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 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 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.

HUBUNGAN PERAN KADER POSYANDU DENGAN STATUS GIZI BALITA

2018 ◽  
Vol 9 (02) ◽  
pp. 192
Author(s):  
Wiwid Wahyuningsih ◽  
Atik Setiyaningsih
Keyword(s):  
Nutritional Status ◽  
Total Sample ◽  
Nutrition Status ◽  
P Value ◽  
Chi Square ◽  
Cross Sectional ◽  
Central Java ◽  
Good Nutrition ◽  
Nutritional Status Of Children

ABSTRAKLatar Belakang : Keberadaan kader di posyandu sebagai salah satu sistem penyelenggarakan pelayanan sangat dibutuhkan. Mereka adalah ujung tombak  pelayanan kesehatan yang merupakan kepanjangtanganan puskesmas Jawa Tengah tahun 2011 jumlah gizi kurang 5,35% dan gizi buruk 0,10%. Untuk Kabupaten Semarang dari 23.562 balita yang ditimbang pada tahun 2011 gizi lebih 1,13%, gizi baik 93,51%, gizi kurang 4,86% dan gizi buruk 0,49% (DepKes Prov Jateng, 2011). Tujuan Penelitian : Penelitian ini bertujuan untuk mengetahui hubungan peran kader posyandu dengan status gizi balita. Metode Penelitian : Desain penelitian ini adalah survey analitik dengan menggunakan pendekatan cross sectional. Populasi dalam penelitian ini adalah seluruh balita di Posyandu Mawar di Desa Gedangan sejumlah 40 responden, dengan teknik total sampling dan analisa data chi square. Hasil Penelitian : Hasil perhitungan chi square di peroleh X² hitung 10.644 pada df=4, P.value 0.031 dimana probabilitas lebih kecil dari level of significant 5 % (0,001 < 0,05) berarti Ha diterima dan Ho ditolak. Kesimpulan : ada hubungan antara peran kader posyandu dengan status gizi pada balita.Kata Kunci : peran kader , status gizi balitaCADERE ROLE RELATIONSHIP WITH NUTRITIONAL STATUS OF CHILDREN POSYANDUABSTRACTBackground : posyandu cadre in Existence as one of the 56th's service system is urgently needed. They are the tip of the Spear is a kepanjangtanganan health services clinics in Central Java in 2011 the amount of nutrition less 5.35% 0.10% and malnutrition. To Semarang from 23.562 toddler who weighed in 2011 more nutritional 1.13%, 93,51%, good nutrition nutrition less 4.86% and 0.49% poor nutrition (Department of Health Central Java Prov., 2011). Objective : the research aims to find out the relationship role of posyandu cadre with the nutritional status of children. Methods : the design of this research is a survey using the analytic approach of cross sectional. The population in this study are all the toddlers at the Rose in the village of Posyandu Gedangan some 38 respondents, with total sample techniques and data analysis a chi square. The results :. The chi square calculation results in getting X ² count 10.644 on df = 4, P. value 0.031 where probability is smaller than the level of significant 5% (0.001 < 0.05) mean Ha Ho accepted and rejected. Conclusion : there is a connection between the role of cadres of posyandu with nutritional status on toddlers.Keywords : the role of cadres, toddler nutrition status

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 The Relationship between Foot Status and Motor Status in Preschool Children: A Simple, Comparative Observational Study

Healthcare ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 936
Author(s):  
Milan Kojić ◽  
Branka Protić Gava ◽  
Milan Bajin ◽  
Marko Vasiljević ◽  
Jasmina Bašić ◽  
...  
Keyword(s):  
Preschool Children ◽  
Observational Study ◽  
Total Sample ◽  
Nonparametric Tests ◽  
Significance Level ◽  
Flat Feet ◽  
Significant Difference ◽  
Left And Right ◽  
The Relationship

Background: The research objective of the study is to determine the differences in the manifestation of the motor status of normally fed preschool test subjects, classified into groups according to foot status. Methods: This is a simple, comparative observational study. Preschool children included in this study have been subjected to anthropometric measurements in order to determine BMI, tests for motor skills assessment (running at 20 m from a high start, standing broad jump, backwards polygon, rectangular seated forward bend, plate tapping, sit-ups for 60 s, and bent arm hang), and a determination of foot status. The total sample was comprised of 202 test subjects who attended a regular sports program, aged 3.9 to 6.5 years of decimal age (M = 141; Age = 5.3 ± 0.74; Height = 117.3 ± 7.1; Weight = 22 ± 3.7; F = 61; Age = 5.1 ± 0.73; Height = 114.9 ± 7.4; Weight = 21.2 ± 3.8), of which 153 (75.7%) were normally fed, 6 (3%) were undernourished, 30 were overweight (14.9%), and 13 were obese (6.4%). Results: In the total sample, 30 (14.9%) subjects had normal arch feet, 90 (44.6%) high arched feet, and 41 (20.3%) flat feet. We found 41 (20.3%) subjects who had different left and right foot statuses within this sample. The data were processed by means of nonparametric tests (the Kruskal–Wallis and Mann–Whitney U tests) at a significance level p ≤ 0.05. Conclusion: The results show that there is a statistically significant difference between groups of subjects with different foot statuses in the manifestation of motor status in most tests, with a significance level of p ≤ 0.01, and in tests of sit-ups for 60 s and the bent arm hang, there is a statistically significant difference, the level of which is p ≤ 0.05. It is only in the inclination test of rectangular seated forward bend that no statistically significant difference was displayed.

