bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the ‘Oat-Like Rice’ Caused by a Novel Allele OsMADS1Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L.
Authors: Li Penghui , Li Hui , Liu Zhijian , Zhuang Yong , Wei Ming , Gu Yuanyang , Liu Yangxuan , Sun Xiuqiang , Tang Yuying , Yue Lu , Lu Longxiang , Luo Dagang , Huang Weizao , Tu Shengbin , Wang Songhu 
Published: October 2020

Abstract
Background
Grain shape is a critical agronomic trait affecting grain yield and quality. Exploration and functional characterization of grain shape-related genes will facilitate rice breeding for higher quality and yield.

Results
Here, we characterized a recessive mutant named Oat-like rice for its unique grain shape which highly resembles oat grains. The Oat-like rice displayed abnormal floral organs, an open hull formed by remarkably elongated leafy lemmas and paleae, occasionally formed conjugated twin brown rice, an aberrant grain shape and a low seed setting rate. By map-based cloning, we discovered that Oat-like rice harbors a novel allele of OsMADS1 gene (OsMADS1Olr), which has a spontaneous point mutation that causes the substitution of an amino acid that is highly conserved in the MADS-box domain of the MADS-box family. Further linkage analysis indicated that the point mutation in the OsMADS1Olr is associated with Oat-like rice phenotype, and expression analysis of the OsMADS1 by qRT-PCR and GUS staining also indicated that it is highly expressed in flower organs as well as in the early stages of grain development. Furthermore, OsMADS1Olr-overexpressing plants showed similar phenotypes of Oat-like rice in grain shape, possibly due to the dominant negative effect. And OsMADS1-RNAi plants also displayed grain phenotypes like Oat-like rice. These results suggested that OsMADS1Olr is responsible for the Oat-like rice phenotype including aberrant grain shape. Moreover, the expression levels of representative genes related to grain shape regulation were apparently altered in Oat-like rice, OsMADS1Olr-overexpressing and OsMADS1-RNAi transgenic plants. Finally, compared with Oat-like rice, OsMADS1Olr-overexpressing and OsMADS1-RNAi plants, mild phenotype of seed-specific OsMADS1-RNAi transgenic plants indicated that OsMADS1 may has has a direct regulation role in grain development and the grain phenotypes of Oat-like rice, OsMADS1Olr-overexpressing and OsMADS1-RNAi plants are majorly caused by the abnormal lemma and palea development.

Conclusions
Altogether, our results showed that grain shape and a low seed setting rate of the notable ‘Oat-like rice’ are caused by a spontaneous point mutation in the novel allele OsMADS1Olr. Furthermore, our findings suggested that OsMADS1 mediates grain shape possibly by affecting the expression of representative genes related to grain shape regulation. Thus, this study not only revealed that OsMADS1 plays a vital role in regulating grain shape of rice but also highlighted the importance and value of OsMADS1 to improve the quality and yield of rice by molecular breeding.
Joint effect of race/ethnicity or location of residence and sex on low density lipoprotein-cholesterol among veterans with type 2 diabetes: a 10-year retrospective cohort study
Authors: Weeda Erin R. , Bishu Kinfe G. , Ward Ralph , Axon R. Neal , Taber David J. , Gebregziabher Mulugeta 
Published: October 2020

Abstract
Background
Cardiovascular (CV) disease is the leading cause of death among United States women. Rural residence and ethnic-minority status are individually associated with increased CV mortality. Managing dyslipidemia is important in the prevention of CV mortality. However, the impact of race/ethnicity and location of residence on sex differences in dyslipidemia management is not well understood. Therefore, we sought to understand the joint effects of race/ethnicity and location of residence on lipid management differences between veteran men and women with type 2 diabetes (T2D).

Methods
Veterans Health Administration and Centers for Medicare and Medicaid Services data were used to perform a longitudinal cohort study of veterans with T2D (2007–2016). Mixed effects logistic regression with a random intercept was used to model the association between sex and low-density lipoprotein (LDL) > 100 mg/dL and its interaction with race/ethnicity and location of residence after adjusting for all measured covariates.

