Miracle-dz/UniFAR-FTUs huggingface dataset:
Different settings, different approaches: a qualitative comparison of Portuguese dietitians’ beliefs, attitudes and practices about obesity in public and private settings

Abstract Objective With obesity being a major public health epidemic, dietitians are charged with the difficult task to assist clients in modifying their behaviours. Since there are inconsistent data about dietitians’ beliefs, attitudes and practices concerning obesity and little is known concerning differences in public and private practice, we conducted the present study to address those gaps. Design Semi-structured interviews analysed according to thematic analysis procedures. Setting Public primary-care and private settings. Subjects Seventeen Portuguese registered dietitians working in public primary-care (n 10) and private settings (n 7). Results Regardless of work context, ‘persistence of efforts’ emerged as the main characteristic of dietitians’ action. Besides holding negative attitudes towards obese patients, their practices are not negatively influenced. They perceive themselves as active agents in promoting lifestyle changes, offering as many management strategies as possible to empower patients, feeling positive about the accomplishment of a successful weight loss, believing in their own efficacy and competency in helping patients. However, differences in reimbursement, work environment, perceived barriers, patient characteristics and availability of resources seem to contribute to differences in persistence according to the setting in which dietitians are working, evidenced by an increase of efforts and engagement in private practice and a decrease in public primary-care practice. Conclusions Portuguese dietitians present a positive mindset and actions about obesity treatment outcomes; however, education in behaviour change strategies should be improved. The public health system requires reorganization to enhance effective obesity management delivery. Motivation driving dietitians’ work in private settings should be addressed.
Inferring Gene Functional Linkages Based on Protein Domain Co-occurrence Patterns

Supplemental Methods Lee, Blom, et al., Prioritizing candidate disease genes by network-based boosting of genome-wide association data Inferring gene functional association from human transcript expression data Functional associations based on mRNA co-expression patterns across multiple microarray datasets were analyzed as in (Lee et al. 2008). A total of 166 microarray datasets (spanning several thousand individual microarrays) were assembled from the Stanford Microarray Database (Gollub et al. 2003) and Gene Expression Omnibus (Barrett et al. 2005) databases. Of these sets, 21 sets (Table S2), composed of 1,603 total microarrays, showed significant correlations between the degree of mRNA co-expression (measured as the Pearson correlation coefficient between expression vectors) and the degree of functional association (measured as the LLS for sharing GO annotations). We assigned 21 LLS to each human gene pair based on regression models between the LLS and correlation coefficients, as well as an additional LLS derived from a similar analysis of the concatenated set of all 1,603 arrays. The resulting 22 scores were integrated into a single overall LLS (HS-CX) for co-expression using the weighted sum method of (Lee et al. 2008). Inferring gene functional associations from genomic context of orthologs To discover functional associations based on genomic context, we compared the human protein sequences to 31 archeaebacterial and 393 eubacterial genomes using phylogenetic profiling (Pellegrini et al. 1999) (HS-PG) and the gene neighbor method of (Bowers et al. 2004) (HS-GN), analyzing them as in (Lee et al. 2008). A subset of 184 genomes, one selected from each unique genus, maximized performance of inferred linkages by the gene neighboring method, judged by recall-precision analysis; a set of 313 genomes, one from each unique species, maximized performance by the phylogenetic profiling method. For phylogenetic profiling, we observed improved performance by considering only human proteins with fewer than two domains annotated by the InterPro database (Hunter et al. 2009), as human proteins with greater numbers of domains tended to generate promiscuous functional associations in this approach. We assigned LLS for each human gene pair based on regression models with the genomic context scores from each method. The occurrence of similar patterns of protein domains is often a good indicator of similar protein function. We therefore analyzed InterPro domains for each protein as follows: We generated a matrix of human proteins versus InterPro domains with binary scores (1 for presence and 0 for absence) indicating domain occurrences. We observed improved performance, judged by …
Cloning and Characterization of Putative Zinc Protease Genes of Ehrlichia canis

