Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential parameter optimization

Sequential parameter optimization is a heuristic that combines classical and modern statistical techniques to improve the performance of search algorithms. To demonstrate its flexibility, three scenarios are discussed: (1) no experience how to choose the parameter setting of an algorithm is available, (2) a comparison with other algorithms is needed, and (3) an optimization algorithm has to be applied effectively and efficiently to a complex real-world optimization problem. Although sequential parameter optimization relies on enhanced statistical techniques such as design and analysis of computer experiments, it can be performed algorithmically and requires basically the specification of the relevant algorithm's parameters
Spatiotemporal Regulation of ERK2 by Dual Specificity Phosphatases*S⃞

Although many stimuli activate extracellular signal-regulated kinases 1 and 2 (ERK1/2), the kinetics and compartmentalization of ERK1/2 signals are stimulus-dependent and dictate physiological consequences. ERKs can be inactivated by dual specificity phosphatases (DUSPs), notably the MAPK phosphatases (MKPs) and atypical DUSPs, that can both dephosphorylate and scaffold ERK1/2. Using a cell imaging model (based on knockdown of endogenous ERKs and add-back of wild-type or mutated ERK2-GFP reporters), we explored possible effects of DUSPs on responses to transient or sustained ERK2 activators (epidermal growth factor and phorbol 12,13-dibutyrate, respectively). For both stimuli, a D319N mutation (which impairs DUSP binding) increased ERK2 activity and reduced nuclear accumulation. These stimuli also increased mRNA levels for eight DUSPs. In a short inhibitory RNA screen, 12 of 16 DUSPs influenced ERK2 responses. These effects were evident among nuclear inducible MKP, cytoplasmic ERK MKP, JNK/p38 MKP, and atypical DUSP subtypes and, with the exception of the nuclear inducible MKPs, were paralleled by corresponding changes in Egr-1 luciferase activation. Simultaneous removal of all JNK/p38 MKPs or nuclear inducible MKPs revealed them as positive and negative regulators of ERK2 signaling, respectively. The effects of JNK/p38 MKP short inhibitory RNAs were not dependent on protein neosynthesis but were reversed in the presence of JNK and p38 kinase inhibitors, indicating DUSP-mediated cross-talk between MAPK pathways. Overall, our data reveal that a large number of DUSPs influence ERK2 signaling. Together with the known tissue-specific expression of DUSPs and the importance of ERK1/2 in cell regulation, our data support the potential value of DUSPs as targets for drug therapy.
PI3-kinase activation is critical for host barrier permissiveness to Listeria monocytogenes

Gessain et al. explore how Listeria monocytogenes facilitates disseminated infection through host epithelial barriers using two of its surface proteins, InlA and InlB. By combining in vitro and in vivo approaches using intestinal and placental mouse and human tissues, they find a differential requirement for InlA and InlB in tissue invasiveness, with a critical role for PI3K activation.
Pharmacokinetic/Pharmacodynamic Modeling of Crizotinib for Anaplastic Lymphoma Kinase Inhibition and Antitumor Efficacy in Human Tumor Xenograft Mouse Models

Crizotinib [Xalkori; PF02341066; (R)-3-[1-(2,6-dichloro-3-fluoro-phenyl)-ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)-pyridin-2-ylamine] is an orally available dual inhibitor of anaplastic lymphoma kinase (ALK) and hepatocyte growth factor receptor. The objectives of the present studies were to characterize: 1) the pharmacokinetic/pharmacodynamic relationship of crizotinib plasma concentrations to the inhibition of ALK phosphorylation in tumors, and 2) the relationship of ALK inhibition to antitumor efficacy in human tumor xenograft models. Crizotinib was orally administered to athymic nu/nu mice implanted with H3122 non–small-cell lung carcinomas or severe combined immunodeficient/beige mice implanted with Karpas299 anaplastic large-cell lymphomas. Plasma concentration-time courses of crizotinib were adequately described by a one-compartment pharmacokinetic model. A pharmacodynamic link model reasonably fit the time courses of ALK inhibition in both H3122 and Karpas299 models with EC50 values of 233 and 666 ng/ml, respectively. A tumor growth inhibition model also reasonably fit the time course of individual tumor growth curves with EC50 values of 255 and 875 ng/ml, respectively. Thus, the EC50 for ALK inhibition approximately corresponded to the EC50 for tumor growth inhibition in both xenograft models, suggesting that >50% ALK inhibition would be required for significant antitumor efficacy (>50%). Furthermore, based on the observed clinical pharmacokinetic data coupled with the pharmacodynamic parameters obtained from the present nonclinical xenograft mouse model, >70% ALK inhibition was projected in patients with non–small-cell lung cancer who were administered the clinically recommended dosage of crizotinib, twice-daily doses of 250 mg (500 mg/day). The result suggests that crizotinib could sufficiently inhibit ALK phosphorylation for significant antitumor efficacy in patients.
An image compression method using sparse representation and grey relation

