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opencc-zeroDec 2020View details →

Methodology data of "A qualitative and quantitative citation analysis toward retracted articles: a case of study"

This document contains the datasets and visualizations generated after the application of the methodology defined in our work: "A qualitative and quantitative citation analysis toward retracted articles: a case of study". The methodology defines a citation analysis of the Wakefield et al. [1] retracted article from a quantitative and qualitative point of view. The data contained in this repository are based on the first two steps of the methodology. The first step of the methodology (i.e. “Data gathering”) builds an annotated dataset of the citing entities, this step is largely discussed also in [2]. The second step (i.e. "Topic Modelling") runs a topic modeling analysis on the textual features contained in the dataset generated by the first step.  Note: the data are all contained inside the "method_data.zip" file. You need to unzip the file to get access to all the files and directories listed below.   Data gathering The data generated by this step are stored in "data/": <ol> <li>"cits_features.csv": a dataset containing all the entities (rows in the CSV) which have cited the Wakefield et al. retracted article, and a set of features characterizing each citing entity (columns in the CSV). The features included are: DOI ("doi"), year of publication ("year"), the title ("title"), the venue identifier ("source_id"), the title of the venue ("source_title"), yes/no value in case the entity is retracted as well ("retracted"), the subject area ("area"), the subject category ("category"), the sections of the in-text citations ("intext_citation.section"), the value of the reference pointer ("intext_citation.pointer"), the in-text citation function ("intext_citation.intent"), the in-text citation perceived sentiment ("intext_citation.sentiment"), and a yes/no value to denote whether the in-text citation context mentions the retraction of the cited entity    ("intext_citation.section.ret_mention"). Note: this dataset is licensed under a <a href="https://creativecommons.org/publicdomain/zero/1.0/legalcode">Creative Commons public domain dedication (CC0)</a>.  </li> <li>"cits_text.csv": this dataset stores the abstract ("abstract") and the in-text citations context ("intext_citation.context") for each citing entity identified using the DOI value ("doi"). Note: the data keep their original license (the one provided by their publisher). This dataset is provided in order to favor the reproducibility of the results obtained in our work.</li> </ol>   Topic modeling We run a topic modeling analysis on the textual features gathered (i.e. abstracts and citation contexts). The results are stored inside the "topic_modeling/" directory. The topic modeling has been done using MITAO, a tool for mashing up automatic text analysis tools, and creating a completely customizable visual workflow [3]. The topic modeling results for each textual feature are separated into two different folders, "abstracts/" for the abstracts, and "intext_cit/" for the in-text citation contexts. Both the directories contain the following directories/files:     <ol> <li> "mitao_workflows/": the workflows of MITAO. These are JSON files that could be reloaded in MITAO to reproduce the results following the same workflows. </li> <li> "corpus_and_dictionary/": it contains the dictionary and the vectorized corpus given as inputs for the LDA topic modeling. </li> <li> "coherence/coherence.csv": the coherence score of several topic models trained on a number of topics from 1 - 40. </li> <li> "datasets_and_views/": the datasets and visualizations generated using MITAO.   </li> </ol>   References <ol> <li>Wakefield, A., Murch, S., Anthony, A., Linnell, J., Casson, D., Malik, M., Berelowitz, M., Dhillon, A., Thomson, M., Harvey, P., Valentine, A., Davies, S., & Walker-Smith, J. (1998). RETRACTED: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. The Lancet, 351(9103), 637–641. <a href="https://doi.org/10.1016/S0140-6736(97)11096-0">https://doi.org/10.1016/S0140-6736(97)11096-0</a></li> <li> Heibi, I., & Peroni, S. (2020). A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article v1 (protocols.io.bdc4i2yw) [Data set]. In protocols.io. ZappyLab, Inc. <a href="https://doi.org/10.17504/protocols.io.bdc4i2yw">https://doi.org/10.17504/protocols.io.bdc4i2yw</a> </li> <li>   Ferri, P., Heibi, I., Pareschi, L., & Peroni, S. (2020). MITAO: A User Friendly and Modular Software for Topic Modelling [JD]. PuntOorg International Journal, 5(2), 135–149. <a href="https://doi.org/10.19245/25.05.pij.5.2.3">https://doi.org/10.19245/25.05.pij.5.2.3</a>   </li> </ol>

opencc-by-4.0Sep 2021View details →

Shared motivations, goals and values in the practice of personal science - Qualitative data set

