Miracle-dz/UniFAR-FTUs huggingface dataset:
An n-gram-based statistical machine translation decoder

In this paper we describe MARIE, an Ngram-based statistical machine translation decoder. It is implemented using a beam search strategy, with distortion (or reordering) capabilities. The underlying translation model is based on an Ngram approach, extended to introduce reordering at the phrase level. The search graph structure is designed to perform very accurate comparisons, what allows for a high level of pruning, improving the decoder efficiency. We report several techniques for efficiently prune out the search space. The combinatory explosion of the search space derived from the search graph structure is reduced by limiting the number of reorderings a given translation is allowed to perform, and also the maximum distance a word (or a phrase) is allowed to be reordered. We finally report translation accuracy results on three different translation tasks.
Ensuring safety in distributed networks

Large-scale distributed networks are not easy to control centrally. Local set-point variations will likely create flooding alarm fluctuations. However, local control can cause emergence of unwanted network behavior. The paper overviews the problems with model-based control in sensory networks, such as currently rolled out for the Electric Grid, and shows how networked intelligence can bridge between central and distributed control.
Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein-Ligand Interactions

To incorporate protein-ligand interaction information into conventional two-dimensional (2D) fingerprint searching, interacting fragments of active compounds were extracted from X-ray structures of protein-ligand complexes and encoded as structural key-type fingerprints. Similarity search calculations with fingerprints derived from interacting fragments were compared to fingerprints of complete ligands and control fragments. In these calculations, fingerprints of interacting fragments produced significantly higher compound recall than other fingerprints. These results indicate that ligand fragments involved in protein-ligand interactions carry much activity-specific chemical information that can be exploited in similarity searching without explicitly accounting for interaction information.
Broadband Dual Circularly Polarized Substrate Integrated Waveguide Antenna

In this letter, a broadband dual circularly polarized substrate integrated waveguide (SIW) antenna is proposed. The proposed antenna consists of a quarter mode SIW cavity, two open-stubs and defected ground structures (DGSs). The antenna has two ports. One of them provides left-hand circular polarization and the other provides right-hand circular polarization. Circular polarization is obtained from TE202 mode of the quarter mode resonator. The cavity loaded with two perpendicular open-stubs at the corner provides dual mode resonance, which is then utilized to increase circular polarization bandwidth of the antenna. Furthermore, DGSs are used to improve isolation between the ports. The measured 3 dB axial ratio (AR) bandwidth of the antenna is approximately 11.2% at 12.5 GHz with a return loss more than 10 dB over the band.
Modulation of heme and myristate binding to human serum albumin by anti‐HIV drugs

Human serum albumin (HSA) has an extraordinary ligand‐binding capacity, and transports Fe(III)heme and medium‐ and long‐chain fatty acids. In human immunodeficiency virus‐infected patients the administered drugs bind to HSA and act as allosteric effectors. Here, the binding of Fe(III)heme to HSA in the presence of three representative anti‐HIV drugs and myristate is investigated. Values of the dissociation equilibrium constant Kd for Fe(III)heme binding to HSA were determined at different myristate concentrations, in the absence and presence of anti‐HIV drugs. Nuclear magnetic relaxation dispersion profiles of HSA–Fe(III)heme were measured, at different myristate concentrations, in the absence and presence of anti‐HIV drugs. Structural bases for anti‐HIV drug binding to HSA are provided by automatic docking simulation. Abacavir and nevirapine bind to HSA with Kd values of 1 × 10−6 and 2 × 10−6 m, respectively. Therefore, at concentrations used in therapy (in the 1–5 × 10−6 m range) abacavir and nevirapine bind to HSA and increase the affinity of heme for HSA. In the presence of abacavir or nevirapine, the affinity is not lowered by myristate. FA7 should therefore be intended as a secondary binding site for abacavir and nevirapine. Binding of atazanavir is limited by the large size of the drug, although preferential binding may be envisaged to a site positively coupled with FA1 and FA2, and negatively coupled to FA7. As a whole, these results provide a foundation for the comprehension of the complex network of links modulating HSA‐binding properties.
Discriminative Learning of the Prototype Set for Nearest Neighbor Classification

