Type inference in flexible model-driven engineering using classification algorithms

Flexible or bottom-up model-driven engineering (MDE) is an emerging approach to domain and systems modelling. Domain experts, who have detailed domain knowledge, typically lack the technical expertise to transfer this knowledge using traditional MDE tools. Flexible MDE approaches tackle this challenge by promoting the use of simple drawing tools to increase the involvement of domain experts in the language definition process. In such approaches, no metamodel is created upfront, but instead the process starts with the definition of example models that will be used to infer the metamodel. Pre-defined metamodels created by MDE experts may miss important concepts of the domain and thus restrict their expressiveness. However, the lack of a metamodel, that encodes the semantics of conforming models has some drawbacks, among others that of having models with elements that are unintentionally left untyped. In this paper, we propose the use of classification algorithms to help with the inference of such untyped elements. We evaluate the proposed approach in a number of random generated example models from various domains. The correct type prediction varies from 23 to 100% depending on the domain, the proportion of elements that were left untyped and the prediction algorithm used

Animal-related factors associated with moderate-to-severe diarrhea in children younger than five years in western Kenya: A matched case-control study

Background Diarrheal disease remains among the leading causes of global mortality in children younger than 5 years. Exposure to domestic animals may be a risk factor for diarrheal disease. The objectives of this study were to identify animal-related exposures associated with cases of moderate-to-severe diarrhea (MSD) in children in rural western Kenya, and to identify the major zoonotic enteric pathogens present in domestic animals residing in the homesteads of case and control children. Methodology/Principal findings We characterized animal-related exposures in a subset of case and control children (n = 73 pairs matched on age, sex and location) with reported animal presence at home enrolled in the Global Enteric Multicenter Study in western Kenya, and analysed these for an association with MSD. We identified potentially zoonotic enteric pathogens in pooled fecal specimens collected from domestic animals resident at children’s homesteads. Variables that were associated with decreased risk of MSD were washing hands after animal contact (matched odds ratio [MOR] = 0.2; 95% CI 0.08–0.7), and presence of adult sheep that were not confined in a pen overnight (MOR = 0.1; 0.02–0.5). Variables that were associated with increased risk of MSD were increasing number of sheep owned (MOR = 1.2; 1.0–1.5), frequent observation of fresh rodent excreta (feces/urine) outside the house (MOR = 7.5; 1.5–37.2), and participation of the child in providing water to chickens (MOR = 3.8; 1.2–12.2). Of 691 pooled specimens collected from 2,174 domestic animals, 159 pools (23%) tested positive for one or more potentially zoonotic enteric pathogens (Campylobacter jejuni, C. coli, non-typhoidal Salmonella, diarrheagenic E. coli, Giardia, Cryptosporidium, or rotavirus). We did not find any association between the presence of particular pathogens in household animals, and MSD in children. Conclusions and significance Public health agencies should continue to promote frequent hand washing, including after animal contact, to reduce the risk of MSD. Future studies should address specific causal relations of MSD with sheep and chicken husbandry practices, and with the presence of rodents

Results of matching valve and root repair to aortic valve and root pathology

ObjectiveFor patients with aortic root pathology and aortic valve regurgitation, aortic valve replacement is problematic because no durable bioprosthesis exists, and mechanical valves require lifetime anticoagulation. This study sought to assess outcomes of combined aortic valve and root repair, including comparison with matched bioprosthesis aortic valve replacement.MethodsFrom November 1990 to January 2005, 366 patients underwent modified David reimplantation (n = 72), root remodeling (n = 72), or valve repair with sinotubular junction tailoring (n = 222). Active follow-up was 99% complete, with a mean of 5.6 ± 4.0 years (maximum 17 years); follow-up for vital status averaged 8.5 ± 3.6 years (maximum 19 years). Propensity-adjusted models were developed for fair comparison of outcomes.ResultsThirty-day and 5-, 10-, and 15-year survivals were 98%, 86%, 74%, and 58%, respectively, similar to that of the US matched population and better than that after bioprosthesis aortic valve replacement. Propensity-score–adjusted survival was similar across procedures (P > .3). Freedom from reoperation at 30 days and 5 and 10 years was 99%, 92%, and 89%, respectively, and was similar across procedures (P > .3) after propensity-score adjustment. Patients with tricuspid aortic valves were more likely to be free of reoperation than those with bicuspid valves at 10 years (93% vs 77%, P = .002), equivalent to bioprosthesis aortic valve replacement and superior after 12 years. Bioprostheses increasingly deteriorated after 7 years, and hazard functions for reoperation crossed at 7 years.ConclusionsValve preservation (rather than replacement) and matching root procedures have excellent early and long-term results, with increasing survival benefit at 7 years and fewer reoperations by 12 years. We recommend this procedure for experienced surgical teams

