Development of a rapid, culture-free, universal microbial identification system using internal transcribed spacer targeting primers.

The indiscriminate administration of broad-spectrum antibiotics is a primary contributor to the increasing prevalence of antibiotic resistance. Unfortunately, culture, the gold standard for bacterial identification is a time intensive process. Due to this extended diagnostic period, broad-spectrum antibiotics are generally prescribed to prevent poor outcomes.

Jointly benchmarking small and structural variant calls with vcfdist.

In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a joint evaluation of small and structural variants uniformly reduces measured errors for SNPs (- 28.9%), INDELs (- 19.

vcfdist: accurately benchmarking phased small variant calls in human genomes.

Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may misrepresent the relative performance of different variant calling pipelines. We propose solutions, first exploring the affine gap parameter design space for complex variant representation and suggesting a standard.

nPoRe: n-polymer realigner for improved pileup-based variant calling.

Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, INDEL recall remains below 80% for standard R9.

A cloud-based pipeline for analysis of FHIR and long-read data.

Motivation: As genome sequencing becomes cheaper and more accurate, it is becoming increasingly viable to merge this data with electronic health information to inform clinical decisions.

Results: In this work, we demonstrate a full pipeline for working with both PacBio sequencing data and clinical FHIR data, from initial data to tertiary analysis. The electronic health records are stored in FHIR (Fast Healthcare Interoperability Resource) format, the current leading standard for healthcare data exchange.

Comparison of the Mechanical Properties of a Conjugated Polymer Deposited Using Spin Coating, Interfacial Spreading, Solution Shearing, and Spray Coating.

The mechanical properties of π-conjugated (semiconducting) polymers are a key determinant of the stability and manufacturability of devices envisioned for applications in energy and healthcare. These properties─including modulus, extensibility, toughness, and strength─are influenced by the morphology of the solid film, which depends on the method of processing. To date, the majority of work done on the mechanical properties of semiconducting polymers has been performed on films deposited by spin coating, a process not amenable to the manufacturing of large-area films.

Towards a better characterisation of deep-diving whales' distributions by using prey distribution model outputs?

In habitat modelling, environmental variables are assumed to be proxies of lower trophic levels distribution and by extension, of marine top predator distributions. More proximal variables, such as potential prey fields, could refine relationships between top predator distributions and their environment. In situ data on prey distributions are not available over large spatial scales but, a numerical model, the Spatial Ecosystem And POpulation DYnamics Model (SEAPODYM), provides simulations of the biomass and production of zooplankton and six functional groups of micronekton at the global scale.

The association of preoperative cardiac stress testing with 30-day death and myocardial infarction among patients undergoing kidney transplantation.

Background: Although periodic cardiac stress testing is commonly used to screen patients on the waiting list for kidney transplantation for ischemic heart disease, there is little evidence to support this practice. We hypothesized that cardiac stress testing in the 18 months prior to kidney transplantation would not reduce postoperative death, total myocardial infarction (MI) or fatal MI.

Methods: Using the United States Renal Data System, we identified ESRD patients ≥40 years old with primary Medicare insurance who received their first kidney transplant between 7/1/2006 and 11/31/2013.

Semiconducting polymer blends that exhibit stable charge transport at high temperatures.

Although high-temperature operation (i.e., beyond 150°C) is of great interest for many electronics applications, achieving stable carrier mobilities for organic semiconductors at elevated temperatures is fundamentally challenging.

Limitations of Current AHA Guidelines and Proposal of New Guidelines for the Preparticipation Examination of Athletes.

Objective: To examine the prevalence of athletes who screen positive with the preparticipation examination guidelines from the American Heart Association, the AHA 12-elements, in combination with 3 screening electrocardiogram (ECG) criteria.

Design: Observational cross-sectional study.

Setting: Stanford University Sports Medicine Clinic.

Are the QRS duration and ST depression cut-points from the Seattle criteria too conservative?

Background: Screening athletes with ECGs is aimed at identifying "at-risk" individuals who may have a cardiac condition predisposing them to sudden cardiac death. The Seattle criteria highlight QRS duration greater than 140 ms and ST segment depression in two or more leads greater than 50 μV as two abnormal ECG patterns associated with sudden cardiac death.

