gebhart/patrepeval huggingface dataset:
A novel diagnostic monoclonal antibody specific for <i>Helicobacter pylori</i> CagA of East Asian type (2009)

Molecular biological and epidemiological studies have suggested that Helicobacter pylori producing East Asian CagA protein variant is more virulent than that producing Western CagA. In the present study, we developed and validated an enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody specifically recognizing East Asian CagA-positive H. pylori. A total of 32 H. pylori strains were tested and the data were subjected to receiver-operator characteristic (ROC) curve analysis. The accuracy of the test, determined by calculating the area under the curve, was 0.96, which indicated a high level of accuracy. At the ROC optimized cutoff, the sensitivity and specificity of our ELISA method were 88.0% and 100%, respectively. The validated ELISA showed good performance in terms of sensitivity and specificity. These results suggest that this test is suitable for the diagnostic detection of East Asian CagA carrying strains. We also analyzed the localization of the CagA protein in H. pylori-infected gastric mucosa with fluorescence immunohistochemistry, and found that CagA protein expression was up-regulated by adhesion to epithelial cells.
Study on the usability evaluation of prosthetic leg products based on ergonomics (2011)

The prosthetic leg (PL) is a typical human-machine system in which the dynamic interaction between the human body and PL (machine) determines a high requirement of ergonomics design for PL and consequently needs to consider an indicator of usability indicating the performance of gait biomechanics. How to evaluate the indexes of usability for PL products is critical to the design technology of PL based on ergonomics. The gait symmetry of PL products, which is a core usability index, was experimentally analyzed by using a specially designed testing device in this paper. The test results show that the swing speed symmetry for intelligent prosthetic leg (IPL) is high up to 96.5%, which indicates a high performance for gait tracking. Then, a comprehensive evaluation was made for the usability of PL products with the analysis method of Grey Correlation Degree. Three types of PL product, including ordinary PL, IPL and Gait-following IPL (GL-IPL), were used in the evaluation. The evaluation results show that the GL-IPL product is the best in usability while both of IPL and GF-IPL products based on ergonomics are obviously better than the ordinary PL. The method of usability evaluation studied here is expected to help directing the design of prosthetic leg products.
Ant Colony Optimization (2004)

An overview of the rapidly growing field of ant colony optimization that describes theoretical findings, the major algorithms, and current applications. The complex social behaviors of ants have been much studied by science, and computer scientists are now finding that these behavior patterns can provide models for solving difficult combinatorial optimization problems. The attempt to develop algorithms inspired by one aspect of ant behavior, the ability to find what computer scientists would call shortest paths, has become the field of ant colony optimization (ACO), the most successful and widely recognized algorithmic technique based on ant behavior. This book presents an overview of this rapidly growing field, from its theoretical inception to practical applications, including descriptions of many available ACO algorithms and their uses. The book first describes the translation of observed ant behavior into working optimization algorithms. The ant colony metaheuristic is then introduced and viewed in the general context of combinatorial optimization. This is followed by a detailed description and guide to all major ACO algorithms and a report on current theoretical findings. The book surveys ACO applications now in use, including routing, assignment, scheduling, subset, machine learning, and bioinformatics problems. AntNet, an ACO algorithm designed for the network routing problem, is described in detail. The authors conclude by summarizing the progress in the field and outlining future research directions. Each chapter ends with bibliographic material, bullet points setting out important ideas covered in the chapter, and exercises. Ant Colony Optimization will be of interest to academic and industry researchers, graduate students, and practitioners who wish to learn how to implement ACO algorithms. Bradford Books imprint
Human femoral artery diameter in relation to knee extensor muscle mass, peak blood flow, and oxygen uptake (2000)

