Miracle-dz/UniFAR-FTUs huggingface dataset:
A multilevel model correction method for parameter identification

Output least-squares formulation with Tikhonov regularization is one of the most frequently used and reliable methods for parameter identification in PDEs. As the discretized optimization system of the formulation is nonlinear, ill-conditioned, and constrained with some PDEs, its numerical solution is very time-consuming and often unstable. In this paper, we present a multilevel model correction method, which aims at solving the general nonlinear output least-squares optimization system in an efficient and robust manner. The multilevel method is conducted iteratively so that larger part of its computations is done on a sequence of nested coarse meshes defined on the concerned physical domain. The key ingredient of the method is to update the output least-squares objective functional on each coarse mesh by using the most updated information of the identifying parameter from a finer mesh. Numerical experiments are provided to demonstrate the robustness and efficiency of the method.
Positive effects of nitric oxide on left ventricular function in humans.

AIMS The myocardial effect of tonically released nitric oxide (NO) in humans is still not known. We tested the hypothesis that low-dose NO exerts positive effects on left ventricular (LV) function. METHODS AND RESULTS Twelve healthy volunteers, 26+/-4 years, were enrolled in this study. Magnetic resonance imaging was used to precisely measure the direct effects of NO on stroke volume index (SVI). The NO pool was monitored by chemiluminescence. We reduced endogenous NO levels with intravenous infusion of the NO synthase-inhibitor N(G)-monomethyl-l-arginine. Replenishment of the NO pool was achieved with the NO donor S-nitrosoglutathione (GSNO) (0.5 micromol iv). To differentiate load-dependent from the direct effects of NO on LV function, changes in SVI in response to GSNO were compared with changes in the NO-independent vasodilator dihydralazine (2.5 mg iv) at matched arterial pressure and heart rate. Inhibition of NO synthesis was followed by reduction in SVI. Subsequent replenishment of the circulating NO with GSNO significantly increased SVI (39+/-8 to 54+/-7 mL m(-2); P=0.001), whereas no significant changes were observed with the NO-independent vasodilator dihydralazine (39+/-8 to 46+/-8 mL m(-2); P=0.0626). CONCLUSION Inhibition of endogenous NO release reduces, whereas replenishment with exogenous NO increases LV function, pointing towards a positive effect of tonically released NO on LV function in healthy humans.
Behavioral and Electrophysiological Effects of Transcranial Direct Current Stimulation of the Parietal Cortex in a Visuo-Spatial Working Memory Task

Impairments of working memory (WM) performance are frequent concomitant symptoms in several psychiatric and neurologic diseases. Despite the great advance in treating the reduced WM abilities in patients suffering from, e.g., Parkinson’s and Alzheimer’s disease by means of transcranial direct current stimulation (tDCS), the exact neurophysiological underpinning subserving these therapeutic tDCS-effects are still unknown. In the present study we investigated the impact of tDCS on performance in a visuo-spatial WM task and its underlying neural activity. In three experimental sessions, participants performed a delayed matching-to-sample WM task after sham, anodal, and cathodal tDCS over the right parietal cortex. The results showed that tDCS modulated WM performance and its underlying electrophysiological brain activity in a polarity-specific way. Parietal tDCS altered event-related potentials and oscillatory power in the alpha band at posterior electrode sites. The present study demonstrates that posterior tDCS can alter visuo-spatial WM performance by modulating the underlying neural activity. This result can be considered an important step toward a better understanding of the mechanisms involved in tDCS-induced modulations of cognitive processing. This is of particular importance for the application of electrical brain stimulation as a therapeutic treatment of neuropsychiatric deficits in clinical populations.
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes

