Miracle-dz/UniFAR-FTUs huggingface dataset:
A Computational Approach to Increase Time Scales in Brownian Dynamics-Based Reaction-Diffusion Modeling

Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling.
Antiviral Resistance Mutations and Genotype-Associated Amino Acid Substitutions in Treatment-Naïve Hepatitis B Virus-Infected Individuals from the Indian Subcontinent

Background/Aims: Antiviral resistance is a major challenge to the treatment currently available for hepatitis B virus (HBV). In this study, mutations that may affect the antiviral efficacy in treatment-naïve HBV-infected individuals were analyzed. Methods: Ninety-seven treatment-naïve HBV-infected individuals were included in this study. HBV reverse transcriptase (rt) domains were sequenced and nucleotide differences were compared to GenBank wild-type sequences. Furthermore, HBV genotypes, subgenotypes and subtypes were determined by analyzing surface gene sequences. Results: An adefovir-related rtI233V mutation was identified in 4 subjects. The rtS213T lamivudine and entecavir refractory mutant was presented in 3 individuals. Altogether, drug-related, atypical and novel HBVrt amino acid substitutions were seen in 73 positions. The HBV genotypes A, C, D and G were depicted in 15, 21, 60 and 1 individuals, respectively. There were 17 HBVrt amino acid substitutions that are associated with certain genotypes of HBV. Mutations in HBVrt corresponded to established surface gene mutations in 9 patients. Conclusion: This data shows that antiviral-resistant HBV strains do exist in treatment-naïve individuals in this region. Further studies are essential to characterize the role of HBVrt amino acid substitutions in response to anti-HBV therapy.
The Precision of 3D Reconstruction from Uncalibrated Views

We consider reconstruction algorithms using points tracked over a sequence of (at least three) images, to estimate the positions of the cameras ( motion parameters), the 3D coordinates (structure parameters), and the calibration matrix of the cameras (calibration parameters). Many algorithms have been reported in literature, and there is a need to know how well they may perform. We show how the choice of assumptions on the camera intrinsic parameters (either fixed, or with a probabilistic prior) influences the precision of the estimator. We associate a Maximum Likelihood estimator to each type of assumptions, and derive analytically their covariance matrices, independently of any specific implementation. We verify that the obtained covariance matrices are realistic, and compare the relative performance of each type of estimator.
Las cerámicas españolas de la Hispanic Society of America (Archer Milton Huntington y su museo)

Archer Milton Huntington. Huntington fundo la Hispanic Society of America para establecer un museo y una bliblioteca publicos y gratuitos con el fin de difundir la cultura de Espana y America Latina. Cuando la Sociedad abrio sus puertas al publico en 1908, Huntington ya habia adquirido y puesto en exposicion una de las colecciones mas importantes de ceramica espanola del mundo, incluyendo 60 piezas hispanomusulmanas de reflejo metalico, contando hoy dia con 150 ejemplares. Continuando con la labor de completar la coleccion, la Sociedad adquirio otras piezas de ceramica espanola y mejicana procedentes de alfares como Talavera de la Reina, Buen Retiro, Alcora, Puente del Arzobispo, Toledo, Sevilla, la ciudad de Mejico y Puebla. En este trabajo se da una vision de la coleccion de ceramicas espanolas y mejicanas que posee la Hispanic Society y de la historia de su adquisicion. Ademas, se examina la difusion e influencia de la ceramica espanola en la ceramica mejicana y su posterior evolucion. El estudio de las colecciones de la Hispanic Society constata que en este museo se encuentran los ejemplares mas sobresalientes de porcelana y de mayolica de Espana y de Mejico.
Machine Vision and Applications Detecting Violent and Abnormal Crowd Activity Using Temporal Analysis of Grey Level Co-occurrence Matrix (glcm)-based Texture Measures

The severity of sustained injury resulting from assault-related violence can be minimised by reducing detection time. However, it has been shown that human operators perform poorly at detecting events found in video footage when presented with simultaneous feeds. We utilise computer vision techniques to develop an automated method of abnormal crowd detection that can aid a human operator in the detection of violent behaviour. We observed that behaviour in city centre environments often occurs in crowded areas, resulting in individual actions being occluded by other crowd members. We propose a real-time descrip-tor that models crowd dynamics by encoding changes in crowd texture using temporal summaries of grey level co-occurrence matrix features. We introduce a measure of inter-frame uniformity and demonstrate that the appearance of violent behaviour changes in a less uniform manner when compared to other types of crowd behaviour. Our proposed method is computationally cheap and offers real-time description. Evaluating our method using a privately held CCTV dataset and the publicly available Violent Flows, UCF Web Abnormality and UMN Abnormal Crowd datasets, we report a receiver operating characteristic score of 0.9782, 0.9403, 0.8218 and 0.9956, respectively.
The coarsening and annihilation kinetics of dislocation loop

