bluuebunny/crossref_metadata_2025_split huggingface dataset:
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data
Authors: Lu Liangqun , Townsend Kevin A. , Daigle Bernie J. 
Published: February 2021

AbstractBackgroundDifferential expression and feature selection analyses are essential steps for the development of accurate diagnostic/prognostic classifiers of complicated human diseases using transcriptomics data. These steps are particularly challenging due to the curse of dimensionality and the presence of technical and biological noise. A promising strategy for overcoming these challenges is the incorporation of pre-existing transcriptomics data in the identification of differentially expressed (DE) genes. This approach has the potential to improve the quality of selected genes, increase classification performance, and enhance biological interpretability. While a number of methods have been developed that use pre-existing data for differential expression analysis, existing methods do not leverage the identities of experimental conditions to create a robust metric for identifying DE genes.ResultsIn this study, we propose a novel differential expression and feature selection method—GEOlimma—which combines pre-existing microarray data from the Gene Expression Omnibus (GEO) with the widely-applied Limma method for differential expression analysis. We first quantify differential gene expression across 2481 pairwise comparisons from 602 curated GEO Datasets, and we convert differential expression frequencies to DE prior probabilities. Genes with high DE prior probabilities show enrichment in cell growth and death, signal transduction, and cancer-related biological pathways, while genes with low prior probabilities were enriched in sensory system pathways. We then applied GEOlimma to four differential expression comparisons within two human disease datasets and performed differential expression, feature selection, and supervised classification analyses. Our results suggest that use of GEOlimma provides greater experimental power to detect DE genes compared to Limma, due to its increased effective sample size. Furthermore, in a supervised classification analysis using GEOlimma as a feature selection method, we observed similar or better classification performance than Limma given small, noisy subsets of an asthma dataset.ConclusionsOur results demonstrate that GEOlimma is a more effective method for differential gene expression and feature selection analyses compared to the standard Limma method. Due to its focus on gene-level differential expression, GEOlimma also has the potential to be applied to other high-throughput biological datasets.
Lipid profile and prognosis in patients with coronary heart disease: a meta-analysis of prospective cohort studies
Authors: Zhao Xiangmei , Wang Dongying , Qin Lijie 
Published: February 2021

Abstract
Background
This meta-analysis based on prospective cohort studies aimed to evaluate the associations of lipid profiles with the risk of major adverse cardiovascular outcomes in patients with coronary heart disease (CHD).

Methods
The PubMed, Embase, and Cochrane Library electronic databases were systematically searched for prospective cohort study published through December 2019, and the pooled results were calculated using the random-effects model.

Results
Twenty-one studies with a total of 76,221 patients with CHD met the inclusion criteria. The per standard deviation (SD) increase in triglyceride was associated with a reduced risk of major adverse cardiovascular events (MACE). Furthermore, the per SD increase in high-density lipoprotein cholesterol (HDL-C) was associated with a reduced risk of cardiac death, whereas patients with lower HDL-C were associated with an increased risk of MACE, all-cause mortality, and cardiac death. Finally, the risk of MACE was significantly increased in patients with CHD with high lipoprotein(a) levels.

Conclusions
The results of this study suggested that lipid profile variables could predict major cardiovascular outcomes and all-cause mortality in patients with CHD.
Interprofessional primary care during COVID-19: a survey of the provider perspective
Authors: Donnelly Catherine , Ashcroft Rachelle , Bobbette Nicole , Mills Christine , Mofina Amanda , Tran Todd , Vader Kyle , Williams Ashley , Gill Sandeep , Miller Jordan 
Published: February 2021

Abstract
Background
Interprofessional primary care (IPC) teams provide comprehensive and coordinated care and are ideally equipped to support those populations most at risk of adverse health outcomes during the COVID-19 pandemic, including older adults, and patients with chronic physical and mental health conditions. There has been little focus on the experiences of healthcare teams and no studies have examined IPC practice during the early phase of the COVID-19 pandemic. The objective of the study was to describe the state of interprofessional health provider practice within IPC teams during the COVID-19 pandemic.

Methods
Observational cross-sectional design. A web-based survey was deployed to IPC providers working in team-based primary care clinics in the province of Ontario, Canada. The survey included 26 close-ended and six open-ended questions. Close-ended questions were analyzed using descriptive statistics. Content analysis was used to analyze the open-ended questions.