It is not known whether the diameter of peripheral conduit arteries may impose a limitation on muscle blood flow and oxygen uptake at peak effort in humans, and it is not clear whether these arteries are dimensioned in relation to the tissue volume they supply or, rather, to the type and intensity of muscular activity. In this study, eight humans, with a peak pulmonary oxygen uptake of 3.90 +/- 0.31 (range 2.29-5.03) l/min during ergometer cycle exercise, performed one-legged dynamic knee extensor exercise up to peak effort at 68 +/- 7 W (range 55-100 W). Peak values for knee extensor blood flow (thermodilution) and oxygen uptake of 6.06 +/- 0.74 (range 4.75-9.52) l/min and 874 +/- 124 (range 590-1,521) ml/min, respectively, were achieved. Pulmonary oxygen uptake reached a peak of 1.72 +/- 0.19 (range 1.54-2.33) l/min. Diameters of common and profunda femoral arteries determined by ultrasound Doppler were 10.6 +/- 0.4 (range 8.2-12.7) and 6.0 +/- 0.4 (range 4.5-8.0) mm, respectively. Thigh and quadriceps muscle volume measured by computer tomography were 10.06 +/- 0.66 (range 6.18-10.95) and 2.36 +/- 0.19 (range 1.31-3.27) liters, respectively. The common femoral artery diameter, but not that of the profunda branch, correlated with the thigh volume and quadriceps muscle mass. There were no relationships between either of the diameters and the absolute or muscle mass-related resting and peak values of blood flow and oxygen uptake, peak pulmonary oxygen uptake, or peak power output during knee extensor exercise. However, common femoral artery diameter correlated to peak pulmonary oxygen uptake during ergometer cycle exercise. In conclusion, common and profunda femoral artery diameters are sufficient to ensure delivery to the quadriceps muscle. However, the common branch may impose a limitation during ergometer cycle exercise.
Dismantling Cell–Cell Contacts during Apoptosis Is Coupled to a Caspase-dependent Proteolytic Cleavage of β-Catenin (1997)

Cell death by apoptosis is a tightly regulated process that requires coordinated modification in cellular architecture. The caspase protease family has been shown to play a key role in apoptosis. Here we report that specific and ordered changes in the actin cytoskeleton take place during apoptosis. In this context, we have dissected one of the first hallmarks in cell death, represented by the severing of contacts among neighboring cells. More specifically, we provide demonstration for the mechanism that could contribute to the disassembly of cytoskeletal organization at cell-cell adhesion. In fact, beta-catenin, a known regulator of cell-cell adhesion, is proteolytically processed in different cell types after induction of apoptosis. Caspase-3 (cpp32/apopain/yama) cleaves in vitro translated beta-catenin into a form which is similar in size to that observed in cells undergoing apoptosis. beta-Catenin cleavage, during apoptosis in vivo and after caspase-3 treatment in vitro, removes the amino- and carboxy-terminal regions of the protein. The resulting beta-catenin product is unable to bind alpha-catenin that is responsible for actin filament binding and organization. This evidence indicates that connection with actin filaments organized at cell-cell contacts could be dismantled during apoptosis. Our observations suggest that caspases orchestrate the specific and sequential changes in the actin cytoskeleton occurring during cell death via cleavage of different regulators of the microfilament system.
Improving supply chain robustness and preventing counterfeiting through authenticated product labels (2010)

Counterfeiting is a serious problem impacting customers and producers in the global economy. We design authenticated product labels (APL), a cryptography based practical counterfeit detection method. Our solution can be used by customers, distributors, and law enforcement alike. APLs not only detects counterfeit goods, but also deters counterfeiting by provably pinpointing its source in the supply chain. Counterfeiting is a serious problem impacting customers and producers in the global economy. We design authenticated product labels (APL), a cryptography based practical counterfeit detection method. Our solution can be used by customers, distributors, and law enforcement alike. APLs not only detects counterfeit goods, but also deters counterfeiting by provably pinpointing its source in the supply chain.
Role of ABCG1 and ABCA1 in Regulation of Neuronal Cholesterol Efflux to Apolipoprotein E Discs and Suppression of Amyloid-β Peptide Generation (2006)