Results
When female sex and rural location of residence were both present, they were associated with an antagonistic harmful effect on LDL. Similar antagonistic harmful effects on LDL were observed when the joint effect of female sex and several minority race/ethnicity groups were evaluated. After adjusting for measured covariates, the odds of LDL > 100 mg/dL were higher for urban women (OR = 2.66, 95%CI 2.48–2.85) and rural women (OR = 3.26, 95%CI 2.94–3.62), compared to urban men. The odds of LDL > 100 mg/dL was the highest among non-Hispanic Black (NHB) women (OR = 5.38, 95%CI 4.45–6.51) followed by non-Hispanic White (NHW) women (OR = 2.59, 95%CI 2.44–2.77), and Hispanic women (OR = 2.56, 95%CI 1.79–3.66).

Conclusion
Antagonistic harmful effects on LDL were observed when both female sex and rural location of residence were present. These antagonistic effects on LDL were also present when evaluating the joint effect of female sex and several minority race/ethnicity groups. Disparities were most pronounced in NHB and rural women, who had 5.4 and 3.3 times the odds of elevated LDL versus NHW and urban men after adjusting for important covariates. These striking effect sizes in a population at high cardiovascular risk (i.e., older with T2D) suggest interventions aimed at improving lipid management are needed for individuals falling into one or more groups known to face health disparities.
Usefulness of preoperative coronary computed tomography angiography in high risk non-cardiovascular surgery old patients with unknown or suspected coronary artery disease
Authors: Li Xue-Ming , Xu Zhong-Zhi , Wen Zhi-Peng , Pei Jiao , Dai Wei , Wang Huai-Ming , Reng Jing , Zhou Peng , Xu Guo-Hui 
Published: October 2020

Abstract
Background
Cumulative evidence has shown that the non-invasive modality of coronary computed tomography angiography (CCTA) has evolved as an alternative to invasive coronary angiography, which can be used to quantify plaque burden and stenosis and identify vulnerable plaque, assisting in diagnosis, prognosis and treatment. With the increasing elderly population, many patients scheduled for non-cardiovascular surgery may have concomitant coronary artery disease (CAD). The aim of this study was to investigate the usefulness of preoperative CCTA to rule out or detect significant CAD in this cohort of patients and the impact of CCTA results to clinical decision-making.

Methods
841 older patients (age 69.5 ± 5.8 years, 74.6% males) with high risk non-cardiovascular surgery including 771 patients with unknown CAD and 70 patients with suspected CAD who underwent preoperative CCTA were retrospectively enrolled. Multivariate logistic regression analysis was performed to determine predictors of significant CAD and the event of cancelling scheduled surgery in patients with significant CAD.

Results
677 (80.5%) patients had non-significant CAD and 164 (19.5%) patients had significant CAD. Single-, 2-, and 3- vessel disease was found in 103 (12.2%), 45 (5.4%) and 16 (1.9%) patients, respectively. Multivariate analysis demonstrated that positive ECG analysis and Agatston score were independently associated with significant CAD, and the optimal cutoff of Agatston score was 195.9. The event of cancelling scheduled surgery was increased consistently according to the severity of stenosis and number of obstructive major coronary artery. Multivariate analysis showed that the degree of stenosis was the only independent predictor for cancelling scheduled surgery. In addition, medication using at perioperative period increased consistently according to the severity of stenosis.

Conclusions
In older patients referred for high risk non-cardiovascular surgery, preoperative CCTA was useful to rule out or detect significant CAD and subsequently influence patient disposal. However, it might be unnecessary for patients with negative ECG and low Agatston score.
Trial registration Retrospectively registered.
Team-based care improves quality of diabetes care -Family Practice Integrated Care Project in Taiwan
Authors: Chang Jerry Che-Jui , Hwang Shinn-Jang , Chen Tzeng-Ji , Chiu Tai-Yuan , Yang Hsiao-Yu , Chen Yu-Chun , Huang Cheng-Kuo , Jan Chyi-Feng 
Published: October 2020

Abstract
Background
The Family Practice Integrated Care Project (FPICP) is a team-based program in Taiwan initiated in 2003. This study investigates the influence of FPICP on the quality of diabetes care.

