Miracle-dz/UniFAR-FTUs huggingface dataset:
Tree Kernels-based Discriminative Reranker for Italian Constituency Parsers

English. This paper aims at filling the gap between the accuracy of Italian and English constituency parsing: firstly, we adapt the Bllip parser, i.e., the most accurate constituency parser for English, also known as Charniak parser, for Italian and trained it on the Turin University Treebank (TUT). Secondly, we design a parse reranker based on Support Vector Machines using tree kernels, where the latter can effectively generalize syntactic patterns, requiring little training data for training the model. We show that our approach outperforms the state of the art achieved by the Berkeley parser, improving it from 84.54 to 86.81 in labeled F1. Italiano. Questo paper mira a colmare il gap di accuratezza tra il constituency parsing dell’Italiano e quello Inglese: come primo miglioramento, abbiamo adattato il parser a costituenti per l’Inglese, Bllip, anche noto come Charniak parser, per l’Italiano e lo abbiamo addestrato sul Turin University Treebank. In seguito, abbiamo progettato un reranker basato sulle Macchine a Vettori di Supporto che usano kernel arborei, i quali possono efficacemente generalizzare pattern sintattici, richiedendo pochi dati di training per addestrare il modello. Il nostro approccio supera lo stato dell’arte ottenuto con il Berkeley parser, migliorando la labeled F1 da 84.54 a 86.81.
Right posterior parietal cortex is involved in disengaging from threat: a 1-Hz rTMS study

Abstract The right posterior parietal cortex (PPC) is implicated in spatial attention, but its specific role in emotional spatial attention remains unclear. In this study, we combined inhibitory transcranial magnetic stimulation (TMS) with a fear-conditioning paradigm to test the role of the right PPC in attentional control of task-irrelevant threatening distractors. In a sham-controlled within-subject design, 1-Hz repetitive TMS was applied to the left and right PPC after which participants performed a visual search task with a distractor that was either associated with a loud noise burst (threat) or not (non-threat). Results demonstrated attentional capture across all conditions as evidenced by the typical reaction time costs of the distractor. However, only after inhibitory rTMS to the right PPC reaction time cost in the threatening distractor condition was increased relative to the non-threatening distractor condition, suggesting that attention lingered longer on the threatening distractor. We propose that the right PPC is involved in disengagement of attention from emotionally salient stimuli in order to re-orient attention to task relevant stimuli and may have implications for anxiety disorders associated with difficulties to disengage from threatening stimuli.
Single-Carrier Frequency Domain Equalization for Hammerstein Communication Systems Using Complex-Valued Neural Networks

Single-carrier (SC) block transmission with frequency-domain equalization (FDE) offers a viable transmission technology for combating the adverse effects of long dispersive channels encountered in high-rate broadband wireless communication systems. However, for high-bandwidth efficiency and high-power-efficiency systems, the channel can generally be modeled by the Hammerstein system, which includes the nonlinear distortion effects of the high-power amplifier (HPA) at transmitter. For such nonlinear Hammerstein channels, the standard SC-FDE scheme no longer works. This paper advocates a complex-valued (CV) B-spline neural-network-based nonlinear SC-FDE scheme for Hammerstein channels. Specifically, we model the nonlinear HPA, which represents the CV static nonlinearity of the Hammerstein channel, by a CV B-spline neural network, and we develop two efficient alternating least squares schemes for estimating the parameters of the Hammerstein channel, including both the channel impulse response coefficients and the parameters of the CV B-spline model. We also use another CV B-spline neural network to model the inversion of the nonlinear HPA, and the parameters of this inverting B-spline model can easily be estimated using the standard least-squares algorithm based on the pseudo training data obtained as a natural byproduct of the Hammerstein channel identification. Equalization of the SC Hammerstein channel can then be accomplished by the usual one-tap linear equalization in the frequency domain as well as the inverse B-spline neural network model obtained in the time domain. Extensive simulation results are included to demonstrate the effectiveness of our nonlinear SC-FDE scheme for Hammerstein channels.
TGF-beta2-induced matrix modification and cell transdifferentiation in the human lens capsular bag.