Polyadenylation of nascent transcripts is one of the key mRNA processing events in eukaryotic cells. A large number of human and mouse genes have alternative polyadenylation sites, or poly(A) sites, leading to mRNA variants with different protein products and/or 3′-untranslated regions (3′-UTRs). PolyA_DB 2 contains poly(A) sites identified for genes in several vertebrate species, including human, mouse, rat, chicken and zebrafish, using alignments between cDNA/ESTs and genome sequences. Several new features have been added to the database since its last release, including syntenic genome regions for human poly(A) sites in seven other vertebrates and cis-element information adjacent to poly(A) sites. Trace sequences are used to provide additional evidence for poly(A/T) tails in cDNA/ESTs. The updated database is intended to broaden poly(A) site coverage in vertebrate genomes, and provide means to assess the authenticity of poly(A) sites identified by bioinformatics. The URL for this database is .
Comparison of the acid resistance of root dentin after treatment with an MIR-FEL emitting at λ=9.0 μm and λ=9.7 μm

Background and Objective: The surface modification of root dentin by mid-infrared (MIR) pulsed-laser irradiation is a potential candidate for non-invasive treatment to prevent root surface caries. The purpose of this study is to compare the relative acid resistance of root dentin treated with an MIR Free Electron Laser emitting at between 9.0 μm and 9.7 μm. Study Design/Materials and Methods: The average power density was varied over the range 7.5-51.5 W/cm2. After irradiation, the samples were immersed in a 0.1 M lactic acid solution. Acid resistance was estimated as the quantity of Ca dissolved in the solution after immersion times (tim) of 1-22 h. Results: The acid resistance of all samples increased markedly, but only until tim = ~3 h. It did not depend significantly on the laser parameters used. Conclusion: The surface modification of root dentin leads to improved acid resistance, but this only persists for a few hours and therefore represents a poor treatment for root surface caries.
Identification of a Signal-Responsive Nuclear Export Sequence in Class II Histone Deacetylases

ABSTRACT Activation of muscle-specific genes by the MEF2 transcription factor is inhibited by class II histone deacetylases (HDACs) 4 and 5, which contain carboxy-terminal deacetylase domains and amino-terminal extensions required for association with MEF2. The inhibitory action of HDACs is overcome by myogenic signals which disrupt MEF2-HDAC interactions and stimulate nuclear export of these transcriptional repressors. Nucleocytoplasmic trafficking of HDAC5 is mediated by binding of the chaperone protein 14-3-3 to two phosphoserine residues (Ser-259 and Ser-498) in its amino-terminal extension. Here we show that HDAC4 and -5 each contain a signal-responsive nuclear export sequence (NES) at their extreme carboxy termini. The NES is conserved in another class II HDAC, HDAC7, but is absent in class I HDACs and the HDAC-related corepressor, MEF2-interacting transcription repressor. Our results suggest that this conserved NES is inactive in unphosphorylated HDAC5, which is localized to the nucleus, and that calcium-calmodulin-dependent protein kinase (CaMK)-dependent binding of 14-3-3 to phosphoserines 259 and 498 activates the NES, with consequent export of the transcriptional repressor to the cytoplasm. A single amino acid substitution in this NES is sufficient to retain HDAC5 in the nucleus in the face of CaMK signaling. These findings provide molecular insight into the mechanism by which extracellular cues alter chromatin structure to promote muscle differentiation and other MEF2-regulated processes.
Tackling the Provenance Challenge one layer at a time

VisTrails is a new workflow and provenance management system that provides support for scientific data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, change is the norm. VisTrails uses a new change‐based provenance mechanism, which was designed to handle rapidly evolving workflows. It uniformly and automatically captures provenance information for data products and for the evolution of the workflows used to generate these products. In this paper, we describe how the VisTrails provenance data are organized in layers and present a first approach for querying this data that we developed to tackle the Provenance Challenge queries. Copyright © 2007 John Wiley & Sons, Ltd.
Unsupervised phonemic Chinese word segmentation using Adaptor Grammars