Maintenance of an adequate supply of cholesterol is important for neuronal function, whereas excess cholesterol promotes amyloid precursor protein (APP) cleavage generating toxic amyloid-beta (Abeta) peptides. To gain insights into the pathways that regulate neuronal cholesterol level, we investigated the potential for reconstituted apolipoprotein E (apoE) discs, resembling nascent lipoprotein complexes in the central nervous system, to stimulate neuronal [3H]cholesterol efflux. ApoE discs potently accelerated cholesterol efflux from primary human neurons and cell lines. The process was saturable (17.5 microg of apoE/ml) and was not influenced by APOE genotype. High performance liquid chromatography analysis of cholesterol and cholesterol metabolites effluxed from neurons indicated that <25% of the released cholesterol was modified to polar products (e.g. 24-hydroxycholesterol) that diffuse from neuronal membranes. Thus, most cholesterol (approximately 75%) appeared to be effluxed from neurons in a native state via a transporter pathway. ATP-binding cassette transporters ABCA1, ABCA2, and ABCG1 were detected in neurons and neuroblastoma cell lines and expression of these cDNAs revealed that ABCA1 and ABCG1 stimulated cholesterol efflux to apoE discs. In addition, ABCA1 and ABCG1 expression in Chinese hamster ovary cells that stably express human APP significantly reduced Abeta generation, whereas ABCA2 did not modulate either cholesterol efflux or Abeta generation. These data indicate that ABCA1 and ABCG1 play a significant role in the regulation of neuronal cholesterol efflux to apoE discs and in suppression of APP processing to generate Abeta peptides.
Indications and morbidity of tube thoracostomy performed for traumatic and non-traumatic free pleural effusions in a low-income setting (2014)

TT is a safe and efficient procedure to drain pleural collections of both traumatic and non-traumatic origins, even in low-income settings. The incidence of complications could be reduced by a better training of general practitioners on this procedure.
Coordinating Mobile Robots By Applying Traffic Rules (2005)

This paper proposes a system to control mobile robots by applying traffic rules. The authors have constructed traffic rules to achieve safe and smooth movement of robots by collectively consid- ering information on the w ork environments of mo- bile objects such as mobile robots and persons. The traffic rules enable respective m obile robots using self-control to j udge their movement. The system a pplies the traffic rules to mobile robots in order to c oordinate a certain range of movement through maximum use of information on the environments of mobile robots s uch as their pas- sages, quantity, performances, and which are usually are known. Applying traffic rules to robot movement in order to coordinate r obots is a new proposal, enabling the realization of a system that needs no direct communi- cation such as a communications system. This paper first outlines a traffic rules application system for mobile robots, and explains how to con- struct the system by showing examples. Also, the paper discusses the effects of the system, and how to apply the traffic rules to actual systems. Finally, the paper explains the effectiveness of the system that applies the traffic rules, and the attainment of mobile robots using the system through experiments with mobile robots mounting ultrasonic sensors.
A 10&#x03BC;m pitch interconnection technology using micro tube insertion into Al-Cu for 3D applications (2011)

Future 3-D applications require a very low pitch for inter-strata vertical interconnection. The last International Technology Roadmap for Semiconductors (ITRS) assessment for vertical interconnection predicts a need for decreasing the interconnection pitch to 10μm. The room-temperature insertion technology has been proposed and developed using micro tubes as inserts to address many assembling difficulties of industrial process. In the present work, we study the mechanical and electrical behavior of a single micro tube insertion into Al-0.5Cu pads. A modified nanoindenter with a very accurate load and displacement control is used, coupled with an electrical measurement device to qualify the insertion process. Finally, the best Die To Wafer (D2W) parameters are determined thanks to a composed experimental design.
A Single Residue in Ebola Virus Receptor NPC1 Influences Cellular Host Range in Reptiles (2016)

