Massively parallel Wang–Landau sampling on multiple GPUs

Wang–Landau sampling is implemented on the Graphics Processing Unit (GPU) with the Compute Unified Device Architecture (CUDA). Performances on three different GPU cards, including the new generation Fermi architecture card, are compared with that on a Central Processing Unit (CPU). The parameters for massively parallel Wang–Landau sampling are tuned in order to achieve fast convergence. For simulations of the water cluster systems, we obtain an average of over 50 times speedup for a given workload.     

Hemifacial hypoplasia and hypomelanosis of Ito

Seventy patients with adolescent idiopathic right thoracic scoliosis had full assessment of their pulmonary function using a computerised pulmonary function system. Their mean age at evaluation was 13.8 years. The following measurements were obtained from anteroposterior and lateral standing and antero-posterior supine bending radiographs: lateral curvature, vertebral rotation, kyphosis, maximum sterno-vertebral distance and apical rib-vertebral angles. Using the above measurements, the flexibility of curve, vertebral rotation and rib-vertebral angle asymmetry were calculated. Patients were classified into three groups on the basis of their predicted vital capacity, to determine whether radiological features of deformity can help identify patients with compromised pulmonary function. The mean Cobb angle and vertebral rotation for the 70 patients were 50 degrees (range 35-100 degrees) and 22 degrees (range 1-44 degrees) respectively. The mean flexibility of curve and vertebral rotation were 52% and 49% respectively. Mean thoracic kyphosis was 25 degrees, ranging from -7 to 55 degrees. Of the patients with Cobb angle less than 90 degrees, 71% had vital capacity less than 80% of predicted values, and of these, 18% had marked compromise of vital capacity (less than 60% of predicted values). Mean values of Cobb angle, vertebral rotational flexibility, kyphosis, rib-vertebral angle asymmetry (in standing as well as supine bending radiographs) differed significantly between patients with more than 80% of predicted vital capacity and those with 60% or less of predicted values. Radiological features indicative of better pulmonary function were: rotational flexibility exceeding 55%, rib-vertebral angle asymmetry (standing) less than 25 degrees and kyphosis greater than 15 degrees. Two deformity parameters--that give a better prediction of pulmonary function than the widely used Cobb angle, vertebral rotational flexibility and rib-vertebral angle asymmetry--were identified in this study.     

The newly identified yeast GRD genes are required for retention of late-Golgi membrane proteins

Processing of A-ALP, a late-Golgi membrane protein constructed by fusing the cytosolic domain of dipeptidyl aminopeptidase A to the transmembrane and lumenal domains of alkaline phosphatase (ALP), serves as a convenient assay for loss of retention of late-Golgi membrane proteins in Saccharomyces cerevisiae. In this study, a large group of novel grd (for Golgi retention defective) yeast mutants, representing 18 complementation groups, were identified on the basis of their mislocalization of A-ALP to the vacuole, where it was proteolytically processed and thus became enzymatically activated. All of the grd mutants exhibited significant mislocalization of A-ALP, as measured by determining the kinetics of A-ALP processing and by analyzing its     

Partial amino acid sequence of gamma-46 gliadin

We have determined the partial amino acid sequence (207 amino acids) of gamma-46 gliadin isolated from wheat cultivar Hardi. The molecular mass of the protein (Mr) estimated by electrospray mass spectrometry is 35191.3. The number of cysteine residues in gamma-46 gliadin was determined as a mass difference of the protein before and after reduction and alkylation with 4-vinylpyridine. It was shown that the protein has no free SH-groups, and all cysteine residues are involved in the formation of four disulfide bonds. The partial structure of gamma-46 gliadin was determined by N-terminal sequencing and sequencing of tryptic and chymotryptic peptides. The tryptic peptides were obtained by enzymatic hydrolysis of the protein, which was preliminarily reduced and immobilized at free SH-groups on thiopropyl-Sepharose 6B. The chymotryptic peptides were isolated by limited digestion of the native protein. The positions of cysteine residues, as well as surrounding amino acid sequences, are conserved in gamma-46 gliadin; this is typical of gliadins.     

Acute and chronic arsenic poisoning associated with treatment of acute promyelocytic leukaemia

Seven relapsed and/or refractory acute promyelocytic leukaemia patients were treated by arsenic trioxide (As2O3). Four patients (4/7, 57%) achieved complete remission after one to three cycles of treatment and the most common acute side-effect was fluid retention (in six patients, 86%), including weight gains and pleuro-pericardial effusions. Evident polyneuropathy compatible with chronic arsenic toxicity was noted in two of the three patients who received As2O3 maintenance therapy and one of them had marked distal muscular atrophy. We suggest that As2O3 may be a useful salvage therapy for relapsed and refractory APL patients, but the acute or chronic arsenic toxicity should be carefully monitored.     

