bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice
Authors: Qu Pingping , Shi Jinhui , Chen Tianxiao , Chen Kai , Shen Congcong , Wang Jiankang , Zhao Xiangqian , Ye Guoyou , Xu Jianlong , Zhang Luyan 
Published: February 2020

AbstractBackgroundThe construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygousindicavarieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice.ResultsWe constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis.ConclusionsIn this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.
A community-wide acute diarrheal disease outbreak associated with drinking contaminated water from shallow bore-wells in a tribal village, India, 2017
Authors: Maramraj Kiran Kumar , Subbalakshmi G. , Ali Mohammed Shahed , Dikid Tanzin , Yadav Rajesh , Sodha Samir V. , Jain Sudhir Kumar , Singh Sujeet Kumar 
Published: February 2020

Abstract
Background
In 2016, India reported 709 acute diarrheal disease (ADD) outbreaks (> 25% of all outbreaks). Tribal populations are at higher risk with 27% not having accessibility to safe drinking water and 75% households not having toilets. On June 26, 2017 Pedda-Gujjul-Thanda, a tribal village reported an acute diarrheal disease (ADD) outbreak. We investigated to describe the epidemiology, identify risk factors, and provide evidence-based recommendations.

Methods
We defined a case as ≥3 loose stools within 24 h in Pedda-Gujjul-Thanda residents from June 24–30, 2017. We identified cases by reviewing hospital records and house-to-house survey. We conducted a retrospective cohort study and collected stool samples for culture. We assessed drinking water supply and sanitation practices and tested water samples for faecal-contamination.

Results
We identified 191 cases (65% females) with median age 36 years (range 4–80 years) and no deaths. The attack-rate (AR) was 37% (191/512). Downhill colonies (located on slope of hilly terrains of the village) reported higher ARs (56%[136/243], p < 0.001) than others (20%[55/269]). Symptoms included diarrhea (100%), fever (17%), vomiting (16%) and abdominal pain (13%). Drinking water from five shallow bore-wells located in downhill colonies was significantly associated with illness (RR = 4.6, 95%CI = 3.4–6.1 and population attributable fraction 61%). In multi-variate analysis, drinking water from the shallow bore-wells located in downhill colonies (aOR = 7.9, [95% CI =4.7–13.2]), illiteracy (aOR =6, [95% CI = 3.6–10.1]), good hand-washing practice (aOR = 0.4, [95%CI = 0.2–0.7]) and household water treatment (aOR = 0.3, [95%CI = 0.2–0.5]) were significantly associated with illness. Two stool cultures were negative for Vibrio cholerae. Heavy rainfall was reported from June 22–24. Five of six water samples collected from shallow bore-wells located in downhill colonies were positive for faecal contamination.

Conclusion
An ADD outbreak with high attack rate in a remote tribal village was associated with drinking water from shallow downhill bore-wells, likely contaminated via runoff from open defecation areas after heavy rains. Based on our recommendations, immediate public health actions including repair of leakages at contaminated water sources and alternative supply of purified canned drinking water to families, and as long-term public health measures construction of house-hold latrines and piped-water supply initiated.
Associations between maternal BMI, breastfeeding practices and infant anthropometric status in Colombia; secondary analysis of ENSIN 2010
Authors: Aldana-Parra Fanny , Vega Gilma Olaya , Fewtrell Mary 
Published: February 2020

Abstract
Background
Maternal malnutrition and infant feeding mode impact short and long term infant and child morbidity and mortality. The period of lactation may provide an opportunity to modulate the risk of disease later in life. Our aim was to estimate the effect of maternal body mass index (BMI) and infant feeding mode, particularly breastfeeding practices, on the anthropometric status of children under 2 years in Colombia.

Methods
A secondary analysis was performed using the data from ENSIN 2010. Term infants under 2y, singleton, with a mother older than 18y, were included in the analysis. Outcomes were wasting (WLZ < -2SD), overweight (WLZ > +2SD) and stunting (LAZ < -2SD). Predictors were infant feeding (exclusive and predominant BF constructed from 24-h recall, age at introduction of liquids, semisolids and solids) and maternal BMI. Socioeconomic variables, maternal education and age, conditions during pregnancy and birth weight were analyzed as covariates.

Results
Mothers of overweight infants had higher BMI (Mean dif = 1.47 kg/m2; 95% CI = 2.1, 0.8) than those with normal weight infants. Stunting and wasting were not predicted by maternal anthropometry or infant feeding mode. Fewer maternal years of education were associated with wasting (OR = 0.90; 95% CI = 0.86, 0.97; p = 0.003) and stunting (OR = 0.92; 95% CI = 0.89, 0.94; p < 0.0001), while more maternal years of education were associated with overweight (OR = 1.06; 95% CI = 1.02, 1.01; p = 0.001); higher birth weight was associated with overweight (OR = 1.001; 95% CI = 1.00, 1.001; p < 0.0001) and lower birth was associated with stunting (OR = 0.99; 95% CI = 0.89; p < 0.0001) in the final regression model.