PURPOSE To study the role of TGF-beta2 in posterior capsule opacification (PCO) and to determine whether CAT-152 (lerdelimumab), a fully human monoclonal antibody that neutralizes the effect of TGF-beta2, can also provide therapeutic benefit for PCO. METHODS In vitro capsular bags were prepared from human donor eyes and maintained in a 5% CO(2) atmosphere at 35 degrees C. To investigate expression of active TGF-beta2, capsular bags were incubated in serum-free EMEM for 2, 28, or more than 100 days and analyzed by ELISA (n > or = 4 at each time point). To study underlying mechanisms, match-pair experiments were also performed, so that the medium was supplemented with 0, 1 or 10 ng/mL TGF-beta2 with or without 10 microg/mL CAT-152 (n = 4 in all cases). On-going observations were by phase-contrast microscopy. In addition, donor material from patients who had undergone cataract surgery was analyzed. Cellular architecture was examined by fluorescence cytochemistry. Expression of matrix metalloproteinase (MMP)-2 and -9 was assessed by gelatin zymography. RESULTS Analysis of capsular bags from donor eyes that had received an intraocular lens (IOL) revealed the presence of endogenous active TGF-beta2, matrix wrinkling, and expression of transdifferentiation markers alphaSMA and fibronectin. When cultured in vitro, donor bags also showed sustained release of MMP-2 and -9. Culture of capsular bags prepared in vitro from whole lenses showed that TGF-beta2 (1-10 ng/mL) stimulated transdifferentiation and contraction of the capsular bag, resulting in light scatter. TGF-beta2 also induced sustained release of MMP-2 and -9. Active TGF-beta2 was detected in these cultures. The human monoclonal anti-TGF-beta2 antibody CAT-152 (10 microg/mL) effectively inhibited all TGF-beta2-induced effects. CONCLUSIONS Addition of TGF-beta2 accelerates transdifferentiation and contraction of the capsular bag, resulting in light scatter. CAT-152 inhibited all the effects of TGF-beta2 that were examined and therefore has the potential to suppress development of PCO and provide potential therapeutic benefit to cataract patients.
Distance Metric Learning with Eigenvalue Optimization

The main theme of this paper is to develop a novel eigenvalue optimization framework for learning a Mahalanobis metric. Within this context, we introduce a novel metric learning approach called DML-eig which is shown to be equivalent to a well-known eigenvalue optimization problem called minimizing the maximal eigenvalue of a symmetric matrix (Overton, 1988; Lewis and Overton, 1996). Moreover, we formulate LMNN (Weinberger et al., 2005), one of the state-of-the-art metric learning methods, as a similar eigenvalue optimization problem. This novel framework not only provides new insights into metric learning but also opens new avenues to the design of efficient metric learning algorithms. Indeed, first-order algorithms are developed for DML-eig and LMNN which only need the computation of the largest eigenvector of a matrix per iteration. Their convergence characteristics are rigorously established. Various experiments on benchmark data sets show the competitive performance of our new approaches. In addition, we report an encouraging result on a difficult and challenging face verification data set called Labeled Faces in the Wild (LFW).
Solubility-Promoting Function of Hsp90 Contributes to Client Maturation and Robust Cell Growth

ABSTRACT The Hsp90 chaperone is required for the maturation of signal transduction clients, including many kinases and nuclear steroid hormone receptors. The binding and hydrolysis of ATP by Hsp90 drive conformational rearrangements in three structure domains. Two intrinsically disordered regions of Hsp90 located between these domains and at the C terminus have traditionally been considered to impart flexibility. We discovered that the charged nature of these acid-rich disordered regions imparts a solubility-promoting function to Hsp90 that is important for its cellular activity in yeast. Both the solubility-promoting function and ATPase activity must occur in the same Hsp90 molecule in order to support robust growth, suggesting that the solubility-promoting function is required during the ATP-driven client maturation process. Expression of model clients together with Hsp90 variants indicated interdependent solubilities mediated by the aggregation propensities of both the client and Hsp90. We propose a model whereby the charge-rich disordered regions of Hsp90 serve a solubility-promoting function important for complexes with aggregation-prone clients. These findings demonstrate a novel biological function of the intrinsically disordered regions in Hsp90 and provide a compelling rationale for why their charged properties are conserved throughout eukaryotic evolution.
Self-Measurement of Blood Pressure at Home Reduces the Need for Antihypertensive Drugs: A Randomized, Controlled Trial

