Complexing Behaviour of 2-Thioorotic Acid: Complexes of Co(II), Fe(II), Rh(III), Pd(IV) & Pt(IV)

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Quasiparticle spectra from a non-empirical optimally-tuned range-separated hybrid density functional

We present a method for obtaining outer valence quasiparticle excitation energies from a DFT-based calculation, with accuracy that is comparable to that of many-body perturbation theory within the GW approximation. The approach uses a range-separated hybrid density functional, with asymptotically exact and short-range fractional Fock exchange. The functional contains two parameters - the range separation and the short-range Fock fraction. Both are determined non-empirically, per system, based on satisfaction of exact physical constraints for the ionization potential and many-electron self-interaction, respectively. The accuracy of the method is demonstrated on four important benchmark organic molecules: perylene, pentacene, 3,4,9,10-perylene-tetracarboxylic-dianydride (PTCDA) and 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA). We envision that for finite systems the approach could provide an inexpensive alternative to GW, opening the door to the study of presently out of reach large-scale systems

Ab initio molecular dynamics using density based energy functionals: application to ground state geometries of some small clusters

The ground state geometries of some small clusters have been obtained via ab initio molecular dynamical simulations by employing density based energy functionals. The approximate kinetic energy functionals that have been employed are the standard Thomas-Fermi $(T_{TF})$ along with the Weizsacker correction $T_W$ and a combination $F(N_e)T_{TF} + T_W$. It is shown that the functional involving $F(N_e)$ gives superior charge densities and bondlengths over the standard functional. Apart from dimers and trimers of Na, Mg, Al, Li, Si, equilibrium geometries for $Li_nAl, n=1,8$ and $Al_{13}$ clusters have also been reported. For all the clusters investigated, the method yields the ground state geometries with the correct symmetries with bondlengths within 5\% when compared with the corresponding results obtained via full orbital based Kohn-Sham method. The method is fast and a promising one to study the ground state geometries of large clusters.Comment: 15 pages, 3 PS figure

Density-functional embedding using a plane-wave basis

The constrained electron density method of embedding a Kohn-Sham system in a substrate system (first described by P. Cortona, Phys. Rev. B {\bf 44}, 8454 (1991) and T.A. Wesolowski and A. Warshel, J. Phys. Chem {\bf 97}, 8050 (1993)) is applied with a plane-wave basis and both local and non-local pseudopotentials. This method divides the electron density of the system into substrate and embedded electron densities, the sum of which is the electron density of the system of interest. Coupling between the substrate and embedded systems is achieved via approximate kinetic energy functionals. Bulk aluminium is examined as a test case for which there is a strong interaction between the substrate and embedded systems. A number of approximations to the kinetic-energy functional, both semi-local and non-local, are investigated. It is found that Kohn-Sham results can be well reproduced using a non-local kinetic energy functional, with the total energy accurate to better than 0.1 eV per atom and good agreement between the electron densities.Comment: 11 pages, 4 figure

CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation

Purpose Internationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier (http://www.cardioclassifier.org), a semiautomated decision-support tool for inherited cardiac conditions (ICCs). Methods CardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretation. Combining disease- and gene-specific knowledge with variant observations in large cohorts of cases and controls, we refined 14 computational ACMG criteria and created three ICC-specific rules. Results We benchmarked CardioClassifier on 57 expertly curated variants and show full retrieval of all computational data, concordantly activating 87.3% of rules. A generic annotation tool identified fewer than half as many clinically actionable variants (64/219 vs. 156/219, Fisher’s P = 1.1  ×  10−18), with important false positives, illustrating the critical importance of disease and gene-specific annotations. CardioClassifier identified putatively disease-causing variants in 33.7% of 327 cardiomyopathy cases, comparable with leading ICC laboratories. Through addition of manually curated data, variants found in over 40% of cardiomyopathy cases are fully annotated, without requiring additional user-input data. Conclusion CardioClassifier is an ICC-specific decision-support tool that integrates expertly curated computational annotations with case-specific data to generate fast, reproducible, and interactive variant pathogenicity reports, according to best practice guidelines

Secretion of Clostridium difficile Toxins A and B Requires the Holin-like Protein TcdE

The pathogenesis of Clostridium difficile, the major cause of antibiotic-associated diarrhea, is mainly associated with the production and activities of two major toxins. In many bacteria, toxins are released into the extracellular environment via the general secretion pathways. C. difficile toxins A and B have no export signature and their secretion is not explainable by cell lysis, suggesting that they might be secreted by an unusual mechanism. The TcdE protein encoded within the C. difficile pathogenicity locus (PaLoc) has predicted structural features similar to those of bacteriophage holin proteins. During many types of phage infection, host lysis is driven by an endolysin that crosses the cytoplasmic membrane through a pore formed by holin oligomerization. We demonstrated that TcdE has a holin-like activity by functionally complementing a λ phage deprived of its holin. Similar to λ holin, TcdE expressed in Escherichia coli and C. difficile formed oligomers in the cytoplamic membrane. A C. difficile tcdE mutant strain grew at the same rate as the wild-type strain, but accumulated a dramatically reduced amount of toxin proteins in the medium. However, the complemented tcdE mutant released the toxins efficiently. There was no difference in the abundance of tcdA and tcdB transcripts or of several cytoplasmic proteins in the mutant and the wild-type strains. In addition, TcdE did not overtly affect membrane integrity of C. difficile in the presence of TcdA/TcdB. Thus, TcdE acts as a holin-like protein to facilitate the release of C. difficile toxins to the extracellular environment, but, unlike the phage holins, does not cause the non-specific release of cytosolic contents. TcdE appears to be the first example of a bacterial protein that releases toxins into the environment by a phage-like system