A putative zinc protease gene operon from Ehrlichia canis was cloned and sequenced. A genomic library was constructed in a pHG165 plasmid vector using Sau 3A partially digested E. canis chromosomal DNA. Sequence analysis of the insert DNA from this clone indicated two open reading frames with a size of 1314 and 1350 bp that encodes for ProA and ProB, respectively. Based on BLAST analyses, ProA and ProB share 20-30% identities with members of the eukaryotic mitochondrial processing peptidase (MPP) subfamily, which are heterodimers containing f and g subunits. The subunits share a 20% of identity, but only MPP- g contains a conserved zinc-binding motif, His-Xaa-Xaa-Glu-His (HXXEH). proA and proB are also detectable in E. canis and Ehrlichia chaffeensis, but not the Anaplasma phagocytophila. 5'-RACE revealed that the 5' end of the proA mRNA is heterogeneous, containing additional adenine residues that may be directed by pseudo-templated transcription. Although ProA was identified in both E. canis and E. chaffeensis, ProB was detected only in E. canis. ProA and ProB were both detectable in E. canis -infected DH82 cells. Sera from dogs, which were either naturally or experimentally infected with E. canis, recognized both the recombinant protein antigens.
Functional organization of sensory input to the olfactory bulb glomerulus analyzed by two-photon calcium imaging

Glomeruli in the olfactory bulb are anatomically discrete modules receiving input from idiotypic olfactory sensory neurons. To examine the functional organization of sensory inputs to individual glomeruli, we loaded olfactory sensory neurons with a Ca2+ indicator and measured odorant-evoked presynaptic Ca2+ signals within single glomeruli by using two-photon microscopy in anaesthetized mice. Odorants evoked patterns of discrete Ca2+ signals throughout the neuropil of a glomerulus. Across glomeruli, Ca2+ signals occurred with equal probability in all glomerular regions. Within single glomeruli, the pattern of intraglomerular Ca2+ signals was indistinguishable for stimuli of different duration, identity, and concentration. Moreover, the response time course of the signals was similar throughout the glomerulus. Hence, sensory inputs to individual glomeruli are spatially heterogeneous but seem to be functionally indiscriminate. These results support the view of olfactory glomeruli as functional units in representing sensory information.
Methods and techniques to identify security incidents using domain knowledge and contextual information

a recent trend in intrusion detection is toward utilizing knowledge-based IDSs. Knowledge-based IDSs store knowledge about cyber-attacks and possible vulnerabilities and use this knowledge to guide the process of attack prediction. One significant limitation of knowledge-based IDSs is the lack of contextual information and domain knowledge used to detect attacks. Contextual information is not only the configuration on the targeted systems and their vulnerabilities. It also covers semantic relationships between malicious activities. In addition, domain knowledge extracted from taxonomies about those activities is a significant contextual factor in attack identification. To overcome these limitations, this work introduces a novel contextual framework which consists of several attack prediction models that are utilized in conjunction with IDSs to detect cyber-attacks.
JoBimText Visualizer: A Graph-based Approach to Contextualizing Distributional Similarity

We introduce an interactive visualization component for the JoBimText project. JoBimText is an open source platform for large-scale distributional semantics based on graph representations. First we describe the underlying technology for computing a distributional thesaurus on words using bipartite graphs of words and context features, and contextualizing the list of semantically similar words towards a given sentential context using graphbased ranking. Then we demonstrate the capabilities of this contextualized text expansion technology in an interactive visualization. The visualization can be used as a semantic parser providing contextualized expansions of words in text as well as disambiguation to word senses induced by graph clustering, and is provided as an open source tool.
The comparative responsiveness of the patient self-report questionnaires and composite disease indices for assessing rheumatoid arthritis activity in routine care.

