gebhart/patrepeval huggingface dataset:
Characterization of extracellular matrix components from the desiccation-tolerant cyanobacterium <i>Nostoc commune</i> (2017)

The terrestrial cyanobacterium Nostoc commune forms macroscopic colonies in its natural habitats, and these colonies consist of both cellular filaments and massive extracellular matrixes. In this study, the biochemical features of the extracellular matrix components were investigated. Naturally growing N. commune was tolerant to desiccation, and produced massive extracellular polysaccharides that contained both neutral sugars and glucuronic acid as constituent monosaccharides. The extracellular polysaccharide contents and desiccation tolerance were compared in laboratory culture strains of Nostoc species. The laboratory culture of N. commune strain KU002 was sensitive to desiccation and produced smaller amounts of extracellular polysaccharides, unlike the field-isolated naturally growing colonies. Nostoc punctiforme strain M-15, which is genetically closed to N. commune, was able to tolerate desiccation, although the other Nostoc strains were desiccation-sensitive. A laboratory culture strain of the aquatic cyanobacterium Nostoc sphaericum produced massive extracellular polysaccharides but was sensitive to desiccation, suggesting that extracellular matrix production is not enough to make this strain tolerant to desiccation. WspA (water stress protein) and SodF (superoxide dismutase) were found to be characteristic protein components of the extracellular matrix of N. commune. Because the WspA proteins were heterogeneous, the wspA genes were highly diverse among the different genotypes of N. commune, although the sodF gene was rather conservative. The heterogeneity of the WspA proteins suggests their complex roles in the environmental adaptation mechanism in N. commune.
Towards the design of a biped jogging robot (2002)

Deals with the design and control of an anthropomorphic autonomous biped robot. The objective is to realize a dynamically stable, three-dimensional walking and jogging motion. The design, sensors and electronics of the robot are introduced. Particular emphasis has been devoted to achieving a high power-to-weight ratio. The corresponding methods for weight reduction are presented. The control scheme is discussed. It is based on the method of feedback linearization employing the equations of motion of the system.
all- <i>Trans</i> -Retinoic Acid Reduces Neointimal Formation and Promotes Favorable Geometric Remodeling of the Rat Carotid Artery After Balloon Withdrawal Injury (1998)

atRA reduces neointimal mass and elicits favorable geometric remodeling of the injured rat carotid artery.
Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration (2010)

Lens epithelium-derived growth factor (LEDGF) fusion proteins can direct HIV-1 DNA integration to novel sites in the host genome. The C terminus of LEDGF contains an integrase binding domain (IBD), and the N terminus binds chromatin. LEDGF normally directs integrations to the bodies of expressed genes. Replacing the N terminus of LEDGF with chromatin binding domains (CBDs) from other proteins changes the specificity of HIV-1 DNA integration. We chose two well-characterized CBDs: the plant homeodomain (PHD) finger from ING2 and the chromodomain from heterochromatin binding protein 1alpha (HP1alpha). The ING2 PHD finger binds H3K4me3, a histone mark that is associated with the transcriptional start sites of expressed genes. The HP1alpha chromodomain binds H3K9me2,3, histone marks that are widely distributed throughout the genome. A fusion protein in which the ING2 PHD finger was linked to the LEDGF IBD directed integrations near the start sites of expressed genes. A similar fusion protein in which the HP1alpha chromodomain was linked to the LEDGF IBD directed integrations to sites that differed from both the PHD finger fusion-directed and LEDGF-directed integration sites. The ability to redirect HIV-1 DNA integration may help solve the problems associated with the activation of oncogenes when retroviruses are used in gene therapy.
Two Sorting Motifs, a Ubiquitination Motif and a Tyrosine Motif, Are Involved in HIV-1 and Simian Immunodeficiency Virus Nef-Mediated Receptor Endocytosis (2011)

