gebhart/patrepeval huggingface dataset:
Kinetic properties of the binding of .alpha.-lytic protease to peptide boronic acids (1988)

The kinetic parameters for peptide boronic acids in their interaction with alpha-lytic protease were determined and found to be similar to those of other serine proteases [Kettner, C., & Shenvi, A. B. (1984) J. Biol. Chem. 259, 15106-15114]. alpha-Lytic protease hydrolyzes substrates with either alanine or valine in the P1 site and has a preference for substrate with a P1 alanine. The most effective inhibitors are tri- and tetrapeptide analogues that have a -boroVal-OH residue in the P1 site. At pH 7.5, MeOSuc-Ala-Ala-Pro-boroVal-OH has a Ki of 6.4 nM and Boc-Ala-Pro-boroVal-OH has a Ki of 0.35 nM. Ac-boroVal-OH and Ac-Pro-boroVal-OH are 220,000- and 500-fold less effective, respectively, than the tetrapeptide analogue. The kinetic properties of the tri- and tetrapeptide analogues are consistent with the mechanism for slow-binding inhibition, E + I in equilibrium EI in equilibrium EI*, while the less effective inhibitors are simple competitive inhibitors. MeO-Suc-Ala-Ala-Pro-boroAla-OH is a simple competitive inhibitor with a Ki of 67 nM at pH 7.5. Other peptide boronic acids, which are analogues of nonsubstrates, are less effective than substrate analogues but still are effective competitive inhibitors. For example, MeOSuc-Ala-Ala-Pro-boroPhe-OH has a Ki of 0.54 microM although substrates with a phenylalanine in the P1 position are not hydrolyzed. Binding for boronic acid analogues of both substrate and nonsubstrate analogues is pH dependent with higher affinity near pH 7.5. Similar binding properties have been observed for pancreatic elastase. Both enzymes have almost identical requirements for an extended peptide inhibitor sequence in order to exhibit highly effective binding and slow-binding characteristics.(ABSTRACT TRUNCATED AT 250 WORDS)
A highly manufacturable 0.2 μm AlGaAs/InGaAs PHEMT fabricated using the single-layer integrated-metal FET (SLIMFET) process (2002)

This work is the development of a single-layer integrated-metal field effect transistor (SLIMFET) process for a high performance 0.2 /spl mu/m AlGaAs/InGaAs pseudomorphic high electron mobility transistor (PHEMT). This process is compatible with MMIC fabrication and minimizes process variations, cycle time, and cost. This process uses non-alloyed ohmic contacts, a selective gate-recess etching process, and a single gate/source/drain metal deposition step to form both Schottky and ohmic contacts at the same time.
Production of a Large Volume Discharge Using a Multiple Arc System (1979)

A multiple arc system using six separate arcs which coalesce to form a large volume of ionized gas is described. The conditions for the maintenance of a stable multiple arc system are analyzed and results using an analog to investigate the current distribution for different electrode configurations are given together with photographs showing the different discharge structures.
The Salivary Adenosine Deaminase Activity of the Mosquitoes <i>Culex quinquefasciatus</i> and <i>Aedes aegypti</i> (2001)

A cDNA coding for a protein with significant similarity to adenosine deaminase (ADA) was found while randomly sequencing a cDNA library constructed from salivary gland extracts of adult female Culex quinquefasciatus. Prompted by this result, we found high ADA activities in two culicine mosquitoes, Culex quinquefasciatus and Aedes aegypti, but not in the anopheline Anopheles gambiae. Homogenates from Culex quinquefasciatus also have an AMP deaminase activity that is three times greater than the ADA activity, whereas in Aedes aegypti the AMP deaminase activity is less than 10% of the ADA activity. Evidence for secretion of ADA during blood feeding by Aedes aegypti includes the presence of ADA activity in warm solutions probed through a membrane by mosquitoes and in serotonin-induced saliva and a statistically significant reduction in the levels of the enzyme in Aedes aegypti following a blood meal. We could not demonstrate, however, that C. quinquefasciatus secrete ADA in their saliva. Male Aedes aegypti and C. quinquefasciatus, which do not feed on blood, have less than 3% of the levels of ADA found in females. We propose that ADA activity in A. aegypti may help blood feeding by removing adenosine, a molecule associated with both the initiation of pain perception and the induction of mast cell degranulation in vertebrates, and by producing inosine, a molecule that potently inhibits the production of inflammatory cytokines. The role of salivary ADA in Culex quinquefasciatus remains unclear.
Conditional gene knock-down by CRE-dependent short interfering RNAs (2004)

