bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of&nbsp;a&nbsp;QTL&nbsp;for&nbsp;grain&nbsp;size&nbsp;and weight&nbsp;using an introgression line from&nbsp;a cross between&nbsp;Oryza&nbsp;sativa&nbsp;and&nbsp;Oryza&nbsp;minuta&nbsp;
Authors: Feng Yue , Yuan Xiaoping , Wang Yiping , Yang Yaolong , Zhang Mengchen , Yu Hanyong , Xu Qun , Wang Shan , Niu Xiaojun , Wei Xinghua 
Published: January 2021

Abstract
Background: Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta. Results: An introgression line ‘IL188’ has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F2 and F2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F2 and F2:3 populations, and explained 15.09-16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F2:3 and four F2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~261 kb region between Indel marker Y7-12 and SSR marker Y7-38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume's epidermal cells showed that the cell length and width of NIL-qGL7IL188 was higher than NIL-qGL7Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion. Conclusions: In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between an Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.
Physical mapping&nbsp;and&nbsp;InDel&nbsp;marker&nbsp;development&nbsp;for&nbsp;the&nbsp;restorer gene&nbsp;Rf2&nbsp;in&nbsp;cytoplasmic male sterile&nbsp;CMS-D8&nbsp;cotton&nbsp;
Authors: Feng Juanjuan , Zhang Xuexian , Zhang Meng , Guo Liping , QI Tingxiang , Tang Huini , Zhu Haiyong , Wang Hailin , Qiao Xiuqin , Xing Chaozhu , Wu Jianyong 
Published: January 2021

Abstract
Background: Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods: The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results: The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on Chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions: This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.
Spatial distribution and determinant factors of anaemia among adults aged 15-59 in Ethiopia; using mixed-effects ordinal logistic regression model
Authors: tusa biruk shalmeno , kebede Sewnet Adem , Weldesenbet Adisu Birhanu Birhanu 
Published: January 2021

Abstract
Background: Anaemia is a global public health problem particularly in developing countries. Assessing the geographical distributions and determinant factors is a key and crucial step in designing targeted prevention and intervention programmes to address anaemia. Thus, the current study aimed to assess the spatial distribution and determinant factors of anaemia among adults aged 15-59 in Ethiopia.Methods: A secondary data analysis was done based on 2016 Ethiopian Demographic and Health Surveys (EDHS). Total weighted samples of 29,140 adults were included. Data processing and analysis were performed using STATA 14; ArcGIS 10.1 and SaTScan 9.6 software. Spatial autocorrelation was checked using Global Moran’s index (Moran’s I). Hotspot analysis was made using Gettis-OrdGi*statistics. Additionally, spatial scan statistics were applied to identify significant primary and secondary cluster of Anaemia. Mixed effect ordinal logistics were fitted to determine factors associated with the level of Anaemia.Result: The spatial distribution of anemia among adults age 15-59 was found to be clustered in Ethiopia (Global Moran’s I = 0.81, p value < 0.0001). In the multivariable mixed-effect ordinal regression analysis; Females [AOR = 1.53; 95% CI: 1.42, 1.66], Never married [AOR = 0.86; 95% CI: 0.77, 0.96], higher educated [AOR = 0.71; 95% CI: 0.60, 0.84], rural residents [AOR = 1.53; 95% CI: 1.23, 1.81], rich wealth status [AOR = 0.77; 95% CI: 0.69, 0.86] and underweight [AOR = 1.15; 1.06, 1.24] were significant predictors of anemia among adults.Conclusions: A significant clustering of anemia among adults aged 15-59 were found in Ethiopia and the significant hotspot areas with high cluster anemia were identified in Somalia, Afar, Gambella, Dire Dewa and Harari regions. Besides, gender, marital status, educational level, place of residence, region, wealth index and BMI were significant predictors of anemia. Therefore, effective public health intervention and nutritional education should be designed in the identified hotspot areas and risk groups to decrease the incidence of anaemia.
Characteristics and Patient-reported Outcomes Associated to Dropout in Severely Affected Oncological Patients
Authors: Gebert Pimrapat , Schindel Daniel , Frick Johann , Schenk Liane , Grittner Ulrike 
Published: January 2021