Sparse LCS Common Substring Alignment

The “Common Substring Alignment” problem is defined as follows. The input consists of a set of strings S₁,S₂…,S_c, with a common substring appearing at least once in each of them, and a target string T. The goal is to compute similarity of all strings S_i with T, without computing the part of the common substring over and over again.In this paper we consider the Common Substring Alignment problem for the LCS (Longest Common Subsequence) similarity metric. Our algorithm gains its efficiency by exploiting the sparsity inherent to the LCS problem. Let Y be the common substring, n be the size of the compared sequences, L_y be the length of the LCS of T and Y, denoted |LCS[T,Y]|, and L be max{|LCS[T,S_i]|}. Our algorithm consists of an O(nL_y) time encoding stage that is executed once per common substring, and an O(L) time alignment stage that is executed once for each appearance of the common substring in each source string. The additional running time depends only on the length of the parts of the strings that are not in any common substring.     

Differential effects of short photoperiod on 2-[125I]iodomelatonin binding in the testis and brain of quail

The affinities and densities of 2-[125I]iodomelatonin binding sites in the brains and gonads of male Japanese quail following short photoperiod treatment were studied. At 6 weeks old, control quail were placed under a 14 hour light/10 hour dark photo-stimulatory cycle and experimental quail were housed under a 7 hour light/17 hour dark photo-inhibitory lighting regime. Eighteen weeks after photic manipulation, the birds were killed at mid-light. The photo-inhibited quail had very small testes. Brains and testes of control and experimental quail were collected for receptor binding studies. The maximum number of binding sites (Bmax) of 2-[125I]iodomelatonin determined by saturation studies and the number of 2-[125I]iodomelatonin binding sites determined by a one-point binding assay in the testes of short-day quail were significantly lower (p < 0.05) than those of the testes in reproductively active birds kept under long photoperiod. There was no significant difference (p > 0.05) between the testicular Kd (equilibrium dissociation constant) values of these two groups. As for the Kd and Bmax of 2-[125I]iodomelatonin binding sites in the whole brain, there were no significant differences (p > 0.05) between the two groups. The higher level of testicular 2-[125I]iodomelatonin binding sites in photostimulated birds may be related to an up-regulation of melatonin receptors by the suppressed pineal melatonin secretion under long photoperiod. The lower testicular 2-[125I]iodomelatonin binding sites under short photoperiod may be the result of down-regulation of melatonin receptors by the stimulated melatonin pattern in the photo-inhibited birds.(ABSTRACT TRUNCATED AT 250 WORDS)     

Electric field-induced changes in agonist-stimulated calcium fluxes of human HL-60 leukemia cells

The mechanism of biological effects of extremely-low-frequency electric and magnetic fields may involve induced changes of Ca2+ transport through plasma membrane ion channels. In this study we investigated the effects of externally applied, low-intensity 60 Hz electric (E) fields (0.5 V/m, current density 0.8 A/m2) on the agonist-induced Ca2+ fluxes of HL-60 leukemia cells. The suspensions of HL-60 cells received E-field or sham exposure for 60 min and were simultaneously stimulated either by 1 microM ATP or by 100 microM histamine or were not stimulated at all. After E-field or sham exposure, the responses of the intracellular calcium levels of the cells to different concentrations of ATP (0.2-100 microM) were assessed. Compared with control cells, exposure of ATP-activated cells to an E-field resulted in a 20-30% decrease in the magnitude of [Ca2+]i elevation induced by a low concentration of ATP (<1 microM). In contrast, exposure of histamine-activated HL-60 cells resulted in a 20-40% increase of ATP-induced elevation of [Ca2+]i. E-field exposure had no effect on non-activated cells. Kinetic analysis of concentration-response plots also showed that compared with control cells, exposure to the E-field resulted in increases of the Michaelis constant, Km, value in ATP-treated cells and of the maximal [Ca2+]i peak rise in histamine-treated HL-60 cells. The observed effects were reversible, indicating the absence of permanent structural damages induced by acute 60 min exposure to electric fields. These results demonstrate that low-intensity electric fields can alter calcium distribution in cells, most probably due to the effect on receptor-operated Ca2+ and/or ion channels.