Miracle-dz/UniFAR-FTUs huggingface dataset:
Limited role of contextual information in adult word recognition

Recognizing a word in a meaningful text involves processes that combine information from many different sources, and poth bottom-up processes (such as feature extraction and letter recognition) and top-down processes (contextual information) are thought to interact when skilled readers recognize words. Two similar experiments investigated word recognition latencies of adult readers who read single words that were manipulated by repetition and/or degradation, and the effects of context were observed. Subjects for the first experiment were 40 introductory psychology students, while those for the second experiment were 60 different students. Findings indicated that repeated words were recognized faster than nonrepeated words, but were not any less affected by semantic context. The two degradation manipulations (inserting asterisks between a word's letters and masking a word) slowed word recognition as compared to a clear presentation. However, only the masking manipulation produced contextual inhibition, and the magnitude of Lontext effects did not always vary monotonically with the word recognition latencies in the neutral condition. A version of the interactive-compensatory model of skilled reading is the most compatible explanation of the results of these experiments, because that model contends that slowed word recognition is not always accompanied by contextual compensation and that adult readers depend on their decoding processes when the processes are slowed, unless the data are inadequate for such analysis. (SEC)
Orlistat and the risk of acute liver injury: self controlled case series study in UK Clinical Practice Research Datalink

Objective To measure the association between orlistat and acute liver injury. Design Self controlled case series study. Setting Population based primary care setting, United Kingdom. Participants 94 695 patients receiving orlistat and registered in the UK Clinical Practice Research Datalink and linked with Hospital Episode Statistics data between 1999 and 2011. Main outcome measure Relative incidence of acute liver injury comparing periods when patients were receiving orlistat with periods of non-usage. Results Among 94 695 patients who received orlistat, 988 cases of acute liver injury were identified, with 335 confirmed as definite cases and 653 as probable cases. For all cases an increased incidence of liver injury was detected during the 90 day period before orlistat was first started, with an incidence rate ratio of 1.50 (95% confidence interval 1.10 to 2.06). The incidence remained raised during the first 30 days of treatment (2.21, 1.43 to 3.42), before returning to baseline levels with prolonged treatment. When the risk during the first 90 days of treatment was compared with the 90 days preceding first treatment, the incidence of liver injury was not increased (1.02, 0.67 to 1.56). An analysis restricted to definite cases showed no evidence of an increased risk of liver injury during treatment. Conclusion The incidence of acute liver injury was higher in the periods both immediately before and immediately after the start of orlistat treatment. This suggests that the observed increased risks of liver injury linked to the start of treatment may reflect changes in health status associated with the decision to begin treatment rather than any causal effect of the drug.
Nasal Speech Sounds Detection Using Connectionist Temporal Classification

Phone attributes, known also as distinctive or phonological features, belong to important classification of the speech sounds used in automatic speech processing. Training of conventional phone attribute detectors (classifiers), either based on acoustic measurements or deep learning approaches, requires decent phone boundary segmentation. This paper proposes a solution to train a phone attribute detector without phone alignment using an end-to-end phone attribute modeling based on the connectionist temporal classification. Experiments, performed for the nasal phone attribute on the LibriSpeech database, confirm that the proposed system outperforms conventional deep neural network detector, trained even on the same training data. Further improvements are observed with more training data. Conventional complex system that consists of feature extraction, phone force-alignment and deep neural network training is replaced by a more simpler Python package based on PyTorch, released as open-source.
Master-slave synchronization of pulse-coupled chaotic spiking oscillators

Studies basic dynamics of a chaotic spiking oscillator and its master-slave type pulse-coupled system. The slaves can exhibit synchronous phenomena for the chaotic spike-trains of the masters not depending on the initial states. Using the mapping procedure, we analyze the synchronous phenomena. Constructing a simple test circuit, we verify typical phenomena in the laboratory.
Collateral Values by Asset Class: Evidence from Primary Securities Dealers

Using data on repurchase agreements by primary securities dealers, we show that three classes of securities (Treasury securities, securities issued by government-sponsored agencies, and mortgage-backed securities) can be formally ranked in terms of their collateral values in the general collateral (GC) market. We then show that GC repurchase agreement (repo) spreads across asset classes display jumps and significant temporal variation, especially at times of predictable liquidity needs, consistent with the "safe haven" properties of Treasury securities: These jumps are driven almost entirely by the behavior of the GC repo rates of Treasury securities. Estimating the "collateral rents" earned by owners of these securities, we find such rents to be sizable for Treasury securities and nearly zero for agency and mortgage-backed securities. Finally, we link collateral values to asset prices in a simple no-arbitrage framework and show that variations in collateral values explain a significant fraction of changes in short-term yield spreads but not those of longer-term spreads. Our results point to securities' role as collateral as a promising direction of research to improve understanding of the pricing of money market securities and their spreads. The Author 2010. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org. , Oxford University Press.
The dual roles of red blood cells in tissue oxygen delivery: oxygen carriers and regulators of local blood flow

