scholarly journals Badges for sharing data and code at Biostatistics: an observational study

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 90
Author(s):  
Anisa Rowhani-Farid ◽  
Adrian G. Barnett
Keyword(s):  
Observational Study ◽  
Data Sharing ◽  
Credible Interval ◽  
Reproducible Research ◽  
P Value ◽  
Online Research ◽  
Regression Modelling ◽  
Psychological Science ◽  
Code Sharing ◽  
Bayesian Logistic Regression

Background: The reproducibility policy at the journal Biostatistics rewards articles with badges for data and code sharing.  This study investigates the effect of badges at increasing reproducible research. Methods:  The setting of this observational study is the Biostatistics and Statistics in Medicine (control journal) online research archives.  The data consisted of 240 randomly sampled articles from 2006 to 2013 (30 articles per year) per journal.  Data analyses included: plotting probability of data and code sharing by article submission date, and Bayesian logistic regression modelling. Results:  The probability of data sharing was higher at Biostatistics than the control journal but the probability of code sharing was comparable for both journals.  The probability of data sharing increased by 3.9 times (95% credible interval: 1.5 to 8.44 times, p-value probability that sharing increased: 0.998) after badges were introduced at Biostatistics.  On an absolute scale, this difference was only a 7.6% increase in data sharing (95% CI: 2 to 15%, p-value: 0.998).  Badges did not have an impact on code sharing at the journal (mean increase: 1 time, 95% credible interval: 0.03 to 3.58 times, p-value probability that sharing increased: 0.378).  64% of articles at Biostatistics that provide data/code had broken links, and at Statistics in Medicine, 40%; assuming these links worked only slightly changed the effect of badges on data (mean increase: 6.7%, 95% CI: 0.0% to 17.0%, p-value: 0.974) and on code (mean increase: -2%, 95% CI: -10.0 to 7.0%, p-value: 0.286). Conclusions:  The effect of badges at Biostatistics was a 7.6% increase in the data sharing rate, 5 times less than the effect of badges at Psychological Science.  Though badges at Biostatistics did not impact code sharing, and had a moderate effect on data sharing, badges are an interesting step that journals are taking to incentivise and promote reproducible research.

scholarly journals Badges for sharing data and code at Biostatistics: an observational study

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 90 ◽  
Author(s):  
Anisa Rowhani-Farid ◽  
Adrian G. Barnett
Keyword(s):  
Observational Study ◽  
Data Sharing ◽  
Credible Interval ◽  
Total Sample ◽  
Reproducible Research ◽  
P Value ◽  
Regression Modelling ◽  
Psychological Science ◽  
Code Sharing ◽  
Bayesian Logistic Regression

Background:  Reproducible research includes sharing data and code.  The reproducibility policy at the journal Biostatistics rewards articles with badges for data and code sharing.  This study investigates the effect of badges at increasing reproducible research, specifically, data and code sharing, at Biostatistics. Methods:  The setting of this observational study is the Biostatistics and Statistics in Medicine (control journal) online research archives.  The data consisted of 240 randomly sampled articles from 2006 to 2013 (30 articles per year) per journal, a total sample of 480 articles.  Data analyses included: plotting probability of data and code sharing by article submission date, and Bayesian logistic regression modelling to test for a difference in the probability of making data and code available after the introduction of badges at Biostatistics.  Results:  The probability of data sharing was higher at Biostatistics than the control journal but the probability of code sharing was comparable for both journals.  The probability of data sharing increased by 3.5 times (95% credible interval: 1.4 to 7.4 times, p-value probability that sharing increased: 0.996) after badges were introduced at Biostatistics.  On an absolute scale, however, this difference was only a 7.3% increase in data sharing (95% CI: 2 to 14%, p-value: 0.996).  Badges did not have an impact on code sharing at the journal (mean increase: 1.1 times, 95% credible interval: 0.45 to 2.14 times, p-value probability that sharing increased: 0.549).  Conclusions:  The effect of badges at Biostatistics was a 7.3% increase in the data sharing rate, 5 times less than the effect of badges on data sharing at Psychological Science (37.9% badge effect).  Though the effect of badges at Biostatistics did not impact code sharing, and was associated with only a moderate effect on data sharing, badges are an interesting step that journals are taking to incentivise and promote reproducible research.