The nearest neighbor rule is a classic yet essential classification model, particularly in problems where the supervising information is given by pairwise dissimilarities and the embedding function are not easily obtained. Prototype selection provides means of generalization and improving efficiency of the nearest neighbor model, but many existing methods assume and rely on the analyses of the input vector space. In this paper, we explore a dissimilarity-based, parametrized model of the nearest neighbor rule. In the proposed model, the selection of the nearest prototypes is influenced by the parameters of the respective prototypes. It provides a formulation for minimizing the violation of the extended nearest neighbor rule over the training set in a tractable form to exploit numerical techniques. We show that the minimization problem reduces to a large-margin principle learning and demonstrate its advantage by empirical comparisons with other prototype selection methods.
Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data

Motivation: The identification of genetic variants influencing gene expression (known as expression quantitative trait loci or eQTLs) is important in unravelling the genetic basis of complex traits. Detecting multiple eQTLs simultaneously in a population based on paired DNA‐seq and RNA‐seq assays employs two competing types of models: models which rely on appropriate transformations of RNA‐seq data (and are powered by a mature mathematical theory), or count‐based models, which represent digital gene expression explicitly, thus rendering such transformations unnecessary. The latter constitutes an immensely popular methodology, which is however plagued by mathematical intractability. Results: We develop tractable count‐based models, which are amenable to efficient estimation through the introduction of latent variables and the appropriate application of recent statistical theory in a sparse Bayesian modelling framework. Furthermore, we examine several transformation methods for RNA‐seq read counts and we introduce arcsin, logit and Laplace smoothing as preprocessing steps for transformation‐based models. Using natural and carefully simulated data from the 1000 Genomes and gEUVADIS projects, we benchmark both approaches under a variety of scenarios, including the presence of noise and violation of basic model assumptions. We demonstrate that an arcsin transformation of Laplace‐smoothed data is at least as good as state‐of‐the‐art models, particularly at small samples. Furthermore, we show that an over‐dispersed Poisson model is comparable to the celebrated Negative Binomial, but much easier to estimate. These results provide strong support for transformation‐based versus count‐based (particularly Negative‐Binomial‐based) models for eQTL mapping. Availability and implementation: All methods are implemented in the free software eQTLseq: https://github.com/dvav/eQTLseq Contact: dimitris.vavoulis@well.ox. ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Fludarabine, Cyclophosphamide, and Mitoxantrone as Initial Therapy of Chronic Lymphocytic Leukemia: High Response Rate and Disease Eradication

Purpose: Fludarabine, cyclophosphamide, and mitoxantrone (FCM) results in a high response rate in previously treated patients with chronic lymphocytic leukemia (CLL). The aim of this study was to investigate FCM as frontline therapy in CLL. Experimental Design: Sixty-nine patients under the age of 65 years with active CLL were treated. Patients received six cycles of fludarabine 25 mg/m2 i.v. × 3 days, cyclophosphamide 200 mg/m2 i.v. × 3 days, and mitoxantrone 6 mg/m2 i.v. × 1 day. Treatment outcome was correlated with clinical and biological variables. The clinical significance of eradicating minimal residual disease (MRD) was also analyzed. Results: The overall response, MRD-negative complete response (CR), MRD-positive CR, nodular partial response (PR), and PR rates were 90%, 26%, 38%, 14%, and 12%, respectively. Severe (grades 3 or 4) neutropenia developed in 10% of the patients. Major and minor infections were reported in 1% and 8% of cases, respectively. Median response duration was 37 months. Patients with del(17p) failed to attain CR. Patients achieving MRD-negative CR had a longer response duration and overall survival than patients with an inferior response. Low serum lactate dehydrogenase levels, low ZAP-70 expression, and mutated IgVH genes predicted longer response duration. Finally, both low ZAP-70 and CD38 expression in leukemic cells correlated with MRD-negativity achievement. Conclusion: FCM induces a high response rate, including MRD-negative CRs in untreated patients with active CLL. Treatment toxicity is acceptable. Both high ZAP-70 and increased CD38 expression predict failure to obtain MRD-negative response. Patients in whom MRD can be eradicated have longer response duration and overall survival than those with inferior response. These results indicate that FCM can be an ideal companion for chemoimmunotherapy of patients with CLL.
The Dynamics of Visual Experience, an EEG Study of Subjective Pattern Formation

