Restrictions on the Material Coefficients in the Constitutive Theories for Non-Classical Viscous Fluent Continua

This paper considers conservation and balance laws and the constitutive theo-ries for non-classical viscous fluent continua without memory, in which in-ternal rotation rates due to the velocity gradient tensor are incorporated in the thermodynamic framework. The constitutive theories for the deviatoric part of the symmetric Cauchy stress tensor and the Cauchy moment tensor are de-rived based on integrity. The constitutive theories for the Cauchy moment tensor are considered when the balance of moments of moments 1) is not a balance law and 2) is a balance law. The constitutive theory for heat vector based on integrity is also considered. Restrictions on the material coefficients in the constitutive theories for the stress tensor, moment tensor, and heat vector are established using the conditions resulting from the entropy inequa-lity, keeping in mind that the constitutive theories derived here based on inte-grity are in fact nonlinear constitutive theories. It is shown that in the case of the simplest linear constitutive theory for stress tensor used predominantly for compressible viscous fluids, Stokes’ hypothesis or Stokes’ assumption has no thermodynamic basis, hence may be viewed incorrect. Thermodynamically consistent derivations of the restrictions on various material coefficients are presented for non-classical as well as classical theories that are applicable to nonlinear constitutive theories, which are inevitable if the constitutive theo-ries are derived based on integrity

Ascorbic Acid is an Abettor in Calcium Urolithiasis: An Experimental Study

Two sets of animal experiments using guinea pigs were planned to evaluate the effect of ascorbic acid supplementation on the lithogenic process. In the first set of experiments, 10, 40, and 60 mg doses of ascorbic acid/100g body weight/day were given for 105 days. Neither of the ascorbic acid doses given induced crystalluria, calcification or stone formation, thereby confirming our previous findings that ascorbic acid in the doses used by clinicians does not cause urolith formation. In the second set of experiments, ascorbic acid was supplemented in hypercalciuric (induced by calcium carbonate feeding) and hyperoxaluric (induced by sodium oxalate feeding) animals for 45 days. The results indicated that it exacerbated the calcification process in renal and bladder tissue

Si nanoparticle interfaces in Si/SiO2 solar cell materials

Novel solar cell materials consisting of Si nanoparticles embedded in SiO2 layers have been studied using positron annihilation spectroscopy in Doppler broadening mode and photoluminescence. Two positron-trapping interface states are observed after high temperature annealing at 1100 °C. One of the states is attributed to the (SiO2/Si bulk) interface and the other to the interface between the Si nanoparticles and SiO2. A small reduction in positron trapping into these states is observed after annealing the samples in N2 atmosphere with 5% H2. Enhanced photoluminescence is also observed from the samples following this annealing step.Peer reviewe

Automated design of DNA origami

Peer reviewe

Diagnostic algorithm for children presenting with epilepsia partialis continua

Objective: To characterize a cohort of children with epilepsia partialis continua (EPC) and develop a diagnostic algorithm incorporating key differential diagnoses. / Methods: Children presenting with EPC to a tertiary pediatric neurology center between 2002 and 2019 were characterized. / Results: Fifty‐four children fulfilled EPC criteria. Median age at onset was 7 years (range 0.6‐15), with median follow‐up of 4.3 years (range 0.2‐16). The diagnosis was Rasmussen encephalitis (RE) in 30 of 54 (56%), a mitochondrial disorder in 12 of 54 (22.2%), and magnetic resonance imaging (MRI) lesion‐positive focal epilepsy in 6 of 54 (11.1%). No diagnosis was made in 5 of 54 (9%). Children with mitochondrial disorders developed EPC earlier; each additional year at presentation reduced the odds of a mitochondrial diagnosis by 26% (P = .02). Preceding developmental concerns (odds ratio [OR] 22, P < .001), no seizures prior to EPC (OR 22, P < .001), bilateral slowing on electroencephalogram (EEG) (OR 26, P < .001), and increased cerebrospinal fluid (CSF) protein level (OR 16) predicted a mitochondrial disorder. Asymmetry or hemiatrophy was evident on MRI at presentation with EPC in 18 of 30 (60%) children with RE, and in the remainder at a median of 6 months (range 3‐15) after EPC onset. The first diagnostic test is brain MRI. Hemiatrophy may permit a diagnosis of RE with unilateral clinical and EEG findings. For children in whom a diagnosis of RE cannot be made on first scan but the clinical and radiological presentation resembles RE, repeat imaging every 6 months is recommended to detect progressive unicortical hemiatrophy, and brain biopsy should be considered. Evidence of intrathecal inflammation (oligoclonal bands and raised neopterin) can be supportive. In children with bihemispheric EPC, rapid polymerase gamma testing is recommended and if negative, sequencing mtDNA and whole‐exome sequencing on blood‐derived DNA should be performed. / Significance: Children presenting with EPC due to a mitochondrial disorder show clinical features distinguishing them from RE and structural epilepsies. A diagnostic algorithm for children with EPC will allow targeted investigation and timely diagnosis

