Miracle-dz/UniFAR-FTUs huggingface dataset:
PhenoHM: human–mouse comparative phenome–genome server

PhenoHM is a human–mouse comparative phenome–genome server that facilitates cross-species identification of genes associated with orthologous phenotypes (http://phenome.cchmc.org; full open access, login not required). Combining and extrapolating the knowledge about the roles of individual gene functions in the determination of phenotype across multiple organisms improves our understanding of gene function in normal and perturbed states and offers the opportunity to complement biologically the rapidly expanding strategies in comparative genomics. The Mammalian Phenotype Ontology (MPO), a structured vocabulary of phenotype terms that leverages observations encompassing the consequences of mouse gene knockout studies, is a principal component of mouse phenotype knowledge source. On the other hand, the Unified Medical Language System (UMLS) is a composite collection of various human-centered biomedical terminologies. In the present study, we mapped terms reciprocally from the MPO to human disease concepts such as clinical findings from the UMLS and clinical phenotypes from the Online Mendelian Inheritance in Man knowledgebase. By cross-mapping mouse–human phenotype terms, extracting implicated genes and extrapolating phenotype-gene associations between species PhenoHM provides a resource that enables rapid identification of genes that trigger similar outcomes in human and mouse and facilitates identification of potentially novel disease causal genes. The PhenoHM server can be accessed freely at http://phenome.cchmc. org.
DAtA: Database of Arabidopsis thaliana Annotation

The Database of Arabidopsis thaliana Annotation (D At A) was created to enable easy access to and analysis of all the Arabidopsis genome project annotation. The database was constructed using the completed A.thaliana genomic sequence data currently in GenBank. An automated annotation process was used to predict coding sequences for GenBank records that do not include annotation. D At A also contains protein motifs and protein similarities derived from searches of the proteins in D At A with motif databases and the non-redundant protein database. The database is routinely updated to include new GenBank submissions for Arabidopsis genomic sequences and new Blast and protein motif search results. A web interface to D At A allows coding sequences to be searched by name, comment, blast similarity or motif field. In addition, browse options present lists of either all the protein names or identified motifs present in the sequenced A.thaliana genome. The database can be accessed at http://baggage. stanford.edu/group/arabprotein/
Measuring and Assessing Software Reliability Growth through Simulation-Based Approaches

In the past decade, several rate-based simulation approaches were proposed to predict software failure process. But most of them did not take the number of available debuggers into consideration and this may not be reasonable. In practice, the number of debuggers is always limited and controlled. If all debuggers or developers are busy, the new detected faults should be willing to wait (for a long time to be corrected and removed). Besides, practical experiences also show that the fault removal time is non-negligible and the number of removed faults generally lags behind the total number of detected faults. Based on these facts, in this paper, we will apply queueing theory to describe and explain the possible debugging behavior during software development. Two simulation procedures are developed based on G/G/ infin and G/G/m queueing models. The proposed methods will be illustrated with real software failure data. Experimental results will be analyzed and discussed in detail. The results we obtained will greatly help to understand the influence of size of debugger teams on the software failure correction activities and other related reliability assessments.
Low back pain.

Procedure Appropriateness Category Relative Radiation Level Radiography lumbar spine Usually Not Appropriate ☢☢☢ MRI lumbar spine with IV contrast Usually Not Appropriate O MRI lumbar spine without and with IV contrast Usually Not Appropriate O MRI lumbar spine without IV contrast Usually Not Appropriate O Bone scan whole body with SPECT or SPECT/CT complete spine Usually Not Appropriate ☢☢☢ CT lumbar spine with IV contrast Usually Not Appropriate ☢☢☢ CT lumbar spine without IV contrast Usually Not Appropriate ☢☢☢ Discography and post-discography CT lumbar spine Usually Not Appropriate ☢☢☢ CT lumbar spine without and with IV contrast Usually Not Appropriate ☢☢☢☢ CT myelography lumbar spine Usually Not Appropriate ☢☢☢☢ FDG-PET/CT whole body Usually Not Appropriate ☢☢☢☢
Seamlessly Expanding a Randomized Phase II Trial to Phase III

Summary. A sequential Bayesian phase II/III design is proposed for comparative clinical trials. The design is based on both survival time and discrete early events that may be related to survival and assumes a parametric mixture model. Phase II involves a small number of centers. Patients are randomized between treatments throughout, and sequential decisions are based on predictive probabilities of concluding superiority of the experimental treatment. Whether to stop early, continue, or shift into phase III is assessed repeatedly in phase II. Phase III begins when additional institutions are incorporated into the ongoing phase II trial. Simulation studies in the context of a non‐small‐cell lung cancer trial indicate that the proposed method maintains overall size and power while usually requiring substantially smaller sample size and shorter trial duration when compared with conventional group‐sequential phase III designs.
TV Viewing and Physical Activity Are Independently Associated with Metabolic Risk in Children: The European Youth Heart Study