It is still uncertain whether one can safely base treatment decisions on self-measurement of blood pressure. In the present study, we investigated whether antihypertensive treatment based on self-measurement of blood pressure leads to the use of less medication without the loss of blood pressure control. We randomly assigned 430 hypertensive patients to receive treatment either on the basis of self-measured pressures (n=216) or office pressures (OPs; n=214). During 1-year follow-up, blood pressure was measured by office measurement (10 visits), ambulatory monitoring (start and end), and self-measurement (8 times, self-pressure group only). In addition, drug use, associated costs, and degree of target organ damage (echocardiography and microalbuminuria) were assessed. The self-pressure group used less medication than the OP group (1.47 versus 2.48 drug steps; P<0.001) with lower costs ($3222 versus $4420 per 100 patients per month; P<0.001) but without significant differences in systolic and diastolic OP values (1.6/1.0 mm Hg; P=0.25/0.20), in changes in left ventricular mass index (−6.5 g/m2 versus −5.6 g/m2; P=0.72), or in median urinary microalbumin concentration (−1.7 versus −1.5 mg per 24 hours; P=0.87). Nevertheless, 24-hour ambulatory blood pressure values at the end of the trial were higher in the self-pressure than in the OP group: 125.9 versus 123.8 mm Hg (P<0.05) for systolic and 77.2 versus 76.1 mm Hg (P<0.05) for diastolic blood pressure. These data show that self-measurement leads to less medication use than office blood pressure measurement without leading to significant differences in OP values or target organ damage. Ambulatory values, however, remain slightly elevated for the self-pressure group.
On thermal stress and fatigue life evaluation in work rolls of hot rolling mill

The paper proposes an approach for thermal stress evaluation and fatigue life assessment of work rolls in hot rolling mills. Temperature and thermal stress distributions are calculated with a simplified finite element approach, based on a plane model of work roll loaded on its boundary by rotating thermal actions for a typical hot rolling configuration. A transient of one hour is simulated and the calculated temperature field is next applied as thermal loading in elastic–plastic mechanical simulation, to get thermal stresses and elastic–plastic strains in work roll. Calculated cyclic stresses and strains are finally used to estimate work roll service life, based on Universal Slopes equation that is modified to account for the multiaxial stress state. A comparison of results by three multiaxial fatigue criteria is provided. The obtained results show that, according to such multiaxial criteria, stress multiaxiality would have a great effect on fatigue life, despite it is generally neglected in approaches usually adopted in literature.
Colouring the rational quantum sphere and the Kochen-Specker theorem

We review and extend recent findings of Godsil and Zaks, who published a constructive colouring of the rational unit sphere with the property that for any orthogonal tripod formed by rays extending from the origin of the points of the sphere, exactly one ray is red, one white and one black. They also showed that any consistent colouring of the real sphere requires an additional colour. We discuss some of the consequences for the Kochen-Specker theorem.
Characterization and Comparative Analyses of Muscle Transcriptomes in Dorper and Small-Tailed Han Sheep Using RNA-Seq Technique

