An interactive online dashboard for tracking COVID-19 in U.S. counties, cities, and states in real time.

Objective: The study sought to create an online resource that informs the public of coronavirus disease 2019 (COVID-19) outbreaks in their area.

Materials And Methods: This R Shiny application aggregates data from multiple resources that track COVID-19 and visualizes them through an interactive, online dashboard.

Results: The Web resource, called the COVID-19 Watcher, can be accessed online (https://covid19watcher.

Correction: The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system.

Purpose: Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care.

Methods: Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements.

Correction: Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data.

In the published version of this article, the degree of author Bo Zhang was incorrectly listed as PhD. The correct degree is BS.

Testing the effects of four urbanization filters on forest plant taxonomic, functional, and phylogenetic diversity.

Ongoing urban development has significant effects on ecosystems, including changes to land cover, environmental conditions, and species' distributions. These various impacts may have opposing or interacting effects on plant communities, making it difficult to predict how plant biodiversity will respond to urban development. A frequently cited conceptual framework predicts how urban development influences plant taxonomic, functional, and phylogenetic diversity by simplifying multiple coincident effects of urbanization into four primary filters of biodiversity: habitat transformation, fragmentation, the urban environment, and human preferences.

Correction: Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data.

In the published version of this article, the name of the 18th author was misspelled as Minjie Lou. The correct name is Minjie Luo. The authors regret the error.

Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data.

PurposeThe objective of this study was to assess the ability of our laboratory's exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test.MethodsWe developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test to detect known variants using a reference HapMap sample, and (ii) an interpretation-based approach that assessed our relative ability to identify and interpret disease-causing variants, by analyzing and comparing the results of 19 randomly selected patients previously tested by external laboratories.ResultsWe demonstrate that this approach is reproducible with >99% analytical sensitivity and specificity for single-nucleotide variants and indels <10 bp.

Investigation of the Use of a Family Health History Application in Genetic Counseling.

The paper-based pedigree is the current standard for family health history (FHH) documentation in genetic counseling. Several tools for electronic capture of family health data have been developed to improve re-use and accessibility, data quality and standardization, ease of updating, and integration with electronic medical records. One such tool, the tablet-based Proband application, provides a flexible approach to data capture in dynamic and diverse clinical settings.

Mapping the Binding Modes of Hemilabile Pincer-Crown Ether Ligands in Solution Using Diamagnetic Anisotropic Effects on NMR Chemical Shift.

A protocol for identifying ligand binding modes in a series of iridium pincer complexes bearing hemilabile aza-crown ether ligands has been developed using readily accessible NMR methods. The approach was tested on a collection of 13 structurally diverse pincer-crown ether complexes that include several newly characterized species. New synthetic routes enable facile interconversion of coordination modes and supporting ligands.

Catalytic Enantioselective [3 + 2] Cycloaddition of α-Keto Ester Enolates and Nitrile Oxides.

An enantioselective [3 + 2] cycloaddition reaction between nitrile oxides and transiently generated enolates of α-keto esters has been developed. The catalyst system was found to be compatible with in situ nitrile oxide-generation conditions. A versatile array of nitrile oxides and α-keto esters could participate in the cycloaddition, providing novel 5-hydroxy-2-isoxazolines in high chemical yield with high levels of diastereo- and enantioselectivity.

Reactivity studies on [Cp'Fe(μ-I)]: nitrido-, sulfido- and diselenide iron complexes derived from pseudohalide activation.

The iron half-sandwich [Cp'Fe(μ-I)] (Cp' = 1,2,4-(MeC)CH, ) reacts with the pseudohalides NCO, SCN, SeCN and N to give [Cp'Fe(μ-NCO)] (), [Cp'Fe(μ-S)] (), [Cp'Fe(μ-Se)] () and [Cp'Fe(μ-N)] (), respectively. Various spectroscopic techniques including X-ray diffraction, solid-state magnetic susceptibility studies and Fe Mössbauer spectroscopy were employed in the characterization of these species. Mössbauer spectroscopy shows a decreasing isomer shift with increasing formal oxidation state, ranging from Fe(ii) to Fe(iv), in complexes to .

Rare copy number variants in patients with congenital conotruncal heart defects.

Background: Previous studies using different cardiac phenotypes, technologies and designs suggest a burden of large, rare or de novo copy number variants (CNVs) in subjects with congenital heart defects. We sought to identify disease-related CNVs, candidate genes, and functional pathways in a large number of cases with conotruncal and related defects that carried no known genetic syndrome.

