Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiscale Stress Analysis Using EDIP Silicon

It is necessary to be able to seamlessly meld molecular dynamics (MD) and continuum stress analysis in many engineering situations. In this paper, we developed a finite volume method (FVM) to solve the continuum stress problem, while the MD simulation employs the environmentally dependent inter-atomic potential (EDIP), a three-body potential suitable for modeling silicon. Fixed-free and fixed-fixed bar bending problems are simulated by both the FVM method and the MD EDIP simulation. The results from the two computations are seen to match well for a cantilever of 32.136times5. 43times5.43 nm3. A one-way multiscale analysis is then performed . Here, the FVM simulation is carried out in the whole domain, while the MD simulation is performed in a sub-domain, with an overlap region in which MD and continuum models are both employed. Material velocities computed by the continuum solution are interpolated to the atomic positions in the MD solver, but velocities from the MD solution do not influence the continuum solution. The method is applied to the beam bending problem and a reasonable match with the pure MD, pure continuum and the multiscale simulation is found
Barcoding in trypanosomes

SUMMARY Trypanosomes (genus Trypanosoma) are parasites of humans, and wild and domestic mammals, in which they cause several economically and socially important diseases, including sleeping sickness in Africa and Chagas disease in the Americas. Despite the development of numerous molecular diagnostics and increasing awareness of the importance of these neglected parasites, there is currently no universal genetic barcoding marker available for trypanosomes. In this review we provide an overview of the methods used for trypanosome detection and identification, discuss the potential application of different barcoding techniques and examine the requirements of the ‘ideal’ trypanosome genetic barcode. In addition, we explore potential alternative genetic markers for barcoding Trypanosoma species, including an analysis of phylogenetically informative nucleotide changes along the length of the 18S rRNA gene.
User-controlled access management to resources on the Web

The rapidly developing Web environment provides users with a wide set of rich services as varied and complex as desktop applications. Those services are collectively referred to as "Web 2.0", with such examples as Facebook, Google Apps, Salesforce, or Wordpress, among many others. These applications are used for creating, managing, and sharing online data between users and services on the Web. With the shift from desktop computers to the Web, users create and store more of their data online and not on the hard drives of their computers. This data includes personal information, documents, photos, as well as other resources. Irrespective of the environment, either desktop or the Web, it is the user who creates the data, who disseminates it and who shares this data. On the Web, however, sharing resources poses new security and usability challenges which were not present in traditional computing. Access control, also known as authorisation, that aims to protect such sharing, is currently poorly addressed in this environment. Existing access control is often not well suited to the increasing amount of highly distributed Web data and does not give users the required flexibility in managing their data. This thesis discusses new solutions to access control for the Web. Firstly, it shows a proposal named User-Managed Access Control (UMAC) and presents its architecture and protocol. This thesis then focuses on the User-Managed Access (UMA) solution that is researched by the UserManaged Access Work Group at Kantara Initiative. The UMA approach allows the user to play a pivotal role in assigning access rights to their resources which may be spread across multiple cloud-based Web applications. Unlike existing authorisation systems, it relies on a user’s centrally located security requirements for these resources. The security requirements are expressed in the form of access control policies and are stored and evaluated in a specialised component called Authorisation Manager. Users are provided with a consistent User Experience for managing access control for their distributed online data and are provided with a holistic view of the security applied to this data. Furthermore, this thesis presents the software that implements the UMA proposal. In particular, this thesis shows frameworks that allow Web applications to delegate their access control function to an Authorisation Manager. It also presents design and implementation of an Authorisation Manager and discusses its evaluation conducted with a user study. It then discusses design and implementation of a second, improved Authorisation Manager. Furthermore, this thesis presents the applicability of the UMA approach and the implemented software to real-world scenarios.
Bioluminescence Imaging of the Response of Rat Gliosarcoma to ALA‐PpIX‐mediated Photodynamic Therapy ¶