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 Determinan Penyalahgunaan Narkoba pada Remaja di SMAN 24 Jakarta

2017 ◽  
Vol 2 (1) ◽  
pp. 135-143
Author(s):  
Oki Fitriani ◽  
Sarah Handayani ◽  
Nur Asiah
Keyword(s):  
High School ◽  
Drug Abuse ◽  
Total Sample ◽  
Senior High School ◽  
Risk Level ◽  
Individual Factors ◽  
P Value ◽  
Cross Sectional ◽  
Big City ◽  
Abuse Risk

Determinants of Drug Abuse Among Adolescents in 24 Senior High School Jakarta  Introduction. The number of drug abuse in adolescents has increased dramatically. Survey conducted in2006 and 2009 shows pattern that drug abuse risk in big city is higher rather than in small city. It is alsoidentified that the risk level of drug abuse in adolescents is different from one to another. The differencesare caused by several factors. This study aims to determine some factors believed to have associationwith the risk of drug abuse in adolescents in 24 Senior High School, Jakarta.Methods. This study is a quantitative analytical research using cross sectional design. Location of thestudy was in 24 Senior High School, Jakarta. Research was conducted during March – August 2016.Population of this study was all student grade 10 and 11 in 24 Senior High School, Jakarta which is 350students. Variable dependent in this study is drug abuse risk and independent variables are individual,drug and environment characteristic. Sampling was chosen using proportional stratified randomsampling. The total sample was 91 people. Data analysis was using uni variate and bivariate analysis.Resulst. The results showed from 8 variables, only 6 variables that have relationship with the risk of drugabuse in teenagers / students. Those variables are drug factors; availability (p value = 0.000 PR = 2,595% CI 1566-3909), and the ease of getting drugs (p value = 0,009 PR = 1,7 95% CI 1114-2437),individual factors; gender (p value = 0,000 PR = 2,6 95% CI 0626-4218), and knowledge (p value =0048 PR = 1,5 95% CI 0966-2340), environmental factors; family (p value = 0.003 PR = 1,8 95% CI1174-2739), and friends (association) (p value = 0,000 PR = 2,4 95% CI 1512-3647).Conclusions. Variables that have relationship with the risk of drug abuse are drug factors (availability,the ease of getting drugs) individual factors (gender, knowladge) and environment factors (family, friend)

scholarly journals Determinant Factor of Childhood Basic Immunization Compliance during the COVID-19 Pandemic in Jambi City, Jambi Province, Indonesia

2021 ◽  
Vol 5 (1) ◽  
pp. 77-88
Author(s):  
Anita Rezeki Carolina ◽  
Defi Efendi ◽  
Maria Dyah Kurniasari
Keyword(s):  
Data Analysis ◽  
Total Sample ◽  
Case Control ◽  
P Value ◽  
Cluster Sampling ◽  
Chi Square ◽  
City Regions ◽  
Improve Compliance ◽  
Determinant Factor ◽  
Descriptive Statistical Analysis

Background: The coverage of immunization among children in Jambi City decreased during COVID-19 pandemic.Purpose: This study aims to identify the factors that might be associated with basic vaccination compliance among mothers in Jambi, Indonesia.Methods: This study uses a case control design in 5 Jambi City Regions in March-May 2021. The sample in this study is mothers who have children in age 9-24 months. The sampling that is used in this study is cluster sampling with total sample of 506 mothers. The data analysis used in this study is descriptive statistical analysis of univariate, bivariate using chi square test.Results: The results of data analysis showed that the variables related to compliance were perceptions of receiving immunization, attitudes, knowledge, husband's support with p value < 0.01, and distance traveled with p value < 0.05.Conclusion: Effort to improve compliance in the pediatric immunization Pandemic are needed to strengthen mother’s perception, knowledge, attitudes during COVID-19. Analysis with predictive models is highly recommended to determine the odd-ratios and adjusted odd-ratios between factors related to the complying for basic vaccination.  

Sign in / Sign up

Export Citation Format

Share Document