Background Since the origin of psychological science a number of studies have reported visual pattern formation in the absence of either physiological stimulation or direct visual-spatial references. Subjective patterns range from simple phosphenes to complex patterns but are highly specific and reported reliably across studies. Methodology/Principal Findings Using independent-component analysis (ICA) we report a reduction in amplitude variance consistent with subjective-pattern formation in ventral posterior areas of the electroencephalogram (EEG). The EEG exhibits significantly increased power at delta/theta and gamma-frequencies (point and circle patterns) or a series of high-frequency harmonics of a delta oscillation (spiral patterns). Conclusions/Significance Subjective-pattern formation may be described in a way entirely consistent with identical pattern formation in fluids or granular flows. In this manner, we propose subjective-pattern structure to be represented within a spatio-temporal lattice of harmonic oscillations which bind topographically organized visual-neuronal assemblies by virtue of low frequency modulation.
Growth in the larval zebrafish pectoral fin and trunk musculature

After initial patterning, muscle in the trunk and fins of teleosts grows extensively. Here, we describe muscle growth in zebrafish, with emphasis on the pectoral fin musculature. In the trunk, slow muscle fibers differentiate first. In contrast, slow muscle does not appear in the pectoral fin until the beginning of the juvenile period. Mosaic hyperplasia contributes to trunk muscle growth, and new fibers are apparent within the muscle as early as 6 mm standard length. In the pectoral fin muscle, mosaic hyperplasia is not evident at any examined stage. Instead, the predominant mode of hyperplasia is stratified. In larval pectoral fin muscle new fibers appear subjacent to the skin, and this correlates with the expression of myogenic genes such as muscle regulatory factors and Pax7. Our results suggest that regulation of fiber type development and muscle growth may differ in the pectoral fin and trunk. Developmental Dynamics 237:307–315, 2008. © 2007 Wiley‐Liss, Inc.
Angiotensin II receptor blockade reduces salt sensitivity of blood pressure through restoration of renal nitric oxide synthesis in patients with diabetic nephropathy

Introduction: We have previously demonstrated the increased salt sensitivity of blood pressure (BP) in diabetic patients with early nephropathy. Here, we examined the effects of an angiotensin II receptor blocker (ARB) on salt sensitivity and renal oxidative stress or nitric oxide (NO) in those patients. Patients and methods: Type 2 diabetic patients with (n = 6) and without (n = 6) microalbuminuria were studied on a high-salt diet for one week and on a salt-restricted diet for one week. The study was repeated in the patients with microalbuminuria during treatment with an ARB, valsartan (80 mg/day). Salt sensitivity was assessed from the BP/sodium excretion curve. Urinary excretion rates of NOx, 8-hydroxy-2-deoxyguanosine as a marker of oxidative stress, and plasma tetrahydrobiopterin as a cofactor for NO synthase were measured. Results: Compared with diabetic patients without microalbuminuria, patients with microalbuminuria showed greater salt sensitivity and lower urinary excretion of NOx. In the patients with microalbuminuria, treatment with valsartan reduced salt sensitivity in association with increased NOx excretion, reduced 8-hydroxy-2,-deoxyguanosine excretion, and increased plasma tetrahydrobiopterin levels. Conclusions: These data support the hypothesis that ARBs reduce the salt sensitivity of BP by decreasing renal oxidative stress and restoring NO activity in diabetic patients with microalbuminuria.
SOLUBLE CD59-ANTIGEN LEVELS ARE INCREASED IN RENAL DISEASE PLASMA

