Polarization and Charge Transfer in the Hydration of Chloride Ions

A theoretical study of the structural and electronic properties of the chloride ion and water molecules in the first hydration shell is presented. The calculations are performed on an ensemble of configurations obtained from molecular dynamics simulations of a single chloride ion in bulk water. The simulations utilize the polarizable AMOEBA force field for trajectory generation, and MP2-level calculations are performed to examine the electronic structure properties of the ions and surrounding waters in the external field of more distant waters. The ChelpG method is employed to explore the effective charges and dipoles on the chloride ions and first-shell waters. The Quantum Theory of Atoms in Molecules (QTAIM) is further utilized to examine charge transfer from the anion to surrounding water molecules. From the QTAIM analysis, 0.2 elementary charges are transferred from the ion to the first-shell water molecules. The default AMOEBA model overestimates the average dipole moment magnitude of the ion compared with the estimated quantum mechanical value. The average magnitude of the dipole moment of the water molecules in the first shell treated at the MP2 level, with the more distant waters handled with an AMOEBA effective charge model, is 2.67 D. This value is close to the AMOEBA result for first-shell waters (2.72 D) and is slightly reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment of the water molecules in the first solvation shell is most strongly affected by the local water-water interactions and hydrogen bonds with the second solvation shell, rather than by interactions with the ion.Comment: Slight revision, in press at J. Chem. Phy

Extending the phenotypic spectrum of Sengers syndrome: Congenital lactic acidosis with synthetic liver dysfunction.

Sengers syndrome is a rare autosomal recessive mitochondrial disease characterized by lactic acidosis, hypertrophic cardiomyopathy and bilateral cataracts. We present here a case of neonatal demise, within the first day of life, who initially presented with severe lactic acidosis, with evidence of both chorioamnionitis and cardiogenic shock. Initial metabolic labs demonstrated a severe lactic acidosis prompting genetic testing which revealed a homozygous pathogenic variant for Sengers syndrome i

Biochemistry of Autoinflammatory Diseases: Catalyzing Monogenic Disease

Monogenic autoinflammatory disorders are a group of conditions defined by systemic or localized inflammation without identifiable causes, such as infection. In contrast to classical primary immunodeficiencies that manifest with impaired immune responses, these disorders are due to defects in genes that regulate innate immunity leading to constitutive activation of pro-inflammatory signaling. Through studying patients with rare autoinflammatory conditions, novel mechanisms of inflammation have been identified that bare on our understanding not only of basic signaling in inflammatory cells, but also of the pathogenesis of more common inflammatory diseases and have guided treatment modalities. Autoinflammation has further been implicated as an important component of cardiovascular, neurodegenerative, and metabolic syndromes. In this review, we will focus on a subset of inherited enzymatic deficiencies that lead to constitutive inflammation, and how these rare diseases have provided insights into diverse areas of cell biology not restricted to immune cells. In this way, Mendelian disorders of the innate immune system, and in particular loss of catalytic activity of enzymes in distinct pathways, have expanded our understanding of the interplay between many seemingly disparate cellular processes. We also explore the overlap between autoinflammation, autoimmunity, and immunodeficiency, which has been increasingly recognized in patients with dysregulated immune responses

BOSS: Bayesian Optimization over String Spaces

This article develops a Bayesian optimization (BO) method which acts directly over raw strings, proposing the first uses of string kernels and genetic algorithms within BO loops. Recent applications of BO over strings have been hindered by the need to map inputs into a smooth and unconstrained latent space. Learning this projection is computationally and data-intensive. Our approach instead builds a powerful Gaussian process surrogate model based on string kernels, naturally supporting variable length inputs, and performs efficient acquisition function maximization for spaces with syntactical constraints. Experiments demonstrate considerably improved optimization over existing approaches across a broad range of constraints, including the popular setting where syntax is governed by a context-free grammar

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Leiomyosarcoma (LMS) is a soft tissue tumor with a significant degree of morphologic and molecular heterogeneity. We used integrative molecular profiling to discover and characterize molecular subtypes of LMS. Gene expression profiling was performed on 51 LMS samples. Unsupervised clustering showed three reproducible LMS clusters. Array comparative genomic hybridization (aCGH) was performed on 20 LMS samples and showed that the molecular subtypes defined by gene expression showed distinct genomic changes. Tumors from the muscle-enriched cluster showed significantly increased copy number changes (P=0.04). A majority of the muscle-enriched cases showed loss at 16q24, which contains Fanconi anemia, complementation group A, known to have an important role in DNA repair, and loss at 1p36, which contains PRDM16, of which loss promotes muscle differentiation. Immunohistochemistry (IHC) was performed on LMS tissue microarrays (n=377) for five markers with high levels of messenger RNA in the muscle-enriched cluster (ACTG2, CASQ2, SLMAP, CFL2 and MYLK) and showed significantly correlated expression of the five proteins (all pairwise P<0.005). Expression of the five markers was associated with improved disease-specific survival in a multivariate Cox regression analysis (P<0.04). In this analysis that combined gene expression profiling, aCGH and IHC, we characterized distinct molecular LMS subtypes, provided insight into their pathogenesis, and identified prognostic biomarkers

