Copper/TEMPO Redox Redux: Analysis of PCET Oxidation of TEMPOH by Copper(II) and the Reaction of TEMPO with Copper(I).

Copper salts and organic aminoxyls, such as TEMPO (2,2,6,6-tetramethylpiperidine-N-oxyl), are versatile catalysts for aerobic alcohol oxidation. Previous reports in the literature contain conflicting proposals concerning the redox interactions that take place between copper(I) and copper(II) salts with the aminoxyl and hydroxylamine species, TEMPO and TEMPOH, respectively. Here, we reinvestigate these reactions in an effort to resolve the conflicting claims in the literature. Under anaerobic conditions, CuIIX2 salts [X = acetate (OAc), trifluoroacetate (TFA), and triflate (OTf)] are shown to promote the rapid proton-coupled oxidation of TEMPOH to TEMPO: CuIIX2 + TEMPOH → CuIX + TEMPO + HX. In the reaction with acetate, however, slow reoxidation of CuIOAc occurs. This process requires both TEMPO and HOAc and coincides with the reduction of TEMPO to 2,2,6,6-tetramethylpiperidine. Analogous reactivity is not observed with trifluoroacetate and triflate species. Overall, the facility of the proton-coupled oxidation of TEMPOH by CuII salts suggests that this process could contribute to catalyst regeneration under aerobic oxidation conditions.

Efficacy of Care for Blind Painful Eyes.

PURPOSE: Pain relief for a blind painful eye often follows an escalating paradigm of interventions. This study compares the efficacy of common interventions. METHODS: A retrospective chart review of blind painful eye cases was conducted at a single tertiary institution from April 2012 to December 2016. Demographics, etiology, treatment, and pain level were assessed. RESULTS: Among 99 blind painful eyes, 96 eyes initially received medical therapy (topical steroids, cycloplegics, and/or hypotensives), with pain relief in 39% of eyes. Minimally invasive interventions (laser cyclophotocoagulation, retrobulbar injection, or corneal electrocautery) were performed 41 times in 36 eyes, 34 of which had failed medical therapy, and led to pain relief in 75% of eyes. Evisceration or enucleation was performed in 28 eyes, and long-term pain relief was achieved in 100% of eyes. Surgery allowed discontinuation of oral analgesics in 100% of cases versus 20% for minimally invasive therapy (p = 0.005) and 14% for medical therapy (p = 0.0001). Compared with medical therapy, minimally invasive therapy was 2.5 times more likely to achieve lasting pain relief (p = 0.003) and surgical therapy 35.6 times more likely to achieve lasting pain relief (p = 0.011). High initial pain score was associated with nonsurgical treatment failure. CONCLUSIONS: Medical therapy provides pain relief in a moderate number of patients with a blind painful eye. When medical therapy fails, minimally invasive therapy and surgical interventions are successively more effective in relieving ocular pain. High initial pain score is a risk factor for nonsurgical therapy failure and may merit an earlier discussion of surgical intervention.

Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.

The Chromosome-centric Human Proteome Project (C-HPP) seeks to comprehensively characterize all protein products coded by the genome, including those expressed sequence variants confirmed via proteogenomics methods. The closely related Biology/Disease-driven Human Proteome Project (B/D-HPP) seeks to understand the biological and pathological associations of expressed protein products, especially those carrying sequence variants that may be drivers of disease. To achieve these objectives, informatics tools are required that interpret potential functional or disease implications of variant protein sequence detected via proteogenomics. Toward this end, we have developed an automated workflow within the Galaxy for Proteomics (Galaxy-P) platform, which leverages the Cancer-Related Analysis of Variants Toolkit (CRAVAT) and makes it interoperable with proteogenomic results. Protein sequence variants confirmed by proteogenomics are assessed for potential structure-function effects as well as associations with cancer using CRAVAT's rich suite of functionalities, including visualization of results directly within the Galaxy user interface. We demonstrate the effectiveness of this workflow on proteogenomic results generated from an MCF7 breast cancer cell line. Our free and open software should enable improved interpretation of the functional and pathological effects of protein sequence variants detected via proteogenomics, acting as a bridge between the C-HPP and B/D-HPP.

Cu-Catalyzed Aerobic Oxidative N-N Coupling of Carbazoles and Diarylamines Including Selective Cross-Coupling.