Abstract Analyses are presented which concern the annealing behaviour of the dislocation loops which are formed during irradiation. The behaviour of isolated loops is briefly reviewed and calculations arc extended to include cases where approximate solutions to the equations which describe the kinetics are no longer accurate. If dislocation loops provide the only available sources and sinks for point defects, then predictions based on isolated-loop behaviour are no longer valid. A coarsening process must occur such that total loop area is conserved. The annihilation of smaller loops is compensated for by the growth of larger ones. This process is treated analytically for the limiting forms of the growth equations and numerically for cases where these simple equations no longer provide sufficiently accurate approximations. Comparisons of the predictions with available experimental data are presented.
T‐Cell Unresponsiveness in vivo and in vitro: Fine Specificity of Induction and Molecular Characterization of the Unresponsive State

Adult induccr T cells are activated by foreign antigens in the context of learned self major hislocompatibility complex (MHC) molecules, but are unresponsive (tolerant) to most sell antigens (reviewed in Schwartz 1984). Recently, our knowledge of T-cell activation has been greatly extended by discoveries concerning the molecular structures of the T-cell receptor (reviewed in Kronenberg et al. 1986) and MHC molecules (reviewed in Germain & Malissen 1986). the role of lymphokines in T-cell proliferatioti and differentiation (reviewed in Smith 1984), and the biochemical events resulting from T-cell receptor occupancy (reviewed in Weiss et al. 1986). In contrast, very little is known about the cellular and molecular mechanisms underlying the induction of T-cell tolerance. Experimentally, T-cell unresponsiveness can be induced in neonates by injection of soluble or particulate antigen, or in adults by the intravenous injection of high doses of soluble antigen or of antigen coupled to syngeneic spleen cells (Borel 1980, Claman et al. 1980, Ramos et at. 1980, Germain & Benacerraf 198K Nossal 1983, Monroe et al. 1984. Oki & Sercarz 1985). These studies have provided evidence for two models of tolerance: 1) indirect inhibition of inducer T cells by suppressor T cells 2) direct inactivation of inducer T cells by antigen. In the suppression model, a complex circuit of interacting suppressor T cells
Effects of net charge and the number of positively charged residues on the biological activity of amphipathic α‐helical cationic antimicrobial peptides

In our previous study, we utilized a 26‐residue amphipathic α‐helical antimicrobial peptide L‐V13K (Chen et al., Antimicrob Agents Chemother 2007, 51, 1398–1406) as the framework to study the effects of peptide hydrophobicity on the mechanism of its antimicrobial action. In this study, we explored the effects of net charge and the number of positively charged residues on the hydrophilic/polar face of L‐V13K on its biological activity (antimicrobial and hemolytic) and biophysical properties (hydrophobicity, amphipathicity, helicity, and peptide self‐association). The net charge of V13K analogs at pH 7 varied between −5 and +10 and the number of positively charged residues varied from 1 to 10. The minimal inhibitory concentrations (MIC) against six strains of Pseudomonas aeruginosa as well as other gram‐negative and gram‐positive bacteria were determined along with the maximal peptide concentration that produces no hemolysis of human red blood cells (MHC). Our results show that the number of positively charged residues on the polar face and net charge are both important for both antimicrobial activity and hemolytic activity. The most dramatic observation is the sharp transition of hemolytic activity on increasing one positive charge on the polar face of V13K i.e., the change from +8 to +9 resulted in greater than 32‐fold increase in hemolytic activity (250 μg/ml to <7.8 μg/ml, respectively). © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 369–383, 2008.
A method to reduce the probability of clipping in DMT-based transceivers

A new method allowing a reduction in the probability of clipping in discrete multitone (DMT)-based transceivers is described. The method does not use any kind of precoding and can easily be implemented within conventional DMT-transceivers. The main advantage of the proposed method is an improvement of system performance in terms of overall signal-to-noise ratios (SNRs): with the simplest implementation option of the proposed method, up to about 8 dB improvement in the SNR as compared with previously reported brute force clipping methods can be achieved.
Functional magnetic resonance imaging neuroactivation studies in normal subjects and subjects with the narcoleptic syndrome. Actions of modafinil

