Miracle-dz/UniFAR-FTUs huggingface dataset:
Frustratingly Simplified Deployment in WLAN Localization by Learning from Route Annotation

Recently wireless LAN (WLAN) localization systems are gaining popularity in pervasive computing, machine learning and sensor networks communities, especially indoor scenarios where GPS coverage is limited. To accurately predict location, a large amount of ngerprints composed of received signal strength values is necessary. Moreover, standard supervised or semi-supervised approaches also require location information to each ngerprint, where annotation work is rather tedious and time consuming. To reduce the eorts and time required to build calibration data, we present a novel calibration methodology \routeannotation" and a self-training algorithm for learning from route information eectively. On the proposed calibration methodology, an annotator walks around while measuring ngerprints, then occasionally stops to annotate ngerprints with route from previous location to current location. This calibration reduces work time even compared to partially annotation, while routes have richer information for learning. The proposed learning algorithm comprises following two iterative steps: 1) inferring locations of each ngerprint under route constraints and 2) updating parameters. Experimental results on real-world datasets demonstrate learning from route-annotated data is comparable to state-of-the-art supervised and semi-supervised approaches trained with large amount of calibration data.
Convolutional neural network architectures for predicting DNA–protein binding

Motivation: Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA–protein binding. Yet inappropriate CNN architectures can yield poorer performance than simpler models. Thus an in-depth understanding of how to match CNN architecture to a given task is needed to fully harness the power of CNNs for computational biology applications. Results: We present a systematic exploration of CNN architectures for predicting DNA sequence binding using a large compendium of transcription factor datasets. We identify the best-performing architectures by varying CNN width, depth and pooling designs. We find that adding convolutional kernels to a network is important for motif-based tasks. We show the benefits of CNNs in learning rich higher-order sequence features, such as secondary motifs and local sequence context, by comparing network performance on multiple modeling tasks ranging in difficulty. We also demonstrate how careful construction of sequence benchmark datasets, using approaches that control potentially confounding effects like positional or motif strength bias, is critical in making fair comparisons between competing methods. We explore how to establish the sufficiency of training data for these learning tasks, and we have created a flexible cloud-based framework that permits the rapid exploration of alternative neural network architectures for problems in computational biology. Availability and Implementation: All the models analyzed are available at http://cnn.csail. mit.edu. Contact: gifford@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Parental and self-reported dietary and physical activity habits in pre-school children and their socio-economic determinants

Abstract Objective To assess the agreement between self-reported and parent-reported dietary and physical activity habits in children; and to evaluate the socio-economic determinants of healthier habits (Mediterranean diet and physical activity) among children. Design Cross-sectional analysis of children recruited to a cluster-randomized controlled trial (Program SI! ). Information about children’s and parents’ dietary and physical activity habits was obtained through validated questionnaires (Program SI! questionnaires, Kidmed, Krece Plus and Predimed scores). Setting Twenty-four schools in Madrid, Spain. Subjects Children (n 2062) aged 3–5 years and their parents (n 1949). Results There was positive agreement between parental- and self-reporting for three of the six children’s habits examined. Parents’ dietary and physical activity patterns were associated with those of their children. The main determinants of higher scores in children were higher parental age, the mother’s scores, Spanish origin and higher awareness of human health (P<0·005). Children from parents with a low educational level had lower odds for scoring positively on items such as using olive oil (OR=0·23; 95 % CI 0·13, 0·41) and not skipping breakfast (OR=0·36; 95 % CI 0·23, 0·55), but higher odds for meeting the recommendations for consuming pulses (OR=1·71; 95 % CI 1·14, 2·55). Other habits being influenced by parental socio-economic status included the consumption of vegetables, fish, nuts, avoidance of fast food, and consumption of bakery products for breakfast. Conclusions Children’s habits may be influenced by their parents’ health awareness and other socio-economic characteristics. These findings suggest that intervention strategies, even in very young children, should also target parents in order to achieve maximum success.
Joint Optimization of Relay-Precoders and Decoders with Partial Channel Side Information in Cooperative Networks