Filoviruses are the causative agents of an increasing number of disease outbreaks in human populations, including the current unprecedented Ebola virus disease (EVD) outbreak in western Africa. One obstacle to controlling these epidemics is our poor understanding of the host range of filoviruses and their natural reservoirs. Here, we investigated the role of the intracellular filovirus receptor, Niemann-Pick C1 (NPC1) as a molecular determinant of Ebola virus (EBOV) host range at the cellular level. Whereas human cells can be infected by EBOV, a cell line derived from a Russell's viper (Daboia russellii) (VH-2) is resistant to infection in an NPC1-dependent manner. We found that VH-2 cells are resistant to EBOV infection because the Russell's viper NPC1 ortholog bound poorly to the EBOV spike glycoprotein (GP). Analysis of panels of viper-human NPC1 chimeras and point mutants allowed us to identify a single amino acid residue in NPC1, at position 503, that bidirectionally influenced both its binding to EBOV GP and its viral receptor activity in cells. Significantly, this single residue change perturbed neither NPC1's endosomal localization nor its housekeeping role in cellular cholesterol trafficking. Together with other recent work, these findings identify sequences in NPC1 that are important for viral receptor activity by virtue of their direct interaction with EBOV GP and suggest that they may influence filovirus host range in nature. Broader surveys of NPC1 orthologs from vertebrates may delineate additional sequence polymorphisms in this gene that control susceptibility to filovirus infection. IMPORTANCE Identifying cellular factors that determine susceptibility to infection can help us understand how Ebola virus is transmitted. We asked if the EBOV receptor Niemann-Pick C1 (NPC1) could explain why reptiles are resistant to EBOV infection. We demonstrate that cells derived from the Russell's viper are not susceptible to infection because EBOV cannot bind to viper NPC1. This resistance to infection can be mapped to a single amino acid residue in viper NPC1 that renders it unable to bind to EBOV GP. The newly solved structure of EBOV GP bound to NPC1 confirms our findings, revealing that this residue dips into the GP receptor-binding pocket and is therefore critical to the binding interface. Consequently, this otherwise well-conserved residue in vertebrate species influences the ability of reptilian NPC1 proteins to bind to EBOV GP, thereby affecting viral host range in reptilian cells.
Dynamic Service Provisioning in Elastic Optical Networks With Hybrid Single-/Multi-Path Routing (2012)

Empowered by the optical orthogonal frequency-division multiplexing (O-OFDM) technology, flexible online service provisioning can be realized with dynamic routing, modulation, and spectrum assignment (RMSA). In this paper, we propose several online service provisioning algorithms that incorporate dynamic RMSA with a hybrid single-/multi-path routing (HSMR) scheme. We investigate two types of HSMR schemes, namely HSMR using online path computation (HSMR-OPC) and HSMR using fixed path sets (HSMR-FPS). Moreover, for HSMR-FPS, we analyze several path selection policies to optimize the design. We evaluate the proposed algorithms with numerical simulations using a Poisson traffic model and two mesh network topologies. The simulation results have demonstrated that the proposed HSMR schemes can effectively reduce the bandwidth blocking probability (BBP) of dynamic RMSA, as compared to two benchmark algorithms that use single-path routing and split spectrum. Our simulation results suggest that HSMR-OPC can achieve the lowest BBP among all HSMR schemes. This is attributed to the fact that HSMR-OPC optimizes routing paths for each request on the fly with considerations of both bandwidth utilizations and lengths of links. Our simulation results also indicate that the HSMR-FPS scheme that use the largest slots-over-square-of-hops first path-selection policy obtains the lowest BBP among all HSMR-FPS schemes. We then investigate the proposed algorithms' impacts on other network performance metrics, including network throughput and network bandwidth fragmentation ratio. To the best of our knowledge, this is the first attempt to consider dynamic RMSA based on both online path computation and offline path computation with various path selection policies for multipath provisioning in O-OFDM networks.
Counteranion Sensitization Approach to Photoinitiated Free Radical Polymerization (2012)

A novel polymeric type II photoinitiator, namely poly(ethylene oxide) dimethylammonium thioxanthonemethyl-carboxylate (PEO-NH+(Me)2 TX-CH2COO–), possessing both photochromophoric and hydrogen donating groups in the structure was synthesized and characterized. In contrast to existing type II photoinitiators, the present photoinitiator initiates free radical polymerization by counteranion excitation even in the absence of added hydrogen donors. The photoinitiator can be applied to the polymerization of monomers soluble in organic solvents or water.
The “sweet” side of a long pentraxin: how glycosylation affects PTX3 functions in innate immunity and inflammation (2013)