A Cu-catalyzed method has been identified for aerobic oxidative dimerization of carbazoles and diarylamines to the corresponding N-N coupled bicarbazoles and tetraarylhydrazines. The reactions proceed under mild conditions (1 atm O2, 60-80 °C) with a catalyst composed of CuBr·dimethylsulfide and N, N-dimethylaminopyridine. Reactions between carbazole and diarylamines show unusually selective cross-coupling, even with a 1:1 ratio of the two substrates. This behavior was found to arise from reversible formation of the tetraarylhydrazine. Formation of this species is kinetically favored, but cleavage of the N-N bond under the reaction conditions leads to selective formation of the thermodynamically favored cross-coupling product.

Assessment of a Tele-education System to Enhance Retinopathy of Prematurity Training by International Ophthalmologists-in-Training in Mexico.

PURPOSE: To evaluate a tele-education system developed to improve diagnostic competency in retinopathy of prematurity (ROP) by ophthalmologists-in-training in Mexico. DESIGN: Prospective, randomized cohort study. PARTICIPANTS: Fifty-eight ophthalmology residents and fellows from a training program in Mexico consented to participate. Twenty-nine of 58 trainees (50%) were randomized to the educational intervention (pretest, ROP tutorial, ROP educational chapters, and posttest), and 29 of 58 trainees (50%) were randomized to a control group (pretest and posttest only). METHODS: A secure web-based educational system was created using clinical cases (20 pretest, 20 posttest, and 25 training chapter-based) developed from a repository of over 2500 unique image sets of ROP. For each image set used, a reference standard ROP diagnosis was established by combining the clinical diagnosis by indirect ophthalmoscope examination and image-based diagnosis by multiple experts. Trainees were presented with image-based clinical cases of ROP during a pretest, posttest, and training chapters. MAIN OUTCOME MEASURES: The accuracy of ROP diagnosis (e.g., plus disease, zone, stage, category) was determined using sensitivity and specificity calculations from the pretest and posttest results of the educational intervention group versus control group. The unweighted kappa statistic was used to analyze the intragrader agreement for ROP diagnosis by the ophthalmologists-in-training during the pretest and posttest for both groups. RESULTS: Trainees completing the tele-education system had statistically significant improvements (P < 0.01) in the accuracy of ROP diagnosis for plus disease, zone, stage, category, and aggressive posterior ROP (AP-ROP). Compared with the control group, trainees who completed the ROP tele-education system performed better on the posttest for accurately diagnosing plus disease (67% vs. 48%; P = 0.04) and the presence of ROP (96% vs. 91%; P < 0.01). The specificity for diagnosing AP-ROP (94% vs. 78%; P < 0.01), type 2 ROP or worse (92% vs. 84%; P = 0.04), and ROP requiring treatment (89% vs. 79%; P < 0.01) was better for the trainees completing the tele-education system compared with the control group. Intragrader agreement improved for identification of plus disease, zone, stage, and category of ROP after completion of the educational intervention. CONCLUSIONS: A tele-education system for ROP education was effective in improving the diagnostic accuracy of ROP by ophthalmologists-in-training in Mexico. This system has the potential to increase competency in ROP diagnosis and management for ophthalmologists-in-training from middle-income nations.

Indenylmetal Catalysis in Organic Synthesis.

Synthetic organic chemists have a long-standing appreciation for transition metal cyclopentadienyl complexes, of which many have been used as catalysts for organic transformations. Much less well known are the contributions of the benzo-fused relative of the cyclopentadienyl ligand, the indenyl ligand, whose unique properties have in many cases imparted differential reactivity in catalytic processes toward the synthesis of small molecules. In this Review, we present examples of indenylmetal complexes in catalysis and compare their reactivity to their cyclopentadienyl analogues, wherever possible.

A Ruthenium/Phosphoramidite-Catalyzed Asymmetric Interrupted Metallo-ene Reaction.

Allylic chlorides prepared from commercially available trans-1,4-dichloro-2-butene were converted to trans-disubstituted 5- and 6-membered ring systems with perfect diastereoselectivity and high enantioselectivity under chiral ruthenium catalysis. These products contain stereodefined secondary and tertiary alcohols that originate from the trapping of an alkylruthenium intermediate with adventitious water. Key to the success of this transformation was the development of a new BINOL-based phosphoramidite ligand containing bulky substitution at its 3- and 3'-positions. As a demonstration of product utility, diastereoselective Friedel-Crafts reactions were performed on the chiral benzylic alcohols in high yield and stereoselectivity.