Background TV viewing has been linked to metabolic-risk factors in youth. However, it is unclear whether this association is independent of physical activity (PA) and obesity. Methods and Findings We did a population-based, cross-sectional study in 9- to 10-y-old and 15- to 16-y-old boys and girls from three regions in Europe (n = 1,921). We examined the independent associations between TV viewing, PA measured by accelerometry, and metabolic-risk factors (body fatness, blood pressure, fasting triglycerides, inverted high-density lipoprotein (HDL) cholesterol, glucose, and insulin levels). Clustered metabolic risk was expressed as a continuously distributed score calculated as the average of the standardized values of the six subcomponents. There was a positive association between TV viewing and adiposity (p = 0.021). However, after adjustment for PA, gender, age group, study location, sexual maturity, smoking status, birth weight, and parental socio-economic status, the association of TV viewing with clustered metabolic risk was no longer significant (p = 0.053). PA was independently and inversely associated with systolic and diastolic blood pressure, fasting glucose, insulin (all p < 0.01), and triglycerides (p = 0.02). PA was also significantly and inversely associated with the clustered risk score (p < 0.0001), independently of obesity and other confounding factors. Conclusions TV viewing and PA may be separate entities and differently associated with adiposity and metabolic risk. The association between TV viewing and clustered metabolic risk is mediated by adiposity, whereas PA is associated with individual and clustered metabolic-risk indicators independently of obesity. Thus, preventive action against metabolic risk in children may need to target TV viewing and PA separately.
IBS-like symptoms in patients with ulcerative colitis

Ulcerative colitis (UC) and irritable bowel syndrome (IBS) are chronic gastrointestinal disorders that, until recently, have been considered dichotomous conditions falling on either side of a functional-organic divide. However, persistent gastrointestinal symptoms, akin to those of IBS, are observed in up to one in three patients with quiescent UC. Whether these lower gastrointestinal symptoms are secondary to coexistent IBS or occult UC disease activity is uncertain, but when objective evidence of disease activity is lacking, escalation of conventional pharmacotherapy in such patients is often ineffective. The etiologies of both UC and IBS remain unclear, but dysregulation of the enteric nervous system, an altered microbiome, low-grade mucosal inflammation, and activation of the brain–gut axis is common to both; this suggests that some overlap between the two conditions is plausible. How best to investigate and manage IBS-type symptoms in UC patients remains unclear. Studies that have assessed patients with UC who meet criteria for IBS for subclinical inflammation have been conflicting in their results. Although evidence-based treatments for IBS exist, their efficacy in UC patients reporting these types of symptoms remains unclear. Given the disturbances in gut microbiota in UC, and the possible role of the brain–gut axis in the generation of such symptoms, treatments such as probiotics, fecal transfer, antidepressants, or psychological therapies would seem logical approaches to use in this group of patients. However, there are only limited data for all of these therapies; this suggests that randomized controlled trials to investigate their efficacy in this setting may be warranted.
Análisis semiparamétrico de la brecha salarial de género en el Ecuador

This paper analyzes the gender wage gap in Ecuador through a semi-parametric estimation of discrimination in the years 2007, 2013 and 2016. A variation of the Tobit III method and the Oaxaca Blinder decomposition are used to conclude that the gender pay gap between 2007 and 2013 was reduced from 10.06%to 3.37 %, only to be increased to 4.09% in 2016. Likewise, it is found that the gender wage differentials in Ecuador are due only to labor market discrimination towards women.
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

The annotation of protein function has not kept pace with the exponential growth of raw sequence and structure data. An emerging solution to this problem is to identify 3D motifs or templates in protein structures that are necessary and sufficient determinants of function. Here, we demonstrate the recurrent use of evolutionary trace information to construct such 3D templates for enzymes, search for them in other structures, and distinguish true from spurious matches. Serine protease templates built from evolutionarily important residues distinguish between proteases and other proteins nearly as well as the classic Ser‐His‐Asp catalytic triad. In 53 enzymes spanning 33 distinct functions, an automated pipeline identifies functionally related proteins with an average positive predictive power of 62%, including correct matches to proteins with the same function but with low sequence identity (the average identity for some templates is only 17%). Although these template building, searching, and match classification strategies are not yet optimized, their sequential implementation demonstrates a functional annotation pipeline which does not require experimental information, but only local molecular mimicry among a small number of evolutionarily important residues.
Reducing Concurrency Bottlenecks in Parallel I/O Workloads

