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 (- 19.3%), and SVs (- 52.4%) across three datasets. vcfdist also corrects a common flaw in phasing evaluations, reducing measured flip errors by over 50%. Lastly, we show that vcfdist is more accurate than previously published works and on par with the newest approaches while providing improved result interpretability.

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. Next, we present our tool vcfdist and demonstrate the importance of enforcing local phasing for evaluation accuracy. We then introduce the notion of partial credit for mostly-correct calls and present an algorithm for clustering dependent variants. Lastly, we motivate using alignment distance metrics to supplement precision-recall curves for understanding variant calling performance. We evaluate the performance of 64 phased Truth Challenge V2 submissions and show that vcfdist improves measured insertion and deletion performance consistency across variant representations from R2 = 0.97243 for baseline vcfeval to 0.99996 for vcfdist.

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 R9.4.1 flow cells. We show that read phasing and realignment can recover a significant portion of false negative INDELs. In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated n-polymer sequences such as homopolymers ([Formula: see text]) and tandem repeats ([Formula: see text]). At the same precision, haplotype phasing improves INDEL recall from 63.76 to [Formula: see text] and nPoRe realignment improves it further to [Formula: see text].

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. For the genomic data, we perform variant calling on long-read PacBio HiFi data using Cromwell on Azure. Both data formats are parsed, processed and merged in a single scalable pipeline which securely performs tertiary analyses using cloud-based Jupyter notebooks. We include three example applications: exporting patient information to a database, clustering patients and performing a simple pharmacogenomic study. Availability and implementation: https://github.com/microsoft/genomicsnotebook/tree/main/fhirgenomics. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

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. Here, we compare the mechanical properties of thin films of regioregular poly(3-heptylthiophene) (P3HpT) produced by three scalable deposition processes─interfacial spreading, solution shearing, and spray coating─and spin coating (as a reference). Our results lead to four principal conclusions. (1) Spray-coated films have poor mechanical robustness due to defects and inhomogeneous thickness. (2) Sheared films show the highest modulus, strength, and toughness, likely resulting from a decrease in free volume. (3) Interfacially spread films show a lower modulus but greater fracture strain than spin-coated films. (4) The trends observed in the tensile behavior of films cast using different deposition processes held true for both P3HpT and poly(3-butylthiophene) (P3BT), an analogue with a higher glass transition temperature. Grazing incidence X-ray diffraction and ultraviolet-visible spectroscopy reveal many notable differences in the solid structures of P3HpT films generated by all four processes. While these morphological differences provide possible explanations for differences in the electronic properties (hole mobility), we find that the mechanical properties of the film are dominated by the free volume and surface topography. In field-effect transistors, spread films had mobilities more than 1 magnitude greater than any other films, likely due to a relatively high proportion of edge-on texturing and long coherence length in the crystalline domains. Overall, spread films offer the best combination of deformability and charge-transport properties.

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. Here, we explored whether generalised additive models fitted to simulated prey distribution data better predicted deep-diver densities (here beaked whales Ziphiidae and sperm whales Physeter macrocephalus) than models fitted to environmental variables. We assessed whether the combination of environmental and prey distribution data would further improve model fit by comparing their explanatory power. For both taxa, results were suggestive of a preference for habitats associated with topographic features and thermal fronts but also for habitats with an extended euphotic zone and with large prey of the lower mesopelagic layer. For beaked whales, no SEAPODYM variable was selected in the best model that combined the two types of variables, possibly because SEAPODYM does not accurately simulate the organisms on which beaked whales feed on. For sperm whales, the increase model performance was only marginal. SEAPODYM outputs were at best weakly correlated with sightings of deep-diving cetaceans, suggesting SEAPODYM may not accurately predict the prey fields of these taxa. This study was a first investigation and mostly highlighted the importance of the physiographic variables to understand mechanisms that influence the distribution of deep-diving cetaceans. A more systematic use of SEAPODYM could allow to better define the limits of its use and a development of the model that would simulate larger prey beyond 1,000 m would probably better characterise the prey of deep-diving cetaceans.

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. Propensity matching created a 1:1 matched sample of patients with and without stress testing in the 18 months prior to kidney transplantation. The outcomes of interest were death, total (fatal and nonfatal) MI or fatal MI within 30 days of kidney transplantation. RESULTS: In the propensity-matched cohort of 17,304 patients, death within 30 days occurred in 72 of 8,652 (0.83%) patients who underwent stress testing and in 65 of 8,652 (0.75%) patients who did not (OR 1.07; 95% CI: 0.79-1.45; P = 0.66). MI within 30 days occurred in 339 (3.9%) patients who had a stress test and in 333 (3.8%) patients who did not (OR 1.03; 95% CI: 0.89-1.21; P = 0.68). Fatal MI occurred in 17 (0.20%) patients who underwent stress testing and 15 (0.17%) patients who did not (OR 0.97; 95% CI: 0.71-1.32; P = 0.84). CONCLUSION: Stress testing in the 18 months prior to kidney transplantation is not associated with a reduction in death, total MI or fatal MI within 30 days of kidney transplantation.