Diagnostic Discrepancies in Retinopathy of Prematurity Classification.

PURPOSE: To identify the most common areas for discrepancy in retinopathy of prematurity (ROP) classification between experts. DESIGN: Prospective cohort study. PARTICIPANTS: A total of 281 infants were identified as part of a multicenter, prospective, ROP cohort study from 7 participating centers. Each site had participating ophthalmologists who provided the clinical classification after routine examination using binocular indirect ophthalmoscopy (BIO) and obtained wide-angle retinal images, which were independently classified by 2 study experts. METHODS: Wide-angle retinal images (RetCam; Clarity Medical Systems, Pleasanton, CA) were obtained from study subjects, and 2 experts evaluated each image using a secure web-based module. Image-based classifications for zone, stage, plus disease, and overall disease category (no ROP, mild ROP, type II or pre-plus, and type I) were compared between the 2 experts and with the clinical classification obtained by BIO. MAIN OUTCOME MEASURES: Inter-expert image-based agreement and image-based versus ophthalmoscopic diagnostic agreement using absolute agreement and weighted kappa statistic. RESULTS: A total of 1553 study eye examinations from 281 infants were included in the study. Experts disagreed on the stage classification in 620 of 1553 comparisons (40%), plus disease classification (including pre-plus) in 287 of 1553 comparisons (18%), zone in 117 of 1553 comparisons (8%), and overall ROP category in 618 of 1553 comparisons (40%). However, agreement for presence versus absence of type 1 disease was >95%. There were no differences between image-based and clinical classification except for zone III disease. CONCLUSIONS: The most common area of discrepancy in ROP classification is stage, although inter-expert agreement for clinically significant disease, such as presence versus absence of type 1 and type 2 disease, is high. There were no differences between image-based grading and clinical examination in the ability to detect clinically significant disease. This study provides additional evidence that image-based classification of ROP reliably detects clinically significant levels of ROP with high accuracy compared with the clinical examination.

Chiral cyclopentadienylruthenium sulfoxide catalysts for asymmetric redox bicycloisomerization.

A full account of our efforts toward an asymmetric redox bicycloisomerization reaction is presented in this article. Cyclopentadienylruthenium (CpRu) complexes containing tethered chiral sulfoxides were synthesized via an oxidative [3 + 2] cycloaddition reaction between an alkyne and an allylruthenium complex. Sulfoxide complex 1 containing a p-anisole moiety on its sulfoxide proved to be the most efficient and selective catalyst for the asymmetric redox bicycloisomerization of 1,6- and 1,7-enynes. This complex was used to synthesize a broad array of [3.1.0] and [4.1.0] bicycles. Sulfonamide- and phosphoramidate-containing products could be deprotected under reducing conditions. Catalysis performed with enantiomerically enriched propargyl alcohols revealed a matched/mismatched effect that was strongly dependent on the nature of the solvent.

ColoWeb: a resource for analysis of colocalization of genomic features.

BACKGROUND: Next-generation sequencing techniques such as ChIP-seq allow researchers to investigate the genomic position of nuclear components and events. These experiments provide researchers with thousands of regions of interest to probe in order to identify biological relevance. As the cost of sequencing decreases and its robustness increases, more and more researchers turn to genome-wide studies to better understand the genomic elements they are studying. One way to interpret the output of sequencing studies is to investigate how the element of interest localizes in relationship to genome annotations and the binding of other nuclear components. Colocalization of genomic features could indicate cooperation and provide evidence for more detailed investigations. Although there are several existing tools for visualizing and analyzing colocalization, either they are difficult to use for experimental researchers, not well maintained, or without measurements for colocalization strength. Here we describe an online tool, ColoWeb, designed to allow experimentalists to compare their datasets to existing genomic features in order to generate hypotheses about biological interactions easily and quickly. RESULTS: ColoWeb is a web-based service for evaluating the colocation of genomic features. Users submit genomic regions of interest, for example, a set of locations from a ChIP-seq analysis. ColoWeb compares the submitted regions of interest to the location of other genomic features such as transcription factors and chromatin modifiers. To facilitate comparisons among various genomic features, the output consists of both graphical representations and quantitative measures of the degree of colocalization between user's genomic regions and selected features. Frequent colocation may indicate a biological relationship. CONCLUSION: ColoWeb is a biologist-friendly web service that can quickly provide an assessment of thousands of genomic regions to identify colocated genomic features. ColoWeb is freely available at: http://projects.insilico.us.com/ColoWeb .

