Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting Parallelism in a X-ray Tomography Reconstruction Algorithm on Hybrid Multi-GPU and Multi-core Platforms

Most small-animal X-ray computed tomography (CT) scanners are based on cone-beam geometry with a flat-panel detector orbiting in a circular trajectory. Image reconstruction in these systems is usually performed by approximate methods based on the algorithm proposed by Feldkamp et al. Currently there are a strong need to speed-up the reconstruction of XRay CT data in order to extend its clinical applications. We present an efficient modular implementation of an FDK-based reconstruction algorithm that takes advantage of the parallel computing capabilities and the efficient bilinear interpolation provided by general purpose graphic processing units (GPGPU). The proposed implementation of the algorithm is evaluated for a high-resolution micro-CT and achieves a speed-up of 46, while preserving the reconstructed image quality.
The Roles of Osteoprotegerin and Osteoprotegerin Ligand in the Paracrine Regulation of Bone Resorption

Although multiple hormones and cytokines regulate various aspects of osteoclast formation, the final two effectors are osteoprotegerin ligand (OPG‐L)/osteoclast differentiation factor (ODF), a recently cloned member of the tumor necrosis factor superfamily, and macrophage colony–stimulating factor. OPG‐L/ODF is produced by osteoblast lineage cells and exerts its biological effects through binding to its receptor, osteoclast differentiation and activation receptor (ODAR)/receptor activator of NF‐κB (RANK), on osteoclast lineage cells, in either a soluble or a membrane‐bound form, the latter of which requires cell‐to‐cell contact. Binding results in rapid differentiation of osteoclast precursors in bone marrow to mature osteoclasts and, at higher concentrations, in increased functional activity and reduced apoptosis of mature osteoclasts. The biological activity of OPG‐L/ODF is neutralized by binding to osteoprotegerin (OPG)/osteoclastogenesis inhibitory factor (OCIF), a member of the TNF‐receptor superfamily that also is secreted by osteoblast lineage cells. The biological importance of this system is underscored by the induction in mice of severe osteoporosis by targeted ablation of OPG/OCIF and by the induction of osteopetrosis by targeted ablation of OPG‐L/ODF or overexpression of OPG/OCIF. Thus, osteoclast formation may be determined principally by the relative ratio of OPG‐L/ODF to OPG/OCIF in the bone marrow microenvironment, and alterations in this ratio may be a major cause of bone loss in many metabolic disorders, including estrogen deficiency and glucocorticoid excess. That changes in but two downstream cytokines mediate the effects of large numbers of upstream hormones and cytokines suggests a regulatory mechanism for osteoclastogenesis of great efficiency and elegance.
Quantized Feedback for Spatial Multiplexing System

In this paper we present a quantized preceding scheme for the spatial multiplexing system equipped with MMSE-SIC receiver. The preceding matrix, consisting of a beamforming matrix and a power allocation matrix, is selected to maximize the minimum post-detection SINR of the MMSE-SIC receiver. Rather than the whole beamforming matrix, the beamforming vector for each data stream is selected sequentially from a predetermined codebook. The advantage of the sequential selection is that the computational burden and storage requirements are significantly reduced while the performance degradation is marginal. This is especially appealing for mobile terminals due to their physical limitation. The codebook is constructed by the Grassmannian beamforming criterion. Moreover, the proposed scheme is flexible enough to allow for a change in the number of data streams without redesigning the codebook. Simulation results are presented to demonstrate the effectiveness of the proposed scheme.
Factors controlling seed dormancy and germination response of Brachypodium hybridum growing in the hot arid mountains of the Arabian Desert