In this paper, we jointly optimize the relay-precoders and decoders with partial channel side information (CSI) in a cooperative network. Specifically, two different CSI assumptions are considered: 1) full CSI at the destination terminal and partial CSI at the relay terminals; 2) partial CSI at the destination terminal and the relay terminals. We show that the optimum relay-precoders and decoders work in a fashion of channel selection. It is demonstrated by numerical results that the proposed optimum relay-precoders and decoders improve the performance considerably
Preoperative quality of life predicts survival following pulmonary resection in stage I non-small-cell lung cancer.

OBJECTIVES The objective of this study was to assess the prognostic role of preoperative quality of life (QoL) in patients operated on for early-stage non-small-cell lung cancer (NSCLC). METHODS This is an observational analysis of 131 consecutive patients (2003-08) submitted to pulmonary lobectomy and systematic nodal dissection for pathological pT1N0 or pT2N0 stages NSCLC with a complete follow-up (median 40 months). QoL was measured by the Short Form 36v2, a multidimensional survey assessing eight domains and two composite scales (physical component score [PCS] and mental component score [MCS]). Survival was calculated by the Kaplan-Meier method. The log-rank test was used to assess differences between groups. The relationships between survival and QoL composite scales were determined by Cox proportional hazards regression analysis adjusting for the effect of several baseline and clinical variables. PCS and MCS were categorized according to their values greater or lower than 50 percentiles (general population norms). RESULTS Fifty-three (40%) patients had PCS <50 and 71 (54%) had MCS <50. Results from physical functioning (P = 0.03) and general health (P = 0.03) scales were directly associated with survival. Multivariable regression showed that significant factors associated with overall survival were age >70 (hazard ratio [HR] 2.4, 95% confidence interval [95% CI] 1.2-4.8, P = 0.01) and PCS <50 (HR 2.3, 95% CI 1.4-4.4, P = 0.01). MCS, pT stage, histology, forced expiratory volume in 1 s, DLCO were not associated with prognosis. Patients with PCS >50 lived longer than those with PCS <50 (5-year overall survival 79 vs 49%, P = 0.01), in both pT1 (5-year overall survival 80 vs 49%) and pT2 stages (5-year overall survival 78 vs 48%). Cancer-specific 5-year survival was better in patients with a preoperative PCS >50 compared with those with PCS <50 (89 vs 73%, P = 0.05). Deaths due to cancer recurrence were similar in patients with PCS <50 and >50 (55 vs 53%, P = 0.9). CONCLUSIONS The physical component of QoL was associated with overall and cancer-specific survivals in patients operated on for early-stage NSCLC. Supportive interventions aimed at improving the perception of physical well-being should be tested to verify whether they can improve long-term prognosis after lung cancer surgery.
Random Walks, Markov Processes and the Multiscale Modular Organization of Complex Networks

Most methods proposed to uncover communities in complex networks rely on combinatorial graph properties. Usually an edge-counting quality function, such as modularity, is optimized over all partitions of the graph compared against a null random graph model. Here we introduce a systematic dynamical framework to design and analyze a wide variety of quality functions for community detection. The quality of a partition is measured by its Markov Stability, a time-parametrized function defined in terms of the statistical properties of a Markov process taking place on the graph. The Markov process provides a dynamical sweeping across all scales in the graph, and the time scale is an intrinsic parameter that uncovers communities at different resolutions. This dynamic-based community detection leads to a compound optimization, which favours communities of comparable centrality (as defined by the stationary distribution), and provides a unifying framework for spectral algorithms, as well as different heuristics for community detection, including versions of modularity and Potts model. Our dynamic framework creates a systematic link between different stochastic dynamics and their corresponding notions of optimal communities under distinct (node and edge) centralities. We show that the Markov Stability can be computed efficiently to find multi-scale community structure in large networks.
Clone-specific T cell receptor antagonists of major histocompatibility complex class I-restricted cytotoxic T cells

