Miracle-dz/UniFAR-FTUs huggingface dataset:
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians

This article describes a method for solving the geometric closure problem for simplified models of nucleic acid structures by using the constant bond lengths approximation. The resulting chain breakage/closure equations, formulated in the space of variable torsion and bond angles, are easy to solve, and have only two solutions. The analytical simplicity is in contrast with the high complexity of the closure problem in the torsion angle space with at most 16 solutions, which has been dealt with by several authors and was solved analytically by Wu and Deem ( J. Chem. Phys. 1999, 111, 6625 ). The discussion on the choice of variables and associated Jacobians is focussed on the question of how conformational equilibration is affected in Monte Carlo simulations of molecular systems. In addition to the closure of the phosphate backbone, it is necessary to also solve the closure problem for the five‐membered flexible furanose sugar ring. Explicit closure equations and the resulting Jacobians are given both for the complete four‐variable model of the furanose ring and simulations in the phase‐amplitude space of the five‐membered ring, which are based on the approximate two‐variable model of furanose introduced by Gabb et al. ( J. Comput. Chem. 1995, 16, 667 ). The suggested closure algorithm can be combined with collective variables defined by translations and rotations of the monomeric nucleotide units. In comparison with simple internal coordinate moves, the resulting concerted moves describe local structural changes that have high acceptance rates and enable fast conformational equilibration. Appropriate molecular models are put forward for prospective Monte Carlo simulations of nucleic acids, but can be easily adapted to other biomolecular systems, such as proteins and lipid structures in biological membranes. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 309–315, 2006
Current status of antifungal resistance and its impact on clinical practice

Mortality linked to invasive fungal diseases remains very high despite the availability of novel antifungals and new therapeutic strategies. Candida albicans and Aspergillus fumigatus account for most invasive mycosis produced by yeast or moulds, respectively. Other Candida non‐albicans are increasingly being reported and newly emerging, as well as cryptic, filamentous fungi often cause disseminated infections in immunocompromised hosts. Management of invasive fungal infections is becoming a challenge as emerging fungal pathogens generally show poor response to many antifungals. The ability of reference antifungal susceptibility testing methods to detect emerging resistance patterns, together with the molecular characterization of antifungal resistance mechanisms, are providing useful information to optimize the effectiveness of antifungal therapy. The current status of antifungal resistance epidemiology with special emphasis on the molecular resistant mechanisms that have been described in the main pathogenic fungal species are reviewed.
Improving exposure estimates by combining exposure information.

OBJECTIVES Any exposure estimation technique has inherent strengths and limitations. In an effort to improve exposure estimates, this study developed and evaluated the performance of several hybrid exposure estimates created by combining information from individual assessment techniques. METHODS Construction workers (n = 68) each completed three full-shift noise measurements over 4 months. Three single exposure assessment techniques [trade mean (TM), task-based (TB), and subjective rating (SR)] were used to estimate exposures for each subject. Hybrid techniques were then developed which incorporated the TM, SR, and TB noise exposure estimates via arithmetic mean combination, linear regression combination, and modification of TM and TB estimates using SR information. Exposure estimates from the single and hybrid techniques were compared to subjects' measured exposures to evaluate accuracy. RESULTS Hybrid estimates generally were more accurate than estimates from single techniques. The best-performing hybrid techniques combined TB and SR estimates and resulted in improvements in estimated exposures compared to single techniques. Hybrid estimates were not improved by the inclusion of TM information in this study. CONCLUSIONS Hybrid noise exposure estimates performed better than individual estimates, and in this study, combination of TB and SR estimates using linear regression performed best. The application of hybrid approaches in other contexts will depend upon the exposure of interest and the nature of the individual exposure estimates available.
The 5α-Androstanedione Pathway to Dihydrotestosterone in Castration-Resistant Prostate Cancer

