Miracle-dz/UniFAR-FTUs huggingface dataset:
Observations and opportunities in architecting shared virtual memory for heterogeneous systems

Computing is becoming increasingly heterogeneous with accelerators like GPUs being tightly integrated with CPUs on the same die. Extending the CPU's virtual addressing mechanism to these accelerators is a key step in making accelerators easily programmable. In this work, we analyze, using real-system measurements, shared virtual memory across the CPU and an integrated GPU. We make several key observations and highlight consequent research opportunities: (1) servicing a TLB miss from the GPU can be an order of magnitude slower than that from the CPU and consequently it is imperative to enable many concurrent TLB misses to hide this larger latency; (2) divergence in memory accesses impacts the GPU's address translation more than the rest of the memory hierarchy, and research in designing address translation mechanisms tolerant to this effect is imperative; and (3) page faults from the GPU are considerably slower than that from the CPU and software-hardware co-design is essential for efficient implementation of page faults from throughput-oriented accelerators like GPUs. We present a detailed measurement study of a commercially available integrated APU that illustrates these effects and motivates future research opportunities.
Intranasal Immunization of Mice with Influenza Vaccine in Combination with the Adjuvant LT-R72 Induces Potent Mucosal and Serum Immunity Which Is Stronger than That with Traditional Intramuscular Immunization

ABSTRACT Immunization of mice by the intranasal route with influenza virus hemagglutinin in combination with the mutant Escherichia coli heat-labile enterotoxin R72 (LT-R72) induced significantly enhanced serum and mucosal antibodies, surpassing, in most cases, responses achieved by traditional intramuscular immunization using inactivated split influenza vaccine. Furthermore, intranasal immunization with LT-R72 induced a potent serum immunoglobulin G2a response, indicating that this adjuvant has Th1 character.
Systems smart effects as the consequence of the systems complexity

Here we show that various effects of systems behavior looking intellectual may be considered as the consequence of the systems special structures. These effects are such as self-organizing processes in robots groups or insects colonies, self-adaptation in business processes of distributed systems and organizing processes in self-adaptive systems at all. We describe systems by special graph structures and the system behavior by the graph transformations. These special structures may be as the structure in the system task set as the structure describing the business process. We estimate different transformation paths by an implication in a logic associated with the graph construction. We discuss the example of some business process describing by a special graph construction with additional structure of linear logic in it. This approach provides a decision making and allows to obtain the automated adaptation choice of the system initially managed manually. The choice follows from the system internal properties only and coincides with the choice obtained by another logic using earlier.
Enhanced Dystrophic Progression in mdx Mice by Exercise and Beneficial Effects of Taurine and Insulin-Like Growth Factor-1

A preclinical screening for prompt-to-use drugs that are safer than steroids and beneficial in Duchenne muscular dystrophy was performed. Compounds able to reduce calcium-induced degeneration (taurine or creatine 10% in chow) or to stimulate regeneration [insulin-like growth factor-1 (IGF-1); 50 or 500 μg/kg s.c. ] were administered for 4 to 8 weeks to mdx mice undergoing chronic exercise on a treadmill, a protocol to worsen dystrophy progression. α-Methyl-prednisolone (PDN; 1 mg/kg) was used as positive control. The effects were evaluated in vivo on forelimb strength and in vitro electrophysiologically on the macroscopic chloride conductance (gCl), an index of degeneration-regeneration events in mdx muscles, and on the mechanical threshold, a calcium-sensitive index of excitation-contraction coupling. The exercise produced a significant weakness and an impairment of gCl, by further decreasing the already low value of degenerating diaphragm (DIA) and fully hampering the increase of gCl typical of regenerating extensor digitorum longus (EDL) mdx muscle. The already negative voltage threshold for contraction of mdx EDL was also slightly worsened. Taurine > creatine > IGF-1 counteracted the exercise-induced weakness. The amelioration of gCl was drug- and muscle-specific: taurine was effective in EDL, but not in DIA muscle; IGF-1 and PDN were fully restorative in both muscles, whereas creatine was ineffective. An acute effect of IGF-1 on gCl was observed in vitro in untreated, but not in IGF-1-treated exercised mdx muscles. Taurine > PDN > IGF-1, but not creatine, significantly ameliorated the negative threshold voltage values of the EDL fibers. The results predict a potential benefit of taurine and IGF-1 for treating human dystrophy.
Separation of helper and suppressor T lymphocytes. II. Ly phenotypes and lack of DNA synthesis requirement for the generation of concanavalin A helper and suppressor cells