A previous report showed that the proliferative response of helper T cells to class II major histocompatibility complex (MHC)-restricted antigens can be inhibited by analogues of the antigen, which act as T cell receptor (TCR) antagonists. Here we define and analyze peptide variants that antagonize various functions of class I MHC-restricted cytotoxic T lymphocyte (CTL) clones. Of 64 variants at individual TCR contact sites of the Kb-restricted octamer peptide ovalbumin257-264 (OVAp), a very high proportion (40%) antagonized lysis by three OVAp- specific CTL clones. This effect was highly clone specific, since many antagonists for one T cell clone have differential effects on another. We show that this inhibition of CTL function is not a result of T cell- T cell interaction, precluding veto-like phenomena as a mechanism for antagonism. Moreover, we present evidence for direct interaction between the TCR and antagonist-MHC complexes. In further analysis of the T cell response, we found that serine esterase release and cytokine production are susceptible to TCR antagonism similarly to lysis. Ca2+ flux, an early event in signaling, is also inhibited by antagonists but may be more resistant to the antagonist effect than downstream responses.
Comparing salt tolerance of beet cultivars and their halophytic ancestor: consequences of domestication and breeding programmes

Our results indicate that the salt tolerance of sugarbeet cultivars is only slightly less than that of their sea beet ancestor and that domestication and selection among sugar beet cultivars have not improved salt tolerance. While the yield of many traditional crops is reduced in salinized soils, sugar beet cultivars are tolerant to increased salinity. It is expected that salt tolerant sugar beet will be productive under seawater and brackish water irrigation in saline agriculture. The use of brackish and saline water for saline agriculture helps to prevent depletion of fresh water on earth.
Unraveling the pathogenesis of ARX polyalanine tract variants using a clinical and molecular interfacing approach

The Aristaless‐related homeobox (ARX) gene is implicated in intellectual disability with the most frequent pathogenic mutations leading to expansions of the first two polyalanine tracts. Here, we describe analysis of the ARX gene outlining the approaches in the Australian and Portuguese setting, using an integrated clinical and molecular strategy. We report variants in the ARX gene detected in 19 patients belonging to 17 families. Seven pathogenic variants, being expansion mutations in both polyalanine tract 1 and tract 2, were identifyed, including a novel mutation in polyalanine tract 1 that expands the first tract to 20 alanines. This precise number of alanines is sufficient to cause pathogenicity when expanded in polyalanine tract 2. Five cases presented a probably non‐pathogenic variant, including the novel HGVS: c. 441_455del, classified as unlikely disease causing, consistent with reports that suggest that in frame deletions in polyalanine stretches of ARX rarely cause intellectual disability. In addition, we identified five cases with a variant of unclear pathogenic significance. Owing to the inconsistent ARX variants description, publications were reviewed and ARX variant classifications were standardized and detailed unambiguously according to recommendations of the Human Genome Variation Society. In the absence of a pathognomonic clinical feature, we propose that molecular analysis of the ARX gene should be included in routine diagnostic practice in individuals with either nonsyndromic or syndromic intellectual disability. A definitive diagnosis of ARX‐related disorders is crucial for an adequate clinical follow‐up and accurate genetic counseling of at‐risk family members.
Long-term dietary supplementation with low-dose nobiletin ameliorates hepatic steatosis, insulin resistance, and inflammation without altering fat mass in diet-induced obesity.