Adaptor grammars are a framework for expressing and performing inference over a variety of non-parametric linguistic models. These models currently provide state-of-the-art performance on unsupervised word segmentation from phonemic representations of child-directed unsegmented English utterances. This paper investigates the applicability of these models to unsupervised word segmentation of Mandarin. We investigate a wide variety of different segmentation models, and show that the best segmentation accuracy is obtained from models that capture interword "collocational" dependencies. Surprisingly, enhancing the models to exploit syllable structure regularities and to capture tone information does improve overall word segmentation accuracy, perhaps because the information these elements convey is redundant when compared to the inter-word dependencies.
Childhood happiness and violence: a retrospective study of their impacts on adult well-being

Objectives To examine the hypothesis that adult well-being is related to childhood experiences independent of current adult sociodemographic conditions. Design A cross-sectional, stratified, randomised sample survey using self-assessed measures of current well-being and retrospective measures of childhood experiences. Setting Households in North West England (September 2012–March 2013). Participants The individual with the next birthday in randomly selected households (n=11 500; compliance 89.6% of eligible households). Analysis was limited to those aged ≥18 years and answering all pertinent questions (n=11 157). Outcomes The primary outcome was a validated multicomponent measure of mental well-being (MWB). Additional outcomes included self-assessed life satisfaction (LS), life worth and trust in others. Results Adult MWB, LS, life worth and trust were all significantly related to childhood violence and happiness. Relationships remained after controlling for sociodemographics. Thus, compared with those with happy, non-violent childhoods, respondents with unhappy, violent childhoods had adjusted ORs (95% CI, significance) of 3.10 (2.59 to 3.71, p<0.001) for low MWB, 3.62 (2.99 to 4.38, p<0.001) for low LS, 4.13 (3.40 to 5.01, p<0.001) for low life worth and 2.62 (2.20 to 3.11, p<0.001) for low trust. The impact of unhappy but non-violent childhoods were smaller but significant (p<0.001). The modelled impact of childhood factors predicted, for instance, that among unemployed white men aged 25–39 years from the most deprived communities, 27% of those with happy non-violent childhoods would have low MWB rising to 53% of those with unhappy violent childhoods. Conclusions Adult well-being is strongly linked to childhood experiences. The addition of well-being measures to outcomes already associated with adverse childhoods (eg, adolescent antisocial behaviour and risks of adult disease) strengthens the case for investment in interventions to improve childhood experiences. Public health systems are well placed to ensure that policy to improve adult well-being exploits the potential for this to be realised through appropriate interventions.
Domain-Oriented Relational Languages

A view of the semantics of a relational data base consists in considering that the data base domains represent the sets of objects of the subject matter and that the relations represent various kinds of associations among these objects. This view is supported by query languages where each variable ranges on a domain of the relational data base and predicates correspond to the associations modeled by relations. This paper defines two domain-oriented relational languages. DRC is a many-sorted calculus, where the structural role of domains is emphasized by defining types for variables and type-checking rules. ILL is an English-like language, which is wholly built upon a structure of expressions nested inside other expressions. "Domain-languages" are contrasted with "tuple languages", which manipulate as basic objects the relation n-tuples. Directly manipulating domains and domain values interacts more directly with the semantics expressed by the relations and produces simpler and more English-like languages.
Epigenetic Regulation of αA-crystallin in High Myopia-Induced Dark Nuclear Cataract