scholarly journals A survey of code sharing practice and policy in computational biology

2021 ◽  
Author(s):  
Iain Hrynaszkiewicz ◽  
James Harney ◽  
Lauren Cadwallader
Keyword(s):  
Computational Biology ◽  
Data Sharing ◽  
Online Survey ◽  
New Products ◽  
Reproducible Research ◽  
The Past ◽  
Code Sharing ◽  
Public Sharing ◽  
Potential Impact ◽  
Survey Responses

Sharing of code supports reproducible research but fewer journals have policies on code sharing compared to data sharing, and there is little evidence on researchers’ attitudes and experiences with code sharing. Before introducing a stronger policy on sharing of code, the Editors and publisher of the journal PLOS Computational Biology wished to test, via an online survey, the suitability of a proposed mandatory code sharing policy with its community of authors. Previous research has established, in 2019, 41% of papers in the journal linked to shared code. We also wanted to understand the potential impact of the proposed policy on authors' submissions to the journal, and their concerns about code sharing.We received 214 completed survey responses, all of whom had generated code in their research previously. 80% had published in PLOS Computational Biology and 88% of whom were based in Europe or North America. Overall, respondents reported they were more likely to submit to the journal if it had a mandatory code sharing policy and US researchers were more positive than the average for all respondents. Researchers whose main discipline is Medicine and Health sciences viewed the proposed policy less favourably, as did the most senior researchers (those with more than 100 publications) compared to early and mid-career researchers.The authors surveyed report that, on average, 71% of their research articles have associated code, and that for the average author, code has not been shared for 32% of these papers. The most common reasons for not sharing code previously are practical issues, which are unlikely to prevent compliance with the policy. A lack of time to share code was the most common reason. 22% of respondents who had not shared their code in the past cited intellectual property (IP) concerns - a concern that might prevent public sharing of code under a mandatory code sharing policy. The results also imply that 18% of the respondents’ previous publications did not have the associated code shared and IP concerns were not cited, suggesting more papers in the journal could share code.To remain inclusive of all researchers in the community, the policy was designed to allow researchers who can demonstrate they are legally restricted from sharing their code to be granted an exemption to public sharing of code.As a secondary goal of the survey we wanted to determine if researchers have unmet needs in their ability to share their own code, and to access other researchers' code. Consistent with our previous research on data sharing, we found potential opportunities for new products or features that support code accessibility or reuse. We found researchers were on average satisfied with their ability to share their own code, suggesting that offering new products or features to support sharing in the absence of a stronger policy would not increase the availability of code with the journal's publications.

scholarly journals POS0441 DEVELOPMENT OF RHEUMATOID ARTHRITIS AMONG ANTI-CITRULLINATED PROTEIN ANTIBODIES POSITIVE ASYMPTOMATIC INDIVIDUALS: A PROSPECTIVE OBSERVATIONAL STUDY

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 449.1-449
Author(s):  
S. Mizuki ◽  
K. Horie ◽  
K. Imabayashi ◽  
K. Mishima ◽  
K. Oryoji
Keyword(s):  
Rheumatoid Arthritis ◽  
Risk Factors ◽  
Observational Study ◽  
Rheumatoid Factor ◽  
Prospective Observational Study ◽  
Enzyme Linked Immunosorbent Assay ◽  
P Value ◽  
Healthy Population ◽  
Asymptomatic Individuals ◽  
Citrullinated Protein