Over-prescription of short-acting β2-agonists for asthma in South Africa: Results from the SABINA III study

Background. Asthma medication prescription trends, including those of short-acting β2-agonists (SABAs), are not well documented for South Africa (SA). Objectives. To describe demographics, disease characteristics and asthma prescription patterns in the SA cohort of the SABA use IN Asthma (SABINA) III study. Methods. An observational, cross-sectional study conducted at 12 sites across SA. Patients with asthma (aged ≥12 years) were classified by investigator-defined asthma severity, guided by the Global Initiative for Asthma (GINA) 2017 recommendations, and practice type (primary/ specialist care). Data were collected using electronic case report forms. Results. Overall, 501 patients were analysed − mean (standard deviation) age, 48.4 (16.6) years; 68.3% female − of whom 70.6% and 29.4% were enrolled by primary care physicians and specialists, respectively. Most patients were classified with moderate-to-severe asthma (55.7%; GINA treatment steps 3 - 5), were overweight or obese (70.7%) and reported full healthcare reimbursement (55.5%). Asthma was partly controlled/uncontrolled in 60.3% of patients, with 46.1% experiencing ≥1 severe exacerbations in the 12 months before the study visit. Overall, 74.9% of patients were prescribed ≥3 SABA canisters in the previous 12 months (over-prescription); 56.5% were prescribed ≥10 SABA canisters. Additionally, 27.1% of patients reported purchasing SABA over-the-counter (OTC); among patients with both SABA purchase and prescriptions, 75.4% and 51.5% already received prescriptions for ≥3 and ≥10 SABA canisters, respectively, in the preceding 12 months. Conclusion. SABA over-prescription and OTC purchase were common in SA, demonstrating an urgent need to align clinical practices with the latest evidence-based recommendations and regulate SABA OTC purchase to improve asthma outcomes

Automated analysis of small intestinal lamina propria to distinguish normal, Celiac Disease, and Non-Celiac Duodenitis biopsy images

Background and objective Celiac Disease (CD) is characterized by gluten intolerance in genetically predisposed individuals. High disease prevalence, absence of a cure, and low diagnosis rates make this disease a public health problem. The diagnosis of CD predominantly relies on recognizing characteristic mucosal alterations of the small intestine, such as villous atrophy, crypt hyperplasia, and intraepithelial lymphocytosis. However, these changes are not entirely specific to CD and overlap with Non-Celiac Duodenitis (NCD) due to various etiologies. We investigated whether Artificial Intelligence (AI) models could assist in distinguishing normal, CD, and NCD (and unaffected individuals) based on the characteristics of small intestinal lamina propria (LP). Methods Our method was developed using a dataset comprising high magnification biopsy images of the duodenal LP compartment of CD patients with different clinical stages of CD, those with NCD, and individuals lacking an intestinal inflammatory disorder (controls). A pre-processing step was used to standardize and enhance the acquired images. Results For the normal controls versus CD use case, a Support Vector Machine (SVM) achieved an Accuracy (ACC) of 98.53%. For a second use case, we investigated the ability of the classification algorithm to differentiate between normal controls and NCD. In this use case, the SVM algorithm with linear kernel outperformed all the tested classifiers by achieving 98.55% ACC. Conclusions To the best of our knowledge, this is the first study that documents automated differentiation between normal, NCD, and CD biopsy images. These findings are a stepping stone toward automated biopsy image analysis that can significantly benefit patients and healthcare providers

The genetic basis of composite spike form in barley and "Miracle-Wheat"

Inflorescences of the tribe Triticeae, which includes wheat (Triticum sp. L.) and barley (Hordeum vulgare L.) are characterized by sessile spikelets directly borne on the main axis, thus forming a branchless spike. "Compositum-Barley" and tetraploid "Miracle-Wheat" (T. turgidum convar. compositum (L.f.) Filat.) display non-canonical spike-branching in which spikelets are replaced by lateral branch-like structures resembling small-sized secondary spikes. As a result of this branch formation "Miracle-Wheat" produces significantly more grains per spike, leading to higher spike yield. In this study, we first isolated the gene underlying spike-branching in "Compositum-Barley", i.e. compositum 2 (com2). Moreover, we found that COM2 is orthologous to the branched head(t) (bh(t)) locus regulating spike-branching in tetraploid "Miracle-Wheat". Both genes possess orthologs with similar functions in maize BRANCHED SILKLESS 1 (BD1) and rice FRIZZY PANICLE/BRANCHED FLORETLESS 1 (FZP/BFL1) encoding AP2/ERF transcription factors. Sequence analysis of the bh(t) locus in a collection of mutant and wild type tetraploid wheat accessions revealed that a single amino acid substitution in the DNA-binding domain gave rise to the domestication of "Miracle-Wheat". mRNA in situ hybridization, microarray experiments, and independent qRT-PCR validation analyses revealed that the branch repression pathway in barley is governed through the spike architecture gene Six-rowed spike 4 regulating COM2 expression, while HvIDS1 (barley ortholog of maize INDETERMINATE SPIKELET 1) is a putative down-stream target of COM2. These findings presented here provide new insights into the genetic basis of spike architecture in Triticeae, and have disclosed new targets for genetic manipulations aiming at boosting wheat's yield potential