Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing Genome-wide Association Study Data with the R Package genMOSS

The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving window approach to identify combinations of single nucleotide polymorphisms associated with a response. The prior used in Bayesian computations is the generalized hyper Dirichlet.
Building annotated resources for automatic text summarisation

Annotated corpora are necessary for automatic summarisation, but given how difficult is to produce them there are only few available. This paper presents an annotation tool which helps the human annotator to select the important units from a text. In addition to the tool, a new annotation scheme is proposed so that phenomena which such as presence of anaphoric expressions and redundancy can be marked. We argue that by annotating these phenomena the results of evaluation can be made more reliable.
Examining Interactions of HIV-1 Reverse Transcriptase with Single-stranded Template Nucleotides by Nucleoside Analog Interference*

Crystallographic studies have implicated several residues of the p66 fingers subdomain of human immunodeficiency virus type-1 reverse transcriptase in contacting the single-stranded template overhang immediately ahead of the DNA polymerase catalytic center. This interaction presumably assists in inducing the appropriate geometry on the template base for efficient and accurate incorporation of the incoming dNTP. To investigate this, we introduced nucleoside analogs either individually or in tandem into the DNA template ahead of the catalytic center and investigated whether they induce pausing of the replication machinery before serving as the template base. Analogs included abasic tetrahydrofuran linkages, neutralizing methylphosphonate linkages, and conformationally locked nucleosides. In addition, several Phe-61 mutants were included in our analysis, based on previous data indicating that altering this residue affects both strand displacement synthesis and the fidelity of DNA synthesis. We demonstrate here that altering the topology of the template strand two nucleotides ahead of the catalytic center can interrupt DNA synthesis. Mutating Phe-61 to either Ala or Leu accentuates this defect, whereas replacement with an aromatic residue (Trp) allows the mutant enzyme to bypass the template analogs with relative ease.
Multiobjectivity and complexity in embodied cognition

We propose a novel perspective on the use of evolutionary multiobjective optimization (EMO) as a paradigm for evolving embodied organisms and as a framework for characterizing complexity. The paper demonstrates novel experiments that show the power of EMO in generating robots with different morphologies, yet with very similar locomotion abilities. The proposed framework for comparing the complexity of an object across different complexity measures allowed meaningful and quantifiable comparisons between the evolved organisms. We show empirically that the partial order feature inherited in the Pareto concept exhibits characteristics which are suitable for comparing between the complexities of artificially evolved embodied organisms.
Potential associations between fecal shedding of Salmonella in feedlot cattle treated for apparent respiratory disease and subsequent adverse health outcomes

A prospective cohort study was used to assess whether Salmonella fecal shedding in commercial feedlot cattle treated with antimicrobials for respiratory disease was associated with subsequent adverse health outcomes. Feces were collected per rectum from cattle that were examined for apparent respiratory disease, had a rectal temperature ≥40 °C, and subsequently received antimicrobial treatment. Salmonella were recovered from 918 (73.7%) of 1 245 fecal samples and weekly prevalence estimates ranged from 49 to 100% over the 3-month study. Genotypic and phenotypic characteristics of Salmonella strains in the population were determined. Serogroup E Salmonella were most common (73.3%), followed by C1 (11.0%), C3 (8.6%), and B (1.1%). Predominant serotypes were Orion (46.5%), Anatum (19.8%), Kentucky (8.7%), Montevideo (7.5%), and Senftenberg (4.9%). Few isolates (36/918) were positive for antimicrobial resistance-associated integron gene intI1. Phenotypic susceptibility was associated with isolate intI1 status. Crude re-pull, re-treatment and case fatality risks were higher for cattle that were Salmonella-positive versus -negative at initial treatment, but not statistically different on multivariable analysis. However, case fatality risk was higher for cattle shedding Group B Salmonella than for cattle shedding other serogroups. Lots (groups) with a higher Salmonella prevalence at first treatment had a higher proportion of mortalities occur in a hospital pen, higher overall re-treatment risks, and were more likely to be sampled later in the study. Results indicate a high prevalence of Salmonella in this population of cattle treated for apparent respiratory disease, but that effects associated with clinical outcomes may depend on the Salmonella strain.
Murine Hepatitis Virus Strain 3 Induces the Macrophage Prothrombinase fgl-2 through p38 Mitogen-activated Protein Kinase Activation*