International audience
Finite-aperture waveguide-laser resonators (1973)

A general theory of finite-aperture waveguide-laser resonators is developed which represents the external reflectors by matrices which couple linearly polarized waveguide modes having the same azimuthal symmetry. The theory allows the determination of resonator efficiency, resonator frequencies, and laser near- and far-field patterns. Computations of the coupling loss for the fundamental waveguide mode as a function of mirror curvature, separation, and aperture are in good agreement with recent infinite-aperture calculations in the limit of large apertures and indicate three low-loss configurations: 1) large radius of curvature mirrors close to the guide; 2) "large" radius of curvature mirrors centered at the guide entrance: and 3) generally smaller curvature mirrors separated by half their curvature from the guide entrance. The importance of higher order waveguide modes in determining laser output power and far-field patterns is demonstrated experimentally and compared to theoretical predictions. Design guidelines for the construction of high-efficiency CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , CO, and He-Ne waveguide-laser resonators are summarized in tabular form.
Evidence for Magnetic Field Decay in the Slowest Known Be/X-ray Pulsars X Per and RX J0146.9+5121 (2000)

Abstract We argue that the slowest known Be/X-ray pulsars X Per and RX J0146.9+5121 currently possess relatively weak (≲ 10 12 G) magnetic fields. Unless these pulsars were born rotating very slowly (initial periods longer than tens of seconds), in order to explain their long spin periods (~ 835 and ~ 1412 s, respectively), they must have had magnetic fields stronger than a few 10 13 G; that is, their magnetic fields must have decayed.
ELECTRONIC SYSTEM TO MEASURE PLANTAR FORCE DISTRIBUTION IN PATIENTS (2007)

This article describes an electronic system, projected to measure the force distribution under patients’ foot soles by instrumented soles with sensors. The system is basically
composed of load cells installed in the soles, signal conditioning circuit, interfacing circuit and a computer, from which the measurement results can be read. It is possible to
measure static and dynamic forces. Data visualization on the computer screen is displayed by a Visual Basic program. The system presents linear response with the applied force, small hysteresis, precision higher than 99.4%, in addition to its simple operation and handling. It could be used by sports and fitness professionals and other health area professionals to assist in the evaluation of specific programs that aim at
increasing athletes’ performance.
Arts-based service learning with First Peoples: Interlocking Communities of Practice (2015)

The core of service learning in post-secondary education is a range of partnerships between higher education institutions and communities, as co-generators of knowledge. This paper, reporting from a national arts-based service learning project involving three Australian universities, is concerned with communities of practice that influence stakeholder values and attitudes as well as enhancing the work readiness of pre-service teachers and university students in music, screen arts and journalism. It builds on seven years of practice and research in arts-based service learning with Aboriginal communities (2009-2015) and a nationally funded project that entailed service-learning programs at three Australia universities in partnership with Aboriginal communities in regional and metropolitan areas Australia (2011-2013). Drawing on the concept of Ubuntu, or humanness, the paper discusses the benefits and challenges of working as an interlocking community of practice. Within this community, inter-relationships underpinned members’ understandings of self as researchers, educators, learners and human beings, and as part of a network of inter-dependence through which our understandings of being human were troubled by our need to rethink our sense of community, culture and history.
Amphiphilic copolymers of glycidol with nonpolar epoxide comonomers (2001)

Abstract To explore the industrially used copolymerization of glycidol with other epoxide species, a series of copolymers of glycidol with various comonomers (epichlorohydrin, isopropyl glycidyl ether, 1,2‐epoxybutane, propylene oxide, and glycidyl phenyl ether) has been synthesized by cationic ring‐opening polymerization in dichloromethane, using boron trifluoride diethyl etherate as the initiator. The facile synthesis proceeded at room temperature under ordinary atmosphere. The air‐ and temperature‐stable products—mostly clear, colorless, viscous liquids—are proposed to consist of a hyperbranched polyglycidol core (incorporating varying fractions of comonomer) with arms made from comonomer‐derived repeat units. These copolymers had low molecular weights and rather broad molecular weight distributions. There was wide variation in the polarity of these copolymers, depending on the comonomer used, resulting in materials that were soluble in solvents ranging from benzene to water. The glass‐transition temperatures observed for these copolymers also varied widely, ranging from −56 to 1°C. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 82: 2290–2299, 2001
Characterization and modeling of SOI RF integrated components (2003)