OBJECTIVES This paper aims to evaluate the internal and external responsiveness of the patient self-report questionnaires, comparatively to the traditional composite indices to assess the activity of rheumatoid arthritis (RA) in everyday practice. METHODS One hundred and ninety-one RA out-patients completed the clinical arthritis activity (PRO-CLARA) index, the rheumatoid arthritis disease activity index (RADAI), the routine assessment of patient index data (RAPID3), and the patient activity score (PAS). Simultaneously, the disease activity score-28 joints based on CRP (DAS28-CRP) and ESR (DAS28-ESR), the simplified disease activity index (SDAI), the clinical disease activity index (CDAI), and the mean overall index for RA (MOI-RA) were computed for each patient. Sensitivity to change was assessed after 6 months of treatment with disease-modifying anti-rheumatic drugs or biologics. Internal responsiveness was evaluated with the effect size (ES) and standardised response mean (SRM). External responsiveness was investigated by receiver operating characteristic (ROC), in categories of respondents, stratified according to the response on an item on change in overall health. In addition, change scores were compared by calculating correlation coefficients. RESULTS No significant differences in internal and external responsiveness were found between self-report questionnaires and composite indices. The internal responsiveness of the self-report questionnaires and composite measures was wide, with SRM and ES ranging from 1.03 (RADAI) to 1.80 (DAS28-ESR) and higher than that of the each individual measures. The responsiveness of the PRO-CLARA was equal to the DAS28-ESR, DAS28-CRP, SDAI or MOI-RA, but better than the CDAI. The RADAI and PAS were less responsive than the PRO-CLARA and RAPID3. The area under ROC curve of the PRO-CLARA gives identical results to those provided by other comparator composite indices. The score changes of all combinations were highly correlated (p<0.0001). CONCLUSIONS The self-report questionnaires showed comparable internal and external responsiveness to the composite activity scores and allow for the detection of rheumatoid disease activity. They appear suitable for clinical decision making, epidemiologic research and clinical trials. Further longitudinal studies are needed to validate these encouraging results.
Iron and Iron Regulatory Proteins in Amoeboid Microglial Cells Are Linked to Oligodendrocyte Death in Hypoxic Neonatal Rat Periventricular White Matter through Production of Proinflammatory Cytokines and Reactive Oxygen/Nitrogen Species

This study was aimed to examine the role of iron in causing periventricular white matter (PWM) damage following a hypoxic injury in the developing brain. Along with iron, the expression of iron regulatory proteins (IRPs) and transferrin receptor (TfR), which are involved in iron acquisition, was also examined in the PWM by subjecting 1-d-old Wistar rats to hypoxia. Apart from an increase in iron levels in PWM, Perls' iron staining showed an increase of intracellular iron in the preponderant amoeboid microglial cells (AMCs) in the tissue. In response to hypoxia, the protein levels of IRP1, IRP2, and TfR in PWM and AMCs were significantly increased. In primary microglial cultures, administration of iron chelator deferoxamine reduced the generation of iron-induced reactive oxygen and nitrogen species and proinflammatory cytokines such as tumor necrosis factor-α and interleukin-1β. Primary oligodendrocytes treated with conditioned medium from hypoxic microglia exhibited reduced glutathione levels, increased lipid peroxidation, upregulated caspase-3 expression, and reduced proliferation. This was reversed to control levels on treatment with conditioned medium from deferoxamine treated hypoxic microglia; also, there was reduction in apoptosis of oligodendrocytes. The present results suggest that excess iron derived primarily from AMCs might be a mediator of oligodendrocyte cell death in PWM following hypoxia in the neonatal brain.
A user-centered approach on combining realism and interactivity in virtual environments

In this paper we describe a project that adopts a user-centered approach in the design of virtual environments (VEs) with enhanced realism and interactivity, guided by real-world applications in the areas of urban planning/architecture and cultural heritage education. In what concerns realism, we introduce an image-based 3D capture process, where realistic models are created from photographs and subsequently displayed in a VR system using a high-quality, view-dependent algorithm. The VE is further enhanced using advanced vegetation and shadow display algorithms as well as 3D sound. A high degree of interactivity is added, allowing users to build and manipulate elements of the VEs according to their needs, as specified through a user task analysis and scenario-based approach which is currently being evaluated. This work is developed as part of the Ell-funded research project CREATE.
Adaptive synchronization of complex networks