Abstract
BackgroundPatient-reported outcome measures (PROMs) are commonly used and are surrogates for clinical outcomes in cancer research. In the research setting of very severe diseases such as cancer, it is difficult to avoid the problem of incomplete questionnaires from drop-out or missing data due to patients who deceased during observation period. We aimed to explore patient characteristics and patient-reported outcomes associated with the time-to-dropout. MethodsIn the Oncological Social Care Project (OSCAR) study the condition of participants was assessed four times within 12 months (t0: baseline, t1: 3 months, t2: 6 months, and t3: 12 months) by validated PROMs. We performed competing-risks regression based on Fine and Gray’s proportional sub-distribution hazards model for exploring factors associated with time-to-dropout. Death was considered as competing risk. ResultsThree hundred sixty-two participants were analyzed in the study. 193 (53.3%) completed follow-up at 12 months, 67 (18.5%) patients dropped out, and 102 patients (28.2%) died during the study period. Poor subjective social support was related to higher risk for drop-out (SHR=2.10; 95%CI: 1.01 – 4.35). Lower values in health-related quality of life were related to drop-out and death. The subscales global health status/QoL, role functioning, physical functioning, and fatigue symptom in the EORTC QLQ-C30 were key characteristics associated with early drop-out.ConclusionSeverely affected cancer patients with poor social support and poor quality of life seem more likely to drop out of studies compared to patients with higher levels of social support and quality of life. This should be considered when planning studies assessing cancer patients. Methods to monitor drop-outs timely and handle missing outcomes might be used. Results of such studies have to be interpreted with caution in light of the particular drop-out mechanisms.
Correlation between Preoperative Ultrasonic Features of Medullary Thyroid Carcinoma and Postoperative Recurrence
Authors: Zhu Qiaodan , Xu Dong 
Published: January 2021

Abstract
Background: To investigate the factors that affect postoperative recurrence in medullary thyroid carcinoma (MTC) patients, including preoperative ultrasonic characteristics and other factors. Method: A retrospective analysis of seventy four MTC patients who underwent the first thyroid surgery from 2009 to 2018 and who had complete follow-up data was conducted. According to the follow-up results, these patients were divided into the recurrence group (17 cases) and non-recurrence group (57 cases). The preoperative ultrasound characteristics, preoperative and postoperative calcitonin levels, and general informations of the two groups were recorded, respectively. Univariate and multivariate analyses were performed. Results: Single factor Kaplan-Meier (K-M) analysis showed that: ① Preoperative ultrasonic characteristics including tumor size > 40.0 mm, capsular invasion, and metastatic cervical lymph nodes, as well as preoperative calcitonin level > 565.8 pg/ml, and postoperative calcitonin (within one week) level > 45.0 pg/ml were positively correlated with the risk of postoperative recurrence of MTC (P <0.05); ② There was no evidence to show that gender and age had a statistically significant effect on postoperative recurrence of MTC (P> 0.05). Multivariate Cox regression analysis showed that metastatic lymph nodes shown by ultrasound (HR=5.368, 95%CI 1.063-27.104, P=0.042) was an independent risk factor for postoperative recurrence of MTC. Conclusions: MTC patients with metastatic lymph nodes shown by ultrasound are prone to postoperative recurrence of MTC. In addition, MTC patients with a tumor > 40.0 mm, capsular invasion, preoperative calcitonin level > 565.8 pg/ml, and postoperative calcitonin level > 45.0 pg/ml are more likely to have postoperative recurrence.
Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson's disease
Authors: Aho Velma T , Houser Madelyn Crawford , Pereira Pedro AB , Chang Jianjun , Rudi Knut , Paulin Lars , Hertzberg Vicki , Auvinen Petri , Scheperjans Filip , Tansey Malu Gamez 
Published: January 2021

Abstract
Background

Previous studies have reported that gut microbiota, permeability, short-chain fatty acids (SCFAs), and inflammation are altered in Parkinson’s disease (PD), but how these factors are linked and contribute to disease processes and symptoms remains uncertain. This study sought to compare and identify associations among these factors in PD patients and controls to elucidate their interrelations and links to clinical manifestations of PD.

Methods

Stool and plasma samples and clinical data were collected from 55 PD patients and 56 controls. Levels of stool SCFAs and stool and plasma inflammatory and permeability markers were compared between patients and controls and related to one another and to the gut microbiota.