The survival and progression of prostate cancer are generally dependent on expression of the androgen receptor (AR), as well as the availability of endogenous AR agonists. Originating from the gonads, testosterone is released into circulation and is converted by steroid-5α-reductase in prostate cancer to 5α-dihydrotestosterone (DHT), potently activating AR and driving tumor progression. Advanced prostate cancer is initially treated with gonadal testosterone depletion, which suppresses this cascade of events and typically leads to a treatment response. Eventually, resistance to testosterone deprivation occurs with “castration-resistant” prostate cancer (CRPC) and is driven by the intratumoral synthesis of DHT. The generation of DHT occurs in large part from adrenal 19-carbon precursor steroids, which are dependent on expression of CYP17A1. Although the path from adrenal precursor steroids to DHT was generally thought to require 5α-reduction of testosterone, recent data suggest that it instead involves conversion from Δ4-androstenedione by steroid-5α-reductase isoenzyme-1 to 5α-androstanedione, followed by subsequent conversion to DHT. The 5α-androstanedione pathway to DHT therefore bypasses testosterone entirely. Abiraterone acetate effectively inhibits CYP17A1, blocks the synthesis of androgens, and extends the survival of men with CRPC. Further progress in the hormonal treatment of CRPC is dependent on an understanding of the mechanisms that underlie CRPC and resistance to abiraterone acetate.
CoMIC: Good features for detection and matching at object boundaries

Feature or interest points typically use information aggregation in 2D patches which does not remain stable at object boundaries when there is object motion against a significantly varying background. Level or iso-intensity curves are much more stable under such conditions, especially the longer ones. In this paper, we identify stable portions on long iso-curves and detect corners on them. Further, the iso-curve associated with a corner is used to discard portions from the background and improve matching. Such CoMIC (Corners on Maximally-stable Iso-intensity Curves) points yield superior results at the object boundary regions compared to state-of-the-art detectors while performing comparably at the interior regions as well. This is illustrated in exhaustive matching experiments for both boundary and non-boundary regions in applications such as stereo and point tracking for structure from motion in video sequences.
Drosophila Homologues of Adenomatous Polyposis Coli (APC) and the Formin Diaphanous Collaborate by a Conserved Mechanism to Stimulate Actin Filament Assembly*

Background: Vertebrate APC collaborates with Dia through its Basic domain to assemble actin filaments. Results: Despite limited sequence homology between the vertebrate and Drosophila APC Basic domains, Drosophila APC1 collaborates with Dia to stimulate actin assembly in vitro. Conclusion: The mechanism of actin assembly is highly conserved over evolution. Significance: APC-Dia collaborations may be crucial in a wide range of animal cells. Adenomatous polyposis coli (APC) is a large multidomain protein that regulates the cytoskeleton. Recently, it was shown that vertebrate APC through its Basic domain directly collaborates with the formin mDia1 to stimulate actin filament assembly in the presence of nucleation barriers. However, it has been unclear whether these activities extend to homologues of APC and Dia in other organisms. Drosophila APC and Dia are each required to promote actin furrow formation in the syncytial embryo, suggesting a potential collaboration in actin assembly, but low sequence homology between the Basic domains of Drosophila and vertebrate APC has left their functional and mechanistic parallels uncertain. To address this question, we purified Drosophila APC1 and Dia and determined their individual and combined effects on actin assembly using both bulk fluorescence assays and total internal reflection fluorescence microscopy. Our data show that APC1, similar to its vertebrate homologue, bound to actin monomers and nucleated and bundled filaments. Further, Drosophila Dia nucleated actin assembly and protected growing filament barbed ends from capping protein. Drosophila APC1 and Dia directly interacted and collaborated to promote actin assembly in the combined presence of profilin and capping protein. Thus, despite limited sequence homology, Drosophila and vertebrate APCs exhibit highly related activities and mechanisms and directly collaborate with formins. These results suggest that APC-Dia interactions in actin assembly are conserved and may underlie important in vivo functions in a broad range of animal phyla.
Microstructure and corrosion behaviour of laser-cladded γ-Ni/Mo2Ni3Si alloy coating

