gebhart/patrepeval huggingface dataset:
Enabling secure high-performance wireless ad hoc networking (2003)

A revolution has occurred in wireless communications over the last decade. Advances in processing power have enabled widespread deployment of radio networks as well as portable devices that can make use of such networks. Wireless networks have become more convenient and affordable and have spread to even fairly stationary applications such as home networking and community networking. Ad hoc networks can extend the range of such wireless networks: in an ad hoc network nodes cooperate to dynamically establish routing among themselves a packet sent by one node may be forwarded in turn by a sequence of other nodes allowing the packet to reach a destination beyond the sender wireless transmission range. This thesis discusses improvements to service in ad hoc network routing. Since different networks require different types of service, I propose several mechanisms to improve service in various network conditions. One example of service is Quality-of-Service (QoS ) since certain networks may desire some flows to have priority over other flows. Many of the mechanisms presented here make no distinction between lower and higher priority traffic and in may evaluation I only examine performance metrics aggregated over all flows rather than the performance of a few select flows. Another area encompassed by service is security. In particular when an attacker is present in the network a protocol that provides security against such an attacker should provide better service than one that does not. For example a secure protocol should deliver more packets incur less overhead or conserve overall network power usage better than in insecure protocol when the network is under attack. As a network experiences attack a secure network routing protocol may continue to provide some level of service whereas a traditional network routing protocol may fail completely.
Characterization of sphingosine kinase (SK) activity in Saccharomyces cerevisiae and isolation of SK-deficient mutants (1998)

Sphingosine kinase (SK) catalyses the phosphorylation of sphingosine to generate sphingosine 1-phosphate, which is a second messenger involved in the proliferative responses of mammalian cells. Although the yeast Saccharomyces cerevisiae has similar phosphorylated sphingoid bases which appear to be involved in growth regulation and the response to stress, SK activity had not been previously demonstrated in yeast. In this study, an in vitro system was set up to characterize yeast SK activity. Activity was detected in the cytosol at neutral pH and 37 degreesC. Yeast SK phosphorylated the sphingoid bases sphingosine, dihydrosphingosine and phytosphingosine. (d,l)-threo-dihydrosphingosine, an inhibitor of mammalian SK, did not inhibit the yeast enzyme. Unique properties of yeast SK were an optimal temperature of 43 degreesC, and in vivo activation during nutrient deprivation. Spontaneous mutants with diminished SK activity were isolated utilizing a screen for resistance to sphingosine in a sphingosine-phosphate-lyase deletion background. Abnormal growth and heat sensitivity were observed in these mutants. These findings suggest that SK may function as a stress-response protein in yeast.
Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs (1995)

Human immunodeficiency virus type 1 (HIV-1) gene expression is modulated by both viral and cellular factors. A regulatory element in the HIV-1 long terminal repeat known as TAR, which extends from nucleotides -18 to +80, is critical for the activation of gene expression by the transactivator protein, Tat. RNA transcribed from TAR forms a stable stem-loop structure which serves as the binding site for both Tat and cellular factors. Although TAR RNA is critical for Tat activation, the role that TAR DNA plays in regulating HIV-1 gene expression is not clear. Several studies have demonstrated that TAR DNA can bind cellular proteins, such as UBP-1/LBP-1, which repress HIV-1 gene expression and other factors which are involved in the generation of short, nonprocessive transcripts. In an attempt to characterize additional cellular factors that bind to TAR DNA, a lambda gt11 expression cloning strategy involving the use of a portion of TAR DNA extending from -18 to +28 to probe a HeLa cDNA library was used. We identified a cDNA, designated TAR DNA-binding protein (TDP-43), which encodes a cellular factor of 43 kDa that binds specifically to pyrimidine-rich motifs in TAR. Antibody to TDP-43 was used in gel retardation assays to demonstrate that endogenous TDP-43, present in HeLa nuclear extract, also bound to TAR DNA. Although TDP-43 bound strongly to double-stranded TAR DNA via its ribonucleoprotein protein-binding motifs, it did not bind to TAR RNA extending from +1 to +80. To determine the function of TDP-43 in regulating HIV-1 gene expression, in vitro transcription analysis was performed. TDP-43 repressed in vitro transcription from the HIV-1 long terminal repeat in both the presence and absence of Tat, but it did not repress transcription from other promoters such as the adenovirus major late promoter. In addition, transfection of a vector which expressed TDP-43 resulted in the repression of gene expression from an HIV-1 provirus. These results indicate that TDP-43 is capable of modulating both in vitro and in vivo HIV-1 gene expression by either altering or blocking the assembly of transcription complexes that are capable of responding to Tat.
Circularly Polarized Patch Antenna Array Fed by Coplanar Waveguide (2004)

