Building Water Models, A Different Approach

Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despite several decades of effort, these models are still far from perfect. Presented here is an alternative approach to constructing point charge water models - currently, the most commonly used type. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than symmetry. Instead, we optimize the distribution of point charges to best describe the "electrostatics" of the water molecule, which is key to many unusual properties of liquid water. The search for the optimal charge distribution is performed in 2D parameter space of key lowest multipole moments of the model, to find best fit to a small set of bulk water properties at room temperature. A virtually exhaustive search is enabled via analytical equations that relate the charge distribution to the multipole moments. The resulting "optimal" 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk water properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures, well outside the ambient conditions at which the fit to experiment was performed. The improvements in the proposed water model extend beyond bulk properties: compared to the common rigid models, predicted hydration free energies of small molecules in OPC water are uniformly closer to experiment, root-mean-square error < 1kcal/mol

Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions

We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior of the approximate potential. A general framework for numerically computing OPCA, for any given number of approximating charges, is described. We then derive a 2-charge practical point charge approximation, PPCA, which approximates the 2-charge OPCA via closed form analytical expressions, and test the PPCA on a set of charge distributions relevant to biomolecular modeling. We measure the accuracy of the new approximations as the RMS error in the electrostatic potential relative to that produced by the original charge distribution, at a distance the extent of the charge distribution–the mid-field. The error for the 2-charge PPCA is found to be on average 23% smaller than that of optimally placed point dipole approximation, and comparable to that of the point quadrupole approximation. The standard deviation in RMS error for the 2-charge PPCA is 53% lower than that of the optimal point dipole approximation, and comparable to that of the point quadrupole approximation. We also calculate the 3-charge OPCA for representing the gas phase quantum mechanical charge distribution of a water molecule. The electrostatic potential calculated by the 3-charge OPCA for water, in the mid-field (2.8 Å from the oxygen atom), is on average 33.3% more accurate than the potential due to the point multipole expansion up to the octupole order. Compared to a 3 point charge approximation in which the charges are placed on the atom centers, the 3-charge OPCA is seven times more accurate, by RMS error. The maximum error at the oxygen-Na distance (2.23 Å ) is half that of the point multipole expansion up to the octupole order

Speed of light in the extended gravity theories

We shall investigate the possibility of formulation of varying speed of light (VSL) in the framework of Palatini non-linear Ricci scalar and Ricci squared theories. Different speeds of light including the causal structure constant, electromagnetic, and gravitational wave speeds are discussed. We shall see that two local frames are distinguishable and discuss about the velocity of light in these two frames. We shall investigate which one of these local frames is inertial.Comment: 19 pages. to appear in Classical Quantum Gravit

Low Compute and Fully Parallel Computer Vision with HashMatch

Numerous computer vision problems such as stereo depth estimation, object-class segmentation and fore-ground/background segmentation can be formulated as per-pixel image labeling tasks. Given one or many images as input, the desired output of these methods is usually a spatially smooth assignment of labels. The large amount of such computer vision problems has lead to significant research efforts, with the state of art moving from CRF-based approaches to deep CNNs and more recently, hybrids of the two. Although these approaches have significantly advanced the state of the art, the vast majority has solely focused on improving quantitative results and are not designed for low-compute scenarios. In this paper, we present a new general framework for a variety of computer vision labeling tasks, called HashMatch. Our approach is designed to be both fully parallel, i.e. each pixel is independently processed, and low-compute, with a model complexity an order of magnitude less than existing CNN and CRF-based approaches. We evaluate HashMatch extensively on several problems such as disparity estimation, image retrieval, feature approximation and background subtraction, for which HashMatch achieves high computational efficiency while producing high quality results

Autologous cricoid cartilage as a graft for airway reconstruction in an emergent technique - A case report