To enable high performance parallel checkpointing we introduced the Parallel Log Structured File System (PLFS). PLFS is middleware interposed on the file system stack to transform concurrent writing of one application file into many non-concurrently written component files. The promising effectiveness of PLFS makes it important to examine its performance for workloads other than checkpoint capture, notably the different ways that state snapshots may be later read, to make the case for using PLFS in the Exascale I/O stack. Reading a PLFS file involved reading each of its component files. In this paper we identify performance limitations on broader workloads in an early version of PLFS, specifically the need to build and distribute an index for the overall file, and the pressure on the underlying parallel file system's metadata server, and show how PLFS's decomposed components architecture can be exploited to alleviate bottlenecks in the underlying parallel file system.
Stochastic Expectation Maximization Algorithm for Long-Memory Fast-Fading Channels

In this paper, we develop a novel statistical detection algorithm following similar principles to that of expectation maximization (EM) algorithm. Our goal is to develop an iterative algorithm for joint channel estimation and data detection in channels that have a long memory and are fast varying in time. At each iteration, starting with an estimate of the channel, we combine a Markov Chain Monte Carlo (MCMC) algorithm for data detection, and an adaptive algorithm for channel tracking, to develop a statistical search procedure that finds joint important samples of possible transmitted data and channel impulse responses. The result of this step, which may be thought as E-step of the proposed algorithm, is used in an M-step that refines the channel estimate, for the next iteration. Excellent behavior of the proposed algorithm is presented by examining it on real data from underwater acoustic communication channels
Disability Studies in Practice: A Work In Progress

Abstract Disability studies, a field of critical study that emerged from the disability rights movement, challenges the medical domination in the lives of people with disabilities and has the potential to transform rehabilitation practice. Significant practical and attitudinal barriers exist to changing rehabilitation practice. Using a point-counterpoint framework, this article examines some common objections to integrating disability studies perspectives into rehabilitation practice and provides solutions, strategies, and rationales for a disability studies informed practice.
In Vivo Monitoring the Intraocular Pressure of Anterior Chamber in Normal Rabbits

To develop a method to monitor the intraocular pressure (IOP) of the anterior chamber in vivo in normal rabbits, to observe the value of the normal IOP, and to detect the distribution regularity in the 24 hours of normal rabbits. Normal IOP was monitored in 15 New Zealand white rabbit eyes. The measurements of IOP of all the experimental rabbits were by Millar transducer which was embedded in the anterior chamber. The analog signal of IOP was filtered, amplified and transformed into digital signal by Powerlab system, and was real-time displayed by Chart software. We successfully obtained the IOP value of 7 anterior chamber groups. The IOP of anterior chamber was (1.31plusmn0.21~2.74plusmn0.83) KPa. The distribution was as follows: the value of the IOP was lower from 0:00 to 5:00 and from 18:00 to 23:00 and gradually increased from 5:00 to 10:00. The peak value of the anterior chamber was at 11:00 and 17:00. The results suggest that we develop a convenient, feasible method to monitor the IOP of rabbits.
Building associations between markers of environmental stressors and adverse human health impacts using frequent itemset mining

Health effects are unknown for the vast majority of the >83,000 chemicals in commerce, creating challenges in balancing industrial needs against the complex landscape of health susceptibilities and exposures. The National Health and Nutritional Examination Survey (NHANES), a large-scale survey aimed at determining the prevalence and risk factors of major diseases, is increasingly used to postulate relationships between chemicals and adverse health effects in the U.S. population. The interpretation of these studies is complicated, however, by the ad hoc data mining approaches typically employed. Here we describe the use of frequent itemset mining for identifying exposure ⇒ health associations in data from the NHANES 2005-2006 cycle. From 9,440 dichotomized samples, 983 two-itemset rules were generated describing associations between markers of health and environmental exposure (lift >1, response threshold >97.5th quantile). A case study using parathyroid hormone levels to develop exposure-health effect hypotheses is presented. This case study demonstrates how association rules can be used in data mining to facilitate hypothesis development and improve traditional regression models by identification of potentially confounding variables even in the presence of missing information. Our approach is designed to enable more effec∗This project was supported in part by an appointment to the Internship/Research Participation Program at the Office of Research and Development, U.S. Environmental Protection Agency, administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and EPA. We thank Drs Lyle Burgoon, Jennifer Richmond-Bryant, and Jon Sobus for helpful discussion and review of early drafts of the paper. The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency. †Oak Ridge Institute for Science and Education. Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA, bell.shannon@epa.gov ‡Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA, edwards.stephen@epa.gov tive knowledge discovery of potential health impacts of environmental chemicals by facilitating comprehensive data mining and meta-analysis of the NHANES dataset. Long-term, our representation of the information allows for integration with other disparate data, such as known biological pathways, to address the current data gaps.
Mutation spectrum of CYP1B1 and MYOC genes in Korean patients with primary congenital glaucoma

