Open Science in Software Engineering

Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other scientific disciplines, in software engineering, we are still struggling in adapting open science to the particularities of our discipline, rendering progress in our scientific community cumbersome. In this chapter, we reflect upon the essentials in open science for software engineering including what open science is, why we should engage in it, and how we should do it. We particularly draw from our experiences made as conference chairs implementing open science initiatives and as researchers actively engaging in open science to critically discuss challenges and pitfalls, and to address more advanced topics such as how and under which conditions to share preprints, what infrastructure and licence model to cover, or how do it within the limitations of different reviewing models, such as double-blind reviewing. Our hope is to help establishing a common ground and to contribute to make open science a norm also in software engineering.Comment: Camera-Ready Version of a Chapter published in the book on Contemporary Empirical Methods in Software Engineering; fixed layout issue with side-note

Do differences in profiling criteria bias performance measurements? Economic profiling of medical clinics under the Korea National Health Insurance program: An observational study using claims data

<p>Abstract</p> <p>Background</p> <p>With a greater emphasis on cost containment in many health care systems, it has become common to evaluate each physician's relative resource use. This study explored the major factors that influence the economic performance rankings of medical clinics in the Korea National Health Insurance (NHI) program by assessing the consistency between cost-efficiency indices constructed using different profiling criteria.</p> <p>Methods</p> <p>Data on medical care benefit costs for outpatient care at medical clinics nationwide were collected from the NHI claims database. We calculated eight types of cost-efficiency index with different profiling criteria for each medical clinic and investigated the agreement between the decile rankings of each index pair using the weighted kappa statistic.</p> <p>Results</p> <p>The exclusion of pharmacy cost lowered agreement between rankings to the lowest level, and differences in case-mix classification also lowered agreement considerably.</p> <p>Conclusions</p> <p>A medical clinic may be identified as either cost-efficient or cost-inefficient, even when using the same index, depending on the profiling criteria applied. Whether a country has a single insurance or a multiple-insurer system, it is very important to have standardized profiling criteria for the consolidated management of health care costs.</p

Minimum follow-up time required for the estimation of statistical cure of cancer patients: verification using data from 42 cancer sites in the SEER database

BACKGROUND: The present commonly used five-year survival rates are not adequate to represent the statistical cure. In the present study, we established the minimum number of years required for follow-up to estimate statistical cure rate, by using a lognormal distribution of the survival time of those who died of their cancer. We introduced the term, threshold year, the follow-up time for patients dying from the specific cancer covers most of the survival data, leaving less than 2.25% uncovered. This is close enough to cure from that specific cancer. METHODS: Data from the Surveillance, Epidemiology and End Results (SEER) database were tested if the survival times of cancer patients who died of their disease followed the lognormal distribution using a minimum chi-square method. Patients diagnosed from 1973–1992 in the registries of Connecticut and Detroit were chosen so that a maximum of 27 years was allowed for follow-up to 1999. A total of 49 specific organ sites were tested. The parameters of those lognormal distributions were found for each cancer site. The cancer-specific survival rates at the threshold years were compared with the longest available Kaplan-Meier survival estimates. RESULTS: The characteristics of the cancer-specific survival times of cancer patients who died of their disease from 42 cancer sites out of 49 sites were verified to follow different lognormal distributions. The threshold years validated for statistical cure varied for different cancer sites, from 2.6 years for pancreas cancer to 25.2 years for cancer of salivary gland. At the threshold year, the statistical cure rates estimated for 40 cancer sites were found to match the actuarial long-term survival rates estimated by the Kaplan-Meier method within six percentage points. For two cancer sites: breast and thyroid, the threshold years were so long that the cancer-specific survival rates could yet not be obtained because the SEER data do not provide sufficiently long follow-up. CONCLUSION: The present study suggests a certain threshold year is required to wait before the statistical cure rate can be estimated for each cancer site. For some cancers, such as breast and thyroid, the 5- or 10-year survival rates inadequately reflect statistical cure rates, and highlight the need for long-term follow-up of these patients

Generalized Painleve-Gullstrand descriptions of Kerr-Newman black holes

Generalized Painleve-Gullstrand metrics are explicitly constructed for the Kerr-Newman family of charged rotating black holes. These descriptions are free of all coordinate singularities; moreover, unlike the Doran and other proposed metrics, an extra tunable function is introduced to ensure all variables in the metrics remain real for all values of the mass M, charge Q, angular momentum aM, and cosmological constant \Lambda > - 3/(a^2). To describe fermions in Kerr-Newman spacetimes, the stronger requirement of non-singular vierbein one-forms at the horizon(s) is imposed and coordinate singularities are eliminated by local Lorentz boosts. Other known vierbein fields of Kerr-Newman black holes are analysed and discussed; and it is revealed that some of these descriptions are actually not related by physical Lorentz transformations to the original Kerr-Newman expression in Boyer-Lindquist coordinates - which is the reason complex components appear (for certain ranges of the radial coordinate) in these metrics. As an application of our constructions the correct effective Hawking temperature for Kerr black holes is derived with the method of Parikh and Wilczek.Comment: 5 pages; extended to include application to derivation of Hawking radiation for Kerr black holes with Parikh-Wilczek metho