Seed dormancy and germination have been studied in the genetic model Brachypodium species complex in cooler, moist higher latitudes. Studying environmental factors in arid mountains affecting dormancy and germination in Brachypodium complex could determine the factors controlling these processes. This study assesses the impacts of temperature during seed maturation, seed after-ripening, drought, photoperiod, and thermoperiod on final germination and germination rate index of B. hybridum in the Arabian Desert. Seeds were germinated under dark or light conditions and under different ratios of red:far-red light, with three diurnal thermoperiods. The final germination percentage was significantly greater at 15/25 °C and 20/30 °C than at 25/35 °C and in light rather than in darkness. Seeds that reached maturity at 15/25 °C attained greater germination rates and faster germination than those that reached maturity at 20/30 °C. One-year after-ripening enhanced the final germination percentage and reduced photoperiod requirements. Light quality did not affect final germination percentage. The seeds tolerated drought of up to –0.8 MPa polyethylene glycol. The tolerance of B. hybridum seeds produced at higher thermoperiods to moderate levels of osmotic stress and their higher dormancy indicate that this species has the potential to survive the projected global warming in its native and introduced ranges.
A Multi-Layered Potential Field Method for Water-Jet Propelled Unmanned Surface Vehicle Local Path Planning with Minimum Energy Consumption

Abstract Focusing on the influence of wind and surface currents on local path planning in the marine environment, a multilayered potential field (MPF) method is proposed to minimize the energy consumption of a water-jet propelled unmanned surface vehicle (USV). A synthetic environment framework that can incorporate the information of the base potential field layer and the environment layer is constructed first. This framework provides a base for minimizing the energy consumption of the water-jet propelled USV through proper force weighting. For the purpose of USV path planning, the traditional potential field method is extended by including the velocity information of the USV and the approached obstacles to avoid collisions with dynamic obstacles. The proposed method integrates kinematic control to prevent considering the vehicle as a point mass or rigid body. Finally, simulation and comparison experiments are performed to demonstrate the energy-saving efficiency of the proposed local path planning approach for the water-jet propelled USV.
Aurora-A Kinase Regulates Telomerase Activity through c-Myc in Human Ovarian and Breast Epithelial Cells

Aurora-A kinase is frequently overexpressed/activated in human ovarian and breast cancers. A rat mammary tumor model study indicates that alterations of Aurora-A are early events during mammary tumor development (T. M. Goepfert et al., Cancer Res., 62: 4115–4122, 2002), suggesting that Aurora-A plays a pivotal role in transformation. However, the molecular mechanism by which Aurora-A induces ovarian and breast cell transformation remains elusive. Here we show that ectopic expression of Aurora-A induces telomerase activity in human ovarian and breast epithelial cell lines HIOSE118 and MCF-10A. The mRNA and promoter activities of human telomerase reverse transcriptase (hTERT) are stimulated by Aurora-A. Furthermore, we have demonstrated that the c-Myc binding sites of hTERT promoter are required for Aurora-A-induced hTERT promoter activity. Ectopic expression of Aurora-A up-regulates c-Myc. Knockdown of c-Myc by RNA interference attenuates Aurora-A-stimulated hTERT expression and telomerase activity. To our knowledge, these findings demonstrate, for the first time, that Aurora-A induces telomerase activity and hTERT by up-regulation of c-Myc and provides an additional mechanism for the role of Aurora-A in malignant transformation in addition to its cell cycle control.
Measurement of spatial colocalization of objects in n-channel confocal images

A method has been developed to measure multi-parametric colocalization of coloror channel-specific light intensities in 3D space using a sequence of planar confocal microscopic images. A region growing algorithm has been implemented that analyzes the 3D image stack produced by a confocal microscope and identifies regions of interest. This algorithm selects threshold values from control images and analyzes the histogram information from each image to intelligently select and categorize object pixels from background pixels. A new technique for measuring the ratio of colocalization has also been proposed in conjunction with the region growing algorithm that results in an intuitive and easily understandable metric for characterization of the spatial colocalization throughout the whole x-y-z image set. This research successfully extends the currently available colocalization metrics by modifying the original equations to work on multi-parametric inputs. The consistency of the results on a range of input channel values is demonstrated via Monte Carlo simulation. A new spatial colocalization metric has also been proposed and implemented which results in a colocalization ratio that includes object information from all images in the colocalization experiment. INDEX WORDS: Colocalization, Confocal microscopy, 3D spatial analysis, 2D spatial analysis, Region growing, Region-of-interest (ROI)
Syntheses and structural characterization of o-carboranylamides with direct cage-amide bond.

