Novel Bacterial Lineages in the Uncultured Candidate Division SR1

Complex and naturally occurring microbial communities are known to be predominantly composed of uncultured bacteria and archaea. A few representatives of uncultured prokaryotes (e.g., from the candidate divisions TM7 and SR1) have been found in environmental samples and in association with animals, including humans. It is not yet clear, however, how uncultured bacteria found at environmental sites relate phylogenetically to their counterparts associated with animal hosts. In this study, we investigated the diversity of the SR1 candidate division to better understand the divide between animal-associated and environmental lineages. We generated 16S rDNA gene clone libraries from samples obtained from the following two habitats: outflow from water in a sulfur cave and spring water sediment in open air. Out of the 421 SR1 clones sequenced, we identified 18 operational taxonomic units (OTUs) that were used in combination with SR1 reference sequences to build an SR1 phylogenetic tree. Phylogenetic analyses indicated that SR1 members associated with animal hosts clustered separately from those collected at the environmental sites. Further in-depth investigation may help to better characterize these bacteria and establish their nutritional requirements and physiological role in their respective communities. In addition, the microbes associated with host animals that are easy to maintain in the laboratory (e.g., termites, cow rumen) or found in habitats easy to access may serve as model organisms for studying the mechanisms by which these bacteria interact with their respective hosts, especially if the sequence homology observed for 16S rDNA to other genes, such as those involved in pathogenicity or mutualism

Using Bad Learners to find Good Configurations

Finding the optimally performing configuration of a software system for a given setting is often challenging. Recent approaches address this challenge by learning performance models based on a sample set of configurations. However, building an accurate performance model can be very expensive (and is often infeasible in practice). The central insight of this paper is that exact performance values (e.g. the response time of a software system) are not required to rank configurations and to identify the optimal one. As shown by our experiments, models that are cheap to learn but inaccurate (with respect to the difference between actual and predicted performance) can still be used rank configurations and hence find the optimal configuration. This novel \emph{rank-based approach} allows us to significantly reduce the cost (in terms of number of measurements of sample configuration) as well as the time required to build models. We evaluate our approach with 21 scenarios based on 9 software systems and demonstrate that our approach is beneficial in 16 scenarios; for the remaining 5 scenarios, an accurate model can be built by using very few samples anyway, without the need for a rank-based approach.Comment: 11 pages, 11 figure

Identification of novel targets in prostate cancer progression

We have developed novel fluorescence bio-imaging based automated models to screen for novel candidate targets involved in prostate cancer metastasis. Utilizing these models and adopting a functional genomics based approach; we identified SYK as a novel regulator of prostate cancer progression. We also identified functional involvement of MST1R in regulating the progression of prostate cancer. For both of these targets, there is supporting human clinical data to validate our results in prostate cancer.UBL - phd migration 201

Is "Better Data" Better than "Better Data Miners"? (On the Benefits of Tuning SMOTE for Defect Prediction)

We report and fix an important systematic error in prior studies that ranked classifiers for software analytics. Those studies did not (a) assess classifiers on multiple criteria and they did not (b) study how variations in the data affect the results. Hence, this paper applies (a) multi-criteria tests while (b) fixing the weaker regions of the training data (using SMOTUNED, which is a self-tuning version of SMOTE). This approach leads to dramatically large increases in software defect predictions. When applied in a 5*5 cross-validation study for 3,681 JAVA classes (containing over a million lines of code) from open source systems, SMOTUNED increased AUC and recall by 60% and 20% respectively. These improvements are independent of the classifier used to predict for quality. Same kind of pattern (improvement) was observed when a comparative analysis of SMOTE and SMOTUNED was done against the most recent class imbalance technique. In conclusion, for software analytic tasks like defect prediction, (1) data pre-processing can be more important than classifier choice, (2) ranking studies are incomplete without such pre-processing, and (3) SMOTUNED is a promising candidate for pre-processing.Comment: 10 pages + 2 references. Accepted to International Conference of Software Engineering (ICSE), 201

We Don't Need Another Hero? The Impact of "Heroes" on Software Development

A software project has "Hero Developers" when 80% of contributions are delivered by 20% of the developers. Are such heroes a good idea? Are too many heroes bad for software quality? Is it better to have more/less heroes for different kinds of projects? To answer these questions, we studied 661 open source projects from Public open source software (OSS) Github and 171 projects from an Enterprise Github. We find that hero projects are very common. In fact, as projects grow in size, nearly all project become hero projects. These findings motivated us to look more closely at the effects of heroes on software development. Analysis shows that the frequency to close issues and bugs are not significantly affected by the presence of project type (Public or Enterprise). Similarly, the time needed to resolve an issue/bug/enhancement is not affected by heroes or project type. This is a surprising result since, before looking at the data, we expected that increasing heroes on a project will slow down howfast that project reacts to change. However, we do find a statistically significant association between heroes, project types, and enhancement resolution rates. Heroes do not affect enhancement resolution rates in Public projects. However, in Enterprise projects, the more heroes increase the rate at which project complete enhancements. In summary, our empirical results call for a revision of a long-held truism in software engineering. Software heroes are far more common and valuable than suggested by the literature, particularly for medium to large Enterprise developments. Organizations should reflect on better ways to find and retain more of these heroesComment: 8 pages + 1 references, Accepted to International conference on Software Engineering - Software Engineering in Practice, 201