HIV-1 and SIV Nef proteins downregulate cell surface CD4 and MHC class I (MHC-I) molecules of infected cells, which are necessary for efficient viral replication and pathogenicity. We previously reported that K144 in HIV-1 Nef is di-ubiquitinated, and K144R substitution impairs Nef-mediated CD4 downregulation. In this report, we extend the role of ubiquitination at this lysine residue from Nef-mediated CD4 downregulation to Nef-mediated MHC-I downregulation and from HIV Nef to SIV Nef. All HIV-1 Nef mutants that contain K144R substitution are inactive in MHC-I downregulation. Tested MHC-I alleles include HLA-ABC endogenously expressed and HLA-A2 exogenously expressed in Jurkat T cells. CD4 downregulation by SIV Nef involves K176 that aligns with K144 in HIV-1 Nef, as well as an N-terminal tyrosine motif Y28Y39 not present in HIV-1 Nef. Dual mutation at K176 and Y28Y39 completely impaired SIV Nef-mediated CD4 and MHC-I downregulation, whereas a single mutation at K176 or Y28Y39 did not. The involvement of tyrosine motif in SIV Nef-mediated CD4 and MHC-I downregulation prompted us to investigate a putative tyrosine motif (Y202Y/F203) in HIV-1 Nef that is conserved among HIV-1 species. Single mutation at the tyrosine motif Y202F203 in HIV-1 Nef (NA7) greatly impaired Nef-mediated CD4 downregulation, which is similar to what we observed previously with the single mutation at lysine K144. Thus, our study demonstrated that Nef-mediated receptor endocytosis involves the ubiquitination motif and tyrosine motif.
Primal Fusion Thought Networking (2009)

Our thoughts are fleeting and immaterial, this mysterious stuff that's locked away in our heads. Painstakingly, we collect our thoughts and transform them into words and documents. This transformation from thought into action is time-consuming and expensive. Thinking is a decidedly "offline" and manual process. What would happen if you could instead make your thoughts tangible and concrete? What if you could collect your thoughts as readily as you can search online? What if your thoughts could self-organize around your tasks while you're off doing other things? Thought networking is the idea that's driving our efforts at Primal Fusion to explore these big questions. In this demonstration Primal Fusion will show the thought networking platform and its applications. This will be an interactive demonstration, where users are invited to try out their own thoughts and actions on the platform. A poster will provide a high-level technical description of the semantic platform components.
119Sn Mössbauer spectroscopy study of the mechanism of lithium reaction with self-organized Ti1/2Sn1/2O2 nanotubes (2014)

Novel self-organized Ti₁/₂Sn₁/₂O₂ nanotubes can be produced by the electrochemical anodization of co-sputtered Ti-Sn thin-films. Combined X-ray photoelectron spectroscopy and (119)Sn Mössbauer spectroscopy of pristine samples evidenced the octahedral substitution of Sn(4+) for Ti(4+) in the TiO₂ structure. In addition to the improved lithium storage behaviour of the Ti₁/₂Sn₁/₂O₂ nanotubes, ex situ(119)Sn Mössbauer spectroscopy of cycled electrodes has sufficiently confirmed that no decomposition of the Ti₁/₂Sn₁/₂O₂ structure occurred, and that no Li-Sn phase was formed during the discharge, corroborating that the electrochemical reaction is due exclusively to Li(+) insertion into the Ti₁/₂Sn₁/₂O₂ nanotubes in the 1 ≤ U/V ≤ 2.6 voltage range.
Compact Swelling in Bi <sub>1.4</sub> Pb <sub>0.6</sub> Sr <sub>2</sub> Ca <sub>2</sub> Cu <sub>3.6</sub> O <sub> <i>y</i> </sub> During the Formation of High‐ <i>T</i> <sub>c</sub> Superconducting Phase (1992)

Compact swelling in Pb‐doped Bi‐Sr‐Ca‐Cu‐O superconductor has been studied by observing the effects of the size of calcined powders, volatilization of materials, and sintering of high‐ T c (2223) powders. The bulk density increases at the early stage of sintering, for about 20 h, and then decreases. Densification occurs when the low‐ T c (2212) phase and a liquid phase exist, whereas dedensification occurs with the formation of the 2223 phase regardless of the presence of the liquid. Gas evolution from specimens does not appear to be responsible for compact swelling. Compact swelling is explained by anisotropic growth of thin, platelike 2223 grains in random orientation. When 2223 grains grow in a preferred direction, compact swelling is suppressed.
Regulation of Cyclooxgenase-2 mRNA Stability by Taxanes (2003)