269 transcribed excerpts coded from 22 interviews to self-researchers for the study "Shared motivations, goals and values in the practice of personal science - A community perspective on self-tracking for empirical knowledge". Interviews with participants were conducted via video conferencing and were based on a list of open-ended questions, separated into key sections around participation and collaboration in personal science. Participants who agreed to be interviewed, gave informed consent in like with the ethics approval by the Inserm Institutional Review Board (IRB) for this study, and regarding this data set, previous agreement in compliance with privacy and anonymity requirements. Academic article based on this dataset: Senabre Hidalgo, E., Ball, M. P., Opoix, M., & Greshake Tzovaras, B. (2022). Shared motivations, goals and values in the practice of personal science: a community perspective on self-tracking for empirical knowledge. Humanities and Social Sciences Communications, 9(1), 1-12. <a href="https://doi.org/10.1057/s41599-022-01199-0">https://doi.org/10.1057/s41599-022-01199-0</a>

opencc-by-4.0Feb 2023View details →

Development Gateway shisha study qualitative data: Understanding factors influencing Shisha smoking in Nigeria

79 qualitative transcripts from semi-structured interviews conducted across 13 states in Nigeria with either six (for Adamawa, Anambra, Ebonyi, Edo, FCT, Gombe, Kaduna, Kogi, Lagos, Oyo, Plateau and Rivers) or seven (Kano) qualitative transcripts per state. The transcripts are from a study exploring the following questions: <ol> <li>What factors (demographic, social, cultural, behavioural, etc.) are associated with the use of shisha in Nigeria?</li> <li>What are the shisha use patterns and behaviours among those who use shisha in Nigeria?</li> </ol> Respondents were self-reported current shisha users identified from public places that are known to provide spaces for use of shisha such as social clubs, night clubs, bars, pubs, cafes, and restaurants. Study participants had to be at least 18 years old to participate in the study. Topics covered in the interviews include respondent’s history of shisha smoking, perceived benefits from smoking shisha, awareness of health implications of smoking shisha, perceptions towards selected health risks of shisha smoking, use of sundry substances and other risky behaviours, and regulations Laws on shisha use in Nigeria. The data was collected between December 2021 and January 2022 Also included with the dataset is the interview guide.

opencc-by-4.0May 2023View details →

Underlying qualitative data for: "What went wrong? A qualitative exploration of the determinants of poor antiretroviral therapy adherence and retention in care among pregnant and postpartum women in the Uganda WiseMama randomized controlled trial"

This dataset is the underlying qualitative data for the paper entitled: "What went wrong? A qualitative exploration of the determinants of poor antiretroviral therapy adherence and retention in care among pregnant and postpartum women in the Uganda WiseMama randomized controlled trial"

dryad36/100

Data from: A qualitative analysis of an Aβ-monomer model with inflammation processes for Alzheimer’s disease

Open the record for dataset details and reuse information.

publicOct 2024View details →

dryad36/100

Qualitative raw data and behavioral analysis for understanding VMMC policy decision-making

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publicJan 2024View details →

opencc-zeroJan 2020View details →

Supplementary material 1 from: Biniari K, Daskalakis I, Bouza D, Stavrakaki M (2019) Comparative study of qualitative and quantitative characters of grape cultivar 'Mavrodafni' (Vitis vinifera L.) and 'Renio' grown in different regions of the Protected Designation of Origin Mavrodafni Patras. Viticulture Data Journal 1: e37852. https://doi.org/10.3897/vdj.1.e37852

This is the raw dataset of the measurements performed on the samples collected from the two varieties from the different locations. There are three repetitions per measurement and no statistical analysis has been performed.