Influence of Fluorescein Angiography on the Diagnosis and Management of Retinopathy of Prematurity.

PURPOSE: To examine the influence of fluorescein angiography (FA) on the diagnosis and management of retinopathy of prematurity (ROP). DESIGN: Prospective cohort study. PARTICIPANTS: Nine recognized ROP experts (3 pediatric ophthalmologists and 6 retina specialists) interpreted 32 sets (16 color fundus photographs and 16 color fundus photographs paired with the corresponding FA images) of wide-angle retinal images from infants with ROP. METHODS: All experts independently reviewed the 32 image sets on a secure website and provided a diagnosis and management plan for the case presented, first based on color fundus photographs alone, and then based on color fundus photographs and corresponding FA images. MAIN OUTCOME MEASURES: Sensitivity and specificity of the ROP diagnosis (zone, stage, plus disease, and category, i.e., no ROP, mild ROP, type 2 ROP, and ROP requiring treatment) were calculated using a consensus reference standard diagnosis, determined from the diagnosis of the color fundus photographs by 3 experienced readers in combination with the clinical diagnosis based on ophthalmoscopic examination. The κ statistic was used to analyze the average intergrader agreement among experts for the diagnosis of zone, stage, plus disease, and category. RESULTS: Addition of FA to color fundus photography resulted in a significant improvement in sensitivity for diagnosis of stage 3 or worse disease (39.8% vs. 74.1%; P = 0.008), type 2 or worse ROP (69.4% vs. 86.8%; P = 0.013), and pre-plus or worse disease (50.5 vs. 62.6%; P = 0.031). There was a nonsignificant trend toward improved sensitivity for diagnosis of ROP requiring treatment (22.2% vs. 40.3%; P = 0.063). Using the κ statistic, addition of FA to color fundus photography significantly improved intergrader agreement for diagnosis of ROP requiring treatment. Addition of FA to color fundus photography did not affect intergrader agreement significantly for the diagnosis of stage, zone, or plus disease. CONCLUSIONS: Compared with color fundus photography alone, FA may improve the sensitivity of diagnosis of ROP by experts, particularly for stage 3 disease. In addition, intergrader agreement for diagnosis of ROP requiring treatment may improve with FA interpretation.

Construction of enantioenriched [3.1.0] bicycles via a ruthenium-catalyzed asymmetric redox bicycloisomerization reaction.

Enantiomerically enriched [3.1.0] bicycles containing vicinal quaternary centers were synthesized from [1,6]-enynes using a cyclopentadienylruthenium catalyst containing a tethered chiral sulfoxide. The reaction was complicated by the fact that the substrates contained a racemic propargyl alcohol that could affect the selectivity of the process. Nonetheless, high levels of enantioinduction were observed, despite complications arising from the use of racemic substrates. Mechanistic studies showed that while the utilization of either enantiomer of the propargyl alcohol led to high product enantiomeric ratios when the reaction was conducted in acetone, a significant matched/mismatched effect was observed in tetrahydrofuran.

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.

SUMMARY: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats. AVAILABILITY AND IMPLEMENTATION: SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. CONTACT: mryan@insilico.us.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

SUMMARY: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. AVAILABILITY AND IMPLEMENTATION: MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

Piperazinobenzodiazepinones: New Encephalitic Alphavirus Inhibitors via Ring Expansion of 2-Dichloromethylquinazolinones.

Venezuelan and eastern equine encephalitis viruses are disease-causing, neuropathic pathogens with no approved treatment options in humans. While expanding the pharmacophoric model of antialphaviral amidines prepared via a quinazolinone rearrangement, we discovered that diamine-treated, 2-dihalomethylquinolinones unexpectedly afforded ring-expanded piperazine-fused benzodiazepinones. Notably, this new chemotype (19 examples) showed potent, submicromolar inhibition of virus-induced cell death, >7-log reduction of viral yield, and tractable structure-activity relationships across both viruses. Antiviral activity was confirmed in primary human neuronal cells. A mechanistic rationale for product formation is proposed, and key structural elements were comparatively modeled between a similarly substituted antiviral amidine and piperazinobenzodiazepinone prototypes to guide future antiviral development.

Ontogenomic study of the relationship between number of gene splice variants and GO categorization.

