Miracle-dz/UniFAR-FTUs huggingface dataset:
RTT measurement and its dependence on the real geographical distance

In recent years, more and more network applications appear to require an accurate knowledge of the Internet station geographical positions in order to operate properly. Real geo-position could play a part in many location-based applications. A typical example is the requirement by the web server owners to be able to find out their websites visitors' geographical position more accurately, than the national level. Thus, the underlying geolocation algorithms are being developed. Most of them use the RTT (round-trip-time) values measurement, whose results are then mapped onto geographical distances. This paper deals with the dependence of RTT on the geographic distance. All the measurements needed for dependence determination took place in a dynamically growing Planetlab network, which tries to simulate real Internet environment. The result of this work is a set of RTT values measured in real IP networks and their brief analysis.
Social status gates social attention in humans

Humans tend to shift attention in response to the averted gaze of a face they are fixating, a phenomenon known as gaze cuing. In the present paper, we aimed to address whether the social status of the cuing face modulates this phenomenon. Participants were asked to look at the faces of 16 individuals and read fictive curriculum vitae associated with each of them that could describe the person as having a high or low social status. The association between each specific face and either high or low social status was counterbalanced between participants. The same faces were then used as stimuli in a gaze-cuing task. The results showed a greater gaze-cuing effect for high-status faces than for low-status faces, independently of the specific identity of the face. These findings confirm previous evidence regarding the important role of social factors in shaping social attention and show that a modulation of gaze cuing can be observed even when knowledge about social status is acquired through episodic learning.
Confidence in Recognition Memory for Words: Dissociating Right Prefrontal Roles in Episodic Retrieval

We used event-related functional magnetic resonance imaging (efMRI) to investigate brain regions showing differential responses as a function of confidence in an episodic word recognition task. Twelve healthy volunteers indicated whether their old-new judgments were made with high or low confidence. Hemodynamic responses associated with each judgment were modeled with an early and a late response function. As predicted by the monitoring hypothesis generated from a previous recognition study [Henson, R. N. A. , Rugg, M. D. , Shallice, T. , Josephs, O. , & Dolan, R. J. (1999a). Recollection and familiarity in recognition memory: An event-related fMRI study. Journal of Neuroscience, 19, 3962-3972], a right dorsolateral prefrontal region showed a greater response to correct low-versus correct high-confidence judgements. Several regions, including the precuneus, posterior cingulate, and left lateral parietal cortex, showed greater responses to correct old than correct new judgements. The anterior left and right prefrontal regions also showed an old-new difference, but for these regions the difference emerged relatively later in time. These results further support the proposal that different subregions of the prefrontal cortex subserve different functions during episodic retrieval. These functions are discussed in relation to a monitoring process, which operates when familiarity levels are close to response criterion and is associated with nonconfident judgements, and a recollective process, which is associated with the confident recognition of old words.
Large-Scale East-Asian eQTL Mapping Reveals Novel Candidate Genes for LD Mapping and the Genomic Landscape of Transcriptional Effects of Sequence Variants

Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5′ untranslated regions and 5′ flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P = 3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P = 4.4E-34) for ulcerative colitis; and IDUA (P = 2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene.
Tardive Dyskinesia in an Outpatient Population: Prevalence and Predisposing Factors*

One hundred and eighty outpatients at the outpatient services of the Douglas Hospital were evaluated for the presence of tardive dyskinesia. Forty-nine (27%) among them had tardive dyskinesia. In this study, female sex, older age and the current administration of antiparkinsonian medication were found to be significantly related to the occurrence of tardive dyskinesia.
Role of Bacterial Biofilms in Catheter-Associated Urinary Tract Infections (CAUTI) and Strategies for Their Control

UTI is considered to be the most common bacterial infection [107]. It is the second most common infection of any organ and is one of the most common infections in humans [157]. UTIs account for nearly 8 million physician visits and 1.5 million visits to emergency rooms annually in the United States [44, 87, 144]. Although every individual is susceptible to UTIs, certain specific subpopulations are more predisposed to the risk of UTIs. This includes infants, pregnant women, elderly, patients with spinal cord injuries and/or catheters, patients with diabetes, multiple sclerosis, or acquired immunodeficiency virus, and patients with underly‐ ing urologic abnormalities [13, 31, 43, 127, 130]. UTIs are usually localized to the bladder, kidneys or prostate. The etiology of UTIs has been regarded as well-established and consistent.
Mast Cell–Restricted, Tetramer-Forming Tryptases Induce Aggrecanolysis in Articular Cartilage by Activating Matrix Metalloproteinase-3 and -13 Zymogens