Results
445 surveys were included in the final analysis. Service delivery shifted from in-person care (77% pre-COVID-19) to telephone (76.5% during the COVID-19 pandemic). Less than half of the respondents (40%) reported receiving any training for virtual delivery. Wait times to access team members were reported to have decreased. There has also been a shift in what IPC providers report as the most commonly seen conditions, with increases in visits related to mental health concerns, acute infections (including COVID-19), social isolation, and resource navigation. Respondents also reported a reduction in healthcare provision for multiple chronic conditions including diabetes, cardiovascular disease, and chronic pain.

Conclusions
IPC teams are rapidly shifting their practice to supporting their patients during the pandemic. A surge in mental health issues has been seen and is expected to continue to increase in response to COVID-19. Understanding early experiences can help plan for future pandemic waves.
The biometric parameters of aniso-astigmatism and its risk factor in Chinese preschool children: the Nanjing eye study
Authors: Tong Haohai , Hao Qingfeng , Wang Zijin , Wang Yue , Li Rui , Zhao Xiaoyan , Sun Qigang , Zhang Xiaohan , Chen Xuejuan , Zhu Hui , Huang Dan , Liu Hu 
Published: February 2021

AbstractBackgroundsAniso-astigmatism may hinder normal visual development in preschool children. Knowing its prevalence, biometric parameters and risk factors is fundamental to children eye care. The purpose of this study was to determine the biometric components of aniso-astigmatism and associated maternal risk factors in Chinese preschool children.MethodsIn the population-based, prospective cohort Nanjing Eye Study, children were measured for noncycloplegic refractive error using an autorefractor and for biometric parameters using an optical low-coherent reflectometry. The difference of total astigmatism (TA) between both eyes was calculated using cylinder power (non-vectorial aniso-TA was defined as ≥1.00 Dioptre Cylinder [DC] between both eyes) and by vector analysis (vectorial aniso-TA was defined as a difference of ≥0.5 inJ0orJ45between both eyes which is equivalent to 1.00 DC). The prevalence of aniso-TA was presented. Interocular biometric parameters were compared between with vs. without aniso-astigmatism group. In addition, risk factors were determined using multivariate logistic regression model.ResultsOf 1131 children (66.90 ± 3.38 months, 53.31% male), the prevalence of non-vectorial aniso-TA was 1.95% (95% Confidence Interval (CI) = 1.14–2.75%), while the prevalence of vectorial aniso-TA was twice as common as non-vectorial aniso-TA, neither varying with sex or age. With aniso-TA eyes were more asymmetric in axial length and corneal curvature radius than without aniso-TA eyes. In multivariate logistic regression model, 5-min Apgar score less than 7 was significantly associated with higher risk of aniso-TA (vectorial aniso-TA: Odds Ratio (OR) = 6.42, 95%CI = 2.63–15.69,P < 0.001; non-vectorial aniso-TA: OR = 4.99, 95%CI = 1.41–17.68,P = 0.01). Being twin or triple was significantly associated with higher risk of vectorial aniso-CA (OR = 2.43, 95%CI = 1.05–5.60,P = 0.04). Pre-term delivery (OR = 2.60, 95%CI = 1.09–6.15,P = 0.03) and post-term delivery (OR = 3.61, 95%CI = 1.31–9.96,P = 0.01) were significantly associated with higher risk of vectorial aniso-CA.ConclusionsBoth corneal curvature radius and axial length asymmetry were correlated with aniso-TA. Children with 5-min Apgar score < 7 were more likely to have aniso-TA, while twin or triple, pre-term or post-term delivery were more likely to have vectorial aniso-CA.
Dopamine D4 receptor gene polymorphism (DRD4 VNTR) moderates real-world behavioural response to the food retail environment in children
Authors: Paquet Catherine , Portella Andre Krumel , Moore Spencer , Ma Yu , Dagher Alain , Meaney Michael J. , Kennedy James L. , Levitan Robert D. , Silveira Patricia P. , Dube Laurette 
Published: February 2021

