Empirical evidence of local seismic effects at sites with pronounced topography: a systematic approach

The recent growth of seismic monitoring networks allows for systematic studies of local seismic effects at sites with pronounced topography.We applied a terrain classification method to identify such sites within Swiss and Japanese networks and compiled a data set of high-quality earthquake recordings. As a number of recent studies have found local effects to be directional at sites with strong topographic features, polarization analysis of particle motion was performed and azimuthally dependent resonant frequencies were estimated. The same procedure was also applied for available ambient vibration recordings. Moreover, average residuals with respect to ground motion prediction models for a reference bedrock were calculated to estimate the average amplification or deamplification for each station. On one hand, observed amplifications are found to be tightly linked with ground motion directionality as estimated by polarization analysis for both earthquake and ambient vibration recordings. On the other hand, we found no clear relation between local topographic features and observed amplification, so the local subsurface properties (i.e. shear wave velocity structure) seem to play the key role and not the geometry itself

Cross-cultural adaptation and linguistic validation of the Hypoglycaemia Symptom Rating Scale (HypoSRQ) among Malaysian patients with diabetes mellitus

The Hypoglycaemia Symptom Rating Questionnaire (HypoSRQ) is potentially useful for local research on hypoglycaemia. However, it requires adaptation and validation in local settings. This study reports the process and results of cross-cultural adaptation and linguistic validation of HypoSRQ for Malay and English versions in our local setting. The HypoSRQ underwent forward and backward translation and adaptation with support from professional translators and a clinical psychologist. Cognitive debriefing was done among patients with Type 1 and Type 2 diabetes mellitus from varying sociodemographic backgrounds. Discussion was done together with the original developers of the HypoSRQ to decide on the best version for local use. The finalised versions were proofread and formatted with the help of Health Psychology Research. Cognitive debriefing for Malay version involved 7 patients and for the English version5 patients. Direct literal translation into Malay language was unsuitable due to technical terms which were difficult for laypersons to understand. Amendments were made based on findings from the cognitive debriefing process. Participants found the questionnaire fairly easy to understand. The HypoSRQ-My (Malay) and HypoSRQ-EMy (English) is easily understood by local participants. These tools may undergo psychometric evaluation for future use in local settings

Microbial Co-occurrence Relationships in the Human Microbiome

The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome

Assessment of associations between transition diseases and reproductive performance of dairy cows using survival analysis and decision tree algorithms

This study aimed to evaluate the associations between transition cow conditions and diseases TD with fertility in Holstein cows, and to compare analytic methods for doing so. Kaplan-Meier, Cox proportional hazard, and decision tree models were used to analyze the associations of TD with the pregnancy risk at 120 and 210 DIM from a 1-year cohort with 1946 calvings from one farm. The association between TD and fertility was evaluated as follows: 1 cows with TD whether complicated with another TD or not TD-all, versus healthy cows, and 2 cows with uncomplicated TD TD-single, versus cows with multiple TD TD+; complicated cases, versus healthy cows. The occurrence of twins, milk fever, retained placenta, metritis, ketosis, displaced abomasum, and clinical mastitis were recorded. Using Kaplan-Meier models, in primiparous cows the 120 DIM pregnancy risk was 62% (95% CI: 57-67 %) for healthy animals. This was not significantly different for TD-single (58%; 95% CI: 51-66 %) but was reduced for TD+ (45%; 95% CI: 33-60 %). Among healthy primiparous cows, 80% (95% CI: 75-84 %) were pregnant by 210 DIM, but pregnancy risk at that time was reduced for primiparous cows with TD-single (72%; 95% CI: 65-79 %) and TD+ (62%; 95% CI: 49-75 %). In healthy multiparous cows, the 120 DIM pregnancy risk was 53% (95% CI: 49-56 %), which was reduced for TD-single (36%; 95% CI: 31-42 %) and TD+ (30%; 95% CI: 24-38 %). The 210 DIM pregnancy risk for healthy multiparous cows was 70% (95% CI: 67-72 %), being higher than the 210 DIM pregnancy risk for multiparous cows with TD-single (47%; 95% CI: 42-53 %) or TD+ (46%; 95% CI: 38-54 %). Cows with TD-all presented similar pregnancy risk estimates as for TD+. Cox proportional hazards regressions provided similar magnitudes of effects as the Kaplan-Meier estimates. Survival analysis and decision tree models identified parity as the most influential variable affecting fertility. Both modeling techniques concurred that TD + had a greater effect than TD-single on the probability of pregnancy at 120 and 210 DIM. Decision trees for individual TD identified that displaced abomasum affected fertility at 120 DIM in primiparous while metritis was the most influential TD at 120 and 210 DIM for multiparous cows. The data were too sparse to assess multiple interactions in multivariable Cox proportional hazard models for individual TD. Machine learning helped to explore interactions between individual TD to study their hierarchical effect on fertility, identifying conditional relationships that merit further investigation