In this paper, the adaptive synchronization of coupled complex networks is investigated. Some controllers and adaptive laws are designed to ensure the synchronization of complex networks. With this new effective method, a general complex network can achieve synchronization. Two examples are simulated, using the chaotic Lorenz system and the delayed neural network as the nodes of the dynamical complex network, which demonstrate the feasibility and effectiveness of the proposed method in this paper.
Chinese College Test Takers’ Individual Differences and Reading Test Performance

This study reports on the relationships between test takers’ individual differences and their performance on a reading comprehension test. A total of 518 Chinese college students (252 women and 256 men; M age = 19.26 year, SD = 0.98) answered a questionnaire and sit for a reading comprehension test. The study found that test takers’ L2 language proficiency was closely linked to their test performance. Test takers’ employment of strategies was significantly and positively associated with their performance on the test. Test takers’ motivation was found to be significantly associated with reading test performance. Test anxiety was negatively related to their use of reading strategies and test performance. The results of the study lent support to the threshold hypothesis of language proficiency. The implications for classroom teaching were provided.
Design methods for CMOS low-current finely tunable voltage references covering a wide output range

This paper introduces methods that were used to design a 0.25 /spl mu/m CMOS low-current tight-tolerance shunt voltage reference circuit. It shows how a recently reported method to produce laser tuned diffused resistors can be applied to the design of continuously tunable voltage references. The methods are validated with a prototype integrated circuit. Measured results show that the output voltage is continuously tunable, from 1.241V to 2.048V, at 0.05% accuracy. The design occupies 0.43 mm/sup 2/ and has a quiescent current of 10 /spl mu/A.
A classification approach to coreference in discharge summaries: 2011 i2b2 challenge

OBJECTIVE To create a highly accurate coreference system in discharge summaries for the 2011 i2b2 challenge. The coreference categories include Person, Problem, Treatment, and Test. DESIGN An integrated coreference resolution system was developed by exploiting Person attributes, contextual semantic clues, and world knowledge. It includes three subsystems: Person coreference system based on three Person attributes, Problem/Treatment/Test system based on numerous contextual semantic extractors and world knowledge, and Pronoun system based on a multi-class support vector machine classifier. The three Person attributes are patient, relative and hospital personnel. Contextual semantic extractors include anatomy, position, medication, indicator, temporal, spatial, section, modifier, equipment, operation, and assertion. The world knowledge is extracted from external resources such as Wikipedia. MEASUREMENTS Micro-averaged precision, recall and F-measure in MUC, BCubed and CEAF were used to evaluate results. RESULTS The system achieved an overall micro-averaged precision, recall and F-measure of 0.906, 0.925, and 0.915, respectively, on test data (from four hospitals) released by the challenge organizers. It achieved a precision, recall and F-measure of 0.905, 0.920 and 0.913, respectively, on test data without Pittsburgh data. We ranked the first out of 20 competing teams. Among the four sub-tasks on Person, Problem, Treatment, and Test, the highest F-measure was seen for Person coreference. CONCLUSIONS This system achieved encouraging results. The Person system can determine whether personal pronouns and proper names are coreferent or not. The Problem/Treatment/Test system benefits from both world knowledge in evaluating the similarity of two mentions and contextual semantic extractors in identifying semantic clues. The Pronoun system can automatically detect whether a Pronoun mention is coreferent to that of the other four types. This study demonstrates that it is feasible to accomplish the coreference task in discharge summaries.
Accounting for data intermittency in a software gnss receiver

In a GNSS software receiver, blocks of digitized intermediate-frequency (IF) data are prepared at the front end and sent to the processing unit for signal acquisition, tracking, demodulation, and position fix. A problem that is observed in practice when the GNSS software module is co-located with a mobile phone device is that the digitized IF data are subject to data intermittency. The intermittency results from the use of mobile phone when the GNSS signals are being received or the execution of higher priority routine in the host computer. An improper buffering scheme at the front end may also lead to such phenomena. Such data intermittency leads to burst-type errors (rather than bit-type errors) on the data to be processed, posing a challenge for the tracking of the GNSS signals. Indeed, if not properly handled, a typical tracking algorithm is not able to accommodate such a large data gap. In the paper, a decision-aided tracking algorithm is developed for a seamless tracking of codes and phases. The effects of data intermittency on code and phase tracking are analyzed. To accounting for the effect without going through the reacquisition process, a detector based on signal power and continuity is then implemented to facilitate decision making. It is shown, through the processing of field gathered data, that the proposed algorithm can indeed be able to continuously track codes and phases in the presence of data intermittency.
Modeling stochasticity and robustness in gene regulatory networks