Methods: High school, college, and professional athletes underwent 12 lead ECGs as part of routine pre-participation physicals.

Class III delocalization and exciton coupling in a bimetallic bis-ligand radical complex.

The geometric and electronic structure of an oxidized bimetallic Ni complex incorporating two redox-active Schiff-base ligands connected via a 1,2-phenylene linker has been investigated and compared to a monomeric analogue. Information from UV/Vis/NIR spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, electrochemistry, and density functional theory (DFT) calculations provides important information on the locus of oxidation for the bimetallic complex. The neutral bimetallic complex is conformationally dynamic at room temperature, which complicates characterization of the oxidized forms.

Double oxidation localizes spin in a Ni bis-phenoxyl radical complex.

The electronic structure of a doubly oxidized Ni salen complex NiSal(tBu) (Sal(tBu) = N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-(1R,2R)-diamine) has been investigated by both experimental and theoretical methods. The doubly oxidized product was probed by resonance Raman spectroscopy, UV-vis-NIR, and EPR to determine the locus of oxidation as well as the spectroscopic signature of the complex. It was determined that double oxidation of NiSal(tBu) affords a bis-ligand radical species in solution via the presence of phenoxyl radical bands at ν(7a) (1504 cm(-1)) and ν(8a) (1579 cm(-1)) in the Raman spectrum, and the loss of the intense NIR transition reported for the mono-radical complex (Angew.

Radical localization in a series of symmetric Ni(II) complexes with oxidized salen ligands.

Square-planar nickel(II) complexes of salen ligands, N,N'-bis(3-tert-butyl-(5R)-salicylidene)-1,2-cyclohexanediamine), in which R=tert-butyl (1), OMe (2), and NMe(2) (3), were prepared and the electronic structure of the one-electron-oxidized species [1-3](+·) was investigated in solution. Cyclic voltammograms of [1-3] showed two quasi-reversible redox waves that were assigned to the oxidation of the phenolate moieties to phenoxyl radicals. From the difference between the first and second redox potentials, the trend of electronic delocalization 1(+·) >2(+·) >3(+·) was obtained.

Non-innocent ligand behaviour of a bimetallic Cu complex employing a bridging catecholate.

The geometric and electronic structure of a bimetallic Cu Schiff-base complex and its one-electron oxidized form have been investigated. The two salen units in the neutral complex 1 are linked via a bridging catecholate function, and the coupling between the two Cu(II) d(9) centres was determined to be weakly antiferromagnetic on the basis of solid-state magnetic studies (J = -3 cm(-1)), and variable-temperature electron paramagnetic resonance (EPR) (J = -3 cm(-1)). Theoretical calculations (DFT) were in agreement with the experimental results (J = -7 cm(-1)), and provided insight into the coupling mechanism for the neutral system.

Non-innocent ligand behavior of a bimetallic Ni Schiff-base complex containing a bridging catecholate.

The geometric and electronic structure of a bimetallic Ni Schiff-base complex and its one-electron oxidized form have been investigated in the solid state and in solution. The two salen units in the neutral complex 1 are linked via a bridging catecholate function. The one-electron oxidized form [1](+) was determined to exist as a ligand radical species in solution, with the electron hole potentially localized on the redox-active dioxolene, the phenolate ligands, or delocalized over the entire ligand system.

Influence of the chelate effect on the electronic structure of one-electron oxidized group 10 metal(II)-(disalicylidene)diamine complexes.

The neutral and one-electron oxidized group 10 metal, Ni(II), Pd(II) and Pt(II), six-membered chelate Salpn (Salpn = N,N'-bis(3,5-di-tert-butylsalicylidene)-1,3-propanediamine) complexes have been investigated and compared to the five-membered chelate Salen (N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-ethanediamine) and Salcn (N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-(1R,2R)-diamine) complexes. Reaction of the Salpn complexes with 1 equivalent of AgSbF(6) affords the oxidized complexes which exist as ligand radical species in solution and in the solid state. The solid state structures of the oxidized complexes have been determined by X-ray crystal structure analysis.