Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects

This article describes a number of algorithms that are designed to improve both the efficiency and accuracy of finite difference solutions to the Poisson–Boltzmann equation (the FDPB method) and to extend its range of application. The algorithms are incorporated in the DelPhi program. The first algorithm involves an efficient and accurate semianalytical method to map the molecular surface of a molecule onto a three‐dimensional lattice. This method constitutes a significant improvement over existing methods in terms of its combination of speed and accuracy. The DelPhi program has also been expanded to allow the definition of geometrical objects such as spheres, cylinders, cones, and parallelepipeds, which can be used to describe a system that may also include a standard atomic level depiction of molecules. Each object can have a different dielectric constant and a different surface or volume charge distribution. The improved definition of the surface leads to increased precision in the numerical solutions of the PB equation that are obtained. A further improvement in the precision of solvation energy calculations is obtained from a procedure that calculates induced surface charges from the FDPB solutions and then uses these charges in the calculation of reaction field energies. The program allows for finite difference grids of large dimension; currently a maximum of 5713 can be used on molecules containing several thousand atoms and charges. As described elsewhere, DelPhi can also treat mixed salt systems containing mono‐ and divalent ions and provide electrostatic free energies as defined by the nonlinear PB equation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 128–137, 2002
Let's Get Closer: Feelings of Connectedness from Using Social Media with Implications for Brand Outcomes

Despite the fact that social media offers consumers opportunities to connect with each other, little work has focused on how what consumers do on social media interacts with why they do it to affect their feelings of connection. Further, the extent to which these social media interactions occur in brand contexts is likely to affect consumers' response to brands and could have important implications for brands' social media marketing efforts. Drawing on regulatory focus theory, we show that the fit conditions of promotion-focused, more social behaviors and prevention-focused, less social behaviors produce higher feelings of connection compared to the nonfit conditions, owing to a subjective sensation that the fit conditions just feel right. We also show that when these fit conditions occur in brand-related contexts, they produce stronger feelings of connection toward the brand and more positive responses to the brand's social media marketing efforts.
Syntactic Dependency Parsers for Biomedical-NLP

Syntactic parsers have made a leap in accuracy and speed in recent years. The high order structural information provided by dependency parsers is useful for a variety of NLP applications. We present a biomedical model for the EasyFirst parser, a fast and accurate parser for creating Stanford Dependencies. We evaluate the models trained in the biomedical domains of EasyFirst and Clear-Parser in a number of task oriented metrics. Both parsers provide stat of the art speed and accuracy in the Genia of over 89%. We show that Clear-Parser excels at tasks relating to negation identification while EasyFirst excels at tasks relating to Named Entities and is more robust to changes in domain.
"It's Kind of a Funny Story...": Exploring Sexual Storytelling Among College Students

“It‟s Kind of a Funny Story. ”: Exploring Sexual Storytelling among College Students. (August 2011) Ashley Spinozzi, B.A., The University of Illinois at Urbana-Champaign Chair of Advisory Committee: Dr. Barbara F. Sharf Sexual health among college students is in jeopardy. College aged men and women face risks associated with sexuality because of college attendance and gender. Through storytelling, college students convey their sexual experiences to their friends and peers, though this process is predominantly focused on the narrator rather than the listener. I investigated how this storytelling influences those who listen to stories through focus groups, using the theory of Communication Privacy Management and grounded theory to understand focus group results. The results revealed themes regarding the context in which storytelling occurs, how storytelling affects listeners, and how listeners interpret the motivation of the narrator. Communication context and communication influence were similar for males and females while perception of narrator motivation differed based on gender. Participants perceived motivation to be highly related to reputation, truth, and relationship status. Additionally, participants reported being impacted by listening to their friends and non-friends share their stories.
Analyzing the Structure of the Centrality-Productivity Literature Created Between 1948 and 1979

Science grows and cumulates on the research fronts of disciplinary specialties, implying that the most fruitful citation analyses will be those looking at well-defined specialties or subspecial ties. The entire literature on centrality and productivity from 1948 to 1979 is used to construct a citation network. Methods are proposed for the analysis of the connective structure of such networks and then applied to the centrality-productivity citation structure. These methods permit identification of the main paths through this literature, distinct intellectual phases, and key articles contributing to the cumulative formation ofknowledge about centrality and productivity in social networks. From 1948 through 1956, centrality and program were integrated in a single research program. By the early 1960s, there were two research streams. One focused on measuring centrality in graphs but lost the substantive focus on productivity. The other branch continued the experimental focus on productivity but lost the idea of centrality.
A Flexible Template Boundary Element in the RNA Subunit of Fission Yeast Telomerase*