Photodynamic therapy (PDT) is a promising modality for the treatment of solid tumors that combines a photosensitizing agent and light to produce cytotoxic reactive oxygen species that lead to tumor cell death. The recent introduction of bioluminescence imaging (BLI), involving the use of the luciferase gene (luc) transferred into target tumor cells, followed by systemic administration of luciferin and detection of the emitted visible chemiluminescence photons, offers the potential for longitudinal imaging of tumor growth and therapeutic response in single animals. We demonstrate in this study the first results of the use of BLI to assess the response of an intracranial brain tumor model (9L rat gliosarcoma) to aminolevulinic acid (ALA)‐mediated PDT. Complementary in vitro experiments with the luciferase‐transfected 9L cells show that the decrease in the luminescent signal after PDT correlates with cell kill. In vivo imaging shows a decrease in the BLI signal from the tumor after ALA‐PDT treatment, followed by tumor regrowth. Furthermore, preliminary studies using cells transfected with a hypoxiaresponsive vector show an increase in bioluminescence within 4 h after Photofrin‐mediated PDT, demonstrating the ability to observe stress‐gene responses. These results suggest that BLI can be used to provide spatiotemporal information of intracranial brain tumor responses after PDT and may serve as a valuable response‐endpoint measure.
GEAMM v.1.4: a versatile program for mixed model analysis of gene expression data.

The research contract of J. Casellas was partially financed by Spain s Ministerio de Educacion y Ciencia (programa Juan de la Cierva). The authors are indebted to J. L. Noguera, R. Quintanilla, R. N. Pena and A. Canovas for their helpful comments. This software has been developed within the frame of research projects AGL2004-08368-C03/GAN, AGL2002-04271-C03 and GEN2003-20658-C05-05. GEAMM v.1. 4 has been extensively tested on several data sets and results were checked for consistency with alternative software when possible.7 The authors would appreciate to be informed of any detected bug.
Modern Probe-Assisted Methods for the Specific Detection of Bacteria

This review intends to present an overview of methods currently under development for the specific and sensitive detection of pathogenic bacteria that exist in a variety of human environments. Bacteria continue to be a major health threat in general, and much effort is being deployed to counteract this problem. In a first instance, current and efficient techniques in use for the detection of bacteria are described. In a second instance, this review serves to compare the more conventional techniques to emerging technologies for the direct (non-labelled) detection of bacteria (referred to as “biosensors”). These approaches are mainly optical, piezoelectric, and electro-chemical in nature. They are cost-effective, quite sensitive, and potentially portable for rapid on-site/real-time detection, and rapid prevention. These devices are comprised of specific chemical/ biochemical probes immobilized onto physical transducers. This work also presents comparisons between the efficiencies (assay time and sensitivity) of various techniques being employed.
Online prediction of an electric vehicle remaining range based on regression analysis

Given the longitudinal average velocity and energy consumption of a Full Electric Vehicle (FEV) for any given part of a targeted road trip, this work solves the problem of online remaining range estimation, i.e., predicting, at any given travelled distance from the beginning of the trip, the actual distance the vehicle can still be driven before recharging is required. Modelling the remaining range is closely related with modelling the energy consumption of an electric vehicle. The latter remains an open problem due to unknown context data that may apply such as driving trip speed, vehicle load and topographical characteristics. In this work, a regression model is formulated in order to learn, from time/location-variant real driving data, a relationship between the future energy consumption on one side, and the following related factors, which are considered known, on the other side: i) the difference in average velocity between the future and the past ii) the difference in elevation rate between the future and the past and iii) the recent past energy consumption. Experimental results on around 2000km of discharge trips, demonstrate the effectiveness of the method over a conventional method that is based solely on historic energy usage evidence. An average Mean Absolute Error (MAE) of 1.64 km and of 1.95 km is obtained when the regression model is evaluated on a model trained without and with elevation respectively.
Solutions diversification in a column generation algorithm

