Miracle-dz/UniFAR-FTUs huggingface dataset:
A N EW S TUDY ON B ICLUSTERING T OOLS , B ICLUSTERS V ALIDATION AND E VALUATION FUNCTIONS Haifa

There are subsets of genes that have similar behavior under subsets of conditions, so we say that they coexpress, but behaveindependently under other subsets of conditions. Discovering such coexpressions can be helpful to uncover genomic knowledge such as gene networks or gene interactions. That is why, it is of utmost importance to make a simultaneous clustering of genes and conditions to identify clusters of genes that are coexpressed under clusters of conditions. This type of clustering is called biclustering. Biclustering is an NP-hard problem. Consequently, heuristic algorithms are typically used to approximate this problem by finding suboptimal solutions. In this paper, we make a new survey on tools , biclusters validation and evaluation functions.
Practical Earley Parsing

Earley’s parsing algorithm isa general algorithm, ableto handleany context-free grammar. As with most parsing algorithms, however, the presence of grammar rules having empty right-hand sides complicates matters. By analyzing why Earley’s algorithm struggles with these grammar rules, we have devised a simple solution to the problem. Our empty-rule solution leads to a new type of finite automaton expressly suited for use in Earley parsers and to a new statement of Earley’s algorithm. We show that this new form of Earley parser is much more time efficient in practice than the original.
Kea: Sentiment Analysis of Phrases Within Short Texts

Sentiment Analysis has become an increasingly important research topic. This paper describes our approach to building a system for the Sentiment Analysis in Twitter task of the SemEval-2014 evaluation. The goal is to classify a phrase within a short piece of text as positive, negative or neutral. In the evaluation, classifiers trained on Twitter data are tested on data from other domains such as SMS, blogs as well as sarcasm. The results indicate that apart from sarcasm, classifiers built for sentiment analysis of phrases from tweets can be generalized to other short text domains quite effectively. However, in crossdomain experiments, SMS data is found to generalize even better than Twitter data.
Dual PECCS: a cognitive system for conceptual representation and categorization

In this article we present an advanced version of Dual-PECCS, a cognitively-inspired knowledge representation and reasoning system aimed at extending the capabilities of artificial systems in conceptual categorization tasks. It combines different sorts of common-sense categorization (prototypical and exemplars-based categorization) with standard monotonic categorization procedures. These different types of inferential procedures are reconciled according to the tenets coming from the dual process theory of reasoning. On the other hand, from a representational perspective, the system relies on the hypothesis of conceptual structures represented as heterogeneous proxytypes. Dual-PECCS has been experimentally assessed in a task of conceptual categorization where a target concept illustrated by a simple common-sense linguistic description had to be identified by resorting to a mix of categorization strategies, and its output has been compared to human responses. The obtained results suggest that our approach can be beneficial to improve the representational and reasoning conceptual capabilities of standard cognitive artificial systems, and – in addition – that it may be plausibly applied to different general computational models of cognition. The current version of the system, in fact, extends our previous work, in that Dual- PECCS is now integrated and tested into two cognitive architectures, ACT-R and CLARION, implementing different assumptions on the underlying invariant structures governing human cognition. Such integration allowed us to extend our previous evaluation.
Evaluation of genome damage in subjects occupationally exposed to possible carcinogens