Purpose To assess the etiology of early-onset dark nucleus in high-myopic patients and its relationship with the epigenetic regulation of αA-crystallin (CRYAA). Methods We reviewed clinical data from patients who underwent cataract surgery at our center in 2012. Lens epithelial samples were collected during capsulorhexis, whereas young lens epithelium was donated. Cataract type and severity were graded according to the Lens Opacity Classification System III (LOCS III). DNA methylation was analyzed by pyrosequencing the CpG islands of the CRYAA promoter in the following groups: Age-Related Cataract (ARC) Nuclear Color (NC) 2–3; High-Myopic Cataract (HMC) NC2–3; ARC NC5–6; HMC NC5–6; and in young lenses graded NC1. We analyzed CRYAA expression by real-time polymerase chain reaction (PCR), reverse transcription PCR, and immunohistochemistry. Results The odds ratio of dark nucleus in high-myopic patients was 5.16 (95% confidence interval: 3.98–6.69; p<0.001). CpG islands in lens epithelial CRYAA promoter in the HMC NC5–6 Group exhibited the highest methylation of all the groups, but no statistically significant differences were evident between the HMC NC2–3 and ARC NC2–3 Groups. Likewise, CRYAA mRNA and protein levels in the HMC NC5–6 Group were significantly lower than the ARC NC5–6 Group and high-myopic controls. Conclusions High myopia is a risk factor for dark nucleus. Downregulation of CRYAA via the hypermethylation of CpG islands in its promoter could underlie the earlier onset of dark nucleus in high-myopic patients.
Chemiluminescence of phagocytic cells caused by N-formylmethionyl peptides

N-formylmethionyl (F-Met) peptides, when added alone to macrophages or polymorphonuclear leukocytes (PMN), were found to induce a chemiluminescent response of shorter duration than that produced by the commonly employed particulate stimulant, zymosan. The cellular nature of F-Met peptide-induced chemiluminescence was indicated by its dependence on cell concentration, and by its inhibition by cell disruption, heat inactivation, or previous maximal stimulation by the peptides. Comparison of PMN and macrophages from different species showed that the maximal chemiluminescent response seen in the dose-response curve of F-Met- Phe was different in different cell types. Chemiluminescence reached highest values in human PMN, it was intermediate in guinea pig macrophages and PMN, and in rabbit PMN; but it was nonexistent in rabbit alveolar macrophages and very low in rabbit peritoneal macrophages. A definite relationship was observed between peptide structure and chemiluminescent activity. Met-Phe, F- Met and Phe were inactive even at millimolar concentrations, while F-Met-Phe caused chemiluminescence at micromolar concentrations. Four active peptides were tested in guinea pig, rabbit, and human PMN, and in guinea pig alveolar and peritoneal macrophages. The relative activity of these peptides was the same in all cells studied, e.g. F-Met-Leu-Phe >> F-Met-Phe > F-Met-Val > F- Met-Ala. The values of ED50 for each peptide were also comparable to previously reported ED50 values of these peptides in inducing lysosomal enzyme release. These results were seen both in the presence and absence ofthe chemiluminescent oxidant indicator, luminol. Low concentrations of superoxide dismutase (10 μg/ml) completely inhibited chemiluminescence caused by the F-Met peptides, suggesting the involvement of 0(2)(-) or O(2)(-)-derived compounds in this response. Sodium azide, an inhibitor of peroxidase reactions, had either no effect or a slight inhibitory effect on chemiluminescence. However, when the extracellular release of lysosomal enzymes was induced by cytochalasin B, an azide- inhibitable enhancement of chemiluminescence was seen in PMN, but not in macrophages. This effect appears to be correlated with the presence of granule-associated myeloperoxidase. Although azide-inhibitable peroxidases could be a potential source of light, they did not appear to be a significant contributor in these experiments. Based on these results and on those of previous investigators, we postulate that the F-Met-peptides stimulate 0(2)(-) production in addition to stimulating lysosomal enzyme release and chemotaxis. The similar structure- activity relationship which appears to exist for these processes may indicate that they are all initiated by a single receptor mechanism. Since F-Met peptides are formed in bacteria it is likely that their actions represent an important physiologic response.
Large-scale Datasets: Faces with Partial Occlusions and Pose Variations in the Wild