Telomerase adds telomeric repeat sequences to chromosome ends using a short region of its RNA subunit as a template. Telomerase RNA subunits are phylogenetically highly divergent, and different strategies have evolved to demarcate the boundary of the template region. The recent identification of the gene encoding telomerase RNA in the fission yeast Schizosaccharomyces pombe (ter1+) has opened the door for structure-function analyses in a model that shares many features with the telomere maintenance machinery of higher eukaryotes. Here we describe a structural element in TER1 that defines the 5′ boundary of the template. Disruption of a predicted long range base pairing interaction between template-adjacent nucleotides and a sequence further upstream resulted in reverse transcription beyond the template region and caused telomere shortening. Normal telomere length was restored by combining complementary nucleotide substitutions in both elements, showing that base pairing, not a specific sequence, limits reverse transcription beyond the template. The template boundary described here resembles that of budding yeasts and some mammalian telomerases. However, unlike any previously characterized boundary element, part of the paired region overlaps with the template itself, thus necessitating disruption of these interactions during most reverse transcription cycles. We show that changes in the paired region directly affect the length of individual telomeric repeat units. Our data further illustrate that marginal alignment of the telomeric 3′ end with RNA sequences downstream of the template is responsible for primer slippage, causing incorporation of strings of guanosines at the start of a subset of repeats.
Alternatives to WIMPy hegemony and pressure-sensitive text input for mobile devices

Even before the advent of the modern windows, icons, menus and pointers (WIMP) interaction paradigm, researchers have focused intently on interfaces which do not chain users to their desks to interact with the same old keyboard, monitor and mouse. The instinct for researchers to explore alternatives to traditional interfaces has been present from the beginning of computing. Indeed, the WIMP paradigm itself was born as an attempt to break away from the text-based, single-threaded computing world that had dominated previously. In defense of the state of the art, many of the limitations on computing interfaces historically resulted from the limitations on the processing capabilities of the computing devices. Moreover, computer scientists and engineers have regularly used additional capacity to improve computing interfaces, showing that the field is at least partially cognizant of the deficiencies in computer interfaces.
Architecture-based Qualitative Risk Analysis for Availability of IT Infrastructures

An IT risk assessment must deliver the best possible quality of results in a time-eﬀective way. Organisations are used to customise the general-purpose standard risk assessment methods in a way that can satisfy their requirements. In this paper we present the QualTD Model and method, which is meant to be employed together with standard risk assessment methods for the qualitative assessment of availability risks of IT architectures, or parts of them. The QualTD Model is based on our previous quantitative model, but geared to industrial practice since it does not require quantitative data which is often too costly to acquire. We validate the model and method in a real-world case by performing a risk assessment on the authentication and authorisation system of a large multinational company and by evaluating the results w.r. t. the goals of the stakeholders of the system. We also perform a review of the most popular standard risk assessment methods and an analysis of which one can be actually integrated with our QualTD Model.
Reverse Engineering of Graphical User Interfaces Using Static Analyses

This paper describes static analyses for reverse engineering graphical user interfaces (GUIs). These analyses, implemented in the Bauhaus tool suite, support typical maintenance tasks like migrating from a hand-written GUI to so-called GUI builders and redocumentation of the GUI. Our tool extracts the program's windows and their structure, the attributes of the widgets and their values, the GUI events that might occur at runtime, and the event handlers associated with those events. We explain our approach and report encouraging results for several programs.
Models for Connected Networks over Random Points and a Route-Length Statistic

We review mathematically tractable models for connected networks on random points in the plane, emphasising the little-studied class of proximity graphs and introducing a new model called the Hammersley network. We introduce and motivate a particular statistic R measuring shortness of routes in a network. We show (via Monte Carlo, in part) the trade-o between normalized network length and R in a oneparameter family of proximity graphs. How close this family comes to the optimal trade-o over all possible networks remains an intriguing open question. xxx Almost finished draft.
Human T cell activation. I. Monocyte-independent activation and proliferation induced by anti-T3 monoclonal antibodies in the presence of tumor promoter 12-o-tetradecanoyl phorbol-13 acetate

