Miracle-dz/UniFAR-FTUs huggingface dataset:
Rat Mcs5a is a compound quantitative trait locus with orthologous human loci that associate with breast cancer risk

Breast cancer risk is a polygenic trait. To identify breast cancer modifier alleles that have a high population frequency and low penetrance we used a comparative genomics approach. Quantitative trait loci (QTL) were initially identified by linkage analysis in a rat mammary carcinogenesis model followed by verification in congenic rats carrying the specific QTL allele under study. The Mcs5a locus was identified by fine-mapping Mcs5 in a congenic model. Here we characterize the Mcs5a locus, which when homozygous for the Wky allele, reduces mammary cancer risk by 50%. The Mcs5a locus is a compound QTL with at least two noncoding interacting elements: Mcs5a1 and Mcs5a2. The resistance phenotype is only observed in rats carrying at least one copy of the Wky allele of each element on the same chromosome. Mcs5a1 is located within the ubiquitin ligase Fbxo10, whereas Mcs5a2 includes the 5′ portion of Frmpd1. Resistant congenic rats show a down-regulation of Fbxo10 in the thymus and an up-regulation of Frmpd1 in the spleen. The association of the Mcs5a1 and Mcs5a2 human orthologs with breast cancer was tested in two population-based breast cancer case-control studies (≈12,000 women). The minor alleles of rs6476643 (MCS5A1) and rs2182317 (MCS5A2) were independently associated with breast cancer risk. The minor allele of rs6476643 increases risk, whereas the rs2182317 minor allele decreases risk. Both alleles have a high population frequency and a low penetrance toward breast cancer risk.
Effects of Ionic Strength on Bacteriophage MS2 Behavior and Their Implications for the Assessment of Virus Retention by Ultrafiltration Membranes

ABSTRACT Bacteriophage MS2 is widely used as a surrogate to estimate pathogenic virus elimination by membrane filtration processes used in water treatment. Given that this water technology may be conducted with different types of waters, we focused on investigating the effects of ionic strength on MS2 behavior. For this, MS2 was analyzed while suspended in solutions of various ionic strengths, first in a batch experiment and second during membrane ultrafiltration, and quantified using (i) quantitative reverse transcriptase PCR (qRT-PCR), which detects the total number of viral genomes, (ii) qRT-PCR without the RNA extraction step, which reflects only particles with a broken capsid (free RNA), and (iii) the PFU method, which detects only infectious viruses. At the beginning of the batch experiments using solutions containing small amounts of salts, losses of MS2 infectivity (90%) and broken particles (20%) were observed; these proportions did not change during filtration. In contrast, in high-ionic-strength solutions, bacteriophage kept its biological activity under static conditions, but it quickly lost its infectivity during the filtration process. Increasing the ionic strength decreased both the inactivation and the capsid breakup in the feed suspension and increased the loss of infectivity in the filtration retentate, while the numbers of MS2 genomes were identical in both experiments. In conclusion, the effects of ionic strength on MS2 behavior may significantly distort the results of membrane filtration processes, and therefore, the combination of classical and molecular methods used here is useful for an effective validation of the retention efficiency of ultrafiltration membranes.
Measurement uncertainty investigation in the multi-probe OTA setups

Extensive efforts are underway to standardize over the air (OTA) testing of the multiple input multiple output (MIMO) capable terminals in COST IC1004, 3GPP RAN4 and CTIA. Due to the ability to reproduce realistic radio propagation environments inside the anechoic chamber and evaluate end user metrics in real world scenarios, the multi-probe based method has attracted huge interest from both industry and academia. This contribution attempts to identify some of the measurement uncertainties of the practical multi-probe setups and provide some guidance to establish the multi-probe anechoic chamber setup. This contribution presents the results of uncertainty measurements carried out in three practical multi-probe setups. Some sources of measurement errors, i.e. cable effect, cable termination, etc. are identified based on the measurement results.
Inter-cell cooperation aided dynamic base station switching for energy efficient cellular networks