Methods
This population-based cohort study used Taiwan’s National Health Insurance Administration data on FPICP (fiscal year 2015–2016, with follow-up duration of one year). Participants included diabetic patients aged ≥30 in primary care clinics.
We used conditional logistic regression modeling of patient characteristics and annual diabetes examinations and compared FPICP participants with non-participating candidates. Main outcome measures included completion of annual diabetes examinations, including glycated hemoglobin (A1c), low-density lipoprotein (LDL), urine microalbumin (MAU), routine urinalysis (UR), and fundus examination (FE).

Results
The sample included 298,208 FPICP participants and 478,778 non-participating candidates. After 1:1 propensity score matching, the examination completion rates for FPICP participants and non-participants, respectively, were 94.4% versus 93.6% in A1c, 84.2% versus 83.8% in LDL, 61.9% versus 60.1% in MAU, 59.2% versus 58.0% in UR, and 30.1% versus 32.4% in FE.

Conclusion
Our findings indicate that a program like FPICP helps improve the quality of diabetes care through regular examinations of Alc, LDL, MAU, and UR.
Comparing proton pump inhibitors with histamin-2 receptor blockers regarding the risk of osteoporotic fractures: a nested case-control study of more than 350,000 Korean patients with GERD and peptic ulcer disease
Authors: Park Joo-Hyun , Lee Jessie , Yu Su-Yeon , Jung Jin-Hyung , Han Kyungdo , Kim Do-Hoon , Rhee Jinnie 
Published: October 2020

Abstract
Background
Patients with peptic ulcer disease (PUD) and gastroesophageal reflux disease (GERD) are more likely to receive long-term therapy with proton pump inhibitors (PPIs). This study aimed to investigate the risk of osteoporotic fractures in PPI users compared to histamine-2 receptor antagonist (H2RA) users and the association between fractures and the duration and regular use of PPI.

Methods
A population-based, nationwide nested case-control study from January 2006 to December 2015 was performed using Korean National Health Insurance Service claims data. We included patients ≥50 years of age, without previous fractures, newly prescribed with PPI or H2RA, and diagnosed with PUD or GERD from 2006 to 2015. Patients with osteoporotic fracture (n = 59,240) were matched with the non-fracture control group (n = 296,200) at a 1:5 ratio based on sex, age, cohort entry date, follow-up duration, and bisphosphonate use. The osteoporotic fractures were defined using the diagnostic codes of claims data (M80, M81, M82, M484, M485, S220, S221, S320, S327, S422, S423, S525, S526, S72).

Results
The higher the cumulative use of PPIs, the higher the osteoporotic fracture risk (P for trend < 0.001). The risk of osteoporotic fracture in the patients whose cumulative use of PPI was more than 1 year was higher than that of others (OR: 1.42, 95% CI: 1.32–1.52). Patients who regularly used PPI in the recent 1 year had a higher risk of osteoporotic fracture than exclusive H2RA users (OR: 1.37, 95% CI: 1.26–1.50).

Conclusions
The risk of osteoporotic fracture increased with the duration of PPI use, especially when PPI was used for ≥1 year and regularly in the recent 1 year.
Robust segmentation of lung in chest x-ray: applications in analysis of acute respiratory distress syndrome
Authors: Reamaroon Narathip , Sjoding Michael W. , Derksen Harm , Sabeti Elyas , Gryak Jonathan , Barbaro Ryan P. , Athey Brian D. , Najarian Kayvan 
Published: October 2020

