bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of prognostic predictor by comprehensive analyzing alternative splicing events for Colon adenocarcinoma
Authors: Qu Yaqi , Chen Yujia , Zhang Le , Tian Lifei 
Published: July 2020

Abstract
Background: Colon adenocarcinoma (COAD) is one of the most common malignant tumors, with high incidence and mortality rates worldwide. Reliable prognostic biomarkers are needed to guide clinical practice. Methods: Comprehensive gene expression with alternative splicing (AS) profiles for each patient were downloaded using the SpliceSeq database from The Cancer Genome Atlas. Cox regression analysis was conducted to screen for prognostic AS events. The R package limma was used to screen differentially expressed genes (DEGs) between normal and tumor samples in the COAD cohort. A Venn plot analysis was performed between DEGs and prognostic AS events, and the DEGs that co-occurred with prognostic AS events (DEGAS) were identified. The top 30 most-connected DEGAS in protein–protein interaction analysis were identified through Cox proportional hazards regression to establish prognostic models. Results: In total, 350 patients were included in the study. A total of 22,451 AS events were detected, of which 2,004 from 1,439 genes were significantly associated with survival time. By overlapping these 1,439 genes with 6,455 DEGs, 211 DEGs with AS events were identified. After construction of the protein–protein interaction network, the top 30 hub genes were included in a multivariate analysis. Finally, a risk score based on 12 genes associated with overall survival was established (P < 0.05). The area under the curve was 0.782. The risk score was an independent predictor (P < 0.001). Conclusions: By exploring survival-associated AS events, a powerful prognostic predictor consisting of 12 DEGAS was built. This study aims to propose a novel method to provide treatment targets for COAD and guide clinical practice in the future.
OPTimizing Irradiation through Molecular Assessment of Lymph node (OPTIMAL): a randomized open label trial.
Authors: Algara Manuel , Rodríguez Elvira , Beato Inmaculada , Martínez Francisco José , Salinas Juan , Rodrígez Jose Reyes , Sanz Xavier , Soler Ana , Juan Germán , Flaquer Amanda 
Published: July 2020

Abstract
Background: Conservative surgery followed by breast and nodal irradiation is the standard loco-regional early breast cancer (BC) treatment for patients with four or more involved lymph nodes (LN). However, the treatment strategy when fewer nodes are involved remains unclear, especially when lymphadenectomy has not been performed. Sensitive nodal status assessment molecular techniques as the OSNA (One-Step Nucleic Acid Amplification) assay can contribute to the definition and standardization of the treatment strategy. Therefore, the OPTIMAL study aims to demonstrate the feasibility of incidental irradiation of axillary nodes in patients with early-stage BC and limited involvement of the SLN. Methods: BC patients who underwent conservative surgery and whose SLN total tumour load assessed with OSNA ranged between 250–15,000 copies/µL will be eligible. Patients will be randomized to receive irradiation on the breast, tumour bed, axillary and supraclavicular lymph node areas (intentional arm) or only on the breast and tumour bed (incidental arm). All areas, including the internal mammary chain, will be contoured. The mean, median, D5% and D95% doses received in all volumes will be calculated. The primary endpoint is the non-inferiority of the incidental irradiation of axillary nodes compared to the intentional irradiation in terms of 5-year disease free survival. Secondary endpoints comprise the comparison of acute and chronic toxicity and loco-regional and distant disease recurrence rates.Discussion: Standardizing the treatment and diagnosis of BC patients with few nodes affected is crucial due to the lack of consensus. Hence, the quantitative score for the metastatic burden of SLN provided by OSNA can contribute by improving the discrimination of which BC patients with limited nodal involvement can benefit from incidental radiation as an adjuvant treatment strategy. Trial registration: ClinicalTrial.gov, NCT02335957; https://clinicaltrials.gov/ct2/show/NCT02335957
Searching for Programme Theories for a realist evaluation: A case study comparing an academic database search and a simple Google search
Authors: Coleman Susanne , WRIGHT Judith M , NIXON Jane , SCHOONHOVEN Lisette , TWIDDY Maureen , GREENHALGH Joanne 
Published: July 2020