The clinical syndrome of acute liver failure produced by fulminant viral hepatitis can be reproduced in mice by infection with murine hepatitis virus strain 3 (MHV-3). Although it is clear that MHV-3-induced hepatitis depends upon macrophage activation and the expression of a specific prothrombinase,fgl-2, the signaling pathways involved in virally stimulated cell activation are unclear. Since we had previously found that MHV-3 induces the tyrosine phosphorylation of cellular proteins, we investigated the roles of the mitogen-activated protein kinase (MAPK) proteins. In a series of Western blots, immunoprecipitation andin vitro kinase assay studies, we found that both the extracellular signal-related kinase (ERK) and p38 MAPK proteins are tyrosine-phosphorylated and activated following exposure of murine peritoneal exudative macrophages (PEM) to MHV-3. Although p38 phosphorylation and activity are induced soon after MHV-3 exposure, peaking by 1–5 min, ERK phosphorylation and activity increase more gradually, peaking at 20–30 min and gradually fading thereafter. Interestingly, whereas selective p38 inhibition with SB203580 (1–20 μm) abolished the virally stimulated induction offgl-2 mRNA, protein, and functional activity, selective ERK inhibition with PD98059 (1–50 μm) limitedfgl-2 functional activity but had little to no effect onfgl-2 mRNA or protein levels. Moreover, whereas inhibition of ERK had no effect on p38 activity, p38 inhibition consistently increased MHV-3-induced ERK activity. To ensure that these pathways were relevant in vivo, MHV-3 was injected intraperitoneally, and peritoneal exudative macrophages were collected. Again, MHV-3 exposure led to increased p38 and ERK tyrosine phosphorylation. These data argue that MHV-3 induces tightly interconnected ERK and p38 MAPK cascades in the macrophage bothin vitro and in vivo. Although the ERK and p38 MAPK proteins have discordant effects at the level of fgl-2expression, both converge at the level of its activity, suggesting that targeted MAPK inhibition may ultimately be useful in the modulation of viral hepatitis.
Mutations in the cytoplasmic tail of influenza A virus neuraminidase affect incorporation into virions

The significance of the conserved cytoplasmic tail sequence of influenza A virus neuraminidase (NA) was analyzed by the recently developed reverse genetics technique (W. Luytjes, M. Krystal, M. Enami, J. D. Parvin, and P. Palese, Cell 59:1107-1113, 1989). A chimeric influenza virus A/WSN/33 NA containing the influenza B virus cytoplasmic tail rescued influenza A virus infectivity. The transfectant virus had less NA incorporated into virions than A/WSN/33, indicating that the cytoplasmic tail of influenza virus NA plays a role in incorporation of NA into virions. However, these results also suggest that the influenza A virus and influenza B virus cytoplasmic tail sequences share common features that lead to the production of infectious virus. Transfectant virus was obtained with all cytoplasmic tail mutants generated by site-directed mutagenesis of the influenza A virus tail, except for the mutant resulting from substitution of the conserved proline residue, presumably because of its contribution to the secondary structure of the tail. No virus was rescued when the cytoplasmic tail was deleted, indicating that the cytoplasmic tail is essential for production of the virus. The virulence of the transfectant viruses in mice was directly proportional to the amount of NA incorporated. The importance of the NA cytoplasmic tail in virus assembly and virulence has implications for use in developing antiviral strategies.
Socioeconomic factors and health risk behaviors among university students in Turkey: questionnaire study.