Mouse mast cell protease (mMCP)-6–null C57BL/6 mice lost less aggrecan proteoglycan from the extracellular matrix of their articular cartilage during inflammatory arthritis than wild-type (WT) C57BL/6 mice, suggesting that this mast cell (MC)–specific mouse tryptase plays prominent roles in articular cartilage catabolism. We used ex vivo mouse femoral head explants to determine how mMCP-6 and its human ortholog hTryptase-β mediate aggrecanolysis. Exposure of the explants to recombinant hTryptase-β, recombinant mMCP-6, or lysates harvested from WT mouse peritoneal MCs (PMCs) significantly increased the levels of enzymatically active matrix metalloproteinases (MMP) in cartilage and significantly induced aggrecan loss into the conditioned media, relative to replicate explants exposed to medium alone or lysates collected from mMCP-6–null PMCs. Treatment of cartilage explants with tetramer-forming tryptases generated aggrecan fragments that contained C-terminal DIPEN and N-terminal FFGVG neoepitopes, consistent with MMP-dependent aggrecanolysis. In support of these data, hTryptase-β was unable to induce aggrecan release from the femoral head explants obtained from Chloe mice that resist MMP cleavage at the DIPEN↓FFGVG site in the interglobular domain of aggrecan. In addition, the abilities of mMCP-6–containing lysates from WT PMCs to induce aggrecanolysis were prevented by inhibitors of MMP-3 and MMP-13. Finally, recombinant hTryptase-β was able to activate latent pro–MMP-3 and pro–MMP-13 in vitro. The accumulated data suggest that human and mouse tetramer-forming tryptases are MMP convertases that mediate cartilage damage and the proteolytic loss of aggrecan proteoglycans in arthritis, in part, by activating the zymogen forms of MMP-3 and MMP-13, which are constitutively present in articular cartilage.
Src-Dependent Syk Activation Controls CD69-Mediated Signaling and Function on Human NK Cells1

CD69 C-type lectin receptor represents a functional triggering molecule on activated NK cells, capable of directing their natural killing function. The receptor-proximal signaling pathways activated by CD69 cross-linking and involved in CD69-mediated cytotoxic activity are still poorly understood. Here we show that CD69 engagement leads to the rapid and selective activation of the tyrosine kinase Syk, but not of the closely related member of the same family, ZAP70, in IL-2-activated human NK cells. Our results indicate the requirement for Src family kinases in the CD69-triggered activation of Syk and suggest a role for Lck in this event. We also demonstrate that Syk and Src family tyrosine kinases control the CD69-triggered tyrosine phosphorylation and activation of phospholipase Cγ2 and the Rho family-specific exchange factor Vav1 and are responsible for CD69-triggered cytotoxicity of activated NK cells. The same CD69-activated signaling pathways are also observed in an RBL transfectant clone, constitutively expressing the receptor. These data demonstrate for the first time that the CD69 receptor functionally couples to the activation of Src family tyrosine kinases, which, by inducing Syk activation, initiate downstream signaling pathways and regulate CD69-triggered functions on human NK cells.
Smoking prevention in school students: positive effects of a hospital-based intervention.

BACKGROUND Adolescents have smoked less in recent years, but 11.7% of 12-to-17-year-olds were still smokers in 2011. The prevalence of smoking has also remained high among 18-to-25-year-olds (36.8%). An intervention program called "Students in the Hospital" was developed in which the health aspects of smoking and its individual and societal consequences were presented in an interactive informational event. In this study, we determine the efficacy of the program. METHODS From September 2007 to July 2008, we performed an anonymous survey by questionnaire, with a quasi-experimental control-group design, two weeks before (t(1)) and six months after (t(2)) the intervention in a group of 760 participating school students in Berlin. RESULTS 40.8% of the participants were smokers, among whom 79% stated that they smoked water pipe. Significantly fewer students in the intervention group than in the control group began smoking in the six months after the intervention (p<0.001). The chance of remaining a non-smoker was four times as high in the intervention group (OR, 4.14; CI, 1.66-10.36). Girls benefited from the intervention more than boys (OR 2.56, CI 1.06-6.19). 16.1% of smokers in the intervention group and 17.6% in the control group gave up smoking (p>0.05). CONCLUSION A clear primary preventive effect of the program was demonstrated, although it apparently did not induce persons who were already smokers to quit.
THE CIRCADIAN CLOCK GENE PER1 SUPPRESSES CANCER CELL PROLIFERATION AND TUMOR GROWTH AT SPECIFIC TIMES OF DAY