Abstract
BackgroundRealist methodologies are increasingly being used to evaluate complex interventions in health and social care. Programme theory (ideas and assumptions of how a particular intervention works) development is the first step in a realist evaluation or a realist synthesis, with literature reviews providing important evidence to support this. Deciding how to search for programme theories is challenging and there is limited guidance available. Using an example of identifying programme theories for a realist evaluation of Pressure Ulcer Risk Assessment Instruments in clinical practice, the authors explore and compare several different approaches to literature searching and highlight important methodological considerations for those embarking on a programme theory review.MethodsWe compared the performance of an academic database search with a simple Google search and developed an optimised search strategy for the identification primary references (i.e. documents providing the clearest examples of programme theories) associated with the use of Pressure Ulcer Risk Assessment Instruments (PU-RAIs). We identified the number of primary references and the total number of references retrieved per source. We then calculated the number needed to read (NNR) expressed as the total number of titles and abstracts screened to identify one relevant reference from each source.ResultsThe academic database search (comprising CINAHL, The Cochrane Library, EMBASE, HMIC, Medline) identified 2 /10 primary references with a NNR of 1395.The Google search identified 7/10 primary references with a NNR of 10.1. The combined NNR was 286.3. The optimised search combining Google and CINAHL identified 10/10 primary references with a NNR of 40.2. ConclusionThe striking difference between the efficiency of the review’s academic database and Google searches in finding relevant references prompted an in-depth comparison of the two types of search. The findings indicate the importance of including grey literature sources such as Google in this particular programme theory search, while acknowledging the need for transparency of methods. Further research is needed to facilitate improved guidance for programme theory searches to enhance practice in the realist field and to save researcher time and therefore resource.
Stakeholder perceptions about the establishment of medical simulation-based learning at a university in a low resource setting: A qualitative study in Uganda
Authors: Najjuma Josephine Nambi , Bajunirwe Francis , Twine Margaret , Namata Tamara , Kyakwera Catherine , Cherop Moses , Data Santorino 
Published: July 2020

Abstract
Background: Simulation based learning (SBL) is a technique where teachers recreate “real life” clinical experiences for health care teams for purposes of gaining clinical skills in a safe environment. There is evidence that SBL is superior to the traditional clinical teaching methods for acquisition of clinical skills. Although it is well established in resource rich settings, there is limited experience in resource limited settings and there is uncertainty regarding how SBL will be perceived among the stakeholders in medical education. As part of the steps leading to implementation of a SBL program at a university in Uganda, we sought to describe the perceptions of various stakeholders regarding the introduction of SBL methodology into learning at a medical school in Uganda. Methods: We conducted a formative qualitative assessment using key informant interviews (KIIs) among faculty members and university administrators and focus group discussions (FGDs) among medical and nursing students at Mbarara University of Science and Technology. Data were collected till saturation point and were transcribed and analyzed manually using open and axial coding approaches to develop themes. Results: We conducted 7 KIIs and 3 FGDs. Overall, findings were categorized into five broad themes: 1. Motivation to adopt simulation based learning 2. Prior experience and understanding of medical simulation 3. Outcomes arising from introduction of medical simulation 4. Drawbacks to establishment of medical simulation; and 5. remedies to the drawbacks. Overall, our data show there was significant buy-in from the institution for SBL, stakeholders were optimistic about the prospects of having a new method of teaching, which they perceived as modern to complement the traditional methods. There was significant knowledge but very limited prior experience of medical simulation. Also, there was some concern regarding how students and faculty would embrace training on lifeless objects, the human resources needed and sustainability of simulation-based learning in the absence of external funding. Conclusion: Stakeholders perceive SBL positively and are likely to embrace the learning methods. Concerns about human resource needs and sustainability need to be addressed to ensure acceptability.
Relationship of metabolic syndrome defined by IDF or revised NCEP ATP III with glycemic control among Malaysians with Type 2 Diabetes
Authors: Saif-Ali Riyadh , Kamaruddin Nor Azmi , AL-Habori Molham , Al-Dubai Sami A , Ngah Wan Zurinah Wan 
Published: July 2020

