bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of 4-genes model in papillary renal cell tumor microenvironment based on comprehensive analysis
Authors: Luo Liang , Zhou Haiyi , Su Hao 
Published: May 2021

Abstract
Background
The tumor microenvironment acts a pivotal part in the occurrence and development of tumor. However, there are few studies on the microenvironment of papillary renal cell carcinoma (PRCC). Our study aims to explore prognostic genes related to tumor microenvironment in PRCC.

Methods
PRCC expression profiles and clinical data were extracted from The Cancer Gene Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Immune/stromal scores were performed utilizing the ESTIMATE algorithm. Three hundred fifty-seven samples were split into two groups on the basis of median immune/stromal score, and comparison of gene expression was conducted. Intersect genes were obtained by Venn diagrams. Hub genes were selected through protein-protein interaction (PPI) network construction, and relevant functional analysis was conducted by DAVID. We used Kaplan–Meier analysis to identify the correlations between genes and overall survival (OS) and progression-free survival (PFS). Univariate and multivariate cox regression analysis were employed to construct survival model. Cibersort was used to predict the immune cell composition of high and low risk group. Combined nomograms were built to predict PRCC prognosis. Immune properties of PRCC were validated by The Cancer Immunome Atlas (TCIA).

Results
We found immune/stromal score was correlated with T pathological stages and PRCC subtypes. Nine hundred eighty-nine differentially expressed genes (DEGs) and 1169 DEGs were identified respectively on the basis of immune and stromal score. Venn diagrams indicated that 763 co-upregulated genes and 4 co-downregulated genes were identified. Kaplan-Meier analysis revealed that 120 genes were involved in tumor prognosis. Then PPI network analysis identified 22 hub genes, and four of which were significantly related to OS in patients with PRCC confirmed by cox regression analysis. Finally, we constructed a prognostic nomogram which combined with influence factors.

Conclusions
Four tumor microenvironment-related genes (CD79A, CXCL13, IL6 and CCL19) were identified as biomarkers for PRCC prognosis.
Posterior pole retinotomy for treatment of recurrent macular hole retinal detachment in highly myopic eyes: a pilot study
Authors: Wang Xianggui , Zhou Xuezhi , Zhu Ying , Xu Huizhuo 
Published: May 2021

Abstract
Background
To investigate the feasibility and efficacy of posterior pole retinotomy to treat recurrent macular hole retinal detachment (MHRD) in highly myopic patients.

Methods
We performed a retrospective study and reviewed the medical records in our hospital between January 1, 2016 and December 31, 2018. Highly myopic patients who received posterior pole retinotomy with silicone oil tamponade for their recurrent MHRD after pars plana vitrectomy were included in the analysis. Postoperative retinal reattachment, best-corrected visual acuity (BCVA), macular hole closure, and complications were evaluated.

Results
There were 11 patients (11 eyes) included in this study. All retinas were reattached. Silicone oil was successfully removed from all eyes 1.5–3 months after the surgery. Macular holes were completely closed in three eyes and remained flat open in eight eyes. The BCVA of all eyes improved significantly at 12 months after surgery (logarithm of the minimal angle of resolution, pre vs. postoperatively, 1.87 ± 0.44 vs. 1.15 ± 0.24, P < 0.05). None of the patients had complications such as endophthalmitis, fundus hemorrhage, retinal redetachment, and proliferative vitreoretinopathy.

Conclusion
Posterior pole retinotomy is a safe and effective surgery to treat recurrent MHRD after pars plana vitrectomy in highly myopic patients.
Sexual and physical abuse and depressive symptoms in the UK Biobank
Authors: Chaplin Anna B. , Jones Peter B. , Khandaker Golam M. 
Published: May 2021

Abstract
Background
The association between sexual and physical abuse and subsequent depression is well-established, but the associations with specific depressive symptoms and sex differences remain relatively understudied. We investigated the associations of sexual and physical abuse with depressive symptoms in men and women in a large population cohort.

Methods
Observational study based on 151,396 UK Biobank participants. Exposures included self-reported experiences of childhood physical abuse and sexual abuse. Mid-life outcomes included current depressive symptoms score, individual depressive symptoms, and lifetime depression. We used logistic regression to test associations of childhood sexual/physical abuse with depressive outcomes.