Purpose To elucidate the incidence of cytochrome P450 1B1 (CYP1B1) and myocillin (MYOC) mutations in Korean patients with primary congenital glaucoma (PCG). Methods Genomic DNA was collected from peripheral blood of 85 unrelated Korean patients who were diagnosed as having PCG by standard ophthalmological examinations and screened for mutations in the CYP1B1 and MYOC genes by using bi-directional sequencing. Results Among 85 patients with PCG, 22 patients (22/85; 25.9%) had either one (n=11) or two (n=11) mutant alleles of the CYP1B1 gene. Among 11 different CYP1B1 mutations identified, a frameshift mutation (c.970_971dupAT; p.T325SfsX104) was the most frequent mutant allele (6/33; 18.2%) while p.G329S and p.V419Gfs11X were novel. In the MYOC gene, two variants of unknown significance (p.L228S and p.E240G) were identified in two PCG patients (2/85; 2.4%), respectively. No patient had mutations in both genes. Conclusions Although CYP1B1 mutations are major causes of PCG in Korea, ~70% of PCG patients have neither CYP1B1 nor MYOC mutations suggesting a high degree of genetic heterogeneity. Furthermore, the fact that 11 out of 22 patients had only one mutant allele in the CYP1B1 gene necessitates further investigation for other genetic backgrounds underlying PCG.
Changing the balance of social care for older people: simulating scenarios under demographic ageing in New Zealand

The demographic ageing of New Zealand society, as elsewhere in the developed world, has dramatically increased the proportion of older people (aged 65 years and over) in the population. This has major policy implications for the future organisation of social care. Our objective was to test the effects on social care use, first, of putative changes in the overall disability profile of older people, and second, of alterations to the balance of their care, i.e. whether it was community-based or residential. In order to undertake these experiments, we developed a microsimulation model of the later life course using individual-level data from two official national survey series on health and disability, respectively, to generate a synthetic version which replicated original data and parameter settings. A baseline projection under current settings from 2001 to 2021 showed moderate increases in disability and associated social care use. Artificially decreasing disability levels, below the baseline projection, only moderately reduced the use of community care (both informal and formal). Scenarios implemented by rebalancing towards informal care use moderately reduced formal care use. However, only moderate compensatory increases in community-based care were required to markedly decrease the transition to residential care. The disability impact of demographic ageing may not have a major negative effect on system resources in developed countries like New Zealand. As well as healthy ageing, changing the balance of social care may alleviate the impact of increasing demand due to an expanding population of older people.
Early and immediately restored and loaded dental implants for single-tooth and partial-arch applications.

PURPOSE The objective of this consensus committee report was to review the available literature published predominantly in refereed journals to summarize findings, data, and conclusions as they related to reduced healing times and protocols for single-tooth and partial-arch clinical situations. Early loading of dental implants has been defined as restoration of implants in or out of occlusion at least 48 hours after implant placement, but at a shorter time interval than conventional healing. Immediate loading or restoration has been defined as attachment of a restoration in or out of direct occlusal function within 48 hours of surgical placement. MATERIALS AND METHODS Six articles addressing early loading, with a mixture of single-tooth and partial-arch clinical conditions and including some controlled cohort studies, were reviewed. Immediate loading or restoration of dental implants in single-tooth and partial-arch applications, was extensively reviewed. An attempt was made to isolate and categorize similar case types to discern trends and relevant factors. Variables that were considered included single- or multiple-tooth conditions, immediate or delayed placement in extraction sockets, effect of implant surface and geometry, bone quality, implant stability, surgical technique, occlusal design, effect of cigarette smoking, and stability of results. RESULTS Combined data from 6 early loading studies on single-tooth and partial-arch applications revealed 1,046 implants with a survival rate of 98.2%. Long-term data for most of the early loading studies were not yet available. Most of the publications on immediate loading or restoration of dental implants were written as case series rather than scientific studies. DISCUSSION AND CONCLUSIONS In general, most publications indicated that with attention to appropriate factors, implant survival with immediate restoration was comparable to the results with conventional and early loading protocols. It should be recognized that, with few exceptions, these conclusions may be misleading statistical phenomena of the authors, as most publications were written by exceptionally experienced, highly skilled practitioners working under tightly controlled clinical conditions on a relatively small, statistically inconclusive number of implants and patients.
Finding Distinct Answers in Web Snippets

This paper presents ListWebQA, a question answering system aimed specifically at discovering answers to list questions in web snippets. ListWebQA retrieves snippets likely to contain answers by means of a query rewriting strategy, and extracts answers according to their syntactic and semantic similarities afterwards. These similarities are determined by means of a set of surface syntactic patterns and a Latent Semantic Kernel. Results show that our strategy is effective in strengthening current web question answering techniques.