AIM To explore relations between socioeconomic factors and health risk behaviors in university students in Turkey. METHODS A total of 650 students currently enrolled at the university in Ankara were selected for the study by means of a circular sampling method. They answered a questionnaire on health risk behaviors. We used multivariate analysis to analyze the relations between socioeconomic variables and each of the following participants' behaviors in the last year: use of cigarettes, alcohol, or drugs; driving under the influence of alcohol; unprotected sex; attempted suicide; self-mutilation; physical fighting; carrying firearms or edged weapon; not wearing a safety belt in motor vehicles; or riding a motorcycle without a helmet. RESULTS Health risk behaviors in university students were in general related to low socioeconomic status, except for alcohol use, which was related to high socioeconomic status. Among female students whose mothers had completed high school, 81.9% used alcohol, compared with less than 68% of female students whose mothers had not completed high school or had completed university (P<0.001). Also, 4.0% of female students whose mothers had completed high school had attempted suicide, compared with less than 1.5% of female students whose mothers had not completed high school or had completed university (P=0.026). In male students, important variables were parental education level and paternal employment status. Among male students who had unemployed fathers, 66.7% used cigarettes (P=0.015), 26.7% engaged in substance use (P<0.010), and 4.4 % attempted suicide (P<0.050) in comparison with 11.9 and 0.7%, respectively, of male students whose fathers were employed. Logistic regression showed male gender to be associated with an increase in all risk behaviors (odds ratio 1.114, 95% confidence interval 1.652-5.622, P<0.001). CONCLUSION This study confirms the findings of similar studies in western developed countries, suggesting that relations between socioeconomic variables and health risk behaviors in young people reflect a basic phenomenon not greatly influenced by culture.
La necesidad de teorías heterodoxas para el acercamiento entre historia y economía [The need of Heterodox theories for a marriage between history and economics]

This paper shows how economic theory and history can be matched with the use of heterodox theories. This matching between history and economics is needed for a better comprehension of reality. Cliometrics, regulationism, institutional economics are some of the tentative approaches that have been used. The use of only orthodox theories is not enough for an understanding of multiple economic phenomena arising in the real world.
Effect of fatigue on joint position sense of the knee

This study was designed to test position sense of the knee joint before and after fatigue in order to determine whether muscle or capsular receptors are the primary sensors for joint position sense. Reproduction of passive positioning and detection of the onset of motion (kinesthesia) were employed to measure joint position sense. Eleven subjects underwent joint position sense measurement before and after a fatigue protocol. A significant worsening of reproduction of knee joint angle after fatigue was noted (p < 0.05). Threshold (kinesthesia) showed no statistically significant change after fatigue. A significant correlation of reproduction measurements and threshold measurements prior to fatigue (p < 0.01) demonstrated that the same neural mechanism is applicable in the rested state, but these variables did not correlate significantly after fatigue. There was a significant correlation between reproduction measurements before and after fatigue (p = 0.018), while no correlation was seen for the pre‐ and postfatigue threshold measurements, suggesting a change in the neural path after fatigue. Since both tests of joint position sense are affected by fatigue, we conclude that muscle receptors are a prominent, if not primary, determinant of joint position sense, and capsular receptors may have a secondary role. Reproduction ability is decreased, presumably through the loss of efficiency of muscle receptors. The threshold data suggest a change in the mechanism of appreciation after fatigue, possibly due to increased sensitivity of capsular receptors from muscle‐fatigue‐induced laxity.
Proximity: Localization vs. Distance in PR News Releases

Charting the use made of 197 news releases mailed from a Mississippi university to 121 daily and weekly state newspapers tested this question: which results in more use, the proximity of the public relations release source or localization of the facts in the story. The influence of proximity proved to be very slight but localization of stories resulted in relatively higher use. This study compared costs and concludes that localization of public relations news releases may be worth — in the age of word processing computers — the small extra expense.
The PROSITE database, its status in 2002

PROSITE [Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219] is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http://www.expasy.org/prosite/) consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains.
Who Said Pedestrian Means Dull: Teaching Methods in the Measurement of Behaviour Through Observational Studies of Pedestrian Behaviour