Cluster of Differentiation antigen 59 (CD59) is a g lycosyl phosphatidylinositol-linked protein that pr otects cells from damage by lytic terminal complexes of co mplement. Soluble forms of CD59 in serum have been little investigated in disease states. In the prese nt study, by using a sandwich ELISA, reactivities w ith antibodies to CD59 were compared for sera and plasma from normal individuals and those with renal, leukemia, heart, liver and lung diseases. In all of 44 renal patients, reactivities were up to three-f old higher than those of normals and patients with other condi tions. The soluble CD59-related antigen displayed epitopes recognized by an anti-CD59 rabbit antiseru m and CD59 monoclonal antibodies MEM-43 and YTH 53.1. Failure to bind the hydrophobic matrix phenyl Sepharose suggested that the CD59-related antigen lacked a membrane-anchoring structure. Although the cellular origin of soluble CD59-related antigen is unknown, some effect common to different renal diseases can promote increased plasma levels of this antigen. In two individuals, monitored before and a fter renal transplantation, plasma levels of CD59-r elated antigen decreased towards normal after receipt of a kidney.
Detection, Characterization, and Modeling Vegetation in Urban Areas From High-Resolution Aerial Imagery

Research in the area of 3-D city modeling from remote sensed data greatly developed in recent years with an emphasis on systems dealing with the detection and representation of man-made objects, such as buildings and streets. While these systems produce accurate representations of urban environments, they ignore information about the vegetation component of a city. This paper presents a complete image analysis system which, from high-resolution color infrared (CIR) digital images, and a Digital Surface Model (DSM), extracts, segments, and classifies vegetation in high density urban areas, with very high reliability. The process starts with the extraction of all vegetation areas using a supervised classification system based on a Support Vector Machines (SVM) classifier. The result of this first step is further on used to separate trees from lawns using texture criteria computed on the DSM. Tree crown borders are identified through a robust region growing algorithm based on tree-shape criteria. A SVM classifier gives the species class for each tree-region previously identified. This classification is used to enhance the appearance of 3-D city models by a realistic representation of vegetation according to the vegetation land use, shape and tree species.
Enhancing real-time full 3D reconstruction of humans with pre-scanned meshes

In this paper, we propose a novel, full-body, real-time 3D reconstruction framework that makes use of pre-scanned body parts (more precisely pre-scanned 3D heads) so as to provide a more detailed 3D reconstruction mainly in the semantically important head area. Our framework deals with 3 major challenges: (a) multiple depth sensors collaboration, (b) pre-scanned head positioning and (c) reconstruction and texturing. In all the above challenges, we propose novel solutions so as to cope with time and space complexity, synchronization and 3D mesh quality. Experimental evaluation provides evidence that superior 3D mesh quality can be achieved compared to simple (not enhanced) use of depth cameras' data.
A Study on the Thermomechanical Properties of Shape Memory Alloys-based Actuators used in Artificial Muscles

Shape memory alloys (SMAs) are a class of smart material having the unique ability to return to a predefined shape when heated. These materials are employed in a variety of emerging applications, and may potentially be used to avoid traditionally voluminous and heavy prosthetic actuators. The primary focus of this article is to convey the design and evaluation of a compact, lightweight, and high-strain SMA ribbon-based artificial muscle for use in such biomimetic applications. A key factor in the design of such an actuator is a thorough understanding of the thermomechanical response of the shape memory material. As such, a review of the relevant constitutive models is included. A selected hysteresis model is evaluated for potential application to ribbon type elements. The proposed actuator achieves strains of 31.6%; a marked improvement over previously documented SMA-based actuators.
Crafting Appealing Text Messages to Encourage Colorectal Cancer Screening Test Completion: A Qualitative Study