In occupational exposures, populations are simultaneously exposed to a mixture of chemicals. We aimed to evaluate DNA damage due to possible carcinogen exposure (phenylhydrazine, ethylene oxide, dichloromethane, and 1,2-dichloroethane) in lymphocytes of pharmaceutical industry workers from the same production line. Population comprised 16 subjects (9 females and 7 males) who were exposed to multiple chemicals for 8 months. Genome damage was assessed using alkaline comet assay, micronucleus assay, and comet assay coupled with fluorescent in situ hybridization (comet-FISH). After 8 months of exposure, the issue of irregular use of all available personal protective equipment (PPE) came into light. To decrease the risk of exposure, strict use of PPE was enforced. After 8 months of strict PPE use, micronuclei frequency and comet assay parameters in lymphocytes of pharmaceutical workers significantly decreased compared with prior period of irregular PPE use. Comet-FISH results indicated a significant shift in distribution of signals for the TP 53 gene toward a more frequent occurrence in the comet tail. Prolonged exposure to possible carcinogens may hinder DNA repair mechanisms and affect structural integrity of TP 53. Two indicators of loss of TP 53 gene integrity have risen, namely, TP 53 fragmentation rate in lymphocytes with persistently elevated primary damage and incidence of TP 53 deletions in undamaged lymphocytes.
Some aspects of the dynamics of Cu and Zn retained in plaque as related to their effect on plaque pH.

The effect of glucose on acid production in dental plaque was measured in vivo after oral rinses with CuSO4 (1.0 mM) or Zn (Ac)2 (20 mM) and compared with the retention of the metals. Plaque samples were analyzed for copper and zinc by neutron activation analysis. A rinse with the cooper salt solution significantly depressed acid formation in plaque for a period of 6 h whereas a rinse with the zinc solution was effective for 2 h. Plaque concentrations of the metals increased from less than 75 p.p.m. to more than 1000 p.p.m. 2 h after a rinse with the metal salts. Twelve hours after a rinse the mean plaque concentrations were 190 p.p.m. Cu or 358 p.p.m. Zn respectively. Reducing the pH of the copper sulfate solution from 5.7 to 2.0 yielded lower Cu concentrations in plaque 2 h after a rinse, indicating lower initial retention. The results clearly demonstrate a high and long lasting retention of metal ions in dental plaque and their biological effect in this environment.
Identification of LIM3 as the principal determinant of paxillin focal adhesion localization and characterization of a novel motif on paxillin directing vinculin and focal adhesion kinase binding

Paxillin is a 68-kD focal adhesion phosphoprotein that interacts with several proteins including members of the src family of tyrosine kinases, the transforming protein v-crk, and the cytoskeletal proteins vinculin and the tyrosine kinase, focal adhesion kinase (FAK). This suggests a function for paxillin as a molecular adaptor, responsible for the recruitment of structural and signaling molecules to focal adhesions. The current study defines the vinculin- and FAK-interaction domains on paxillin and identifies the principal paxillin focal adhesion targeting motif. Using truncation and deletion mutagenesis, we have localized the vinculin-binding site on paxillin to a contiguous stretch of 21 amino acids spanning residues 143-164. In contrast, maximal binding of FAK to paxillin requires, in addition to the region of paxillin spanning amino acids 143-164, a carboxyl-terminal domain encompassing residues 265-313. These data demonstrate the presence of a single binding site for vinculin, and at least two binding sites for FAK that are separated by an intervening stretch of 100 amino acids. Vinculin- and FAK-binding activities within amino acids 143-164 were separable since mutation of amino acid 151 from a negatively charged glutamic acid to the uncharged polar residue glutamine (E151Q) reduced binding of vinculin to paxillin by >90%, with no reduction in the binding capacity for FAK. The requirement for focal adhesion targeting of the vinculin- and FAK-binding regions within paxillin was determined by transfection into CHO.K1 fibroblasts. Significantly and surprisingly, paxillin constructs containing both deletion and point mutations that abrogate binding of FAK and/or vinculin were found to target effectively to focal adhesions. Additionally, expression of the amino-terminal 313 amino acids of paxillin containing intact vinculin- and FAK-binding domains failed to target to focal adhesions. This indicated other regions of paxillin were functioning as focal adhesion localization motifs. The carboxyl-terminal half of paxillin (amino acids 313-559) contains four contiguous double zinc finger LIM domains. Transfection analyses of sequential carboxyl-terminal truncations of the four individual LIM motifs and site-directed mutagenesis of LIM domains 1, 2, and 3, as well as deletion mutagenesis, revealed that the principal mechanism of targeting paxillin to focal adhesions is through LIM3. These data demonstrate that paxillin localizes to focal adhesions independent of interactions with vinculin and/or FAK, and represents the first definitive demonstration of LIM domains functioning as a primary determinant of protein subcellular localization to focal adhesions.
Circular dichroism of collagen, gelatin, and poly(proline) II in the vacuum ultraviolet

