Miracle-dz/UniFAR-FTUs huggingface dataset:
A Coclustering Approach for Mining Large Protein-Protein Interaction Networks

Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonoverlapping clusters. The density of the clusters to search for can also be set by the user. We tested our method on the two networks of yeast and human, and compared it to other five well-known techniques on the same interaction data sets. The results showed that, for all the examples considered, our approach always reaches a good compromise between accuracy and network coverage. Furthermore, the behavior of our algorithm is not influenced by the structure of the input network, different from all the techniques considered in the comparison, which returned very good results on the yeast network, while on the human network their outcomes are rather poor.
A test of numerical instability and stiffness in the parametrizations of the ARPÉGE and ALADIN models

Abstract. Meteorological numerical weather prediction (NWP) models solve a system of partial differential equations in time and space. Semi-lagrangian advection schemes allow for long time steps. These longer time steps can result in instabilities occurring in the model physics. A system of differential equations in which some solution components decay more rapidly than others is stiff. In this case it is stability rather than accuracy that restricts the time step. The vertical diffusion parametrization can cause fast non-meteorological oscillations around the slowly evolving true solution (fibrillations). These are treated with an anti-fibrillation scheme, but small oscillations remain in operational weather forecasts using ARPEGE and ALADIN models. In this paper, a simple test is designed to reveal if the formulation of particular a physical parametrization is a stiff problem or potentially numerically unstable in combination with any other part of the model. When the test is applied to a stable scheme, the solution remains stable. However, applying the test to a potentially unstable scheme yields a solution with fibrillations of substantial amplitude. The parametrizations of the NWP model ARPEGE were tested one by one to see which one may be the source of unstable model behaviour. The test identified the set of equations in the stratiform precipitation scheme (a diagnostic Kessler-type scheme) as a stiff problem, particularly the combination of terms arising due to the evaporation of snow.
Pharmacists' self-perception of their professional role: insights into community pharmacy culture.

OBJECTIVE To obtain an understanding of how community pharmacists self-describe their professional role, in order to begin understanding some of the assumptions underlying pharmacy culture. DESIGN Cross-sectional qualitative study. SETTING Edmonton, Canada, and surrounding area. PARTICIPANTS 115 community pharmacists. INTERVENTION Brief telephone interview. MAIN OUTCOMES MEASURE Pharmacists' self-description/perception of their professional role and its relation to underlying assumptions of pharmacy culture. RESULTS 100 pharmacists provided usable responses. The majority of pharmacists practiced in a community chain setting (76%) and within the city of Edmonton (81%). The median length of time in practice was 15 years. A total of 278 separate response items were obtained. Of these responses, 45% were categorized as product focused, 29% as patient centered, and 26% as ambiguous. The first response of 52 of the 100 pharmacists was a product-focused description of their role. Overall, in either their first or second response, 57% of the pharmacists used the term "dispensing" or dispensing-related terms to describe their professional role. CONCLUSION The results of this study seem to suggest that community pharmacists who participated viewed themselves primarily as "dispensers of medication," not patient-centered practitioners. Sustainable pharmacy practice change will be possible only if the current culture aligns with change initiatives. Our findings may suggest that pharmacists' self-perception of what they do and, perhaps by extension, the culture of pharmacy itself, could be important barriers to implementing practice change initiatives. We need to better understand the culture of pharmacy to foster meaningful practice change.
Top and bottom: A brane of their own

We consider extra-dimensional descriptions of models where there are two separate strongly interacting sectors contributing to electroweak symmetry breaking ('topcolor' type models). In the extra-dimensional picture there would be two separate (anti-de Sitter) bulks meeting on the Planck brane, with each bulk having its own corresponding IR (TeV) brane. Sources for electroweak symmetry breaking can then be localized on both of these IR branes, while the different generations of fermions may be separated from each other. We describe the modes propagating in such a setup, and consider the cases where the electroweak symmetry breaking on either of the two IR branes come either from a Higgsless scenario (via boundary conditions) or a (top-)Higgs. We show that the tension that exists between obtaining a large top quark mass and the correct value of the Zbb couplings in ordinary Higgsless models can be largely relieved in the Higgsless-top-Higgs versions of the two IR brane models. This may also be true in the purely Higgsless-Higgsless case, however since that model is necessarily in the strongly coupled regime the tree-level results for the properties of the third generation may get large corrections. A necessary consequence of such models is the appearance of additional pseudo-Goldstonemore » bosons ('top-pions'), which would be strongly coupled to the third generation. « less
Ball impact localization on table tennis rackets using piezo-electric sensors

