bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data
Authors: Dadaneh Siamak Zamani , de Figueiredo Paul , Sze Sing-Hoi , Zhou Mingyuan , Qian Xiaoning 
Published: September 2020

AbstractBackgroundSingle-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the underlying cellular process to better understand development and disease mechanisms. The unique analytic challenge is to appropriately model highly over-dispersed scRNA-seq count data with prevalent dropouts (zero counts), making zero-inflated dimensionality reduction techniques popular for scRNA-seq data analyses. Employing zero-inflated distributions, however, may place extra emphasis on zero counts, leading to potential bias when identifying the latent structure of the data.ResultsIn this paper, we propose a fully generative hierarchical gamma-negative binomial (hGNB) model of scRNA-seq data, obviating the need for explicitly modeling zero inflation. At the same time, hGNB can naturally account for covariate effects at both the gene and cell levels to identify complex latent representations of scRNA-seq data, without the need for commonly adopted pre-processing steps such as normalization. Efficient Bayesian model inference is derived by exploiting conditional conjugacy via novel data augmentation techniques.ConclusionExperimental results on both simulated data and several real-world scRNA-seq datasets suggest that hGNB is a powerful tool for cell cluster discovery as well as cell lineage inference.
First insights on value-based healthcare of elders using ICHOM older person standard set reporting
Authors: Lee Wei-Ju , Peng Li-Ning , Lin Chi-Hung , Lin Shinn-Zong , Loh Ching-Hui , Kao Sheng-Lun , Hung Tzu-Shing , Chang Chia-Yun , Huang Chun-Feng , Tang Ting-Ching , Chen Liang-Kung 
Published: September 2020

Abstract
Background
Clinical guidelines for specific conditions fragment care provision for elders. The International Consortium for Health Outcomes Measurement (ICHOM) has developed a global standard set of outcome measures for comprehensive assessment of older persons. The goal of this study was to report value-based health metrics in Taiwan using this ICHOM toolset.

Methods
The cross-sectional study of baseline data excerpted from a prospective longitudinal cohort, which recruited people ≥65 years old with ≥3 chronic medical conditions between July and December 2018. All participants received measurements of physical performance, anthropometric characteristics, health-related behaviors, Charlson Comorbidity Index, and Montreal Cognitive Assessment. The ICHOM toolset comprises three tiers: 1 includes frailty and having chosen a preferred place of death; 2 includes polypharmacy, falls, and participation in decision-making; and 3 includes loneliness, activities of daily living, pain, depression, and walking speed. These items were converted into a 0–10 point value-based healthcare score, with high value-based health status defined as ≥8/10 points.

Results
Frequencies of individual ICHOM indicators were: frail 11.7%, chose preferred place of death 14.4%, polypharmacy 31.5%, fell 17.1%, participated in decision-making 81.6%, loneliness 26.8%, limited activities of daily living 22.4%, pain 10.4%, depressed mood 13.0%, and slowness 38.5%. People with high disease burden (OR 0.40, 95% CI 0.21–0.76, p = 0.005) or cognitive impairment (OR 0.49, 95%CI 0.27–0.87, p = 0.014) were less likely to have high value-based healthcare status.

Conclusions
The ICHOM Standard Set Older Person health outcome measures provide an opportunity to shift from a disease-centric medical paradigm to whole person-focused goals. This study identified advanced age, chronic disease burden and cognitive impairment as important barriers to achieving high value-based healthcare status.
Do multiple community-based interventions on health promotion tackle health inequalities?
Authors: Nickel Stefan , von dem Knesebeck Olaf 
Published: September 2020

Abstract
Background
Previous systematic reviews of the impact of multi-component community-based health promotion interventions on reducing health inequalities by socio-economic status (SES) were restricted to physical activity and smoking behavior, and revealed limited and rather disillusioning evidence. Therefore, we conducted a comprehensive review worldwide to close this gap, including a wide range of health outcomes.

Methods
The Pubmed and PsycINFO databases were screened for relevant articles published between January 1999 and August 2019, revealing 87 potentially eligible publications out of 2876 hits. In addition, three studies out of a prior review on the effectiveness of community-based interventions were reanalyzed under the new research question. After a systematic review process, 23 papers met the inclusion criteria and were included in the synthesis.