Results
Recalled childhood sexual and physical abuse were both associated with current depressive symptoms score in adults. Results for individual symptoms-based analyses suggest that sexual and physical abuse are associated with all depressive symptoms, particularly suicidal behaviours. The associations between lifetime depression and sexual/physical abuse were not fully explained by current depressive symptoms score, indicating that these findings may not be fully attributable to recall bias. There was no indication of differential risk for specific depressive symptoms among men and women.

Conclusions
Sexual and physical abuse are robust risk factors for depression/depressive symptoms regardless of sex. Higher risk of suicidal behaviours associated with childhood sexual/physical abuse are of particular concern. Longitudinal research into sex-specific associations for individual depressive symptoms is required.
Sarcopenia screening strategies in older people: a cost effectiveness analysis in Iran
Authors: Darvishi Ali , Hemami Mohsen Rezaei , Shafiee Gita , Daroudi Rajabali , Mohseni Mahsa , Shekarabi Farkhondeh Hosseini , Heshmat Ramin 
Published: May 2021

Abstract
Background and objectives
Sarcopenia is an important age-related disease which can lead to an increased risk of mortality, falls, fractures, and poor quality of life. So, timely detection can be effective in reducing the burden of disease. The aim of this study was to identify the most cost-effective strategy for sarcopenia screening in Iran.

Materials and methods
We constructed a Markov transition model over a life-time horizon based on natural history. Compared strategies included Sarcopenia scoring assessment models (SarSA-Mod), European working group on sarcopenia in older people (EWGSOP), Mini sarcopenia risk assessment (MSRA) and SARC-F. Parameters values were extracted from primary data and the literature, and the costs and Quality-adjusted life years (QALYs) were calculated for each strategy. Sensitivity analysis of uncertain parameters was also performed to determine the robustness of the model. Analysis was performed using 2020 version of TreeAge Pro software.

Results
All four screening strategies increased life time QALYs. After removing dominated strategy, the incremental cost per QALY gained for sarcopenia screening varied from $1875.67 for EWGSOP to $1898.33 for MSRA. Our base-case analysis showed that the most cost-effective strategy was EWGSOP and 2nd best was SarSA-Mod with $43,414.3 and $42,663.3 net monetary benefits given one GDP per capita ($5520.311) as willingness to pay, respectively. Sensitivity analysis of model parameters also showed robustness of results.

Conclusions
The results of the study, as the first economic evaluation of sarcopenia screening, showed that the EWGSOP strategy is more cost-effective than other strategies.
The extent to which the design of available reproductive health interventions fit the reproductive health needs of adolescents living in urban poor settings of Kisenyi, Kampala, Uganda
Authors: Tuhebwe Doreen , Babirye Susan , Ssendagire Steven , Ssengooba Freddie 
Published: May 2021

Abstract
Background
The rate at which informal urban settlements (slums) are developing in Low and Middle Income. Countries (LMICs) like Uganda is high. With this, comes the growing intersection between urbanization and the reproductive health of key populations. Currently, a number of interventions are being implemented to improve the Reproductive Health (RH) of adolescents in Kisenyi, the largest informal urban settlement in Kampala, the capital of Uganda. Despite these efforts, adolescent RH indicators have persistently remained poor in Kisenyi. This could be indicative of a gap between the provided and needed adolescent RH interventions. We assessed the fit between the available interventions and the RH needs of adolescents living in Kisenyi.

Methods
We conducted a qualitative study in July 2019–February 2020 in Kisenyi. The methodology was guided by the Word Health Organization global standards for quality-health care services for adolescents, the “For whom? Where? By whom? and What?” Framework of sexual RH service delivery and the realist evaluation approach. Eight focus group discussions were conducted with adolescents 15–19 years to explore their RH needs. The design and implementation of the available adolescent RH interventions were assessed by conducting Key Informant interviews with 10 RH service providers in Kisenyi. Validation meetings were held with adolescents and they scored the extent to which the various design features of the existing interventions fit the adolescents’ RH needs.