Three monoclonal antibodies (mAb), of IgG1, IgG2a, and IgM isotypes, raised against the T3 complex, were used to probe the activation of human T cells. The IgM antibody 235 was not mitogenic for peripheral blood mononuclear cells (PMC). It efficiently blocked the proliferation of PMC induced by T cell mitogens, alloantigens, and soluble antigens. The other two antibodies were mitogenic, and behaved similarly to Leu 4 and OKT3, respectively. In T cell preparations with less than 0.1% monocytes (as assayed by nonspecific esterase staining), all three mAb were not mitogenic. They failed to induce either interleukin 2 (IL-2) receptor expression or IL-2 secretion. Addition of IL-1 failed to collaborate with anti-T3 mAb to induce these T cells to proliferate, but IL-2 enhanced T cell proliferation slightly. Monocyte-depleted T cells, however, proliferated in response to all three anti-T3 mAb, when TPA was added, in a dose-dependent manner. TPA induced a low level of IL-2 receptor expression in monocyte-depleted T cells, without inducing IL-2 secretion. Anti-T3 plus TPA induced a marked enhancement in both quantity and intensity of IL-2 receptor expression. IL-2 secretion was also detected. These results indicate that anti-T3 IgM can deliver an inductive signal despite its blockage of T cell proliferation, and that two signals are necessary and perhaps sufficient to induce human T cell activation and proliferation.
Thrust loss saving design of overlapping rotor arrangement on small multirotor unmanned aerial vehicles

Small multirotor unmanned aerial vehicles (UAVs) are suitable for surveillance or inspection operations, such as disaster site observations or building inspections, as they can hover. Therefore, engineers and associations plan to use them for civilian applications. However, the payload capacity of current UAVs is too small to carry heavy sensors or batteries. Thus, improving payload capacity by increasing the number of rotors has been considered to achieve an increase in the thrust for a limited body size. Although, most rotor arrangements cause rotor flow interaction, which degrade the total thrust. To design a rotor arrangement on small multirotor UAVs, it is necessary to first evaluate the thrust from an aerodynamic perspective. In this study, we evaluated the effect of rotor flow interactions on thrust for three two-rotor configurations. The investigation showed that the thrust of rotors in wake flow is degraded. Thus, we proposed a new octorotor UAV configuration based on the results of our evaluation of the rotor flow interaction and verified the thrust improvement compared to a coaxial octorotor UAV configuration. This investigation demonstrated a thrust improvement of 24% over the total thrust of the coaxial octorotor UAV.
Olanzapine-Induced Mania in Bipolar Spectrum Disorder:A Case Report

Objective: To report the case of a 46-year old male with major depressive disorder, who represented manic symptoms, when olanzapine was added to his treatment. Method: A 46-year old female, with a diagnosis of treatment resistant depression was referred to the authors. He had past history of depression for more than 20 years. The symptoms were present nearly every day since 1981, without any distinct period of remission, nor any noticeable fluctuation. His irritability had been disruptive to his family all these years. His doctor had prescribed maprotiline 25 mg/day, and lorazepam, 2mg/day, in addition to fluoxetine for the last 5 months. He is also a father of two children with methylphenidateresistant and sodium valproate-responsive attention-deficit hyperactivity disorder. Considering the antidepressant effects of olanzapine and its positive effects on irritability, the authors added olanzapine, to the patient’s previous medications. Results: After one week, he showed new problems such as talkativeness and beginning to smoke for the first time in his life, elevated mood, grandiosity about his intelligence and abilities, talkativeness, and shopping sprees. The score on the mania rating scale was 14. Fluoxetine was discontinued and sodium valproate, were prescribed. It took around 2 months to completely control the manic symptoms. Conclusions: In the patients with depression who show bipolar spectrum disorder features, adding mood stabilizers may be preferred to the drugs as olanzapine which could induce mania.
Regulation of SIK1 abundance and stability is critical for myogenesis

cAMP signaling can both promote and inhibit myogenic differentiation, but little is known about the mechanisms mediating promyogenic effects of cAMP. We previously demonstrated that the cAMP response element-binding protein (CREB) transcriptional target salt-inducible kinase 1 (SIK1) promotes MEF2 activity in myocytes via phosphorylation of class II histone deacetylase proteins (HDACs). However, it was unknown whether SIK1 couples cAMP signaling to the HDAC-MEF2 pathway during myogenesis and how this response could specifically occur in differentiating muscle cells. To address these questions, we explored SIK1 regulation and function in muscle precursor cells before and during myogenic differentiation. We found that in primary myogenic progenitor cells exposed to cAMP-inducing agents, Sik1 transcription is induced, but the protein is rapidly degraded by the proteasome. By contrast, sustained cAMP signaling extends the half-life of SIK1 in part by phosphorylation of Thr475, a previously uncharacterized site that we show can be phosphorylated by PKA in cell-free assays. We also identified a functional PEST domain near Thr475 that contributes to SIK1 degradation. During differentiation of primary myogenic progenitor cells, when PKA activity has been shown to increase, we observe elevated Sik1 transcripts as well as marked accumulation and stabilization of SIK1 protein. Depletion of Sik1 in primary muscle precursor cells profoundly impairs MEF2 protein accumulation and myogenic differentiation. Our findings support an emerging model in which SIK1 integrates cAMP signaling with the myogenic program to support appropriate timing of differentiation.
Crossover of Burnout and Engagement in Work Teams