AbstractBackgroundThis study outlines an image processing algorithm for accurate and consistent lung segmentation in chest radiographs of critically ill adults and children typically obscured by medical equipment. In particular, this work focuses on applications in analysis of acute respiratory distress syndrome – a critical illness with a mortality rate of 40% that affects 200,000 patients in the United States and 3 million globally each year.MethodsChest radiographs were obtained from critically ill adults (n = 100), adults diagnosed with acute respiratory distress syndrome (ARDS) (n = 25), and children (n = 100) hospitalized at Michigan Medicine. Physicians annotated the lung field of each radiograph to establish the ground truth. A Total Variation-based Active Contour (TVAC) lung segmentation algorithm was developed and compared to multiple state-of-the-art methods including a deep learning model (U-Net), a random walker algorithm, and an active spline model, using the Sørensen–Dice coefficient to measure segmentation accuracy.ResultsThe TVAC algorithm accurately segmented lung fields in all patients in the study. For the adult cohort, an averaged Dice coefficient of 0.86 ±0.04 (min: 0.76) was reported for TVAC, 0.89 ±0.12 (min: 0.01) for U-Net, 0.74 ±0.19 (min: 0.15) for the random walker algorithm, and 0.64 ±0.17 (min: 0.20) for the active spline model. For the pediatric cohort, a Dice coefficient of 0.85 ±0.04 (min: 0.75) was reported for TVAC, 0.87 ±0.09 (min: 0.56) for U-Net, 0.67 ±0.18 (min: 0.18) for the random walker algorithm, and 0.61 ±0.18 (min: 0.18) for the active spline model.ConclusionThe proposed algorithm demonstrates the most consistent performance of all segmentation methods tested. These results suggest that TVAC can accurately identify lung fields in chest radiographs in critically ill adults and children.
Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles
Authors: Molinari Elisa , Srivastava Shalabh , Dewhurst Rebecca M. , Sayer John A. 
Published: October 2020

Abstract
Background
PKHD1 is the main genetic cause of autosomal recessive polycystic kidney disease (ARPKD), a hereditary hepato-renal fibrocystic disorder which is the most important cause of end-stage renal disease during early childhood. ARPKD can also present in adulthood with milder phenotypes. In this study, we describe a 24-year-old woman with atypical polycystic kidney, no family history of renal disease and no obvious extra-renal manifestations who was referred for genetic investigation.

Methods
We used a combination of next generation sequencing, Sanger sequencing and RNA and microscopy studies performed on urine-derived renal epithelial cells (URECs) to provide a genetic diagnosis of ARPKD.

Results
A next generation sequencing panel of cystic ciliopathy genes allowed the identification of two heterozygous sequence changes in PKHD1 (c.6900C > T; p.(Asn2300=) and c.7964A > C; p.(His2655Pro)). The pathogenicity of the synonymous PKHD1 variant is not clear and requires RNA studies, which cannot be carried out efficiently on RNA extracted from proband blood, due to the low expression levels of PKHD1 in lymphocytes.
Using URECs as a source of kidney-specific RNA, we show that PKHD1 is alternatively spliced around exon 43, both in control and proband URECs. The variant p.(Asn2300=) shifts the expression ratio in favour of a shorter, out-of-frame transcript. To further study the phenotypic consequence of these variants, we investigated the ciliary phenotype of patient URECs, which were abnormally elongated and presented multiple blebs along the axoneme.

Conclusions
We confirm the power of URECs as a tool for functional studies on candidate variants in inherited renal disease, especially when the expression of the gene of interest is restricted to the kidney and we describe, for the first time, ciliary abnormalities in ARPKD patient cells.
Effects of prenatal mindfulness-based childbirth education on child-bearers’ trajectories of distress: a randomized control trial
Authors: Sbrilli Marissa D. , Duncan Larissa G. , Laurent Heidemarie K. 
Published: October 2020

Abstract
Background
The perinatal period is a time of immense change, which can be a period of stress and vulnerability for mental health difficulties. Mindfulness-based interventions have shown promise for reducing distress, but further research is needed to identify long-term effects and moderators of mindfulness training in the perinatal period.

Methods
The current study used data from a pilot randomized control trial (RCT) comparing a condensed mindfulness-based childbirth preparation program—the Mind in Labor (MIL)—to treatment as usual (TAU) to examine whether prenatal mindfulness training results in lower distress across the perinatal period, and whether the degree of benefit depends on child-bearers’ initial levels of risk (i.e., depression and anxiety symptoms) and protective (i.e., mindfulness) characteristics. Child-bearers (N = 30) in their third trimester were randomized to MIL or TAU and completed assessments of distress—perceived stress, anxiety, and depressive symptoms—at pre-intervention, post-intervention, six-weeks post-birth, and one-year postpartum.

Results
Multilevel modeling of distress trajectories revealed greater decreases from pre-intervention to 12-months postpartum for those in MIL compared to TAU, especially among child-bearers who were higher in anxiety and/or lower in dispositional mindfulness at baseline.