Different γ-Ni/Mo2Ni3Si alloy coatings were fabricated on 0.45 wt-% C steel applying the DISTA300 semiconductor laser system. The microstructures, phase components and corrosion behaviour of the alloy coatings were investigated. Research results showed that laser-cladded coatings with different compositions were all composed of ductile phase γ-Ni and reinforced phase Mo2Ni3Si. Electrochemical parameters and anodic polarisation curves revealed that the γ-Ni/Mo2Ni3Si alloy coatings exhibited a good corrosion performance in 3.5% NaCl solution in comparison with 0Cr18Ni9Ti stainless steel. The corrosion current density of the laser-cladded layer increased first and then decreased with the increasing volume fraction of Mo2Ni3Si. Moreover, the addition of Cr can significantly improve the passivation and anti-pitting ability of the γ-Ni/Mo2Ni3Si alloy coating.
Transport in semiconductor nanowire superlattices described by coupled quantum mechanical and kinetic models

In this paper we develop a kinetic model for the analysis of semiconductor superlattices, accounting for quantum effects. The model consists of a Boltzmann–Poisson type system of equations with simplified Bhatnagar–Gross–Krook collisions, obtained from the general time-dependent Schrödinger–Poisson model using Wigner functions. This system for superlattice transport is supplemented by the quantum mechanical part of the model based on the Ben-Daniel–Duke form of the Schrödinger equation for a cylindrical superlattice of finite radius. The resulting energy spectrum is used to characterize the Fermi–Dirac distribution that appears in the Bhatnagar–Gross–Krook collision, thereby coupling the quantum mechanical and kinetic parts of the model. The kinetic model uses the dispersion relation obtained by the generalized Kronig–Penney method, and allows us to estimate radii of quantum wire superlattices that have the same miniband widths as in experiments. It also allows us to determine more accurately the time-dependent characteristics of superlattices, in particular their current density. Results, for several experimentally grown superlattices, are discussed in the context of self-sustained coherent oscillations of the current density which are important in an increasing range of current and potential applications.
Mechanisms of antiplatelet activity of nifedipine: role of peroxisome proliferator-activated receptor-&bgr;-&ggr;-dependent processes

Objective: Nifedipine, an L-type calcium channel blocker, is widely used in the treatment of hypertension and coronary heart diseases, and also exhibits an antiplatelet activity. Activation of peroxisome proliferator-activated receptors (PPARs; &agr;, &bgr;/&dgr;, and &ggr;) inhibits the platelet aggregation. Therefore, the purpose of this study was to evaluate the contribution of PPAR-mediated processes to the antiplatelet activity of nifedipine. Methods and results: We assessed human platelet aggregation by using an aggregometer and measured several platelet activating markers and related signaling pathways in platelets treated with nifedipine in the presence or absence of PPAR agonists. Nifedipine treatment (1, 5 &mgr;mol/l) dose-dependently increased the activity and intracellular expression of PPAR-&bgr;/-&ggr; by inhibiting the release of PPAR-&bgr;/-&ggr; from activated platelets. Nifedipine treatment also upregulated cyclic 3′,5′-cyclic monophosphate (GMP)/protein kinase G (PKG) expression, and increased PI3K/Akt pathway, endothelial nitric oxide synthase, and soluble guanylyl cyclase activities. In the presence of a selective PPAR-&bgr; antagonist (GSK0660) or PPAR-&ggr; antagonist (GW9662), the inhibitory effects of nifedipine on collagen-induced platelet aggregation, intracellular Ca2+ mobilization, and protein kinase C (PKC-&agr;) activation were abrogated. Similarly, PPAR-&bgr;-&ggr; antagonists markedly attenuated nifedipine-mediated upregulation of nitric oxide/cyclic GMP/PKG cascade. In a mouse model of thrombosis, the administration of nifedipine substantially inhibited fluorescein sodium-induced vessel thrombus formation; however, the antithrombotic effect was considerably reduced in the presence of PPAR-&bgr;/-&ggr; antagonists. Conclusion: This study is the first to show that the PPAR-&bgr;/-&ggr;-dependent upregulation of PI3K/Akt/nitric oxide/cyclic GMP/PKG pathway and the inhibition of PKC-&agr; activity and intracellular Ca2+ mobilization in platelets may be the mechanisms underlying the antiplatelet and antithrombotic activities of nifedipine.
Vision-Aided Inertial Navigation Using a Geomatics Approach