opencc-by-4.0Jan 2020View details →

The Qualitative Analysis of Repertory Grid Data: Interpretive Clustering (datasets only)

Datasets accompanying the publication "The Qualitative Analysis of Repertory Grid Data: Interpretive Clustering" by  Burr, King, and Heckmann.

opencc-by-4.0Mar 2020View details →

Data file: a qualitative social media content analysis of the Dutch #breakthesilence campaign on negative and traumatic experiences of labour and birth

Data file with typed out quotes from the Dutch #breakthesilence campaign analysed for the study 'Left powerless: a qualitative social media content analysis of the Dutch #breakthesilence campaign on negative and traumatic experiences of labour and birth'.

opencc-zeroAug 2020View details →

Data from: Understanding families' experiences following a diagnosis of non-syndromic Craniosynostosis: A qualitative study

Objectives: Craniosynostosis, a congenital anomaly producing an abnormal cranial morphology, is typically diagnosed and surgically corrected within the first year of life. Given the young age of this patient population at the time of diagnosis, it is reasonable to expect this experience to be a very significant and stressful ordeal for patient families. Despite this, there is little research exploring the impact that craniosynostosis has on families, especially in the early stages. In this study, the authors aimed to qualitatively examine the psychosocial experience of families with a child diagnosed with craniosynostosis. Design: Qualitative study. Setting: Tertiary care paediatric health centre. Participants: Parents of children newly diagnosed with single-suture, non-syndromic craniosynostosis Intervention: Semistructured interviews regarding parental experience with the initial diagnosis, their decision on corrective surgery for their child, the operative experience, the impact of craniosynostosis on the family and the challenges they encountered throughout their journey. Primary and Secondary Outcome Measures: Interpretive phenomenological analysis, a type of qualitative analysis that provides an in-depth account of participant's experiences and their meanings, was used to analyze the interview data. Results: Over a four-year period, twelve families meeting eligibility criteria completed the study. Three main themes (6 subthemes) emerged from the pre-operative interviews: frustration with diagnostic delays (parental intuition and advocacy, hope for improved awareness), understanding what to expect (healthcare supports, interest in connecting with other families), and justifying the need for corrective surgery (influence of the surgeon, struggle with cosmetic indications). Two main themes (4 subthemes) were drawn from the post-operative interviews: pushing through fear (the role of healthcare professionals, transition home) and relief (reduction in parental anxiety, cosmetic improvements). Conclusions: Overall, the diagnosis of craniosynostosis has a profound impact on families, leading them to face many struggles throughout their journey. A better understanding of these experiences will help to inform future practice, with a hope to improve this experience for other families moving forward.

opencc-zeroAug 2020View details →

Qualitative data on: Sustainability drivers and inhibitors for the health system performance improvement projects in selected health facilities in Kenya

Objectives to investigate the health managers perceived sustainability status of the health facilities institutional improvement projects and their experiences on factors that facilitated or constrained their maintenance, with intentions of informing relevant strategies or policies in Kenya's health sector. Methods A qualitative study, nested within a quasi-experimental study. Thirty-three project-teams of health managers were purposively selected and interviewed based on their project implementation success rates post-training. The managers had previously undergone a 9-month leadership training, complimented with facility-based team coaching around the chosen projects. The training was funded by the USAID; however, the implementation of the projects was based on how the participants could innovatively utilize the existing resource to create a positive change. The projects were housed within 20 public, nine faith-based, and four private health facilities in 19 Counties in Kenya. The interviews explored the manager's experiences in sustaining the successfully implemented projects within the (24-60 months post-training period). We asked Managers to describe factors they perceived enabled or hindered the sustainability of the successfully implemented institutional improvement project. The digitally audio-recorded interviews were transcribed verbatim. Data on barriers and enablers were thematically analyzed. Results Twenty-seven out of the 33 successfully implemented projects reported sustainability within periods ranging from 24-60 months post-training. Seven themes related to drivers of sustainability emerged, namely; program design, stakeholder's buy-in, board members, communication, coaching, presence of change champion, devolution and political good-will. Four sustainability inhibitors identified were; human resources constraints, policy implementation, misalignment of projects with daily operations, devolution and political interference. Conclusions The sustainability of institutional improvement strategies such as projects implemented post-leadership training in public and private health facilities depends on the quality of board members, communication management and institutionalization of coaching culture. These findings are pertinent for planning and implementing similar health systems strengthening intervention in low-income countries.