A novel design of a circularly polarized linear patch antenna array fed by a coplanar waveguide (CPW) is presented. The array elements are placed in the direction transverse to the feeding CPW line and are excited by a couple of 100 /spl Omega/ slotlines, which are combined to form the 50 /spl Omega/ feeding CPW. The circularly polarized radiation is obtained by placing similar perturbation segments to each of the array elements. The simulated and measured axial ratios, return losses, and radiation patterns are presented for an 1 /spl times/ 2 and an 1 /spl times/ 4 arrays with good results. The proposed feeding structure can be extended to design a two dimensional array with good front-to-back ratio on a single substrate with only one straight CPW line.
A Specific Domain of the Chikungunya Virus E2 Protein Regulates Particle Formation in Human Cells: Implications for Alphavirus Vaccine Design (2012)

Virus-like particles (VLPs) can be generated from Chikungunya virus (CHIKV), but different strains yield variable quantities of particles. Here, we define the genetic basis for these differences and show that amino acid 234 in E2 substantially affects VLP production. This site is located within the acid-sensitive region (ASR) known to initiate a major conformational change in E1/E2. Selected other mutations in the ASR, or changes in pH, also increased VLP yield. These results demonstrate that the ASR of E2 plays an important role in regulating particle generation.
Basics of Cutaneous Wound Repair (1993)

The dynamic reciprocity among cells, cytokines, and matrix material helps explain how integrated wound healing networks are sequential as well as tightly controlled.
A language with distributed scope (1995)

Obliq is a lexically-scoped, untyped, interpreted language that supports distributed object-oriented computation. Obliq objects have state and are local to a site. Obliq computations can roam over the network, while maintaining network connections. Distributed lexical scoping is the key mechanism for managing distributed computation.
The Role of Functional Neuroimaging in the Neuropsychology of Depression (2001)

Depressed individuals show impaired performance in tests of attention and concentration. They also exhibit PET resting state abnormalities in dorsal prefrontal cortex and anterior cingulate, regions known to be substrates of attentional processing in healthy individuals. This chapter outlines a strategy to study neuropsychological mechanisms in emotional disorders using functional imaging methods. It reviews evidence strongly implicating the dorsolateral prefrontal cortex, particularly in the right hemisphere, as a key brain structure in emotion/cognition interactions in negative mood states. It will be argued that this neocortical region is a crucial convergence zone, being the substrate of sustained attention to the external environment, and the main target of limbic-cortical influences during changes in mood state across health and disease.
Solid-State Lithium Metal Batteries Promoted by Nanotechnology: Progress and Prospects (2017)

Driven by an increasing demand on storage devices with higher energy outputs and better safety, solid-state lithium metal batteries have shown their potential to replace the traditional liquid-based Li-ion batteries and power the future storage market. In this Perspective, we will show our views on improving this emerging battery system by nanoscience. Discussions will be placed, from both scientific and engineering points of view, on the fundamentals and problems of the battery and its key components. The corresponding “nano” strategies will also be addressed, as well as recent progress in related fields including materials synthesis, battery design, and characterization techniques. With these efforts, we want to provide insights on rational design of the solid-state Li metal battery for optimized performance.
Interleukin 6 and its receptor in the immune response and hematopoiesis (1990)