Innate immunity represents the first line of defense against pathogens and plays key roles in activation and orientation of the adaptive immune response. The innate immune system comprises both a cellular and a humoral arm. Components of the humoral arm include soluble pattern recognition molecules (PRMs) that recognize pathogen-associated molecular patterns and initiate the immune response in coordination with the cellular arm, therefore acting as functional ancestors of antibodies. The long pentraxin PTX3 is a prototypic soluble PRM that is produced at sites of infection and inflammation by both somatic and immune cells. Gene targeting of this evolutionarily conserved protein has revealed a non-redundant role in resistance to selected pathogens. Moreover, PTX3 exerts important functions at the crossroad between innate immunity, inflammation, and female fertility. The human PTX3 protein contains a single N-glycosylation site that is fully occupied by complex type oligosaccharides, mainly fucosylated and sialylated biantennary glycans. Glycosylation has been implicated in a number of PTX3 activities, including neutralization of influenza viruses, modulation of the complement system, and attenuation of leukocyte recruitment. Therefore, this post translational modification might act as a fine tuner of PTX3 functions in native immunity and inflammation. Here we review the studies on PTX3, with emphasis on the glycan-dependent mechanisms underlying pathogen recognition and crosstalk with other components of the innate immune system.
What a difference a cloud makes: cognitive abilities, tasks, and the search results interface (2009)

Introduction. The objective of this study is to expand our understanding of the relationships between selected cognitive abilities, search result interfaces, and tasks. The overarching objective is to understand how to match search result presentations with different tasks and user contexts.
Method. Twenty three participants conducted four search tasks of two types and used two interfaces (List and Overview) to refine and examine search results. Clickthrough data were recorded. This controlled study employed a mixed model design, with two within-subject factors (task and interface) and two between-subject factors (two cognitive abilities: memory span and verbal closure).
Analysis. Quantitative analyses were carried out by means of the statistical package SPSS. Specifically, multivariate analysis of variance with repeated measures and non-parametric tests were performed on the collected data. 
Results. The overview of search results appeared to have benefited users in several ways. It made searchers faster; it facilitated formulation of more effective queries and helped to assess search results. The List interface discriminated between searchers with different cognitive abilities. Searchers with higher cognitive abilities were fastest in less demanding situations and expended more search effort in more demanding situations (in the List interface and on more complex tasks).
Conclusions. These findings have implications for the design of search interfaces. They suggest benefits of providing result overviews. They also suggest the importance of considering cognitive abilities in the design of search results presentation and interaction.
Establishment and characterization of bone marrow stromal cell lines that support osteoclastogenesis (1995)

We established bone marrow stromal cell lines that support tartrate-resistant acid phosphatase-positive multinucleated cell [TRAcP(+)MNC] formation by using transgenic mice harboring simian virus 40 large T antigen gene. The morphology of these TM cell lines (large T-immortalized marrow cells) was spindle-like at sparse cell density, whereas it became smaller and cuboidal at confluence. The TM cell lines showed diverse ranges of activity in supporting TRAcP(+)MNC formation when they were examined in the cocultures with spleen cells in the presence of 1 alpha,25-dihydroxyvitamin D3. Among these cell lines, TM8 supported the TRAcP(+)MNC formation most efficiently (from 400-1500 cells/well) when cocultured with spleen cells. Another bone marrow-derived cell line, TM5, supported TRAcP(+)MNC formation in the coculture assay, whereas the efficiency was approximately one fifth that of TM8. Interestingly, TM8 cells also supported TRAcP(+)MNC formation even in the cocultures at low serum concentration (0.5% fetal bovine serum) with an efficiency yielding over 200 TRAcP(+)MNCs/well. TM8 cells expressed certain levels of macrophage colony-stimulating factor and stem cell factor messenger RNAs (mRNAs), but low levels of c-fms mRNA. Expression of c-kit mRNA in TM5 and TM8 cells was undetectable. 1 alpha,25-Dihydroxyvitamin D3 treatment enhanced the expression of osteopontin mRNA more than 10-fold in these cells, indicating the presence of the receptor for this steroid. These TRAcP(+)MNCs, which developed in the cocultures of the TM8 and spleen cells, formed pits when cultured on bone slices, indicating that they were capable of resorbing bone. The various levels of expression of these genes and the difference in the supporting activities for the TRAcP(+)MNC development in the diverse TM cell lines suggest the heterogeneity in the marrow cell populations in vivo regarding their activity in supporting osteoclastogenesis.