Results
The available RH interventions focused on meeting the sexual RH needs like providing family planning services but less on social needs like livelihood and sanitation which the adolescents identified as equally important. While the providers designed intervention to target 10-24 year olds, the adolescents preferred to have interventions that specifically targeted the study population 15-19 years. Most interventions were facility-based while, the adolescents desired community based outreaches.

Conclusion
The packaging and mode of delivery of interventions were perceived less holistic to meet the adolescents’ needs. Most interventions were designed to address the sexual and family planning needs while ignoring the wider social and livelihood needs. More holistic and outreach-based programming that addresses RH within the broader context of livelihood and sanitation requirements are more likely to be effective.
A qualitative study documenting unmet needs in the management of diabetic kidney disease (DKD) in the primary care setting
Authors: Datar Manasi , Ramakrishnan Saranya , Montgomery Elizabeth , Coca Steven G. , Vassalotti Joseph A. , Goss Thomas 
Published: May 2021

Abstract
Background
A majority of diabetic kidney disease (DKD) patients receive medical care in the primary care setting, making it an important opportunity to improve patient management. There is limited evidence evaluating whether primary care physicians (PCPs) are equipped to effectively manage these patients in routine clinical practice. The present study was undertaken to identify gaps in primary care and unmet needs in the diagnosis and monitoring of DKD in type 2 diabetes (T2D) patients among PCPs.

Methods
This was a qualitative analysis based on 30–45-min interviews with PCPs treating T2D patients. PCPs were recruited via email and were board-certified, in practice for more than 3 years, spent most of their time in direct clinical care, and provided care for more than three T2D patients in a week. Descriptive data analysis was conducted to identify and examine themes that were generated by interviews. Two reviewers evaluated interview data to identify themes and developed consensus on the priority themes identified.

Results
A total of 16 PCPs satisfying the inclusion criteria were recruited for qualitative interviews. Although the PCPs recognized kidney disease as an important comorbidity in T2D patients, testing for kidney disease was not consistently top of mind, with 56% reportedly performing kidney function testing in their T2D patients. PCPs most frequently reported using estimated glomerular filtration rate (eGFR) alone to monitor and stage DKD; only 25% PCPs reported testing for albuminuria. Most PCPs incorrectly believed that a majority of DKD patients are diagnosed in early stages. Also, early stages of DKD emerged as ambiguous areas of decision-making, wherein treatments prescribed greatly varied among PCPs. Lastly, early and accurate risk stratification of DKD patients emerged as the most important unmet need; which, if it could be overcome, was consistently identified by PCPs as a key to monitoring, appropriate nephrologist referrals, and intervening to improve outcomes in patients with DKD.

Conclusions
Our study highlights important unmet needs in T2D DKD testing, staging, and stratification in the PCP setting that limit effective patient care. Health systems and insurers in the U.S. should prioritize the review and approval of new strategies that can improve DKD staging and risk stratification.
ORMDL3 regulates poly I:C induced inflammatory responses in airway epithelial cells
Authors: Laura Gemma , Liu Yi , Fernandes Kieran , Willis-Owen Saffron A. G. , Ito Kazuhiro , Cookson William O. , Moffatt Miriam F. , Zhang Youming 
Published: May 2021

Abstract
Background
Oroscomucoid 3 (ORMDL3) has been linked to susceptibility of childhood asthma and respiratory viral infection. Polyinosinic-polycytidylic acid (poly I:C) is a synthetic analog of viral double-stranded RNA, a toll-like receptor 3 (TLR3) ligand and mimic of viral infection.

Methods
To investigate the functional role of ORMDL3 in the poly I:C-induced inflammatory response in airway epithelial cells, ORMDL3 knockdown and over-expression models were established in human A549 epithelial cells and primary normal human bronchial epithelial (NHBE) cells. The cells were stimulated with poly I:C or the Th17 cytokine IL-17A. IL-6 and IL-8 levels in supernatants, mRNA levels of genes in the TLR3 pathway and inflammatory response from cell pellets were measured. ORMDL3 knockdown models in A549 and BEAS-2B epithelial cells were then infected with live human rhinovirus (HRV16) followed by IL-6 and IL-8 measurement.