Face detection methods have relied on face datasets for training. However, existing face datasets tend to be in small scales for face learning in both constrained and unconstrained environments. In this paper, we first introduce our large-scale image datasets, Large-scale Labeled Face (LSLF) and noisy Large-scale Labeled Non-face (LSLNF). Our LSLF dataset consists of a large number of unconstrained multi-view and partially occluded faces. The faces have many variations in color and grayscale, image quality, image resolution, image illumination, image background, image illusion, human face, cartoon face, facial expression, light and severe partial facial occlusion, make up, gender, age, and race. Many of these faces are partially occluded with accessories such as tattoos, hats, glasses, sunglasses, hands, hair, beards, scarves, microphones, or other objects or persons. The LSLF dataset is currently the largest labeled face image dataset in the literature in terms of the number of labeled images and the number of individuals compared to other existing labeled face image datasets. Second, we introduce our CrowedFaces and CrowedNonFaces image datasets. The crowedFaces and CrowedNonFaces datasets include faces and non-faces images from crowed scenes. These datasets essentially aim for researchers to provide a large number of training examples with many variations for large scale face learning and face recognition tasks.
Least square based sliding mode control for a quad-rotor helicopter

In this paper, we design a least square based sliding mode control to solve the over determined problem in translation motion of a quad-rotor helicopter while in rotational motion we employ a regular sliding mode control. A saturation function is designed around a boundary layer to reduce the chattering phenomenon that occurs in a sliding mode control. The dynamics of the quad-rotor helicopter is derived by the Newton-Euler formulation for a rigid body. A constant plus proportional reaching law is utilized to increase reaching rate of the sliding mode controller. The stability of the proposed algorithm is evaluated on the basis of Lyapunov stability theory. Experimental results under wind disturbance are presented to show the robustness and effectiveness of the proposed control algorithm.
LexOnto: A Model for Ontology Lexicons for Ontology-based NLP

In this paper we present a model and a corresponding ontology for associating lexical information to entities of a given domain ontology. In particular, we focus on representing subcategorization frames as well as their mapping to ontological structures. The lexicon model and ontology can thus be used to specify the syntax-semantic interface for ontology-based NLP systems which are expected to produce output compliant with a specific domain ontology. Our lexicon ontology itself is formalized in the OWL language, thus allowing the lexica to be published together with the domain ontologies. We also discuss different ways how the creation of appropriate lexica can be supported.
Spatial analysis of the exposure of dogs in rural north-coastal California to vectorborne pathogens

Between 0 and 50 per cent of the dogs in eight rural villages in far northern California with a high risk of tickborne diseases were seropositive for Anaplasma phagocytophilum and Bartonella vinsonii subspecies berkhoffii, and between 0 and 10 per cent were seropositive for Borrelia burgdorferi. The odds ratio for the co-exposure of individual dogs to B vinsonii berkhoffii and A phagocytophilum was 18·2. None of the diseases was associated with the sex of the dogs, whether they slept out of doors, or whether tick-preventive measures were taken. When the villages were assessed for landscape risk factors, a particularly high seroprevalence for B vinsonii berkhoffii and A phagocytophilum was observed in a village at a relatively high altitude and greater distance from the Pacific coast, and montane hardwood conifer woodland was most associated with a high seroprevalence for these two pathogens.
What and how much to gain by spectrum agility?

Static spectrum allocation prohibits radio devices from using spectral bands designated for others. As a result, some bands are under-utilized while other bands are over-populated with radio devices. To remedy this problem, the concept of spectrum agility has been considered so as to enable devices to opportunistically utilize others' spectral bands. In order to help realize this concept, we establish an analytical model to derive performance metrics, including spectrum utilization and spectrum-access blocking time in spectral-agile communication systems. We then propose three basic building blocks for spectral-agile systems, namely spectrum opportunity discovery, spectrum opportunity management, and spectrum usage coordination, and develop protocols for each blocks. These protocols are integrated with the IEEE 802.11 protocol, and simulated using ns-2 to evaluate the protocol overhead. The simulation results show that our proposed protocols can improve the throughput of an IEEE 802.11 wireless LAN by 90% for the simulated scenarios, and the improvements matched well our analytical model. These results demonstrate the great potential of using spectrum agility for improving spectral utilization in an efficient, distributed, and autonomous manner