This paper proposes and tests a method for bridging GPS outages during short and long periods with a vision-based inertial navigation. This method is similar to the Simultaneous Lacalisation And Mapping (SLAM), which is the problem of mapping the environment and at the same time using this map to determine the location of the mapping device.
Bluetooth standard v4.1: Simulating the Bluetooth low energy data channel selection algorithm

Bluetooth Low Energy (BLE) is gaining notoriety as a low cost and low energy standard for wireless communication in the ISM band. The technology has been adapted in a wide range of applications, including smartphones, medical devices, and electrical household equipment. BLE introduces a simplified channel-hopping algorithm as an alternative to Classic Bluetooth - one that masks unfair usage of available spectrum. This paper details a simulation of BLE's data channel selection algorithm. The authors describe a pseudo-code for simulation software to calculate selection probability for each data channel. Results demonstrate that data channels in a BLE system are not selected equitably and the algorithm is more inclined to select data channels with indices between 1 and 21. The probability of collision between multiple BLE communicating pairs is found to be higher than that of Classic Bluetooth which results in a reduced maximum achievable aggregate throughput of 3.18 Mbps.
Security analysis of transformed-key asymmetric watermarking system

Asymmetric watermarking schemes have been widely discussed recently. Transformed-key asymmetric watermarking (TKAW) system is one of the schemes, which was proposed by Choi et al. This letter discusses the weaknesses of TKAW. In TKAW, the inner product of the received signal and public key almost equals to zero. As a result, it cannot resist projection attack. To prove this point, we will demonstrate how to find the most relevant unwatermarked signal y/spl tilde/ for a given watermark embedded signal y and prove that /spl par/y-y/spl par//spl les/|/spl alpha/|, where /spl alpha/ is a constant adjusted to a value that makes the watermark imperceptible. Moreover, we also find that the feature y-y/spl tilde/, a predicted watermark of a stego image, can be copied from a stego image to another image, which means that the TKAW system cannot resist copy attack either.
Named Entity Extraction using AdaBoost

This paper presents a Named Entity Extraction (NEE) system for the CoNLL 2002 competition. The two main sub-tasks of the problem, recognition (NER) and classification (NEC), are performed sequentially and independently with separate modules. Both modules are machine learning based systems, which make use of binary AdaBoost classifiers.
A Maturity Model For Information Systems Action-research Project Management

Action-Research is a research method broadly used in Information Systems. However, it requires improving its rigor and quality. To address this situation, several proposals have appeared, that give relevance to use Information Systems Action-Research through a vision of project management. This work is based on this vision by presenting a CMM-based maturity model to apply the project management practices in an incremental way with the aim of guaranteeing an improvement of the rigor and quality in Information Systems Action-Research projects.
It’s Harder to Break a Relationship When you Commit Long

Past research has produced evidence that parsing commitments strengthen over the processing of additional linguistic elements that are consistent with the commitments and undoing strong commitments takes more time than undoing weak commitments. It remains unclear, however, whether this so-called digging-in effect is exclusively due to the length of an ambiguous region or at least partly to the extra cost of processing these additional phrases. The current study addressed this issue by testing Japanese relative clause structure, where lexical content and sentence meaning were controlled for. The results showed evidence for a digging-in effect reflecting the strengthened commitment to an incorrect analysis caused by the processing of additional adjuncts. Our study provides strong support for the dynamical, self-organizing models of sentence processing but poses a problem for other models including serial two-stage models as well as frequency-based probabilistic models such as the surprisal theory.
AMED E NTITY R ECOGNITION IN T URKISH U SING A SSOCIATION M EASURES