In ricordo di Paolo Sylos Labini

Background: Diarrheal disease is the second leading cause of disease in children less than 5 y of age. Poor water, sanitation, and hygiene conditions are the primary routes of exposure and infection. Sanitation and hygiene interventions are estimated to generate a 36% and 48% reduction in diarrheal risk in young children, respectively. Little is known about whether the number of households sharing a sanitation facility affects a child's risk of diarrhea. The objective of this study was to describe sanitation and hygiene access across the Global Enteric Multicenter Study (GEMS) sites in Africa and South Asia and to assess sanitation and hygiene exposures, including shared sanitation access, as risk factors for moderate-to-severe diarrhea (MSD) in children less than 5 y of age. Methods/Findings: The GEMS matched case-control study was conducted between December 1, 2007, and March 3, 2011, at seven sites in Basse, The Gambia; Nyanza Province, Kenya; Bamako, Mali; Manhiça, Mozambique; Mirzapur, Bangladesh; Kolkata, India; and Karachi, Pakistan. Data was collected for 8,592 case children aged 93%) had access to a sanitation facility, while 70% of households in rural Kenya had access to a facility. Practicing open defecation was a risk factor for MSD in children <5 y old in Kenya. Sharing sanitation facilities with 1–2 or ≥3 other households was a statistically significant risk factor for MSD in Kenya, Mali, Mozambique, and Pakistan. Among those with a designated handwashing area near the home, soap or ash were more frequently observed at control households and were significantly protective against MSD in Mozambique and India. Conclusions: This study suggests that sharing a sanitation facility with just one to two other households can increase the risk of MSD in young children, compared to using a private facility. Interventions aimed at increasing access to private household sanitation facilities may reduce the burden of MSD in children. These findings support the current World Health Organization/ United Nations Children's Emergency Fund (UNICEF) system that categorizes shared sanitation as unimproved

Sanitation and Hygiene-Specific Risk Factors for Moderate-to-Severe Diarrhea in Young Children in the Global Enteric Multicenter Study, 2007-2011: Case-Control Study.

Background: Diarrheal disease is the second leading cause of disease in children less than 5 y of age. Poor water, sanitation, and hygiene conditions are the primary routes of exposure and infection. Sanitation and hygiene interventions are estimated to generate a 36% and 48% reduction in diarrheal risk in young children, respectively. Little is known about whether the number of households sharing a sanitation facility affects a child's risk of diarrhea. The objective of this study was to describe sanitation and hygiene access across the Global Enteric Multicenter Study (GEMS) sites in Africa and South Asia and to assess sanitation and hygiene exposures, including shared sanitation access, as risk factors for moderate-to-severe diarrhea (MSD) in children less than 5 y of age. Methods/Findings: The GEMS matched case-control study was conducted between December 1, 2007, and March 3, 2011, at seven sites in Basse, The Gambia; Nyanza Province, Kenya; Bamako, Mali; Manhiça, Mozambique; Mirzapur, Bangladesh; Kolkata, India; and Karachi, Pakistan. Data was collected for 8,592 case children aged 93%) had access to a sanitation facility, while 70% of households in rural Kenya had access to a facility. Practicing open defecation was a risk factor for MSD in children <5 y old in Kenya. Sharing sanitation facilities with 1–2 or ≥3 other households was a statistically significant risk factor for MSD in Kenya, Mali, Mozambique, and Pakistan. Among those with a designated handwashing area near the home, soap or ash were more frequently observed at control households and were significantly protective against MSD in Mozambique and India. Conclusions: This study suggests that sharing a sanitation facility with just one to two other households can increase the risk of MSD in young children, compared to using a private facility. Interventions aimed at increasing access to private household sanitation facilities may reduce the burden of MSD in children. These findings support the current World Health Organization/ United Nations Children's Emergency Fund (UNICEF) system that categorizes shared sanitation as unimproved

A Case-Control Study of Hantavirus Pulmonary Syndrome during an Outbreak in the Southwestern United States

In May 1993, an outbreak of hantavirus pulmonary syndrome( HPS) occurred in the south-western United States. A case-control study determined risk factors for HPS. Seventeen case-patients were compared with 3 groups of controls: members of case-patient households( household controls), members of neighboring households( near controls), and members of randomly selected households ≥ 24 km away ( far controls). Investigators trapped more small rodents at case households than at near ( P = .03) or far control households( P = .02). After the number of small rodents was controlled for,case-patients were more likely than household controls to hand plow (odds ratio [OR], 12.3; 95% confidence interval [ CI], 1.1-143.0) or to clean feed storage areas (OR, 33.4; 95% CI, 1.7-666.0). Case-patients were more likely than near controls to plant( OR, 6.2; 95% CI, 1.1-34.0) and more likely than far controls to clean animal sheds( OR, 11.9;95% CI, 1.4-103.0). Peridomestic cleaning, agricultural activities, and an increased number of small rodents at the household were associated with HPS