Introduction: Laryngotracheal stenosis can be caused after traumatic injuries to the neck from the subglottic larynx to the trachea. Patients with laryngotracheal stenosis often need a tracheotomy and occasionally may become tracheotomy dependent. Different procedures have been described for the management of these lesions. Management options include techniques of endoscopic dilation, laser resection, laryngo-fissure, and an innovative array of plastic reconstructions with or without the use of stents. Case Report: This paper presents airway reconstruction in a young patient with severe subglottic stenosis due to a blunt trauma to the neck, who was treated using particles of an autologous fractured cricoid cartilage as the source for airway augmentation. An incision was made in the anterior midline of the cricoid lamina and deepened through the scar tissue to the posterior cricoid lamina. Then two lateral incisions (right&left) were made in the cricoid lamina and fractured cartilage particles and the scar tissue were removed via these two lateral incisions. The mucosal lining at the right and left of the midline incision, after debulking, were sutured to a lateral position. Thereafter three cartilage particles were used to reconstruct the anterior cricoid lamina and augment the lumen. Conclusion: It is worth to mention that an autologus cartilage graft can be used for certain cases with traumatic airway stenosis. Further follow up and more patients are needed to approve this method of reconstructive surgery in emergent situations

Exploring conserved mRNA-miRNA interactions in colon and lung cancers

Aim: The main goal of this analysis was prioritization of co-expressed genes and miRNAs that are thought to have important influences in the pathogenesis of colon and lung cancers. Background: MicroRNAs (miRNAs) as small and endogenous noncoding RNAs which regulate gene expression by repressing mRNA translation or decreasing stability of mRNAs; they have proven pivotal roles in different types of cancers. Accumulating evidence indicates the role of miRNAs in a wide range of biological processes from oncogenesis and tumor suppressors to contribution to tumor progression. Colon and lung cancers are frequently encountered challenging types of cancers; therefore, exploring trade-off among underlying biological units such as miRNA with mRNAs will probably lead to identification of promising biomarkers involved in these malignancies. Methods: Colon cancer and lung cancer expression data were downloaded from Firehose and TCGA databases and varied genes extracted by DCGL software were subjected to build two gene regulatory networks by parmigene R package. Afterwards, a network-driven integrative analysis was performed to explore prognosticates genes, miRNAs and underlying pathways. Results: A total of 192 differentially expressed miRNAs and their target genes within gene regulatory networks were derived by ARACNE algorithm. BTF3, TP53, MYC, CALR, NEM2, miR-29b-3p and miR-145 were identified as bottleneck nodes and enriched via biological gene ontology (GO) terms and pathways chiefly in biosynthesis and signaling pathways by further screening. Conclusion: Our study uncovered correlated alterations in gene expression that may relate with colon and lung cancers and highlighted the potent common biomarker candidates for the two diseases

Conforming to accreditation in Iranian hospitals

This paper examines the operation of an accreditation programme for hospitals in Iran. It explores the process of accreditation as a regulatory control system and analyses hospitals’ responses to this type of control. We draw on the notion of steering and argue that the accreditation system is transactional in nature. Our findings show that hospitals conform to the scheme, although they also resist some of its requirements. On a wider policy level, we suggest that accreditations offer the accreditor the opportunity to impact on how activities are undertaken, but hospitals require incentives in order to make the necessary organisational changes

Contovir - A new adjuvant therapy in recurrent respiratory papillomatosis: A case study

Background: Contovir is a mixture of herbal extracts (Tanacetum vulgare, Rossa canina, Urtica dioica) that is supplemented with selenium. Objectives: This study aimed to add Contovir to the classic treatment of recurrent respiratory papillomatosis (RRP) in order to decrease the severity and extent of the disease, elongate the surgical intervals and improve the sense of patient well-being. Furthermore, we had to adjust the prescribed drug dosage, since there were no previous findings available. Patients and Methods: This is a case study of RRP patients treated with Contovir as an adjuvant to the classic treatment, from March 2011 to February 2013, at an academic tertiary hospital (Rasoul-e-Akram hospital). All patients underwent surgical removal of papilloma and then were prescribed Contovir. Disease severity was quantified based on Derkay�s staging system. Results: Eight patients were enrolled in this study. The extent and severity of the disease improved in six cases. One had no response, and the severity of disease increased in one patient. Patients with supraglottic lesions had better responses to Contovir adjuvant therapy. No immediate or long-term side effects were reported. Conclusions: Although Contovir has been found to be an advantageous adjuvant for RRP treatment, further studies are called for to verify these findings. © 2016, Iranian Red Crescent Medical Journal