NICHE: A Curated Dataset of Engineered Machine Learning Projects in Python

Machine learning (ML) has gained much attention and been incorporated into our daily lives. While there are numerous publicly available ML projects on open source platforms such as GitHub, there have been limited attempts in filtering those projects to curate ML projects of high quality. The limited availability of such a high-quality dataset poses an obstacle in understanding ML projects. To help clear this obstacle, we present NICHE, a manually labelled dataset consisting of 572 ML projects. Based on evidences of good software engineering practices, we label 441 of these projects as engineered and 131 as non-engineered. This dataset can help researchers understand the practices that are followed in high-quality ML projects. It can also be used as a benchmark for classifiers designed to identify engineered ML projects.Comment: Accepted by MSR 202

Prevalence and impacts of upper limb morbidity after treatment for breast cancer: a cross-sectional study of lymphedema and function.

A cross-sectional study screened lymphedema, impaired upper limb function (ULF) and quality of life (QOL) in women post-breast cancer. Women attending review appointments who had completed surgery, chemotherapy and radiotherapy, were without recurrence, and could complete questionnaires in English were invited. Medical records were reviewed and questionnaires completed: the Morbidity Screening Tool (MST), Disability of the Arm, Shoulder and Hand questionnaire (DASH), and Functional Assessment of Cancer Therapy for breast cancer QOL questionnaire (FACTB+4). The vertical perometer (400T) measured percentage upper limb volume difference (%LVD), with 10% or greater difference diagnosed as lymphedema. Of 617 participants (mean age 62.3y, SD 10.0; mean time since treatment 63.0 months, SD 46.6), sufficient questionnaire data were available for 613 and perometry data for 417. Using the MST, 21.9% self-reported impaired ULF, 19.8% lymphedema, and 9.2% both. Based on %LVD, 26.5% had lymphedema. Histogram analysis for individuals in the first eight twelve-month intervals after treatment found impaired ULF prevalence peaked at three to five years and lymphedema at three years. Significantly worse function (DASH) and QOL (FACT B+4) resulted for those with morbidity (p<0.000). This provides evidence that impaired ULF and lymphedema negatively affect QOL years after treatment and are not necessarily linked.sch_phy1pub3633pub

Cervical ripening at home or in-hospital-prospective cohort study and process evaluation (CHOICE) study: a protocol.

IntroductionThe aim of the cervical ripening at home or in-hospital-prospective cohort study and process evaluation (CHOICE) study is to compare home versus in-hospital cervical ripening to determine whether home cervical ripening is safe (for the primary outcome of neonatal unit (NNU) admission), acceptable to women and cost-effective from the perspective of both women and the National Health Service (NHS).Methods and analysisWe will perform a prospective multicentre observational cohort study with an internal pilot phase. We will obtain data from electronic health records from at least 14 maternity units offering only in-hospital cervical ripening and 12 offering dinoprostone home cervical ripening. We will also conduct a cost-effectiveness analysis and a mixed methods study to evaluate processes and women/partner experiences. Our primary sample size is 8533 women with singleton pregnancies undergoing induction of labour (IOL) at 39+0 weeks' gestation or more. To achieve this and contextualise our findings, we will collect data relating to a cohort of approximately 41 000 women undergoing IOL after 37 weeks. We will use mixed effects logistic regression for the non-inferiority comparison of NNU admission and propensity score matched adjustment to control for treatment indication bias. The economic analysis will be undertaken from the perspective of the NHS and Personal Social Services (PSS) and the pregnant woman. It will include a within-study cost-effectiveness analysis and a lifetime cost-utility analysis to account for any long-term impacts of the cervical ripening strategies. Outcomes will be reported as incremental cost per NNU admission avoided and incremental cost per quality adjusted life year gained.Research ethics approval and disseminationCHOICE has been funded and approved by the National Institute of Healthcare Research Health Technology and Assessment, and the results will be disseminated via publication in peer-reviewed journals.Trial registration numberISRCTN32652461

Constructing a measure of balance recovery confidence for older persons: Content themes from different stakeholders

