Miracle-dz/UniFAR-FTUs huggingface dataset:
The detection of protective antigen ( PA ) associated with spores of Bacillus anthracis and the effects of anti-PA antibodies on spore germination and macrophage interactions

The protective antigen (PA) component of the anthrax toxins is an essential virulence factor of Bacillus anthracis and is the major protective immunogen. The kinetics of PA production during growth of B. anthracis, and the roles of anti-PA antibody in host immunity are not clearly defined. Production of PA by the vegetative organisms peaks during the shift from exponential to stationary phase of growth. Recently, PA was also found to be associated with spores. In our study, PA-specific mRNA was detected in spores by RT-PCR within 15-min of exposure to germinant. PA protein was detected by immunomagnetic electrochemiluminescence (ECL) on spores within 1 h of exposure to a germination medium and was rapidly released into the supernatant. PA was not demonstrated on ungerminated spores by RNA analysis, ECL, or spore-based anti-PA ELISA; however, it was detected on ungerminated spores by immunoelectron microscopy (immunoem). In rabbits, PA induces polyclonal antibodies (Abs) that, in addition to their anti-toxin neutralizing activities, exhibit anti-spore activities. In this study, the anti-spore effects of a human monoclonal Ab specific for PA (AVP-hPA mAb, Avanir Pharmaceuticals) were characterized. AVPhPA mAb retarded germination in vitro, and enhanced the phagocytic and sporicidal activities of macrophages. The activities were comparable to those of the polyclonal rabbit anti-rPA Ab. Assays to detect germination inhibitory activity (GIA) in serum from vaccinated mice and guinea pigs suggested a possible role for anti-PA Abs in protection. Thus, anti-PA Ab-mediated, anti-spore activities may play a role in protection during the early stages of an anthrax infection. q 2005 Elsevier Ltd. All rights reserved.
Flexible 3D localization of planar objects for industrial bin-picking with monocamera vision system

In this paper, we present a robust and flexible vision system for 3D localization of planar parts for industrial robots. Our system is able to work with nearly any object with planar shape, randomly placed inside a standard industrial bin or on a conveyor belt. Differently from most systems based on 2D image analysis, which usually can manage parts disposed in single layers, our approach can estimate the 6 degrees of freedom (DoF) pose of planar objects from a single 2D image. The choice of a single camera solution makes our system cheaper and faster with respect to systems using expensive industrial 3D cameras, or laser triangulation systems, or laser range finders. Our system can work virtually with any planar piece, without changing the software parameters, because the input for the recognition and localization algorithm is the CAD data of the planar part. The localization software is based on a two step strategy: i) a candidates selection step based on a well-engineered voting scheme ii) a refinement and best match selection step based on a robust iterative optimize-and-score procedure. During this second step, we employ a novel strategy we called search-in-the-stack that avoids the optimization from being stuck on local minima (representing false positives) created when objects are almost regularly stacked. Our system is currently installed in seven real world industrial plants, with different setups, working with hundreds of different models and successfully guiding the manipulators to pick several hundreds of thousands of pieces per year. In the experiment section, we report statistics about our system at work in real production plants on more than 60000 cycles.
Feature-space structural MAPLR with regression tree-based multiple transformation matrices for DNN

Feature-space maximum-likelihood linear regression (fMLLR) transforms acoustic features to adapted ones by a multiplication operation with a single transformation matrix. This property realizes an efficient adaptation performed within a pre-precessing, which is independent of a decoding process, and this type of adaptation can be applied to deep neural network (DNN). On the other hand, constrained MLLR (CMLLR) uses multiple transformation matrices based on a regression tree, which provides further improvement from fMLLR. However, there are two problems in the model-space adaptations: first, these types of adaptation cannot be applied to DNN because adaptation and decoding must share the same generative model, i.e. Gaussian mixture model (GMM). Second, transformation matrices tend to be overly fit when the amount of adaptation data is small. This paper proposes to use multiple transformation matrices within a feature-space adaptation framework. The proposed method first estimates multiple transformation matrices in the GMM framework according to the first-pass decoding results and the alignments, and then takes a weighted sum of these matrices to obtain a single feature transformation matrix frame-by-frame. In addition, to address the second problem, we propose feature-space structural maximum a posteriori linear regression (fSMAPLR), which introduces hierarchal prior distributions to regularize the MAP estimation. Experimental results show that the proposed fSMAPLR outperformed fMLLR.
From uncertainty to belief: inferring the specification within