Results
More than half (56.5%) of the studies reported improvements of socially disadvantaged communities overall (i.e. reduced inequalities at the area level) in at least one health behavior and/or health status outcome. Amongst the remaining studies we found some beneficial effects in the most deprived sub-groups of residents (8.2%) and studies with no differences between intervention and control areas (34.8%). There was no evidence that any program under review resulted in an increase in health disparity.

Conclusions
Our results confirm that community-based interventions may be reducing absolute health inequalities of deprived and disadvantaged populations, but their potential so far is not fully realized. For the future, greater attention should be paid to inequalities between sub-groups within communities when analyzing changes in health inequality over time.
Is insulin resistance a predictor for complete response in breast cancer patients who underwent neoadjuvant treatment?
Authors: Alan Ozkan , Akin Telli Tugba , Aktas Bilge , Koca Sinan , Ökten Ilker Nihat , Hasanov Rahib , Basoglu Tugba , Arikan Rukiye , Demircan Nazim Can , Ercelep Ozlem , Kaya Serap , Ugurlu Mustafa Umit , Kaya Handan , Akgul Babacan Nalan , Dane Faysal , Yumuk Perran Fulden 
Published: September 2020

Abstract
Purpose
Neoadjuvant chemotherapy is the standard front-line treatment modality in locally advanced breast cancer. Achieving pathological complete response (pCR) is a significant prognostic factor for prolonged disease-free and overall survival. Insulin resistance is defined as a pathological condition in which insulin effect is impaired in peripheral target tissues such as the skeletal muscle, liver, and adipose tissue. The relationship between breast cancer and insulin resistance is controversial. In this study, our aim is to evaluate the role of insulin resistance, body mass index (BMI), metabolic syndrome, and inflammation markers to predict complete response in breast cancer patients who underwent neoadjuvant treatment.

Methods
Data from 55 locally advanced non-diabetic breast cancer patients, treated with neoadjuvant chemotherapy between 2015 and 2017, were retrospectively evaluated. Homeostatic model assessment, IR = insulin resistance (HOMA-IR) was calculated by using the obtained insulin and fasting blood glucose values before neoadjuvant chemotherapy (fasting insulin × fasting glucose/405). We considered a cut-off of 2.5 for insulin resistance. The systemic inflammatory index (SII), neutrophil-lymphocyte ratio (NLR), and platelet-lymphocyte ratio (PLR) were calculated.

Results
Twenty-five patients had no insulin resistance. The most common pathologic subtype (56%) was hormone receptor (HR) positive and human epidermal growth factor receptor-2 (Her-2)-negative invasive ductal carcinoma. Sixteen (29%) patients had a pathological complete response (pCR). We found that the probability of pCR in patients with insulin resistance was 4.7 times lower than that in patients without insulin resistance [OR: 4.7 (95%CI 1.7–17.2), p = 0.01].

Conclusion
Our results revealed that insulin resistance may have a negative effect on pathological complete response (pCR) following neoadjuvant therapy particularly with hormone-positive and Her-2-negative cases of non-diabetic breast cancer.
Association of the MTHFR 677C>T and 1298A>C polymorphisms and male infertility risk: a meta-analysis
Authors: Aliakbari Fereshteh , Pouresmaeili Farkhondeh , Eshghifar Nahal , Zolghadr Zahra , Azizi Faezeh 
Published: September 2020

Abstract
Background and objectives
One of the possible male sterility risk factors are polymorphisms of Methylenetetrahydrofolate reductase (MTHFR). However, the epidemiologic investigations described inconsistent results regarding MTHFR polymorphism and the risk of male infertility. For that reason, we carried out a meta-analysis of published case-control studies to re-examine the controversy.

Methods
Electronic searches of Cochrane, EMBASE, Google Scholar, and PubMed were conducted to select eligible studies for this meta-analysis (updated to May 2019). According to our exclusion and inclusion criteria, only high-quality studies that remarked the association between MTHFR polymorphisms and male infertility risk were included. The Crude odds ratio (OR) with a confidence interval of 95% (CI) was used to assess the relationship between MTHFR polymorphism and male infertility risk.