In this paper, we present an approach for a ball impact localization on table tennis rackets using piezo-electric sensors. Three sensors were used as vibration sensors at the outer edge of the racket. We analyzed ball impact vibration appearances and measured time differences of arriving wave fronts for each sensor pair. A study was conducted comprising six different racket-rubber combinations. Firstly, we calculated a time difference distribution model based on training sets of impact data constructed by a grid of measuring points. Secondly, this model was used to estimate the impact position of test data sets using three different methods. Best performance for each racket-rubber combination was achieved with a linear regression based method yielding a RMSE in x-direction (transversal racket direction) of 22.1 mm and a RMSE of 19.8 mm in y-direction (longitudinal racket direction). The measuring system is small enough to be completely invisibly integrated into table tennis rackets. This contribution is the first attempt to address a ball impact localization system for table tennis rackets that has the potential to be used in real-world training exercises and competitions to assist table tennis players during matches and to support the athletes' training progress.
Novel porous scaffolds of pH responsive chitosan/carrageenan-based polyelectrolyte complexes for tissue engineering.

Polyelectrolyte complexes (PECs) represent promising materials for drug delivery and tissue engineering applications. These substances are obtained in aqueous medium without the need for crosslinking agents. PECs can be produced through the combination of oppositely charged medical grade polymers, which include the stimuli responsive ones. In this work, three-dimensional porous scaffolds were produced through the lyophilization of pH sensitive PECs made of chitosan (CS) and carrageenan (CRG). CS:CRG molar ratios of 1:1 (CSCRG1), 2:1 (CSCRG2), and 3:1 (CSCRG3) were used. The chemical compositions of the PECs, as well as their influence in the final structure of the scaffolds were meticulously studied. In addition, the pH responsiveness of the PECs in a range including the physiological pH values of 7.4 (simulating normal physiological conditions) and 4.5 (simulating inflammatory response) was assessed. Results showed that the PECs produced were stable at pH values of 7.4 and under but dissolved as the pH increased to nonphysiological values of 9 and 11. However, after dissolution, the PEC could be reprecipitated by decreasing the pH to values close to 4.5. The scaffolds obtained presented large and interconnected pores, being equally sensitive to changes in the pH. CSCRG1 scaffolds appeared to have higher hydrophilicity and therefore higher water absorption capacity. The increase in the CS:CRG molar ratios improved the scaffold mechanical properties, with CSCRG3 presenting the higher compressive modulus under wet conditions. Overall, the PEC scaffolds appear promising for tissue engineering related applications that require the use of pH responsive materials stable at physiological conditions.
Personal Bankruptcy Law, Debt Portfolios, and Entrepreneurship

Bankruptcy provides entrepreneurs with insurance against the financial consequences of failure at the cost of worsened credit conditions. Using a quantitative general equilibrium model of entrepreneurship, we show that the presence of secured credit in addition to unsecured credit substantially alters this trade-off. If secured credit is not available the optimal bankruptcy law is harsh since the negative effect dominates. If secured credit is available the optimal law is lenient since entrepreneurs rationed out of the unsecured credit market can still obtain secured credit, lowering the costs of worse credit conditions. We find significant welfare gains from reforming the law.
Enhancing the Standard Operating Range of a Placido Disk Videokeratoscope for Corneal Surface Estimation

Corneal topography estimation that is based on the Placido disk principle relies on good quality of precorneal tear film and sufficiently wide eyelid (palpebral) aperture to avoid reflections from eyelashes. However, in practice, these conditions are not always fulfilled resulting in missing regions, smaller corneal coverage, and subsequently poorer estimates of corneal topography. Our aim was to enhance the standard operating range of a Placido disk videokeratoscope to obtain reliable corneal topography estimates in patients with poor tear film quality, such as encountered in those diagnosed with dry eye, and with narrower palpebral apertures as in the case of Asian subjects. This was achieved by incorporating in the instrument's own topography estimation algorithm an image processing technique that comprises a polar-domain adaptive filter and a morphological closing operator. The experimental results from measurements of test surfaces and real corneas showed that the incorporation of the proposed technique results in better estimates of corneal topography, and, in many cases, to a significant increase in the estimated coverage area making such an enhanced videokeratoscope a better tool for clinicians.
The structure of paranoia in the general population

