Toward Accurate Quantum Mechanical Thermochemistry: (1) Extensible Implementation and Comparison of Bond Additivity Corrections and Isodesmic Reactions.

Obtaining accurate enthalpies of formation of chemical species, ΔHf, often requires empirical corrections that connect the results of quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state. One approach is to use atomization energy corrections followed by bond additivity corrections (BACs), such as those defined by Petersson et al. or Anantharaman and Melius. Another approach is to utilize isodesmic reactions (IDRs) as shown by Buerger et al. We implement both approaches in Arkane, an open-source software that can calculate species thermochemistry using results from various QM software packages. In this work, we collect 421 reference species from the literature to derive ΔHf corrections and fit atomization energy corrections and BACs for 15 commonly used model chemistries. We find that both types of BACs yield similar accuracy, although Anantharaman- and Melius-type BACs appear to generalize better. Furthermore, BACs tend to achieve better accuracy than IDRs for commonly used model chemistries, and IDRs can be less robust because of the sensitivity to the chosen reference species and reactions. Overall, Anantharaman- and Melius-type BACs are our recommended approach for achieving accurate QM corrections for enthalpies.

RMG Database for Chemical Property Prediction.

The Reaction Mechanism Generator (RMG) database for chemical property prediction is presented. The RMG database consists of curated datasets and estimators for accurately predicting the parameters necessary for constructing a wide variety of chemical kinetic mechanisms. These datasets and estimators are mostly published and enable prediction of thermodynamics, kinetics, solvation effects, and transport properties. For thermochemistry prediction, the RMG database contains 45 libraries of thermochemical parameters with a combination of 4564 entries and a group additivity scheme with 9 types of corrections including radical, polycyclic, and surface absorption corrections with 1580 total curated groups and parameters for a graph convolutional neural network trained using transfer learning from a set of >130 000 DFT calculations to 10 000 high-quality values. Correction schemes for solvent-solute effects, important for thermochemistry in the liquid phase, are available. They include tabulated values for 195 pure solvents and 152 common solutes and a group additivity scheme for predicting the properties of arbitrary solutes. For kinetics estimation, the database contains 92 libraries of kinetic parameters containing a combined 21 000 reactions and contains rate rule schemes for 87 reaction classes trained on 8655 curated training reactions. Additional libraries and estimators are available for transport properties. All of this information is easily accessible through the graphical user interface at https://rmg.mit.edu. Bulk or on-the-fly use can be facilitated by interfacing directly with the RMG Python package which can be installed from Anaconda. The RMG database provides kineticists with easy access to estimates of the many parameters they need to model and analyze kinetic systems. This helps to speed up and facilitate kinetic analysis by enabling easy hypothesis testing on pathways, by providing parameters for model construction, and by providing checks on kinetic parameters from other sources.

Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation.

In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. Most notably, RMG can now generate heterogeneous catalysis models in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release includes parallelization for faster model generation and a new molecule isomorphism approach to improve computational performance. RMG has also been updated to use Python 3, ensuring compatibility with the latest cheminformatics and machine learning packages. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.

Inducing remission in paediatric Crohn's disease using nutritional therapies - A systematic review.

BACKGROUND: Exclusive enteral nutrition (EEN) is known to be a safe and effective treatment option for managing active Crohn's disease (CD) in children, although no uniform protocol exists. The aim of this systematic review was to evaluate and compare the clinical effectiveness of aspects of EEN protocols to ascertain whether an optimum regimen can be identified. METHODS: A systematic search of the Cochrane Library, PubMed, MEDLINE, EMBASE, CINAHL and AMED was conducted for studies published between 1998 and 2018 that examined paediatric patients being treated with an enteral nutrition protocol to induce remission. Studies that included patients receiving concurrent medication for active disease were excluded. Quality assessment was performed using separate tools for randomised controlled trials, cohort studies and for studies without a control group. RESULTS: Sixteen studies met the inclusion criteria. Of these, six found insufficient evidence to support use of a specific formula. One study examined the route of EEN, finding no difference between oral or nasogastric tube administration with respect to inducing remission. Three examined the use of partial enteral nutrition to induce remission, although conflicting results were seen. No studies explored the effect of length of treatment or energy prescription on remission rates CONCLUSIONS: An optimum enteral nutrition protocol for inducing remission cannot be identified. Further focused research is required by well designed, adequately powered prospective clinical trials to examine aspects of enteral feeding protocols that remain uncertain, including the use of partial enteral nutrition as a potential alternative to EEN.