The sheep is an important domestic animal and model for many types of medically relevant research. An investigation of gene expression in ovine muscle would significantly advance our understanding of muscle growth. RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing. Although RNA-seq has been recently applied to a wide variety of organisms, few RNA-seq studies have been conducted in livestock, particularly in sheep. In this study, two cDNA libraries were constructed from the biceps brachii of one Small-tailed Han sheep (SH) and one Dorper sheep (DP). The Illumina high-throughput sequencing technique and bioinformatics were used to determine transcript abundances and characteristics. For the SH and DP libraries, we obtained a total of 50,264,608 and 52,794,216 high quality reads, respectively. Approximately two-thirds of the reads could be mapped to the sheep genome. In addition, 40,481 and 38,851 potential coding single nucleotide polymorphisms (cSNPs) were observed, respectively, of which a total of 59,139 cSNP coordinates were different between the two samples. Up to 5,116 and 5,265 respective reference genes had undergone 13,827 and 15,684 alternative splicing events. A total of 6,989 reference genes were extended at the 5’, 3’ or both ends, and 123,678 novel transcript units were found. A total of 1,300 significantly differentially expressed genes were identified between the two libraries. These results suggest that there are many differences in the muscle transcriptomes between these two animals. This study addresses a preliminary analysis and offers a foundation for future genomic research in the sheep.
A major surface protein on group A streptococci is a glyceraldehyde-3- phosphate-dehydrogenase with multiple binding activity

The surface of streptococci presents an array of different proteins, each designed to perform a specific function. In an attempt to understand the early events in group A streptococci infection, we have identified and purified a major surface protein from group A type 6 streptococci that has both an enzymatic activity and a binding capacity for a variety of proteins. Mass spectrometric analysis of the purified molecule revealed a monomer of 35.8 kD. Molecular sieve chromatography and sodium dodecyl sulfate (SDS)-gel electrophoresis suggest that the native conformation of the protein is likely to be a tetramer of 156 kD. NH2-terminal amino acid sequence analysis revealed 83% homology in the first 18 residues and about 56% in the first 39 residues with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of eukaryotic or bacterial origin. This streptococcal surface GAPDH (SDH) exhibits a dose-dependent dehydrogenase activity on glyceraldehyde-3-phosphate in the presence of beta-nicotinamide adenine dinucleotide both in its pure form and on the streptococcal surface. Its sensitivity to trypsin on whole organism and its inability to be removed with 2 M NaCl or 2% SDS support its surface location and tight attachment to the streptococcal cell. Affinity-purified antibodies to SDH detected the presence of this protein on the surface of all M serotypes of group A streptococcal tested. Purified SDH was found to bind to fibronectin, lysozyme, as well as the cytoskeletal proteins myosin and actin. The binding activity to myosin was found to be localized to the globular heavy meromyosin domain. SDH did not bind to streptococcal M protein, tropomyosin, or the coiled-coil domain of myosin. The multiple binding capacity of the SDH in conjunction with its GAPDH activity may play a role in the colonization, internalization, and the subsequent proliferation of group A streptococci.
Secure State Estimation for Cyber-Physical Systems Under Sensor Attacks: A Satisfiability Modulo Theory Approach

Secure state estimation is the problem of estimating the state of a dynamical system from a set of noisy and adversarially corrupted measurements. Intrinsically a combinatorial problem, secure state estimation has been traditionally addressed either by brute force search, suffering from scalability issues, or via convex relaxations, using algorithms that can terminate in polynomial time but are not necessarily sound. In this paper, we present a novel algorithm that uses a satisfiability modulo theory approach to harness the complexity of secure state estimation. We leverage results from formal methods over real numbers to provide guarantees on the soundness and completeness of our algorithm. Moreover, we discuss its scalability properties, by providing upper bounds on the runtime performance. Numerical simulations support our arguments by showing an order of magnitude decrease in execution time with respect to alternative techniques. Finally, the effectiveness of the proposed algorithm is demonstrated by applying it to the problem of controlling an unmanned ground vehicle.
Supporting Online Material Materials and Methods Som Text Figs. S1 to S3 Table S1 References Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops

29. Overlapping buffers in multiple PAs were combined for analysis, which decreased the sample of 306 PAs to 284 buffer areas. Countries and ecoregions with one park were excluded from statistical analysis of median buffer growth rates, although results did not vary with their inclusion. A simple negative feedback loop of interacting genes or proteins has the potential to generate sustained oscillations. However, many biological oscillators also have a positive feedback loop, raising the question of what advantages the extra loop imparts. Through computational studies, we show that it is generally difficult to adjust a negative feedback oscillator's frequency without compromising its amplitude, whereas with positive-plus-negative feedback, one can achieve a widely tunable frequency and near-constant amplitude. This tunability makes the latter design suitable for biological rhythms like heartbeats and cell cycles that need to provide a constant output over a range of frequencies. Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant. T he mammalian heart rate is normally established by the sino-atrial node. The node generates constant-amplitude action potentials at a tunable frequency of ~50 to 150 action potentials per minute, depending on the body's oxygen demands. The cell cycle oscillator may also require this combination of an adjustable frequency and invariant amplitude. The period of the cell cycle ranges from about 10 min in rapidly dividing embryos to tens of hours in rapidly dividing somatic cells (and longer in slowly dividing somatic cells), but variations in the amplitude [the peak concentration of active cyclin-dependent kinase-1 (CDK1)] of the oscillations seem neither necessary nor desirable. Two basic types of circuits have been proposed for biological oscillators: (i) those that contain both positive and negative feedback loops and (ii) those containing only negative feedback (Table 1) (1–6). Both the sino-atrial node oscil-lator and the cell cycle oscillator fall into the positive-plus-negative feedback class, suggesting that this design might be better suited for generating oscillations with a tunable frequency and constant amplitude. We tested this idea through computational studies, beginning with an ordinary differential equation model of CDK1 oscillations in the Xenopus embryonic cell cycle (7). The model includes a negative feedback loop [active CDK1 brings about its inactivation through the anaphase-promoting complex (APC)] and a pair of positive feedback loops (active CDK1 activates its acti-vator Cdc25 and inactivates its inhibitor Wee1) (Fig. 1A). …
Investigating the linkage between disease‐causing amino acid variants and their effect on protein stability and binding

Single amino acid variations (SAV) occurring in human population result in natural differences between individuals or cause diseases. It is well understood that the molecular effect of SAV can be manifested as changes of the wild type characteristics of the corresponding protein, among which are the protein stability and protein interactions. Typically the effect of SAV on protein stability and interactions was assessed via the changes of the wild type folding and binding free energies. However, in terms of SAV affecting protein functionally and disease susceptibility, one wants to know to what extend the wild type function is perturbed by the SAV. Here it is demonstrated that relative, rather than the absolute, change of the folding and binding free energy serves as a good indicator for SAV association with disease. Using HumVar as a source for disease‐causing SAV and experimentally determined free energy changes from ProTherm and SKEMPI databases, correlation coefficients (CC) between the disease index (Pd) and relative folding (Ppr,f) and binding (Ppr,b) probability indexes, respectively, was achieved. The obtained CCs demonstrated the applicability of the proposed approach and it served as good indicator for SAV association with disease. Proteins 2016; 84:232–239. © 2015 Wiley Periodicals, Inc.
Learning in a game context: strategy choice by some keeps learning from evolving in others

Behavioural decisions in a social context commonly have frequency-dependent outcomes and so require analysis using evolutionary game theory. Learning provides a mechanism for tracking changing conditions and it has frequently been predicted to supplant fixed behaviour in shifting environments; yet few studies have examined the evolution of learning specifically in a game-theoretic context. We present a model that examines the evolution of learning in a frequency-dependent context created by a producer–scrounger game, where producers search for their own resources and scroungers usurp the discoveries of producers. We ask whether a learning mutant that can optimize its use of producer and scrounger to local conditions can invade a population of non-learning individuals that play producer and scrounger with fixed probabilities. We find that learning provides an initial advantage but never evolves to fixation. Once a stable equilibrium is attained, the population is always made up of a majority of fixed players and a minority of learning individuals. This result is robust to variation in the initial proportion of fixed individuals, the rate of within- and between-generation environmental change, and population size. Such learning polymorphisms will manifest themselves in a wide range of contexts, providing an important element leading to behavioural syndromes.