Functional magnetic resonance imaging (fMRI) can be used to detect regional brain responses to changes in sensory stimuli. We have used fMRI to determine the amount of visual and auditory cortical activation in 12 normal subjects and 12 subjects with the narcoleptic syndrome, using a multiplexed visual and auditory stimulation paradigm. In both normal and narcoleptic subjects, mean cortical activation levels during the presentation of periodic visual and auditory stimulation showed no appreciable differences with either age or sex. Normal subjects showed higher levels of visual activation at 10:00 hours than 15:00 hours, with a reverse pattern in narcoleptic subjects (P=0.007). The group differences in spatial extent of cortical activation between control and narcoleptic subjects were small and statistically insignificant. The alerting action, and imaging response, to a single oral dose of the sleep‐preventing drug modafinil 400 mg were then determined and compared with placebo in both the 12 normal (8 given modafinil, 4 placebo) and 12 narcoleptic subjects (8 modafinil, 4 placebo). Modafinil caused an increase in self‐reported levels of alertness in 7 of 8 narcoleptic subjects, but there was no significant difference between mean pretreatment and post‐treatment activation levels as determined by fMRI for either normal or narcoleptic syndrome subjects given modafinil. However, in the modafinil‐treated group of 8 normal and 8 narcoleptic subjects, there was a clock time independent correlation between the initial level of activation as determined by the pretreatment scan and the post‐treatment change in activation (visual, P=0.002; and auditory, P=0.001). No correlation was observed in placebo‐treated subjects (P=0.99 and 0.77, respectively).
A Processing Platform for Optoelectronic/Optogenetic Retinal Prosthesis

The field of retinal prosthesis has been steadily developing over the last two decades. Despite the many obstacles, clinical trials for electronic approaches are in progress and already demonstrating some success. Optogenetic/optoelectronic retinal prosthesis may prove to have even greater capabilities. Although resolutions are now moving beyond recognition of simple shapes, it will nevertheless be poor compared to normal vision. If we define the aim to be to return mobility and natural scene recognition to the patient, it is important to maximize the useful visual information we attempt to transfer. In this paper, we highlight a method to simplify the scene, perform spatial image compression, and then apply spike coding. We then show the potential for translation on standard consumer processors. The algorithms are applicable to all forms of visual prosthesis, but we particularly focus on optogenetic approaches.
A climate-change risk analysis for world ecosystems

We quantify the risks of climate-induced changes in key ecosystem processes during the 21st century by forcing a dynamic global vegetation model with multiple scenarios from 16 climate models and mapping the proportions of model runs showing forest/nonforest shifts or exceedance of natural variability in wildfire frequency and freshwater supply. Our analysis does not assign probabilities to scenarios or weights to models. Instead, we consider distribution of outcomes within three sets of model runs grouped by the amount of global warming they simulate: <2°C (including simulations in which atmospheric composition is held constant, i.e., in which the only climate change is due to greenhouse gases already emitted), 2–3°C, and >3°C. High risk of forest loss is shown for Eurasia, eastern China, Canada, Central America, and Amazonia, with forest extensions into the Arctic and semiarid savannas; more frequent wildfire in Amazonia, the far north, and many semiarid regions; more runoff north of 50°N and in tropical Africa and northwestern South America; and less runoff in West Africa, Central America, southern Europe, and the eastern U.S. Substantially larger areas are affected for global warming >3°C than for <2°C; some features appear only at higher warming levels. A land carbon sink of ≈1 Pg of C per yr is simulated for the late 20th century, but for >3°C this sink converts to a carbon source during the 21st century (implying a positive climate feedback) in 44% of cases. The risks continue increasing over the following 200 years, even with atmospheric composition held constant.
A scalable system for primal-dual optimization

We present some of the most widely used architectures for Big Data, \textit{Hadoop} and \textit{Spark}, and develop several implementations exploiting, the advantages of each. We implement a simplified version of the primal-dual optimization algorithm, described briefly in this paper, by choosing the smoothing functions to be $\Vert \cdot \Vert^2$ with a zero center point. Under the assumption that data is provided as a sparse matrix, we assess the scalability of the designed systems empirically by running them on sample tests.
Toroidal Dipolar Response in Metamaterials Composed of Metal–Dielectric–Metal Sandwich Magnetic Resonators

Toroidal metamaterials have been drawing increasing interest recently because of their unusual electromagnetic properties and a variety of potential applications. In this work, we have investigated numerically toroidal dipolar response at optical frequency in metamaterials whose unit cell includes three magnetic resonators. The magnetic resonators are metal-dielectric-metal sandwich nanostructures, which are composed of two Ag rods and a SiO2 spacer. They have the same shape and dimension, but they are placed at different positions to break the space-inversion symmetry. The near-field plasmon coupling between magnetic resonators leads to the excitation of a toroidal dipolar mode, which is characterized by a head-to-tail distribution of magnetic dipoles within magnetic resonators. In our designed toroidal metamaterials, space-inversion symmetry breaking is needed only in the polarization direction of incident light, and light can be normally incident on the toroidal metamaterials.
Validation of AD-CSF-Index in Chinese Patients With Alzheimer’s Disease and Nondemented Controls

