Miracle-dz/UniFAR-FTUs huggingface dataset:
A investigation on solving dense systems of linear equations with high performance verified computing on shared memory architectures

In Computer Science the guarantee that an algorithm has been verified to be correct does not guarantees that the numerical result obtained by it is correct. Hence, automatic result verification is an important additional tool to reduce the impact of arithmetic errors in numerical computation. As in traditional computation, one fundamental problem in verified computing is bounding the solution set of systems of linear equations. However, even using highly optimized libraries, solving interval linear systems, that is, those where input data are interval instead of point numbers, stills representing a considerable computational cost when dealing with large dense interval systems. Thus, the use of high performance computing techniques appears as a solution. Several works have been developed along the years using parallel computing techniques on clusters with message passing paradigm. However, many changes have been occurring in high performance computing. Given the number of cores on multicore chips expected to reach tens in a few years, efficient implementations of numerical libraries using shared memory programming models is of urgent interest. In this context, this work presents a revision of high performance verified computing basis, like interval arithmetic, and investigates implementation of the widely used libraries and tools for verified computing. Finally, the paper discusses some issues about implementing an system of linear equations solver using verified computing on shared memory architectures.
Oxygen radicals released during ischemic preconditioning contribute to cardioprotection in the rabbit myocardium.

Previous studies have proposed that oxygen radicals may play a role in the triggering of ischemic preconditioning. However, studies evaluating the effects of radical scavengers have yielded conflicting results, possibly because of differences in the number of preconditioning episodes used. The present study tested whether N-2-mercaptopropionylglycine (MPG) could block protection of both single and multiple episodes of preconditioning in in situ and in vitro rabbit hearts. All hearts were subjected to 30 min of regional ischemia followed by reperfusion for 2 (in vitro) or 3 (in situ) h. Infarct size was measured by tetrazolium. Infarction in control in situ hearts was 37.5+/-3.5% of the risk zone. A single cycle of preconditioning (PC1), with 5 min ischemia/10 min reperfusion, reduced infarct size to 12.3+/-2.0% (P<0.05). Four cycles of preconditioning (PC4) were equally protective. MPG (1 mg/kg/min i.v.) alone had no effect on infarction but abolished protection afforded by PC1 (35.4+/-3.9%). However, MPG failed to block protection in the PC4 group. In isolated control hearts, infarct size was 31.1+/-1.8% and was reduced to 10.2+/-2.2% (P<0.05) by preconditioning. MPG (300 microM) aborted protection. Infusion of hypoxanthine or xanthine oxidase separately in lieu of preconditioning had no effect on infarct size, but induced protection when combined (14.1+/-2.2%; P<0.05). Polymyxin B, an inhibitor of protein kinase C (PKC), abolished this protection (53.1+/-4.1%). In conclusion, oxygen radicals contribute to ischemic preconditioning in the rabbit and appear to do so via activation of PKC. The fact that MPG could not block protection by PC4 suggests that oxygen radicals act in concert with other triggers of preconditioning such as adenosine and bradykinin.
On Specification Informatics in Discrete-event Systems - State-transparency for Clarity of Finite Automata as Control Specifications

In control of discrete-event systems (DES’s), the formalization of control requirements from natural language statements is essentially a human endeavor. Without automated support tools, human designers often face the uncertainty of not knowing if the control requirements formalized in the rudimentary DES formalism of automata are as intended, motivating the automata-theoretic study of specification informatics in the field of DES’s. A specification automaton that renders its linguistic description more transparent should help designers ascertain the prescribed requirement. Such transparency may be formalized in either the state space or the event space of the DES. In this paper, treating the former as fundamental, a state-transparent specification automaton is conceptualized with respect to a full specification automaton (‘full’ in the sense of having all the a priori transitional constraints of the DES embedded in it). It contains only specification relevant states called specification epochs. Each epoch denotes a “well-defined” disjoint subset of states of the full specification automaton in the same phase of execution, meaningfully aggregated such that the resultant specification automaton retains the original restrictiveness on the DES. The problem of maximizing the state-transparency of specification automata for DES’s is then theoretically formulated. Subject to human perceptive or cognition limits, we believe that such a maximally state-transparent specification automaton could be more comprehensible, showing clearly the compliant execution of the system through a minimum number of specification epochs, and should aid designers in clarifying if the requirement prescribed is the one intended.
Uncorrected or untreated vision problems and occupational injuries among the adolescent and adult population in Australia