opencc-zeroDec 2016View details →

Data from: Radar wind profilers and avian migration - a qualitative and quantitative assessment verified by thermal imaging and moon watching

1. Radars of various types have been used in ornithological research for about 70 years. However, the potential of radar wind profiler (RWP) as a tool for biological purposes remains poorly understood. The aim of this study is to assess the suitability of RWP for ornithological research questions. 2. A 1290 MHz RWP at the southeastern coast of the Bay of Biscay has been known to exhibit seasonally occurring nocturnal signals attributed to migrating birds. As a first step to verify the origin of these seasonal patterns, historical radar data from 2010-2012 were analysed, and both bird patterns and temporal occurrence were identified in RWP data at different levels of the signal processing. A thermal-imaging (TI) camera in conjunction with moon watching was used as verification systems at the radar site to confirm the ornithological origin of the radar echoes. The simultaneous data on spring migration served as a basis for the identification of biological signatures (qualitative parameters) on time series level (raw data) and to derive quantitative migration parameters (flight altitude, migration traffic rates) thereof. Finally the quantitative measurements of the TI camera and the radar were compared considering meteorological conditions. 3. The approach allowed identifying reproducible criteria based on time series to calculate migration traffic rates and altitudinal flight distribution. General flight directions were only available in the final wind data. In clear weather conditions the calibration methods coincided well with the wind profiler data. 4. Findings show that wind profiler raw data offers reliable information on migration intensity, flight altitudes and flight directions in a variety of meteorological conditions. The method presented can be applied as a complement to present efforts to use weather radars for large-scale bird monitoring. Furthermore it is also interesting for the meteorological community to refine signal-processing methods.

opencc-zeroDec 2016View details →

Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.

opencc-zeroDec 2018View details →

Data from: Perceived impact of community kitchens on the food security of Syrian refugees and kitchen workers in Lebanon: Qualitative evidence in a displacement context

Community kitchens (CKs) have been recommended as public health strategies with social and nutritional health benefits for low-income participants and their families in different settings. The benefit of CKs in improving the food security status of participants in the context of conflict and displacement is less conclusive. This study aimed to qualitatively explore the impact of CKs on the food security status of community kitchen workers (CWs) and Syrian refugee (SR) families in Lebanon. An exploratory qualitative descriptive approach was adopted. Focus group discussions were conducted with 15 CWs and 49 SRs, and transcripts were analyzed thematically. Emerging themes included: motivation to join the CKs (CWs only), perception towards CKs, impact of these CKs, and their sustainability (both groups). Motivating factors for CWs included financial, internal and societal drivers, and the favorable type of work in kitchens. The perception towards CKs was overall positive among CWs and SR beneficiaries. Both groups reported the positive impact of CKs on their food security and financial status, which in turn affected positively their psychological health. At the social level, CWs indicated that the kitchen's friendly atmosphere increased social cohesion and companionship between Syrians and Lebanese within the kitchen. In addition, CWs reported increased sense of empathy towards SRs benefiting from the CK services. According to study participants, the positive impact of the CKs was almost completely reversed when their operation and services were interrupted for two months. Both CWs and SRs identified facilitators and barriers that can affect the sustainability of the kitchens, including financial and entrepreneurial skills. In conclusion, findings from this study highlight that CKs can be promising programs to improve the food security and livelihoods of participants, while also increasing social cohesion and integration of refugees within host communities in protracted crisis contexts.

opencc-zeroJul 2019View details →

Data from: Genetic rescue by distant trees mitigates qualitative pollen limitation imposed by fine-scale spatial genetic structure