Reactions of lithio-o-carborane with isocyanates under various conditions were studied, and the structural features of the resulting carboranylamides are described. The reactions of o-carborane (o-C2B10H12), n-BuLi (two equiv.) and two equiv. of (substituted) phenylisocyanate, pentylisocyanate and p-ethylphenylthioisocyanate in diethyl ether, respectively, led, after workup, to the corresponding mono-substituted carboranylamide 2a-g and carboranylthioamide 5 in low to moderate yields, and only with RNCO (R = Ph, m-MeOC6H4, pentyl) could disubstituted products 3a-c be isolated. The reaction with phenylisocyanate afforded the mono-amide and di-amide products in a ratio of approximately 1 : 2, whereas in the other two reactions the ratios are approximately 4 : 1 and 3 : 2, respectively. In tetrahydrofuran all the reactions attempted with RNCO (R = Ph, p-IC6H4, m-NCC6H4 and pentyl) gave more monoamide products than those in diethyl ether. With phenylisocyanate no diamide product was isolated and with pentylisocyanate the ratio between monoamide and diamide is approximately 3.5 : 1. The new carboranylamides were characterized by means of elemental analyses, IR and NMR spectroscopy and mass spectrometry, as well as single-crystal X-ray diffraction analyses of 2a-f, 3a and 5.
A Process Mining Approach Based on Trace Alignment Information for Very Large Sequential Processes with Duplicated Activities

This paper presents an approach to construct models for very large sequential processes with duplicated activities. Very large meaning processes containing hundreds of activities. The algorithm uses traces of the process we are interested in modeling and construct an alignment between them. The alignment obtained is then used to guide the model construction. We present also the application of our approach to STMicroelectronics’ manufacturing processes. The constant modifications of semiconductor specifications forces engineers to continuously update processes. For this reason, STMicroelectronics is interested in re-constructing models of its manufacturing processes to being able to control their definitions and quickly react in case a problem is detected.
Escitalopram and enhancement of cognitive recovery following stroke.

CONTEXT Adjunctive restorative therapies administered during the first few months after stroke, the period with the greatest degree of spontaneous recovery, reduce the number of stroke patients with significant disability. OBJECTIVE To examine the effect of escitalopram on cognitive outcome. We hypothesized that patients who received escitalopram would show improved performance in neuropsychological tests assessing memory and executive functions than patients who received placebo or underwent Problem Solving Therapy. DESIGN Randomized trial. SETTING Stroke center. PARTICIPANTS One hundred twenty-nine patients were treated within 3 months following stroke. The 12-month trial included 3 arms: a double-blind placebo-controlled comparison of escitalopram (n = 43) with placebo (n = 45), and a nonblinded arm of Problem Solving Therapy (n = 41). OUTCOME MEASURES Change in scores from baseline to the end of treatment for the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and Trail-Making, Controlled Oral Word Association, Wechsler Adult Intelligence Scale-III Similarities, and Stroop tests. RESULTS We found a difference among the 3 treatment groups in change in RBANS total score (P < .01) and RBANS delayed memory score (P < .01). After adjusting for possible confounders, there was a significant effect of escitalopram treatment on the change in RBANS total score (P < .01, adjusted mean change in score: escitalopram group, 10.0; nonescitalopram group, 3.1) and the change in RBANS delayed memory score (P < .01, adjusted mean change in score: escitalopram group, 11.3; nonescitalopram group, 2.5). We did not observe treatment effects in other neuropsychological measures. CONCLUSIONS When compared with patients who received placebo or underwent Problem Solving Therapy, stroke patients who received escitalopram showed improvement in global cognitive functioning, specifically in verbal and visual memory functions. This beneficial effect of escitalopram was independent of its effect on depression. The utility of antidepressants in the process of poststroke recovery should be further investigated. Trial Registration clinicaltrials.gov Identifier: NCT00071643.
Quantum games with decoherence

A protocol for considering decoherence in quantum games is presented. Results for two-player, two-strategy quantum games subject to decoherence are derived and some specific examples are given. Decoherence in other types of quantum games is also considered. As expected, the advantage that a quantum player achieves over a player restricted to classical strategies is diminished for increasing decoherence but only vanishes in the limit of maximum decoherence.
RISAS: A novel rotation, illumination, scale invariant appearance and shape feature