Taxanes are widely used to treat malignancies and are known to modulate the transcription of several genes. We investigated the effects of taxanes (docetaxel and paclitaxel) on cyclooxygenase-2 (COX-2) transcription and mRNA stability in human mammary epithelial cells. As reported previously for paclitaxel, docetaxel stimulated COX-2 transcription by an AP-1-dependent mechanism. Treatment with taxanes also enhanced the stability of COX-2 mRNA. To define the mechanism by which taxanes stabilized COX-2 mRNA, transient transfections were carried out using luciferase expression constructs containing the COX-2 3'-untranslated region (3'-untranslated region (UTR)). The stabilizing effects of taxanes were localized to the AU-rich region of COX-2 3'-UTR. RNA binding studies indicated that taxanes stimulated the binding of HuR to the AU-rich region of the COX-2 3'-UTR. Overexpression of antisense HuR suppressed taxane-mediated induction of COX-2 3'-UTR activity. We next investigated the signal transduction pathway responsible for taxane-mediated induction of COX-2. Taxanes enhanced protein kinase C activity; overexpressing dominant negative PKC-alpha suppressed taxane-mediated stimulation of both COX-2 3'-UTR and 5'-promoter activities. Interestingly, ERK1/2, JNK, and p38 MAPKs were important for taxane-mediated activation of COX-2 transcription, but only p38 MAPK appeared to be responsible for the increase in COX-2 mRNA stability. MAPKAPK-2, a known target of p38 MAPK, contributed to increased COX-2 mRNA stability following taxane treatment. SB 202190, a selective p38 MAPK inhibitor, and dexamethasone suppressed taxane-mediated stimulation of the COX-2 3'-UTR and binding of HuR. Taken together, these data indicate that taxanes induce COX-2 by stimulating both transcription and mRNA stability. To the best of our knowledge, this is the first evidence that taxanes can promote stabilization of mRNA in addition to modulating gene transcription.
Segment-based packet combining in a cluster: To combine or not to combine? (2010)

Segment-based packet combining schemes are an attractive approach towards link-layer packet combining for memory-constrained sensor nodes. We consider the usage of segment-based combining schemes in a dense cluster of relayers. We show that with two or more relayers the segment-based scheme provides a higher probability for the cluster to possess the full information sent by the source node than an unsegmented protocol. Secondly, to achieve an (almost) perfect average per-segment diversity, it suffices if each relayer transmits only once.
Global river inflow with Navy Coastal Ocean Model (2005)

One of the primary concerns driving the development of U.S. Navy global models has been improved performance and nesting support in shelf and nearshore regions with short notice applicability anywhere on the globe. A global implementation of the Navy Coastal Ocean Model (NCOM) is a product of some of the efforts to meet this need. One purpose of Global NCOM is to provide a global capability for initializing, nesting, and evaluating fixed and relocatable coastal ocean models. In support of that objective, a database of river flow estimates is needed. Perry et al. (1996) provides a start with estimates of annual mean river discharges for 981 of the largest global rivers. However, many rivers exhibit a strong seasonal variability, which we would like to reflect in our ocean models. Through the use of multiple Internet sources and published data sets we have expanded on the Perry (1996) data to provide a global database of monthly mean river discharge and incorporated this data in global and nested NCOM runs. Where sufficient data is unavailable to construct monthly means, a seasonal cycle is imputed from nearby rivers and scaled to the appropriate annual mean. Real time discharge rates are routinely available for almost no rivers outside of the United States, so a monthly mean is likely to be the most appropriate estimate of real time flow for analyses and forecasts in most areas. The monthly river outflow can contribute to more accurate seasonal representation of areas near coastlines. Seasonality particularly affects the polar areas, where river outflow can become quite small during winter months and quite large during the summer melting season. Multiannual daily USGS observations for selected US rivers are used to quantify the improvement in estimation of daily flow by the monthly means versus a multiannual mean. Case studies examine the impact of river input into NCOM.
Push-based information delivery in two stage satellite-terrestrial wireless systems (2001)