In this paper, a cell zooming based dynamic base stations (BS) switching scheme is conceived for energy saving in cellular networks. A cell zooming algorithm is developed for leveraging the BS's coverage with inter-cell cooperation and downlink power control. Meanwhile, we design a feasible working strategy for the cell zooming scheme to maximizing the energy saving. Simulations are provided to demonstrate the advantages of the proposed scheme.
Effect of charged dust particles on the ion cyclotron and firehose instabilities

[1] Effects due to the presence of charged dust particles on the growth rate of instabilities of low frequency electromagnetic waves propagating along the ambient magnetic field are investigated, using a kinetic theory which takes into account the collisional charging of the dust particles. For perpendicular ion temperature larger than the parallel ion temperature the dustless plasma features the proton cyclotron anisotropy instability, which is gradually reduced by the presence of the dust population, until complete disappearance for sufficiently large dust density. For perpendicular ion temperature smaller than the parallel ion temperature the dustless plasma features the proton fire-hose instability, which is also reduced by the presence of the dust population. The results obtained show that the fire-hose instability is more easily quenched by the presence of the dust than the proton cyclotron instability. For both instabilities, the presence of the dust affects the dispersion relation by the charge imbalance produced by the electron capture by the dust particles, and by the damping effect originated from the collisional charging of the dust particles.
Perceptual training: A tool for both modifying the brain and exploring it

During the past 20 years it became increasingly clear that sensory areas in the brain of adult primates, including humans, retain a large degree of plasticity (reviewed in ref. 1). Consequently, experiences continuously modify our perception of the world even as adults. When perceptual experience is monitored, for example, in a training regime that includes intensive practice with a limited set of stimuli, the neuronal representations of these stimuli are gradually modified (e.g., ref. 2). But the nature of the changes that are induced by practice and the degree of modifiability of different sensory sites are still not well understood. The study of Wright and Fitzgerald (3), reported in this issue of PNAS, is an important contribution to these largely open questions. They found that the ability to discriminate between stimuli that cue for neighboring sound locations significantly improves with practice. Yet, the susceptibility to improvement seems to differ between the two prominent cues for sound localization—interaural time and intensity differences.
Human Immunode®ciency Virus Type 1 Tat Protein Induces Adhesion Molecule Expression in Astrocytes

AIDS encephalitis is a frequent consequence of CNS HIV infection, especially in children. One of its many characteristics is a leukocyte in®ltrate that is believed to contribute to the production of cytokines, chemokines and neurotoxic factors resulting in CNS damage. Entry of such leukocytes into the CNS is mediated in part by the expression of adhesion molecules by blood ± brain barrier (BBB) endothelial cells. Expression of these proteins by astrocytes, the other main component of the BBB, also serves to target leukocytes to the CNS parenchyma. We now demonstrate that HIV-1-derived Tat, a soluble protein secreted by infected cells, induced astrocyte VCAM-1 and ICAM-1 expression in a dose-and time-dependent manner. The functional role of Tat in monocyte binding in vitro was also demonstrated. These data suggest that the presence of extracellular Tat may be a signi®cant factor in the traf®cking of HIV-infected and in¯ammatory cells into the CNS via its effect on adhesion molecule expression by astrocytes.
Finding Strongly Knit Clusters in Social Networks

Social networks are ubiquitous. The discovery of closely knit clusters in these networks is of fundamental and practical interest. Existing clustering criteria are limited in that clusters typically do not overlap, all vertices are clustered, and/or external sparsity is ignored. We introduce a new criterion that overcomes these limitations by combining internal density with external sparsity in a natural way. This paper explores combinatorial properties of internally dense and externally sparse clusters. A simple algorithm is given for provably finding such clusters assuming a sufficiently large gap between internal density and external sparsity. Experimental results show that the algorithm is able to identify over 90% of the clusters in real graphs, assuming conditions on external sparsity.
Laplace-Beltrami Eigenfunctions Towards an Algorithm That "Understands" Geometry