Background Psychotic phenomena appear to form a continuum with normal experience and beliefs, and may build on common emotional interpersonal concerns. Aims We tested predictions that paranoid ideation is exponentially distributed and hierarchically arranged in the general population, and that persecutory ideas build on more common cognitions of mistrust, interpersonal sensitivity and ideas of reference. Method Items were chosen from the Structured Clinical Interview for DSM-IV Axis II Disorders (SCID-II) questionnaire and the Psychosis Screening Questionnaire in the second British National Survey of Psychiatric Morbidity (n = 8580), to test a putative hierarchy of paranoid development using confirmatory factor analysis, latent class analysis and factor mixture modelling analysis. Results Different types of paranoid ideation ranged in frequency from less than 2% to nearly 30%. Total scores on these items followed an almost perfect exponential distribution (r = 0.99). Our four a priori first-order factors were corroborated (interpersonal sensitivity; mistrust;ideas of reference; ideas of persecution). These mapped onto four classes of individual respondents:a rare, severe, persecutory class with high endorsement of all item factors, including persecutory ideation; a quasi-normal class with infrequent endorsement of interpersonal sensitivity, mistrust and ideas of reference, and no ideas of persecution; and two intermediate classes, characterised respectively by relatively high endorsement of items relating to mistrust and to ideas of reference. Conclusions The paranoia continuum has implications for the aetiology, mechanisms and treatment of psychotic disorders, while confirming the lack of a clear distinction from normal experiences and processes.
Relationships between epidemiological features and tumor characteristics of breast cancer.

OBJECTIVES Breast cancer is a histological, morphological and molecular heterogenous disease. Like clinical outcomes and prognoses of different subtypes, etiologies might also be different. Therefore, epidemiologic risk factors like sociologic, demographic, antropometric, reproductive, and menstrual factors can be considered as an entity reflected in tumor features. This study was planned to explore the relation between well known risk factors of breast cancer and histological and molecular features of the tumor. MATERIALS AND METHODS Epidemiologic data for 250 breast cancer patients followed-up by our clinic and 250 healthy individuals without any diagnosis of malignancy were obtained. The data displaying a relation to breast cancer are age, height, weight, body mass index (BMI), place of birth and province, educational level, menstrual status, age of menarche and menopause, number of births, age at first childbirth, family history of breast cancer, history of smoking and hormone treatment, mammographic screening, and presence of benign lesions. The tumor characteristics of patients in the breast cancer group were recorded. RESULTS Advanced age, nulliparity, low educational level, irregular mammographic screening, early menarche and late menopause, and high BMI in postmenopausal period were found to be related to increased breast cancer risk. Striking results in terms of the relation between epidemiological factors and tumor features were the early diagnosis of breast cancer in patients with regular mammographic screening. Tumor size was decreased with increased age and increased with increased BMI. Advanced age, prolonged lactation, increased number of births, and high education level were found to decrease axillary involvement. CONCLUSIONS Multiparity still continues to be the strongest protective factor against breast cancer in our society. The decrease in menarche age may be an early sign of the increased breast cancer incidence. Women should be informed about the relation between postmenopausal obesity and breast cancer and encouraged to attend physical activity and exercise programmes. Regular physical examination and mammographic screening are protective against breast cancer.
Cues for Haptic Perception of Compliance

For the perception of the hardness of compliant materials, several cues are available. In this paper, the relative roles of force/displacement and surface deformation cues are investigated. We have measured discrimination thresholds with silicone rubber stimuli of differing thickness and compliance. Also, the influence of the finger span is assessed. When compliance is expressed as the Young's modulus, the thresholds in the different conditions follow Weber's law with a Weber fraction of 15 percent. When the surface deformation cue was removed, thresholds more than trebled. Under the assumption of optimal cue combination, this suggests that a large fraction of the information comes from the surface deformation cue. Using a matching experiment, we found that differences in object thickness are correctly taken into account. When cues appear to contradict each other, the conflict is resolved by means of a compromise.
The Intersection of Working Memory and Emotion Recognition in Autism Spectrum Disorders