Toward Reliable Characterization of Sites With Pronounced Topography and Related Effects on Ground Motion

Here we present first results of a joint effort undertaken in ongoing European project NERA -JRA1, which aims at establishing scientifically solid and practically acceptable propositions to incorporate surface topography effects in seismic hazard estimates. We assembled a dataset of both ambient vibration and earthquake recordings acquired at 40 European sites with pronounced topography. It comprises a wide variety of sites including populated hills and even extreme cases of unstable rock slopes in Alpine regions. Results of the polarisation analysis for the two sites presented here show the peculiarity of the topographic site effects

A description and qualitative comparison of the elements of heterogeneous bovine viral diarrhea control programs that influence confidence of freedom

For endemic infections in cattle that are not regulated at the European Union level, such as bovine viral diarrhea virus (BVDV), European Member States have implemented control or eradication programs (CEP) tailored to their specific situations. Different methods are used to assign infection-free status in CEP; therefore, the confidence of freedom associated with the “free” status generated by different CEP are difficult to compare, creating problems for the safe trade of cattle between territories. Safe trade would be facilitated with an output-based framework that enables a transparent and standardized comparison of confidence of freedom for CEP across herds, regions, or countries. The current paper represents the first step toward development of such a framework by seeking to describe and qualitatively compare elements of CEP that contribute to confidence of freedom. For this work, BVDV was used as a case study. We qualitatively compared heterogeneous BVDV CEP in 6 European countries: Germany, France, Ireland, the Netherlands, Sweden, and Scotland. Information about BVDV CEP that were in place in 2017 and factors influencing the risk of introduction and transmission of BVDV (the context) were collected using an existing tool, with modifications to collect information about aspects of control and context. For the 6 participating countries, we ranked all individual elements of the CEP and their contexts that could influence the probability that cattle from a herd categorized as BVDV-free are truly free from infection. Many differences in the context and design of BVDV CEP were found. As examples, CEP were either mandatory or voluntary, resulting in variation in risks from neighboring herds, and risk factors such as cattle density and the number of imported cattle varied greatly between territories. Differences were also found in both testing protocols and definitions of freedom from disease. The observed heterogeneity in both the context and CEP design will create difficulties when comparing different CEP in terms of confidence of freedom from infection. These results highlight the need for a standardized practical methodology to objectively and quantitatively determine confidence of freedom resulting from different CEP around the world

Propensity score analysis in the Genetic Analysis Workshop 17 simulated data set on independent individuals

Genetic Analysis Workshop 17 provided simulated phenotypes and exome sequence data for 697 independent individuals (209 case subjects and 488 control subjects). The disease liability in these data was influenced by multiple quantitative traits. We addressed the lack of statistical power in this small data set by limiting the genomic variants included in the study to those with potential disease-causing effect, thereby reducing the problem of multiple testing. After this adjustment, we could readily detect two common variants that were strongly associated with the quantitative trait Q1 (C13S523 and C13S522). However, we found no significant associations with the affected status or with any of the other quantitative traits, and the relationship between disease status and genomic variants remained obscure. To address the challenge of the multivariate phenotype, we used propensity scores to combine covariates with genetic risk factors into a single risk factor and created a new phenotype variable, the probability of being affected given the covariates. Using the propensity score as a quantitative trait in the case-control analysis, we again could identify the two common single-nucleotide polymorphisms (C13S523 and C13S522). In addition, this analysis captured the correlation between Q1 and the affected status and reduced the problem of multiple testing. Although the propensity score was useful for capturing and clarifying the genetic contributions of common variants to the disease phenotype and the mediating role of the quantitative trait Q1, the analysis did not increase power to detect rare variants