One of the challenges in geometry processing is to automatically reconstruct a higher-level representation from raw geometric data. For instance, computing a parameterization of an object helps attaching information to it and converting between various representations. More generally, this family of problems may be thought of in terms of constructing structured function bases attached to surfaces. In this paper, we study a specific type of hierarchical function bases, defined by the eigenfunctions of the Laplace-Beltrami operator. When applied to a sphere, this function basis corresponds to the classical spherical harmonics. On more general objects, this defines a function basis well adapted to the geometry and the topology of the object. Based on physical analogies (vibration modes), we first give an intuitive view before explaining the underlying theory. We then explain in practice how to compute an approximation of the eigenfunctions of a differential operator, and show possible applications in geometry processing
The rise of internal fertilization in the Anablepidae (Teleostei, Cyprinodontiformes): two new genera and species from the Miocene of Tucumán, Argentina

Two new genera and species of Cyprinodontiformes from the Miocene of Tucumán, Argentina, are described: Tucmanableps cionei and Sachajenynsia pacha. Both exhibit sexual dimorphism, indicated by the modification of the male anal fin into an intromittent organ; tricuspid teeth in the jaws; abdominal pelvic fins and other features that demonstrate a relationship with the family Anablepidae. Males of Sachajenynsia pacha gen. et sp. nov. present modifications of the anal fin, herein interpreted as an incipient gonopodium, whereas the anal fin of Tucmanableps cionei gen. et sp. nov. is modified into a complex gonopodium with a median distal plate, which is unique among the Anablepidae. In extant genera of the family, modification of the anal fin into an intromittent organ is related to internal fertilization; this condition is inferred for S. pacha but was clearly the reproductive mode of T. cionei. In our phylogenetic analysis, S. pacha is recovered as the sister group of all anablepids with evident internal fertilization, while T. cionei forms a clade with Anableps species. The occurrence of two new anablepid genera showing distinct and unique morphologies suggests that the fossil diversity of the Anablepidae may be higher than the extant one. Also, the new taxa were found in open lake deposits with coastal and inner lake sediments of the Río Salí Formation associated with the Miocene Entrerrian–Paranense Marine Ingression, supporting the idea that coastal environments and brackish waters are related to the generic diversification of the Anablepidae, as was suggested for the species of Jenynsia.
Computer-supported cooperative work - concepts and trends

The research field Computer-Supported Cooperative Work (CSCW) is concerned with understanding social interaction and the design, development, and evaluation of technical systems supporting social interaction in teams and communities - or in other words it is about researching the use of computer-based technology for supporting collaboration. The field was coined in the 1980th by researchers from computer science, information science and social science. In this paper we will briefly introduce CSCW - its concepts and current trends - and thereby focus on the role of Informatics in the field - from application integration to ubiquitous user interfaces.
Effects of the coastal forests, sea embankment and sand dune on reducing washout region of houses at the tsunami caused by the Great East Japan Earthquake

The tsunami caused by the Great East Japan Earthquake on 11 March 2011, broke most of the sea embankment and coastal forests, and caused dreadful damage to people and buildings in Tohoku and Kanto districts of Japan. This study hypothesized that the coastal forest had a tsunami mitigation effect even when the coastal vegetation was bent down, because most of the vegetation was not washed out, hence could acts as a dense roughness element. Therefore, the objective of this study is to evaluate the vegetation effect on reducing the washout region of houses under severe tree breaking phenomenon using numerical simulation and data from field investigation in April and May 2011. Numerical simulations estimated the effects of a 640m-coastal forest, sea embankment around 5.4m in height or sand dune (2m increase) on reducing the washout region of houses by around 100 m, 600m and 600m for 10m height tsunami at coast. It was observed/concluded that although the quantitative effect of coastal forest is smaller than sea embankment, the coastal forest and sand dune is not a negligible component of the mitigation measures when a large tsunami occurs and overflows the sea embankment.
Correlates of Successful Aging in Racial and Ethnic Minority Women Age 80 Years and Older: Findings from the Women's Health Initiative.

