bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment success and mortality among adults with tuberculosis in rural eastern Uganda: a retrospective cohort study
Authors: Izudi Jonathan , Tamwesigire Imelda K. , Bajunirwe Francis 
Published: February 2020

Abstract
Background

Successful treatment of tuberculosis leads to clinical and public health benefits such as reduction in transmission, complications, and mortality among patients. However, data are limited on treatment outcomes and the associated factors among persons with bacteriologically confirmed pulmonary (BC-PTB) in rural areas of high tuberculosis and Human Immunodeficiency Virus (HIV) burden countries such as Uganda. We investigated factors associated with successful treatment of tuberculosis and mortality among adult persons with BC-PTB in rural eastern Uganda.

Methods

We constructed a retrospective cohort of patients with BC-PTB from a routine tuberculosis clinic database in eastern Uganda. We performed bivariate and multivariate analysis. Using a 5% level of significance, we used the modified Poisson regression analysis to determine factors independently associated with treatment success and mortality.

Results

We retrieved 1,123 patient records. Of these, 477(42.5%) had a cure, 323 (28.0%) had treatment completion, 17(1.5%) had failed treatment, 81(7.2%) had died, 89(7.9%) were lost to follow-up, and 136(12.1%) had missing treatment outcome. Overall, 800 (81.1%) of the 987 persons with BC-PTB that had an outcome, were successfully treated. Successful treatment of tuberculosis was less likely to occur among those with HIV infection (Adjusted risk ratio (aRR), 0.88; 95% Confidence Interval (CI), 0.82-0.95), older than 50 years (aRR, 0.89; 95% CI, 0.81-0.97), or male (aRR, 0.92; 95% CI, 0.87-0.98). Mortality was associated with HIV infection (aRR, 4.48; 95% CI, 2.95-6.79), older than 50 years (aRR, 2.93; 95% CI, 1.74-4.92), year of enrollment into treatment from 2015 (aRR, 0.80; 95% CI, 0.66-0.97), and Community-Based Directly Observed Therapy Short Course (aRR, 0.26; 95% CI, 0.13-0.50).

Conclusions

Treatment success rate among adult persons with BC-PTB in rural eastern Uganda is suboptimal and mortality is high. HIV infection and older age reduce the chance of successful treatment of tuberculosis, and increase risk of mortality. Older and HIV infected persons with BC-PTB will require special consideration to optimize treatment success and reduce risk of mortality.
Real-world questions and concerns about disease-modifying antirheumatic drugs (DMARDs): a retrospective analysis of questions to a medicine call center
Authors: Masri Hiba EL , Hollingworth Samantha , Driel Mieke van , Benham Helen , McGuire Treasure 
Published: February 2020

Abstract
Background Disease modifying antirheumatic drugs (DMARDs) have transformed the treatment of numerous autoimmune and inflammatory diseases but their perceived risk of harm be a barrier to use.Methods In a retrospective mixed-methods study, we analysed conventional (c) and biologic (b) DMARDs-related calls and compared them with rest of calls (ROC) from consumers to an Australian national medicine call center operated by clinical pharmacists from September 2002 to June 2010. This includes the period where bDMARDs became available on the Pharmaceutical Benefits Scheme, the government-subsidized prescription medicines formulary. We compared caller and patient demographics, enquiry types and motivation to information-seek for both cDMARDs and bDMARDs with ROC, using a t-test for continuous data and a chi-square test for categorical data. We explored call narratives to identify common themes.Results There were 1,547 calls involving at least one DMARD. The top three cDMARD enquiry types were side effects (27.2%), interactions (21.9%), and risk versus benefit (11.7%). For bDMARDs, the most common queries involved availability and subsidized access (18%), mechanism and profile (15.8%), and side effects (15.1%). The main consumer motivations to information-seek were largely independent of medicines type and included: inadequate information (44%), wanting a second opinion (23.6%), concern about a worrying symptom (18.8%), conflicting information (6.9%), or information overload (2.3%). Question themes common to conventional and biological DMARDs were caller overemphasis on medication risk and the need for reassurance. Callers seeking information about bDMARDs generally overestimated effectiveness and focused their attention on availability, cost, storage, and medicine handling.Conclusion Consumers have considerable uncertainty regarding DMARDs and may overemphasise risk. Patients cautiously assess the benefits and risks of their DMARDs but when new treatments emerge, they tend to overestimate their effectiveness.
Histone deacetylase inhibitors Induce Expression of Chromosomally Tagged Variant-Specific Surface Protein Genes in Giardia lamblia
Authors: Orozco Daniel Roberto , Garlapati Srinivas 
Published: February 2020