Circular dichroism spectra for acid‐soluble calfskin collagen, gelatin, and poly(proline) II in solution have been extended into the vacuum ultraviolet region. The extended spectrum of gelatin reveals that the circular dichroism of this unordered polymer is more closely related to the spectrum of charged polypeptides than might be evident from near ultraviolet work. A short‐wavelength band is found at about 172 nm, which corresponds in position, magnitude, and sign to a band recorded earlier for poly(L‐glutamic acid) at pH 8.0. This band is observed in a helical structure for the first time in the vacuum ultraviolet circular dichroism and absorption spectra of poly(proline) II. Both circular dichroism and absorption spectra point to the assignement of this band as the nσ*. Neither the nσ* nor the expected positive lobe of the ππ* helix band is observed in the extended circular dichroism spectrum of collagen. We postulate that these two bands cancel here in analogy to the case of α‐helical poly(L‐glutamic acid).
A directional visual descriptor for large-scale coverage problems

Visual coverage of large scale environments is a challenging problem that has many practical applications such as large scale 3D reconstruction, search and rescue and active video surveillance. In this paper, we consider a setting where mobile robots must acquire visual information using standard cameras, while minimizing associated movement costs. The main source of complexity for such scenario is the lack of a priori knowledge of 3D structures for the surrounding environment. To address this problem, we propose a novel descriptor for visual coverage that aims at measuring the orientation dependent visual information of an area, based on a regular discretization of the 3D environment in voxels. Next, we use the proposed visual descriptor to define an autonomous cooperative exploration approach, which controls the robot movements so to maximize information accuracy and minimizing movement costs. We empirically evaluate our approach in a simulation scenario based on real data for large scale 3D environments, and on widely used robotic tools (such as ROS and Stage). Experimental results show that the proposed method significantly outperforms a baseline random approach and an uncoordinated one, thus being a valid proposal for visual coverage in large scale outdoor scenarios.
Akt Deficiency Attenuates Muscle Size and Function but Not the Response to ActRIIB Inhibition

Background Akt is a critical mediator of developmental skeletal muscle growth. Treatment with a soluble ActRIIB fusion protein (ActRIIB-mFc) increases skeletal muscle mass and strength by inhibiting myostatin and related peptides. Recent in vitro studies have suggested that Akt signaling is necessary for the ability of ActRIIB inhibition to induce muscle hypertrophy. Thus, we hypothesized that mice deficient in either Akt1 or Akt2 would not respond to in vivo inhibition of ActRIIB with ActRIIB-mFc treatment. Methodology and Principal Findings We analyzed body composition and muscle parameters in wild-type C57BL/6J and Akt1 and Akt2 knockout mice, and compared the responses to blockade of ActRIIB signaling via ActRIIB-mFc treatment. Mice lacking Akt1 or Akt2 had reduced muscle mass, grip strength and contractile force. However, deficiency of Akt1 or Akt2 did not prevent the ability of ActRIIB-mFc treatment to induce muscle hypertrophy, or increase grip strength and contractile force. Akt1 and Akt2 deficient mice responded similarly as wild type mice to ActRIIB-mFc treatment by increasing fiber size. Conclusions and Significance Akt1 and Akt2 are important for the regulation of skeletal muscle mass and function. However, these Akt isoforms are not essential for the ability of ActRIIB inhibition to regulate muscle size, fiber type, strength or contractile force.
Hierarchical semantic segmentation using modular convolutional neural networks