Objective: To investigate the relationship between uncorrected or untreated vision problems and occupational injuries in the adolescent and adult population in Australia. Design: National Health Survey conducted via personal interviews with a stratified random sample. Setting: Population-based. Subjects: Individuals selected from the total population aged 15 or older. Exposure measures: Information on uncorrected or untreated vision problems was collected by personal interview via responses to screening questions. Main outcome measures: Information on occupational injuries also collected via personal interview. Results: After adjustment for potential confounders, the odds of occupational injury increased by ∼60% (OR = 1.57, 95% CI = 1.11 to 2.24) for those who had any uncorrected or untreated vision problems, and by 3½ times (OR = 3.52, 95% CI = 1.64 to 7.55) for those with untreated macular degeneration compared with healthy subjects. Conclusions: Uncorrected or untreated vision problems, particularly macular degeneration, significantly increased the risk of occupational injury. Vision examination should be recommended and implemented regularly for all workers.
Impact of synaptic noise and conductance state on spontaneous cortical firing

Cortical neurons in-vivo operate in a continuum of overall conductance states, depending on the average level of background synaptic input throughout the dendritic tree. We compare how variability, or fluctuations, in this input affects the statistics of the resulting ‘spontaneous’ or ‘background’ firing activity, between two extremes of the mean input corresponding to a low-conductance (LC) and a high-conductance (HC) state. In the HC state, we show that both firing rate and regularity increase with increasing variability. In the LC state, firing rate also increases with input variability, but in contrast to the HC state, firing regularity first decreases and then increases with an increase in the variability. At high levels of input variability, firing regularity in both states converge to similar values.
Network analysis of dendritic fields of pyramidal cells in neocortex and Purkinje cells in the cerebellum of the rat.

The connectivity within the dendritic array of Purkinje cells in the cerebellum and pyramidal cells of the neocortex of the rat, stained by the Golgi-Cox method, has been quantified by the method of network analysis. Connectivity was characterized either by applying the system of Strahler ordering, which assigns a relative order of magnitude to each branch of the arborescence or by the identification of unique topological branching patterns within the tree. The former method has been used to define the entire dendritic array of the Purkinje cell and the apical system of neocortical pyramids. It has been shown that the relation between the numbers of branches of successive Strahler order in Purkinje cells form an inverse geometric series in which the highest order is unity and the ratio between successive orders approximates to 3. On the other hand, the apical dendrites of neocortical pyramids exhibit two bifurcation ratios, i.e. a ratio of 3 between low orders and a ratio of 4 between higher orders. A computer simulation technique was used to generate networks of a size comparable with the Purkinje cell networks and grown according to two hypotheses namely, a 'terminal growth model' in which additional segments were added randomly to the terminal branches only and a 'segmental growth model' in which additional segments were added randomly to any branch within the array including terminal branches. Subsequent ordering of the simulated trees revealed that the relation between the numbers of successive orders for networks generated according to the 'segmental model' tended towards an inverse geometric series with a ratio of 4 and that generated according to the 'terminal model' tended towards a ratio of 3. This result showed that the dendritic tree of Purkinje cells grow in a manner indistinguishable from a system adding branches to random terminal segments and that neocortical apical dendrites add their collateral branches to random segments of the apical shaft but that the collateral branches themselves grow by random terminal branching. The possibility that such conclusions may be influenced by loss of branches incurred by either a failure of impregnation, by sectioning, or by environmental influences was investigated by means of a computer technique.
Colorectal cancer incidence, mortality and survival in South-east England between 1972 and 2001

We report incidence, mortality and survival from colorectal cancer in South-east England using data from 162 022 incident cases and 97 697 deaths collected between 1972 and 2001 at the Thames Cancer Registry, which currently covers 14 million people. Overall, there was an increase in the incidence of colorectal cancer among men aged 50 years and over, and a decrease among the youngest age groups. In women, there was a clear decrease in incidence among those aged less than 60 years but a slight increase among those aged 60–79 years. Furthermore, there has been a steady decrease in mortality for all ages, larger in women than in men, and an increase in the 10-year relative survival for both sexes from just over 30% among those followed-up during 1981–1986 to just over 45% among those followed-up during 1997–2001.
A measure of linear diagonals-parameter symmetry for square contingency tables with ordered categories

For square contingency tables with ordered categories, Agresti (1) considered the linear diagonals-parameter symmetry (LDPS) model being an extension of the symmetry model. This paper proposes a measure which represents the degree of departure from the LDPS model. The measure proposed is expressed using the Cressie-Read power-divergence or Patil-Taillie diversity index. The measure is useful for comparing the degree of departure from LDPS in several tables, and it may be appropriate for comparing the degrees of departure from the equality of the marginal variances for several square ordinal tables if it is reasonable to assume underlying bivariate normal distributions. Examples are also given.
Elevated Methylmalonic Acid Is Related to Cognitive Impairment in Older Adults Enrolled in an Elderly Nutrition Program