Abstract
Objective RNA interference and miRNA mediated mechanisms have been proposed to explain the expression of a specific variant of VSP at a time on the surface of Giardia lamblia. Recently, epigenetic mechanisms involving histone acetylations have been proposed to explain the process of antigenic switching in Giardia lamblia. However, due to the limited availability of specific antibodies for all the vsp variants present in the genome, it was difficult to monitor vsp gene switching. In this study, we have used an endogenous tagging method to tag specific vsp genes vsp1267 and vsp9B10A with a sequence encoding hemagglutinin (HA) epitope at the 3’end of the coding sequences without altering the 5’ upstream elements. With this method, we have monitored the expression of the tagged vsp genes in cells treated with histone deacetylase inhibitors using RT-PCR. Results Our results show that vsp1267-3XHA can be induced by treatment with sodium 4-phenylbutyrate, M344 and splitomicin but not by apicidin and Trichostatin A, while vsp9B10A-3XHA expression can be induced by Trichostatin A and splitomicin but not by sodium 4-phenylbutyrate, M344 and apicidin. The induced expression of these variants was not due to growth inhibition. These results support the role of histone acetylations in vsp expression.
Reducing Suicidal Ideation among Turkish Migrants in the Netherlands and in the UK A Pilot RCT of a guided Online Intervention
Authors: Eylem Ozlem , Straten Annemieke van , de Wit Leonore , Rathod Shanaya , Bhui Kamaldeep , Kerkhof Ad J.F.M. 
Published: February 2020

Abstract
Background: The evidence for the effectiveness of e-mental health interventions among ethnic minorities is still preliminary. This mixed methods study investigates the feasibility of a culturally adapted, guided online intervention with the intention to understand how it works and for whom to inform refinement. It also examines indications for its effectiveness in reducing suicidal ideation when compared with the treatment as usual. Methods: Turkish migrants (first and second generation) with mild to moderate suicidal thoughts were recruited from the general population using social media and newspaper advertisements. The intervention group obtained direct access to a 6 weeks guided online intervention while participants in the waiting list condition had to wait for 6 weeks. The intervention is based on an existing online intervention and was culturally adapted. Participants in both conditions completed baseline, post-test, and follow up questionnaires on suicidal ideation (primary outcome), depression, worrying, hopelessness, suicide attempt and self-harm, acculturation, quality of life, and usability. In addition, participants were interviewed to examine the feasibility and mechanisms of action in more depth. The responses were analysed by inductive thematic analysis. Results: A total of 85 people signed up via the study website and 18 (10 intervention, 8 waitlist control) were included. While the therapeutic benefits were emphasised (e.g. feeling connected with the intervention), the feasibility was judged to be low. The main reasons given were: not having severe suicidal thoughts and not being represented by the culturally adapted intervention. No suicide attempts were recorded during the study. The suicidal ideation, depression and hopelessness scores were improved in both groups. Conclusion: The online intervention, as might be expected in a small feasibility study, was not superior to the control condition. Future studies need to attend the implementation issues raised including measures of stigma, acculturation, careful cultural adaptations alongside more attention to coaching and relational support. They should also consider how to improve engagement alongside selection of those who are motivated to use online interventions and offer alternatives for those who are not. Trial registration: NTR5028. Registered 1 March 2015, https://www.trialregister.nl/trial/4926
Supervisors’ intention to observe clinical task performance: an exploratory study using the Theory of Planned Behaviour during postgraduate medical training
Authors: de Jonge Laury PJWM , Mesters Ilse , Govaerts Marjan JB , Timmerman Angelique A , Muris Jean WM , Kramer Anneke WM , Vleuten Cees PM van der 
Published: February 2020