Conclusions
Maternal BMI is a modifiable target for public health policy to promote healthy infant growth. Infant nutritional status is affected by direct and indirect factors that need to be addressed in further studies.
RETRACTED ARTICLE: Chinese medicine Di-Huang-Yi-Zhi protects PC12 cells from H2O2-induced apoptosis by regulating ROS-ASK1-JNK/p38 MAPK signaling
Authors: Zhang Li-Min , Zhen Rong-Rong , Gu Chao , Zhang Tian-Li , Li Yue , Jin Miao , Hu Bing , An Hong-Mei 
Published: February 2020

Abstract
Background
Oxidative stress mediates the nerve injury during the pathogenesis of Alzheimer’s disease (AD). Protecting against oxidative stress damage is an important strategy to prevent and treat AD. Di-Huang-Yi-Zhi (DHYZ) is a Chinese medicine used for the treatment of AD, but its mechanism remains unknown. This study is aimed to investigate the effect of DHYZ on H2O2 induced oxidative damage in PC12 cells.

Methods
PC12 cells were treated with H2O2 and DHYZ. Cell proliferation was detected by Cell counting kit-8 (CCK-8) assay. Cytotoxicity of H2O2 was measured by lactate dehydrogenase (LDH) release assay. Apoptosis were identified by Annexin V-FITC/PI staining. Caspase 3 activity was detected by commercial kit. Mitochondrial membrane potential (MMP) was detected by JC-1 staining. Reactive oxygen species (ROS) was 2′, 7′-Dichlorodihydrofluorescein diacetate (DCFH-DA) staining. Protein expression and phosphorylation was identified by western blot.

Results
The results showed that DHYZ antagonized H2O2-mediated cytotoxicity and proliferation inhibition. DHYZ reduced ROS production, stabilize mitochondrial membrane potential, inhibit Caspase-3 activity and apoptosis induced by H2O2. In addition, DHYZ inhibited the phosphorylation of ASK1, JNK1/2/3 and p38 MAPK which were up-regulated by H2O2.

Conclusions
The present study suggested that DHYZ protected PC12 cells from H2O2-induced oxidative stress damage and was related to inhibition of ROS production and ASK1-JNK/p38 MAPK signaling. The present study provides experimental evidence for the application of DHYZ for the management of oxidative stress damage and AD.
Understanding the Athena SWAN award scheme for gender equality as a complex social intervention in a complex system: analysis of Silver award action plans in a comparative European perspective
Authors: Kalpazidou Schmidt Evanthia , Ovseiko Pavel V. , Henderson Lorna R. , Kiparoglou Vasiliki 
Published: February 2020

Abstract
Background
Given the complex mix of structural, cultural and institutional factors that produce barriers for women in science, an equally complex intervention is required to understand and address them. The Athena SWAN Award Scheme for Gender Equality has become a widespread means to address barriers for women’s advancement and leadership in the United Kingdom, Ireland, Australia, the United States of America and Canada, while the European Commission is exploring the introduction of a similar award scheme across Europe.

Methods
This study analyses the design and implementation of 16 departmental Athena SWAN Silver Action Plans in Medical Sciences at one of the world’s leading universities in Oxford, United Kingdom. Data pertaining to the design and implementation of gender equality interventions were extracted from the action plans, analysed thematically, coded using categories from the 2015 Athena SWAN Charter Awards Handbook and synthesised against a typology of gender equality interventions in the European Research Area. The results were further analysed against the complexity research literature framework, where research organisations are perceived as dynamic systems that adapt, interact and co-evolve with other systems.

Results
Athena SWAN is a complex contextually embedded system of action planning within the context of universities. It depends on a multitude of contextual variables that relate in complex, non-linear ways and dynamically adapt to constantly moving targets and new emergent conditions. Athena SWAN Silver Action Plans conform to the key considerations of complexity – (1) multiple actions and areas of intervention with a focus on the complex system being embedded in local dynamics, (2) the non-linearity of interventions and the constantly emerging conditions, and (3) impact in terms of contribution to change, improved conditions to foster change and the increased probability that change can occur.