Nitrous Oxide for Pain Management in the Emergency Department

The clinical practice problem addressed was pain control in emergency department (ED) patients. The purpose of this project was to establish situations when inhaled nitrous oxide (N2O) could be used to manage pain in the ED. Specifically, a systematic review provided answers to questions related to appropriate uses of N2O in acute pain management, the effectiveness of inhaled N2O in managing acute pain, and the benefits of and barriers to N2O use in the ED. The middle range nursing theory of acute pain management published by the Agency for Health Care Policy and Research served as the theoretical support for the project. A systematic literature review using the PRISMA checklist yielded 5 studies that were incorporated into the synthesis of evidence. Inhaled N2O was found to be safe and effective for managing pain in some ED patients and in women undergoing labor. N2O can be used in pediatric and adult patients for minor procedural pain relief and pain associated with burns and cancer. N2O was associated with improved outcomes and increased patient and family satisfaction. However, extensive adoption was hindered by the scarcity of the delivery equipment, untrained medical staff, and the increasing use of N2O as a recreational drug with addictive properties. Although integrating the use of inhaled N2O to mitigate pain may improve patient outcomes, more research is indicated before the widespread use of the drug can be encouraged. The findings were communicated to the ED staff for consideration of the limited adoption of N2O in the ED. The use of this alternative evidence-based and effective pain control agent may result in positive social change by lessening acute or procedural pain experienced by patients in specific ED situations

Software configuration management (SCM) support process capability maturity model

Software Configuration Management (SCM) is a concept of trying to group the changing artifacts of software development to try to manage the complexity of modern day software. This paper provides a roadmap for improving the SCM support process based on a meta-model. I developed a model that defines key practice areas that are important for the SCM support group. The model deals with the process, quality assurance and usability aspect of the SCM activities. A questionnaire to assess the state of the current process and a mapping of the questions to the model is also presented. This is the first attempt at dealing with the support aspect of the SCM part of software development.Keywords: Software Configuration Management, process improvement, meta­model, key practices, quality assurance, usability

A cross-sectional study to evaluate uploader-based quality and reliability of content on YouTube about endometriosis

Background: Endometriosis is characterized by the development and presence of endometrial glands and stroma outside of the uterine cavity. Reflux of endometrial tissue fragments, cells, and protein-rich fluid into the pelvis during menstruation is considered the most important mechanism for the development of endometriosis, which is termed reflux menstruation. This study aims to assess quality and reliability of information on YouTube related to endometriosis. Methods: A cross-sectional observational study of YouTube videos was conducted in April 2023. Videos related to endometriosis were searched by six authors, easy using one search term. Relevant videos in English or Hindi language of duration 1-20 minutes were included in the study. These were evaluated for type of uploader, popularity, type of content and lastly quality and reliability using global quality score (GQS) and DISCERN scores respectively. Results: The 67 relevant videos conveying Endometriosis related information had 21,620,808 views, 120,830 likes and 11,655 comments. Around 31 (46.3%) of videos uploaded were by doctors and health care organizations, outnumbering those uploaded by news channels 14 (20.9%), patients 5 (7.5%), and others 17 (25.4%). 59 (88.06%) of these videos described symptoms of endometriosis, and 67.1% presented the cause or etiology. A total of 47 (70.1%) of videos discussed information regarding treatment options. Conclusions: YouTube videos have a wide reach among audience. In this study it was found that there was no significant difference in the quality, reliability or video power index (VPI) of videos uploaded by different types of uploaders. It is important to ensure that content with high quality and reliability is available from qualified medical professionals and organizations; for viewers to understand their disease and take treatment decisions

Airway Management in Pan Facial Fracture: An Outcome Analysis of Elective Tracheostomy and Submental Endotracheal Intubation

Background and Aims. Pan facial fractures are complex and often requiring complex airway management. Elective tracheostomy (ET) and submental endotracheal intubation (SEI) are the two major techniques for airway management. The aim of this article is to compare the management outcome between these techniques. Methods. This study was done in a tertiary care hospital from Jan 2019 to Dec 2019. Data were retrieved for all patients from hospital admission-discharge reports, operation room records, follow-up notes, and clinical photograph records which was recorded prospectively after ethical clearance. Total 38 patients were included in the study after the exclusion criteria into two groups: submental endotracheal intubation (SEI) and elective tracheostomy (ET). Demographic data, intraoperative time (IOT), length of hospital stay (LOHS), postoperative pain score at three and seven days, and Vancouver Scar Score (VSS) at 4 and 12 weeks was compared between the two groups. Results. SEI consisted of 23 patients (60%) while ET had 15 (40%) patients. The mean age was 32.77±8.24 years in the SEI and 29.36±7.32 years in the ET. The IOT in SEI was 15.36±1.53 min and 24.60±1.40 min in the ET which was statistically significant (p = 0.00001). The LOHS was 11±3.87 days in SEI and 25.2±3.88 days in ET (p = 0.0001). The mean VSS at 4 and 12 weeks for SEI were moderate and mild respectively and for the ET was moderate and mild respectively. Both were statistically significant with a p = 0.003 and p = 0.006. Conclusion. Submental intubation is a safe airway management technique in pan facial fracture. It provides the surgeon with an excellent operative field for achieving the proper dental occlusion. Both short- and long-term outcomes are better compared to the alternative airway method of elective tracheostomy