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Phenotype standardization for drug-induced kidney disease.

Drug-induced kidney disease is a frequent cause of renal dysfunction; however, there are no standards to identify and characterize the spectrum of these disorders. We convened a panel of international, adult and pediatric, nephrologists and pharmacists to develop standardized phenotypes for drug-induced kidney disease as part of the phenotype standardization project initiated by the International Serious Adverse Events Consortium. We propose four phenotypes of drug-induced kidney disease based on clinical presentation: acute kidney injury, glomerular, tubular, and nephrolithiasis, along with the primary and secondary clinical criteria to support the phenotype definition, and a time course based on the KDIGO/AKIN definitions of acute kidney injury, acute kidney disease, and chronic kidney disease. Establishing causality in drug-induced kidney disease is challenging and requires knowledge of the biological plausibility for the specific drug, mechanism of injury, time course, and assessment of competing risk factors. These phenotypes provide a consistent framework for clinicians, investigators, industry, and regulatory agencies to evaluate drug nephrotoxicity across various settings. We believe that this is the first step to recognizing drug-induced kidney disease and developing strategies to prevent and manage this condition

Note and Comment

Unliquidated Tort Claims as Provable Debts in Bankruptcy; May a State, in the Exercise of its Police Power, Regulate Insurace Rates?; Interest upon Legacies which are not Payable Until Legatee Attains Certain Age; Validity of a Classification of Banks Based Upon the Amount of Their Average Annual Deposit

Twenty-Four-Month Longitudinal Study Suggests Little to No Horizontal Gene Transfer In Situ between Third-Generation Cephalosporin-Resistant \u3ci\u3eSalmonella\u3c/i\u3e and Third-Generation Cephalosporin-Resistant \u3ci\u3eEscherichia coli\u3c/i\u3e in a Beef Cattle Feedyard

Third-generation cephalosporins (3GCs) are preferred treatments for serious human Salmonella enterica infections. Beef cattle are suspected to contribute to human 3GC-resistant Salmonella infections. Commensal 3GC-resistant Escherichia coli are thought to act as reservoirs of 3GC resistance because these strains are isolated more frequently than are 3GC-resistant Salmonella strains at beef cattle feedyards. During each of 24 consecutive months, four samples of pen surface material were obtained from five pens (N = 480) at a Nebraska feedyard to determine to the contribution of 3GC-resistant E. coli to the occurrence of 3GC-resistant Salmonella. Illumina whole genome sequencing was performed, and susceptibility to 14 antimicrobial agents was determined for 121 3GC-susceptible Salmonella, 121 3GC-resistant Salmonella, and 203 3GCresistant E. coli isolates. 3GC-susceptible Salmonella isolates were predominantly from serotypes Muenchen (70.2%) and Montevideo clade 1 (23.1%). 3GC-resistant Salmonella isolates were predominantly from serotypes Montevideo clade 2 (84.3%). One bla gene type (blaCMY-2) and the IncC plasmid replicon were present in 100 and 97.5% of the 3GC-resistant Salmonella, respectively. Eleven bla gene types were detected in the 3GC-resistant E. coli, which were distributed across 42 multilocus sequence types. The blaCMY-2 gene and IncC plasmid replicon were present in 37.9 and 9.9% of the 3GC-resistant E. coli, respectively. These results suggest that 3GC resistance in Salmonella was primarily due the persistence of Salmonella Montevideo clade 2 with very minimal or no contribution from 3GC-resistant E. coli via horizontal gene transfer and that 3GCresistant E. coli may not be a useful indicator for 3GC-resistant Salmonella in beef cattle production environments

Conventional niche overlap measurements are not effective for assessing interspecific competition

Interspecific competition is notoriously difficult to detect and quantify, especially in species that are wide-ranging or otherwise difficult to track in the wild. Research investigating interspecific competition usually relies on niche overlap measurements despite that this approach alone does not yield rigorous inference. As an illustration, we review published research assessing interspecific competition in mid-sized carnivores in North America (bobcat – Lynx rufus; Canada lynx – Lynx canadensis; coyote – Canis latrans), and report on shortcomings associated with commonly used study designs and types of inference. Niche overlap measurements typically focus on one or two resources (e.g., food, space, habitat), often using non-independent sampling units and inadequate replication. Few studies measure overlap variation through space, time, or resource variability, which is crucial for robust assessment. Niche overlap (or lack thereof) is used as evidence both for and against interspecific competition, reflecting a weak link between competition theory, predicted responses, and observations. Overall, challenges associated with conducting competition research in the field promote over-reliance on simple measurements, flawed study designs and weak inference. Minimally, niche overlap studies should include assessment across multiple niche dimensions and spatial or temporal variation in competitor density or resource availability. Dynamic investigative approaches should include new technologies for tracking inter-individual interactions, study designs that leverage quasi-experiments (e.g., decline in shared resources, biological control of one competitor), and synthetic analyses (e.g., meta-regression). Ultimately, better understanding of competition theory vis-à-vis study design and data needs will promote improved understanding of the role of interspecific competition in nature

Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 4994-4999, doi:10.1128/AEM.00809-16.Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.This work, including the efforts of Mitchell L. Sogin and Steven D’Hondt, was funded by Sloan Foundation (Census of Deep Life). This work, including the efforts of Steven D’Hondt, was funded by U.S. Science Support Program for IODP. This work, including the efforts of Steven D’Hondt, was funded by National Science Foundation (NSF) (OCE- 0752336 and OCE-0939564). The work of E. A. Walsh, J. B. Kirkpatrick, R. Pockalny, and J. Sauvage was funded by the grants to S. D’Hondt

Rationale and Design of the Genetic Contribution to Drug Induced Renal Injury (DIRECT) Study

IntroductionNephrotoxicity from drugs accounts for 18% to 27% of cases of acute kidney injury. Determining a genetic predisposition may potentially be important in minimizing risk. The aims of this study are as follows: to determine whether a genetic predisposition exists for the development of drug-induced kidney disease (DIKD), using genome-wide association and whole-genome sequencing studies; to describe the frequency, course, risk factors, resolution and outcomes of DIKD cases; to investigate the role of ethnic/racial variability in the genetics of DIKD; and to explore the use of different tools establishing causality of DIKD.MethodsA total of 800 patients will be enrolled worldwide and blood samples for DNA collected. Data on the patient risk factors, vital signs, laboratory parameters, drug exposure, and DIKD course will be recorded. A panel of nephrologists will adjudicate all cases. Genome-wide association studies will be conducted using population controls matched on biogeographic ancestry to determine whether there is a genetic predisposition to DIKD. The primary endpoint is the identification of specific drug-related polymorphisms associated with DIKD. Secondary endpoints include the following: frequency of DIKD by causal drug and drug combinations; DIKD genetic variability; exploration of causality assessment tools; risk factor identification; description of the course of DIKD, including mortality and dialysis dependency at hospital discharge and 28 and 90 days post-event.ResultsData are currently being analyzed. Results are pending.DiscussionThe Genetic Contribution to Drug Induced Renal Injury (DIRECT) study will be the first observational cohort study to investigate the genetic determinants of DIKD. If the trial is positive, its findings will potentially translate into safer patient outcomes, by genotypic individualization of therapy and minimization of harm

Estimating the horizontal and vertical direction-of-arrival of water-borne seismic signals in the northern Philippine Sea

Author Posting. © Acoustical Society of America, 2013. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 134 (2013): 3282, doi:10.1121/1.4818843.Conventional and adaptive plane-wave beamforming with simultaneous recordings by large-aperture horizontal and vertical line arrays during the 2009 Philippine Sea Engineering Test (PhilSea09) reveal the rate of occurrence and the two-dimensional arrival structure of seismic phases that couple into the deep ocean. A ship-deployed, controlled acoustic source was used to evaluate performance of the horizontal array for a range of beamformer adaptiveness levels. Ninety T-phases from unique azimuths were recorded between Yeardays 107 to 119. T-phase azimuth and S-minus-P-phase time-of-arrival range estimates were validated using United States Geological Survey seismic monitoring network data. Analysis of phases from a seismic event that occurred on Yearday 112 near the east coast of Taiwan approximately 450 km from the arrays revealed a 22° clockwise evolution of T-phase azimuth over 90 s. Two hypotheses to explain such evolution—body wave excitation of multiple sources or in-water scattering—are presented based on T-phase origin sites at the intersection of azimuthal great circle paths and ridge/coastal bathymetry. Propagation timing between the source, scattering region, and array position suggests the mechanism behind the evolution involved scattering of the T-phase from the Ryukyu Ridge and a T-phase formation/scattering location estimation error of approximately 3.2 km.This research is supported by the Office of Naval Research, both the Applied Research Laboratory program and Code 322(OA)

Patterning and process parameter effects in 3D suspension near-field electrospinning of nanoarrays

The extracellular matrix (ECM) contains nanofibrous proteins and proteoglycans. Nanofabrication methods have received growing interest in recent years as a means of recapitulating these elements within the ECM. Near-field electrospinning (NFES) is a versatile fibre deposition method, capable of layer-by-layer nano-fabrication. The maximum layer height is generally limited in layer-by-layer NFES as a consequence of electrostatic effects of the polymer at the surface, due to residual charge and polymer dielectric properties. This restricts the total volume achievable by layer-by-layer techniques. Surpassing this restriction presents a complex challenge, leading to research innovations aimed at increasing patterning precision, and achieving a translation from 2D to 3D additive nanofabrication. Here we investigated a means of achieving this translation through the use of 3D electrode substrates. This was addressed by in-house developed technology in which selective laser melt manufactured standing pillar electrodes were combined with a direct suspension near-field electrospinning (SNFES) technique, which implements an automated platform to manoeuvre the pillar electrodes around the emitter in order to suspend fibres in the free space between the electrode support structures. In this study SNFES was used in multiple operation modes, investigating the effects of varying process parameters, as well as pattern variations on the suspended nanoarrays. Image analysis of the nanoarrays allowed for the assessment of fibre directionality, isotropy, and diameter; identifying optimal settings to generate fibres for tissue engineering applications