The boom of mobile communications leads to an increasing request of low cost and low power mixed mode integrated circuits. Maturity of SOI technology, and recent progresses of MOSFET's microwave performances, explain the success of silicon as compared to III-V technologies for low-cost multigigahertz analog applications. The design of efficient circuits requires accurate, wide-band models for both active and passive elements. Within this frame, passive components fabricated in SOI technologies have been studied, and a physical model of integrated square spiral inductors has been developed. Also, the performances of integrated MOSFETs have been analyzed. New alternative structures of transistor (the Graded Channel MOSFET and the Dynamic Threshold MOSFET) have been proposed and studied from Low to High frequencies. These transistors show very interesting properties for analog, low power, low voltage, and microwave applications. Furthermore, as their fabrication processes are fully CMOS compatible, they allow us to increase the performances of a CMOS technology without any modification of its process, and without extra-cost.
The Molecular Chaperone Calnexin Associates with the Vacuolar H<sup>+</sup>-ATPase from Oat Seedlings (1998)

Acidification of endomembrane compartments by the vacuolar-type H(+)-ATPase (V-ATPase) is central to many cellular processes in eukaryotes, including osmoregulation and protein sorting. The V-ATPase complex consists of a peripheral sector (V1) and a membrane integral sector (V0); however, it is unclear how the multimeric enzyme is assembled. A 64-kD polypeptide that had copurified with oat V-ATPase subunits has been identified as calnexin, an integral protein on the endoplasmic reticulum. To determine whether calnexin interacted physically with the V-ATPase, microsomal membranes were Triton X-100 solubilized, and the protein-protein interaction was analyzed by coimmunoprecipitation. Monoclonal antibodies against calnexin precipitated both calnexin and V-ATPase subunits, including A and B and those of 44, 42, 36, 16, and 13 kD. A monoclonal antibody against subunit A precipitated the entire V-ATPase complex as well as calnexin and BiP, an endoplasmic reticulum lumen chaperone. The results support our hypothesis that both calnexin and BiP act as molecular chaperones in the folding and assembly of newly synthesized V1V0-ATPases at the endoplasmic reticulum.
Eclipse Attacks on Overlay Networks: Threats and Defenses (2006)

Overlay networks are widely used to deploy functionality at edge nodes without changing network routers. Each node in an overlay network maintains connections with a number of peers, forming a graph upon which a distributed application or service is implemented. In an “Eclipse” attack, a set of malicious, colluding overlay nodes arranges for a correct node to peer only with members of the coalition. If successful, the attacker can mediate most or all communication to and from the victim. Furthermore, by supplying biased neighbor information during normal overlay maintenance, a modest number of malicious nodes can eclipse a large number of correct victim nodes. This paper studies the impact of Eclipse attacks on structured overlays and shows the limitations of known defenses. We then present the design, implementation, and evaluation of a new defense, in which nodes anonymously audit each other’s connectivity. The key observation is that a node that mounts an Eclipse attack must have a higher than average node degree. We show that enforcing a node degree limit by auditing is an effective defense against Eclipse attacks. Furthermore, unlike most existing defenses, our defense leaves flexibility in the selection of neighboring nodes, thus permitting important overlay optimizations like proximity neighbor selection (PNS).
Effects of daily oral administration of quercetin chalcone and modified citrus pectin on implanted colon-25 tumor growth in Balb-c mice. (2000)