The present study investigates the intersection of working memory and emotion recognition in young adults with autism spectrum disorders (ASD) and neurotypical controls. The executive functioning theory of autism grounds key impairments within the cognitive realm, whereas social-cognitive theories view social functioning impairments as primary. Executive functioning theory of ASD has been criticized because executive functioning is too broad and is composed of separable, component skills. In the current study, the focus is narrowed to one of those components, working memory. It has been suggested that executive functioning may play a role in effective social interactions. Emotion recognition is an important aspect of social reciprocity, which is impaired in ASD. The current study investigates this hypothesis by combining working memory and emotion recognition into a single task, the n-back, as a model of social interaction and comparing performance between adults with ASD and controls. A validated set of facial expression stimuli (NimStim) was modified to remove all extraneous detail, and type of emotion was tightly controlled across 1-, 2-, and 3-back conditions. Results include significantly lower accuracy in each of the working memory load conditions in the ASD group compared to the control group, as well as in a baseline, maintenance memory task. The control group’s reaction time increased as working memory load increased, whereas the ASD group’s reaction time did not significantly vary by n-back level. The pattern of results suggests that the limit for n-back with emotional expressions is 2-back, due to near chance level performance in both groups for 3-back, as well as definitive problems in short term memory for facial expressions of emotion in high-functioning individuals with ASD, in contrast to previous findings of near perfect short memory for facial expressions in controls. INDEX WORDS: Autism, Emotion recognition, Working memory, Faces THE INTERSECTION OF WORKING MEMORY AND EMOTION RECOGNITION IN AUTISM SPECTRUM DISORDERS
Influence of instruments performance and material properties on exposure assessment of airborne engineered nanomaterials

Dustiness testing using a down-scaled EN15051 rotating drum was used to investigate the effects of storage conditions such as relative humidity and physical loading on the dustiness of five inorganic metal oxide nanostructured powder materials. The tests consisted of measurements of gravimetrical respirable dustiness index and particle size distributions. Water uptake of the powders during 7 days of incubation was investigated as an explanatory factor of the changes. Consequences of these varying storage conditions in exposure modelling were tested using the control banding and risk management tool NanoSafer. Drastic material-specific effects on powder respirable dustiness index were observed with the change in TiO2 from 30 % RH (639 mg/kg) to 50 % RH (1.5 mg/kg). All five tested materials indicate a decreasing dustiness index with relative humidity increasing from 30 to 70 % RH. Test of powder water uptake showed an apparent link with the decreasing dustiness index. Effects of powder compaction appeared more material specific with both increasing and decreasing dustiness indices observed as an effect of compaction. Tests of control banding exposure models using the measured dustiness indices in three different exposure scenarios showed that in two of the tested materials, one 20 % change in RH changed the exposure banding from the lowest level to the highest. The study shows the importance of powder storage conditions prior to tests for classification of material dustiness indices. It also highlights the importance of correct storage information and relative humidity and expansion of the dustiness test conditions specifically, when using dustiness indices as a primary parameter for source strength in exposure assessment. Electronic supplementary material The online version of this article (doi:10.1007/s11051-015-3139-6) contains supplementary material, which is available to authorized users. M. Levin (&) K. Mølhave Department of Micro and Nanotechnology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark e-mail: mle@nrcwe.dk M. Levin B. Liguori K. I. Kling I. K. Koponen K. A. Jensen National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen, Denmark E. Rojas D. Gregurec S. Moya CIC biomaGUNE, Paseo Miramón 182 C, 20009 San Sebastián, Gipuzkoa, Spain E. Vanhala M. Vippola T. Tuomi Finnish Institute of Occupational Health, Topeliuksenkatu 41 A, 00250 Helsinki, Finland M. Vippola Department of Materials Science, Tampere University of Technology, Korkeakoulunkatu 6, 33720 Tampere, Finland B. Liguori Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark 123 J Nanopart Res (2015) 17:337 DOI 10.1007/s11051-015-3139-6
Stochastic Optimal Control and Estimation Methods Adapted to the Noise Characteristics of the Sensorimotor System

Optimality principles of biological movement are conceptually appealing and straightforward to formulate. Testing them empirically, however, requires the solution to stochastic optimal control and estimation problems for reasonably realistic models of the motor task and the sensorimotor periphery. Recent studies have highlighted the importance of incorporating biologically plausible noise into such models. Here we extend the linear-quadratic-gaussian frameworkcurrently the only framework where such problems can be solved efficientlyto include control-dependent, state-dependent, and internal noise. Under this extended noise model, we derive a coordinate-descent algorithm guaranteed to converge to a feedback control law and a nonadaptive linear estimator optimal with respect to each other. Numerical simulations indicate that convergence is exponential, local minima do not exist, and the restriction to nonadaptive linear estimators has negligible effects in the control problems of interest. The application of the algorithm is illustrated in the context of reaching movements. A Matlab implementation is available at www.cogsci. ucsd.edu/todorov.