Traditional wavelet transform needs to be improved and perfected in sparse representation. In this paper, we proposed an image compression algorithm based on grey relational theory in wavelet domain. We use the character of wavelet coefficients, and apply the grey relational theory in coefficients relational description, and then propose an image compression method via grey relational theory. We classify the coefficients according to their characters in different domains and construct the sparse representation method under different types of coefficients. The algorithm reduces the computational complexity and improves the ability of image sparse representation. It achieves an efficient way of image compression. The simulation results show that the proposed compression algorithm based on grey relational theory is superior to the other algorithms both in the visual quality and PSNR.
Long term activity monitoring with a wearable sensor node

This paper introduces an encapsulated sensor node that is devised to monitor and record motion patterns over long, quotidian periods of time with potential application in psychological studies. Its design fuses different sensing modalities to allow efficient capturing of tilt and acceleration stimuli, as well as embedded algorithms that abstract from the raw sensory data to indicative features. By combining tilt switches and accelerometers with customized processing techniques, it is argued that a power-efficient yet information-rich approach is reached for the observation and logging of human motion-based activity
Evidence of Dengue Virus Transmission and Factors Associated with the Presence of Anti-Dengue Virus Antibodies in Humans in Three Major Towns in Cameroon

Background Dengue is not well documented in Africa. In Cameroon, data are scarce, but dengue infection has been confirmed in humans. We conducted a study to document risk factors associated with anti-dengue virus Immunoglobulin G seropositivity in humans in three major towns in Cameroon. Methodology/Principal Findings A cross sectional survey was conducted in Douala, Garoua and Yaounde, using a random cluster sampling design. Participants underwent a standardized interview and were blood sampled. Environmental and housing characteristics were recorded. Randomized houses were prospected to record all water containers, and immature stages of Aedes mosquitoes were collected. Sera were screened for anti-dengue virus IgG and IgM antibodies. Risk factors of seropositivity were tested using logistic regression methods with random effects. Anti-dengue IgG were found from 61.4% of sera in Douala (n = 699), 24.2% in Garoua (n = 728) and 9.8% in Yaounde (n = 603). IgM were found from 0.3% of Douala samples, 0.1% of Garoua samples and 0.0% of Yaounde samples. Seroneutralization on randomly selected IgG positive sera showed that 72% (n = 100) in Douala, 80% (n = 94) in Garoua and 77% (n = 66) in Yaounde had antibodies specific for dengue virus serotype 2 (DENV-2). Age, temporary house walls materials, having water-storage containers, old tires or toilets in the yard, having no TV, having no air conditioning and having travelled at least once outside the city were independently associated with anti-dengue IgG positivity in Douala. Age, having uncovered water containers, having no TV, not being born in Garoua and not breeding pigs were significant risk factors in Garoua. Recent history of malaria, having banana trees and stagnant water in the yard were independent risk factors in Yaounde. Conclusion/Significance In this survey, most identified risk factors of dengue were related to housing conditions. Poverty and underdevelopment are central to the dengue epidemiology in Cameroon.
Predicting the number of forks for open source software project