Background:In the idividuals with genetic and enviromental risk factors, immune events at mucosal surfaces occur and may precede systemic autoimmunity. Anti-citrullinated protein antibodies (ACPA) are present in the serum for an average of 3-5 years prior to the onset of rheumatoid arthritis (RA) during an asymptomatic period. In ACPA-positivite individuals, the additional presence of RA-related risk factors appears to add significant power for the development of RA. To date, there have been few reports in which clinical courses of ACPA-positive asymptomatic individuals were investigated prospectively.Objectives:To observe the clinical time course of ACPA-positive healthy population for the development of RA.Methods:Healthy volunteers without joint pain or stiffness, who attended the comprehensive health screening of our hospital, were enrolled in this prospective observational study. The serum ACPA levels were quantified by Ig-G anti-cyclic citrullinated peptide enzyme-linked immunosorbent assay with levels > 4.4 U/mL considered positive. ACPA-positive subjects were followed by rheumatologists of our department clinically or a questionnaire sent by mail for screening to detect arthritis.Results:5,971 healthy individuals without joint symptons were included. Ninty-two (1.5%) were positive for ACPA. Of these, 19 (20.7%) developed RA and two were suspected as RA by mail questionnaire. Their average age were 58-years, and women were 68%. The average duration between the date of serum sampling and diagnosis was 10.7 months. ACPA-positive individuals who developed to RA had higher serum ACPA and Ig-M rheumatoid factor levels than ACPA-positive individuals who did not (P value by Mann-Whitney U test: 0.002, 0.005, respectively).Conclusion:Among ACPA-positive asymptomatic individuals, 20% developed RA. The higher titer of ACPA and Ig-M rheumatoid factor levels are risk factors for devoloping RA.Disclosure of Interests:None declared

scholarly journals Helicobacter pylori eradication in patients with type 2 diabetes mellitus: Multicenter prospective observational study

2019 ◽  
Vol 7 ◽  
pp. 205031211983209 ◽  
Author(s):  
Seung-Joo Nam ◽  
Sung Chul Park ◽  
Sang Hoon Lee ◽  
Dong Wook Choi ◽  
Sung Joon Lee ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Observational Study ◽  
Prospective Observational Study ◽  
Eradication Rate ◽  
Laboratory Data ◽  
P Value ◽  
Diabetic Patients ◽  
Multicenter Prospective Observational Study ◽  
H Pylori

Objective: To compare Helicobacter pylori ( H. pylori) eradication rate of type 2 diabetic patients with non-diabetic subjects. Methods: In this multicenter prospective observational study, H. pylori-infected subjects were enrolled from three university-affiliated hospitals. Eradication regimen was triple therapy with standard dose of proton pump inhibitors (b.i.d), amoxicillin (1.0 g b.i.d), and clarithromycin (500 mg b.i.d) for 7 days. Urea breath test was performed 4 weeks after treatment. Various clinical and laboratory data were collected for identification of factors associated with successful eradication. Results: Totally, 144 subjects were enrolled and 119 (85 non-diabetic and 34 diabetic patients) were finally analyzed. Eradication rate was 75.6% and there was no difference between diabetic patients and non-diabetic subjects (73.5% vs 76.5%, p value: 0.814). Adverse drug reactions were reported in 44.5% of patients. In multivariate analysis for predicting H. pylori eradication in diabetic patients, HbA1c (⩾7.5%) was a significant factor affecting eradication rate (adjusted odds ratio: 0.100, 95% confidence interval: 0.011–0.909, p value: 0.041). Conclusion: Diabetes itself is not a major factor affecting H. pylori eradication. However, poor glucose control may harmfully affect H. pylori eradication.

Prospective observational study of prevalence, assessment and treatment of pancreatic exocrine insufficiency (PEI) in patients with advanced pancreatic cancer (aPC): PanDA.