Interleukin 6 (IL-6) plays critical roles in the immune response and hematopoiesis. It is a potent B cell differentiation factor inducing antibody-forming plasma cells. It enhances interleukin 3-induced proliferation of hematopoietic stem cells. Furthermore, IL-6 induces maturation of megakaryocytes. In IL-6 transgenic mice, a massive polyclonal plasmacytosis and an increase in the number of mature megakaryocytes in the bone marrow were observed. The data indicated that deregulated expression of the IL-6 gene induced a polyclonal plasmacytosis and could be involved in the oncogenesis of plasma cell neoplasias. IL-6 receptor (IL-6R) was molecularly cloned and found to be an immunoglobulin superfamily having an MW of 80 kDa. Upon the binding of IL-6 to its 80 kDa IL-6R, a second non-binding molecule, gp130 was shown to associate with IL-6R. The complex of IL-6 and soluble IL-6R lacking both transmembrane and cytoplasmic domains could bind gp130 and transduce the signal. The results indicate that the IL-6R system consists of two polypeptide chains: one is an 80 kDa ligand-binding molecule and the other is a possible signal transducer, gp130.
Manometric Calibration and Comparison of TonoLab and TonoPen Tonometers in Rats With Experimental Glaucoma and in Normal Mice (2006)

In mouse and rat eyes, including rats with chronic IOP elevation, the TonoLab accurately reflected manometrically set IOP in an efficient manner.
Expression of enteropeptidase in differentiated enterocytes, goblet cells, and the tumor cells in human duodenum (2003)

Enteropeptidase (EP) is a serine proteinase and activates trypsinogen to trypsin, thus playing an important role in food digestion. Nevertheless, the localization of EP is still controversial, likely due to a lack of studies using specific antibodies against EP. The aim of this study was to define cellular localization of EP in human duodenum and expression in tumor cells at the duodenal region. Immunohistochemical staining for resected tissues was performed with two antibodies against recombinant EP light and heavy chains, respectively. In situ hybridization was done with two RNA probes that include either the light or the heavy chain sequences of proEP, respectively. The two antibodies reacted with enterocytes, accentuated on the brush border, and goblet cells, with increasing intensity from the bottom of crypts to the top of villi. Paneth cells, neuroendocrine cells, Brunner's glands, lymphocytes, smooth muscle, or connective tissue did not react with the antibodies. The two RNA probes detected EP mRNA expression only in enterocytes and goblet cells. EP is produced in enterocytes and goblet cells, and the localization on the brush border of the cells is reasonable for the physiological activation of digestive enzymes. Interestingly, the antibodies reacted with tumor cells in duodenal polyps and adenocarcinoma at the duodenum but not in Brunner's gland adenoma. EP seems to be a marker of differentiated enterocytes and goblet cells, which suggests the existence of a common progenitor of these cells. Furthermore, EP may be a useful marker of tumor cells originating from these cells.
Differential Expression of Thrombospondin (THBS1) in Tumorigenic and Nontumorigenic Prostate Epithelial Cells in Response to a Chromatin-Binding Soy Peptide (2011)

The chemopreventive properties of the chromatin-binding soy peptide, lunasin, are well documented, but its mechanism of action is unclear. To elucidate the mechanism by which lunasin reduces tumor foci formation in cultured mammalian cells, nontumorigenic (RWPE-1) and tumorigenic (RWPE-2) human prostate epithelial cells were treated with lunasin followed by gene expression profiling and characterization of the chromatin acetylation status for certain chemopreventive genes. The genes HIF1A, PRKAR1A, TOB1, and THBS1 were upregulated by lunasin in RWPE-1 but not in RWPE-2 cells. Using histone acetyltransferase (HAT) assays with acid-extracted histones as templates, we showed that lunasin specifically inhibited H4K8 acetylation while enhanced H4K16 acetylation catalyzed by HAT enzymes p300, PCAF, and HAT1A. These results suggest a novel mechanism for lunasin-dependent upregulation of gene expression. Chromatin immunoprecipitation (ChIP) revealed hypoacetylation of H4K16 in RWPE-2 cells, specifically at the 5' end of THBS1 containing a CpG island. Moreover, bisulfite PCR (BSP) and subsequent DNA sequencing indicated that this CpG island was hypomethylated in RWPE-1 but hypermethylated in RWPE-2 cells. Histone hypoacetylation and DNA hypermethylation in the 5' region of THBS1 may explain the inability of lunasin to upregulate this gene in RWPE-2 cells.
Tolerability comparison of adapalene gel, 0.3% versus tazarotene cream, 0.05% in subjects with healthy skin. (2007)