Abstract
Background Direct observation of clinical task performance plays a pivotal role in competency-based medical education. Although formal guidelines require supervisors to engage in direct observations, research demonstrates that trainees are infrequently observed. Supervisors may not only experience practical and socio-cultural barriers to direct observations in healthcare settings, they may also question usefulness or have low perceived self-efficacy in performing direct observations. A better understanding of how these multiple factors interact to influence supervisors’ intention to perform direct observations may help us to more effectively implement the aforementioned guidelines and increase the frequency of direct observations. Methods We conducted an exploratory quantitative study, using the Theory of Planned Behaviour (TPB) as our theoretical framework. In applying the TPB, we transfer a psychological theory to medical education to get insight in the influence of cognitive and emotional processes on intentions to use direct observations in workplace based learning and assessment. We developed an instrument to investigate supervisors intention to perform direct observations. The relationships between the TPB measures of our questionnaire were explored by computing bivariate correlations using Pearson’s R tests. Hierarchical regression analysis was performed in order to assess the impact of the respective TPB measures as predictors on the intention to perform direct observations. Results In our study 82 GP supervisors completed our TPB questionnaire. We found that supervisors had a positive attitude towards direct observations. Our TPB model explained 45% of the variance in supervisors’ intentions to perform them. Normative beliefs and past behaviour were significant determinants of this intention. Conclusion Our study suggests that supervisors use their past experiences to form intentions to perform direct observations in a careful, thoughtful manner and, in doing so, also take the preferences of the learner and other stakeholders potentially engaged in direct observations into consideration. These findings have potential implications for research into work-based assessments and the development of training interventions to foster a shared mental model on the use of direct observations.
Overdose-Associated Admissions Among People Who Inject Opioids at a County Safety-Net Hospital Following Implementation of a Syringe Services Program
Authors: Bornstein Kasha , Coye Austin , Onge Joan St. , Li Hua , Muller Amanda , Bartholomew Tyler , Tookes Hansel 
Published: February 2020

Abstract
Background Syringe service programs (SSPs) are an evidence-based harm reduction strategy that reduce dangerous sequelae of injection drug use among people who inject drugs (PWID) such as overdose. SSP services include safer injection education and community-based naloxone distribution programs. This study evaluates differences in overdose-associated hospital admissions following implementation of the first legal SSP in Florida, based in Miami-Dade County. Methods We performed a retrospective analysis of hospitalizations for injection drug-related sequelae at a county hospital before and after the implementation of the SSP. An algorithm utilizing ICD-10 codes for opioid use and sequelae was used to identify people who inject opioids (PWIO). Florida Department of Law Enforcement Medical Examiners Commission Report data was used to analyze concurrent overdose death trends in Florida counties. Results Over the 25-month study period, 302 PWIO admissions were identified; 146 in the pre-index vs. 156 in post-index. A total of 26 admissions with PWIO overdose were found; 20 pre-index and 6 post-index (p=0.0034). Conclusions Declining overdose-associated admissions among PWIO suggests early impacts following SSP implementation.
The efficacy of Bifidobacterium quadruple viable tablet in the treatment of diarrhea predominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled, multicenter trial.
Authors: Bai Tao , Zeng Haoyu , Long Yanqin , Li Xiaoqing , Sun Xiaohong , Lan Yu , Gao Lingling , Zhang Lu , Feng Zenghui , Hou Xiaohua 
Published: February 2020