Automatic tools for finding software errors require a set of specifications before they can check code: if they do not know what to check, they cannot find bugs. This paper presents a novel framework based on factor graphs for automatically inferring specifications directly from programs. The key strength of the approach is that it can incorporate many disparate sources of evidence, allowing us to squeeze significantly more information from our observations than previously published techniques. We illustrate the strengths of our approach by applying it to the problem of inferring what functions in C programs allocate and release resources. We evaluated its effectiveness on five codebases: SDL, OpenSSH, GIMP, and the OS kernels for Linux and Mac OS X (XNU). For each codebase, starting with zero initially provided annotations, we observed an inferred annotation accuracy of 80--90%, with often near perfect accuracy for functions called as little asfive times. Many of the inferred allocator and deallocator functions are functions for which we both lack the implementation and are rarely called---in some cases functions with at most one or two callsites. Finally, with the inferred annotations we quickly found both missing and incorrect properties in a specification used by a commercial static bug-finding tool.
A Critical Discussion of the Rates of Progression and Causes of Optic Nerve Damage in Glaucoma: International Glaucoma Think Tank II: July 25-26, 2008, Florence, Italy

The International Glaucoma Think Tank II brought together glaucoma clinicians and researchers from all over the world to discuss current practices in glaucoma diagnosis and management, and the neurobiology of glaucoma. The meeting focused on several themes, including rates of deterioration in glaucoma patients, mechanisms of optic nerve damage, and implications for treatment. Issues such as how to measure and integrate progression information into clinical practice, screening protocols, or trials were discussed, as were promising new technologies and limitations of currently available measurement tools. Clinical applications for genetic testing were considered. Study of the neurobiology of glaucoma continues to inform our understanding of underlying degenerative processes, as well as to introduce possibilities for early detection or prevention. Many questions regarding glaucoma pathophysiology and best treatment practices remain unanswered, but with continued research and discussion, we will advance our understanding of this disease and ensure that patients receive optimal care.
- 1-From Protocol-based to Distributed Object-based Management Architectures

OSI Systems Management (OSI-SM) and Internet SNMP have been conceived as protocolbased management frameworks, adopting the manager-agent model that governs interactions between management applications assuming the manager and agent roles. The manager-agent model is objectoriented in information specification terms but addresses only "on the wire" interactions, leaving deliberately unspecified aspects relevant to the internal structure of management applications. On the other hand, OMG CORBA and similar technologies emerge from the distributed systems world and can be thought as pragmatic counterparts of Open Distributed Processing (ODP). They project an objectoriented paradigm and address mainly programmatic interface aspects, while they use a general purpose Remote Procedure Call (RPC) protocol as opposed to a specialized management protocol. The benefits of using distributed object technologies for management are easy programmabilit y, multiple programming language bindings, application portabilit y and distribution. On the contrary, management protocol approaches offer optimized mechanisms for accessing management information, including event dissemination, and do not constrain implementations. This paper examines the basic characteristics of the two types of architectures, explains their relevant similarities and differences and proposes a future architecture based on distributed objects. This retains the operational paradigm of OSISM model over the relevant distributed object framework, bridging the two worlds and maintaining the best aspects of both. The proposed framework has been prototyped over OMG CORBA and management applications based on it have been used in real field trials.
Design and development of a debris flow tracking "Smart Rock"