Results

Calprotectin was increased and SCFAs decreased in stool in PD in a sex-dependent manner. Inflammatory markers in plasma and stool were neither intercorrelated nor strongly associated with SCFA levels. Age at PD onset was positively correlated with SCFAs and negatively correlated with CXCL8 and IL-1β in stool. Fecal zonulin correlated positively with fecal NGAL and negatively with PD motor and non-motor symptoms. Microbiota diversity and composition were linked to levels of stool SCFAs, inflammation, and zonulin. Certain relationships differed between patients and controls and by sex.

Conclusions

Intestinal inflammatory responses and reductions in fecal SCFAs occur in PD, are related to the microbiota and to disease onset, and are not reflected in plasma inflammatory profiles. Some of these relationships are PD- and sex-dependent. Alterations in microbiota-host interactions and links between intestinal inflammation and reduced SCFA levels and earlier PD onset warrant further investigation.
An Intersectional Analysis Providing More Precise Information on Inequities in Self-Rated Health
Authors: Wemrell Maria , Karlsson Nadja , Vicente Raquel Perez , Merlo Juan 
Published: January 2021

Abstract
Background: Intersectionality theory combined with an analysis of individual heterogeneity and discriminatory accuracy (AIHDA) can facilitate our understanding of health disparities. This enables the application of proportionate universalism for resource allocation in public health. Analyzing self-rated health (SRH) in Sweden, we show how an intersectional perspective allows for a detailed mapping of health inequalities while avoiding simplification and stigmatization based on indiscriminate interpretations of differences between group averages. Methods: We analyzed participants (n=133,244) in 14 consecutive National Public Health Surveys conducted in Sweden in 2004-2016 and 2018. Applying AIHDA, we investigated the risk of bad SRH across 12 intersectional strata defined by gender, income and migration status, adjusted by age and survey year. We calculated odds ratios (with 95% confidence intervals) to evaluate between-strata differences, using native-born men with high income as the comparison reference. We calculated the area under the receiver operating characteristic curve (AU-ROC) to evaluate the discriminatory accuracy of the intersectional strata for identifying individuals according to their SRH status. Results: The analysis of intersectional strata showed clear average differences in the risk of bad SRH. For instance, the risk was seven times higher for immigrated women with low income (OR 7.00 [95% CI 6.14-7.97]) than for native men with high income. However, the discriminatory accuracy of the intersectional strata was small (AU-ROC=0.67). Conclusions: The intersectional AIHDA approach provides more precise information on the existence (or the absence) of health inequalities, and can guide public health interventions according to the principle of proportionate universalism. The low discriminatory accuracy of the intersectional strata found in this study warrants universal interventions rather than interventions exclusively focused on strata with a higher average risk of bad SRH.
CircTP63 promotes hepatocellular carcinoma progression by sponging miR-155-5p and upregulating ZBTB18
Authors: Wang Jiantao , Che Jinbiao 
Published: January 2021

Abstract
Background: Hepatocellular carcinoma (HCC) is the leading cause of tumor-related death worldwide due to high morbidity and mortality, yet lacking effective biomarkers and therapies. Circular RNAs (circRNAs) are a group of non-coding RNAs that regulate gene expression through interacting with miRNAs, implicating in the tumorigenesis and progression. A novel circRNA, circTP63, was reported to be an oncogene in HCC. However, its role in HCC remains unclear.Methods: qRT-PCR was used to assess the mRNA levels of CircTP63 in 90 pairs of tumor and adjacent normal tissues from HCC patients, one human normal hepatic epithelial cell line and HCC cell lines. CCK-8, colony formation, transwell, and flow cytometry assays were performed to detect the cellular function of circTP63/miR-155-5p/ZBTB18 in HCC cells. HCC xenograft mice models were established to assess the in vivo effect of circTP63. Bioinformatic analysis, RNA pull-down and luciferase assays were used to determine the interaction among circTP63/miR-155-5p/ZBTB18. Results: circTP63 was significantly upregulated in HCC tissues and cell lines. High circTP63 expression is closely associated with the tumor stages, lymph node metastasis, and poor prognosis of HCC patients. Functionally, knockdown of circTP63 inhibited cell proliferation, migration, invasion, and promoted cell apoptosis of HCC. Meanwhile, overexpression of circTP63 enhanced HCC progression. Mechanically, circTP63 was a sponge of miR-155-5p to facilitate the ZBTB18 expression, and the ZBTB18 expression in HCC tissues was negatively associated with the survival rate of HCC patients. Furthermore, rescued assays revealed that the reduced tumor-promoting effect on HCC cells induced by knockdown of circTP63 can be reversed by miR-155-5p inhibitor or ZBTB18 overexpression. Conclusion: Our data highlight a critical circTP63-miR-155-5p-ZBTB18 regulatory network involved in the HCC progression, gaining mechanistic insights into the function of circRNAs in HCC progression, and providing effective biomarkers and therapeutic targets for HCC treatment.
Maternal Death Surveillance and Response in Tanzania: Comprehensiveness of narrative summaries and action points from maternal death reviews
Authors: Said Ali , Pembe Andrea B. , Massawe Siriel , Hanson Claudia , Malqvist Mats 
Published: January 2021