This paper presents a novel appearance and shape feature, RISAS, which is robust to viewpoint, illumination, scale and rotation variations. RISAS consists of a keypoint detector and a feature descriptor both of which utilise texture and geometric information present in the appearance and shape channels. A novel response function based on the surface normals is used in combination with the Harris corner detector for selecting keypoints in the scene. A strategy that uses the depth information for scale estimation and background elimination is proposed to select the neighbourhood around the keypoints in order to build precise invariant descriptors. Proposed descriptor relies on the ordering of both grayscale intensity and shape information in the neighbourhood. Comprehensive experiments which confirm the effectiveness of the proposed RGB-D feature when compared with CSHOT [1] and LOIND[2] are presented. Furthermore, we highlight the utility of incorporating texture and shape information in the design of both the detector and the descriptor by demonstrating the enhanced performance of CSHOT and LOIND when combined with RISAS detector.
An Abstract Machine for Curry and Its Concurrent Implementation in Java

Curry is a multi-paradigm declarative language aiming to amalgamate functional, logic, and concurrent programming paradigms. Curry combines in a seamless way features from functional programming and (concurrent) logic programming. Curry’s operational semantics is based on the combination of lazy reduction of expressions together with a possibly non-deterministic binding of free variables occurring in expressions. Moreover, (equational) constraints can be executed concurrently which provides for passive constraints and concurrent computation threads that are synchronized on logical variables. This paper describes in an object-oriented style an abstract machine for executing Curry programs. The machine is designed to provide a link for compiling Curry programs into Java but it can also be a basis for implementations of Curry in other (object-oriented) languages. The main emphasis of the Java-based implementation is the exploitation of Java threads to implement the concurrent and nondeterministic features of Curry.
Biocontrol Potential of Trichoderma and Bacillus Species on Fusarium oxysporum f. sp vasinfectum

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum, is one of the major diseases of cotton. Preventive methods to manage this disease should be adopted what includes the seed treatment with biocontrol agents as a good alternative. This work aimed to evaluate the efficiency of biological products based on Trichoderma spp. and Bacillus subtilis in the control of Fusarium oxysporum f. sp. vasinfectum (Fov) applied in seeds and seedlings of cotton. The experiment was carried out at the Laboratório de Fitopatologia of the Centro de Ciências Agrárias, of the Universidade Federal de Paraíba (CCA-UFPB), located in the city of Areia, Paraíba - Brazil. The disease transmission of the seeds to the seedlings was evaluated. After the transmission test, cotton seeds of the variety Mocó (Gossypium hirsutum var. Marie-gallante (Watt) Hutch. ), BRS 286 and Topázio cultivar (Gossypium hirsutum L.) were submitted to the treatments T1 - Control, T2 - Trichodel® (0,5 mL); T3-Trichodel® (1.0 mL); T4-Trichodel® (1.5 mL); T5-Trichodel® (2.0 mL); T6-Bactel® (2.0 mL); T7-Bactel® (2.5 mL); T8-Bactel® (3.0 mL); T9-Bactel® (3.5 mL) diluted in 100 mL SDW; T10 - Fungicide Captana (240 g / 100 kg of seeds) and inoculated with Fov. The pathogen incidence of the seeds was evaluated seven days after the inoculation (DAI). To evaluate the biological control of Fov in the seedlings, the treated seeds were submitted to the following inoculation methods: 1 - inoculation of the substrate with a pathogen conidia suspension; 2 - immersion of the seeds in the conidia suspension and 3 - direct contact of the seeds with the pathogen mycelium. Twenty-one DAI the disease severity and percentage of seedlings with vascular darkening were evaluated. It was observed a transmission rate of 64.0 to 89.0% of the seeds to the seedlings. Trichodel® reduced the incidence and severity of Fov in the cotton seedlings and was the most efficient product.
Diffusion-tensor MR imaging of corticospinal tract in amyotrophic lateral sclerosis and progressive muscular atrophy.