The Measuring Behaviour class (PSYO 3161) at Dalhousie University is designed to teach third year undergraduate students the theoretical and methodological procedures for the measurement of behaviour. For this class, students complete laboratory projects on the behaviour of mice and humans. For one of these projects, students completed observational studies on the behaviour of pedestrians at cross-walks. Students worked in groups to design an experiment to answer a question concerning pedestrian behaviour, and by doing so applied knowledge learned in the class on experimental design, sampling rules, objective definition of behavioural measures and statistical analysis. The students collected data, analyzed the data and then completed written reports describing the results. This poster describes some of the studies completed by students in the Measuring Behaviour class, and demonstrates the value of pedestrian behaviour as an educational tool for classes designed to teach methods for measuring behaviour. Author Keywords Teaching, pedestrian behaviour.
Reproducing Knowledge: Replication Without Imitation at Moderate Complexity

The complexity of a firm's strategy affects both the ease with which the firm can replicate the strategy in a new setting and the ease with which rivals can imitate it. Simple strategies are as readily imitated as replicated, and highly intricate strategies resist imitation and replication equally. At moderate levels of complexity, however, a wedge develops between the ease of replication and the difficulty of imitation, so long as the replicator has better information than the imitator about the original success. An agent-based simulation model clarifies the structural reasons that this is so. The model also shows how the wedge-maximizing level of complexity varies with the replicator's informational edge over the imitator.The results help to pinpoint situations in which strategies requiring replication are likely to defy imitation and generate sustained competitive advantage. More generally, the analysis sheds light on the value of superior but imperfect information about good solutions to hard problems. Finally, the results suggest that a pattern long observed by organization scholars--that "loosely coupled organizations" are especially effective competitors--may arise for a very different reason than is normally posited.
Cooperative inhibition of renal cancer growth by anti-epidermal growth factor receptor antibody and protein kinase A antisense oligonucleotide.

BACKGROUND The expression of epidermal growth factor receptor (EGFR) and type I cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKAI) is associated with neoplastic transformation. By use of human renal cancer cell lines (i.e., 769-P, ACHN, A498, and SW839), we investigated the antiproliferative activity and the antitumor activity of an anti-EGFR humanized chimeric mouse monoclonal antibody, MAb C225, and a novel mixed backbone 18-mer antisense oligonucleotide, HYB 190, that targets expression of the RIalpha regulatory subunit of PKAI. METHODS The antiproliferative activity of MAb C225 and oligonucleotide HYB 190, alone or in combination, on different renal cancer cell lines was determined by monitoring cell growth in soft agar. In addition, the induction of apoptosis by treatment with the anti-EGFR antibody and/or antisense PKAI oligonucleotides was evaluated by flow cytometric analysis of fragmented DNA. The antitumor activity of MAb C225 and oligonucleotide HYB 190 was determined in athymic mice bearing established ACHN tumor xenografts. Cell proliferation and tumor growth data were evaluated for statistical significance using Student's t test; reported P values are two-sided. RESULTS MAb C225 and oligonucleotide HYB 190 inhibited colony formation in soft agar in a dose-dependent manner for all renal cancer cell lines tested. We observed a potentiation of growth inhibition and induction of apoptosis when 769-P cells and ACHN cells were treated with both agents. Combination treatment with MAb C225 and oligonucleotide HYB 190 caused regression of ACHN tumor xenografts, whereas single-agent treatment only delayed tumor growth. CONCLUSION The combination of anti-EGFR MAb C225 and ited cooperative antiproliferative effects and cooperative antitumor effects on EGFR and PKAI-expressing human renal cancer cell lines.
Modeling of bulk acoustic wave devices built on piezoelectric stack structures: Impedance matrix analysis and network representation

The fundamental electro-acoustic properties of a solid layer are deduced in terms of its impedance matrix (Z) and represented by a network for modeling the bulk acoustic wave devices built on piezoelectric stacked structures. A piezoelectric layer is described by a three-port equivalent network, a nonpiezoelectric layer, and a short- or open-circuit piezoelectric layer by a two-port one. Electrical input impedance of the resonator is derived in terms of the Z-matrix of both the piezoelectric layer and an external load, the unique expression applies whether the resonator is a mono- or electroded-layer or a solidly mounted resonator (SMR). The loading effects of AZ-electrodes on the resonating frequencies of the piezoelectric ZnO-layer are analyzed. Transmission and reflection properties of Bragg mirrors are investigated along with the bulk radiation in SMR. As a synthesizing example, a coupled resonator filter (CR.F) is analyzed using the associated two-port equivalent network and by calculating the power transmission to a 50 Omega-load. The stacked crystal filter is naturally included in the model as a special case of CRF. Combining a comprehensive matrix analysis and an instructive network representation and setting the problem with a full vectorial formalism are peculiar features of the presented approach.
Competence and performance in child language: are children really competent to judge?