Methods: Cases and control samples were divided into two cohorts and genotyped to assess each subject's CNV content.

Ammonia Synthesis from a Pincer Ruthenium Nitride via Metal-Ligand Cooperative Proton-Coupled Electron Transfer.

The conversion of metal nitride complexes to ammonia may be essential to dinitrogen fixation. We report a new reduction pathway that utilizes ligating acids and metal-ligand cooperation to effect this conversion without external reductants. Weak acids such as 4-methoxybenzoic acid and 2-pyridone react with nitride complex [(H-PNP)RuN] (H-PNP = HN(CHCHPBu)) to generate octahedral ammine complexes that are κ-chelated by the conjugate base.

Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins.

We report a functional synthetic model for studying the noncovalent networks (NCNs) required for complex protein functions. The model [2]-catenane is self-assembled from dipeptide building blocks and contains an extensive network of hydrogen bonds and aromatic interactions. Perturbations to the catenane cause compensating changes in the NCNs structure and dynamics, resulting in long-distance changes reminiscent of a protein.

Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death.

Background: Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural and electrical abnormalities prior to symptomatic events and allow appropriate surveillance and treatment. This study investigated the diagnostic utility of exome sequencing (ES) by evaluating the capture and coverage of genes related to SCA/D.

Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data.

Rationale: Congenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown pathogenesis.

Objective: To determine the contribution of de novo copy number variants (CNVs) in the pathogenesis of sporadic CHD.

Analysis of chromosomal structural variation in patients with congenital left-sided cardiac lesions.

Background: We sought to characterize the landscape of structural variation associated with the subset of congenital cardiac defects characterized by left-sided obstruction.

Methods: Cases with left-sided cardiac defects (LSCD) and pediatric controls were uniformly genotyped and assessed for copy number variant (CNV) calls. Significance testing was performed to ascertain differences in overall CNV incidence, and for CNV enrichment of specific genes and gene functions in LSCD cases relative to controls.

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology.

Background: Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype.

Oxygen atom transfer to a half-sandwich iridium complex: clean oxidation yielding a molecular product.

The oxidation of [Ir(Cp*)(phpy)(NCAr(F))][B(Ar(F))4] (1; Cp* = η(5)-pentamethylcyclopentadienyl, phpy = 2-phenylene-κC(1')-pyridine-κN, NCAr(F) = 3,5-bis(trifluoromethyl)benzonitrile, B(Ar(F))4 = tetrakis[3,5-bis(trifluoromethyl)phenyl]borate) with the oxygen atom transfer (OAT) reagent 2-tert-butylsulfonyliodosobenzene (sPhIO) yielded a single, molecular product at -40 °C. New Ir(Cp*) complexes with bidentate ligands derived by oxidation of phpy were synthesized to model possible products resulting from oxygen atom insertion into the iridium-carbon and/or iridium-nitrogen bonds of phpy. These new ligands were either cleaved from iridium by water or formed unreactive, phenoxide-bridged iridium dimers.

Efficient digest of high-throughput sequencing data in a reproducible report.

Background: High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research. Processing and summarizing the large amount of data generated by HTS presents a non-trivial challenge to bioinformatics. A commonly adopted standard is to store sequencing reads aligned to a reference genome in SAM (Sequence Alignment/Map) or BAM (Binary Alignment/Map) files.

Harvest: a web-based biomedical data discovery and reporting application development platform.

Biomedical researchers share a common challenge of making complex data understandable and accessible. This need is increasingly acute as investigators seek opportunities for discovery amidst an exponential growth in the volume and complexity of laboratory and clinical data. To address this need, we developed Harvest, an open source framework that provides a set of modular components to aid the rapid development and deployment of custom data discovery software applications.

Microclimate moderates plant responses to macroclimate warming.

Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., "thermophilization" of communities).

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications.

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications.

A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record.

Purpose: Genome-scale clinical sequencing is being adopted more broadly in medical practice. The National Institutes of Health developed the Clinical Sequencing Exploratory Research (CSER) program to guide implementation and dissemination of best practices for the integration of sequencing into clinical care. This study describes and compares the state of the art of incorporating whole-exome and whole-genome sequencing results into the electronic health record, including approaches to decision support across the six current CSER sites.