BACKGROUND Most research has focused on definitions and predictors of successful aging. However, racial/ethnic minorities are often under represented in this research. Given that the U.S. population is aging and becoming more racially diverse, we examined correlates of "successful aging," as defined by physical functioning and overall quality of life (QOL), among racial/ethnic minority women aged 80 years and older in the Women's Health Initiative. METHODS Participants included 1,924 racial/ethnic minority women (African Americans, Asian/Pacific Islanders, Hispanic/Latinos, and American Indian/Alaskan Natives) 80 years of age and older who are enrolled in the Women's Health Initiative and have physical functioning data after turning 80 years of age. Analysis of covariance was used to examine between and within group differences in physical functioning and selfrated overall QOL for African Americans, Asian/Pacific Islanders, and Hispanic/Latinos. RESULTS We found no significant differences in physical functioning between racial/ethnic minority groups in adjusted analyses. However, overall QOL was significantly different between racial/ethnic minority groups. Age, recreational physical activity, and overall selfrated health were independent correlates of physical functioning across racial/ethnic minority groups, whereas overall selfrated health was the only consistent correlate of overall QOL across the minority groups for the within minority group comparisons. CONCLUSIONS Between racial/ethnic minority group differences in physical functioning are largely explained by demographic, psychosocial, behavioral, and health-related variables. We found statistically significant differences in selfrated overall QOL between racial/ethnic minority groups.
A randomized prospective comparison of CartoMerge and CartoXP to guide circumferential pulmonary vein isolation for the treatment of paroxysmal atrial fibrillation.

BACKGROUND CartoXP and CartoMerge have been used to treat atrial fibrillation (AF) for several years. Our randomized prospective study compared clinical outcomes of these two versions of three dimensional electroanatomic mapping system in guiding catheter ablation for paroxysmal atrial fibrillation (PAF). METHODS Eighty-one patients with symptomatic, drug refractory PAF were randomly assigned to CartoMerge group (n=42, mean age (54.5+/-13.1) years, history of AF=3.2 years) or CartoXP group (n=39, mean age (59.8+/-15.6) years, history of AF = 2.9 years). All patients underwent 64-slice computed tomography (MSCT) 1 to 3 days prior to ablation procedure. Using CartoMerge(TM) Image Integration Module, 3D anatomical images of the left atrium (LA) and pulmonary veins (PVs) derived from MSCT of CartoMerge group were established and merged with the electroanatomical map. The integrated images were used to guide the procedure of circumferential pulmonary vein isolation (CPVI). In the other group, CPVI was guided just by CartoXP. The endpoint of CPVI in both groups was abolition or dissociation of pulmonary vein potentials (PVPs). RESULTS Mapping points to establish the electroanatomical model of the LA/PVs were 48.7+/-13.4 in CartoMerge group and 62.5+/-15.7 in CartoXP group (P<0.001). Mean distance between mapping points and the MSCT surfaces in CartoMerge group was (1.59+/-0.33) mm. Accomplishment of abolition or dissociation of PVPs was achieved 95.2% in CartoMerge group and 92.3% in CartoXP group. Durations of procedure and exposure to X-ray were (156+/-25) minutes, (179+/-21) minutes (P<0.001) and (19.6+/-7.5) minutes, (28.5+/-12.8) minutes (P<0.001), respectively. After a follow-up with duration of (11.9+/-3.1) months vs (12.4+/-3.6) months post the first ablation procedure, patients free of AF were 33 (78.6%) in CartoMerge group and 29 (74.4%) in CartoXP group (P>0.50). No patient suffered pulmonary vein stenosis, atrioesophageal fistula, stroke or death. CONCLUSION Compared to CartoXP, CartoMerge shortened the catheter ablation procedure and exposure to X-ray, without affecting the clinical outcomes of circumferential pulmonary vein isolation for the treatment of paroxysmal atrial fibrillation in experienced centres.
A Relational Representation for Procedural Task Knowledge