Abstract
Background The chronic complications of Type 2 Diabetes (T2D) such as macrovascular disease is amplified with the increase in the number of metabolic syndrome (MetS) risk factors. This research aims to study the relationship of MetS, diagnosed by the International Diabetes Federation (IDF) or revised National Cholesterol Education Programs Adult Treatment Panel III (NCEP ATP III) criteria, with glycemic control, Fasting blood glucose (FBG), glycated hemoglobin (HbA1c), C-peptide, and insulin resistance in T2D patients.Methods The study is a cross-sectional observational study which, involved 485 T2D patients who are receiving treatment at the University Kebangsaan Malaysia Medical Center (UKMMC), Kuala Lumpur, Malaysia. The MetS among the T2D patients was diagnosed based on IDF and revised NCEP ATP III criteria. C-peptide and HbA1c levels were determined by an automated quantitative immunoassay analyzer and high-performance liquid chromatography, respectively. The MetS factors; FBG, triglyceride, and high-density lipoprotein cholesterol were measured by spectrophotometer. Results Application of the IDF and revised NCEP ATP III criteria respectively resulted in 73% and 85% of the T2D subjects being diagnosed with MetS. The concordance of these criteria in diagnosing MetS among T2D patients was low (κ =0.33, P<0.001). Both IDF and revised NCEP ATP III criteria indicated that T2D patients with 5 MetS factors had higher insulin resistance (P=2.1×10-13;1.4×10-11), C-peptide (P=1.21×10-13; 4.1×10-11), FBG (P=0.01; 0.021), and HbA1c (P=0.039; 0.018) than those T2D patients without MetS, respectively. Conclusion Although there is a low concordance between IDF and revised NCEP ATP III criteria in the diagnosis of MetS among T2D patients, both criteria showed that T2D patients with 5 MetS factors had higher insulin resistance, C-peptide, FBG, and HbA1c.
Prediction of Treatment Failure and Compliance in Patients with Tuberculosis
Authors: Koo Hyeon-Kyoung , Min Jinsoo , Kim Hyung Woo , Lee Joosun , Kim Ju Sang , Park Jae Seuk , Lee Sung-Soon 
Published: July 2020

Abstract
Background: To improve treatment outcomes for tuberculosis (TB), efforts to reduce treatment failure are necessary. The aim of our study was to describe the characteristics of subjects who had failed treatment of tuberculosis and identify the risk factors for treatment failure and poor compliance using national data.Methods: A multicenter cross-sectional study was performed on tuberculosis subjects whose final outcome was reported as treatment failure during 2015-2017. The same number of subjects with treatment success during the same study period were randomly selected for comparison. Demographics, microbiological, radiographic, and clinical data were collected based on in-depth interviews by TB nurse specialists at all Public Private Mix (PPM) participating hospitals in South Korea. Results: A total of 52 tuberculosis patients with treatment failure were enrolled. In a multivariable analysis, the presence of diabetes, previous history of tuberculosis, and cavity were identified as risk factors for treatment failure; and Medicaid support was a favorable factor for treatment success (area under the curve [AUC]: 0.79). Age, low body mass index (BMI), presence of diabetes, preexisting lung disease, positive sputum acid-fast bacilli (AFB) smear result, and the presence of multidrug-resistant tuberculosis (MDR-TB) were significantly associated with presence of cavities. Younger age, lower BMI and previous history of TB were associated with poor compliance during treatment (AUC: 0.76). Conclusion: To reduce treatment failure, careful evaluation of the presence of diabetes, previous TB history, underlying lung disease, cavity, results of sputum AFB smears, and socioeconomic status are needed. To enhance treatment compliance, more attention should be paid to younger patients with lower BMIs during follow-up.
High burden of Self-reported Sexually Transmitted Infections among Key Populations in Mozambique: The Urgent Need for an Integrated Surveillance System
Authors: Boothe Makini A.S. , Comé Charlotte , Baltazar Cynthia Semá , Chicuecue Noela , Seleme Jessica , Langa Denise Chitsondzo , Sathane Isabel , Raymond Henry Fisher , Fazito Erika , Temmerman Marleen , Luchters Stanley 
Published: July 2020