Conclusions
The current study offers preliminary evidence for durable perinatal mental health benefits following a brief mindfulness-based program and suggests further investigation of these effects in larger samples is warranted.

Trial registration
The ClinicalTrials.gov identifier for the study is: NCT02327559. The study was retrospectively registered on June 23, 2014.
Detection of MCM5 as a novel non-invasive aid for the diagnosis of endometrial and ovarian tumours
Authors: Stockley J. , Akhand R. , Kennedy A. , Nyberg C. , Crosbie E. J. , Edmondson R. J. 
Published: October 2020

AbstractBackgroundMCM5 is a protein involved in DNA replication, facilitating cell proliferation. In normal epithelium MCM5 expression is restricted to the cells in the basal proliferative compartments, however in the presence of a tumour MCM5 positive cells are present at the surface epithelium and are shed into bodily fluids. The aim of this study was to determine the sensitivity of MCM5 as a biomarker for the detection of endometrial and ovarian cancer.MethodsPatients with known ovarian or endometrial cancers, or known benign gynaecological conditions, were enrolled. Informed consent was obtained prior to the collection of full void urine, and either a vaginal tampon (worn for 6–8 h), or a vaginal swab. Vaginal secretions were extracted from the tampon or swab, centrifuged and lysed. Urine samples were centrifuged and lysed. MCM5 levels were determined by MCM5-ELISA (Arquer Diagnostics Ltd).Results125 patients completed the study protocol, 41 patients had endometrial cancer, 26 ovarian cancer, and 58 benign controls. All patients provided a urine sample and either a tampon or vaginal swab sample. Urine MCM5 levels were higher in cancer patients than controls (p < 0.0001), there was no significant difference in levels between tampon samples or vaginal swab samples in cancer patients when compared to controls.Performance of MCM5 to discriminate cancer from benign disease was high with an area under the ROC curve of 0.83 for endometrial cancer and 0.68 for ovarian cancer. Using a cut off of 12 pg/mL, overall sensitivity for endometrial cancer was 87.8, and 61.5% for ovarian cancer with a specificity of 75.9%.ConclusionsMCM5 is a novel sensitive and specific biomarker for the detection of ovarian and endometrial tumours in urine samples, which is likely to have clinical utility as a diagnostic aid.
Prevalence of intimate partner violence in Malaysia and its associated factors: a systematic review
Authors: Kadir Shahar Hayati , Jafri Faridah , Mohd Zulkefli Nor Afiah , Ahmad Norliza 
Published: October 2020

Abstract
Background
Intimate partner violence (IPV) is any behaviour within an intimate relationship that causes physical, psychological or sexual harm to those in the relationship. IPV is an important public health problem with substantial consequences on physical, mental, sexual, and reproductive health. Data on the systematic review of IPV are vital as basis for policy and program recommendations. The purpose of this systematic review was to ascertain the prevalence of IPV and its associated factors in Malaysia.

Materials and methods
A systematic review was conducted on published research studies from four databases which included Scopus, Medline, Sage and Google Scholar using keywords of intimate partner violence OR IPV AND associated factors OR risk factors OR protective factors AND Malaysia. Articles included were either cross-sectional, cohort or case-control studies which were published between the year 2005 till present. Excluded articles were the non-Malaysian origin, irrelevant topics being studied and articles not written in English.

Results and discussion
Out of 1983 records identified and screened, five were included for the analysis and interpretation of the data. All of the included studies were of cross-sectional design in which one of the studies was secondary data. IPV prevalence in Malaysia has a wide range between 4.94 and 35.9%. Two studies reported emotional or psychological abuse as the most common form of IPV (13% out of 22%) and (29.8%; CI = [0.27, 0.32]). Significant factors associated with IPV were lower education background, lower socio-economic status, history/ current substance abuse, exposure to prior abuse or violence, violence-condoning attitude; husbands or partners controlling behaviour, substance abuse and involvement in fights and lack of social support.

Conclusion
Specific IPV intervention should focus on lower socio-economic groups, high-risk institutionalised groups, the involvement of partners or husband and addressing issues of substance abuse.