GitHub is successful open source software platform which attract many developers. In GitHub, developers are allowed to fork repositories and copy repositories without asking for permission, which make contribution to projects much easier than it has ever been. It is significant to predict the number of forks for open source software projects. The prediction can help GitHub to recommend popular projects, and guide developers to find projects which are likely to succeed and worthy of their contribution. In this paper, we use stepwise regression and design a model to predict the number of forks for open source software projects. Then we collect datasets of 1,000 repositories through GitHub’s APIs. We use datasets of 700 repositories to compute the weight of attributes and realize the model. Then we use other 300 repositories to verify the prediction accuracy of our model. Advantages of our model include: (1) Some attributes used in our model are new. This is because GitHub is different from traditional open source software platforms and has some new features. These new features are used to build our model. (2) Our model uses project information within t month after its creation, and predicts the number of forks in the month T (t < T). It allows users to set the combination of time parameters and satisfy their own needs. (3) Our model predicts the exact number of forks, rather than the range of the number of forks (4) Experiments show that our model has high prediction accuracy. For example, we use project information with 3 months to prediction the number of forks in month 6 after its creation. The correlation coefficient is as high as 0.992, and the median number of absolute difference between prediction value and actual value is only 1.8. It shows that the predicted number of forks is very close to the actual number of forks. Our model also has high prediction accuracy when we set other time parameters.
Update on the clinical utility and optimal use of cefditoren

This article reviews and updates published data on cefditoren. The in vitro activity of cefditoren and its potential pharmacokinetic/pharmacodynamic adequacy to cover emerging resistance phenotypes in the present decade is reviewed. Cefditoren’s in vitro activity against most prevalent bacterial respiratory pathogens in the community and its pharmacokinetic/pharmacodynamic profile suggests a significant role for cefditoren in the treatment of respiratory tract infections. Clinical trials (in acute exacerbations of chronic bronchitis, community-acquired pneumonia, pharyngotonsillitis, and sinusitis) performed during clinical development outside Japan, mainly in adults, are reviewed, together with new clinical studies in the treatment of pharyngotonsillitis, sinusitis, and otitis media in children, mainly in Japan, for efficacy and safety assessment. The results of these studies support the adequacy of cefditoren for the treatment of community-acquired respiratory tract infections with a safety profile similar to previous oral antibiotics. From the data reviewed, it is concluded that cefditoren is an adequate option for the treatment of mild-to-moderate community-acquired respiratory infections, especially in geographical areas with a reported prevalence of phenotypes exhibiting nonsusceptibility to common oral antibiotics.
Reaching volumes generated by means of octal trees and Cartesian constraints

We present a system to analyze the reachability of the human body. The inverse kinematics technique is employed to find which regions of space are reachable using a certain reach strategy. This information is stored in a data structure called volume approximation tree (VATree). This tree has proven itself to be an appropriate data structure for two reasons: it provides an efficient representation of the reachable volumes and it reduces the number of inverse kinematics simulations necessary for its construction. Once the VATrees are constructed for the different reach strategies, that information can be used to determine in real time which strategy is most suitable for a given reach task.
Legionella pneumophila Sequence Type 1/Paris Pulsotype Subtyping by Spoligotyping

ABSTRACT Endemic strains of Legionella pneumophila sequence type 1 (ST1), in particular the ST1/Paris pulsotype, are dispersed worldwide and represent about 10% of culture-proven clinical cases of Legionnaires' disease in France. The high rate of isolation of this strain from both clinical and environmental samples makes identification of the source of infection difficult during epidemiological investigations. The full-length genome sequence of this strain was recently determined, and it revealed the presence of a CRISPR/cas complex. The aim of this study was to develop and evaluate a spoligotyping tool based on the diversity of this CRISPR locus that would allow the accurate subtyping of the L. pneumophila serogroup 1 ST1/Paris pulsotype. The CRISPR loci of 28 L. pneumophila ST1/Paris pulsotype isolates were sequenced, and 42 different spacers regions were characterized. A membrane-based spoligotyping method was developed and used to determine the subtypes of 406 L. pneumophila isolates, including 233 with the ST1/Paris pulsotype profile that were collected in France from 2000 to 2011. A total of 46 different spoligotypes were detected, and 41 of these were specifically identified in the ST1/Paris pulsotype isolates. In 27 of 33 epidemiological investigations, the environmental source of contamination was confirmed by comparing spoligotypes of clinical isolates with those of environmental isolates. With an index of discrimination of 79.72% (95% confidence interval, 75.82 to 83.63), spoligotyping of the L. pneumophila ST1/Paris pulsotype has the potential to be a useful complementary genotyping tool for discriminating isolates with undistinguishable pulsed-field gel electrophoresis (PFGE) and ST genotypes, which could help to identify environmental sources of infection.
Dietary intake of acrylamide and pancreatic cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort.