Column generation algorithms have been specially designed for solving mathematical programs with a huge number of variables. Unfortunately, this method suffers from slow convergence that limits its efficiency and usability. Several accelerating approaches are proposed in the literature such as stabilization-based techniques. A more classical approach, known as “intensification”, consists in inserting a set of columns instead of only the best one. Unfortunately, this intensification typically overloads the master problem, and generates a huge number of useless variables. This article covers some characteristics of the generated columns from theoretical and experimental points of view. Two selection criteria are compared. The first one is based on column reduced cost and the second on column structure. We conclude our study with computational experiments on two kinds of problems: the acyclic vehicle routing problem with time windows and the one-dimensional cutting stock problem.
Local excitation black blood imaging at 3T: Application to the carotid artery wall

A novel approach for imaging large sections of the carotid artery wall at isotropic spatial resolution is presented. Local excitation by means of 2D excitation pulses was combined with a diffusion‐prepared segmented steady‐state black‐blood gradient echo technique enabling the assessment of the carotid arterial wall over a range of up to 15 cm. The carotid arteries of five healthy volunteers were imaged with the proposed technique. Signal‐to‐noise ratio (SNR), wall‐lumen contrast‐to‐noise ratio (CNR), and vessel dimensions were assessed and compared to conventional excitation techniques. In all experiments black‐blood contrast could be realized over the covered carotid arteries with similar SNR and CNR as the conventional technique covering the region of the bulbus only. The proposed technique enables the time‐efficient coverage of the carotid arteries without compromising wall‐lumen CNR and geometrical accuracy. Furthermore, the proposed technique appears to be less sensitive to motion and swallowing artifacts due to the local character of the excitation. Magn Reson Med, 2008. © 2008 Wiley‐Liss, Inc.
[FAB: a preliminar Spanish application of the frontal assessment battery to 11 groups of patients].

INTRODUCTION We consider in this paper the applicability of the FAB in Spain, a battery at bedside devised to assess frontal lobe function and able to identify a dysexecutive syndrome, which takes few minutes to administer, and useful for neuropsychological diagnosis in diseases involving frontal lobe dysfunctions. PATIENTS AND METHODS We study dual application of FAB and Folstein s MMSE to 195 subjects belonging to 11 subgroups (controls, neurodegenerative disorders and psychiatric conditions), and they were related to: cortical/subcortical normality, cortical/subcortical cognitive impairment, or cortical/subcortical dementia. STATISTICS mean, standard deviation, U test (p< 0.05) and Pearson s correlation index. CONCLUSIONS Data suggest FAB reflects in Spanish environment the reality of frontosubcortical deterioration in studied groups. FAB and MMSE showed a variable grade of positive lineal correlation in different diseases.
PPAR-alpha and -gamma agonists attenuate diabetic kidney disease in the apolipoprotein E knockout mouse.

BACKGROUND Peroxisome proliferator-activated receptor (PPAR)-alpha and PPAR-gamma agonists are widely used in diabetes. In addition to their effects on lipid and glucose homeostasis, these agents have been postulated to have independent renoprotective actions. In the current study, we assess the efficacy of the PPAR-alpha agonist, gemfibrozil, the PPAR-gamma agonist rosiglitazone and the non-thiazolidinedione PPAR-alpha/gamma coagonist, compound 3q, on kidney structure and function in streptozotocin-treated apolipoprotein E knockout mice. METHODS Control and streptozotocin-diabetic mice were randomized to receive rosiglitazone (20 mg/kg/day), gemfibrozil (100 mg/kg/day), or compound 3q (3 mg/kg/day) by gavage, or no treatment for a period of 20 weeks. Renal fibrosis was assessed by standard histology and collagen IV immunohistochemistry. Kidney function was assessed by urinary albumin excretion and creatinine clearance. RESULTS Diabetes in this model was associated with an increase in glomerulosclerosis, tubulointerstitial fibrosis and increased collagen IV deposition in the glomeruli and tubules. All three agents significantly attenuated glomerulosclerosis, tubulointerstitial expansion and collagen IV deposition. The increase in albuminuria and the decline in kidney function associated with diabetes in this model were also attenuated by each of these agents, with no superiority observed among various treatment groups. These renoprotective effects were observed in the absence of changes in glucose, insulin or lipid levels or a reduction in blood pressure. CONCLUSIONS Combined with their independent anti-atherosclerotic actions, and their important effects on dyslipidaemia and insulin resistance, PPAR agonists may be useful for the prevention of diabetic complications, including kidney disease, even in type 1 diabetes.
Stub-loaded ridge waveguides for frequency-scanning antenna application