This thesis covers the design and development of a Smart Rock sensor package to be used in U.S. Geological Survey research of debris flow phenomena. This instrumented Rock, containing inertial sensors and pressure sensors, provides information about the movement of the flow as well as the pressures seen within the flow. The goal of the sensor package is to use this information to track the position of a particle in the flow with an accuracy of 1 m over the course of 10 s. It is found that using an ad hoc filtering method provides the required level of accuracy. Any known positions are incorporated into the filter. Large scale motions over tens of meters can be distinguished as well as small scale motions on the order of centimeters. Thus, the data gathered by the Smart Rock can be used to help verify and refine debris flow models.
Evolutionary Design of FreeCell Solvers

In this paper, we evolve heuristics to guide staged deepening search for the hard game of FreeCell, obtaining top-notch solvers for this human-challenging puzzle. We first devise several novel heuristic measures using minimal domain knowledge and then use them as building blocks in two evolutionary setups involving a standard genetic algorithm and policy-based, genetic programming. Our evolved solvers outperform the best FreeCell solver to date by three distinct measures: 1) number of search nodes is reduced by over 78%; 2) time to solution is reduced by over 94%; and 3) average solution length is reduced by over 30%. Our top solver is the best published FreeCell player to date, solving 99.65% of the standard Microsoft 32 K problem set. Moreover, it is able to convincingly beat high-ranking human players.
Unique botanical values in a metropolitan area and the landscape history reasons of their occurrence on the Széchenyi Hill, Budapest

Urban areas host several threatened species in small reserves that face habitat loss and fragmentation due to land-use change. Despite historical and current disturbances, these areas sometimes still maintain high biological diversity. As only 5% of the European Union territory was classified as natural, the permanent grasslands represent overriding value, especially in metropolitan areas. Our aim was to explore protected and adventive plant species in a small and valuable, but till now, not deeply studied area of the densely inhabited 12th district in the metropolitan city Budapest (Hungary), which is visited by large numbers of people. We compared various historical map sources in order to explain how the extension of the grasslands has changed during the past centuries and, thus, which patches are permanent grassland habitats. We found 29 protected and 1 strictly protected plant species. The highest number of protected plant species and their stands were found in the permanent grasslands. Besides urbanisation, a heavy load of tourism (especially on non-designated routes), off-road mountain biking, airsoft races, some illegal shelters for homeless people and game damage threaten this unique refuge of high natural values. The extension of grasslands between 1783 and 2016 varies from 6.7 ha to 21.5 ha. Their area constantly increased due to deforestation until 1867 and exceeded 20 ha, probably due to the mass increase in livestock grazing; then it stagnated until the 1920s, with a slight decrease due to expanding urban areas. Golf greens appeared, walker and skiing tourism increased and these apparently have not decreased the coverage of grasslands, but surely affected the composition of their species. Recent scrub encroachment and re-forestation caused a further decrease. Our distribution maps show the highest density of protected plant species on the southern slopes (2.4 hectare) that have constantly been grasslands since 1783 to date. Contrarily, the cutting of grasslands from 1861 to date contains only half of their number per area unit. Thus, the number of valuable plant specimens refers to the age of the grassland. Three species occur only in the oldest grasslands. Conservation actions should first and foremost focus on these patches.
The impact of boundary spanning capability, cultural differences on success of offshore information system outsourcing - from the vendors' perspective

Effective communication between clients and vendors in offshore IS outsourcing requires spanning various boundaries such as cultural differences, language barriers and domain knowledge gaps to ensure efficacious information transmission through clients and vendors. How to overcome these boundaries is an important question. This paper takes culture differences as a mediator to study the impact of vendors' boundary spanning capability on success of offshore IS outsourcing. The research model is empirically tested on 102 offshore IS outsourcing projects from 20 vendors in China. The results suggest that vendors' boundary spanning capability significantly improves outsourcing success. Moreover, we find that culture differences partial mediate the relationship between boundary spanning capability and outsourcing success.
GUIDO: visualizing document retrieval