Cerebrospinal fluid (CSF) biomarkers of Alzheimer’s disease (AD), especially Aβ42/t-tau and Aβ42/p-tau, showed high diagnostic sensitivities and specificities. But significant interassay and interlaboratory variabilities hinder the widespread clinical applications of CSF biomarkers. The objective of this study was to validate the diagnostic accuracy of AD-CSF-Index in our local Chinese patients with AD compared to nondemented controls. A total of 36 patients, which included 24 patients with AD and 12 nondemented controls, were recruited. Chinese patients with AD showed higher mean AD-CSF-Indices than nondemented controls (AD = 1.25-1.3, normal = 0.62-0.63; P < .001). The AD-CSF-indices have a high sensitivity and specificity of 86.4% to 90.9% and 83.3%, respectively, in differentiating patients with AD from nondemented controls. After selecting the patients with “pure AD” and “pure normal” controls, the AD-CSF-indices have a high sensitivity and specificity of 94.1% and 90%, respectively, in differentiating patients with AD from nondemented controls. Most importantly, our AD-CSF-indices cutoff was highly similar to that reported in Western studies.
Adalimumab and pustular psoriasis

Adalimumab (Humira ® ) is a fully human recombinant monoclonal immunoglobulin G1 antibody expressed in Chinese hamster ovary cells that inhibits the action of tumor necrosis factor-α (TNFα) by binding specifically to TNF-α and neutralizing the biological function of TNF-α by blocking its interaction with the p55 and p75 cell surface TNF receptors [1]. Adalimumab was granted marketing authorization on 8 September 2003 in Europe [1]. Therapeutic indications include rheumatoid arthritis (RA), polyarticular juvenile idiopathic arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn’s disease and psoriasis. In RA adalimumab is used either as monotherapy or in combination with methotrexate in patients with an inadequate response to classic disease-modifying antirheumatic drugs. Adalimumab is indicated for the treatment of moderate to severe chronic plaque psoriasis in adult patients who failed to respond to, or have a contraindication for other systemic therapy including cyclosporine, methotrexate or PUVA [1]. The SmPC of adalimumab mentions psoriasis as an uncommon adverse drug reaction, but pustular psoriasis is not mentioned [1]. This report describes pustular psoriasis in association with the use of adalimumab.
On the parallelisation of MCMC by speculative chain execution

The increasing availability of multi-core and multiprocessor architectures provides new opportunities for improving the performance of many computer simulations. Markov Chain Monte Carlo (MCMC) simulations are widely used for approximate counting problems, Bayesian inference and as a means for estimating very high-dimensional integrals. As such MCMC has had a wide variety of applications in fields including computational biology and physics, financial econometrics, machine learning and image processing. One method for improving the performance of Markov Chain Monte Carlo simulations is to use SMP machines to perform ‘speculative moves’, reducing the runtime whilst producing statistically identical results to conventional sequential implementations. In this paper we examine the circumstances under which the original speculative moves method performs poorly, and consider how some of the situations can be addressed by refining the implementation. We extend the technique to perform Markov Chains speculatively, expanding the range of algorithms that maybe be accelerated by speculative execution to those with non-uniform move processing times. By simulating program runs we can predict the theoretical reduction in runtime that may be achieved by this technique. We compare how efficiently different architectures perform in using this method, and present experiments that demonstrate a runtime reduction of up to 35–42% where using conventional speculative moves would result in execution as slow, if not slower, than sequential processing.
Flexible, in-plane, and all-solid-state micro-supercapacitors based on printed interdigital Au/polyaniline network hybrid electrodes on a chip

A simple and rapid fabrication method involving laser printing technology and in situ anodic electropolymerization is introduced to fabricate interdigital Au/polyaniline network hybrid electrodes on polyethylene terephthalate films for flexible, in-plane, and all-solid-state micro-supercapacitors. The as-obtained micro-supercapacitors acquire a maximum energy density of 5.83 mW h cm−3 and a maximum power density of 0.45 W cm−3 that are both comparable to or superior to the values obtained for currently available state-of-the-art planar supercapacitors/micro-supercapacitors. In addition, the micro-supercapacitors exhibit remarkably high mechanical flexibility and show a good cycling stability, with 72.7% retention of the specific capacity after 1000 cycles. Moreover, the micro-supercapacitors can be optionally connected in series or in parallel to meet the voltage and capacity requirements for a given application. Compared to traditional fabrication approaches for flexible micro-supercapacitors with an interdigital in-plane design, the method demonstrated here does not involve a complicated lithography process, toxic chemical treatments, expensive rigid template, and cumbersome fabrication of jettable and stable precursor ink, which provides a simple route for fabrication of flexible planar micro-supercapacitors with high-practicality and high-performance.
Light quark correlators in a mixed-action setup

We report our progress in simulating Neuberger valence fermions on Nf = 2 Wilson O(a)improved sea quarks. We compute correlators with valence quark masses both in the p- and in the e-regime, and we match the results with the predictions of the Chiral Effective Theory in the mixed regime. This allows us to extract the Low Energy Couplings (LECs) of the Nf = 2 theory and to test the validity of the approach.