Adapalene gel 0.3% is very well-tolerated with good cosmetic acceptability.
Experiment-based modeling, simulation and validation of interactions between virtual walkers (2009)

An interaction occurs between two humans when they walk with converging trajectories. They need to adapt their motion in order to avoid and cross one another at respectful distance. This paper presents a model for solving interactions between virtual humans. The proposed model is elaborated from experimental interactions data. We first focus our study on the pair-interaction case. In a second stage, we extend our approach to the multiple interactions case. Our experimental data allow us to state the conditions for interactions to occur between walkers, as well as each one's role during interaction and the strategies walkers set to adapt their motion. The low number of parameters of the proposed model enables its automatic calibration from available experimental data. We validate our approach by comparing simulated trajectories with real ones. We also provide comparison with previous solutions. We finally discuss the ability of our model to be extended to complex situations.
Hiding seams in high dynamic range panoramas (2006)

This poster presents a simple and efficient method for stitching sections of a high dynamic range (HDR) panorama, taking advantage of perception to minimize visible seams. Most approaches to panoramic stitching require exact or nearly exact overlay of the input images in order to produce a seamless blend. Most methods also require identical image exposures, and do not work in HDR. We overcome these limitations with an approach that is fast and memory-efficient, working on a scanline at a time within each overlapping rectangle. Input to the algorithm is a set of HDR images with correspondence points between each pair to be joined, one point pair per seam. These correspondence pairs may be selected manually, or generated automatically using a technique such as [Pollefeys & Van Gool 2002].
Isolation and Characterization of the Kininogen-binding Protein p33 from Endothelial Cells (1996)

Kininogens, the precursor proteins of the vasoactive kinins, bind specifically, reversibly, and saturably to platelets, neutrophils, and endothelial cells. Two domains of the kininogens expose major cell binding sites: domain D3 that is shared by H- and L-kininogen and domain D5H that is exclusively present in H-kininogen. Previously we have mapped the kininogen cell binding sites to 27 residues of D3 ("LDC27") and 20 residues of D5H ("HKH20"", respectively (Herwald, H., Hasan, A. A. K., Godovac-Zimmermann, J., Schmaier, A. H., and Müller-Esterl, W. (1995) J. Biol. Chem. 270, 14634-14642; Hasan, A. A. K., Cines, D. B., Herwald, H., Schmaier, A. H., and Müller-Esterl, W. (1995) J. Biol. Chem. 270, 19256-19261). The corresponding kininogen acceptor site(s) exposed by the cell surfaces are still poorly defined. Using a non-ionic detergent, Nonidet P-40, we have been able to solubilize kininogen binding sites from an endothelial cell line, EA.hy926, in their functionally active form. Affinity chromatography of the solubilized kininogen binding sites on HKH20, a synthetic peptide representing the D5H cell binding site, allowed us to isolate a 33-kDa protein ("p33") that binds specifically and reversibly to H-kininogen with a KD (apparent dissociation constant) of 9 +/- 2 nM. Preparative SDS electrophoresis followed by NH2-terminal amino acid sequence analysis identified the kininogen-binding protein p33 as the gC1q receptor ("gC1qR"), an extrinsic membrane protein that interacts with the globular domains of the complement component C1q. The purified p33 binds C1q with moderate affinity, KD = 240 +/- 10 nM. Recombinant expression of the corresponding cDNA in Escherichia coli demonstrated that p33 binds H-kininogen, but not L-kininogen. Peptide HKH20 but not peptide LDC27 inhibited binding of H-kininogen to the recombinant p33 in a concentration-dependent manner, indicating that H-kininogen binds to p33 via domain D5H. Recombinant p33 efficiently inhibited the binding of H-kininogen to EA.hy926 cells. Factor XII, but not prekallikrein, competed with H-kininogen binding to p33. These findings suggest that an endothelial binding protein mediates the assembly of critical components of the kinin-generating pathway on the surface of endothelial cells, thereby linking the early events of kinin formation and complement activation.
Endoscopic Treatment of Early-Stage Lung Cancer (2000)

