Slope Stability Analysis: A Computerized Solution of Bishop’s Simplified Method of Slices

A computer program based on Bishop\u27s simplified method of slices (1954) and capable of analyzing the slope stability of a multilayered soil mass is described. The computer program was specifically developed for analyzing the slope stability of highway bridge approach embankments; however, it can be applied to a broad spectrum of practical slope configurations and bearing capacity problems. Details of the use, applications, and accuracy of the program are presented. Important features of the computer program include a grid type, search operation for locating the critical shear surface and a ledger printout of the forces acting on each individual slice. The latter feature was included so that results of the computer program could be compared to those obtained from manual computations. Pore pressures in the computer program are handled in a manner described by Bishop (1954). Additionally, for seepage cases, infinite slope conditions are assumed and used to simulate a flow net

Stability of a Side-Hill Embankment

The report submitted herein is a case history describing observations and in-depth analyses made at a highway site involving a massive, unstable side-hill embankment located on I-64 in Boyd County. The in-depth study was initiated in January 1973. The I-64 site was selected for study because it contained several design, construction and maintenance features as well as soil types that are typical of many highway embankments in Kentucky. Side-hill fill situations are common design problems and oftentimes have required extensive maintenance after construction. Major objectives of the study were to 1) determine the causes of instability of the I-64 embankment, 2) check a remedial solution previously reported for the I-64 site and present alternative solutions if necessary, 3) determine short-term (initial) and long-term safety factors of the embankment slopes, and 4) compare theoretical shear surfaces obtained from a slope stability program based on Bishop\u27s simplified method of slices with actual failure points obtained from slope indicators and surface observations. All slope stability computations were carried out in terms of effective stress using shear strength parameters obtained from consolidated, isotropic, undrained triaxial tests with pore pressure measurements

A Novel Soluble Immune-Type Receptor (SITR) in Teleost Fish: Carp SITR Is Involved in the Nitric Oxide-Mediated Response to a Protozoan Parasite

Background- The innate immune system relies upon a wide range of germ-line encoded receptors including a large number of immunoglobulin superfamily (IgSF) receptors. Different Ig-like immune receptor families have been reported in mammals, birds, amphibians and fish. Most innate immune receptors of the IgSF are type I transmembrane proteins containing one or more extracellular Ig-like domains and their regulation of effector functions is mediated intracellularly by distinct stimulatory or inhibitory pathways. Methodology/Principal Findings - Carp SITR was found in a substracted cDNA repertoire from carp macrophages, enriched for genes up-regulated in response to the protozoan parasite Trypanoplasma borreli. Carp SITR is a type I protein with two extracellular Ig domains in a unique organisation of a N-proximal V/C2 (or I-) type and a C-proximal V-type Ig domain, devoid of a transmembrane domain or any intracytoplasmic signalling motif. The carp SITR C-proximal V-type Ig domain, in particular, has a close sequence similarity and conserved structural characteristics to the mammalian CD300 molecules. By generating an anti-SITR antibody we could show that SITR protein expression was restricted to cells of the myeloid lineage. Carp SITR is abundantly expressed in macrophages and is secreted upon in vitro stimulation with the protozoan parasite T. borreli. Secretion of SITR protein during in vivo T. borreli infection suggests a role for this IgSF receptor in the host response to this protozoan parasite. Overexpression of carp SITR in mouse macrophages and knock-down of SITR protein expression in carp macrophages, using morpholino antisense technology, provided evidence for the involvement of carp SITR in the parasite-induced NO production. Conclusion/Significance - We report the structural and functional characterization of a novel soluble immune-type receptor (SITR) in a teleost fish and propose a role for carp SITR in the NO-mediated response to a protozoan parasite

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

Should We Be Concerned About Jejunoileal Atresia During Repair of Duodenal Atresia?

Introduction: During repair for duodenal atresia, it has been emphasized that inspection of the small bowel to identify a second atresia is required. The laparoscopic approach for repair of duodenal atresia has been criticized for its limitation to perform this step. Given that duodenal atresia and jejunoileal atresias do not share common embryologic origins, we question the validity of this concern. Therefore, we conducted a multicenter retrospective review of duodenal atresia patients to quantify the incidence of jejunoileal atresia in this population.Methods: After institutional review board approval (IRB #07-12-187X), a retrospective review was conducted on all patients who have undergone duodenal atresia repair at seven institutions over the past 7-12 years. Demographics and the presence or absence of a jejunoileal atresia were recorded.Results: Four hundred eight patients with duodenal atresia were identified. The mean gestaational age was 36.3 ± 2.9 weeks, and the mean weight was 2.5 ± 0.8 kg. Mean age at operation was 19 days (range, 1-1314). There was a 28% incidence of trisomy 21. Two patients (0.5%) were identified as having a second intestinal atresia, and both were type IIIb. One patient was diagnosed at the time of duodenal atresia repair; the other was a delayed diagnosis. Both patients did well after repair.Conclusions: In this, the largest series of duodenal atresia patients compiled to date, the rate of a concomitant jejunoileal atresia is less than 1%. This low incidence is not high enough to mandate extensive inspection of the entire bowel in these patients, and a second atresia should not be a concern during laparoscopic repair of duodenal atresia

Fig. S1_TNT-RAXML-MorphoOnlyRed2

Fig. S1. Results for morphological character data only: RAxML single best known likelihood tree and parsimony (Equal Weights TNT New Technology Search) results