Using a Ficoll velocity sedimentation gradient, we have been able to fractionate concanavalin A (Con A)-induced helper and suppressor cells into separate pools. Cells activated by Con A to mediate helper activity are Ly1+, do not require DNA synthesis for induction, and remain as small cells after activation. Suppressor cells are Ly23+, are found in the blast cell fraction and their induction is not inhibitable by prior treatment with mitomycin C or irradiation, both of which inhibit DNA synthesis. The implications of such findings are discussed.
Visual influence on the magnitude of somatogravic illusion evoked on advanced spatial disorientation demonstrator.

BACKGROUND The somatogravic illusion (SGI) is a kind of spatial disorientation caused by a linear sustained acceleration. Pilots believe that visual cues, such as a visible horizon or texture flow, reduce this illusion. This study was performed to evaluate the influence of visual stimuli on the SGI using the Advanced Spatial Disorientation Demonstrator (ASDD). METHODS There were eight healthy males who were exposed to a 0.58 g x axis linear acceleration on the ASDD, where the direction of the resultant gravitoinertial force was equivalent to 30 degrees pitch-up. One of the following visual stimuli was presented during each acceleration: BLANK (no visual cues); HORIZON (a visible horizon without motion); and TEXTURE (vertical lines moving toward the subject evoking vection). The subjective magnitude of the SGI in ordinal scale was observed; and in interval scale, the deviation of the moving point kept at the subjective horizon was observed. The differences among visual stimuli were analyzed. RESULTS The subjective magnitude of the SGI (p < 0.01) and the deviation of the moving point (p < 0.05) were significantly smaller in HORIZON than in BLANK and TEXTURE. No difference was demonstrated between BLANK and TEXTURE. The linear vection produced by the TEXTURE stimulus did not affect the SGI. CONCLUSION The data indicated that the presence of a visible horizon reduced the magnitude of the SGI. On the other hand, the presence of a vection stimulus did not influence the magnitude of the SGI.
Catechol-O-methyltransferase and Monoamine Oxidase A Genotypes and Drug Response to Conventional Neuroleptics in Schizophrenia

Biogenic amine synthesis and degradation are involved in the pathogenesis of schizophrenia. Catechol-O-methyltransferase and monoamine oxidase enzymes are important agents in the metabolic inactivation of these neurotransmitters (ie, dopamine, serotonin, and norepinephrine). Functional polymorphism in the catechol-O-methyltransferase and monoamine oxidase A genes causes variation in enzyme activities. We investigated the relationship of catechol-O-methyltransferase Val158Met and monoamine oxidase A promoter repeat polymorphism with response to conventional neuroleptic treatment in schizophrenia. Ninety-four schizophrenic patients formed 2 different study populations. The responders had experienced a fair and steady response to conventional neuroleptics. The nonresponders had failed to achieve an acceptable response to conventional neuroleptics. We also used a control population of 94 age-matched and gender-matched blood donors. Genotyping of the catechol-O-methyltransferase and monoamine oxidase A genes was performed by polymerase chain reaction. Forty-three percent of the nonresponders had a low activity catechol-O-methyltransferase genotype compared with 16% of the responders (P = 0.009). Monoamine oxidase A genotype alone did not differ significantly between the groups. Moreover, the risk of having both low-activity catechol-O-methyltransferase and monoamine oxidase A genotypes was over 6 times more common (odds ratio = 6.16, P = 0.03) in the nonresponders compared with responders. The whole population of patients with schizophrenia did not differ from the controls. The low-activity catechol-O-methyltransferase genotype may be associated with unsatisfactory drug response to conventional neuroleptics or alternatively be involved in a subset of schizophrenics. The role of monoamine oxidase A genotype seems to be additive in this respect.
Reduced Gradient Method and its Generalization via Stochastic Perturbation