PURPOSE To prospectively evaluate several diffusion-tensor magnetic resonance (MR) imaging indexes (mean diffusivity [MD], fractional anisotropy [FA], and eigenvalues) of corticospinal tract impairment in patients with progressive muscular atrophy (PMA) and patients with amyotrophic lateral sclerosis (ALS). MATERIALS AND METHODS This study had institutional review board approval, and written informed consent was obtained from all subjects. Eight male patients with PMA (mean age, 63 years +/- 13 [standard deviation]), eighteen patients with ALS (14 men and four women; mean age, 64 years +/- 7), and twelve control subjects (four men and eight women; mean age, 65 years +/- 6) underwent diffusion-tensor MR imaging at which 25 spin-echo echo-planar imaging diffusion-weighted images (b = 1000 sec/mm2) were acquired along noncollinear directions. MD and FA were measured along the corticospinal tracts in each patient and subject. Changes in diffusion along and orthogonal to fiber bundles in patients were evaluated by using diffusion-tensor eigenvalues. Differences in diffusion-tensor imaging indexes between patients with PMA and those with ALS, as compared with these indexes in control subjects, were evaluated with Mann-Whitney testing. Correlations between diffusion-tensor imaging indexes and clinical variables were estimated with Pearson and Spearman rank correlation testing. RESULTS As compared with MD (697.1 x 10(-6) mm2/sec +/- 28.1) and FA (0.585 +/- 0.032) in control subjects, MD was typically significantly increased (734.7 x 10(-6) mm2/sec +/- 41.2, P = . 035) and FA significantly decreased (0.534 +/- 0.053, P = .037) along the corticospinal tracts in patients with ALS, while these parameters showed no significant change in patients with PMA (MD, 707.0 x 10(-6) mm2/sec +/- 44.2; FA, 0.559 +/- 0.028). Estimation of diffusion-tensor eigenvalues revealed normal diffusion along fiber tracts in all patients, while diffusion was increased orthogonal to fiber tracts only in patients with typical ALS. In patients with ALS, MD correlated with disease duration while FA correlated with disease severity. CONCLUSION Diffusion-tensor MR imaging reveals corticospinal tract impairment in ALS but not in PMA.
Optimal Bidding/Offering Strategy for EV Aggregators under a Novel Business Model

Realizing the full potential of plug-in electric vehicle (PEVs) in power systems requires the development of business models for PEV owners and electric vehicle aggregators (EVAs). Most business models neglect the significant economic potential of PEV demand response. This paper addresses this challenge by proposing a novel business model to optimize the charging energy of PEVs for maximizing the owners’ profits. The proposed business model aims to overcome the opportunity cost neglect for PEV owners, whose charging energy and charging profiles are optimized with full consideration of the demand curves and market conditions. Lagrangian relaxation technology is used for the relaxation of the constraint of satisfying the charging demand, and as a result, the optimization potential becomes greater. The bidding/offering strategy is formulated as a two-stage stochastic optimization problem, considering the different market prices and initial and target state of energy (SOE) of the PEVs. By case studies and analyses, we demonstrate that the proposed business model can effectively overcome the opportunity cost neglect and increase the PEV owners’ profits. Furthermore, we demonstrate that the proposed business model is incentive-compatible. The PEV owners will be attracted by the proposed business model.
On the Performance of Cooperative-Diversity Networks with the Nth Best-Relay Selection Scheme

In this letter, we consider the adaptive decode-and-forward (DF) and amplify-and-forward (AF) cooperative-diversity systems with the Nth best-relay selection scheme. In the best-relay selection scheme, from the set of M relays the best relay only forwards the source signal to the destination. However, the best relay might be unavailable; hence we might resort to the second, third or generally the Nth best relay. We derive closed-form expressions for the symbol error probability, outage probability and asymptotic error probability. In particular, we derive a closed-form expression for the probability density function (PDF) of the signal-to-noise ratio (SNR) of the relayed signal at the destination node. Then, we find a closed-form expression for the moment generating function (MGF) of the output SNR at the destination. This MGF is used to derive the closed-form expressions of the performance metrics. All these expressions are derived over identical and non-identical Rayleigh fading channels. Results show that with the Nth best relay the diversity order is equal to (M - N + 2) where M is the number of relays.