2021 ◽  
Vol 39 (28_suppl) ◽  
pp. 196-196
Author(s):  
Angela Lamarca ◽  
Lindsay Carnie ◽  
Dinakshi Shah ◽  
Kate Vaughan ◽  
Zainul Abedin Kapacee ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
High Risk ◽  
Observational Study ◽  
Breath Test ◽  
Cox Regression ◽  
Pancreatic Enzyme ◽  
Palliative Therapy ◽  
Advanced Pancreatic Cancer ◽  
P Value ◽  
Screening Methods

196 Background: PEI in patients with advanced pancreatic cancer is well documented, but there is a lack of consensus regarding optimal screening. Methods: Eligible patients for this observational study (NCT03616431) were those diagnosed with aPC referred for consideration of palliative therapy who consented to evaluation by a research dietitian. In addition to symptom and full dietetic assessment (including Mid-Upper Arm Circumference (MUAC), handgrip and stair climb test), full nutritional blood panel, faecal elastase (FE) and 13C mixed triglyceride breath test (for diagnostic cohort (DiC)) were performed. Primary objectives: prospective assessment of PEI prevalence (dietitian-assessed; demographic cohort (DeC)), and to design (using breath test as gold standard; DiC) and validate (follow-up cohort (FuC)) the most suitable screening tool for PEI in patients with aPC. Logistic and Cox regression were used for statistical analysis (Stat v.12). Results: Between 1st July 2018 and 30th October 2020, 112 eligible patients [50 (DeC), 25 (DiC), 37 (FuC)]. Prevalence of PEI in the DeC was 64.0% (PEI-related symptoms were flatus (84.0%), weight loss (84.0%), abdominal discomfort (50.0%) and steatorrhea (48.0%)); 70.0% of patients required pancreatic enzyme replacement therapy and 74.0% had anorexia (low appetite); 44.0% and 18.0% had low vitamin D and vitamin A levels, respectively. Designed PEI screening panel (DiC; 19 patients with breath test completed) included FE [normal/missing (0 points); low (1 point)] and MUAC [normal/missing ( > percentile 25 for age/gender) (0 points); low (2 points)] and identified patients at high-risk (2-3 total points) of PEI [vs. low-medium risk (0-1 total points)]. When patients from DeC and DiC) were analysed together, those classified as “high-risk of PEI” according to the screening panel had shorter overall survival (multivariable Hazard Ratio (mHR) 1.86 (95% CI 1.03-3.36); p-value 0.040) when adjusted for other prognostic factors, including presence of PEI symptoms (mHR 2.28 (95% CI 1.19-4.35); p-value 0.013). The screening panel was tested in the FuC; 78.38% were classified as patients at “high-risk of PEI”; of these, 89.6% were confirmed to have PEI by the dietitian. The panel was feasible for use in clinical practice, (64.8% of patients completed fully the assessments required) and acceptability was high (87.5% of patients would do it again). The majority of patients (91.3%) recommended that all future patients with aPC should have dietitian input. Conclusions: PEI is present in the majority of patients with aPC, and early dietetic input is important to provide a holistic nutritional overview, including, but not limited to, PEI. This proposed screening panel could be used to prioritise patients at higher risk of PEI requiring urgent dietitian input. Its prognostic role needs further validation. Clinical trial information: NCT03616431.

scholarly journals Immediate and delayed complications of adenotonsillectomy

2019 ◽  
Vol 5 (4) ◽  
pp. 1013
Author(s):  
Gerald P. Sebastian ◽  
Balasubramanian Thiagarajan ◽  
Pethuru Devadason
Keyword(s):  
Postoperative Complications ◽  
Observational Study ◽  
Endotracheal Tube ◽  
Surgical Complications ◽  
Surgical Complication ◽  
P Value ◽  
Secondary Haemorrhage ◽  
Delayed Complications ◽  
Primary Hemorrhage ◽  
Anesthetic Complications