In this paper, we first investigate the structural parameters for recently developed leaky waveguide by Tsuji et al. (2005) to design a leaky-wave antenna with low sidelobes. Such an antenna requires to keep the phase constant the fixed value and then to vary the leakage constant over the wide range along an antenna axis. The guide structure under consideration includes many conductor edges at which the fields diverge, so its leakage characteristics are accurately calculated by the modified mode-matching method incorporating the singular field behavior into the aperture-field expressions. As an example, the antenna with the Taylor distribution of -30dB sidelobes is designed. Finally we investigate the excitation problem of this stub-loaded ridge guide and verify that the usefulness of both the coaxial feed for the present antenna structure and also the designed antenna from the numerical calculation.
Expression of Cell Death‐Associated Proteins in Neuronal Apoptosis Associated with Pontosubicular Neuron Necrosis

Expression of apoptosis‐associated proteins p53, bcl‐2, bax, and caspase‐3/CPP32, activation of caspase‐3, and modification of proteins via poly(ADP‐ribosyl)ation was studied in pontosubicular neuron necrosis (PSN), a form of perinatal brain damage revealing the morphological hallmarks of neuronal apoptosis. Immunoreactivity for p53 was completely absent. The majority of cells stained with the bax and procaspase‐3 antibodies did not show morphological signs of apoptosis. In contrast, an antibody against activated caspase‐3 almost exclusively stained cells with apoptotic morphology. Poly(ADP‐ribosyl)ated proteins were only rarely detected in cells with apoptotic morphology. The expression patterns of bax, procaspase‐3, bcl‐2, and p53 in PSN were similar to that found in age‐matched control brains. However, activated caspase‐3 and poly‐ADP‐ribosylated proteins were exclusively found in apoptotic cells. These data indicate that detection of active caspase‐3 is a reliable marker for apoptosis in formalin‐fixed human tissue, and that neuronal apoptosis in pontosubicular neuron necrosis is accompanied by a pronounced activation of caspase‐3.
Structural Proteins of Simian Virus 40: Phosphoproteins

All five structural polypeptides of infectious simian virus 40 grown in African green monkey kidney cells were found to be phosphorylated. The polypeptides with the largest and smallest molecular weights are phosphorylated to a somewhat lower extent than the other polypeptides. The protein moiety of “empty” virus, which is essentially devoid of deoxyribonucleic acid, exhibited a degree of phosphorylation similar to that of infectious virus. In the major polypeptide (molecular weight: 49,000), the phosphate appears to be bound to the seryl or threonyl residues, or both. The nature of the phosphate-polypeptide bond in the other viral polypeptides remains obscure.
MULTI-SQUINT ANALYSIS TO SEPARATE GEOMETRIC AND ATMOSPHERIC PHASE ARTIFACTS IN SPACEBORNE INSAR

The main issue during phase calibration of spaceborne SAR system is to properly identify and separate different contributions to the interferometric phase. In this paper we suggest to exploit the Multi-Squint (MS) interferometric phase in order to remove InSAR fringes due to a linear orbital error, under the key assumption that the MS phase is very poorly affected by contributions from the atmospheric delay. Preliminary results obtained by processing TerraSAR-X stripmap data appear to confirm the validity of this assumption, and suggest that MS processing can be operationally employed for the calibration of spaceborne InSAR datastacks.
Detections of water ice, hydrocarbons, and 3.3um PAH in z~2 ULIRGs