Shawn Leng-Hsien Soh - ORCID: https://orcid.org/0000-0002-8725-5182 0000-0002-8725-5182Judith Lane - ORCID: 0000-0003-0413-8421 https://orcid.org/0000-0003-0413-8421Fiona Gilmour - ORCID: 0000-0002-9106-3618 https://orcid.org/0000-0002-9106-3618Background: The absence of patient-reported outcome measures (PROMs) for a specific construct or target population suggests a need for such measures to be developed. A case in point is the domain of falls efficacy; a PROM for balance recovery confidence was proposed to improve older persons ’agency to arrest a fall. Appropriate participation in its development by relevant stakeholders was identified as essential to maximise the utility of the PROM and its potential to enhance patient care. There is a gap in the practice development literature in terms of PROMs for older persons. This article aims to encourage researchers to use the principles of practice development to address this gap by involving relevant stakeholders to gain greater insight.Methods: The nominal group technique and the Delphi technique were used to generate and refine the content of the measure, and content analysis was applied to assess and summarise the data.Findings: Unique themes emerged, such as ‘agency of older people in the prevention of falls ’from the community-dwelling older adults in Singapore, and ‘clinical specificity ’from an international panel of healthcare professionals. Common themes including ‘relevance to the target population’, ‘comprehensibility ’and ‘cultural and contextual sensitivity ’were found in both groups.Conclusion: A collaborative, inclusive and participatory approach involving different stakeholders, underpinned by practice development methodology, can offer rich insights for PROM developers.Implications for practice: Meaningful perspectives are generated from a diversity of views shared by representatives from all stakeholder groups involved in caregiving Participation of different stakeholders, such as physiotherapists, occupational therapists, nurses, doctors, podiatrists and older persons, provides a more robust and authentic approach to developing a PROM for older personshttps://doi.org/10.19043/ipdj.111.00911pubpub

Comparison of breast cancer-related lymphedema (Upper Limb Swelling) prevalence estimated using objective and subjective criteria and relationship with quality of life

This study aimed to investigate lymphedema prevalence using three different measurement/diagnostic criterion combinations and explore the relationship between lymphedema and quality of life for each, to provide evaluation of rehabilitation. Cross-sectional data from 617 women attending review appointments after completing surgery, chemotherapy, and radiotherapy included the Morbidity Screening Tool (MST; criterion: yes to lymphedema); Lymphedema and Breast Cancer Questionnaire (LBCQ; criterion: yes to heaviness and/or swelling); percentage limb volume difference (perometer: %LVD; criterion: 10%+ difference); and the Functional Assessment of Cancer Therapy breast cancer-specific quality of life tool (FACT B+4). Perometry measurements were conducted in a clinic room. Between 341 and 577 participants provided sufficient data for each analysis, with mean age varying from 60 to 62 (SD 9.95-10.03) and median months after treatment from 49 to 51. Lymphedema prevalence varied from 26.2% for perometry %LVD to 20.5% for the MST and 23.9% for the LBCQ; differences were not significant. Limits of agreement analysis between %LVD and the subjective measures showed little consistency, while moderate consistency resulted between the subjective measures. Quality of life differed significantly for women with and without lymphedema only when subjective measurements were used. Results suggest that subjective and objective tools investigate different aspects of lymphedema. 2013 Catherine Bulley et al.sch_phy2013pub3233pub80756

Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing

Legionella pneumophila is the most common cause of the severe respiratory infection known as Legionnaires' disease. However, the microorganism is typically a symbiont of free-living amoeba, and our understanding of the bacterial factors that determine human pathogenicity is limited. Here we carried out a population genomic study of 902 L. pneumophila isolates from human clinical and environmental samples to examine their genetic diversity, global distribution and the basis for human pathogenicity. We find that the capacity for human disease is representative of the breadth of species diversity although some clones are more commonly associated with clinical infections. We identified a single gene (lag-1) to be most strongly associated with clinical isolates. lag-1, which encodes an O-acetyltransferase for lipopolysaccharide modification, has been distributed horizontally across all major phylogenetic clades of L. pneumophila by frequent recent recombination events. The gene confers resistance to complement-mediated killing in human serum by inhibiting deposition of classical pathway molecules on the bacterial surface. Furthermore, acquisition of lag-1 inhibits complement-dependent phagocytosis by human neutrophils, and promoted survival in a mouse model of pulmonary legionellosis. Thus, our results reveal L. pneumophila genetic traits linked to disease and provide a molecular basis for resistance to complement-mediated killing. The bacterium Legionella pneumophila can cause severe respiratory infection, but is typically a symbiont of free-living amoeba. Here, the authors analyse the genomes of 902 clinical and environmental isolates, and identify a bacterial gene that is strongly associated with human infection and confers resistance to complement-mediated killing.Peer reviewe