Image recognition tasks that involve identifying parts of an object or the contents of a vessel can be viewed as a hierarchical problem, which can be solved by initial recognition of the main object, followed by recognition of its parts or contents. To achieve such modular recognition, it is necessary to use the output of one recognition method (which identifies the general object) as the input for a second method (which identifies the parts or contents). In recent years, convolutional neural networks have emerged as the dominant method for segmentation and classification of images. This work examines a method for serially connecting convolutional neural networks for semantic segmentation of materials inside transparent vessels. It applies one fully convolutional neural net to segment the image into vessel and background, and the vessel region is used as an input for a second net which recognizes the contents of the glass vessel. Transferring the segmentation map generated by the first nets to the second net was performed using the valve filter attention method that involves using different filters on different segments of the image. This modular semantic segmentation method outperforms a single step method in which both the vessel and its contents are identified using a single net. An advantage of the modular neural net is that it allows networks to be built from existing trained modules, as well the transfer and reuse of trained net modules without the need for any retraining of the assembled net.
OVER UNCERTAIN MOVING OBJECTS

Data uncertainty inherently exists in a large number of applications due to factors such as limitations of measuring equipments, update delay, and network bandwidth. Recently, modeling and querying uncertain data have attracted considerable attention from the database community. However, how to perform advanced analysis on uncertain data remains an interesting question. In this paper, we focus on the execution of skyline computation over uncertain moving objects. We propose a novel probabilistic skyline model where an uncertain object may take a probability to be in the skyline at a certain time point, therefore a p-t-skyline contains those moving objects whose skyline probabilities are at least p at time point t. Computing probabilistic skyline over a large number of uncertain moving objects is a daunting task in practice. In order to efficiently compute the probabilistic skyline query, we propose a discrete-and-conquer strategy, which follows the sampling-bounding-pruning-refining procedure. To further reduce the skyline computation cost, we propose an enhanced framework that is based on a multi988 X.F. Ding, H. Jin, H. Xu, W. Song dimensional indexing structure combined with the discrete-and-conquer strategy. Through extensive experiments with synthetic datasets, we show that the framework can efficiently support skyline queries over uncertain moving object and is scalable on large data sets.
[Fabry's disease in Spain. Study of 24 cases].

BACKGROUND AND OBJECTIVE Fabry's disease is a rare metabolic disorder inherited as an X-linked trait resulting from a decreased activity of the alpha-galactosidase A lysosomal enzyme. This defect leads to an accumulation of unmetabolized neutral glycosphingolipids in all cell types. This condition displays a high rate of early mortality and affects both hemizygous males and heterozygous females. We present data from Spanish patients admitted to the Fabry Outcome Survey (FOS), a multicenter European registry for patients suffering from Fabry's disease, at the time of their inclusion. PATIENTS AND METHOD The study presents baseline data from 24 Spanish patients upon inclusion in the registry, with an analysis of their overall clinical characteristics and relationship to gender. RESULTS The median age of onset of symptoms was 13 years, while it was 25.5 years for diagnosis. In 7 patients, the manifestations of the disease had been attributed to other processes. Predominant manifestations in males were angiokeratomas (86%), pain (71%), cardiovascular involvement (71%), kidney involvement (50%), digestive symptoms (43%) and ophthalmologic complications (43%). Among females, ophthalmologic complications were present in 50%, followed by cardiovascular involvement (40%); 30% of females had a painful clinical condition which is characteristic of the process. CONCLUSIONS We present the clinical characteristics of the largest Spanish cohort of Fabry's disease sufferers reported so far. Due to the wide spectrum of clinical manifestations, their awareness allows an early diagnosis as well as the possibility of starting the specific therapy currently available.
Evaluation of commonly used filter substrates for the measurement of aerosol trace element solubility