Restricted seed dispersal frequently leads to fine-scale spatial genetic structure (i.e., FSGS) within plant populations. Depending on its spatial extent and the mobility of pollinators, this inflated kinship at the immediate neighbourhood can critically impoverish pollen quality. Despite the common occurrence of positive FSGS within plant populations, our knowledge regarding the role of long-distance pollination preventing reproductive failure is still limited. Using microsatellite markers, we examined the existence of positive FSGS in two low-density populations of the tree Pyrus bourgaeana. We also designed controlled crosses among trees differing in their kinship to investigate the effects of increased local kinship on plant reproduction. We used six pollination treatments and fully monitored fruit production, fruit and seed weight, proportion of mature seeds per fruit, and seed germination. Our results revealed positive FSGS in both study populations and lower fruit initiation in flowers pollinated with pollen from highly-genetically related individuals within the neighbourhood, with this trend intensifying as the fruit development progressed. Besides, open-pollinated flowers exhibited lower performance of compared to those pollinated by distant pollen donors, suggesting intense qualitative pollen limitation in natural populations. We found positive fine-scale spatial genetic structure is translated into impoverished pollen quality from nearby pollen donors which negatively impacts the reproductive success of trees in low-density populations. Under this scenario of intrapopulation genetic rescue by distant pollen donors, the relevance of highly-mobile pollinators for connecting spatially and genetically distant patches of trees may be crucial to safeguarding population recruitment.

opencc-zeroDec 2015View details →

Data from: How do patients and health workers interact around malaria rapid diagnostic testing, and how are the tests experienced by patients in practice? A qualitative study in western Uganda

Background: Successful scale-up in the use of malaria rapid diagnostic tests (RDTs) requires that patients accept testing and treatment based on RDT results and that healthcare providers treat according to test results. Patient-provider communication is a key component of quality care, and leads to improved patient satisfaction, higher adherence to treatment and better health outcomes. Voiced or perceived patient expectations are also known to influence treatment decision-making among healthcare providers. While there has been a growth in literature on provider practices around rapid testing for malaria, there has been little analysis of inter-personal communication around the testing process. We investigated how healthcare providers and patients interact and engage throughout the diagnostic and treatment process, and how the testing service is experienced by patients in practice. Methods: This research was conducted alongside a larger study which explored determinants of provider treatment decision-making following negative RDT results in a rural district (Kibaale) in mid-western Uganda, ten months after RDT introduction. Fifty-five patients presenting with fever were observed during routine outpatient visits at 12 low-level public health facilities. Observation captured communication practices relating to test purpose, results, diagnosis and treatment. All observed patients or caregivers were immediately followed up with in-depth interview. Analysis followed the 'framework' approach. A summative approach was also used to analyse observation data. Results: Providers failed to consistently communicate the reasons for carrying out the test, and particularly to RDT-negative patients, a diagnostic outcome or the meaning of test results, also leading to confusion over what the test can detect. Patients appeared to value testing, but were frustrated by the lack of communication on outcomes. RDT-negative patients were dissatisfied by the absence of information on an alternative diagnosis and expressed uncertainty around adequacy of proposed treatment. Conclusions: Poor provider communication practices around the testing process, as well as limited inter-personal exchange between providers and patients, impacted on patients' perceptions of their proposed treatment. Patients have a right to health information and may be more likely to accept and adhere to treatment when they understand their diagnosis and treatment rationale in relation to their perceived health needs and visit expectations.

opencc-zeroDec 2016View details →

Data from: Taxonomic revision of the Malagasy Camponotus grandidieri and niveosetosus species groups (Hymenoptera, Formicidae) using qualitative and quantitative morphology