Abstract
Background: Irritable bowel syndrome (IBS) is one of the most acommon functional gastrointestinal disorders characterized by recurrent abdominal pain associated with defecation or a change in bowel habits. Leading to significant negative effect on patients’ quality of life and huge financial burden to health system, the management of IBS is a great challenge. Probiotics are considered as an effective therapy, however, in a lack of high-quality evidence of efficacy, no specific strain- and dose-probiotics were recommended in clinical guidelines. This study aims to evaluate the efficacy of the bifidobacterium quadruple viable tablet in the treatment of IBS-D.Methods/design: A multicenter randomized controlled trial will be performed in fourteen hospitals. A total of three hundred patients fulfill the eligible criteria will be stratified divided into an experimental group and a control group randomly in a ratio of 1:1. The experimental group is treated with the bifidobacterium quadruple viable tablet while the control group is treated with placebo. All the patients will receive a 4-week treatment and a 2-week follow-up. The primary outcome is the effectiveness in improving abdominal pain and stool consistency, the secondary outcome include evaluation of overall symptom relief, frequency of defecation, bloating, urgency of defecation, remedial medication, score of IBS-QOL and changes of microbiota and metabonomics. Physical examination, vital signs, laboratory tests, adverse events and concomitant medication will be taken into account for intervention safety assessment during the trial.Discussion: This multicenter randomized controlled trial may provide high-quality evidence on the efficacy of the bifidobacterium quadruple viable tablet for IBS-D on both physical and mental dimensions in China. To fill the gap of previous probiotics intervention studies, in addition, this study will also present safety assessment which will be a significant emphasis.Trial registration: Chinese Clinical Trial Registry, ID: ChiCTR1800017721 ( http://www.chictr.org.cn/showproj.aspx?proj=29440 ). Registered on 10 August 2018.
The rescue intervention strategy for asthma patients under severe air pollution: a protocol for a single-center prospective randomized controlled trial
Authors: Yang Xiaoyu , Huang Junjun , Hu Yan , Guo Cuiyan , Wang Xi , Yang Zhao , Zhou Tianyu , Wang Guangfa 
Published: February 2020

Abstract
Background Asthma is a common chronic airway inflammatory disease. Exacerbation of asthma not only accelerates the progression of the disease, but also increases the incidence of hospitalization and death. Studies have shown that air pollution is a high-risk factor of exacerbation of asthma. However, there are rare treatment strategies recommended to reduce severe air pollution related exacerbation of asthma. Methods/design This is a single-center, prospective, randomized and standard treatment parallel control clinical trial. Seventy-two asthma patients in non-exacerbation stage according to GINA guidelines 2017 will be recruited and equally assigned to Rescue Intervention Strategy (RIS) group or the control group. Original treatments for participants include unused inhaled drug, use short-acting β-agonists (SABA) on demand or use Budesonide/Formoterol (160μg/4.5μg/ dose, 1-2 dose / time, b.i.d). The rescue intervention strategy for RIS group is Budesonide / Formoterol plus the original treatment until the end of severe pollution (air quality index, AQI<200). Control group will maintain the original treatment. The intervention will last for one year. Primary outcome is the frequency of exacerbation asthma per year. And the secondary outcomes include the number of unplanned outpatient visits, emergency visits, hospitalization, medical cost and mortality caused by exacerbation asthma per year. Discussion The rescue intervention strategy is a novel strategy for asthma management under severe air pollution. Results of the study will provide reference information to guide clinical practice in reducing the air pollution related exacerbation of asthma.
18F-FDG PET/CT Metabolic Parameters and HER2 Expression in Colorectal Cancer
Authors: Yang Ziyi , Liu Shuai , Sun Yuyun , Xu Junyan , Jiang Jinjin , Ma Xiaoxi , Zhang Yingjian , Song Shaoli 
Published: February 2020