Abstract
Background: Key populations - men who have sex with men (MSM), female sex workers (FSW) and people who inject drugs (PWID) – are at high risk for sexually transmitted infections (STI) given their sexual risk behaviours along with social, legal and structural barriers to prevention, care and treatment services. The purpose of this secondary analysis is to assess the prevalence of self-reported STIs and to describe associated risk factors among participations of the first Biological Behavioural Surveillance (BBS) in Mozambique. Methods: Responses from the first BBS surveys conducted in 2011-2014 were aggregated across survey-cities to produce pooled estimates for each population. Aggregate weighted estimates were computed to analyse self-reported STI prevalence. Unweighted pooled estimates were used in multivariable logistic regression to identify risk factors associated with self-reported STI. Results: The prevalence of self-reported STI was 11.9% (95% CI: 7.8-16.0), 33.6% (95% CI: 29.0-41.3), and 22.0% (95% CI: 17.0-27.0) among MSM, FSW and PWID, respectively. MSM who were circumcised, had HIV, reported drug use, reported receptive anal sex, and non-condom use with their last male partner had greater odds of STI self-report. STI-self report among FSW was associated with living in Beira, being married, employment aside from sex work, physical violence, sexual violence, drug use, access to comprehensive HIV prevention services, non-condom use with last client, and sexual relationship with a non-client romantic partner. Among PWID, risk factors for self-reported STI included living in Nampula/Nacala, access to HIV prevention services, and sex work.Conclusion: The high-burden of STIs among survey participants requires integrated HIV and STI prevention, treatment, and harm reduction services that address overlapping risk behaviours, especially injection drug use and sex work. A robust public health response requires the creation of a national STI surveillance system for better screening and diagnostic procedures within these vulnerable populations.
Adjuvant instant preoperative renal artery embolization facilitates the radical nephrectomy and thrombectomy in locally advanced renal cancer with venous thrombus: A retrospective study of 54 cases
Authors: Tang Guangxin , chen xiaoxu , Wang Jianwei , He Wei , Niu Zhihong 
Published: July 2020

Abstract
Background: The role of renal artery embolization (RAE) in the therapeutic armamentarium is always controversial. The present study aimed to assess the safety and the surgical outcomes of the instant renal artery embolization (I-RAE) prior to nephrectomy and thrombectomy in patients with locally advanced renal cell carcinoma (RCC) with venous thrombus.Methods: We performed a retrospective analysis of 54 patients treated with nephrectomy and thrombectomy between January 2012 and January 2019. Twenty-four patients were treated with I-RAE before surgery. Thirty patients received surgery alone (non-RAE group). The patient demographics, operation time, blood loss, transfusion requirements, complications and other surgical parameters were analyzed between the two groups.Results: The mean tumor size in the I-RAE group was significantly larger than that in the non-RAE group (11.1 cm versus 7.9 cm; p = .001). The mean estimated blood loss was significantly lower in the I-RAE group compared to that in the non-RAE group (596 ml versus 827 ml; p = .015), and the patients in the Non-RAE group were more likely to receive blood transfusion (red blood cell, RBC units, 4 U versus 6 U, p = .025; plasma volume, 200 ml versus 400 ml, p = .01). No differences were found in operative duration, ICU stay, perioperative complications and length of postoperative hospitalization. Conclusions: Instant preoperative adjuvant renal artery embolization (I-RAE) is a safe technique. It facilitates nephrectomy and thrombectomy by reducing blood loss, transfusion requirements and complications of delayed operations, providing urologists with a reliable option for treatment of locally advanced RCC with tumor thrombus.
Genetic Analysis of Children with Congenital Ocular Anomalies in Three Ecological Regions of Nepal: A Phase II of Nepal Pediatric Ocular Diseases Study
Authors: Adhikari Srijana , Thakur Neelam , Shrestha Ujjowala , Shrestha Mohan , Shrestha Murari Man , Thapa Bijaya , Poudel Manish , Kunwar Ajay 
Published: July 2020