BugsInPy: A database of existing bugs in Python programs to enable controlled testing and debugging studies

Lee Kuan Yew Fellowship, Singapore Management Universit

Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system

Abstract: Remyelination following CNS demyelination restores rapid signal propagation and protects axons; however, its efficiency declines with increasing age. Both intrinsic changes in the oligodendrocyte progenitor cell population and extrinsic factors in the lesion microenvironment of older subjects contribute to this decline. Microglia and monocyte-derived macrophages are critical for successful remyelination, releasing growth factors and clearing inhibitory myelin debris. Several studies have implicated delayed recruitment of macrophages/microglia into lesions as a key contributor to the decline in remyelination observed in older subjects. Here we show that the decreased expression of the scavenger receptor CD36 of aging mouse microglia and human microglia in culture underlies their reduced phagocytic activity. Overexpression of CD36 in cultured microglia rescues the deficit in phagocytosis of myelin debris. By screening for clinically approved agents that stimulate macrophages/microglia, we have found that niacin (vitamin B3) upregulates CD36 expression and enhances myelin phagocytosis by microglia in culture. This increase in myelin phagocytosis is mediated through the niacin receptor (hydroxycarboxylic acid receptor 2). Genetic fate mapping and multiphoton live imaging show that systemic treatment of 9–12-month-old demyelinated mice with therapeutically relevant doses of niacin promotes myelin debris clearance in lesions by both peripherally derived macrophages and microglia. This is accompanied by enhancement of oligodendrocyte progenitor cell numbers and by improved remyelination in the treated mice. Niacin represents a safe and translationally amenable regenerative therapy for chronic demyelinating diseases such as multiple sclerosis

Correction to: Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system.

The article Niacin‑mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system, written by Khalil S. Rawji, Adam M.H. Young, Tanay Ghosh, Nathan J. Michaels, Reza Mirzaei, Janson Kappen, Kathleen L. Kolehmainen, Nima Alaeiilkhchi, Brian Lozinski, Manoj K. Mishra, Annie Pu, Weiwen Tang, Salma Zein, Deepak K. Kaushik, Michael B. Keough, Jason R. Plemel, Fiona Calvert, Andrew J. Knights, Daniel J. Gaffney, Wolfram Tetzlaff, Robin J. M. Franklin and V. Wee Yong, was originally published electronically on the publisher's internet

Doxycycline versus prednisolone as an initial treatment strategy for bullous pemphigoid: a pragmatic non-inferiority randomised controlled trial

Background: Bullous pemphigoid (BP) is a blistering skin disorder with increased mortality. We tested whether a strategy of starting treatment with doxycycline conveys acceptable short-term blister control whilst conferring long-term safety advantages over starting treatment with oral corticosteroids. Methods: Pragmatic multi-centre parallel-group randomised controlled trial of adults with BP (≥3 blisters ≥2 sites and linear basement membrane IgG/C3) plus economic evaluation. Participants were randomised to doxycycline (200 mg/day) or prednisolone (0·5 mg/kg/day). Localised adjuvant potent topical corticosteroids (<30 g/week) was permitted weeks 1-3. The non-inferiority primary effectiveness outcome was the proportion of participants with ≤3 blisters at 6 weeks. We assumed that doxycycline would be 25% less effective than corticosteroids with a 37% acceptable margin of noninferiority. The primary safety outcome was the proportion with severe, life-threatening or fatal treatment-related adverse events by 52 weeks. Analysis used a regression model adjusting for baseline disease severity, age and Karnofsky score, with missing data imputed. Results: 132 patients were randomised to doxycycline and 121 to prednisolone from 54 UK and 7 German dermatology centres. Mean age was 77·7 years and 68.4% had moderate to severe baseline disease. For those starting doxycycline, 83/112 (74·1%) had ≤3 blisters at 6 weeks compared with 92/101 (91·1%) for prednisolone, a difference of 18·6% favouring prednisolone (upper limit of 90% CI, 26·1%, within the predefined 37% margin). Related severe, life-threatening and fatal events at 52 weeks were 18·5% for those starting doxycycline and 36·6% for prednisolone (mITT analysis), an adjusted difference of 19·0% (95% CI, 7·9%, 30·1%, p=0·001). Conclusions: A strategy of starting BP patients on doxycycline is non-inferior to standard treatment with oral prednisolone for short-term blister control and significantly safer long-term