Results
Thirty-four case-control studies with 9662 cases and 9154 controls concerning 677C/T polymorphism and 22 case-control studies with 5893 cases and 6303 controls concerning 1298A/C polymorphism were recruited. Both MTHFR polymorphisms had significant associations with male infertility risk (CT + TT vs. CC: OR = 1.37, 95% CI: 1.21–1.55, P = 0.00, I2 = 41.9%); (CC vs. CA + AA: OR = 0.82, 95% CI: 0.52–1.30, P = 0.04, I2 = 50.1%). Further, when stratified by ethnicity, the significant association results were observed in Asians and Caucasians for 677C/T and just Asians for 1298A/C.

Conclusions
Some of MTHFR polymorphisms like MTHFR 677C > T are associated with an elevated male infertility risk. To confirm our conclusion and to provide more accurate and complete gene-environment communication with male infertility risk, more analytical studies are needed.
Disease burden metrics and the innovations of leading pharmaceutical companies: a global and regional comparative study
Authors: Jung Ye Lim , Hwang JeeNa , Yoo Hyoung Sun 
Published: September 2020

Abstract
Background
The recent innovation activities of global top-tier pharmaceutical companies in accordance with global and regional health concerns were investigated in order to identify their innovations contributing to population health.

Methods
“Innovation activity” was defined as the number of drugs for which R&D activities have been reported within the last three years. Such activities were measured by collecting the data on drug developments and classifying them by developer company, phase of development, therapeutic use, and the country in which the development conducted. Subsequently, we examined and compared the correlations between the global innovation activities of the top 20 pharmaceutical companies and the disease burden measured in disability-adjusted life years (DALYs) by income level and region. In addition, this study analyzed the association between country-specific innovations and DALYs in the corresponding countries.

Results
At a global level, the innovation activities were not associated with global DALYs. However, when analyzed by income level, the innovation activities were associated with DALYs in high income and upper middle income countries while it was not associated with DALYs in low middle income and low income countries. In terms of region, correlations were found between the innovation activities and DALYs in the European region, the Americas, and the Western Pacific region whereas such correlations were not found in the African, Eastern Mediterranean, and South-East Asian regions. Similar to the analyses by income level and region, correlations between country-specific innovations and DALYs were only found in high income or high GDP countries. In addition, an empirical analysis of several cases including Canada, Germany, South Korea, and the United Kingdom revealed that pharmaceutical innovation is more closely related to market size than disease burden.

Conclusions
This study identified that discrepancies between pharmaceutical innovation and public health needs, i.e., disease burden values, have persisted until recently. To alleviate this imbalance, both public and private sectors should not only fulfill their respective roles and responsibilities regarding these issues, but also make strategic and collaborative efforts such as Product Development Partnerships (PDPs) directed toward public health improvement.
Factors associated with duration of breastfeeding in Spain: a cohort study
Authors: Lechosa-Muñiz Carolina , Paz-Zulueta María , Sota Sonia Mateo , de Adana Herrero María Sáez , del Rio Elsa Cornejo , Llorca Javier , Cabero-Perez María J. 
Published: September 2020

Abstract
Background
Factors associated with duration of breastfeeding have been usually studied at specific times after birth. Little is known about how much time is added to breastfeeding by each associated factor.

Methods
A cohort of 969 mother-child dyads was followed-up for twelve months at the Marqués de Valdecilla University Hospital, Spain, in 2018. Data on mother characteristics, pregnancy, delivery and children characteristics were obtained from medical records. Length of breastfeeding was reported by the mothers and recorded in paediatric medical record at hospital discharge and 2, 4, 6, 9 and 12 months of life. Factors associated with duration of breastfeeding were analysed via multivariate Weibull regression parameterized as accelerated time of failure. Results are presented as time ratios.

Results
About four out of five children were breastfed at hospital discharge, although this proportion dropped to 65% in children born from smoker women, 70% in preterm children and 68% in neonates weighting less than 2500 g. Mother’s age was associated with longer breastfeeding, adding 2% more breastfeeding time per year (adjusted time ratio 1.02; 95% confidence interval 1.00, 1.04). Children born from mothers with university studies were breastfed 53% more time than those born from mothers with primary studies (adjusted time ratio 1.53; 95% confidence interval 1.21, 1.95); smoking in pregnancy decreased length of breastfeeding by 41% (adjusted time ratio 0.59; 95% confidence interval 0.46, 0.76). Other factors associated with longer breastfeeding were single pregnancy and newborn weight over 2500 g.