The reliability of the Cutaneous Dermatomyositis Disease Area and Severity Index (CDASI) among dermatologists, rheumatologists and neurologists.

BACKGROUND: Previous studies have shown that skin disease in dermatomyositis (DM) is best assessed using the Cutaneous Dermatomyositis Disease Area and Severity Index (CDASI). Although the CDASI has been validated for use by dermatologists, it has not been validated for use by other physicians such as rheumatologists and neurologists, who also manage patients with DM and assess skin activity in clinical trials. OBJECTIVES: To assess the reliability of the CDASI among dermatologists, rheumatologists and neurologists. METHODS: Fifteen patients with cutaneous DM were assessed using the CDASI and the Physician Global Assessment (PGA) by five dermatologists, five rheumatologists and five neurologists. RESULTS: The mean CDASI activity scores for dermatologists, rheumatologists and neurologists were 21·0, 21·8 and 20·8, respectively. These mean scores were not different among the specialists. The CDASI damage score means for dermatologists, rheumatologists and neurologists were 5·3, 7·0 and 4·8, respectively. The mean scores between dermatologists and rheumatologists were significantly different, but the means between dermatologists and neurologists were not. The intraclass correlation coefficients (ICCs) for interrater reliability for CDASI activity and damage were good to excellent for dermatologists and rheumatologists, and moderate to excellent for neurologists. The ICCs for intrarater reliability for CDASI activity and damage were excellent for dermatologists and rheumatologists and moderate to excellent for neurologists. The PGA displayed lower interrater and intrarater reliability relative to the CDASI. CONCLUSIONS: Our results confirm the reliability of the CDASI when used by dermatologists and rheumatologists. The data for its use by neurologists were not as robust.

Adrenal medulla of AS/AGU rats: a histological and immunohistochemical study.

BACKGROUND: The outcome of the autograft therapy for Parkinson's disease including autologous cells from adrenal medulla was disappointing. This could be attributed to the pathological process in Parkinson's disease affecting cells of the adrenal medulla. This study was performed to investigate the histopathological changes in the adrenal medulla of AS/AGU rat, a model of Parkinson's disease, in comparison with Albino Swiss (AS) rats. MATERIALS AND METHODS: A total of 24 male AS rats were divided into four groups, each of 6 animals: AS W1 - AS rats aged 1 week; AS adult - AS adult rats; AS/ /AGU W1 - AS/AGU rats aged 1 week; and AS/AGU adult - AS/AGU adult rats. The rats were sacrificed and the adrenal glands were dissected and processed for histological staining with haematoxylin and eosin and periodic acid Schiff and for immunohistochemical staining for S100 protein, ubiquitin and tyrosine hydroxylase. RESULTS: The histological investigation of the adrenal medulla of AS/AGU rats showed vascular congestion, inflammatory cellular infiltration, pyknotic nuclei, necrotic chromaffin cells and medullary inclusion bodies. The immunohistochemical investigation of AS/AGU rats showed a statistically significant decrease in the expression of S100 protein, ubiquitin and tyrosine hydroxylase compared to AS rats. CONCLUSIONS: The histological and immunohistological changes in the adrenal medulla could explain the failure of outcome of adrenal autograft therapy in Parkinson's disease.

Xenogeneic collagen matrix for periodontal plastic surgery procedures: a systematic review and meta-analysis.