Abstract
Background: Genetic eye diseases constitute a large and heterogeneous group of childhood ocular morbidity. Individual diseases may cause multiple structural anomalies and developmental features. Nepal Pediatric Ocular Disease Study (NPODS) was a population-based epidemiological study conducted across three ecological regions of Nepal to determine the prevalence and etiology of childhood ocular morbidity and blindness. In Phase II of this study, genetic analysis was performed for children who were found to have congenital ocular anomalies. Method: It was a cross sectional descriptive study. A total of 10,270 children across three different ecological regions in Nepal (Low lands, hills, and mountains) underwent ocular examinations in NPODS. Out of 374 (3.6%) of children with ocular abnormalities, 30 were thought to be congenital in nature. Targeted genetic analysis, including genotyping for genes specific to presenting phenotype, was performed for 25 children using serum samples. Results: Out of 25 children, 18 had meaningful genetic results. Analysis revealed one missense alteration G12411T of Zinc Finger Homeobox 4 (ZFHX4) gene in one participant among 10 with congenital ptosis and another missense variation T>C P. Y374 C of Signaling Receptor and Transporter Retinol 6 (STRA6) gene in one participant among 3 with microphthalmos.Conclusion: The study is first of its kind from Nepal and mutant genes were unique to Nepalese Population. Further analysis of genetic factors is crucial to better understand genetic association with ocular diseases and conditions. This helps further in genetic counseling and probably gene therapy to prevent blindness from these conditions.
Impact of viral coinfection and macrolide-resistant mycoplasma infection in children with refractory Mycoplasma pneumoniae pneumonia
Authors: Zhou Yajuan , Wang Jing , Chen Wenjuan , Shen Nan , Tao Yue , Zhao Ruike , Luo Lijuan , Li Biru , Cao Qing 
Published: July 2020

Abstract
Background: Cases of refractory Mycoplasma pneumoniae pneumonia have been increasing recently; however, whether viral coinfection or macrolide-resistant M. infection contribute to the development of refractory M. pneumoniae pneumonia remains unclear. This study aimed to investigate the impacts of viral coinfection and macrolide-resistant M. pneumoniae infection on M. pneumoniae pneumonia in hospitalized children and build a model to predict a severe disease course. Methods: Nasopharyngeal swabs or sputum specimens were collected from patients with community-acquired pneumonia meeting our protocol who were admitted to Shanghai Children’s Medical Center from December 1, 2016, to May 31, 2019. The specimens were tested with the FilmArray Respiratory Panel, a multiplex polymerase chain reaction assay that detects 16 viruses, Bordetella pertussis, M. pneumoniae, and Chlamydophila pneumoniae. Univariate and multivariate logistic regression models were used to identify the risk factors for adenovirus coinfection and macrolide-resistant mycoplasma infection.Results: Among the 107 M. pneumoniae pneumonia patients, the coinfection rate was 56.07%, and 60 (60/107, 56.07%) patients were infected by drug-resistant M. pneumoniae. Adenovirus was the most prevalent coinfecting organism, accounting for 22.43% (24/107). The classification tree confirmed that viral coinfection was more common in patients younger than 3 years old. Adenovirus coinfection and drug-resistant M. pneumoniae infection occurred more commonly in patients with refractory M. pneumoniae pneumonia (P=0.019; P=0.001). A prediction model including wheezing, lung consolidation and extrapulmonary complications was used to predict adenovirus coinfection. The area under the receiver operating characteristic curve of the prediction model was 0.795 (95% CI 0.679-0.893, P<0.001). A prolonged fever duration after the application of macrolides for 48 hours was found more commonly in patients infected by drug-resistant M. pneumoniae (P=0.002). A fever duration longer than 7 days was an independent risk factor for drug-resistant Mycoplasma infection (OR=3.500, 95% CI=1.310-9.353, P=0.012).Conclusions: The occurrence of refractory M. pneumoniae pneumonia is associated with adenovirus coinfection and infection by drug-resistant M. pneumoniae. A prediction model combining wheezing, extrapulmonary complications and lung consolidation can be used to predict adenovirus coinfection in children with M. pneumoniae pneumonia. A prolonged fever duration indicates drug-resistant M. pneumoniae infection, and a reasonable change in antibiotics is necessary.