Cell cycle progression is tightly regulated. The expressions of cell cycle regulators, the products of which either promote or inhibit cell proliferation, oscillate during each cell cycle. Cellular proliferation and the expression of cell cycle regulators are also controlled by the circadian clock. Disruption of the circadian clock may thereby lead to deregulated cell proliferation. Mammalian Per2 is a core clock gene, the product of which suppresses cancer cell proliferation and tumor growth in vivo and in vitro. Because Per1, another key clock gene, is mutated in human breast cancers, and because its clock functions are similar and complementary to those of Per2, we have studied its role in modulating breast cancer cell proliferation and tumor growth. We find that breast cancer growth rate is gated by the circadian clock with two daily peaks and troughs, and that they are coupled to the daily expression patterns of clock-controlled genes that regulate cell proliferation. Down-regulation of the expression of tumor Per1 increases cancer cell growth in vitro and tumor growth in vivo by enhancing the circadian amplitude of the two daily tumor growth peaks. The data of the study suggest Per1 has tumor-suppressor function that diminishes cancer proliferation and tumor growth, but only at specific times of day. (Author correspondence: williamhrushesky@gmail.com).
Genetic manipulation of Bacillus methanolicus, a gram-positive, thermotolerant methylotroph

We report the fist genetic transformation system, shuttle vectors, and integrative vectors for the thermotolerant, methylotrophic bacterium Bacillus methanolicus. By using a polyethylene glycol-mediated transformation procedure, we have successfully transformed B. methanolicus with both integrative and multicopy plasmids. For plasmids with a single BmeTI recognition site, dam methylation of plasmid DNA (in vivo or in vitro) was found to enhance transformation efficiency from 7- to 11-fold. Two low-copy-number Escherichia coli-B, methanolicus shuttle plasmids, pDQ507 and pDQ508, are described. pDQ508 caries the replication origin cloned from a 17-kb endogenous B. methanolicus plasmid, pBM1. pDQ507 carries a cloned B. methanolicus DNA fragment, pmr-1, possibly of chromosomal origin, that supports maintenance of pDQ507 as a circular, extrachromosomal DNA molecule. Deletion analysis of pDQ507 indicated two regions required for replication, i.e., a 90-bp AT-rich segment containing a 46-bp imperfect, inverted repeat sequence and a second region 65% homologous to the B. subtilis dpp operon. We also evaluated two E. coli-B. subtilis vectors, pEN1 and pHP13, for use as E. coli-B. methanolicus shuttle vectors. The plasmids pHP13, pDQ507, and pDQ508 were segregationally and structurally stable in B. methanolicus for greater than 60 generations of growth under nonselective conditions; pEN1 was segregationally unstable. Single-stranded plasmid DNA was detected in B. methanolicus transformants carrying either pEN1, pHP13, or pDQ508, suggesting that pDQ508, like the B. subtilis plasmids, is replicated by a rolling-circle mechanism. These studies provide the basic tools for the genetic manipulation of B. methanolicus.
HLA-G/C, miRNAs, and Their Role in HIV Infection and Replication

In recent years, a number of different mechanisms regulating gene expressions, either in normal or in pathological conditions, have been discovered. This review aims to highlight some of the regulatory pathways involved during the HIV-1 infection and disease progression, focusing on the novel discovered microRNAs (miRNAs) and their relation with immune system's agents. Human leukocyte antigen (HLA) family of proteins plays a key role because it is a crucial modulator of the immune response; here we will examine recent findings, centering especially on HLA-C and -G, novel players lately discovered to engage in modulation of immune system. We hope to provide novel perspectives useful to find out original therapeutic roads against HIV-1 infection and AIDS progression.
Ancient maya stone tools and ritual use of deep valley rockshelter, Belize