This paper proposes a methodology for learning joint probability estimates regarding the effect of sensorimotor features on the predicated quality of desired behavior. These relationships can then be used to choose actions that will most likely produce success. relational dependency networks are used to learn statistical models of procedural task knowledge. An example task expert for picking up objects is learned through actual experience with a humanoid robot. We believe that this approach is widely applicable and has great potential to allow a robot to autonomously determine which features in the world are salient and should be used to recommend policy for action.
Time‐invariant feed‐forward inhibition of Purkinje cells in the cerebellar cortex in vivo

We performed extracellular recording of pairs of interneuron–Purkinje cells in vivo. A single interneuron produces a substantial, short‐lasting, inhibition of Purkinje cells. Feed‐forward inhibition is associated with characteristic asymmetric cross‐correlograms. In vivo, Purkinje cell spikes only depend on the most recent synaptic activity.
Improving Accuracy and Cost of Two-class and Multi-class Probabilistic Classifiers Using ROC Curves

The probability estimates of a naive Bayes classifier are inaccurate if some of its underlying independence assumptions are violated. The decision criterion for using these estimates for classification therefore has to be learned from the data. This paper proposes the use of ROC curves for this purpose. For two classes, the algorithm is a simple adaptation of the algorithm for tracing a ROC curve by sorting the instances according to their predicted probability of being positive. As there is no obvious way to upgrade this algorithm to the multi-class case, we propose a hillclimbing approach which adjusts the weights for each class in a pre-defined order. Experiments on a wide range of datasets show the proposed method leads to significant improvements over the naive Bayes classifier's accuracy. Finally, we discuss an method to find the global optimum, and show how its computational complexity would make it untractable.
A ROLE OF METRICAL STRUCTURE IN IMPLICIT MEMORY OF RHYTHM PERCEPTION : TOWARD A COMPUTATIONAL MODELING OF PERCEPTION PROCESS OF METRICAL STRUCTURE

Memory for rhythmic tone sequence plays an important roll in rhythm perce ption and variety of study has been made on it. Previous study suggests, for instance, that more easily it is perceived, more easily it is memorized. In recent years there has been renewal of interest in implicit memory for musical information. In this study, the implicit memory for rhythmic tone sequence was examined. The aim of this study was to investigate the implicit memory for musical rhythm from the viewpoint of cognitive psychology. An experiment using priming and recognition tasks was performed to clarify the nature of implicit memory for rhythmic tone sequences. Two types of measure, “ binary”meter tone sequence and “ ternary”meter tone sequence, were used in experimental variables. In the experiment, encoding strategy was manipulated as an independent measure. In the study phase, half of participants were asked to perform “foot tapping task” and the others were asked to “note counting task. ” Foot tapping task means that participants tap their foot to the tone sequence. Note counting task means that participants count the number of the tones. In the test phase, half of the participants performed a priming task: they were asked to judge the familiarity on a 7-point scale (1= not familiar at all, 7= completely familiar). The rest of the participants performed a yes/no recognition test. The pitch height (A4) and timber (piano sound) were the same in both the study phase and the test phase. Priming effect was defined as difference between rating value of familiarity for old tone sequence and new one. The following results were obtained: 1) priming effect was observed in both binary meter and ternary meter tone sequence when listeners were asked to performed “foot tapping task”, 2) priming effect for binary meter tone sequence was bigger than that for ternary meter tone sequence, 3) no significant main effect was observed in the recognition task. These results lead to the conclusion that an implicit memory for musical rhythm exists and the type of metrical structure plays an important role in perceptual priming of rhythmic tone sequences. This may associate with the preference for binary metrical type in rhythm perception.
Nonuniform Sampling for Global Optimization of Kinetic Rate Constants in Biological Pathways

Global optimization has proven to be a powerful tool for solving parameter estimation problems in biological applications, such as the estimation of kinetic rate constants in pathway models. These optimization algorithms sometimes suffer from slow convergence, stagnation or misconvergence to a non-optimal local minimum. Here we show that a nonuniform sampling method (implemented by running the optimization in a transformed space) can improve convergence and robustness for evolutionary-type algorithms, specifically differential evolution and evolutionary strategies. Results are shown from two case studies exemplifying the common problems of stagnation and misconvergence