Abstract
Background Maternal deaths reviews are proposed as one strategy to address high maternal mortality in low and middle-income countries, including Tanzania. Review of maternal deaths relies on comprehensive documentation of medical records that can reveal the sequence of events leading to death. The World Health Organization’s and the Tanzanian Maternal Death and Surveillance (MDSR) system propose the use of narrative summaries during maternal death reviews for discussing the case to categorize causes of death, identify gaps in care and recommend action plans to prevent deaths. Suggested action plans are recommended to be Specific, Measurable, Attainable, Relevant and Time bound (SMART). To identify gaps in documenting information and developing recommendations, comprehensiveness of written narrative summaries and action plans were assessed. Methods A total of 76 facility maternal deaths that occurred in two regions in Southern Tanzania in 2018 were included for analysis. Using a prepared checklist from Tanzania 2015 MDSR guideline, we assessed comprehensiveness by presence or absence of items in four domains, each with several attributes. These were socio-demographic characteristics, antenatal care, referral information and events that occurred after admission. Less than 75% completeness of attributes in all domains was considered poor while 95% and above were good/comprehensive. Action plans were assessed by application of SMART criteria and according to the place of planned implementation (community, facility or higher level of health system).Results Almost half of narrative summaries (49%) scored poor, and only1% scored good/comprehensive. Summaries missed key information such as demographic characteristics, time between diagnosis of complication and commencing treatment (65%), investigation results (47%), summary of case evolution (51%) and referral information (47%). A total of 285 action points were analysed. Most action points, 242(85%), recommended strategies to be implemented at health facilities and were mostly about service delivery, 120(42%). Only 42% (32/76) of the action points were deemed to be SMART.Conclusions Abstraction of information to prepare narrative summaries used in the MDSR system is inadequately done. Most recommendations were unspecific with a focus on improving quality of care in health facilities
Impact of Post-diagnosis Weight Change on Survival Outcomes in Black and White Breast Cancer Patients
Authors: Shang Lihua , Hattori Masaya , Fleming Gini , Jaskowiak Nora , Hedeker Donald , Olopade Olufunmilayo I , Huo Dezheng 
Published: January 2021

Abstract
Purpose: To evaluate weight change patterns over time following the diagnosis of breast cancer, and to examine the association of post-diagnosis weight change and survival outcomes in Black and White patients.Methods: The study included 2,888 women diagnosed with non-metastatic breast cancer in 2000-2017 in Chicago. Longitudinal repeated measures of weight and height were collected, along with a questionnaire survey including questions on body size. Multilevel mixed-effects models were used to examine changes in body mass index (BMI). Delayed entry Cox proportional hazards models were used to investigate the impacts of changing slope of BMI on survival outcomes. Results: At diagnosis, most patients were overweight or obese with a mean BMI of 27.5 kg/m2 and 31.5 kg/m2 for Blacks and Whites, respectively. Notably, about 45% of the patients had cachexia before death and substantial weight loss started about 30 months before death. In multivariable-adjusted analyses, compared to stable weight, BMI loss (>0.5 kg/m2/year) showed greater than 2-fold increased risk in overall survival (hazard ratio [HR]=2.60, 95%CI 1.88-3.59), breast cancer specific survival (HR=3.05, 95%CI 1.91-4.86), and disease-free survival (HR=2.12, 95%CI 1.52-2.96). The associations were not modified by race, age at diagnosis, and pre-diagnostic weight. BMI gain (>0.5 kg/m2/year) was also related to worse survival, but the effect was weak (HR=1.60, 95%CI 1.10-2.33 for overall survival).Conclusion: BMI loss is a strong predictor of worse breast cancer outcomes. Growing prevalence of obesity may hide diagnosis of cancer cachexia, which can occur in a large proportion of breast cancer patients long before death.