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

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

Lee Kuan Yew Fellowship, Singapore Management Universit

A systemic infection involved in lung, brain and spine caused by Scedosporium apiospermum species complex after near-drowning: a case report and literature review

Abstract Scedosporium apiospermum species complex are widely distributed fungi that can be found in a variety of polluted environments, including soil, sewage, and decaying vegetation. Those opportunistic pathogens with strong potential of invasion commonly affect immunosuppressed populations However, few cases of scedosporiosis are reported in immunocompetent individuals, who might be misdiagnosed, leading to a high mortality rate. Here, we reported an immunocompetent case of systemtic infection involved in lung, brain and spine, caused by S. apiospermum species complex (S. apiospermum and S. boydii). The patient was an elderly male with persistent fever and systemtic infection after near-drowning. In the two tertiary hospitals he visited, definite diagnosis was extremely difficult. After being admitted to our hospital, he was misdiagnosed as tuberculosis infection, before diagnosis of S. apiospermum species complex infection by the metagenomic next-generation sequencing. His symptoms were alleviated after voriconazole treatment. In the present case, the details associated with its course were reported and published studies on Scedosporium spp. infection were also reviewed, for a better understanding of this disease and reducing the misdiagnosis rate

The early-onset febrile reaction following vaccination and associated factors: An exploratory sub-study based on the Ebola vaccine clinical trial

A phase-1 clinical trial aimed to assess the safety and immunogenicity of the type-5 adenovirus vector based Ebola vaccine (Ad5-EBOV) was conducted in China. To provide more evidence for the safety evaluation and dose-selection, an exploratory sub-study using a wireless automatic temperature measuring platform was done based on the phase-1 clinical trial. The main aim of the sub-study was to obtain more information about the occurrence of fever and detect the potential associated factors, second was to assess the feasibility of the temperature measuring platform in vaccine clinical trials. Temperature data of 3 treatment groups all presented a rising tendency during the first 6 hours after vaccination, the incidence of elevated temperature and possible associated factors were analyzed. For the incidence of elevated temperature, no marked dose-response relationship was found in 6 hours with wireless thermometers; the information from mercury thermometers showed that the grade-1 fever proportion peaked at 6 hours and there was no difference between groups, while grade-2 fever proportion peaked at 24 hours and was significantly higher in high-dose group than those in the other 2 groups. Significant differences were found between sex groups (males vs. female, incidence rate ratios (IRR) = 2.93 and 7.62 for any-grade, grade-2 fever respectively, P<0.001); a decline in grade-2 fever incidence was found with the increasing age groups (IRR = 0.78, P = 0.003) and body mass index (BMI, IRR = 0.67, P<0.001) .Our findings show that the dose-dependent manner between fever and the dose of Ad5-EBOV in this study might emerge after 6 hours, and which is slight and transient. Wireless thermometers secured on the skin surface are not suitable for a long time (longer than 6 hours) measurement, new methods for temperature monitoring, like ear temperature measurement, should be tested in the further research

Long non-coding RNA LHX1-DT regulates cardiomyocyte differentiation through H2A.Z-mediated LHX1 transcriptional activation

Summary: Long non-coding RNAs (lncRNAs) play widespread roles in various processes. However, there is still limited understanding of the precise mechanisms through which they regulate early stage cardiomyocyte differentiation. In this study, we identified a specific lncRNA called LHX1-DT, which is transcribed from a bidirectional promoter of LIM Homeobox 1 (LHX1) gene. Our findings demonstrated that LHX1-DT is nuclear-localized and transiently elevated expression along with LHX1 during early differentiation of cardiomyocytes. The phenotype was rescued by overexpression of LHX1 into the LHX1-DT−/− hESCs, indicating LHX1 is the downstream of LHX1-DT. Mechanistically, we discovered that LHX1-DT physically interacted with RNA/histone-binding protein PHF6 during mesoderm commitment and efficiently replaced conventional histone H2A with a histone variant H2A.Z at the promoter region of LHX1. In summary, our work uncovers a novel lncRNA, LHX1-DT, which plays a vital role in mediating the exchange of histone variants H2A.Z and H2A at the promoter region of LHX1