ABSTRACT The notion of competence as it applies to child language is critically assessed in the light of evidence collected from a number of linguistic performances which share the same word-order rule. These performances – production, comprehension, judgment and correction – parallel Moravcsik's (1969) formulation of Chomsky's criteria for tacit knowledge of a rule, i.e. competence. It was found that these criteria are not all satisfied until the child is four or five years old, as the performances appear at very different points in time. Alternative criteria for tacit knowledge are suggested, with specific models of each performance replacing a general model of competence for early child speech.
SDF‐1α/CXCR4 axis is involved in glucose‐potentiated proliferation and chemotaxis in rat vascular smooth muscle cells

Excessive proliferation of vascular smooth muscle cells (VSMCs), which migrate from the tunica media to the subendothelial region, is one of the primary lesions involved in atherogenesis in diabetes. Here, we investigated whether high glucose potentiated the proliferation and chemotaxis of VSMCs by activating SDF‐1α/CXCR4/PI‐3K/Akt signalling. The expression of SDF‐1α, CXCR4 and PCNA was up‐regulated in tunica media of thoracic aortas by streptozotocin‐induced hyperglycaemic Sprague–Dawley rats. Exposure of primary VSMCs to high glucose (25 mM) led to the up‐regulated expression of SDF‐1α and CXCR4, activated PI‐3K/Akt signalling, and consequently promoted the proliferation and chemotaxis of VSMCs. Interestingly, the administration of SDF‐1 siRNA or neutralizing antibody against SDF‐1α abolished high glucose‐induced up‐regulation of CXCR4. Moreover, pretreatment with SDF‐1α neutralizing antibody, CXCR4 specific inhibitor (AMD3100) or PI‐3K inhibitor (LY294002) attenuated the high glucose‐potentiated proliferation and chemotaxis in VSMCs. These results suggested that high glucose activated the SDF‐1α/CXCR4/PI‐3K/Akt signalling pathway in VSMCs in an autocrine manner, which enhanced the proliferation and chemotaxis of VSMCs.
Beeinflussung der Wirkung von Ernährungsinformation durch Framing: Analyse am Beispiel von Folsäure

Die Bereitstellung und verbrauchergerechte Aufbereitung von Informationen stellt eine MA¶glichkeit dar, Konsumenten darin zu unterstA¼tzen, Gesundheitsaspekte vermehrt in das Kauf- und Essverhalten zu integrieren. In der VerhaltensA¶konomik gelten Framing-Effekte als wichtige Bestimmungsfaktoren fA¼r die Wahrnehmung von Informationen. Im Rahmen des vorliegenden Beitrags werden Framing-Effekte am Beispiel von ErnA¤hrungsinformationen A¼ber FolsA¤ure mit Hilfe eines Experiments untersucht. Die Ergebnisse zeigen, dass der Frame einen, wenn auch nur geringen, Einfluss auf die Wahrnehmung, das InformationsbedA¼rfnis und den Entscheidungsprozess ausA¼bt. Insgesamt verursacht der negative Frame, wie erwartet, stA¤rkere Effekte als der positive. One way to support consumers in integrating health aspects into their purchase and eating behaviour is to make information available to consumers in a comprehensible manner. In behavioural economics framing effects are acknowledged as important factors influencing perception of information. In this paper framing effects are analysed by means of an experiment using the example of information about folic acid. The results give evidence that framing influences consumersâ€™ perception, the need for information and decision process even though the effect is small. Overall, a negative frame results in a stronger effect than a positive one.