Abstract
Purpose: The relationship between 18F-FDG uptake and HER2 expression in colorectal cancer has not been investigated yet. This study aimed to investigate the predictive efficiency of preoperative 18F-FDG PET/CT for HER2 expression and prognosis in colorectal cancer.Results: Over all 131 colorectal cancer patients, there were 27 (20.6%) patients were HER2 positive. SUVmax of primary tumor (Mean ± SD) in HER2-positive and HER2-negative group was 18.238 ± 8.912 and 14.455 ± 6.531, respectively. SUVmax in HER2-positive group were higher than in negative group (p = 0.034). When the cutoff was based on 5cm, tumor size demonstrated significant positive correlations with SUVmax (p = 0.012) and HER2 expression (p = 0.014). Multivariate analysis showed that both SUVmax and tumor size had significant correlation with HER2 expression (p = 0.049 vs p = 0.043, respectively). In addition, statistical analysis showed that patients with higher SUVmax had better PFS (p = 0.029). There was no statistical difference of PFS between HER2-positive and HER2-negative group (p = 0.28).Conclusion: 18F-FDG metabolic parameters had significant correlation with HER2 expression in colorectal cancer. SUVmax combined with primary tumor size were better for predicting the HER2 status of colorectal cancer.
Indocyanine green fluorescence imaging to assess bowel perfusion during totally laparoscopic surgery for colon cancer
Authors: Su Hao , Wu Hongliang , Mandula Bao , Luo Shou , Wang Xuewei , Zhao Chuanduo , Liu Qian , Wang Xishan , Zhou Zhixiang , Zhou Haitao 
Published: February 2020

Abstract
Aim: To retrospectively evaluate the feasibility and safety of intraoperative assessment of bowel perfusion in totally laparoscopic surgery for colon cancer using indocyanine green fluorescence imaging (IGFI).
Methods: From October 2017 to June 2019, consecutive patients with colon cancer who underwent totally laparoscopic surgery were enrolled retrospectively and grouped into the IGFI group (n=84) and control group (n=105). In the IGFI group, indocyanine green (ICG) was injected intravenously, and the bowel perfusion was observed using a fluorescence camera system prior to and after completion of the anastomosis.
Results: The two groups were demographically comparable. The IGFI group exhibited a significantly shorter operative time (p=0.0374) while intraoperative blood loss did not significantly differ among the groups (p=0.062). In the IGFI group, average time to perfusion fluorescence was 48.4±14.0 s after ICG injection, and four patients (4.8%) were required to choose a more proximal point of resection due to the lack of adequate fluorescence at the point previously selected. There were no differences in terms of pathological outcomes, postoperative recovery and the postoperative complication rates between the groups (p＞0.05).
Conclusion: IGFI shows promise as a safe and feasible tool to assess bowel perfusion during a totally laparoscopic surgery for colon cancer and may reduce the operative time.
High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status
Authors: Hall Lauren , Hendricks Audrey E 
Published: February 2020

Abstract
Background: A low replication rate has been reported in some scientific areas motivating the creation of resource-intensive collaborations to estimate the replication rate by repeating individual studies. The substantial resources required by these projects limits the number of studies that can be repeated and consequently the generalizability of the findings. We extend the use of a method from Jager and Leek to estimate the false discovery rate (FDR) for 94 journals over a five-year period using p-values from 30,000 abstracts enabling the study of how the FDR varies by journal characteristics. Results: We find that the empirical FDR is higher for cancer vs. general medicine journals (p = 5.14E-6), especially for those with lower journal impact factors. Conversely, we find no significant evidence of a higher FDR, on average, for Open Access vs. closed access journals (p = 0.256, 95% CI: -0.014, 0.051). Conclusions: Our results identify areas of research that may need additional scrutiny and support to facilitate replicable science. Given our publicly available R code and data, others can complete a broad assessment of the empirical FDR across other subject areas and characteristics of published research.
NIPT technique based on the use of long chimeric DNA reads
Authors: Belova Vera , Plakhina Daria , Evfratov Sergey , Tsukanov Kirill , Khvorykh Gennady , Rakitko Alexander , Konoplyannikov Alexander , Ilinsky Valery , Rebrikov Denis , Korostin Dmitriy 
Published: February 2020

Abstract

Background: Non-invasive prenatal testing for aneuploidy on chromosomes 21, 18 and 13 is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as the high throughput sequencing is still relatively expensive. At the same time, there is a trend of increase of the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140-160 bp, it is not possible to effectively use long reads.Results: The authors used high-performance sequencing of cfDNA libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples of pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV and NPV of the results.Conclusions: The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99, 93% and 99.14% for 21 trisomy; 100% and 98.34% for 18 trisomy; 100% and 99.17% for 13 trisomy, respectively).