Several clinical trials describe the effectiveness of xenogeneic collagen matrix (XCM) as an alternative option to surgical mucogingival procedures for the treatment of marginal tissue recession and augmentation of insufficient zones of keratinized tissue (KT). The aim of this systematic review and meta-analysis was to evaluate the clinical and patient-centred outcomes of XCM compared to other mucogingival procedures. Applying guidelines of the Preferred Reporting Items for Systematic Reviews and Meta analyses statement, randomized controlled trials were searched for in electronic databases and complemented by hand searching. The risk of bias was assessed using the Cochrane Collaboration's Risk of Bias tool and data were analysed using statistical software. A total of 645 studies were identified, of which, six trials were included with 487 mucogingival defects in 170 participants. Overall meta-analysis showed that connective tissue graft (CTG) in conjunction with the coronally advanced flap (CAF) had a significantly higher percentage of complete/mean root coverage and mean recession reduction than XCM. Insufficient evidence was found to determine any significant differences in width of KT between XCM and CTG. The XCM had a significantly higher mean root coverage, recession reduction and gain in KT compared to CAF alone. No significant differences in patient's aesthetic satisfaction were found between XCM and CTG, except for postoperative morbidity in favour of XCM. Operating time was significantly reduced with the use of XCM compared with CTG but not with CAF alone. There is no evidence to demonstrate the effectiveness of XCM in achieving greater root coverage, recession reduction and gain in KT compared to CTG plus CAF. Superior short-term results in treating root coverage compared with CAF alone are possible. There is limited evidence that XCM may improve aesthetic satisfaction, reduce postoperative morbidity and shorten the operating time. Further long-term randomized controlled trials are required to endorse the supposed advantages of XCM.

First molecular detection of Mycobacterium bovis in environmental samples from a French region with endemic bovine tuberculosis.

AIMS: The aim of the study was to determine the prevalence of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in environmental matrices within a French region (Côte d'Or) affected by this zoonotic disease. METHODS AND RESULTS: We report here the development and the use of molecular detection assays based on qPCR (double fluorescent dye-labelled probe) to monitor the occurrence of Mycobacterium tuberculosis complex (MTBC) or Myco. bovis in environmental samples collected in pastures where infected cattle and wildlife had been reported. Three qPCR assays targeting members of the MTBC (IS1561' and Rv3866 loci) or Myco. bovis (RD4 locus) were developed or refined from existing assays. These tools were validated using Myco. bovis spiked soil, water and faeces samples. Environmental samples were detected positive for the presence of MTBC strains and Myco. bovis in the environment of bTB-infected farms in the Côte d'Or region. CONCLUSIONS: The development of molecular assays permitted testing of several types of environmental samples including spring water, sediment samples and soils from badger setts entrance located in the vicinity of these farms, which were repeatedly contaminated with Myco. bovis (up to 8·7 × 10(3) gene copies per gram of badger sett soil). For the first time, direct spoligotyping of soil DNA enabled identification of Myco. bovis genotypes from environmental matrices. SIGNIFICANCE AND IMPACT OF THE STUDY: All together, these results suggest that Myco. bovis occurs at low levels in environmental matrices in Côte d'Or within the bTB-infected area. Drinking contaminated water or inhaling contaminated bioaerosols might explain cattle infection in some cases.

Lysine mediation of neuroendocrine food regulation in guinea fowl.

In poultry, obesity is partly influenced by food intake, and is increasingly becoming a nationwide problem. Hypothalamic food intake mechanisms are involved metabolically and neurologically via two peptide hormones, leptin and ghrelin, and the amino acid glutamate, which is enzymatically derived from lysine metabolism. We hypothesize that lysine homeostasis mediates regulation of feed intake and performance characteristics via the brain-liver axis through glutamate sensing. The objective was to examine the effects of lysine homeostasis in avian food regulation and performance through neuroendocrine signaling. One-day-old male French Guinea fowl (GF) keets (n = 270) were weighed and randomly assigned to 5 dietary treatments (0.80%, 0.86%, 0.92%, 1.10% control, and 1.22% lysine) in 3 replicates. At 4 and 8 wk of age 20% of experimental birds were randomly selected, weighed and euthanatized. The liver, pancreas, and hypothalamus were excised, snap frozen in liquid nitrogen and stored at -80°C until use. Tissue mRNA was extracted and cDNA synthesized for qPCR assays. Lysine at 0.80 and 0.86% hindered growth, development of digestive organs, expression of brain and liver glutamate and leptin receptors, and caused high mortality in GF. The fold change for metabotropic glutamate receptor I was lower (P < 0.05) in liver and higher in brain at 0.86 and 0.92% than the control (1.10%) and 1.22% lysine. The 1.22% lysine exhibited highest expression of ionotropic glutamate receptor, while brain ghrelin receptor expression was highest at 0.86 and 0.92% lysine. Therefore, dietary lysine concentration may influence signaling pathways regulating food intake in brain-liver axis via glutamate synthesis.