Results
ORMDL3 knockdown and over-expression had little influence on the transcript levels of TLR3 in airway epithelial cells. Time course studies showed that ORMDL3-deficient A549 and NHBE cells had an attenuated IL-6 and IL-8 response to poly I:C stimulation. A549 and NHBE cells over-expressing ORMDL3 released relatively more IL-6 and IL-8 following poly I:C stimulation. IL-17A exhibited a similar inflammatory response in ORMDL3 knockdown and over-expressing cells, but co-stimulation of poly I:C and IL-17A did not significantly enhance the IL-6 and IL-8 response. Transcript abundance of IFNB following poly I:C stimulation was not significantly altered by ORMDL3 knockdown or over-expression. Dampening of the IL-6 response by ORMDL3 knockdown was confirmed in HRV16 infected BEAS-2B and A549 cells.

Conclusions
ORMDL3 regulates the viral inflammatory response in airway epithelial cells via mechanisms independent of the TLR3 pathway.
A study of the association of cognitive abilities and emotional function with allergic disorders in young women
Authors: Fereidouni Mohammad , Rezapour Hadis , Saharkhiz Mansoore , Mahmoudzadeh Sara , Ayadilord Malaksima , Askari Masoumeh , Karbasi Samira , Abbaszadeh Arefeh , Hoseini Zahra Sadat , Ferns Gordon A. , Bahrami Afsane 
Published: May 2021

Abstract
Background
Allergic disorders may have a bidirectional causal relationship with mental disorders. In this cross-sectional study, we aimed to assess the associations between cognitive abilities and emotional function tests and quality of life with the presence of allergic disease in young women.

Methods
A diagnosis of allergic disorders, comprising allergic rhinitis (AR), asthma and atopic dermatitis (AD), was confirmed by a specialist in allergy. The presence and severity of depression, anxiety, stress, insomnia and sleepiness were evaluated using validated questionnaires. Cognitive abilities and quality of life were assessed using standard instruments.

Results
Among 181 female young participants, the prevalence of AR, asthma and AD were 26.5%, 2.8%, and 14.9% respectively. The AR group had higher scores than the non-AR group for depression, anxiety, insomnia, and lower scores for physical and mental health-related quality of life. Moreover, the AD cases had higher scores on the depression and stress scale compared to those without it (p < 0.05). Asthmatic patients also had significantly higher insomnia severity and lower physical health-related quality of life than non-asthmatic.

Conclusion
There was a high prevalence of psychological/psychiatric disorders that included: anxiety, and sleep problems among allergic women, and a reduced quality of life that may be associated with it.
Genome-wide copy number variations in a large cohort of bantu African children
Authors: Yilmaz Feyza , Null Megan , Astling David , Yu Hung-Chun , Cole Joanne , Santorico Stephanie A. , Hallgrimsson Benedikt , Manyama Mange , Spritz Richard A. , Hendricks Audrey E. , Shaikh Tamim H. 
Published: May 2021

AbstractBackgroundCopy number variations (CNVs) account for a substantial proportion of inter-individual genomic variation. However, a majority of genomic variation studies have focused on single-nucleotide variations (SNVs), with limited genome-wide analysis of CNVs in large cohorts, especially in populations that are under-represented in genetic studies including people of African descent.MethodsWe carried out a genome-wide copy number analysis in > 3400 healthy Bantu Africans from Tanzania. Signal intensity data from high density (> 2.5 million probes) genotyping arrays were used for CNV calling with three algorithms including PennCNV, DNAcopy and VanillaICE. Stringent quality metrics and filtering criteria were applied to obtain high confidence CNVs.ResultsWe identified over 400,000 CNVs larger than 1 kilobase (kb), for an average of 120 CNVs (SE = 2.57) per individual. We detected 866 large CNVs (≥ 300 kb), some of which overlapped genomic regions previously associated with multiple congenital anomaly syndromes, including Prader-Willi/Angelman syndrome (Type1) and 22q11.2 deletion syndrome. Furthermore, several of the common CNVs seen in our cohort (≥ 5%) overlap genes previously associated with developmental disorders.ConclusionsThese findings may help refine the phenotypic outcomes and penetrance of variations affecting genes and genomic regions previously implicated in diseases. Our study provides one of the largest datasets of CNVs from individuals of African ancestry, enabling improved clinical evaluation and disease association of CNVs observed in research and clinical studies in African populations.
Biosynthesis of pinene in purple non-sulfur photosynthetic bacteria
Authors: Wu Xiaomin , Ma Guang , Liu Chuanyang , Qiu Xin-yuan , Min Lu , Kuang Jingyu , Zhu Lingyun 
Published: May 2021