A gene signature for post-infectious chronic fatigue syndrome

Background: At present, there are no clinically reliable disease markers for chronic fatigue syndrome. DNA chip microarray technology provides a method for examining the differential expression of mRNA from a large number of genes. Our hypothesis was that a gene expression signature, generated by microarray assays, could help identify genes which are dysregulated in patients with post-infectious CFS and so help identify biomarkers for the condition. Methods: Human genome-wide Affymetrix GeneChip arrays (39,000 transcripts derived from 33,000 gene sequences) were used to compare the levels of gene expression in the peripheral blood mononuclear cells of male patients with post-infectious chronic fatigue (n = 8) and male healthy control subjects (n = 7). Results: Patients and healthy subjects differed significantly in the level of expression of 366 genes. Analysis of the differentially expressed genes indicated functional implications in immune modulation, oxidative stress and apoptosis. Prototype biomarkers were identified on the basis of differential levels of gene expression and possible biological significance Conclusion: Differential expression of key genes identified in this study offer an insight into the possible mechanism of chronic fatigue following infection. The representative biomarkers identified in this research appear promising as potential biomarkers for diagnosis and treatment

The impact of hyperhidrosis on patients' daily life and quality of life : A qualitative investigation

Background: An understanding of the daily life impacts of hyperhidrosis and how patients deal with them, based on qualitative research, is lacking. This study investigated the impact of hyperhidrosis on the daily life of patients using a mix of qualitative research methods. Methods: Participants were recruited through hyperhidrosis patient support groups such as the Hyperhidrosis Support Group UK. Data were collected using focus groups, interviews and online surveys. A grounded theory approach was used in the analysis of data transcripts. Data were collected from 71 participants, out of an initial 100 individuals recruited. Results: Seventeen major themes capturing the impacts of hyperhidrosis were identified; these covered all areas of life including daily life, psychological well-being, social life, professional /school life, dealing with hyperhidrosis, unmet health care needs and physical impact. Conclusions: Psychosocial impacts are central to the overall impacts of hyperhidrosis, cutting across and underlying the limitations experienced in other areas of life.Peer reviewe

Associations between cardiorespiratory fitness, physical activity and clustered cardiometabolic risk in children and adolescents: the HAPPY study

Clustering of cardiometabolic risk factors can occur during childhood and predisposes individuals to cardiometabolic disease. This study calculated clustered cardiometabolic risk in 100 children and adolescents aged 10-14 years (59 girls) and explored differences according to cardiorespiratory fitness (CRF) levels and time spent at different physical activity (PA) intensities. CRF was determined using a maximal cycle ergometer test, and PA was assessed using accelerometry. A cardiometabolic risk score was computed as the sum of the standardised scores for waist circumference, blood pressure, total cholesterol/high-density lipoprotein ratio, triglycerides and glucose. Differences in clustered cardiometabolic risk between fit and unfit participants, according to previously proposed health-related threshold values, and between tertiles for PA subcomponents were assessed using ANCOVA. Clustered risk was significantly lower (p < 0.001) in the fit group (mean 1.21 ± 3.42) compared to the unfit group (mean -0.74 ± 2.22), while no differences existed between tertiles for any subcomponent of PA. Conclusion These findings suggest that CRF may have an important cardioprotective role in children and adolescents and highlights the importance of promoting CRF in youth

Mixed Feelings of Children and Adolescents with Unilateral Congenital Below Elbow Deficiency: An Online Focus Group Study

The existing literature is inconsistent about the psychosocial functioning of children and adolescents with Unilateral Congenital Below Elbow Deficiency (UCBED). The objective of this qualitative study was to explore the psychosocial functioning of children and adolescents with UCBED in terms of their feelings about the deficiency and what helps them to cope with those feelings. Additionally, the perspectives of prosthesis wearers and non-wearers were compared, as were the perspectives of children, adolescents, parents and health professionals. Online focus group interviews were carried out with 42 children and adolescents (aged 8–12, 13–16 and 17–20), 16 parents and 19 health professionals. Questions were asked about psychosocial functioning, activities, participation, prosthetic use or non-use, and rehabilitation care. This study concerned remarks about psychosocial functioning. Children and adolescents with UCBED had mixed feelings about their deficiency. Both negative and positive feelings were often felt simultaneously and mainly depended on the way people in the children’s environment reacted to the deficiency. People staring affected the children negatively, while support from others helped them to cope with the deficiency. Wearing a prosthesis and peer-to-peer contact were also helpful. Non-wearers tended to be more resilient than prosthesis wearers. Wearers wore their prosthesis for cosmetic reasons and to prevent them from negative reactions from the environment. We recommend that rehabilitation teams make parents aware of their great influence on the psychosocial functioning of their child with UCBED, to adjust or extend the currently available psychosocial help, and to encourage peer-to-peer contact

Prediction of 60 day case-fatality after aneurysmal subarachnoid haemorrhage: results from the International Subarachnoid Aneurysm Trial (ISAT)

Aneurysmal subarachnoid haemorrhage (aSAH) is a devastating event with substantial case-fatality. Our purpose was to examine which clinical and neuro-imaging characteristics, available on admission, predict 60 day case-fatality in aSAH and to evaluate performance of our prediction model. We performed a secondary analysis of patients enrolled in the International Subarachnoid Aneurysm Trial (ISAT), a randomised multicentre trial to compare coiling with clipping in aSAH patients. Multivariable logistic regression analysis was used to develop a prognostic model to estimate the risk of dying within 60 days from aSAH based on clinical and neuro-imaging characteristics. The model was internally validated with bootstrapping techniques. The study population comprised of 2,128 patients who had been randomised to either endovascular coiling or neurosurgical clipping. In this population 153 patients (7.2%) died within 60 days. World Federation of Neurosurgical Societies (WFNS) grade was the most important predictor of case-fatality, followed by age, lumen size of the aneurysm and Fisher grade. The model discriminated reasonably between those who died within 60 days and those who survived (c statistic = 0.73), with minor optimism according to bootstrap re-sampling (optimism corrected c statistic = 0.70). Several strong predictors are available to predict 60 day case-fatality in aSAH patients who survived the early stage up till a treatment decision; after external validation these predictors could eventually be used in clinical decision making