A study of prospective surveillance for inhibitors among persons with haemophilia in the United States.

Inhibitors are a rare but serious complication of treatment of patients with haemophilia. Phase III clinical trials enrol too few patients to adequately assess new product inhibitor risk. This project explores the feasibility of using a public health surveillance system to conduct national surveillance for inhibitors. Staff at 17 U.S. haemophilia treatment centres (HTC) enrolled patients with haemophilia A and B into this prospective study. HTC staff provided detailed historic data on product use and inhibitors at baseline, and postenrolment patients provided monthly detailed infusion logs. A central laboratory performed inhibitor tests on blood specimens that were collected at baseline, annually, prior to any planned product switch or when clinically indicated. The central laboratory also performed genotyping of all enrolled patients. From January 2006 through June 2012, 1163 patients were enrolled and followed up for 3329 person-years. A total of 3048 inhibitor tests were performed and 23 new factor VIII inhibitors were identified, 61% of which were not clinically apparent. Infusion logs were submitted for 113,205 exposure days. Genotyping revealed 431 distinct mutations causing haemophilia, 151 of which had not previously been reported elsewhere in the world. This study provided critical information about the practical issues that must be addressed to successfully implement national inhibitor surveillance. Centralized testing with routine monitoring and confirmation of locally identified inhibitors will provide valid and representative data with which to evaluate inhibitor incidence and prevalence, monitor trends in occurrence rates and identify potential inhibitor outbreaks associated with products.

An exploratory study of positive and incongruent communication in young children with type 1 diabetes and their mothers.

BACKGROUND: The incidence of type 1 diabetes is increasing in young children. However, they are overlooked in treatment adherence and intervention research despite evidence that parents often experience difficulty securing their treatment cooperation, especially with the diet. We investigated positive and incongruent (i.e. the co-occurrence of contradictory verbal and non-verbal messages) communication in the mother-child dyad and their association with child adjustment and dietary adherence outcomes. METHODS: Participants were 23 6- to 8-year-old children with type 1 diabetes and their mothers. We conducted dietary adherence interviews with mothers and performed nutritional analyses to assess children's consumption of extrinsic sugars (e.g. confectionary). Mothers completed a standardized assessment of child psychological adjustment. Mothers and children engaged in a videotaped problem-solving task related to the dietary regimen, with maternal and child utterances and non-verbal behaviours analysed for positive dyadic and incongruent communication. RESULTS: Positive dyadic communication correlated with lower levels of child incongruent communication, fewer behavioural problems and better overall adjustment. Higher levels of maternal and child incongruent communication correlated with more behavioural and emotional problems and poorer overall adjustment. Higher levels of maternal incongruent communication correlated with poorer dietary adherence. CONCLUSIONS: Results converged to form a conceptually and empirically coherent pattern in that behavioural indices of poorer communication in both mother and child consistently correlated with poorer child adjustment outcomes. This study shows that specific features of dyadic, child and maternal communication could be targeted in developmentally sensitive interventions to promote positive communication in the home management of type 1 diabetes care for young children.

An 11-channel radio frequency phased array coil for magnetic resonance guided high-intensity focused ultrasound of the breast.

In this study, a radio frequency phased array coil was built to image the breast in conjunction with a magnetic resonance guided high-intensity focused ultrasound (MRgHIFU) device designed specifically to treat the breast in a treatment cylinder with reduced water volume. The MRgHIFU breast coil was comprised of a 10-channel phased array coil placed around an MRgHIFU treatment cylinder where nearest-neighbor decoupling was achieved with capacitive decoupling in a shared leg. In addition a single loop coil was placed at the chest wall making a total of 11 channels. The radio frequency coil array design presented in this work was chosen based on ease of implementation, increased visualization into the treatment cylinder, image reconstruction speed, temporal resolution, and resulting signal-to-noise ratio profiles. This work presents a dedicated 11-channel coil for imaging of the breast tissue in the MRgHIFU setup without obstruction of the ultrasound beam and, specifically, compares its performance in signal-to-noise, overall imaging time, and temperature measurement accuracy to that of the standard single chest-loop coil typically used in breast MRgHIFU.