In this paper, the global optimization of a nonconvex objective function under linear and nonlinear dierentiable constraints is studied, a reduced gradient and GRG descent methods with random perturbation is proposed and it is desired to establish the global convergence of the algorithm. Some numerical examples are also given by the problems of statistical, octagon, mixture, alkylation and pooling.
Angiography alone versus angiography plus optical coherence tomography to guide decision-making during percutaneous coronary intervention: the Centro per la Lotta contro l'Infarto-Optimisation of Percutaneous Coronary Intervention (CLI-OPCI) study.

AIMS Angiographic guidance for percutaneous coronary intervention (PCI) has substantial limitations. The superior spatial resolution of optical coherence tomography (OCT) could translate into meaningful clinical benefits. We aimed to compare angiographic guidance alone versus angiographic plus OCT guidance for PCI. METHODS AND RESULTS Patients undergoing PCI with angiographic plus OCT guidance (OCT group) were compared with matched patients undergoing PCI with angiographic only guidance (Angio group) within 30 days. The primary endpoint was the one-year rate of cardiac death or myocardial infarction (MI). A total of 670 patients were included, 335 in the OCT group and 335 in the Angio group. OCT disclosed adverse features requiring further interventions in 34.7%. Unadjusted analyses showed that the OCT group had a significantly lower one-year risk of cardiac death (1.2% vs. 4.5%, p=0.010), cardiac death or MI (6.6% vs. 13.0%, p=0.006), and the composite of cardiac death, MI, or repeat revascularisation (9.6% vs. 14.8%, p=0.044). Angiographic plus OCT guidance was associated with a significantly lower risk of cardiac death or MI even at extensive multivariable analysis adjusting for baseline and procedural differences between the groups (OR=0.49 [0.25-0.96], p=0.037) and at propensity-score adjusted analyses. CONCLUSIONS This observational study, the first ever formally to appraise OCT guidance for PCI decision-making, suggests that the use of OCT can improve clinical outcomes of patients undergoing PCI.
A new framework for balancing both local and global optimizations in evolutionary algorithms

This paper presents a completely new approach to fulfill both local and global optimization goals simultaneously of the conventional evolutionary algorithm. The basis of the proposed framework is repeatedly alternating three different stages of evolution, each with its own objective and genetic operators. As the stages execute repeatedly, the conflicting goals of local optimization and global exploration are distributed gracefully across the generations of the different stages. The proposed system is compared with classical evolutionary programming (CEP), fast evolutionary programming (FEP) and improved fast evolutionary programming (IFEP) on a number of standard benchmark problems. The experimental results show that the new approach performs better optimization with a higher rate of convergence for most of the problems.
Arbitrary numbers counter fair decisions: trails of markedness in card distribution

Converging evidence from controlled experiments suggests that the mere processing of a number and its attributes such as value or parity might affect free choice decisions between different actions. For example the spatial numerical associations of response codes (SNARC) effect indicates the magnitude of a digit to be associated with a spatial representation and might therefore affect spatial response choices (i.e., decisions between a “left” and a “right” option). At the same time, other (linguistic) features of a number such as parity are embedded into space and might likewise prime left or right responses through feature words [odd or even, respectively; markedness association of response codes (MARC) effect]. In this experiment we aimed at documenting such influences in a natural setting. We therefore assessed number-space and parity-space association effects by exposing participants to a fair distribution task in a card playing scenario. Participants drew cards, read out loud their number values, and announced their response choice, i.e., dealing it to a left vs. right player, indicated by Playmobil characters. Not only did participants prefer to deal more cards to the right player, the card’s digits also affected response choices and led to a slightly but systematically unfair distribution, supported by a regular SNARC effect and counteracted by a reversed MARC effect. The experiment demonstrates the impact of SNARC- and MARC-like biases in free choice behavior through verbal and visual numerical information processing even in a setting with high external validity.
Strong Selection at MHC in Mexicans since Admixture