Abstract Vitamin B12 status has been linked to cognitive impairment among older adults. Deficit in methylmalonic acid (MMA) may be reflective of cognitive impairment because it is a biochemically sensitive marker of B12 deficiency. In a cross-sectional study the contributions of different indices of B12 status, including serum B12, MMA and total homocysteine (tHcy), were measured in relation to cognitive functioning. B12 deficiency as measured by elevated MMA concentrations appeared to be most reflective of cognitive impairment and appeared to contribute unique variance to cognitive measures after controlling for other biochemical variables. Demographic variables, particularly education and age, were more strongly associated with cognitive measures than was MMA. Monitoring and reducing serum MMA concentrations by increasing the intake of vitamin B12 may provide protection against cognitive decline in this and other older populations.
The 185delAG mutation (c.68_69delAG) in the BRCA1 gene triggers translation reinitiation at a downstream AUG codon

The 185delAG mutation (c.68_69delAG; ter39) in the BRCA1 gene is a founder Jewish Ashkenazi mutation that is carried by 1% of this population and has been identified in thousands of breast or ovarian cancer patients. We have previously described that transcripts bearing this mutation, as well as transcripts bearing the 188del11 mutation (c.71_81del; ter36), are not degraded by nonsense‐mediated mRNA decay (NMD), contrary to our observations of other truncating mutations that introduce premature termination codons (PTCs) farther downstream in the coding sequence [Perrin‐Vidoz et al., 2002]. To test the hypothesis that these two mutations fail to trigger NMD because of translation reinitiation, we have constructed BRCA1 minigenes and studied their protein expression after transient expression in HeLa cells. We show here that in the presence of a (PTC) at position 36 or 39, translation reinitiation occurs in the BRCA1 minigenes at position 128. Hum Mutat 27(10), 1024–1029, 2006. © 2006 Wiley‐Liss, Inc.
Peripheral levels of superoxide dismutase and glutathione peroxidase in youths in ultra-high risk for psychosis: a pilot study

Introduction Oxidative stress has been documented in chronic schizophrenia and in the first episode of psychosis, but there are very little data on oxidative stress prior to the disease onset. Objective This work aimed to compare serum levels of superoxide dismutase (SOD) and glutathione peroxidase (GPx) in young individuals at ultra-high risk (UHR) of developing psychosis with a comparison healthy control group (HC). Methods Thirteen UHR subjects and 29 age- and sex-matched healthy controls (HC) were enrolled in this study. Clinical assessment included the Comprehensive Assessment of At-Risk Mental States (CAARMS), the Semi-Structured Clinical Interview for DSM-IV Axis-I (SCID-I) or the Kiddie-SADS-Present and Lifetime Version (K-SADS-PL), and the Global Assessment of Functioning (GAF) scale. Activities of SOD and GPx were measured in serum by the spectrophotometric method using enzyme-linked immunosorbent assay kits. Results After adjusting for age and years of education, there was a significant lower activity of SOD and lower GPX activity in the UHR group compared to the healthy control group (rate ratio [RR]=0.330, 95% CI 0.187; 0.584, p<0.001 and RR=0.509, 95% CI 0.323; 0.803, p=0.004, respectively). There were also positive correlations between GAF functioning scores and GPx and SOD activities. Conclusion Our results suggest that oxidative imbalances could be present prior to the onset of full-blown psychosis, including in at-risk stages. Future studies should replicate and expand these results.
Integrin signaling and cell spreading mediated by phorbol 12‐myristate 13‐acetate treatment

Spreading of SNU16mAd gastric carcinoma cells was previously shown to be regulated via a signaling network from transforming growth factor β1 (TGFβ1) to integrins signaling, through a mediation of protein kinase C δ (PKCδ). However, in the previous study, the roles of PKCδ appeared complicated. In this study to clarify the roles of PKCδ in the spreading of the gastric carcinoma cells, we questioned if PKC activation via phorbol 12‐myristate 13‐acetate (PMA) treatment could mimic the TGFβ1 effects. An acute PMA treatment increased phosphorylations of focal adhesion (FA) kinase, paxillin, c‐Src, and cofilin, just as TGFβ1 did. Furthermore, cell spreading mediated by TGFβ1‐ or acute PMA treatment correlated with activation of RhoA, which regulates actin reorganization and FA formation. However, stress fiber formation was prominent in TGFβ1‐treated cells, compared to cortical actin organization in PMA‐treated cells. Altogether, these observations indicate that acute PMA treatment could mimic the TGFβ1 mechanisms for cell spreading through subtly different effects on actin reorganization. J. Cell. Biochem. © 2006 Wiley‐Liss, Inc.
Isolation and cDNA Cloning of Ovarian Cortical Rod Protein in Kuruma Prawn Marsupenaeus japonicus (Crustacea: Decapoda: Penaeidae)