Abstract
Background
Pinene is a monoterpene, that is used in the manufacture of fragrances, insecticide, fine chemicals, and renewable fuels. Production of pinene by metabolic-engineered microorganisms is a sustainable method. Purple non-sulfur photosynthetic bacteria belong to photosynthetic chassis that are widely used to synthesize natural chemicals. To date, researches on the synthesis of pinene by purple non-sulfur photosynthetic bacteria has not been reported, leaving the potential of purple non-sulfur photosynthetic bacteria synthesizing pinene unexplored.

Results
Rhodobacter sphaeroides strain was applied as a model and engineered to express the fusion protein of heterologous geranyl diphosphate synthase (GPPS) and pinene synthase (PS), hence achieving pinene production. The reaction condition of pinene production was optimized and 97.51 μg/L of pinene was yielded. Then, genes of 1-deoxy-d-xylulose 5-phosphate synthase, 1-deoxy-d-xylulose 5-phosphate reductoisomerase and isopentenyl diphosphate isomerase were overexpressed, and the ribosome binding site of GPPS-PS mRNA was optimized, improving pinene titer to 539.84 μg/L.

Conclusions
In this paper, through heterologous expression of GPPS-PS, pinene was successfully produced in R. sphaeroides, and pinene production was greatly improved by optimizing the expression of key enzymes. This is the first report on pinene produce by purple non-sulfur photosynthetic bacteria, which expands the availability of photosynthetic chassis for pinene production.
Community support model on breastfeeding and complementary feeding practices in remote areas in Vietnam: implementation, cost, and effectiveness
Authors: Nguyen Tuan T. , Hajeebhoy Nemat , Li Jia , Do Chung T. , Mathisen Roger , Frongillo Edward A. 
Published: May 2021

Abstract
Background
Poor access to healthcare facilities and consequently nutrition counseling services hinders the uptake of recommended infant and young child feeding (IYCF) practices. To address these barriers and improve IYCF practices, Alive & Thrive (A&T) initiated community support groups in remote villages across nine provinces in Vietnam.

Objective
This study examines the effectiveness of the support group model and related project costs for reaching underserved areas to improve IYCF practices.

Methods
To evaluate the model’s implementation and project costs, we reviewed implementation guidelines, expenditure and coverage reports, monitoring data, and budgets for the nine provinces. To evaluate the model’s effectiveness, we used a 3-stage sampling method to conduct a cross-sectional survey from April to May 2014 in three provinces entailing interviewing mothers of children aged 0–23 months in communes with (intervention; n = 551) and without support groups (comparison; n = 559).

Findings
Coverage: From November 2011 to November 2014, in partnership with the government, A&T supported training for 1513 facilitators and the establishing 801 IYCF support groups in 267 villages across nine provinces. During this period, facilitators provided ~ 166,000 meeting/support contacts with ~ 33,000 pregnant women and mothers with children aged 0–23 months in intervention villages. Costs: The average project costs for supporting the meetings, compensating village collaborators, and providing supportive supervision through staff in commune health stations were USD 5 per client and USD 1 per contact. After adding expenditures for training, supportive supervision, and additional administrative costs at central and provincial levels, the average project cost was USD 15 per client and USD 3 per contact. Effectiveness: Survey participants in intervention and comparison communes had similar maternal, child, and household characteristics. Multiple logistic regression models showed that living in intervention communes was associated with higher odds of early initiation of breastfeeding (OR: 1.7; 95% CI: 1.1, 2.7), exclusive breastfeeding from 0 to 5 months (OR: 12.5; 95% CI: 6.7, 23.4), no bottle feeding (OR: 2.69; 95% CI: 1.82, 3.99), and minimum acceptable diet (OR: 1.51; 95% CI: 0.98, 2.33) compared to those living in comparison communes.

Conclusion
The IYCF support group model was effective in reaching populations residing in remote areas and likely contributed to improved IYCF practices. The study suggests that the model could be scaled up to promote equity in breastfeeding support.