We present the first detections of the 3μm water ice and 3. 4μm amorphous hydrocarbon (HAC) absorption features in z∼ 2 ULIRGs. These are based on deep rest-frame 2 – 8μm Spitzer IRS spectra of 11 sources selected for their appreciable silicate absorption. The HAC-to-silicate ratio for our z∼ 2 sources is typically higher by a factor of 2 – 5 than that observed in the Milky Way. This HAC ‘excess’ suggests compact nuclei with steep temperature gradients as opposed to predominantly host obscuration. Beside the above molecular absorption features, we detect the 3. 3μm PAH emission feature in one of our sources with three more individual spectra showing evidence for it. Stacking analysis suggests that water ice, hydrocarbons, and PAH are likely present in the bulk of this sample even when not individually detected. The most unexpected result of our study is the lack of clear detections of the 4. 67μm CO gas absorption feature. Only three of the sources show tentative signs of this feature and at significantly lower levels than has been observed in local ULIRGs. Overall, we find that the closest local analogs to our sources, in terms of 3 – 4μm color, HAC-to-silicate and ice-to-silicate ratios, as well as low PAH equivalent widths are sources dominated by deeply obscured nuclei. Such sources form only a small fraction of
Remote-controlled robots for repair and recovery in the zones of high radiation levels

The Chernobyl accident in 1986 raised the acuteness of the problem of designing mobile robot based systems capable of carrying out long-term reconstruction operations in zones of high-level radiation. The authors examine the design and control features of two types of such systems and the results of their operation. Remote-controlled robots of two types were developed and manufactured with due regard for varied conditions and technological requirements; a heavy robotic complex for engineering work comprising an unmanned remote-controlled vehicle and a command vehicle, and a small robotic complex designed for operating on the roofing of the Chernobyl nuclear power plant buildings and structures. <<ETX>>
Middleware-based Security for Future In-Car Networks

This thesis presents novel insights and solutions for middleware-based security in future in-car networks and defines a car-wide access control model enforced at the middleware level for on-board and C2X communications. An authorization model based on information flow control was developed and coupled to two approaches for safe integration of third-party applications: a monitoring one based on isolation techniques and a controlling one relying on a custom data flow tracking framework. The implementation shows that this architecture can be realistically applied for the automotive purpose.
Identifying Convectively Coupled Equatorial Waves Using Theoretical Wave Eigenvectors

AbstractConvectively coupled equatorial waves (CCEWs) are often identified by space–time filtering techniques that make use of the eigenvalues of linear shallow water theory. Here, instead, a method is presented for identifying CCEWs by projection onto the eigenvectors of the theory. This method does not use space–time filtering; instead, wave signals corresponding to the first baroclinic Kelvin, Rossby, and mixed Rossby–gravity (MRG) waves are constructed from reanalysis data by a series of projections onto (i) vertical and meridional modes and (ii) the wave eigenvectors. In accordance with the theory, only dry variables, that is, winds and geopotential height, are used; no proxy for convection is used. Using lag–lead regression, composites of the structures associated with each eigenvector signal during boreal summer are shown to contain all the features of the theory as well as some additional features seen in previous observational studies, such as vertical tilts. In addition, these composites exhibit.
Surface magnetism in iron, cobalt, and nickel.

We have calculated magnetic moments, work functions, and surface energies for several of the most closely packed surfaces of iron, cobalt, and nickel by means of a spin-polarised Green's-function technique based on the linear muffin-tin orbitals method within the tight-binding and atomic sphere approximations. We find enhanced spin moments at all the surfaces considered except for Ni fcc(111), where the moment at the surface reverts to its bulk value. This is in close agreement with earlier slab calculations