One of the prominent objectives of National/Global Information Infrastructure is to provide all types of users global access to information. Satellite broadcast data delivery has inherent advantages, such as scalability and location independent availability, in achieving this objective. However, users need expensive and cumbersome equipment to receive and transmit satellite signals. Furthermore, as the amount of information being broadcast increases, average user latency increases as well. Often, users in a geographical locality have similar interests, which can be better served by employing a local broadcast schedule. In this context, a two stage satellite terrestrial wireless broadcast system can provide more efficient service in terms of lower average user latency and cheaper and more convenient user equipment. In such a system, the main server broadcasts information via satellite to the geographically distributed local ground stations. Every ground station has limited buffer capacity to store the data broadcast by the satellite. According to their buffer content, and the interests of their users, local stations deliver the information to their users via terrestrial wireless channel. We develop novel methods for the joint cache management and scheduling problem encountered in these systems. Our results demonstrate that such two stage systems are feasible and they can provide more efficient data delivery compared to the single stage systems.
Pharmaceutical and pharmacological importance of peptide transporters (2008)

Peptide transport is currently a prominent topic in membrane research. The transport proteins involved are under intense investigation because of their physiological importance in protein absorption and also because peptide transporters are possible vehicles for drug delivery. Moreover, in many tissues peptide carriers transduce peptidic signals across membranes that are relevant in information processing. The focus of this review is on the pharmaceutical relevance of the human peptide transporters PEPT1 and PEPT2. In addition to their physiological substrates, both carriers transport many beta-lactam antibiotics, valaciclovir and other drugs and prodrugs because of their sterical resemblance to di- and tripeptides. The primary structure, tissue distribution and substrate specificity of PEPT1 and PEPT2 have been well characterized. However, there is a dearth of knowledge on the substrate binding sites and the three-dimensional structure of these proteins. Until this pivotal information becomes available by X-ray crystallography, the development of new drug substrates relies on classical transport studies combined with molecular modelling. In more than thirty years of research, data on the interaction of well over 700 di- and tripeptides, amino acid and peptide derivatives, drugs and prodrugs with peptide transporters have been gathered. The aim of this review is to put the reports on peptide transporter-mediated drug uptake into perspective. We also review the current knowledge on pharmacogenomics and clinical relevance of human peptide transporters. Finally, the reader's attention is drawn to other known or proposed human peptide-transporting proteins.
NERVE- A Three-Dimensional Patient Simulation for Evaluating Cranial Nerve Function (2011)

Abstract This module portrays a simulated patient who presents to a clinic or Emergency Room with a complaint of blurry vision. The purpose of this simulation is to promote effective history taking and evaluation in order to differentiate cranial nerve disorders from less worrisome pathologies. A significant limitation of live standardized patient interaction is the difficulty in reproducing clinical findings in various conditions. Therefore, medical students are often taught diagnostic skills for evaluation of cranial nerve injuries in a low fidelity manner, mainly where the injury is described, and the student is able to visualize still images of the anticipated clinical findings. The current simulation incorporates not only an accurate depiction of the clinical findings, but an opportunity to dialogue with the patient to ascertain important history information. By integrating the ability to perform a history and evaluate a realistic representation of the clinical examination findings, we anticipate a significant enhancement in medical student learning of various pathologies.
Validation of Noninvasive Functional Cardiac Electrical Source in a 43-year old Male Patient (1999)

Article Validation of Noninvasive Functional Cardiac Electrical Source in a 43-year old Male Patient was published on January 1, 1999 in the journal Biomedical Engineering / Biomedizinische Technik (volume 44, issue s2).
Dyadic Wavelets Energy Zero-Crossings (1988)

An important problem in signal analysis is to define a general purpose signal representation which is well adapted for developing pattern recognition algorithms. In this paper we will show that such a representation can be defined from the position of the zero-crossings and the local energy values of a dyadic wavelet decomposition. This representation is experimentally complete and admits a simple distance for pattern matching applications. It provides a multiscale decomposition of the signal and at each scale characterizes the locations of abrupt changes in the signal. We have developed a stereo matching algorithm to illustrate the application of this representation to pattern matching.
G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA (2003)