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. We report a general strategy to make thermally stable high-temperature semiconducting polymer blends, composed of interpenetrating semicrystalline conjugated polymers and high glass-transition temperature insulating matrices. When properly engineered, such polymer blends display a temperature-insensitive charge transport behavior with hole mobility exceeding 2.0 cm2/V·s across a wide temperature range from room temperature up to 220°C in thin-film transistors.

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. PARTICIPANTS: Total of 1596 participants, including 297 (167 male; mean age, 16.2 years) high school athletes, 1016 (541 male; mean age, 18.8 years) collegiate athletes, and 283 (mean age, 26.3 years) male professional athletes. MAIN OUTCOME MEASURES: Athletes were screened using the 8 personal and family history questions from the AHA 12-elements. Electrocardiograms were obtained for all participants and interpreted using Seattle criteria, Stanford criteria, and European Society of Cardiology (ESC) recommendations. RESULTS: Approximately one-quarter of all athletes (23.8%) had at least 1 positive response to the AHA personal and family history elements. High school and college athletes had similar rates of having at least 1 positive response (25.9% vs 27.4%), whereas professional athletes had a significantly lower rate of having at least 1 positive response (8.8%, P < 0.05). Females reported more episodes of unexplained syncope (11.4% vs 7.5%, P = 0.017) and excessive exertional dyspnea with exercise (11.1% vs 6.1%, P = 0.001) than males. High school athletes had more positive responses to the family history elements when compared with college athletes (P < 0.05). The percentage of athletes who had an abnormal ECG varied between Seattle criteria (6.0%), Stanford criteria (8.8%), and ESC recommendations (26.8%). CONCLUSIONS: Many athletes screen positive under current screening recommendations, and ECG results vary widely by interpretation criteria. CLINICAL RELEVANCE: In a patient population without any adverse cardiovascular events, the currently recommended AHA 12-elements have an unacceptably high rate of false positives. Newer screening guidelines are needed, with fewer false positives and evidence-based updates.

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. Prevalence of prolonged QRS duration was measured using cut-points of 120, 125, 130, and 140 ms. ST segment depression was measured in all leads except leads III, aVR, and V1 with cut-points of 25 µV and 50 µV. RESULTS: Between June 2010 and November 2013, 1595 participants including 297 (167 male, mean age 16.2) high school athletes, 1016 (541 male, mean age 18.8) college athletes, and 282 (mean age 26.6) male professional athletes underwent screening with an ECG. Only 3 athletes (0.2%) had a QRS duration greater than 125 ms. ST segment depression in two or more leads greater than 50 µV was uncommon (0.8%), while the prevalence of ST segment depression in two or more leads increased to 4.5% with a cut-point of 25 µV. CONCLUSION: Changing the QRS duration cut-point to 125 ms would increase the sensitivity of the screening ECG, without a significant increase in false-positives. However, changing the ST segment depression cut-point to 25 µV would lead to a significant increase in false-positives and would therefore not be justified.

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. Comparison to an oxidized monomer analogue 1 provides critical insight into the electronic structure of the oxidized bimetallic complex 2. Oxidation of 1 provides [1˙](+), which is characterized as a fully delocalized ligand radical complex; the spectroscopic signature of this derivative includes an intense NIR band at 4500 cm(-1). Oxidation of 2 to the bis-oxidized form affords a bis-ligand radical species [2˙˙](2+). Variable temperature EPR spectroscopy of [2˙˙](2+) shows no evidence of coupling, and the triplet and broken symmetry solutions afforded by theoretical calculations are essentially isoenergetic. [2˙˙](2+) is thus best described as incorporating two non-interacting ligand radicals. Interestingly, the intense NIR intervalence charge transfer band observed for the delocalized ligand-radical [1˙](+) exhibits exciton splitting in [2˙˙](2+), due to coupling of the monomer transition dipoles in the enforced oblique dimer geometry. Evaluating the splitting of the intense intervalence charge transfer band can thus provide significant geometric and electronic information in less rigid bis-ligand radical systems. Addition of excess pyridine to [2˙˙](2+) results in a shift in the oxidation locus from a bis-ligand radical species to the Ni(III) /Ni(III) derivative [2(py)4](2+), demonstrating that the ligand system can incorporate significant bulk in the axial positions.

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. Chem., Int. Ed., 2007, 46, 5198). Spectroscopic experiments, complemented by DFT calculations, show that the two radical spins are predominantly localized on the phenolate moieties, in opposition to the extensive delocalization over the ligand framework observed for the mono-radical analogue.