BACKGROUND In 1994, acrylamide (AA) was classified as a probable human carcinogen by the International Agency for Research on Cancer. In 2002, AA was discovered at relatively high concentrations in some starchy, plant-based foods cooked at high temperatures. PATIENTS AND METHODS A prospective analysis was conducted to evaluate the association between the dietary intake of AA and ductal adenocarcinoma of the exocrine pancreatic cancer (PC) risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort using Cox regression modeling. EPIC includes >500,000 men and women aged 35-75 at enrollment from 10 European countries. AA intake was estimated for each participant by combining questionnaire-based food consumption data with a harmonized AA database derived from the EU monitoring database of AA levels in foods, and evaluated in quintiles and continuously. RESULTS After a mean follow-up of 11 years, 865 first incident adenocarcinomas of the exocrine pancreas were observed and included in the present analysis. At baseline, the mean dietary AA intake in EPIC was 26.22 µg/day. No overall association was found between continuous or quintiles of dietary AA intake and PC risk in EPIC (HR:0.95, 95%CI:0.89-1.01 per 10 µg/day). There was no effect measure modification by smoking status, sex, diabetes, alcohol intake or geographic region. However, there was an inverse association (HR: 0.73, 95% CI: 0.61-0.88 per 10 µg/day) between AA intake and PC risk in obese persons as defined using the body mass index (BMI, ≥ 30 kg/m(2)), but not when body fatness was defined using waist and hip circumference or their ratio. CONCLUSIONS Dietary intake of AA was not associated with an increased risk of PC in the EPIC cohort.
Decline in the Frequencies of Borrelia burgdorferi OspA161–175-Specific T Cells after Antibiotic Therapy in HLA-DRB1*0401-Positive Patients with Antibiotic-Responsive or Antibiotic-Refractory Lyme Arthritis1

Synovitis in patients with antibiotic-refractory Lyme arthritis persists for months to several years after antibiotic therapy. This course, which may result from infection-induced autoimmunity, is associated with T cell recognition of Borrelia burgdorferi outer surface protein A (OspA161–175) and with HLA-DR molecules that bind this epitope, including the DRB1*0401 molecule. In this study, we used tetramer reagents to determine the frequencies of OspA161–175-specific T cells in samples of PBMC and synovial fluid mononuclear cells (SFMC) from 13 DRB1*0401-positive patients with antibiotic-responsive or antibiotic-refractory arthritis. Initially, three of the six patients (50%) with antibiotic-responsive arthritis and four of the seven patients (57%) with antibiotic-refractory arthritis had frequencies of OspA161–175-specific CD4+ T cells in peripheral blood above the cutoff value of 4 per 105 cells. Among the five patients with concomitant PBMC and SFMC, four (80%) had OspA tetramer-positive cells at both sites, but the mean frequency of such cells was 16 times higher in SFMC, reaching levels as high as 1,177 per 105 cells. In the two patients in each patient group in whom serial samples were available, the frequencies of OspA161–175-specific T cells declined to low or undetectable levels during or soon after antibiotic therapy, months before the resolution of synovitis in the two patients with antibiotic-refractory arthritis. Thus, the majority of patients with Lyme arthritis initially have increased frequencies of OspA161–175-specific T cells. However, the marked decline in the frequency of such cells with antibiotic therapy suggests that persistent synovitis in the refractory group is not perpetuated by these cells.
Study and Implementation of CHAMELEON algorithm for [ 1 ] Gene Clustering

The vast amount of gathered genomic data from Microarray and other experiments makes it extremely difficult for the researcher to interpret the data and form conclusions about the functions of the discovered genes. We can make use of extensive biomedical literature databases to find the functional similarity between genes using various clustering techniques. There are very few tailored information retrieval systems for this purpose.
Defining and Assessing Individual Differences in Attachment Relationships: Q-Methodology and the Organization of Behavior in Infancy and Early Childhood.