A Case-Control Study of Hantavirus Pulmonary Syndrome during an Outbreak in the Southwestern United States

In May 1993, an outbreak of hantavirus pulmonary syndrome( HPS) occurred in the south-western United States. A case-control study determined risk factors for HPS. Seventeen case-patients were compared with 3 groups of controls: members of case-patient households( household controls), members of neighboring households( near controls), and members of randomly selected households ≥ 24 km away ( far controls). Investigators trapped more small rodents at case households than at near ( P = .03) or far control households( P = .02). After the number of small rodents was controlled for,case-patients were more likely than household controls to hand plow (odds ratio [OR], 12.3; 95% confidence interval [ CI], 1.1-143.0) or to clean feed storage areas (OR, 33.4; 95% CI, 1.7-666.0). Case-patients were more likely than near controls to plant( OR, 6.2; 95% CI, 1.1-34.0) and more likely than far controls to clean animal sheds( OR, 11.9;95% CI, 1.4-103.0). Peridomestic cleaning, agricultural activities, and an increased number of small rodents at the household were associated with HPS

Mapping and monitoring carbon stocks with satellite observations: a comparison of methods

Mapping and monitoring carbon stocks in forested regions of the world, particularly the tropics, has attracted a great deal of attention in recent years as deforestation and forest degradation account for up to 30% of anthropogenic carbon emissions, and are now included in climate change negotiations. We review the potential for satellites to measure carbon stocks, specifically aboveground biomass (AGB), and provide an overview of a range of approaches that have been developed and used to map AGB across a diverse set of conditions and geographic areas. We provide a summary of types of remote sensing measurements relevant to mapping AGB, and assess the relative merits and limitations of each. We then provide an overview of traditional techniques of mapping AGB based on ascribing field measurements to vegetation or land cover type classes, and describe the merits and limitations of those relative to recent data mining algorithms used in the context of an approach based on direct utilization of remote sensing measurements, whether optical or lidar reflectance, or radar backscatter. We conclude that while satellite remote sensing has often been discounted as inadequate for the task, attempts to map AGB without satellite imagery are insufficient. Moreover, the direct remote sensing approach provided more coherent maps of AGB relative to traditional approaches. We demonstrate this with a case study focused on continental Africa and discuss the work in the context of reducing uncertainty for carbon monitoring and markets

Vegetation phenology and habitat discrimination : impacts for E.multilocularis transmission host modelling

Echinococcus multilocularis (Em), a parasitic tapeworm, is responsible for a significant burden of human disease across continental Asia. Here, we use a time-series of MODIS 16-day 250 m Enhanced Vegetation Index (EVI) satellite data to quantify the seasonal vegetation dynamics across a study area in Serxu County, Sichuan Province, China, in relation to the presence of the Em intermediate host Ochotona curzoniae (plateau pika) and Ochotona cansus (Gansu pika) (here merged to Ochotona spp.). A series of derived phenological metrics are analysed using the random forests statistical method to determine the relative importance of seasonal vegetation characteristics. Results indicate negative relationships between Ochotona spp. presence and EVI showing a preference for low-biomass habitats. However, EVI values during green-up and senescence periods are also shown to be important, potentially resulting from improved detectability of low-biomass grassland habitats at these times. Improved detection of Ochotona spp. preferred habitats via time-series EVI imagery offers better understanding of the distributions of this Em host, and the potential for monitoring the changes in Ochotona spp. optimal habitat distributions resulting from landscape change. This could aid the identification of villages at increased risk of infection, enabling preventive strategies to be adopted

High-throughput mapping of regulatory DNA

Quantifying the effects of cis-regulatory DNA on gene expression is a major challenge. Here, we present the multiplexed editing regulatory assay (MERA), a high-throughput CRISPR-Cas9–based approach that analyzes the functional impact of the regulatory genome in its native context. MERA tiles thousands of mutations across ~40 kb of cis-regulatory genomic space and uses knock-in green fluorescent protein (GFP) reporters to read out gene activity. Using this approach, we obtain quantitative information on the contribution of cis-regulatory regions to gene expression. We identify proximal and distal regulatory elements necessary for expression of four embryonic stem cell–specific genes. We show a consistent contribution of neighboring gene promoters to gene expression and identify unmarked regulatory elements (UREs) that control gene expression but do not have typical enhancer epigenetic or chromatin features. We compare thousands of functional and nonfunctional genotypes at a genomic location and identify the base pair–resolution functional motifs of regulatory elements.National Institutes of Health (U.S.) (1U01HG007037