SUMMARY Vertebrate red blood cells (RBCs) seem to serve tissue oxygen delivery in two distinct ways. Firstly, RBCs enable the adequate transport of O2 between respiratory surfaces and metabolizing tissues by means of their high intracellular concentration of hemoglobin (Hb), appropriate allosteric interactions between Hb ligand-binding sites, and an adjustable intracellular chemical environment that allows fine-tuning of Hb O2 affinity. Secondly, RBCs may sense tissue O2 requirements via their degree of deoxygenation when they travel through the microcirculation and release vasodilatory compounds that enhance blood flow in hypoxic tissues. This latter function could be important in matching tissue O2 delivery with local O2 demand. Three main mechanisms by which RBCs can regulate their own distribution in the microcirculation have been proposed. These are: (1) deoxygenation-dependent release of ATP from RBCs, which stimulates production of nitric oxide (NO) and other vasodilators in the endothelium; (2) release of vasoactive NO from S-nitroso-Hb upon deoxygenation; and (3) reduction of naturally occurring nitrite to vasoactive NO by deoxygenated Hb. This Commentary inspects all three hypotheses with regard to their mechanisms, experimental evidence in their support and details that remain unresolved. The prime focus is on human/mammalian models, where most evidence for a role of erythrocyte ATP and NO release in blood flow regulation have accumulated. Information from other vertebrate groups is integrated in the analysis and used to discuss the evolutionary origin and general relevance of each hypothesis.
Accurate Torque Control of Interior Permanent Magnet Synchronous Machine

A novel parameters estimation strategy of interior permanent magnet synchronous machine (IPMSM) for accurate torque control is proposed and investigated in this paper. The difference of q-axis inductance and d-axis inductance is estimated by a PI regulator using the deviation between actual output power and reference power. The estimated difference of dq inductance can be used to achieve maximum torque per ampere control and accurate toque control. This strategy is most effective when IPMSM works under high-power high-speed working conditions. It provides an effective way for IPMSM accurate torque control. The effectiveness of the proposed method is verified by both simulation and experimental results.
Extrinsic modulation of theta field activity in the entorhinal cortex of the anesthetized rat

Field recordings of the entorhinal cortex (EC) were studied and compared to those recorded concomitantly in the dentate region of the hippocampal formation (HPC) in the urethane anesthetized rat. The EC, like the HPC, showed two main variations of spontaneous field activity: a desynchronized, large amplitude irregular activity and a synchronized, rhythmic, slow frequency field activity (RSA or theta). Corroborating previous research, a phase reversal was seen across layer II of the EC and when recorded superficial to this layer, EC theta was phase‐locked to that recorded from the HPC (dentate). Entorhinal cortex (and HPC) theta could be evoked by the application of moderate tail pinches (sensory stimulation), by pharmacological treatments enhancing cholinergic transmission, and by electrical stimulation of the posterior hypothalamus. Spectral analysis revealed that in all cases, theta was produced coherently across the two limbic structures. Entorhinal cortex (and HPC) production of theta could be abolished by pharmacological treatments disrupting cholinergic transmission, and by reversible procaine inactivation of the medial septal region. Therefore, it was concluded that limbic theta is modulated spontaneously, and with sensory and hypothalamic stimulation through the activity of cells in the medial septal region via muscarinic neurotransmission. It was also hypothesized that the activation of cells in the posterior hypothalamus linearly codes the frequency, and to a lesser extent the power, of EC and HPC theta. Given these findings and the coincidence and coherence of the occurrence of theta across the EC and HPC, it was postulated that it occurs via a parallel mechanism in the two areas.
Myocardin-related transcription factors control the motility of epicardium-derived cells and the maturation of coronary vessels

An important pool of cardiovascular progenitor cells arises from the epicardium, a single layer of mesothelium lining the heart. Epicardium-derived progenitor cell (EPDC) formation requires epithelial-to-mesenchymal transition (EMT) and the subsequent migration of these cells into the sub-epicardial space. Although some of the physiological signals that promote EMT are understood, the functional mediators of EPDC motility and differentiation are not known. Here, we identify a novel regulatory mechanism of EPDC mobilization. Myocardin-related transcription factor (MRTF)-A and MRTF-B (MKL1 and MKL2, respectively) are enriched in the perinuclear space of epicardial cells during development. Transforming growth factor (TGF)-β signaling and disassembly of cell contacts leads to nuclear accumulation of MRTFs and the activation of the motile gene expression program. Conditional ablation of Mrtfa and Mrtfb specifically in the epicardium disrupts cell migration and leads to sub-epicardial hemorrhage, partially stemming from the depletion of coronary pericytes. Using lineage-tracing analyses, we demonstrate that sub-epicardial pericytes arise from EPDCs in a process that requires the MRTF-dependent motile gene expression program. These findings provide novel mechanisms linking EPDC motility and differentiation, shed light on the transcriptional control of coronary microvascular maturation and suggest novel therapeutic strategies to manipulate epicardium-derived progenitor cells for cardiac repair. Highlighted article: Myocardin-related transcription factors respond to TGFβ signalling and control both the motility of mouse epicardium-derived progenitors and the maturation of coronary vessels.
Predicting students' grades based on free style comments data by artificial neural network