Conclusions
To enact effective sustainable structural and cultural change for gender equality, it is necessary to acknowledge and operationalise complexity as a frame of reference. Athena SWAN is the single most comprehensive and systemic gender equality scheme in Europe. It can be further strengthened by promoting the integration of sex and gender analysis in research and education. Gender equality policies in the wider European Research Area can benefit from exploring Athena SWAN’s contextually embedded systemic approach to dynamic action planning and inclusive focus on all genders and categories of staff and students.
Activation of the PDGFRα-Nrf2 pathway mediates impaired adipocyte differentiation in bone marrow mesenchymal stem cells lacking Nck1
Authors: Haider Nida , Larose Louise 
Published: February 2020

Abstract
Background
The limited options to treat obesity and its complications result from an incomplete understanding of the underlying molecular mechanisms regulating white adipose tissue development, including adipocyte hypertrophy (increase in size) and hyperplasia (increase in number through adipogenesis). We recently demonstrated that lack of the adaptor protein Nck1 in mice is associated with reduced adiposity and impaired adipocyte differentiation. In agreement, Nck1 depletion in 3 T3-L1 cells also attenuates adipocyte differentiation by enhancing PDGFRα activation and signaling. This is accompanied by higher expression of PDGF-A, a specific PDGFRα ligand, that may contribute to enhanced activation of PDGFRα signaling in the absence of Nck1 in white adipose tissue. However, whether Nck1 deficiency also impairs adipogenic differentiation in bone marrow still remains to be determined.

Methods
To address this point, Nck1-deficient derived bone marrow mesenchymal stem/stromal cells (BM-MSCs) and C3H10T1/2 mesenchymal stem cells were differentiated into adipocytes in vitro. Genes and proteins expression in these cellular models were determined using qPCR and western blotting respectively. Pharmacological approaches were used to assess a role for Nrf2 in mediating Nck1 deficiency effect on mesenchymal stem cells adipocyte differentiation.

Results
Nck1 deficiency in both BM-MSCs and C3H10T1/2 results in impaired adipocyte differentiation, accompanied by increased activation of the transcription factor Nrf2, as shown by increased mRNA levels of Nrf2 target genes, including PDGF-A. Using pharmacological activator and inhibitor of Nrf2, we further provide evidence that Nrf2 is an important player in PDGFRα signaling that mediates expression of PDGF-A and impaired adipogenesis in Nck1-deficient BM-MSCs and C3H10T1/2 cells.

Conclusion
This study demonstrates that Nck1 deficiency in mesenchymal stem cells impairs adipogenesis through activation of the PDGFRα-Nrf2 anti-adipogenic signaling pathway.
Secretory clusterin promotes hepatocellular carcinoma progression by facilitating cancer stem cell properties via AKT/GSK-3β/β-catenin axis
Authors: Zheng Wenjie , Yao Min , Wu Mengna , Yang Junling , Yao Dengfu , Wang Li 
Published: February 2020

Abstract
Background
To explore the modulatory effects and mechanism of secretory clusterin (sCLU) on cancer stem cell (CSC) properties in hepatocellular carcinoma (HCC).

Methods
The effects of sCLU repression or overexpression on chemoresistance, migration, invasion, and tumor growth were detected by MTT, wound healing, transwell assays, and xenograft assay, respectively. The tumor sphere assay was performed to evaluate the self-renewal ability of HCC cells. In addition, the molecular regulation between sCLU and AKT/GSK-3β/β-catenin axis in HCC cells were discovered by western blotting, quantitative real-time PCR (qRT-PCR), and immunofluorescence. The expression status of sCLU and β-catenin in HCC tissues were investigated by immunohistochemistry.

Results
Knockdown or overexpressing sCLU remarkably inhibited or promoted the chemoresistance against sorafenib/doxorubicin, metastasis, and tumor growth of HCC cells, respectively. HepG2 and HCCLM3-derived spheroids showed higher expression of sCLU than that in attached cells. Additionally, repressing sCLU impaired the self-renewal capacity of HCC cells and CSC-related chemoresistance while overexpression of sCLU enhanced these CSC properties. Knockdown or overexpression of sCLU inhibited or increased the expressions of β-catenin, cyclinD1, MMP-2 and MMP-9, and the phosphorylation of AKT or GSK3β signaling, respectively. However, LiCl or LY294002 abrogated the effects mediated by sCLU silencing or overexpression on chemoresistance, metastasis, and CSC phenotype. Furthermore, co-expression of sCLU and β-catenin in HCC tissues indicated poor prognosis of HCC patients.

Conclusions
Taken together, the oncogenic sCLU might promote CSC phenotype via activating AKT/GSK3β/β-catenin axis, suggesting that sCLU was a potential molecular-target for HCC therapy.
A scoping review of full-spectrum knowledge translation theories, models, and frameworks
Authors: Esmail Rosmin , Hanson Heather M , Holroyd-Leduc Jayna , Brown Sage , Strifler Lisa , Straus Sharon E , Niven Daniel J. , Clement Fiona M. 
Published: February 2020

Abstract
Background
Application of knowledge translation (KT) theories, models, and frameworks (TMFs) is one method for successfully incorporating evidence into clinical care. However, there are multiple KT TMFs and little guidance on which to select. This study sought to identify and describe available full-spectrum KT TMFs to subsequently guide users.