AbstractBackgroundEvidence for the impact of the food retailing environment on food-related and obesity outcomes remains equivocal, but only a few studies have attempted to identify sub-populations for whom this relationship might be stronger than others. Genetic polymorphisms related to dopamine signalling have been associated with differences in responses to rewards such as food and may be candidate markers to identify such sub-populations. This study sought to investigate whether genetic variation of the dopamine D4 receptor gene (DRD4 exon III 48 bp VNTR polymorphism) moderated the association between local exposure to food retailers on BMI and diet in a sample of 4 to12-year-old children.MethodsData collected from a birth cohort and a community cross-sectional study conducted in Montreal, Canada, were combined to provide DRD4 VNTR polymorphism data in terms of presence of the 7-repeat allele (DRD4-7R) for 322 children aged between 4 and 12 (M (SD): 6.8(2.8) y). Outcomes were Body Mass Index (BMI) for age and energy density derived from a Food Frequency Questionnaire. Food environment was expressed as the proportion of local food retailers classified as healthful within 3 km of participants’ residence. Linear regression models adjusted for age, sex, income, cohort, and geographic clustering were used to test gene*environment interactions.ResultsA significant gene*food environment interaction was found for energy density with results indicating that DRD4-7R carriers had more energy dense diets than non-carriers, with this effect being more pronounced in children living in areas with proportionally more unhealthy food retailers. No evidence of main or interactive effects of DRD4 VNTR and food environment was found for BMI.ConclusionsResults of the present study suggest that a genetic marker related to dopamine pathways can identify children with potentially greater responsiveness to unhealthy local food environment. Future studies should investigate additional elements of the food environment and test whether results hold across different populations.
Social and behavioral risk reduction strategies for tuberculosis prevention in Canadian Inuit communities: a cost-effectiveness analysis
Authors: Uppal Aashna , Oxlade Olivia , Nsengiyumva Ntwali Placide , N’Diaye Dieynaba S. , Alvarez Gonzalo G. , Schwartzman Kevin 
Published: February 2021

Abstract
Background
Tuberculosis (TB) is an important public health problem in Inuit communities across Canada, with an annual incidence rate in 2017 that was nearly 300 times higher than in Canadian-born non-Indigenous individuals. Social and behavioral factors that are prevalent in the North, such as commercial tobacco use, excessive alcohol use, food insecurity and overcrowded housing put individuals at higher risk for TB morbidity and mortality. We examined the potential impact of mitigation strategies for these risk factors, in reducing TB burden in this setting.

Methods
We created a transmission model to simulate the epidemiology of TB in Nunavut, Canada. We then used a decision analysis model to assess the potential impact of several evidence-based strategies targeting tobacco use, excessive alcohol use, food insecurity and overcrowded housing. We predicted TB incidence, TB-related deaths, quality adjusted life years (QALYs), and associated costs and cost-effectiveness over 20 years. All costs were expressed in 2018 Canadian dollars.

Results
Compared to a status quo scenario with no new interventions for these risk factors, the reduction strategy for tobacco use was most effective and cost-effective, reducing TB incidence by 5.5% (95% uncertainty range: 2.7–11%) over 20 years, with an estimated cost of $95,835 per TB case prevented and $49,671 per QALY gained. The addition of the food insecurity reduction strategy reduced incidence by a further 2% (0.5–3%) compared to the tobacco cessation strategy alone, but at significant cost.

Conclusions
Strategies that aim to reduce commercial tobacco use and improve food security will likely lead to modest reductions in TB morbidity and mortality. Although important for the communities, strategies that address excess alcohol use and overcrowding will likely have a more limited impact on TB-related outcomes at current scale, and are associated with much higher cost. Their benefits will be more substantial with scale up, which will also likely have important downstream impacts such as improved mental health, educational attainment and food security.
LncRNA LINC01116 sponges miR-93-5p to promote cell invasion and migration in small cell lung cancer
Authors: Liu Wenzhou , Liang Feihai , Yang Guangyu , Xian Lei 
Published: February 2021

Abstract
Background
LINC01116 is a recently identified oncogenic lncRNA in glioma. Differential expression analysis using the public gene expression analysis tool GEPIA revealed the upregulation of LINC01116 in lung cancer. We studied the functions of LINC01116 in small cell lung cancer (SCLC).

Methods
The expression of LINC01116 in several types of cancer tissue and the paired non-tumor tissues was evaluated by GEPIA. The effects of the overexpression of LINC01116 and miR-93-5p on the expression of STAT3 were evaluated. The effects of the overexpression of LINC01116, miR-93-5p and STAT3 on SHP-77 cell behaviors were evaluated by Transwell assays.