Mexicans are a recent admixture of Amerindians, Europeans, and Africans. We performed local ancestry analysis of Mexican samples from two genome-wide association studies obtained from dbGaP, and discovered that at the MHC region Mexicans have excessive African ancestral alleles compared to the rest of the genome, which is the hallmark of recent selection for admixed samples. The estimated selection coefficients are 0.05 and 0.07 for two datasets, which put our finding among the strongest known selections observed in humans, namely, lactase selection in northern Europeans and sickle-cell trait in Africans. Using inaccurate Amerindian training samples was a major concern for the credibility of previously reported selection signals in Latinos. Taking advantage of the flexibility of our statistical model, we devised a model fitting technique that can learn Amerindian ancestral haplotype from the admixed samples, which allows us to infer local ancestries for Mexicans using only European and African training samples. The strong selection signal at the MHC remains without Amerindian training samples. Finally, we note that medical history studies suggest such a strong selection at MHC is plausible in Mexicans.
Gene Methylation in Breast Ductal Fluid from BRCA1 and BRCA2 Mutation Carriers

Purpose: Genomic alterations (including gene hypermethylation) are likely to precede the phenotypic changes associated with breast tumorigenesis. From a prospective collection of ductal lavage (DL) samples from women with a known mutation in BRCA1 or BRCA2, we have assessed promoter methylation with a comparison of results with several variables, including breast cancer (BC) outcome. Experimental Design: Hypermethylation of p16, RASSF1A, twist, and RARβ was assessed using a qualitative, real-time, nested PCR assay. Associations between methylation status and variables were tested using Fisher's exact test or logistic regression. Analyses were done at three levels: a single breast, a single duct (both over time), and each DL sample in isolation. Results: A total of 168 samples from 93 ducts in 54 breasts have been analyzed in 34 women (16 BRCA1 and 18 BRCA2 mutation carriers). A median of 2 DL was done (range, 1–5), with 7 women developing BC on study, 1 bilateral. Methylation of p16 was associated with a known BRCA1 mutation (P = 0.001, P < 0.001, and P < 0.001 for breast, duct, and sample levels, respectively) and women with a history of contralateral BC (P = 0.001 and P < 0.001 for duct and sample levels, respectively). An association was seen for women who developed BC on study and RASSF1A methylation (P = 0.001 for sample level). Conclusions: Genetic methylation patterns could potentially be used to predict future BC risk. In addition, p16 methylation may be a predictor of BRCA1 mutation status. Further research is required to corroborate these findings. Cancer Epidemiol Biomarkers Prev; 19(1); 265–74
Detection and typing of herpes simplex viruses by using recombinant immunoglobulin fragments produced in bacteria

Thirty-seven bacterial clones producing human recombinant monoclonal antibody Fab fragments (rFabs) reactive to herpes simplex virus (HSV) antigens were selected from a human combinatorial antibody library constructed in a phage-display vector by a panning procedure against an HSV lysate. Thirty-four of the HSV-specific rFabs were able to specifically recognize HSV-infected cells in indirect immunofluorescence (IF) assays; of these, 25 recognized cells infected by either HSV type 1 (HSV-1) or HSV-2, while 9 recognized only HSV-1-infected cells. One HSV type-common rFab (rFab H37) and one HSV-1-specific rFab (rFab H85) were further evaluated as reagents for viral detection and typing by IF staining in 134 HSV-positive (72 HSV-1 and 62 HSV-2) viral cultures from clinical specimens. The results obtained with these two rFabs were fully consistent with those obtained with a commercial preparation of fluorescein-labeled anti-HSV type-specific murine monoclonal antibodies. The detection sensitivity with the type-common rFab in indirect IF assays was higher overall than that provided by the type-specific murine monoclonal antibodies. Preparations of rFabs suitable for IF staining can be easily and inexpensively obtained in a clinical microbiology laboratory from Escherichia coli cultures. Similar HSV-specific rFabs, therefore, could be advantageous for in vitro diagnostic purposes.
An Energy Efficient Virtual Machine Placement Algorithm with Balanced Resource Utilization