This paper discusses the technological and microscopic use-wear analyses of the chert debitage excavated from Deep Valley Rockshelter. This rockshelter, located in the Caves Branch River Valley of central Belize, was primarily used by the ancient Maya from the Late Preclassic to Terminal Classic periods (AD 80–950) and may demonstrate a pattern of rockshelter usage by the Classic period Maya. To test whether such a pattern exists, lithic data from Caves Branch Rockshelter and other rockshelters in Belize, specifically those in the Sibun Valley and the Ek Xux Valley, are compared. Interpretations are complicated, however, by the severe mixing of deposits, which makes segregating the lithic artifacts into different reduction or use events nearly impossible. Moreover, this mixing severely hampers reconstructions of diachronic change in stone-tool use in the rockshelter. While acknowledging these limitations, our analysis suggests that the lithics in the rockshelter are primarily the result of reduction and use-related activities that originally occurred at other nearby surface sites rather than in the rockshelter itself. Consequently, the chipped-stone artifacts recovered from this rockshelter most likely result from secondary deposition of debitage for ritual purposes and represent accumulation over many years. We suspect this type of secondary deposition of debitage was also occurring at other rockshelters in Belize, based on comparisons to the chipped stone assemblages from these locations. We cannot discount the possibility that some stone tool production and use may have originally occurred in Deep Valley Rockshelter, but support for this is minimal.
Prevalence of teeth and dentures among elderly in Norway receiving social care

The aim of this study was to estimate the prevalence of teeth and dentures in individuals aged 67 years and over receiving social care in Norway. A representative sample of 2893 individuals was selected from all 19 counties of Norway. In all, 1910 individuals (1358 living in institutions, 552 living at home) could be interviewed and examined by calibrated local dental teams in 1996-97. Overall response rate was 66%. Out of the examined, 1359 (71%) were women and 551 (29%) were men. The mean age was 85.1 years for women and 82.2 years for men. In all, 19.6% had 'own teeth only', 21% 'own teeth and dentures', 54% 'dentures only', and 5.3% 'neither teeth nor dentures'. Previous findings in a random sample of elderly Norwegians from three regions with markedly different dental health were confirmed by using plychotomous logistic regressin. Three regions of Norway could be identified with respect to the occurence of teeth and dentures: region A (South-East counties of Norway including the capital Oslo), region B (West-Central counties), and region C (Northern counties). Significant differences existed between them and non-significant differences between them. A mean number of 12.3 teeth were observed in 773 (40.5%) dentate individuals, 13.4 in reion A, 11.4 in region B, and 9.0 in region C, respectively. In conclusion, there are large geographic disparities with respect to dental/denture status also in individuals receiving social care in Norway. When the data were collected (1996-97), the oral health goal for the year 2000 suggested by WHO/FDI aiming at 50% of people aged 65 years and above having a minimum of 20 remaining functional teeth was not fulfilled for individuals receiving social care in large parts of Norway.
Dynamic Thermal Management Considering Accurate Temperature-Leakage Interdependency

In this paper, we develop an accurate dynamic thermal management DTM approach considering the interdependency of temperature and leakage. By modeling the leakage-thermal interdependence as a quadratic polynomial, we develop accurate analytical equations that capture the thermal transient. We also identify all the situations in which thermal runaway would occur, which should be avoided by DTM. We then present a discrete dynamic programming algorithm that performs thermalaware task and speed scheduling using the model we derived. Compared to a linear leakage-thermal model [1], owing to our more accurate model, our scheme resulted in 18.2% better performance while maintaining the temperature below constraint.
Clustering validity assessment: finding the optimal partitioning of a data set

Clustering is a mostly unsupervised procedure and the majority of clustering algorithms depend on certain assumptions in order to define the subgroups present in a data set. As a consequence, in most applications the resulting clustering scheme requires some sort of evaluation regarding its validity. In this paper we present a clustering validity procedure, which evaluates the results of clustering algorithms on data sets. We define a validity index, S Dbw, based on well-defined clustering criteria enabling the selection of optimal input parameter values for a clustering algorithm that result in the best partitioning of a data set. We evaluate the reliability of our index both theoretically and experimentally, considering three representative clustering algorithms run on synthetic and real data sets. We also carried out an evaluation study to compare S Dbw performance with other known validity indices. Our approach performed favorably in all cases, even those in which other indices failed to indicate the correct partitions in a data set.
Query evaluation via tree-decompositions

A number of efficient methods for evaluating first-order and monadic-second order queries on finite relational structures are based on tree-decompositions of structures or queries. We systematically study these methods.In the first part of the article, we consider arbitrary formulas on tree-like structures. We generalize a theorem of Courcelle [1990] by showing that on structures of bounded tree-width a monadic second-order formula (with free first- and second-order variables) can be evaluated in time linear in the structure size plus the size of the output.In the second part, we study tree-like formulas on arbitrary structures. We generalize the notions of acyclicity and bounded tree-width from conjunctive queries to arbitrary first-order formulas in a straightforward way and analyze the complexity of evaluating formulas of these fragments. Moreover, we show that the acyclic and bounded tree-width fragments have the same expressive power as the well-known guarded fragment and the finite-variable fragments of first-order logic, respectively.