Predicting students' academic achievement with high accuracy has an important vital role in many academic disciplines. Most recent studies indicate the important role of the data type selection. They also attempt to understand individual students more deeply by analyzing questionnaire for a particular purpose. The present study uses free-style comments written by students after each lesson, to predict their performance. These comments reflect their learning attitudes to the lesson, understanding of subjects, difficulties to learn, and learning activities in the classroom. To reveal the high accuracy of predicting student's grade, we employ (LSA) latent semantic analysis technique to extract semantic information from students' comments by using statistically derived conceptual indices instead of individual words, then apply (ANN) artificial neural network model to the analyzed comments for predicting students' performance. We chose five grades instead of the mark itself to predict student's final result. Our proposed method averagely achieves 82.6% and 76.1% prediction accuracy and F-measure of students' grades, respectively.
Distribution, age, and origin of a submarine landslide deposit in the Pleistocene Kiwada Formation, forearc basin fill on the Boso Peninsula, east‐central Japan: Constraints from tephro‐ and biostratigraphy

A mass‐transport deposit named MTD1 (up to 100 m in thickness) is intercalated in the upper Kiwada Formation, a Pleistocene forearc basin fill on the Boso Peninsula, east‐central Japan. The present study aims to examine the origin, age, and distribution of MTD1. MTD1 consists mainly of mudstone blocks containing thin very fine‐ to medium‐grained sandstones, and ranges from tens of centimeters to more than tens of meters in length and thickness. Correlation of marker tuff beds and application of the biostratigraphy of calcareous nannofossils suggest that the blocks in MTD1 were derived from the underlying strata. The total thickness of the stratified blocks from the different stratigraphic horizons exceeds 60 m, implying that MTD1 originated from deeply‐excavated slope failure. The slope failure occurred in a short time interval at ca 1.3 Ma. MTD1 provides an estimate of the height of the escarpment on the basis of the stratigraphic origin of the blocks.
Early Cretaceous granitic rocks from the southern Jiaodong Peninsula, eastern China: implications for lithospheric extension

ABSTRACT Zircon U–Pb ages, major element and trace element compositions, and Sr, Nd, and Pb isotopic compositions for late Mesozoic granites from the southern Jiaodong Peninsula (eastern China) were determined. Ages for the Wulianshan, Xiaozhushan, and Dazhushan plutons are 119.1–122.3, 114.2, and 108.9 Ma, respectively. Major and trace element characteristics show that these granitic rocks belong to alkaline, A-type granites formed in an extensional setting. Trace element compositions show strong, variable negative anomalies in Ba, K, P and Ti, and positive anomalies in Rb, Th, U, Pb, Ce, Zr, and Hf, which are typical characteristics of A-type granites. Variable Sr and Nd isotopic compositions, 87Sr/86Sr(i) = 0.70540–0.7071 and εNd(t) = −14.5 to −20.9. Whole-rock Pb isotopic compositions have the following ranges, (206Pb/204Pb)t = 15.707–16.561, (207Pb/204Pb)t = 15.376–16.462, and (208Pb/204Pb)t = 36.324 to 37.064. Isotopic modelling indicates an origin that lies between mantle tapped by Cenozoic basalts around the Tan-Lu megafault and lower continental crust (LCC), and which can be explained by mixing of 11–18% mantle and 82–89% LCC. Based on new and compiled data, we suggest that the southern Jiaodong Peninsula, as well as the Laoshan area, was in a regional extensional setting of an orogenic belt during 106–126 Ma. The granitic rocks may be the result of late Mesozoic lithospheric thinning and decratonization (i.e. late Mesozoic craton destruction event occurring throughout eastern China). GRAPHICAL ABSTRACT
Bmc Structural Biology Crystal Structure of a Dna Polymerase Sliding Clamp from a Gram-positive Bacterium

Background: Sliding DNA clamps are processivity factors that are required for efficient DNA replication. DNA polymerases maintain proximity to nucleic acid templates by interacting with sliding clamps that encircle DNA and thereby link the polymerase enzyme to the DNA substrate. Although the structures of sliding clamps from Gram-negative bacteria (E. coli), eukaryotes, archaea, and T4-like bacteriophages are well-known, the structure of a sliding clamp from Gram-positive bacteria has not been reported previously.
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors

This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein–DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites: http://protedna.csbb. ntu.edu. tw/ http://protedna.csie. ntu.edu. tw/ http://bio222.esoe. ntu.edu. tw/ProteDNA/.
Functional Analysis of Conserved Polar Residues in Vc-NhaD, Na+/H+ Antiporter of Vibrio cholerae*

Vc-NhaD is a Na+/H+ antiporter from Vibrio cholerae with a sharp maximum of activity at pH ∼ 8.0. NhaD homologues are present in many bacteria as well as in higher plants. However, very little is known about structure-function relations in NhaD-type antiporters. In this work 14 conserved polar residues associated with putative transmembrane segments of Vc-NhaD have been screened for their possible role in the ion translocation and pH regulation of Vc-NhaD. Substitutions S150A, D154G, N155A, N189A, D199A, T201A, T202A, S389A, N394G, S428A, and S431A completely abolished the Vc-NhaD-mediated Na+-dependent H+ transfer in inside-out membrane vesicles. Substitutions T157A and S428A caused a significant increase of apparent Km values for alkali cations, with the Km for Li+ elevated more than that for Na+, indicating that Thr-157 and Ser-428 are involved in alkali cation binding/translocation. Of six conserved His residues, mutation of only His-93 and His-210 affected the Na+(Li+)/H+ antiport, resulting in an acidic shift of its pH profile, whereas H93A also caused a 7-fold increase of apparent Km for Na+ without affecting the Km for Li+. These data suggest that side chains of His-93 and His-210 are involved in proton binding and that His-93 also contributes to the binding of Na ions during the catalytic cycle. These 15 residues are clustered in three distinct groups, two located at opposite sides of the membrane, presumably facilitating the access of substrate ions to the third group, a putative catalytic site in the middle of lipid bilayer. The distribution of these key residues in Vc-NhaD molecule also suggests that transmembrane segments IV, V, VI, X, XI, and XII are situated close to one another, creating a transmembrane relay of charged/polar residues involved in the attraction, coordination, and translocation of transported cations.
Hemodynamic Signals Correlate Tightly with Synchronized Gamma Oscillations

Functional imaging methods monitor neural activity by measuring hemodynamic signals. These are more closely related to local field potentials (LFPs) than to action potentials. We simultaneously recorded electrical and hemodynamic responses in the cat visual cortex. Increasing stimulus strength enhanced spiking activity, high-frequency LFP oscillations, and hemodynamic responses. With constant stimulus intensity, the hemodynamic response fluctuated; these fluctuations were only loosely related to action potential frequency but tightly correlated to the power of LFP oscillations in the gamma range. These oscillations increase with the synchrony of synaptic events, which suggests a close correlation between hemodynamic responses and neuronal synchronization.
Conventional PCR for molecular diagnosis of human strongyloidiasis

SUMMARY Strongyloidiasis is frequently asymptomatic and diagnosis of latent infection is difficult due to limitations of current parasitological and serological methods. This study aimed to verify the use of conventional polymerase chain reaction (PCR) assay for molecular diagnosis of Strongyloides stercoralis infection. Fresh stool samples were obtained from 103 individuals: 33 S. stercoralis positive, 30 positive for other parasites and 40 negative for parasitological methods. These samples were examined by the Lutz, Rugai and agar plate culture methods and conventional PCR assay. Two sets of primers (S. stercoralis species-specific and genus-specific sets), located in the 18S ribosomal RNA gene, were used for PCR. Of the 33 samples positive for S. stercoralis by parasitological methods, 28 (84·8%) were also detected by PCR assay using species-specific primers and 26 (78·8%) using genus-specific primers. Among the stool samples negative by parasitological methods, seven (17·5%) were positive by PCR using species-specific primers and two (5·0%) using genus-specific primers. In conclusion, the conventional PCR assay described in this study using a species-specific primer pair provided a molecular method for S. stercoralis diagnosis in human stool samples.
Generating reliable video annotations by exploiting the crowd

In computer vision and machine learning, the availability of annotated datasets is of crucial importance for both learning and performance evaluation. However, annotating visual datasets is a tedious and error-prone task and computer vision researchers usually dedicate a large amount of their time for collecting and generating annotations, which most of the time cannot be re-used in other scenarios. In this paper, we propose a simple, but effective, interactive video object segmentation method exploiting large noisy data gathered from crowd of users while playing a web game. Experimental results, carried out on two challenging video benchmarks, show how it is possible to generate reliable object segmentations in videos with a small human effort, achieving an accuracy comparable to the one obtained with manually-labeled annotations and also outperforming state-of-the-art video object segmentation approaches.