The d(TTGGGGGGTACAGTGCA) sequence, derived from the human immunodeficiency virus type 1 (HIV-1) central DNA flap, can form in vitro an intermolecular parallel DNA quadruplex. This work demonstrates that the HIV-1 nucleocapsid protein (NCp) exhibits a high affinity (10(8) M(-1)) for this quadruplex. This interaction is predominantly hydrophobic, maintained by a stabilization between G-quartet planes and the C-terminal zinc finger of the protein. It also requires 5 nt long tails flanking the quartets plus both the second zinc-finger and the N-terminal domain of NCp. The initial binding nucleates an ordered arrangement of consecutive NCp along the four single-stranded tails. Such a process requires the N-terminal zinc finger, and was found to occur for DNA site sizes shorter than usual in a sequence-dependent manner. Concurrently, NCp binding is efficient on a G'2 quadruplex also derived from the HIV-1 central DNA flap. Apart from their implication within the DNA flap, these data lead to a model for the nucleic acid architecture within the viral nucleocapsid, where adjacent single-stranded tails and NCp promote a compact assembly of NCp and nucleic acid growing from stably and primary bound NCp.
Mo<sub>6</sub>S<sub>9</sub><sub>-</sub><i><sub>x</sub></i>I<i><sub>x</sub></i> Nanowire Recognitive Molecular-Scale Connectivity (2007)

We report on a new highly reproducible route to recognitive self-assembly of molecular-scale circuits using sulfur-terminated subnanometer diameter Mo6S9-xIx (MoSIx) molecular nanowires. We demonstrate solution-processed attachment of MoSIx connecting leads to gold nanoparticles (GNPs). We also show that naked nanowires have the potential to bind thiolated proteins such as green fluorescent protein directly, thus providing a universal construct to which almost any protein could be attached. We further demonstrate three-terminal branched circuits with GNPs, opening a self-assembly route to multiscale complex molecular-scale architectures at the single-molecule level.
Susceptibility of cartilage collagens type II, IX, X, and XI to human synovial collagenase and neutrophil elastase (1988)

The action of purified rheumatoid synovial collagenase and human neutrophil elastase on the cartilage collagen types II, IX, X and XI was examined. At 25 degrees C, collagenase attacked type II and type X (45-kDa pepsin-solubilized) collagens to produce specific products reflecting one and at least two cleavages respectively. At 35 degrees C, collagenase completely degraded the type II collagen molecule to small peptides whereas a large fragment of the type X molecule was resistant to further degradation. In contrast, collagen type IX (native, intact and pepsin-solubilized type M) and collagen type XI were resistant to collagenase attack at both 25 degrees C and 35 degrees C even in the presence of excess enzyme. Mixtures of type II collagen with equimolar amounts of either type IX or XI did not affect the rate at which the former was degraded by collagenase at 25 degrees C. Purified neutrophil elastase, shown to be functionally active against soluble type III collagen, had no effect on collagen type II at 25 degrees C or 35 degrees C. At 25 degrees C collagen types IX (pepsin-solubilized type M) and XI were also resistant to elastase, but at 35 degrees C both were susceptible to degradation with type IX being reduced to very small peptides. Collagen type X (45-kDa pepsin-solubilized) was susceptible to elastase attack at 25 degrees C and 35 degrees C as judged by the production of specific products that corresponded closely with those produced by collagenase. Although synovial collagenase failed to degrade collagen types IX and XI, all the cartilage collagen species examined were degraded at 35 degrees C by conditioned culture medium from IL1-activated human articular chondrocytes. Thus chondrocytes have the potential to catabolise each cartilage collagen species, but the specificity and number of the chondrocyte-derived collagenase(s) has yet to be resolved.
TLR4 Mediates Pneumolysin-Induced ATF3 Expression through the JNK/p38 Pathway in Streptococcus pneumoniae-Infected RAW 264.7 Cells (2014)

Activating transcription factor-3 (ATF3) acts as a negative regulator of cytokine production during Gram-negative bacterial infection. A recent study reported that ATF3 provides protection from Streptococcus pneumoniae infection by activating cytokines. However, the mechanism by which S. pneumoniae induces ATF3 after infection is still unknown. In this study, we show that ATF3 was upregulated via Toll-like receptor (TLR) pathways in response to S. pneumoniae infection in vitro. Induction was mediated by TLR4 and TLR2, which are in the TLR family. The expression of ATF3 was induced by pneumolysin (PLY), a potent pneumococcal virulence factor, via the TLR4 pathway. Furthermore, ATF3 induction is mediated by p38 mitogen-activated protein kinase (MAPK) and c-Jun N-terminal kinase (JNK). Thus, this study reveals a potential role of PLY in modulating ATF3 expression, which is required for the regulation of immune responses against pneumococcal infection in macrophages.