SCOPE We evaluated the long-term effect of low-dose nobiletin (NOB), a polymethoxylated flavone, on diet-induced obesity and related metabolic disturbances. METHODS AND RESULTS C57BL/6J mice were fed a high-fat diet (HFD, 45 kcal% fat) with or without NOB (0.02%, w/w) for 16 weeks. NOB did not alter food intake or body weight. Despite increases in fatty acid oxidation-related genes expression and enzymes activity in adipose tissue, NOB did not affect adipose tissue weight due to simultaneous increases in lipogenic genes expression and fatty acid synthase activity. However, NOB significantly decreased not only pro-inflammatory genes expression in adipose tissue but also proinflammatory cytokine levels in plasma. NOB-supplemented mice also showed improved glucose tolerance and insulin resistance, along with decreased levels of plasma insulin, free fatty acids, total cholesterol, non-HDL-cholesterol, and apolipoprotein B. In addition, NOB caused significant decreases in hepatic lipid droplet accumulation and triglyceride content by activating hepatic fatty acid oxidation-related enzymes. Hepatic proinflammatory TNF-α mRNA expression, collagen accumulation, and plasma levels of aminotransferases, liver damage indicators, were also significantly lower in NOB-supplemented mice. CONCLUSION These findings suggest that long-term supplementation with low-dose NOB can protect against HFD-induced inflammation, insulin resistance, dyslipidemia, and nonalcoholic fatty liver disease, without ameliorating adiposity.
Influence of zirconia surface treatments on resin cement bonding and phase transformation

Abstract It evaluated the effects of different zirconia surface treatments on the bond strength of a resin cement to Y-TZP (yttria-stabilized tetragonal zirconia) ceramics, as well as their phase-transformations. 75 blocks (5 mm × 5 mm × 4 mm) of Y-TZP were assigned into five groups (n = 15): (tribochemical silica coating - TBS) zirconia surface was abraded by silica coated alumina particles followed by silanization; (GLZ1) zirconia surface received the application of a thin layer of low-fusing porcelain glaze, followed by hydrofluoric acid (HF) etching for 1 min; (GLZ5) glaze application + HF etching by 5 min; (GLZ10) glaze application + HF etching by 10 min; (GLZ15) glaze application + HF etching by 15 min. After etching, all the specimens were washed, dried and silanized. Cylinders of composites (diameter: 3.25 mm; height: 3 mm) were cemented to the Y-TZP blocks using a resin cement. All the specimens were subjected to aging (10,000 thermal cycles and 90 days storage), tested under shear conditions, and finally analyzed by a stereomicroscope (failure analysis). In addition, we also performed topographical and phase transformation analyses of the treated zirconia surfaces. The TBS group presented the highest bond strength value (23.34 MPa). The glazed groups presented low bond values and high prevalences of pretest failures. X-ray diffraction analysis showed a phase transformation for the TBS group (13.14%); however, there was no clear phase change observed for the GLZ groups. From our results, we concluded that tribochemical silica coating is the main Y-TZP surface conditioning for resin bond improvements.
Protecting the ingroup stereotype: ingroup identification and the management of deviant ingroup members.

In two experiments, we investigated the impact of the presentation of a deviant ingroup member on the perception of the ingroup among participants who differed in their degree of identification with the ingroup. In Study 1, we measured psychology students' level of identification with the group of psychologists (i.e. the ingroup) and presented them with an anti-norm versus a pro-norm psychologist. Results showed that in the anti-norm condition (but not in the pre-norm condition), identification predicted the ratings of psychologists as a group and the perception of typicality of the deviant psychologist. Also, in this condition, the impact of the level of identification on the ratings of psychologists proved to be mediated by the perceived typicality of the deviant. In Study 2, group measures were taken both before and after presentation of a deviant among members of an environmentalist group who differed in their level of identification with the ingroup. The level of identification had an impact on the modification of the ratings of environmentalists as a group, and this effect was mediated by the perceived typicality of the deviant environmentalist. The results are discussed in terms of their implications for the black sheep effect and the stereotype change literature.
Strain Differences in Stress Responsivity Are Associated with Divergent Amygdala Gene Expression and Glutamate-Mediated Neuronal Excitability