Background mHealth interventions that incorporate text messages have great potential to increase receipt of preventive health services such as colorectal cancer screening. However, little is known about older adult perspectives regarding the receipt of text messages from their health care providers. Objective To assess whether older adults would value and access text messages from their physician’s practice regarding colorectal cancer screening. Methods We conducted four focus groups with 26 adults, aged 50 to 75 years, who had either recently completed or were overdue for colorectal cancer screening. A trained moderator followed a semistructured interview guide covering participant knowledge and attitudes regarding colorectal cancer screening, potential barriers to colorectal cancer screening, attitudes about receiving electronic communications from a doctor’s office, and reactions to sample text messages. Results Participant responses to three primary research questions were examined: (1) facilitators and barriers to colorectal cancer screening, (2) attitudes toward receiving text messages from providers, and (3) characteristics of appealing text messages. Two themes related to facilitators of colorectal cancer screening were perceived benefits/need and family experiences and encouragement. Themes related to barriers included unpleasantness, discomfort, knowledge gaps, fear of complications, and system factors. Four themes emerged regarding receipt of text messages from health care providers: (1) comfort and familiarity with technology, (2) privacy concerns/potential for errors, (3) impact on patient-provider relationship, and (4) perceived helpfulness. Many participants expressed initial reluctance to receiving text messages but responded favorably when shown sample messages. Participants preferred messages that contained content that was important to them and were positive and reassuring, personalized, and friendly to novice texters (eg, avoided the use of texting shorthand phrases and complicated replies); they did not want messages that contain bad news or test results. They wanted the ability to choose alternative options such as email or phone calls. Conclusions Older adults are receptive to receiving cancer screening text messages from health care providers. Sharing sample messages with patients may increase acceptance of this tool in the clinic setting. Supportive tailored text messaging reminders could enhance uptake of colorectal cancer screening by enhancing patient self-efficacy and providing cues to action to complete colonoscopy or fecal occult blood testing.
Privacy-enhanced sharing of personal content on the web

Publishing personal content on the web is gaining increased popularity with dramatic growth in social networking websites, and availability of cheap personal domain names and hosting services. Although the Internet enables easy publishing of any content intended to be generally accessible, restricting personal content to a selected group of contacts is more difficult. Social networking websites partially enable users to restrict access to a selected group of users of the same network by explicitly creating a "friends' list. " While this limited restriction supports users' privacy on those (few) selected websites, personal websites must still largely be protected manually by sharing passwords or obscure links. Our focus is the general problem of privacy-enabled web content sharing from any user-chosen web server. By leveraging the existing "circle of trust" in popular Instant Messaging (IM) networks, we propose a scheme called IM-based Privacy-Enhanced Content Sharing (IMPECS) for personal web content sharing. IMPECS enables a publishing user's personal data to be accessible only to her IM contacts. A user can put her personal web page on any web server she wants (vs. being restricted to a specific social networking website), and maintain privacy of her content without requiring site-specific passwords. Our prototype of IMPECS required only minor modifications to an IM server, and PHP scripts on a web server. The general idea behind IMPECS extends beyond IM and IM circles of trust; any equivalent scheme, (ideally) containing pre-arranged groups, could similarly be leveraged.
A Computationally Efficient Design Technique for Electric-Vehicle Traction Machines

This paper describes a new design technique for electric-vehicle traction machines in order to achieve high efficiency against a defined driving cycle such as the New European Drive Cycle, while satisfying the required torque-speed operating range and other volumetric and thermal design constraints. This paper is undertaken as a part of the Personal Mobility Project funded by the European Union. By analyzing the energy distribution of a given driving cycle, the energy efficiency of the traction machine over the driving cycle can be characterized against a number of representative points, and the design optimization can be carried out with respect to these points. This dramatically reduces the computation time of the design optimization process, while improving the energy efficiency of the traction machines. The utility of the design technique has been illustrated through design case studies and its effectiveness validated by experimental results.