GUIDO (GUI for DOcuments) is a visual information retrieval interface (VIRI) that focuses on retrieval rather than on document organization. This visual document retrieval system utilizes two reference points at a time, three metrics (the city block metric, the Euclidean metric and the maximal distance metric) and four retrieval caps (the disjunctive, conjunctive, elliptical and Cassini oval models). User tests on the system are described.
Dicarbonyls and Advanced Glycation End-Products in the Development of Diabetic Complications and Targets for Intervention

Advanced glycation end-products (AGEs) are non-enzymatic protein and amino acid adducts as well as DNA adducts which form from dicarbonyls and glucose. AGE formation is enhanced in diabetes and is associated with the development of diabetic complications. In the current review, we discuss mechanisms that lead to enhanced AGE levels in the context of diabetes and diabetic complications. The methylglyoxal-detoxifying glyoxalase system as well as alternative pathways of AGE detoxification are summarized. Therapeutic approaches to interfere with different pathways of AGE formation are presented.
Comparison of Coupled and Uncoupled Currents during Glutamate Uptake by GLT-1 Transporters

The transport of glutamate across the plasma membrane is coupled to the movement of cations (Na+, K+, and H+) that are necessary for glutamate uptake and transporter cycling as well as anions that are uncoupled from the flux of glutamate. Although the relationship between these coupled (stoichiometric) and uncoupled (anion) transporter currents is poorly understood, transporter-associated anion currents often are used to monitor transporter activity. To define the kinetic relationship between these two components, we have recorded transporter currents associated with stoichiometric and anion charge movements occurring in response to the rapid application of l-glutamate to outside-out patches from human embryonic kidney cells expressing GLT-1 transporters. Transporter-associated anion currents were approximately twice as slow to rise and decay as stoichiometric transport currents, but the presence of permeant anions did not slow transporter cycling. A kinetic model for GLT-1 was developed to simulate the behavior of both components of the transporter current and to estimate the capture efficiency of GLT-1. In this model the K+counter-transport step was defined as rate-limiting, consistent with the slowing of transporter cycling after the substitution of internal K+ with Cs+ or Na+. The model predicts that in physiological conditions ∼35% of GLT-1 transporters function as buffers, releasing glutamate back into the extracellular space after binding.
Crystal structure of 2-{[(naphthalen-1-yl)oxy]methyl}-5-(2,4,5-trifluorophenyl)-1,3,4-oxadiazole

In the title compound C19H11F3N2O2, the oxadiazole ring and the naphthalene ring system are approximately planar (r.m.s. deviations of 0.001 and 0.020 Å, respectively) and the oxadiazole ring makes dihedral angles of 13.11 (1) and 7.59 (1)° with the naphthalene ring system and the trifluorophenyl ring, respectively. In the crystal, C—H⋯N hydrogen bonds link molecules into chains along the a-axis direction, while C—H⋯F contacts form additional chains along the ac diagonal. These contacts generate sheets of molecules approximately parallel to the (011) plane.
Core Proteomic Analysis of Unique Metabolic Pathways of Salmonella enterica for the Identification of Potential Drug Targets