Decontamination of materials contaminated with Bacillus anthracis and Bacillus thuringiensis Al Hakam spores using PES-Solid, a solid source of peracetic acid.

AIMS: To develop test methods and evaluate survival of Bacillus anthracis Ames, B. anthracis ∆Sterne and B. thuringiensis Al Hakam spores after exposure to PES-Solid (a solid source of peracetic acid), including PES-Solid formulations with bacteriostatic surfactants. METHODS AND RESULTS: Spores (≥ 7 logs) were dried on seven different test materials and treated with three different PES-Solid formulations (or preneutralized controls) at room temperature for 15 min. There was either no spore survival or less than 1 log (<10 spores) of spore survival in 56 of 63 test combinations (strain, formulation and substrate). Less than 2.7 logs (<180 spores) survived in the remaining seven test combinations. The highest spore survival rates were seen on water-dispersible chemical agent resistant coating (CARC-W) and Naval ship topcoat (NTC). Electron microscopy and Coulter analysis showed that all spore structures were intact after spore inactivation with PES-Solid. CONCLUSIONS: Three PES-Solid formulations inactivated Bacillus spores that were dried on seven different materials. SIGNIFICANCE AND IMPACT OF THE STUDY: A test method was developed to show that PES-Solid formulations effectively inactivate Bacillus spores on different materials.

Mutations in a new photoreceptor-pineal gene on 17p cause Leber congenital amaurosis.

Leber congenital amaurosis (LCA, MIM 204000) accounts for at least 5% of all inherited retinal disease and is the most severe inherited retinopathy with the earliest age of onset. Individuals affected with LCA are diagnosed at birth or in the first few months of life with severely impaired vision or blindness, nystagmus and an abnormal or flat electroretinogram (ERG). Mutations in GUCY2D (ref. 3), RPE65 (ref. 4) and CRX (ref. 5) are known to cause LCA, but one study identified disease-causing GUCY2D mutations in only 8 of 15 families whose LCA locus maps to 17p13.1 (ref. 3), suggesting another LCA locus might be located on 17p13.1. Confirming this prediction, the LCA in one Pakistani family mapped to 17p13.1, between D17S849 and D17S960-a region that excludes GUCY2D. The LCA in this family has been designated LCA4 (ref. 6). We describe here a new photoreceptor/pineal-expressed gene, AIPL1 (encoding aryl-hydrocarbon interacting protein-like 1), that maps within the LCA4 candidate region and whose protein contains three tetratricopeptide (TPR) motifs, consistent with nuclear transport or chaperone activity. A homozygous nonsense mutation at codon 278 is present in all affected members of the original LCA4 family. AIPL1 mutations may cause approximately 20% of recessive LCA, as disease-causing mutations were identified in 3 of 14 LCA families not tested previously for linkage.

Mutations in a human homologue of Drosophila crumbs cause retinitis pigmentosa (RP12).

Retinitis pigmentosa (RP) comprises a clinically and genetically heterogeneous group of diseases that afflicts approximately 1.5 million people worldwide. Affected individuals suffer from a progressive degeneration of the photoreceptors, eventually resulting in severe visual impairment. To isolate candidate genes for chorioretinal diseases, we cloned cDNAs specifically or preferentially expressed in the human retina and the retinal pigment epithelium (RPE) through a novel suppression subtractive hybridization (SSH) method. One of these cDNAs (RET3C11) mapped to chromosome 1q31-q32.1, a region harbouring a gene involved in a severe form of autosomal recessive RP characterized by a typical preservation of the para-arteriolar RPE (RP12; ref. 3). The full-length cDNA encodes an extracellular protein with 19 EGF-like domains, 3 laminin A G-like domains and a C-type lectin domain. This protein is homologous to the Drosophila melanogaster protein crumbs (CRB), and denoted CRB1 (crumbs homologue 1). In ten unrelated RP patients with preserved para-arteriolar RPE, we identified a homozygous AluY insertion disrupting the ORF, five homozygous missense mutations and four compound heterozygous mutations in CRB1. The similarity to CRB suggests a role for CRB1 in cell-cell interaction and possibly in the maintenance of cell polarity in the retina. The distinct RPE abnormalities observed in RP12 patients suggest that CRB1 mutations trigger a novel mechanism of photoreceptor degeneration.