<p class="abstract"><strong>Background:</strong> Tonsillectomy with or without adenoidectomy is the commonest pediatric otorhinolaryngological procedure. The aim of the present study was to compare the intraoperative (immediate) and postoperative (delayed) complications between in conventional and coablation tonsillectomy in children.</p><p class="abstract"><strong>Methods:</strong> This observational study was conducted among 100 children between 5 and 15 years who had conventional tonsillectomy and 50 children who had coblation tonsillectomy. Intraoperative and postoperative complications were observed and compared between two groups.  </p><p class="abstract"><strong>Results:</strong> Of the total 150 children, 64 (42.7%) were males and 86 (57.3%) were females with mean age of 9.42±2.67 years. Common preoperative symptoms were odynophagia (96.0%), throat pain (95.3%) and difficult swallowing (89.3%). Among the intraoperative anesthetic complications, compression of endotracheal tube was observed in 19 (12.7%), accidental extubation in 10 (6.7%) and dislodging of loose tooth in 9 (6.0%) patients. Regarding intraoperative surgical complications, primary hemorrhage was seen in 43 (28.7%), edema uvula in 39 (26.0%) and pillar injury in 33 (22.0%) patients. Commonest postoperative complication was oropharyngeal pain (18.7%) followed by primary hemorrhage (14.0%) and nausea, vomiting (13.3%). Immediate complications like primary haemorrhage (p value 0.0001) and uvula edema (p value 0.018) were significantly associated with conventional tonsillectomy group while delayed complications like secondary haemorrhage (p value 0.011) and referred otalgia (p value 0.0001) were with coblation tonsillectomy group.</p><p class="abstract"><strong>Conclusions:</strong> Compression of endotracheal tube and primary hemorrhage were the commonest intraoperative anesthetic and surgical complication respectively. Immediate complications were significantly associated with conventional tonsillectomy group while delayed complications were with coblation tonsillectomies.</p>

scholarly journals Comparison of hospitalizations in patients on first generation versus second generation long acting injectable (LAI) antipsychotics

BJPsych Open ◽  
2021 ◽  
Vol 7 (S1) ◽  
pp. S283-S283
Author(s):  
Seemab Rasool ◽  
Paster Venan
Keyword(s):  
Drug Abuse ◽  
Observational Study ◽  
First Generation ◽  
Second Generation ◽  
Hospital Admissions ◽  
Paranoid Schizophrenia ◽  
Bipolar Affective Disorder ◽  
Community Treatment ◽  
P Value ◽  
Targeted Interventions

AimsThere is limited data on the comparison of efficacy between first and second antipsychotic LAIs. One good indicator of efficacy is the rates of hospitalization. Some studies have shown that second generation depot antipsychotics, significantly reduce hospitalizations as compared to conventional depots.Our aim was to compare hospitalizations in patients on first and second generation LAI antipsychotics.MethodA retrospective observational study was done by reviewing the records of all the depot clinics in South Essex, United Kingdom. A list of patients enrolled and receiving LAI antipsychotics was obtained from the 6 depot clinics. Data were collected by going through the electronic records of the patients on the depot clinic lists and taking down the demographics, diagnosis and the hospital admissions. Other variables like comorbid drug abuse were also recorded.ResultAmongst a total of 346 patients 223 (64 %) were males and 123 (36%) were females. Average age was 50.3 (range 21 to 88 years) and 290 (83%) patients were single. An overwhelming majority of patients 299 (87 %) were not in employment. Regarding the diagnosis, the majority, 237 patients were diagnosed with Paranoid Schizophrenia, 49 patients were diagnosed with Schizoaffective disorder, 38 patients were diagnosed with Bipolar affective disorder, 20 patients had a diagnosis of Delusional disorder and only 2 patients had a primary diagnosis of Mental and Behavioral disorders due to substance abuse. Of the total 346 only 17 patients were on a Community treatment Order.Risperidone was the most commonly used second generation LAI at 26%,Aripiprazole in 10% and Paliperidone was used in 5% patients. Olanzapine LAI was only used in 2 patients. Amongst first generation LAIs Zuclopenthixol, Fluclopentixol were both used in 24%, and Haloperidol in 10% patients. 21 % of patients were reported to be actively abusing drugs.65 (32.6%) of the total 200 patients on Ist Generation LAIs had hospital admissions55 (39.8%) of the total 138 patients on 2nd Generation LAIs had hospital admissionsThis difference was not statistically significant (Z test)- P value of 0.082427ConclusionThe results in our observational study are equivocal, both LAIs providing equitable decrease in the hospital admissions albeit with a slightly favourable outcome (not statistically significant though) attributable to the first generation LAIs. There was a high incidence of unemployment and drug abuse in our cohort of patients, thus targeted interventions can be established in rehabilitation of such individuals.