The identification of early-stage lung cancer provides no advantage if we have little to offer the patient short of traditional therapy. The value of newer treatment techniques and methods requires verification.
Comparison of the Transcription and Replication Strategies of Marburg Virus and Ebola Virus by Using Artificial Replication Systems (1999)

The members of the family Filoviridae, Marburg virus (MBGV) and Ebola virus (EBOV), are very similar in terms of morphology, genome organization, and protein composition. To compare the replication and transcription strategies of both viruses, an artificial replication system based on the vaccinia virus T7 expression system was established for EBOV. Specific transcription and replication of an artificial monocistronic minireplicon was demonstrated by reporter gene expression and detection of the transcribed and replicated RNA species. As it was shown previously for MBGV, three of the four EBOV nucleocapsid proteins, NP, VP35, and L, were essential and sufficient for replication. In contrast to MBGV, EBOV-specific transcription was dependent on the presence of the fourth nucleocapsid protein, VP30. When EBOV VP30 was replaced by MBGV VP30, EBOV-specific transcription was observed but with lower efficiency. Exchange of NP, VP35, and L between the two replication systems did not lead to detectable reporter gene expression. It was further observed that neither MBGV nor EBOV were able to replicate the heterologous minigenomes. A chimeric minigenome, however, containing the EBOV leader and the MBGV trailer was encapsidated, replicated, transcribed, and packaged by both viruses.
Secreted Antigens of Mycobacterium tuberculosis: Characterization with T Lymphocytes from Patients and Contacts after Two-Dimensional Separation (1992)

Little is known about T cell antigens involved in immunity against Mycobacterium tuberculosis. Most model systems use in vitro culture of human T lymphocytes with bacterial lysates or secreted proteins as antigens. In this study, proteins from 3-week-old M. tuberculosis culture filtrates were separated by two-dimensional PAGE and subsequently transferred into soluble phase. The resulting 480 fractions were screened with T lymphocytes from tuberculosis patients and healthy contacts. T cells from all 9 patients and from 8 of 10 tuberculin-positive contacts preferentially responded to a cluster of acidic proteins (pI 4-5) with molecular masses of 30-100 kDa, although they also recognized a number of other fractions. In contrast, of 7 tuberculin-negative contacts, 4 were not and 3 were only weakly stimulated by this cluster region. Therefore, this distinct cluster of secreted proteins seems to comprise dominant T cell antigens of M. tuberculosis.
The role of an autoantigen, histidyl-tRNA synthetase, in the induction and maintenance of autoimmunity. (1990)

Patients with systemic autoimmune diseases make specific autoantibodies that are directed against self structures. According to one view, these autoantibodies arise as a result of an immune response to foreign antigens such as infectious agents that share, by molecular mimicry, common structures with host proteins. An alternative view is that the target autoantigen itself initiates, selects, and sustains autoantibody synthesis. We show here that anti-Jo-1 autoantibodies directed against histidyl-tRNA synthetase in the human autoimmune muscle disease polymyositis undergo, in addition to spectrotype broadening and class switching, the sine qua non of an immune response to the target antigen--affinity maturation to that antigen. We demonstrate further that these autoantibodies, unlike anti-synthetase antibodies induced in mice immunized with heterologous antigen, bind only nonlinear epitopes on the native human synthetase that remain exposed when the enzyme is complexed to tRNA(His). These data suggest that the native target autoantigen itself has played a direct role in selecting and sustaining the autoantibody response and sharply restrict the time and the way in which a molecular mimic might act to provoke autoantibodies.
Origin of the matching effect in a superconducting film with a hole array (2007)

We investigate the origin of the matching effect observed in superconducting Nb films containing regular arrays of holes near the zero-field critical temperature. We find ``dips'' in the resistance vs magnetic field curves at matching fields where the magnitude of the magnetic flux threading each unit cell is an integer number of the flux quantum. By comparing the magnetic field dependences of the resistance and critical temperature in perpendicular and parallel magnetic field directions, we find that the matching effect in Nb films containing triangular hole arrays originates from hole-induced suppression of the critical temperature rather than the widely assumed flux pinning enhancement.