Conclusions
Analysing factors associated with duration of breastfeeding as time parameters allows us to quantify the amount of time gained or lost by each factor, which could make it easier to evaluate the relevance of programmes directed to promote facilitating breastfeeding factors.
A qualitative assessment of factors influencing implementation and sustainability of evidence-based tobacco use treatment in Vietnam health centers
Authors: VanDevanter Nancy , Vu Milkie , Nguyen Ann , Nguyen Trang , Van Minh Hoang , Nguyen Nam Truong , Shelley Donna R. 
Published: September 2020

Abstract
Background
Effective strategies are needed to increase implementation and sustainability of evidence-based tobacco dependence treatment (TDT) in public health systems in low- and middle-income countries (LMICs). Our two-arm cluster randomized controlled trial (VQuit) found that a multicomponent implementation strategy was effective in increasing provider adherence to TDT guidelines in commune health center (CHCs) in Vietnam. In this paper, we present findings from a post-implementation qualitative assessment of factors influencing effective implementation and program sustainability.

Methods
We conducted semi-structured qualitative interviews (n = 52) with 13 CHC medical directors (i.e., physicians), 25 CHC health care providers (e.g., nurses), and 14 village health workers (VHWs) in 13 study sites. Interviews were transcribed and translated into English. Two qualitative researchers used both deductive (guided by the Consolidated Framework for Implementation Research) and inductive approaches to analysis.

Results
Facilitators of effective implementing of TDT included training and point-of-service tools (e.g., desktop chart with prompts for offering brief counseling) that increased knowledge and self-efficacy, patient demand for TDT, and a referral system, available in arm 2, which reduced the provider burden by shifting more intensive cessation counseling to a trained VHW. The primary challenges to sustainability were competing priorities that are driven by the Ministry of Health and may result in fewer resources for TDT compared with other health programs. However, providers and VHWs suggested several options for adapting the intervention and implementation strategies to address challenges and increasing engagement of local government committees and other sectors to sustain gains.

Conclusion
Our findings offer insights into how a multicomponent implementation strategy influenced changes in the delivery of evidence-based TDT. In addition, the results illustrate the dynamic interplay between barriers and facilitators for sustaining TDT at the policy and community/practice level, particularly in the context of centralized public health systems like Vietnam’s. Sustaining gains in practice improvement and clinical outcomes will require strategies that include ongoing engagement with policymakers and other stakeholders at the national and local level, and planning for adaptations and subsequent resource allocations in order to meet the World Health Organization’s goals promoting access to effective treatment for all tobacco users.

Trial registration
NCT02564653, registered September 2015
Uniportal versus multiportal video-assisted thoracoscopic anatomical resection for NSCLC: a meta-analysis
Authors: Yan Yueren , Huang Qingyuan , Han Han , Zhang Yang , Chen Haiquan 
Published: September 2020

Abstract
Background
Uniportal video-assisted thoracoscopic surgery (U-VATS) has recently emerged as an alternative procedure for non-small cell lung cancer (NSCLC); however, whether U-VATS has advantages over multiportal VATS (M-VATS) remains unknown.

Methods
We performed a systematic review of two databases (Pubmed and Web of Science) to search comparative studies of U-VATS and M-VATS anatomical pulmonary resection for NSCLC. Operative time, blood loss, number of resected lymph nodes, drainage duration, length of postoperative stay, pain in postoperative day 1(POD1) and conversion rates were retrieved to estimate the comparison of outcomes. A subgroup analysis stratified by study type (propensity-matched analysis and randomized-controlled trial versus non-propensity matched analysis) was performed.

Result
A total of 20 studies with 4142 patients were included in this meta-analysis. U-VATS was performed on 1869 patients, whereas the other 2173 patients underwent M-VATS. This meta-analysis showed that there was no significant difference in operative time (U-VATS: 146.48 ± 55.07 min versus M-VATS: 171.70 ± 79.40 min, P = 0.81), blood loss (74.49 ± 109.03 mL versus 95.48 ± 133.67 mL, P = 0.18), resected lymph nodes (17.28 ± 9.46 versus 18.31 ± 10.17, P = 0.62), conversion rate (6.18% versus 4.34%, P = 0.14), drainage duration (3.90 ± 2.94 days versus 4.44 ± 3.12 days, p = 0.09), length of postoperative stay (6.16 ± 4.40 days versus 6.45 ± 4.80 days, P = 0.22), and pain in POD1 (3.94 ± 1.68 versus 3.59 ± 2.76, p = 0.07). Subgroup analysis showed the value of PSM and RCT group consistency with overall value.