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. The cations [1-3](+·) exhibited isotropic g tensors of 2.045, 2.023, and 2.005, respectively, reflecting a lower metal character of the singly occupied molecular orbital (SOMO) for systems that involve strongly electron-donating substituents. Pulsed-EPR spectroscopy showed a single population of equivalent imino nitrogen atoms for 1(+·), whereas two distinct populations were observed for 2(+·). The resonance Raman spectra of 2(+·) and 3(+·) displayed the ν(8a) band of the phenoxyl radicals at 1612 cm(-1), as well as the ν(8a) bands of the phenolates. In contrast, the Raman spectrum of 1(+·) exhibited the ν(8a) band at 1602 cm(-1), without any evidence of the phenolate peak. Previous work showed an intense near-infrared (NIR) electronic transition for 1(+·) (Δν(1/2) =660 cm(-1), ε=21,700 M(-1) cm(-1)), indicating that the electron hole is fully delocalized over the ligand. The broader and moderately intense NIR transition of 2(+·) (Δν(1/2) =1250 cm(-1) , ε=12,800 M(-1) cm(-1)) suggests a certain degree of ligand-radical localization, whereas the very broad NIR transition of 3(+·) (Δν(1/2) =8630 cm(-1), ε=2550 M(-1) cm(-1)) indicates significant localization of the ligand radical on a single ring. Therefore, 1(+·) is a Class III mixed-valence complex, 2(+·) is Class II/III borderline complex, and 3(+·) is a Class II complex according to the Robin-Day classification method. By employing the Coulomb-attenuated method (CAM-B3LYP) we were able to predict the electron-hole localization and NIR transitions in the series, and show that the energy match between the redox-active ligand and the metal d orbitals is crucial for delocalization of the radical SOMO.

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. One-electron oxidation provided [1](+) which was observed to have limited stability in solution. The oxidized complex was determined to be 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. Electrochemical experiments and UV-vis-NIR spectroscopy, in combination with density functional theory (DFT) calculations, provided insight into the locus of oxidation and the degree of delocalization in this system. The ligand radical for [1˙](+) was determined experimentally to be localized on the dioxolene bridge with a small amount of spin density on the outer phenolate moieties predicted by the calculations. This assignment was aided via comparison to data for the Ni analogue (Inorg. Chem., 2011, 50, 6746). The resonance Raman spectrum of [1˙](+) (λ(ex) = 413 nm) in CH(2)Cl(2) solution clearly exhibited a new band at 1308 cm(-1) in comparison to 1, supporting semiquinone formation. Variable-temperature EPR on the three-spin system [1˙](+) did not provide definitive information on the coupling interaction, possibly due to a very small difference in energy between the S = 3/2 and S = 1/2 states and/or a very small zero-field splitting, in combination with significant line-broadening. The data is consistent with a description of the overall electronic structure of [1˙](+) as a bimetallic Cu(II) complex with a bridge-localized semiquinone ligand radical species.

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. Electrochemical experiments and UV-vis-NIR spectroscopy, in combination with density functional theory (DFT) calculations, provide insight into the locus of oxidation and the degree of delocalization in this system. The one-electron hole for [1](+) was determined experimentally to be localized on the dioxolene bridge with a small amount of spin density on the outer phenolate moieties predicted by the calculations. The resonance Raman spectrum of [1](+) (λ(ex) = 413 nm) in CH(2)Cl(2) solution clearly exhibited a new band at 1315 cm(-1) in comparison to 1, which is predicted to be a combination of dioxolene ring and C-O bond stretching modes, consistent with oxidation of the bridging moiety in [1](+). Analysis of the NIR bands for [1](+), in association with time-dependent DFT calculations, suggests that the low energy bands are ligand to ligand charge transfer transitions from the terminal phenolates to the central dioxolene unit. In combination, this data is consistent with a description of the overall electronic structure of [1](+) as a bridge-localized semiquinone ligand radical species. This is in contrast to the mixed-valence ground state description for many one-electron oxidized Ni salen monomer systems, and analysis in terms of intervalence charge transfer (IVCT) theory.

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. While the Ni and Pt analogues exhibit an essentially symmetric coordination sphere contraction upon oxidation, the oxidized Pd derivative exhibits an asymmetric metal binding environment demonstrating at least partial ligand radical localization. In comparison to the oxidized Salen and Salcn complexes, the propyl backbone of the Salpn complexes leads to a larger deviation from a planar geometry in the solid state. The electronic structure of the oxidized Salpn complexes was further probed by UV-vis-NIR measurements, electrochemistry, EPR spectroscopy, and theoretical calculations. The intense NIR band for the one-electron oxidized Salpn complexes shifts to lower energy in comparison to the 5-membered chelate analogues, which is attributed to lower metal d(xz) character in the ß-LUMO for the Salpn series. The reactivity of the one-electron oxidized Salpn complexes with exogenous ligands was also studied. In the presence of pyridine, the oxidized Ni analogue exhibits a shift in the locus of oxidation to a Ni(III) species. The oxidized PtSalpn complex rapidly decomposes in the presence of pyridine, even at low temperature. Interestingly, electronic and EPR spectroscopy suggests that the addition of pyridine to the oxidized Pd analogue results in initial dissociation of the phenoxyl radical ligand, likely due to the increased flexibility of the propyl backbone.