Results
LINC01116 was highly expressed in SCLC and predicted poor survival. In SCLC tissues, the expression of LINC01116 was positively correlated with STAT3. Bioinformatics analysis revealed that miR-93-5p may target LINC01116. Overexpression of LINC01116 increased STAT3 but did not affect the expression of miR-93-5p. Transwell assay showed that LINC01116 and STAT3 increased cell invasion and migration rates. MiR-93-5p played an suppressed cell behaviors and suppressed the role of LINC01116.

Conclusion
Therefore, LINC01116 might upregulate STA3 by sponging miR-93-5p, thereby promoting cell invasion and migration in SCLC.
Circumferential dissection of deep fascia as ancillary technique in circumcision: is it possible to correct phimosis increasing penis size?
Authors: Carmine Pagano , Mario Faenza , Antonio Guastafierro , Vincenzo Manfellotto , Elisa Grella , Angelo Cosenza , Gorizio Pieretti , Sara Izzo 
Published: February 2021

AbstractBackgroundPhimosis is the inability to retract the preputium downward over the glans penis. Despite the various techniques of preputial plasty described in literature, the most performed surgical treatment is still the conventional circumcision.MethodsIn this paper we retrospectively reviewed data of a homogeneous population of 36 consecutive adult patients who underwent phimosis correction by circumcsion with dissection of the Deep Fascia. Patients were followed up by one independent plastic surgeon that measured penis length and circumference in nonerected state preoperatively and at 6 month time postoperatively.ResultsThe Wilcoxon Signed Rank Test showed a significant (p < 0.0001) difference between the two groups both in terms of length and circumference.ConclusionsIn conclusion, the ancillary technique we described leads to an increase of penis size, is safe and easy to perform and does not increase significantly operative time nor complication rate to the conventional procedure.
Partial hepatectomy for treatment of multiple liver abscess in a calf: a case report
Authors: Sato Reiichiro , Yamada Kazutaka , Yokoyama Taiki , Tanimoto Koki , Takeuchi Shoko , Tatsuzawa Natsumi , Nakui Shiho , Satoh Hiroyuki , Fadul Mahmoud , Steiner Adrian 
Published: February 2021

AbstractBackgroundUmbilical vein bacterial infections may cause liver abscesses during bacterial ascent. A single liver abscess can be surgically treated by marsupialization, but a risk of recurrence or non-healing remains. Moreover, there is no effective treatment for multiple abscesses.Case presentationA 17-day-old Holstein female calf exhibited reduced general condition, swelling and drainage of the umbilicus, and pressure sores in the area of the carpus, resulting in reluctance to stand up. The umbilicus showed pain at palpation; deep abdominal palpation indicated a swollen umbilical vein coursing from the umbilicus toward the liver. Ultrasonography confirmed a swollen umbilical vein with pus accumulation and multiple abscesses in the liver. Contrast-enhanced computed tomography (CT) examination confirmed that the swollen umbilical vein with fluid continued to the liver, and multiple unenhanced lesions, most likely abscesses, were confirmed in the liver. Partial hepatectomy was performed to remove as many abscesses as possible. For the resection, a vessel sealing device (LigaSureTM) was used to excise a part of the left liver lobe. As we could not remove all the abscesses in the liver during the operation, cefazolin sodium (5 mg/kg) was administered for 14 days after surgery. Post-operatively, blood accumulation was observed in the abdominal cavity, but no signs of peritonitis were found. The calf returned to the farm on day 38 after surgery. Follow-up information was obtained after 1 year, and complications were not reported.ConclusionsTo our knowledge, this is the first report of partial hepatectomy using a vessel sealing device for a calf with multiple liver abscesses. This case report suggests that the combination of partial hepatectomy and long-term administration of antibacterial drugs may restore the health of calves with multiple liver abscesses.
Integrated transcriptome and proteome analyses identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration
Authors: Xu Chen , Luo Shengchang , Wei Leixin , Wu Huiqiao , Gu Wei , Zhou Wenchao , Sun Baifeng , Hu Bo , Zhou Hongyu , Liu Yang , Chen Huajiang , Ye Xiaojian , Yuan Wen 
Published: February 2021