Methods
A scoping review was completed. Articles were identified through searches within electronic databases, previous reviews, grey literature, and consultation with KT experts. Search terms included combinations of KT terms and theory-related terms. Included citations had to describe full-spectrum KT TMFs that had been applied or tested. Titles/abstracts and full-text articles were screened independently by two investigators. Each KT TMF was described by its characteristics including name, context, key components, how it was used, primary target audience, levels of use, and study outcomes. Each KT TMF was also categorized into theoretical approaches as process models, determinant frameworks, classic theories, implementation theories, and evaluation frameworks. Within each category, KT TMFs were compared and contrasted to identify similarities and unique characteristics.

Results
Electronic searches yielded 7160 citations. Additional citations were identified from previous reviews (n = 41) and bibliographies of included full-text articles (n = 6). Thirty-six citations describing 36 full-spectrum were identified. In 24 KT TMFs, the primary target audience was multi-level including patients/public, professionals, organizational, and financial/regulatory. The majority of the KT TMFs were used within public health, followed by research (organizational, translation, health), or in multiple contexts. Twenty-six could be used at the individual, organization, or policy levels, five at the individual/organization levels, three at the individual level only, and two at the organizational/policy level. Categorization of the KT TMFs resulted in 18 process models, eight classic theories, three determinant frameworks, three evaluation frameworks, and four that fit more than one category. There were no KT TMFs that fit the implementation theory category. Within each category, similarities and unique characteristics emerged through comparison.

Conclusions
A systematic compilation of existing full-spectrum KT TMFs, categorization into different approaches, and comparison has been provided in a user-friendly way. This list provides options for users to select from when designing KT projects and interventions.

Trial registration
A protocol outlining the methodology of this scoping review was developed and registered with PROSPERO (CRD42018088564).
3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency: one disease - many faces
Authors: Grünert Sarah C. , Sass Jörn Oliver 
Published: February 2020

Abstract
Background
3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency (HMGCLD) is an autosomal recessive disorder of ketogenesis and leucine degradation due to mutations in HMGCL.

Method
We performed a systematic literature search to identify all published cases. Two hundred eleven patients of whom relevant clinical data were available were included in this analysis. Clinical course, biochemical findings and mutation data are highlighted and discussed. An overview on all published HMGCL variants is provided.

Results
More than 95% of patients presented with acute metabolic decompensation. Most patients manifested within the first year of life, 42.4% already neonatally. Very few individuals remained asymptomatic. The neurologic long-term outcome was favorable with 62.6% of patients showing normal development.

Conclusion
This comprehensive data analysis provides a systematic overview on all published cases with HMGCLD including a list of all known HMGCL mutations.
Toll-like receptor 4 deficiency ameliorates β2-microglobulin induced age-related cognition decline due to neuroinflammation in mice
Authors: Zhong Qi , Zou Yufeng , Liu Hongchao , Chen Ting , Zheng Feng , Huang Yifei , Chen Chang , Zhang Zongze 
Published: February 2020

AbstractToll-like receptor 4 (TLR4) is a crucial receptor in neuroinflammation and apoptotic neuronal death, and increasing evidences indicated that β2-microglobulin (B2M) is thought to be a major contributor to age-related cognitive decline. In present study, we designed to investigate the effects of TLR4 on B2M-induced age-related cognitive decline. Wild-type (WT) C57BL/6, TLR4 knockout (TLR4 -KO) mice and hippocampal neurons from the two type mice were respectively divided into two groups: (1) Veh group; (2) B2M-treated group. The behavioral responses of mice were measured using Morris Water Maze. Hippocampal neurogenesis and neuronal damage, inflammatory response, apoptosis, synaptic proteins and neurotrophic factors, and TLR4/MyD88/NF-κB signaling pathway proteins were examined using molecular biological or histopathological methods. The results showed that WT mice received B2M in the DG exhibited age-related cognitive declines, increased TLR4 mRNA expression and high levels of interleukin-1β (IL-1β), tumor necrosis factor-alpha (TNF-α) and apoptotic neuronal death in the hippocampus, which were partially attenuated in TLR4-KO mice. Moreover, in absence of TLR4, B2M treatment improved hippocampus neurogenesis and increased synaptic related proteins. Our cell experiments further demonstrated that deletion of TLR4 could significantly increase synaptic related protein, decrease neuroinflammatory fators, inhibited apoptotic neuronal death, and regulated MyD88/NF-κB signal pathway after B2M treatment. In summary, our results support the TLR4 contributes to B2M-induced age-related cognitive decline due to neuroinflammation and apoptosis through TLR4/MyD88/NF-κB signaling pathway via a modulation of hippocampal neurogenesis and synaptic function. This may provide an important neuroprotective mechanism for improving age-related cognitive decline.