Stress is a major risk factor for numerous neuropsychiatric diseases. However, susceptibility to stress and the qualitative nature of stress effects on behavior differ markedly among individuals. This is partly because of the moderating influence of genetic factors. Inbred mouse strains provide a relatively stable and restricted range of genetic and environmental variability that is valuable for disentangling gene–stress interactions. Here, we screened a panel of inbred strains for anxiety- and depression-related phenotypes at baseline (trait) and after exposure to repeated restraint. Two strains, DBA/2J and C57BL/6J, differed in trait and restraint-induced anxiety-related behavior (dark/light exploration, elevated plus maze). Gene expression analysis of amygdala, medial prefrontal cortex, and hippocampus revealed divergent expression in DBA/2J and C57BL/6J both at baseline and after repeated restraint. Restraint produced strain-dependent expression alterations in various genes including glutamate receptors (e.g., Grin1, Grik1). To elucidate neuronal correlates of these strain differences, we performed ex vivo analysis of glutamate excitatory neurotransmission in amygdala principal neurons. Repeated restraint augmented amygdala excitatory postsynaptic signaling and altered metaplasticity (temporal summation of NMDA receptor currents) in DBA/2J but not C57BL/6J. Furthermore, we found that the C57BL/6J-like changes in anxiety-related behavior after restraint were absent in null mutants lacking the modulatory NMDA receptor subunit Grin2a, but not the AMPA receptor subunit Gria1. Grin2a null mutants exhibited significant (∼30%) loss of dendritic spines on amygdala principal neurons under nonrestraint conditions. Collectively, our data support a model in which genetic variation in glutamatergic neuroplasticity in corticolimbic circuitry underlies phenotypic variation in responsivity to stress.
Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models

Background The advent of various high-throughput experimental techniques for measuring molecular interactions has enabled the systematic study of biological interactions on a global scale. Since biological processes are carried out by elaborate collaborations of numerous molecules that give rise to a complex network of molecular interactions, comparative analysis of these biological networks can bring important insights into the functional organization and regulatory mechanisms of biological systems. Methodology/Principal Findings In this paper, we present an effective framework for identifying common interaction patterns in the biological networks of different organisms based on hidden Markov models (HMMs). Given two or more networks, our method efficiently finds the top matching paths in the respective networks, where the matching paths may contain a flexible number of consecutive insertions and deletions. Conclusions/Significance Based on several protein-protein interaction (PPI) networks obtained from the Database of Interacting Proteins (DIP) and other public databases, we demonstrate that our method is able to detect biologically significant pathways that are conserved across different organisms. Our algorithm has a polynomial complexity that grows linearly with the size of the aligned paths. This enables the search for very long paths with more than 10 nodes within a few minutes on a desktop computer. The software program that implements this algorithm is available upon request from the authors.
The cephalosporin antibiotics.

Introduction The first cephalosporin released for clinical use was cephalothin in 1964. Since that time, more than 20 cephalosporin antibiotics have been introduced. These are the most commonly prescribed antibiotics in the United States and account for the largest share of hospital expenditures. To determine which agent to use for an infection in a particular patient involves weighing competing claims of improved antibacterial spectrum, side effects, pharmacokinetics, and cost. This review will address these issues, as well as the basic mechanisms of action of the cephalosporins and their mechanisms of bacterial resistance. In addition, instances in which cephalosporins serve as appropriate alternatives or in which they offer distinct advantages over previously available antimicrobial agents will be described. Chemistry and Mechanism of Action Cephalosporins resemble penicillins (Fig.1) in that they have a β-lactam structure, but the five-member thiazolidine ring characteristic of the penicillins is replaced by a six-member dihydrothiazine ring (Fig. 2). The dihydrothiazine ring of the cephalosporins provides the molecule with the ability to resist bacterial enzymes; the antibacterial activity emanates from the β-lactam ring shared by penicillins and cephalosporins. Modifications at position 7 of the cephalosporin nucleus generally affect the antibacterial spectrum, and substitutions at position 3 of the dihydrothiazine ring alter the pharmacokinetics and metabolic parameters of the drug.