This study investigates the crossover of burnout and work engagement among 2,229 Royal Dutch constabulary officers, working in one of 85 teams. The authors hypothesized that both states may transfer from teams to individual team members. The results of multilevel analyses confirm this crossover phenomenon by showing that team-level burnout and work engagement are related to individual team members’ burnout (i.e., exhaustion, cynicism, and reduced professional efficacy) and work engagement (vigor, dedication, and absorption), after controlling for individual members’ job demands and resources. The implications of these findings for interventions aimed at the promotion of employee well-being are discussed.
MIAR ICT Participation at Robot Vision 2013

This paper describes the participation of our team - MIAR ICT in the ImageCLEF 2013 Robot Vision Challenge. The task of the Challenge asked participants to classify imaged indoor scenes and recog- nize the predefined objects appeared in the imaged scene. Our approach is based on the recently proposed Kernel Descriptors framework, which is an effective representation for images. For the provided visual and depth sequences, we make a simple fusion at feature level. Then we use Linear Support Vector Machine (L-SVM) classifiers for both scene clas- sification and object recognition. At last, the temporal continuity of the given sequences is considered. Our team ranked the first among all the participants, showing the effectiveness of our proposed scheme.
Procedural Model of Requirements Elicitation Techniques

Software requirement elicitation is one of the most sensitive phases in software requirements knowledge area; it extracts useful requirement and help software engineers to select the right elicitation techniques. This paper presents a proposed elicitation model to facilitate the selection requirement elicitation techniques on the basis of the previous published work in academia, including the combination of situational characteristics, in addition technique characteristics, project characteristic and use guidelines to avoid misunderstanding of the requirements.
Real women on real beauty

This experiment tested the effectiveness of manipulated images of a Dove model, of varying shapes and sizes, to assess how or if exposure to an average or plus-size model would decrease women’s short-term internalisation of body image ideals. The objective of this study was to assess adult women’s beliefs about beauty and attractiveness in themselves and in others using several variables as possible predictors: exposure to thin-ideal or plus-size models, social comparison and societal views of thinness. Using an image of a model from the Dove Campaign for Real Beauty and three manipulated images of the same model, this study tested participants’ evaluations of each model’s attractiveness and thinness, and further tested participants’ level of self-discrepancy and societal views of thinness to assess if the campaign was at all effective in influencing the way women perceive beauty and attractiveness in themselves and in others. While exposure to the Dove model versus an ultra-thin model was not related to decreased levels of self-discrepancy across experimental groups, numerous other statistically significant relationships emerged based on exposure to the Dove or plus-size model. These and other findings are discussed.
Radial artery pressure monitoring underestimates central arterial pressure during vasopressor therapy in critically ill surgical patients.

OBJECTIVES Radial artery pressure is known to differ from central arterial pressure in normal patients (distal pulse amplification) and in the early postcardiopulmonary bypass period. The adequacy of the radial artery as a site for blood pressure monitoring in critically ill patients receiving high-dose vasopressors has not been carefully examined. DESIGN Prospective observational study comparing simultaneous intra-arterial measurements of radial (peripheral) and femoral artery (central) pressures. SETTING Clinical investigation in a university-based surgical intensive care unit. PATIENTS Fourteen critically ill patients with presumed sepsis who received norepinephrine infusions at a rate of > or =5 microg/min. INTERVENTIONS All patients were managed in accordance with our standard practice for presumed sepsis, which consisted of intravascular volume repletion followed by vasopressor administration titrated to a mean arterial pressure of > or =60 mm Hg. MEASUREMENTS AND MAIN RESULTS Systolic and mean arterial pressures were significantly higher when measured from the femoral vs. radial site (p < .005). The higher mean arterial pressures enabled an immediate reduction in norepinephrine infusions in 11 of the 14 patients. No change in cardiac output or pulmonary artery occlusion pressure was noted after dose reduction. In the two patients in whom simultaneous recordings were made after discontinuation of norepinephrine infusions, equalization of mean arterial pressures was observed. CONCLUSIONS Radial artery pressure underestimates central pressure in hypotensive septic patients receiving high-dose vasopressor therapy. Clinical management, based on radial pressures, may lead to excessive vasopressor administration. Awareness of this phenomena may help minimize adverse effects of these potent agents by enabling dosage reduction.