MOTIVATION: Splice variation plays important roles in evolution and cancer. Different splice variants of a gene may be characteristic of particular cellular processes, subcellular locations or organs. Although several genomic projects have identified splice variants, there have been no large-scale computational studies of the relationship between number of splice variants and biological function. The Gene Ontology (GO) and tools for leveraging GO, such as GoMiner, now make such a study feasible. RESULTS: We partitioned genes into two groups: those with numbers of splice variants b (b=1,..., 10). Then we used GoMiner to determine whether any GO categories are enriched in genes with particular numbers of splice variants. Since there was no a priori 'appropriate' partition boundary, we studied those 'robust' categories whose enrichment did not depend on the selection of a particular partition boundary. Furthermore, because the distribution of splice variant number was a snapshot taken at a particular point in time, we confirmed that those observations were stable across successive builds of GenBank. A small number of categories were found for genes in the lower partitions. A larger number of categories were found for genes in the higher partitions. Those categories were largely associated with cell death and signal transduction. Apoptotic genes tended to have a large repertoire of splice variants, and genes with splice variants exhibited a distinctive 'apoptotic island' in clustered image maps (CIMs). AVAILABILITY: Supplementary tables and figures are available at URL http://discover.nci.nih.gov/OG/supplementaryMaterials.html. The Safari browser appears to perform better than Firefox for these particular items.

Feasibility and Clinical Utility of Ultra-Widefield-Navigated Swept-Source Optical Coherence Tomography Imaging.

Purpose: This work aims to evaluate the clinical utility and feasibility of a novel scanning laser ophthalmoscope-based navigated ultra-widefield swept-source optical coherence tomography (UWF SS-OCT) imaging system. Methods: A retrospective, single-center, consecutive case series evaluated patients between September 2019 and October 2020 with UWF SS-OCT (modified Optos P200TxE, Optos PLC) as part of routine retinal care. The logistics of image acquisition, interpretability of images captured, nature of the peripheral abnormality, and clinical utility in management decisions were recorded. Results: Eighty-two eyes from 72 patients were included. Patients were aged 59.4 ± 17.1 years (range, 8-87 years). During imaging, 4.4 series of images were obtained in 4.1 minutes, with 86.4% of the image series deemed to be diagnostic of the peripheral pathology on blinded image review. The most common pathologic findings were chorioretinal scars (18 eyes). In 31 (38%) eyes, these images were meaningful in supporting clinical decision-making with definitive findings. Diagnoses imaged included retinal detachment combined with retinoschisis, retinal hole with overlying vitreous traction and subretinal fluid, vitreous inflammation overlying a peripheral scar, Coats disease, and peripheral retinal traction in sickle cell retinopathy. Conclusions: Navigated UWF SS-OCT imaging was clinically practical and provided high-quality characterization of peripheral retinal lesions for all eyes. Images directly contributed to management plans, including laser, injection or surgical treatment, for a clinically meaningful set of patients (38%). Future studies are needed to further assess the value of this imaging modality and its role in diagnosing, monitoring, and treating peripheral lesions.

Ruthenium-Catalyzed Asymmetric Allylic Alkylation of Isatins.

A new ruthenium-based catalytic system for branched-selective asymmetric allylic alkylation is disclosed and applied to the synthesis of chiral isatin derivatives. The catalyst, which is generated in situ from commercially available CpRu(MeCN)3PF6 and a BINOL-derived phosphoramidite, is both highly active (TON up to 180) and insensitive to air and moisture. Additionally, the N-alkylated isatins accessible using this methodology are versatile building blocks that are readily transformed into chiral analogs of achiral drug molecules.

Mechanistic insights into copper-catalyzed aerobic oxidative coupling of N-N bonds.

Catalytic N-N coupling is a valuable transformation for chemical synthesis and energy conversion. Here, mechanistic studies are presented for two related copper-catalyzed oxidative aerobic N-N coupling reactions, one involving the synthesis of a pharmaceutically relevant triazole and the other relevant to the oxidative conversion of ammonia to hydrazine. Analysis of catalytic and stoichiometric N-N coupling reactions support an "oxidase"-type catalytic mechanism with two redox half-reactions: (1) aerobic oxidation of a CuI catalyst and (2) CuII-promoted N-N coupling. Both reactions feature turnover-limiting oxidation of CuI by O2, and this step is inhibited by the N-H substrate(s). The results highlight the unexpected facility of the N-N coupling step and establish a foundation for development of improved catalysts for these transformations.