scholarly journals The Evolution of Data Sharing Practices in the Psychological Literature

2021 ◽  
Author(s):  
Judith Neve ◽  
Guillaume A Rousselet
Keyword(s):  
Data Sharing ◽  
Linear Models ◽  
Generalized Additive Models ◽  
Additive Models ◽  
Future Research ◽  
Science Data ◽  
Editorial Policies ◽  
Psychological Science ◽  
The Impact

Sharing data has many benefits. However, data sharing rates remain low, for the most part well below 50%. A variety of interventions encouraging data sharing have been proposed. We focus here on editorial policies. Kidwell et al. (2016) assessed the impact of the introduction of badges in Psychological Science; Hardwicke et al. (2018) assessed the impact of Cognition’s mandatory data sharing policy. Both studies found policies to improve data sharing practices, but only assessed the impact of the policy for up to 25 months after its implementation. We examined the effect of these policies over a longer term by reusing their data and collecting a follow-up sample including articles published up until December 31st, 2019. We fit generalized additive models as these allow for a flexible assessment of the effect of time, in particular to identify non-linear changes in the trend. These models were compared to generalized linear models to examine whether the non-linearity is needed. Descriptive results and the outputs from generalized additive and linear models were coherent with previous findings: following the policies in Cognition and Psychological Science, data sharing statement rates increased immediately and continued to increase beyond the timeframes examined previously, until reaching close to 100%. In Clinical Psychological Science, data sharing statement rates started to increase only two years following the implementation of badges. Reusability rates jumped from close to 0% to around 50% but did not show changes within the pre-policy nor the post-policy timeframes. Journals that did not implement a policy showed no change in data sharing rates or reusability over time. There was variability across journals in the levels of increase, so we suggest future research should examine a larger number of policies to draw conclusions about their efficacy. We also encourage future research to investigate the barriers to data sharing specific to psychology subfields to identify the best interventions to tackle them.

scholarly journals A prospective observational study conducted in tertiary teaching hospital of Uttar Pradesh to compare safety and efficacy of PPIUCD and interval IUCD (380A)

2018 ◽  
Vol 8 (1) ◽  
pp. 295
Author(s):  
Nidhi Gupta ◽  
Akanksha .
Keyword(s):  
Observational Study ◽  
Prospective Observational Study ◽  
Uttar Pradesh ◽  
P Value ◽  
Efficacy And Safety ◽  
Puerperal Sepsis ◽  
Medical College ◽  
Tertiary Teaching ◽  
Reversible Method ◽  
Tertiary Teaching Hospital

Background: The objective of this study was to compare the efficacy and safety of PPIUCD and interval IUCD.Methods: This was a prospective observational study conducted on women attending the OPD and indoor services of S.N. Medical college, Agra. 800 women willing for PPIUCD insertion were included in the study after informed consent excluding chorioamnionitis, PROM>18 hours, unresolved PPH and puerperal sepsis. Another 200 willing women were inserted interval IUCD according to MEC criteria of WHO. All were followed up for 1 year.Results: It was found that rate of expulsion was more in PPIUCD group compared to interval IUCD group (6%vs 1.5% p value <.05),rate of removal was almost similar in both groups (11.5%inPPIUCD and 14%in interval IUCD group), cause of removal was mainly social in PPIUCD group while bleeding was more in interval IUCD group compared to PPIUCD (85.7%vs26%).Conclusions: Postpartum insertion of IUCD is a safe effective, feasible and reversible method of contraception.

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