Conclusion
This up-to-date meta-analysis shows that the perioperative outcomes of U-VATS and M-VATS anatomical pulmonary resection are equivalent. In addition, the differences in long-term outcomes of these two approaches are still unclear. Thoracic surgeons should pay more emphasize on providing high-quality and personalized surgical care for patients, to improve the survival ultimately.
Primary and secondary aortopathy associated with adult congenital heart disease - retrospective study
Authors: Schusterova Ingrid , Banovcinova Alžbeta , Vachalcova Marianna , Jakubova Marta , Artemiou Panagiotis 
Published: September 2020

Abstract
Background
Primary and secondary aortopathy are frequently encountered in patients with congenital heart disease. The aim of this study is to present our experience and the incidence of primary and secondary adult CHD-associated aortopathy.

Methods
The cohort is comprised of adult patients with congenital heart disease from the registry of the Eastern Slovakia Institute of Cardiovascular Diseases. Data from the last follow-up examinations are included in this study. In the primary and secondary aortopathy groups were 35 and 12 patients respectively. As a control group were selected 64 patients with non aortopathy associated congenital heart disease (atrial and ventricular septal defect).

Results
Patients with primary and secondary aortopathy had larger ascending aorta/aortic root diameters than the control group (36.28 (26–49) mm vs 30.25 (21–41) mm p = 0.000113, 33.82 27–49) mm vs 29.03 (19–38)mm p = 0.000366 and 42.1 (30–50) mm vs 30.25 (21–41) mm, p = 0.000106, 35.67 (27–48) mm vs 29.03 (19–38) mm, p = 0.000119 respectively). Moreover, patients with secondary aortopathy had statistically significant larger ascending aorta diameter compared to the patients with primary aortopathy (42.1 (30–50) mm vs 36.28 (26–49) mm p = 0.030). During the follow-up period, were performed only in 2 patients (one from each group) operations on the aortic root and the ascending aorta due to aortic root or ascending aorta dilatation.

Conclusion
More patients with secondary aortopathy had dilated ascending aorta/ aortic root, as well as larger aortic diameters compare to the patients with primary aortopathy. Routine follow-up of these patients with attention to aortic diameter is necessary.
Meta-analysis of association between CT-based features and tumor spread through air spaces in lung adenocarcinoma
Authors: Yin Qifan , Wang Huien , Cui Hongshang , Wang Wenhao , Yang Guang , Qie Peng , Xun Xuejiao , Han Shaohui , Liu Huining 
Published: September 2020

Abstract
Objective
Spread through air space (STAS) is a novel invasive pattern of lung adenocarcinoma and is also a risk factor for recurrence and worse prognosis of lung adenocarcinoma after sublobar resection. The aims of this study are to evaluate the association between computed tomography (CT)-based features and STAS for preoperative prediction of STAS in lung adenocarcinoma, eventually, which could help us choose appropriate surgical type.

Methods
Systematic research was conducted to search for studies published before September 1, 2019. The association between CT-based features of radiological tumor size>2 cm、pure solid nodule、 part-solid nodule or Percentage of solid component (PSC)>50% and STAS was evaluated. According to rigorous inclusion and exclusion criteria. Eight studies including 2385 patients published between 2015 and 2018 were finally enrolled in our meta-analysis.

Results
Our results clearly depicted that there is no significant relationship between radiological tumor size>2 cm and STAS with the combined OR of 1.47(95% CI:0.86–2.51). Meta-analysis of 3 studies showed that pure solid nodule in CT image were more likely to spread through air spaces with pooled OR of 3.10(95%CI2.17–4.43). Meta-analysis of 5 studies revealed the part-solid nodule in CT image may be more likely to appear STAS in adenocarcinoma (ADC) (combined OR:3.10,95%CI:2.17–4.43). PSC>50% in CT image was a significant independent predictor in the diagnosis of STAS in ADC from our meta-analysis with combined OR of 2.95(95%CI:1.88–4.63).

Conclusion
In conclusion, The CT-based features of pure solid nodule、part-solid nodule、PSC>50% are promising imaging biomarkers for predicting STAS in ADC and may substantially influence the choice of surgical type. In future, more studies with well-designed and large-scale are needed to confirm the conclusion.