Named Entity Recognition which is an important subject of Natural Language Processing is a key technology of information extraction, information retrieval, question answering and other text processing applications. In this study, we evaluate previously well-established association measures as an initial attempt to extract two-worded named entities in a Turkish corpus. Furthermore we propose a new association measure, and compare it with the other methods. The evaluation of these methods is performed by precision and recall measures.
Detecting Dependencies between Semantic Verb Subclasses and Subcategorization Frames in Text Corpora

There is a widespread belief among linguists that a predicate's subcategorization frames are largely determined by its lexical-semantic properties [23, 11, 12]. Consider the domain of movement verbs. Following Talmy [23], these can he semantically classified with reference to the meaning components: MOTION, MANNER, CAUSATION, THEME (MOVING ENTITY), PATH AND REFERENCE LOCATIONS (GOAL, SOURCE). Lexicalization patterns which arise from identifying clusters of such meaning components in verb senses can be systematically related to distinct subcategorization frames. 1 For example, the arguments of a verb expressing directed caused motion (e.g. bring, put, give) are normally a causative subject (agent), a theme direct object (moving entity) and a directional argument expressing path and reference location (goal), e.g.
Algebraic-graphical approach for signed dynamical networks

A signed network is a network with each link associated with a positive or negative sign. Models for nodes interacting over such signed networks, where two types of interactions are defined along the positive and negative links, respectively, arise from various biological, social, political, and economical systems. Starting from standard consensus dynamics, there are two basic types of negative interactions along negative links, namely state flipping or relative-state flipping. In this paper, we provide an algebraic-graphical method serving as a systematic tool of studying these dynamics over signed networks. Utilizing generalized Perron-Frobenius theory, graph theory, and elementary algebraic recursions, we show this method is useful to establish a series of basic convergence results for dynamics over signed networks.
Concussion Symptom Scales and Sideline Assessment Tools: A Critical Literature Update

Sports-related concussion remains a diagnostic and management challenge for the sports medicine practitioner. Numerous symptom scales and sideline assessment tools are available for team physicians and athletic trainers to objectively assess this difficult injury. The purpose of this article is to update the reader on literature published within the past year relevant to concussion symptom scales and sideline assessment tools. A critical evaluation of pertinent articles is presented. We conclude that multiple symptom scales and assessment tools are available, with no single tool showing clear superiority. Many tools remain based more on expert opinion than rigorous scientific evaluation. A multifaceted approach to sports concussion is advised. The sports medicine practitioner must not rely on any one tool in managing concussion and must be aware of the strengths and limitations of whichever method is chosen to incorporate into a concussion evaluation and management plan.
Interconnecting device opportunities for gigascale integration (GSI)

In recent years interconnecting devices have become primary limits on the performance, energy dissipation, signal integrity, and productivity of gigascale integration (GSI). Opportunities to address the interconnect problem include new materials and processes, reverse scaling, novel microarchitectures, three-dimensional integration, input/output interconnect enhancements, RF wireless interconnects and microphotonics.
Using ATL to Support Model-Driven Development of RubyTL Model Transformations

Model transformations are the main artefact in any Model-Driven Engineering proposal. However, being software artefacts more effort should be dedicated to apply model-driven principles in the development of model transformations. In this context, this work presents some tooling to ease the model-driven development of RubyTL model transformations. In particular, we present a metamodel for RubyTL, a model transformation to move from highlevel to RubyTL transformation models and finally a TCS injector/extractor to move from RubyTL models to RubyTL source-code and back.