Abstract Two cortical rod proteins having molecular weights of 28.6 kDa and 30.5 kDa were isolated from the mature ovary of Marsupenaeus japonicus using gel filtration and reversed-phase HPLC. Analysis of the N-terminal amino acid sequence of the 28.6 kDa molecule revealed that amino acid residues 1–21 corresponded to residues 9–29 of the 30.5 kDa molecule. Examination of homology using BLAST showed that 21 amino acids out of 29 residues of the 28.6 kDa molecule, and 14 out of 29 residues of the 30.5 kDa molecule were identical to that of the ovarian cortical rod proteins of Penaeus semisulcatus. Positive immunohistochemical reaction to antiserum raised against the 28.6 kDa protein was observed on cortical rods forming around the periphery of oocytes at the maturation stages. Western blotting analysis revealed that both the 28.6 kDa and 30.5 kDa molecules stained with the anti-28.6 kDa antiserum. Furthermore, the 28.6 kDa and 30.5 kDa proteins were both glycosylated, as evidenced by positive carbohydrate staining using Concanavalin A and production of positive PAS reaction. These results indicate that the cortical rods are comprised of the 28.6 kDa and 30.5 kDa molecules. We subsequently cloned two full-length cDNAs based on the N-terminal sequences of the 28.6 kDa and 30.5 kDa molecules. The open reading frame of 28.6 kDa and 30.5 kDa encoded 276 amino acid residues. Comparison analysis of the two cDNAs revealed that the location of the processing site and sequence of signal peptides differed, indicating that the two cDNAs are products of two separate genes and encode the 28.6 kDa molecule and 30.5 kDa molecule, respectively. Both proteins possessed one potential N-linked glycosylation site. It is considered that both molecules are components of the cortical rods, forming a jelly layer after fertilization.
Progression of Nephropathy in Spontaneous Diabetic Rats Is Prevented by OPB-9195, a Novel Inhibitor of Advanced Glycation

Levels of tissue advanced glycation end products (AGEs) that result from nonenzymatic reactions of glucose and proteins are high in both diabetic and aging people. Irreversible AGE formation is based on increases in AGE-derived protein-to-protein cross-linking and is considered to be a factor contributing to the complications of diabetes. A novel inhibitor of advanced glycation, OPB-9195, belongs to a group of thiazolidine derivatives, known as hypoglycemic drugs; however, they do not lower blood glucose levels. We did studies to determine if OPB-9195 would prevent the progression of nephropathy in spontaneous diabetic rats. In vitro inhibitory effects of OPB-9195 on AGE formation and AGE-derived cross-linking were examined by enzyme-linked immunosorbent assay (ELISA) and SDS-PAGE, respectively. Otsuka-Long-Evans-Tokushima-Fatty (OLETF) rats, a model of NIDDM, were used to evaluate the therapeutic effect of OPB-9195. Light microscopic findings by periodic acid-Schiff (PAS) staining, the extent of AGE accumulation detected by immunohistochemical staining in the kidneys, the levels of serum AGEs by AGE-specific ELISA, and urinary albumin excretion were examined. OPB-9195 effectively inhibited both AGE-derived cross-linking and the formation of AGEs, in a dose-dependent manner in vitro. In addition, the administration of OPB-9195 prevented the progression of glomerular sclerosis and AGE deposition in glomeruli. Elevation of circulating AGE levels and urinary albumin excretion were dramatically prevented in rats, even at 56 weeks of age and with persistent hyperglycemia. We concluded that a novel thiazolidine derivative, OPB-9195, prevented the progression of diabetic glomerular sclerosis in OLETF rats by lowering serum levels of AGEs and attenuating AGE deposition in the glomeruli.
Real-time observation of light-controlled transcription in living cells

ABSTRACT Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed blue light-induced chromatin recruitment (BLInCR) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a cluster of reporter genes in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 min after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light. Quantitative assessment of the activation process revealed biphasic activation kinetics with a pronounced early phase in cells treated with the histone deacetylase inhibitor SAHA. Comparison with kinetic models of transcription activation suggests that the gene cluster undergoes a maturation process when activated. We anticipate that BLInCR will facilitate the study of transcription dynamics in living cells. This article has an associated First Person interview with the first author of the paper. Summary: Blue light-induced chromatin recruitment (BLInCR) enables rapid and reversible targeting of effector proteins to nuclear loci with high temporal resolution for analyzing transcription activation.
The dynamics of perception: modelling subjective wellbeing in a short panel

Summary. We consider the issue of the dynamics of perceptions, as expressed in responses to survey questions on subjective wellbeing. We develop a simulated maximum likelihood method for estimation of dynamic linear models, where the dependent variable is partially observed through ordinal scales. This latent auto‐regression model is often more appropriate than the usual state dependence model for attitudinal and interval variables. The paper contains an application to a model of households’ perceptions of their financial wellbeing, demonstrating the superior fit of the latent auto‐regression model to both the usual static model and the state dependence model.