality of life (Short Form Health Survey-36, SF-36), chronic somatic conditions, number of sick days (past 12 months) or days with limitations in normal daily life activities (past 4 weeks), and health service utilization (past 12 months) were compared for PDD vs. NCMDD.

Results
PDD cases from the clinical sample had a significantly earlier depression onset, a higher proportion of self-classification as persistent course, and treatment resistance than PDD and NCMDD cases in DEGS1-MH. At a population level, PDD cases showed worse outcomes compared with NCMDD cases in terms of somatic comorbidity, SF-36 mental component score, and activity limitations owing to mental health problems, as well as a higher risk for outpatient mental health care contact.

Conclusions
The distinction between PDD and NCMDD proposed for DSM-5 seems warranted. Early onset depression, self-classification as persistent depressive course, and treatment resistance are suggested as markers of more severe and chronic depression courses. At a population level, PDD is associated with remarkably higher individual and economic disease burden than NCMDD, highlighting the need to improve medical recognition of chronic courses and establish specific treatment concepts for chronic depression.