The published literature describing aerosol trace element fractional solubility measurements is characterized by a wide range of observed fractional solubilities. Whereas some of this variability is derived from natural differences in the chemical characteristics of the aerosol source material, the use of different sample collection and processing protocols by the scientific community has also confounded efforts to understand aerosol solubility. Bulk aerosol samples were collected at a coastal site over a nine‐month period and used to assess the influence of filter material on aerosol solubility measurements. Two hundred samples were extracted with ultrapure deionized water and focused on the solubility of ten trace elements (Al, P, Ti, V, Mn, Fe, Ni, Cu, Zn, and Pb) of interest to the GEOTRACES program. Aerosol samples were collected on eight different filter types and extracted using a flow‐through “instantaneous” extraction method. In many cases, the operationally defined aerosol trace element solubility differed depending on filter type. Major anion concentrations and trace element fractional solubility were found to differ 58% and 60% of the time, respectively. Filter blank concentrations are also reported for the various filter types. This work, in conjunction with the 2008 GEOTRACES Aerosol Intercalibration study, should aid the design of future research efforts by the wider marine aerosol community and allow better comparisons among published data.
Researching children and young people's lives: the problem of interpretation in vignette methodology : BPS Qualitative Research in Psychology Section QMiP conference

In this paper we explore important issues that are raised when interpretation is dealt with by researchers using a vignette methodology. Researchers using vignette methodology often struggle with interpretation: how to interpret the responses when participants shift between discussing the vignettes as themselves, taking the perspective of the character in the vignette and commenting on what 'ought' to happen. We argue that by foregrounding a consideration of the method with an explicitly articulated theoretical position of dialogicality, issues inherent in the process of interpretation become a valuable addition to the research rather than an obstacle to be overcome. In the paper we discuss 'Louise' a young carer, detailing the various positions she takes in her talk about the vignette of Mary, a fictitious young carer, to illustrate how a perspective based on the dialogical theory contributed to the analysis of her various moves through different identity positions
Assessing Recent Smoking Status by Measuring Exhaled Carbon Monoxide Levels

Background Cigarette smoke causes both acute and chronic changes of the immune system. Excluding recent smoking is therefore important in clinical studies with chronic inflammation as primary focus. In this context, it is common to ask the study subjects to refrain from smoking within a certain time frame prior to sampling. The duration of the smoking cessation is typically from midnight the evening before, i.e. 8 hours from sampling. As it has been shown that a proportion of current smokers underestimates or denies smoking, objective assessment of recent smoking status is of great importance. Our aim was to extend the use of exhaled carbon monoxide (CObreath), a well-established method for separating smokers from non-smokers, to assessment of recent smoking status. Methods and Findings The time course of CObreath decline was investigated by hourly measurements during one day on non-symptomatic smokers and non-smokers (6+7), as well as by measurements on three separate occasions on non-smokers (n = 29), smokers with normal lung function (n = 38) and smokers with chronic obstructive pulmonary disease (n = 19) participating in a clinical study. We used regression analysis to model the decay, and receiver operator characteristics analysis for evaluation of model performance. The decline was described as a mono-exponential decay (r2 = 0.7) with a half-life of 4.5 hours. CO decline rate depends on initial CO levels, and by necessity a generic cut-off is therefore crude as initial CObreath varies a lot between individuals. However, a cut-off level of 12 ppm could classify recent smokers from smokers having refrained from smoking during the past 8 hours with a specificity of 94% and a sensitivity of 90%. Conclusions We hereby describe a method for classifying recent smokers from smokers having refrained from smoking for >8 hours that is easy to implement in a clinical setting.
Split string field theory II

We describe the ghost sector of cubic string field theory in terms of degrees of freedom on the two halves of a split string. In particular, we represent a class of pure ghost BRST operators as operators on the space of half-string functionals. These BRST operators were postulated by Rastelli, Sen, and Zwiebach to give a description of cubic string field theory in the closed string vacuum arising from condensation of a D25-brane in the original tachyonic theory. We find a class of solutions for the ghost equations of motion using the pure ghost BRST operators. We find a vanishing action for these solutions, and discuss possible interpretations of this result. The form of the solutions we find in the pure ghost theory suggests an analogous class of solutions in the original theory on the D25-brane with BRST operator Q_B coupling the matter and ghost sectors.