Bone morphogenetic protein-5 (BMP-5) promotes dendritic growth in cultured sympathetic neurons

BACKGROUND: BMP-5 is expressed in the nervous system throughout development and into adulthood. However its effects on neural tissues are not well defined. BMP-5 is a member of the 60A subgroup of BMPs, other members of which have been shown to stimulate dendritic growth in central and peripheral neurons. We therefore examined the possibility that BMP-5 similarly enhances dendritic growth in cultured sympathetic neurons. RESULTS: Sympathetic neurons cultured in the absence of serum or glial cells do not form dendrites; however, addition of BMP-5 causes these neurons to extend multiple dendritic processes, which is preceded by an increase in phosphorylation of the Smad-1 transcription factor. The dendrite-promoting activity of BMP-5 is significantly inhibited by the BMP antagonists noggin and follistatin and by a BMPR-IA-Fc chimeric protein. RT-PCR and immunocytochemical analyses indicate that BMP-5 mRNA and protein are expressed in the superior cervical ganglia (SCG) during times of initial growth and rapid expansion of the dendritic arbor. CONCLUSIONS: These data suggest a role for BMP-5 in regulating dendritic growth in sympathetic neurons. The signaling pathway that mediates the dendrite-promoting activity of BMP-5 may involve binding to BMPR-IA and activation of Smad-1, and relative levels of BMP antagonists such as noggin and follistatin may modulate BMP-5 signaling. Since BMP-5 is expressed at relatively high levels not only in the developing but also the adult nervous system, these findings suggest the possibility that BMP-5 regulates dendritic morphology not only in the developing, but also the adult nervous system

Quantum Monte Carlo Dynamics: the Stationary Phase Monte Carlo Path Integral Calculation of Finite Temperature Time Correlation Functions

We present a numerically exact procedure for the calculation of an important class of finite temperature quantum mechanical time correlation functions. The present approach is based around the stationary phase Monte Carlo (SPMC) method, a general mathematical tool for the calculation of high dimensional averages of oscillatory integrands. In the present context the method makes possible the direct numerical path integral calculation of real-time quantum dynamical quantities for times appreciably greater than the thermal time (βħ). Illustrative applications involving finite temperature anharmonic motion are presented. Issues of importance with respect to future applications are identified and discussed

IgG4-Related Disease Is Not Associated with Antibody to the Phospholipase A2 Receptor

Patients with IgG4-related disease (IgG4-RD) share histopathological characteristics that are similar across affected organs. The finding of infiltration with IgG4+ plasma cells in the proper clinical and histopathological contexts connects a large number of clinical entities that were viewed previously as separate conditions. The renal involvement in IgG4-RD is usually characterized by tubulointerstitial nephritis, but membranous nephropathy has also been reported to be one of the renal complications of IgG4-RD. The recent discovery that a high proportion of patients with idiopathic membranous nephropathy (IMN) have IgG4 autoantibodies to the M-type phospholipase A2 receptor (PLA2R) in the circulation and glomerular immune deposits, together with the profound IgG4 hypergammaglobulinemia and occasional reports of membranous nephropathy in IgG4-RD, raised the question of a common antigen. To assess the presence of anti-PLA2R antibody in patients with IgG4-RD, we screened sera from 28 IgG4-RD patients by immunoblot. None of the patients in this cohort had detectable circulating anti-PLA2R antibodies. This study suggests that despite some clinical and serological overlaps between IgG4-RD and IMN,anti-PLA2R antibodies do not play a role in the pathogenesis of IgG4-RD. Additional studies of IgG4-RD with evidence of membranous nephropathy are important to exclude any definite relationship

The association between care co-ordination and emergency department use in older managed care enrollees

OBJECTIVE: To investigate the association between care co-ordination and use of the Emergency Department (ED) in older managed care enrollees. DESIGN: Nested case-control with 103 cases (used the ED) and 194 controls (did not use the ED). PATIENTS AND METHODS: Older patients with multiple chronic illnesses enrolled in a care management programme of a large group-model health maintenance organisation with more than 50,000 members over the age of 64. Better care co-ordination was defined as timely follow-up after a change in treatment; fewer decision-makers involved with the care plan; and a higher patient-perceived rating of overall care co-ordination. Logistic regression was used to assess the relationship between ED use (the outcome variable) and measures of care co-ordination (the predictor variables). RESULTS: Self-reported care co-ordination was not significantly different between cases and controls for any of the four classifications of inappropriate ED use. Similarly, no differences were found in the number of different physicians or medication prescribers involved in the patients' care. Four-week follow-up after potentially high-risk events for subsequent ED use, including changes in chronic disease medications, missed encounters, and same day encounters, did not differ between subjects with inappropriate ED use and controls. CONCLUSION: Existing measures of care co-ordination were not associated with inappropriate ED use in this study of older adults with complex care needs. The absence of an association may, in part, be attributable to the paucity of validated measures to assess care co-ordination, as well as the methodological complexity inherent in studying this topic. Future research should focus on the development of new measures and on approaches that better isolate the role of care co-ordination from other potential variables that influence utilisation