Virtualization is a key technology for resource sharing in IaaS/PaaS cloud infrastructures. One primary issue in virtualization is the virtual machine placement (VMP) problem, which is to choose proper physical machine (PM) to deploy virtual machines (VMs) in runtime. In this paper, we study the VMP problem with the goal of minimizing the total energy consumption. We first present a multi-dimensional space partition model to characterize the resource usage states of PMs. Based on this model, we then propose a virtual machine placement algorithm, which can balance the utilization of multi-dimensional resources, reduce the number of running PMs and thus lower down the energy consumption. We also evaluate our proposed balanced algorithm via extensive simulations. Simulation results show that our approach can save as much as 15% energy compared to the first fit algorithm over a long run.
Islands Containing Slowly Hydrolyzable GTP Analogs Promote Microtubule Rescues

Microtubules are dynamic polymers of GTP- and GDP-tubulin that undergo stochastic transitions between growing and shrinking phases. Rescues, the conversion from shrinking to growing, have recently been proposed to be to the result of regrowth at GTP-tubulin islands within the lattice of growing microtubules. By introducing mixed GTP/GDP/GMPCPP (GXP) regions within the lattice of dynamic microtubules, we reconstituted GXP islands in vitro (GMPCPP is the slowly hydrolyzable GTP analog guanosine-5′-[(α,β)-methyleno]triphosphate). We found that such islands could reproducibly induce rescues and that the probability of rescue correlated with both the size of the island and the percentage of GMPCPP-tubulin within the island. The islands slowed the depolymerization rate of shortening microtubules and promoted regrowth more readily than GMPCPP seeds. Together, these findings provide new mechanistic insights supporting the possibility that rescues could be triggered by enriched GTP-tubulin regions and present a new tool for studying such rescue events in vitro.
Hidden Population Structure and Cross-species Transmission of Whipworms (Trichuris sp.) in Humans and Non-human Primates in Uganda

Background Whipworms (Trichuris sp.) are a globally distributed genus of parasitic helminths that infect a diversity of mammalian hosts. Molecular methods have successfully resolved porcine whipworm, Trichuris suis, from primate whipworm, T. trichiura. However, it remains unclear whether T. trichiura is a multi-host parasite capable of infecting a wide taxonomic breadth of primate hosts or a complex of host specific parasites that infect one or two closely related hosts. Methods and Findings We examined the phylogenetic structure of whipworms in a multi-species community of non-human primates and humans in Western Uganda, using both traditional microscopy and molecular methods. A newly developed nested polymerase chain reaction (PCR) method applied to non-invasively collected fecal samples detected Trichuris with 100% sensitivity and 97% specificity relative to microscopy. Infection rates varied significantly among host species, from 13.3% in chimpanzees (Pan troglodytes) to 88.9% in olive baboons (Papio anubis). Phylogenetic analyses based on nucleotide sequences of the Trichuris internal transcribed spacer regions 1 and 2 of ribosomal DNA revealed three co-circulating Trichuris groups. Notably, one group was detected only in humans, while another infected all screened host species, indicating that whipworms from this group are transmitted among wild primates and humans. Conclusions and Significance Our results suggest that the host range of Trichuris varies by taxonomic group, with some groups showing host specificity, and others showing host generality. In particular, one Trichuris taxon should be considered a multi-host pathogen that is capable of infecting wild primates and humans. This challenges past assumptions about the host specificity of this and similar helminth parasites and raises concerns about animal and human health.