From START to FINISH : the influence of osmotic stress on the cell cycle

Peer reviewedPublisher PD

Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks

<p>Abstract</p> <p>Background</p> <p>A reverse engineering of gene regulatory network with large number of genes and limited number of experimental data points is a computationally challenging task. In particular, reverse engineering using linear systems is an underdetermined and ill conditioned problem, i.e. the amount of microarray data is limited and the solution is very sensitive to noise in the data. Therefore, the reverse engineering of gene regulatory networks with large number of genes and limited number of data points requires rigorous optimization algorithm.</p> <p>Results</p> <p>This study presents a novel algorithm for reverse engineering with linear systems. The proposed algorithm is a combination of the orthogonal least squares, second order derivative for network pruning, and Bayesian model comparison. In this study, the entire network is decomposed into a set of small networks that are defined as unit networks. The algorithm provides each unit network with P(D|H_i), which is used as confidence level. The unit network with higher P(D|H_i) has a higher confidence such that the unit network is correctly elucidated. Thus, the proposed algorithm is able to locate true positive interactions using P(D|H_i), which is a unique property of the proposed algorithm.</p> <p>The algorithm is evaluated with synthetic and <it>Saccharomyces cerevisiae </it>expression data using the dynamic Bayesian network. With synthetic data, it is shown that the performance of the algorithm depends on the number of genes, noise level, and the number of data points. With Yeast expression data, it is shown that there is remarkable number of known physical or genetic events among all interactions elucidated by the proposed algorithm.</p> <p>The performance of the algorithm is compared with Sparse Bayesian Learning algorithm using both synthetic and <it>Saccharomyces cerevisiae </it>expression data sets. The comparison experiments show that the algorithm produces sparser solutions with less false positives than Sparse Bayesian Learning algorithm.</p> <p>Conclusion</p> <p>From our evaluation experiments, we draw the conclusion as follows: 1) Simulation results show that the algorithm can be used to elucidate gene regulatory networks using limited number of experimental data points. 2) Simulation results also show that the algorithm is able to handle the problem with noisy data. 3) The experiment with Yeast expression data shows that the proposed algorithm reliably elucidates known physical or genetic events. 4) The comparison experiments show that the algorithm more efficiently performs than Sparse Bayesian Learning algorithm with noisy and limited number of data.</p

Protein Domain of Unknown Function 3233 is a Translocation Domain of Autotransporter Secretory Mechanism in Gamma proteobacteria

Vibrio cholerae, the enteropathogenic gram negative bacteria is one of the main causative agents of waterborne diseases like cholera. About 1/3rd of the organism's genome is uncharacterised with many protein coding genes lacking structure and functional information. These proteins form significant fraction of the genome and are crucial in understanding the organism's complete functional makeup. In this study we report the general structure and function of a family of hypothetical proteins, Domain of Unknown Function 3233 (DUF3233), which are conserved across gram negative gammaproteobacteria (especially in Vibrio sp. and similar bacteria). Profile and HMM based sequence search methods were used to screen homologues of DUF3233. The I-TASSER fold recognition method was used to build a three dimensional structural model of the domain. The structure resembles the transmembrane beta-barrel with an axial N-terminal helix and twelve antiparallel beta-strands. Using a combination of amphipathy and discrimination analysis we analysed the potential transmembrane beta-barrel forming properties of DUF3233. Sequence, structure and phylogenetic analysis of DUF3233 indicates that this gram negative bacterial hypothetical protein resembles the beta-barrel translocation unit of autotransporter Va secretory mechanism with a gene organisation that differs from the conventional Va system