The Camponotus grandidieri species group and Camponotus niveosetosus species group of the Malagasy region are revised. Species delimitation was inferred from the evidence of both qualitative morphological analysis and multivariate morphometry. The multivariate method combined the Nest Centroid (NC)-clustering method and Partitioning Algorithm based on Recursive Thresholding (PART) function to generate hypotheses about species boundaries (clusters) based on 19 continuous morphological traits of minor workers. The proposed species hypotheses were tested by cumulative cross-validated Linear Discriminant Analysis (LOOCV-LDA) and Principal Component Analysis in a shape space (shape PCA). Morphometric ratios for the subsets of minor and major workers were used in species descriptions and redefinitions. Here, eight species are recognized, of which three are newly described and five are redescribed. Four species belong to the Camponotus grandidieri species group: auropubens Forel, efitra n. sp., grandidieri Forel, and maintikibo n. sp.; and four species belong to the Camponotus niveosetosus species group: descarpentriesi Santschi, madagascarensis Forel stat. rev., mita n. sp., and voeltzkowii Forel. Camponotus auropubens aldabrensis Forel and C. olivieri freyeri Santschi are synonymized under C. auropubens. Camponotus grandidieri atrabilis Santschi and C. grandidieri comorensis Santschi are synonymized under C. grandidieri. Illustrated species identification keys for both minor and major castes, taxonomic discussions, images, and distribution maps for each species superimposed on the ecoregions of Madagascar are also provided.

opencc-zeroDec 2014View details →

Data from: Newspaper coverage of maternal health in Bangladesh, Rwanda, and South Africa: a quantitative and qualitative content analysis

Objective: To examine newspaper coverage of maternal health in three countries that have made varying progress towards Millennium Development Goal 5 (MDG 5): Bangladesh (on track), Rwanda (making progress, but not on track) and South Africa (no progress). Design: We analysed each country's leading national English-language newspaper: Bangladesh's The Daily Star, Rwanda's The New Times/The Sunday Times, and South Africa's Sunday Times/The Times. We quantified the number of maternal health articles published from 1 January 2008 to 31 March 2013. We conducted a content analysis of subset of 190 articles published from 1 October 2010 to 31 March 2013. Results: Bangladesh's The Daily Star published 579 articles related to maternal health from 1 January 2008 to 31 March 2013, compared to 342 in Rwanda's The New Times/The Sunday Times and 253 in South Africa's Sunday Times/The Times over the same time period. The Daily Star had the highest proportion of stories advocating for or raising awareness of maternal health. Most maternal health articles in The Daily Star (83%) and The New Times/The Sunday Times (69%) used a 'human-rights' or 'policy-based' frame compared to 41% of articles from Sunday Times/The Times. Conclusions: In the three countries included in this study, which are on different trajectories towards MDG 5, there were differences in the frequency, tone and content of their newspaper coverage of maternal health. However, no causal conclusions can be drawn about this association between progress on MDG 5 and the amount and type of media coverage of maternal health.

opencc-zeroDec 2012View details →

Data from: The interactions of ethical notions and moral values of immediate stakeholders of immunisation services in two Indian states: a qualitative study

OBJECTIVES: This study examines the existing norms regarding immunization within the communities and the ethical notions that govern the action of different health professionals and their collective synergistic or conflicting effect on governance of the programme. Design: We used descriptive and analytical qualitative methods as it suited the research question. SETTING: The data was collected from areas under 16 Primary Health Centres in Kerala and Tamil Nadu identified through three-step sampling process. PARTICIPANTS: This involved in-depth interview with stakeholders including providers, beneficiaries and other stakeholders, focus group discussions with mother of under five children and participant and non-participant observations of vaccination related activities. RESULTS: Unlike most other ethical analysis that looks at ethics of vaccination policies, the interactions of normative principles and notions are analysed in this article. Moral obligation of parents towards their children, beneficence of health care providers and the utilitarian aspirations of the state are the key normative principles involved. Our analysis points to the interplay of both synergy and conflict in ethical notions and moral values in the context of immunisation services. Paternalistic interventions like special immunisation campaigns against polio and Japanese encephalitis are a case in point: they generate conflict at the normative level and create mistrust. CONCLUSIONS: Analysis of vaccination policies and programmes need to go beyond factors that assess monitory benefits or herd immunity. Understanding the interactions normative notions that shape the social organisation of the providers and the users of vaccination is important in creating a sustainable environment for the programme.