Motivation: Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed interest in Boolean modeling techniques for gene regulatory networks (GRNs). However, due to their deterministic nature, it is often difficult to identify whether these modeling approaches are robust to the addition of stochastic noise that is widespread in gene regulatory processes. Stochasticity in Boolean models of GRNs has been addressed relatively sparingly in the past, mainly by flipping the expression of genes between different expression levels with a predefined probability. This stochasticity in nodes (SIN) model leads to over representation of noise in GRNs and hence non-correspondence with biological observations. Results: In this article, we introduce the stochasticity in functions (SIF) model for simulating stochasticity in Boolean models of GRNs. By providing biological motivation behind the use of the SIF model and applying it to the T-helper and T-cell activation networks, we show that the SIF model provides more biologically robust results than the existing SIN model of stochasticity in GRNs. Availability: Algorithms are made available under our Boolean modeling toolbox, GenYsis. The software binaries can be downloaded from http://si2.epfl.ch/∼garg/genysis.html. Contact: abhishek.garg@epfl.ch
Maintaining flow isolation in work-conserving flow aggregation

In order to improve the scalability of scheduling protocols with bounded end-to-end delay, much effort has focused on reducing the amount of per-flow state at routers. One technique to reduce this state is flow aggregation, in which multiple individual flows are aggregated into a single aggregate flow. In addition to reducing per-flow state, flow aggregation has the advantage of a per-hop delay that is inversely proportional to the rate of the aggregate flow, while in the case of no aggregation, the per-hop delay is inversely proportional to the (smaller) rate of the individual flow. Flow aggregation in general is non-work-conserving. Recently, a work-conserving flow aggregation technique has been proposed. However, it has the disadvantage that the end-to-end delay of an individual flow is related to the burstiness of other flows sharing its aggregate flow. Here, we show how work-conserving flow aggregation may be performed without this drawback, that is, the end-to-end delay of an individual flow is independent of the burstiness of other flows.
Effects of CalmodulinAntagonistsand Cytochalasinson Proliferationand Differentiationof HumanPromyelocyticLeukemiaCell Line HL-601

To identify the possible roles of Ca2+-related proteins, calmodulin and microfilaments in leukemic cells, we tested the effect of calmodulin antagonists and cytochalasins on proliferation and differentiation of human promyelocytic leukemic HL-60 cells. The growth of HL-60 was inhibited by A/-(6-aminohexyl)-5-chloro-1 naphthalenesulfonamide, A/-(4-aminobutyl)-5-chloro-2-naphthalenesulfonamide, and trifluoperazine dihydrochloride. In contrast, the 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3]-induced differentia tion of HL-60, as judged by plasma-membrane antigenic changes detected by monoclonal antibodies (OKM1, OKT9), nitroblue tetrazolium reduction, and induction of phagocytotic capacity, was not inhibited by A/-(6-aminohexyl)-5-chloro-1-naphthalene sulfonamide or A/-(4-aminobutyl)-5-chloro-2-naphthalenesulfonamide, although phagocytosis was depressed by A/-(6-aminohexyl)-5-chloro-1 -naphthalenesulfonamide or A/-(4-aminobutyl)-5chloro-2-naphthalenesulfonamide. Trifluoperazine dihydrochlo ride also failed to inhibit the antigenic change induced by 1,25(OH)2D3. Cytochalasins B and D, microfilament-disrupting agents, inhibited the cytoplasmic division and the growth of HL60 but did not inhibit the 1Â¿S-fOHfeDs-induced differentiation. These findings suggest that the calmodulinand microfilamentdependent process may be involved in the proliferation of HL60, but not in the differentiation induced by 1Â¿S-iOHfeDa.