AbstractBackgroundDegeneration of intervertebral disc is a major cause of lower back pain and neck pain. Studies have tried to unveil the regulatory network using either transcriptomic or proteomic analysis. However, neither have fully elucidated the exact mechanism of degeneration process. Since post-transcriptional regulation may affect gene expression by modulating the translational process of mRNA to protein product, a combined transcriptomic and proteomic study may provide more insight into the key regulatory network of Intervertebral disc degeneration.MethodsIn order to obtain the proteomic and transcriptomic data, we performed label-free proteome analysis on freshly isolated nucleus pulposus cells and obtained transcriptome profiling data from the Gene Expression Omnibus repository. To identify the key regulatory network of intervertebral disc degeneration in nucleus pulposus cells, we performed bioinformatic analyses and established a protein-RNA interacting network. To validate the candidate genes, we performed in vitro experimentation and immunochemistry labeling to identify their potential function during nucleus pulposus degeneration.ResultsThe label-free proteome analysis identified altogether 656 proteins, and 503 of which were differentially expressed between nucleus pulposus cells from degenerated or normal disc cells. Using the existing nucleus pulposus transcriptomic profiling data, we integrated the proteomic and transcriptomic data of nucleus pulposus cells, and established a protein-RNA interacting network to show the combined regulatory network of intervertebral disc degeneration. In the network, we found 9 genes showed significant changes, and 6 of which (CHI3L1, KRT19, COL6A2, DPT, TNFAIP6 and COL11A2) showed concordant changes in both protein and mRNA level. Further functional analysis showed these candidates can significantly affect the degeneration of the nucleus pulposus cell when altering their expression.ConclusionsThis study is the first to use combined analysis of proteomic and transcriptomic profiling data to identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration. Our established protein-RNA interacting network demonstrated novel regulatory mechanisms and key genes that may play vital roles in the pathogenesis of intervertebral disc degeneration.
Impact of Haemophilus influenzae type b combination vaccination on asthma symptoms and pneumonia in 5-year-old children in rural Bangladesh: a longitudinal study and comparison with a previous cross-sectional study
Authors: Takeuchi Haruko , Hasan S. M. Tafsir , Zaman Khalequ , Takanashi Sayaka , Hore Samar Kumar , Yeasmin Sultana , Ahmad Shaikh Meshbahuddin , Alam Md Jahangir , Jimba Masamine , Iwata Tsutomu , Khan Md Alfazal 
Published: February 2021

Abstract
Background
Although the prevalence of bronchial asthma has been increasing worldwide since the 1970′s, the prevalence among 5-year-old children was significantly lower in 2016 than in 2001 in rural Bangladesh. We aimed to determine whether the Haemophilus influenzae type b (Hib) combination vaccination (without booster) started in 2009 contributed to this decrease.

Methods
A case–control study was conducted among 1658 randomly selected 5-year-old children from Matlab, Bangladesh. Data on wheezing were collected using the International Study of Asthma and Allergies in Childhood questionnaire. The vaccination data were collected from the records of the Matlab Health and Demographic Surveillance System, while data on pneumonia were obtained from the clinical records of Matlab Hospital. Adjusted odds ratios (aORs) were calculated for the risk for wheezing. The reduction rate was calculated to determine the impact of the vaccination on pneumonia history between the present study and our previous study conducted in 2001 by using the following formula: (percentage of pneumonia cases in 2001 − percentage of pneumonia cases in 2016)/(percentage of pneumonia cases in 2001) times 100 (%).

Results
Hib combination vaccination was a protecting factor against wheezing (aOR: 0.50; p = 0.010), while pneumonia at 1, 2, 3–4 years of age were risk factors for wheezing (aOR: 2.86, 3.19, 2.86; p = 0.046, 0.030, 0.030, respectively). The history of pneumonia was significantly lower in the 2016 study participants than those in 2001 both in the overall cohort and the wheezing group (paired t-test: p = 0.012, p < 0.001, respectively). Whereas the history of pneumonia decreased when the children grew older in the 2001 overall cohort, it peaked at the age of 2 years in 2016 wheezing group. The reduction rate decreased when children grew older in both the overall cohort and the wheezing group, however, it decreased faster in the wheezing group.

Conclusions
Hib combination vaccination was a protective factor against wheezing in 0-year-old children. However, the effects of vaccination might have attenuated at the ages of 1–4 years, because no booster dose was administered. The addition of a booster dose might further decrease the prevalence of asthma and wheezing.