Background Infections caused by Salmonella enterica, a Gram-negative facultative anaerobic bacteria belonging to the family of Enterobacteriaceae, are major threats to the health of humans and animals. The recent availability of complete genome data of pathogenic strains of the S. enterica gives new avenues for the identification of drug targets and drug candidates. We have used the genomic and metabolic pathway data to identify pathways and proteins essential to the pathogen and absent from the host. Methods We took the whole proteome sequence data of 42 strains of S. enterica and Homo sapiens along with KEGG-annotated metabolic pathway data, clustered proteins sequences using CD-HIT, identified essential genes using DEG database and discarded S. enterica homologs of human proteins in unique metabolic pathways (UMPs) and characterized hypothetical proteins with SVM-prot and InterProScan. Through this core proteomic analysis we have identified enzymes essential to the pathogen. Results The identification of 73 enzymes common in 42 strains of S. enterica is the real strength of the current study. We proposed all 73 unexplored enzymes as potential drug targets against the infections caused by the S. enterica. The study is comprehensive around S. enterica and simultaneously considered every possible pathogenic strain of S. enterica. This comprehensiveness turned the current study significant since, to the best of our knowledge it is the first subtractive core proteomic analysis of the unique metabolic pathways applied to any pathogen for the identification of drug targets. We applied extensive computational methods to shortlist few potential drug targets considering the druggability criteria e.g. Non-homologous to the human host, essential to the pathogen and playing significant role in essential metabolic pathways of the pathogen (i.e. S. enterica). In the current study, the subtractive proteomics through a novel approach was applied i.e. by considering only proteins of the unique metabolic pathways of the pathogens and mining the proteomic data of all completely sequenced strains of the pathogen, thus improving the quality and application of the results. We believe that the sharing of the knowledge from this study would eventually lead to bring about novel and unique therapeutic regimens against the infections caused by the S. enterica.
A lifting line model to investigate the influence of tip feathers on wing performance

Bird wings have been studied as prototypes for wing design since the beginning of aviation. Although wing tip slots, i.e. wings with distinct gaps between the tip feathers (primaries), are very common in many birds, only a few studies have been conducted on the benefits of tip feathers on the wingʼs performance, and the aerodynamics behind tip feathers remains to be understood. Consequently most aircraft do not yet copy this feature. To close this knowledge gap an extended lifting line model was created to calculate the lift distribution and drag of wings with tip feathers. With this model, is was easily possible to combine several lifting surfaces into various different birdwing-like configurations. By including viscous drag effects, good agreement with an experimental tip slotted reference case was achieved. Implemented in C++ this model resulted in computation times of less than one minute per wing configuration on a standard notebook computer. Thus it was possible to analyse the performance of over 100 different wing configurations with and without tip feathers. While generally an increase in wing efficiency was obtained by splitting a wing tip into distinct, feather-like winglets, the best performance was generally found when spreading more feathers over a larger dihedral angle out of the wing plane. However, as the results were very sensitive to the precise geometry of the feather fan (especially feather twist) a careless set-up could just as easily degrade performance. Hence a detailed optimization is recommended to realize the full benefits by simultaneously optimizing feather sweep, twist and dihedral angles.
Effects of palmitoylethanolamide on intestinal injury and inflammation caused by ischemia‐reperfusion in mice

Our primary aim in this study was to test the hypothesis that PEA, a member of the fatty acid ethanolamide family and an endogenous PPAR‐α ligand, exerts anti‐inflammatory effects on SAO shock, causing a severe form of circulatory shock and enhanced formation of ROS. SAO shock was induced by clamping the superior mesenteric artery and the celiac trunk, resulting in a total occlusion of these arteries for 30 min. After this period of occlusion, the clamps were removed. In this study, we demonstrated that the administration of PEA, 5 min before reperfusion, significantly reduced all of the parameters involved during inflammation, such as proinflammatory cytokine production (TNF‐α, IL‐1β), adhesion molecules (ICAM‐1, P‐selectin) expression, NF‐κB expression, and apoptosis (Bax, Bcl‐2, TUNEL assay) activation. In addition, to study whether the protective action of PEA on SAO shock is also related to the activation of PPAR‐α, we have investigated the effect of PEA in PPAR‐α KO mice subjected to SAO shock. Our study clearly demonstrates that PEA significantly attenuated the degree of intestinal injury and inflammation caused by I/R injury. Moreover, the positive effects of PEA were at least in part dependent on the PPAR‐α pathway. The results clearly indicate that PEA exerts an anti‐inflammatory effect, also in a SAO shock model, which could imply a future use of PEA in the treatment of I/R shock.