At times, it seems as if attachment research could fall victim to its own success. In the span of barely 15 years, we have come to accept Freud's view that attachment in infancy constitutes a genuine love relationship. We have recognized that this relationship is closely tracked by patterns of behavior toward caregivers and that this behavior is complexly organized, goalcorrected, and sensitive to environmental input. We have also adapted observational techniques employed by behavioral biologists and learned to examine infant behavior in detail and in context. As a result we have learned
On construction and analysis of sparse random matrices and expander graphs with applications to compressed sensing

We revisit the probabilistic construction of sparse random matrices where each column has a fixed number of nonzeros whose row indices are drawn uniformly at random. These matrices have a one-to-one correspondence with the adjacency matrices of lossless expander graphs. We present tail bounds on the probability that the cardinality of the set of neighbors for these graphs will be less than the expected value. The bounds are derived through the analysis of collisions in unions of sets using a {\em dyadic splitting} technique. This analysis led to the derivation of better constants that allow for quantitative theorems on existence of lossless expander graphs and hence the sparse random matrices we consider and also quantitative compressed sensing sampling theorems when using sparse non mean-zero measurement matrices.
A Chroma-based Salience Function for Melody and Bass Line Estimation from Music Audio Signals

In this paper we present a salience function for melody and bass line estimation based on chroma features. The salience functionisconstructedbyadaptingtheHarmonicPitchClass Profile (HPCP) and used to extract a mid-level representation of melodies and bass lines which uses pitch classes rather than absolute frequencies. We show that our salience function has comparable performance to alternative state of the art approaches, suggesting it could be successfully used as a first stage in a complete melody and bass line estimation system.
Dinosaurs, Methicillin-Resistant Staphylococcus aureus, and Infection Control Personnel: Survival Through Translating Science Into Prevention

Some believe that dinosaurs became extinct because they failed to learn from their experiences and evolve in a changing world. The infection control community currently is witnessing an evolution in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). How the infection control (and infectious diseases) community responds to this evolution will illustrate what it has learned from past science and experiences, whether it is capable of translating the science into prevention, and whether it will be successful ultimately in controlling antimicrobial-resistant pathogens in healthcare settings and the community. In other words, will the members of the infection control community become dinosaurs and irrelevant or will they apply the science in applied public health prevention and reverse the inexorable upward secular trends seen for many antimicrobial-resistant pathogens in healthcare settings?
Adaptive conjoint analysis for the vitalisation of angel investments by entrepreneurs

ABSTRACT In order to promote angel investments, attracting those who have entrepreneurial experience is necessary because their capital, unique managing experience, and business insight are highly beneficial to the performance of the investment. This can be accomplished by providing a preferred investment environment for potential angels who have entrepreneurial backgrounds. In this paper, we use an adaptive conjoint analysis to identify preferred investment environments represented as a combination of support policies for business angels who have entrepreneurial experience in Korea. Of particular interest is a preference for angel insurance. This insurance is newly proposed based on prospect theory, which explains that people tend to be more sensitive to a loss than to a gain. The value of the angel insurance is compared to those of tax policies and matching funds for business angels. The empirical results are expected to contribute to promoting angel investments by attracting entrepreneurs to become business angels.
Polysyllabic shortening and word-final lengthening in English

We investigate Polysyllabic shortening effects in three prosodic domains, the word, the inter-stress interval (ISI) and the narrow rhythm unit (NRU), in a large corpus of English broadcast speech. Results confirm and extend earlier findings, indicating that these effects are interpretable as artifacts of word-final lengthening. We do, however, find effects compatible with the assumption of eurhythmic principles in speech production.