The health benefits of fruits and vegetables have been the subject of numerous investigations over many years. Two natural substances, quercetin (a flavonoid) and citrus pectin (a polysaccharide found in the cell wall of plants) are of particular interest to cancer researchers. Two modified versions of these substances - quercetin chalcone (QC) and a pH-modified citrus pectin (MCP) - are the focus of this study. Previous research has confirmed that quercetin exhibits antitumor properties, likely due to immune stimulation, free radical scavenging, alteration of the mitotic cycle in tumor cells, gene expression modification, anti-angiogenesis activity, or apoptosis induction, or a combination of these effects. MCP has inhibited metastases in animal studies of prostate cancer and melanoma. To date, no study has demonstrated a reduction in solid tumor growth with MCP, and there is no research into the antitumor effect of QC. This study examines the effects of MCP and QC on the size and weight of colon-25 tumors implanted in balb-c mice. Fifty mice were orally administered either 1 ml distilled water (controls), low-dose QC (0.8 mg/ml), high-dose QC (1.6 mg/ml), low-dose MCP (0. 8 mg/ml) or high-dose MCP (1.6 mg/ml) on a daily basis, beginning the first day of tumor palpation (usually eight days post-implantation). A significant reduction in tumor size was noted at day 20 in all groups compared to controls. The groups given low-dose QC and MCP had a 29-percent (NS) and 38-percent (p<0.02) decrease in size, respectively. The high-dose groups had an even more impressive reduction in size; 65 percent in the QC group and 70 percent in the mice given MCP (both p<0.001). This is the first evidence that MCP can reduce the growth of solid primary tumors, and the first research showing QC has antitumor activity. Additional research on these substances and their effect on human cancers is warranted.
Attenuation of the induced differentiation of HL-60 leukemia cells by mitochondrial chaperone HSP70. (1999)

The HSP70 family of heat shock proteins, which are involved in development and cellular differentiation, is elevated in various tumor cell lines. To examine the role of these proteins in neoplastic cell differentiation, four members of the HSP70 multiple gene family (i.e., HSP70, HSC70, GRP78, and mtHSP70) were examined during the induced differentiation of HL-60 promyelocytic leukemia cells. Western analyses showed that continuous exposure for 48 h of HL-60 cells to the differentiation-inducing agents, all-trans retinoic acid, 1,25-dihydroxyvitamin D3, or N-methylformamide, resulted in decreases in mitochondrial HSP70 (mtHSP70), with little change in the levels of HSP70, HSC70, and GRP78. To gain information on the role of mtHSP70 in the differentiation process, HL-60 cells were transfected with either murine mthsp70 cDNA or vector alone. Slightly greater than twofold increases in mtHSP70 protein levels occurred in cells transfected with the mthsp70 cDNA. In vector-transfected HL-60 cells, myeloid differentiation, measured as an increase in CD31 expression and nitroblue tetrazolium positivity, was observed following 3-6 days of treatment with each of the three inducing agents. In contrast, cell differentiation induced by each agent was markedly attenuated in mthsp70-transfected HL-60 cells. These findings suggest that a decrease in mtHSP70 is important for the induced differentiation of HL-60 cells.
Immunosuppressive properties of tissues obtained from eyes with experimentally manipulated corneas. (1996)

The cornea plays an active role in ocular immune privilege and ACAID by creating a local immunosuppressive microenvironment, providing neural afferent stimuli that affect immunosuppressive properties of I/CB, and preventing neovascularization and infiltration with Langerhans cells.
Real-time video transport optimization using streaming agent over 3G wireless networks (2005)

Feedback adaptation has been the basis for many media streaming schemes, whereby the media being sent is adapted in real time according to feedback information about the observed network state and application state. Central to the success of such adaptive schemes, the feedback must: 1) arrive in a timely manner and 2) carry enough information to effect useful adaptation. In this paper, we examine the use of feedback adaptation for media streaming in 3G wireless networks, where the media servers are located in wired networks while the clients are wireless. We argue that end-to-end feedback adaptation using only information provided by 3G standards is neither timely nor contain enough information for media adaptation at the server. We first show how the introduction of a streaming agent (SA) at the junction of the wired and wireless network can be used to provide useful information in a timely manner for media adaptation. We then show how optimization algorithms can be designed to take advantage of SA feedbacks to improve performance. The improvement of SA feedbacks in peak signal-to-noise ratio is significant over nonagent-based systems.
Tracking real-time user experience (TRUE) (2008)

Automatic recording of user behavior within a system (instrumentation) to develop and test theories has a rich history in psychology and system design. Often, researchers analyze instrumented behavior in isolation from other data. The problem with collecting instrumented behaviors without attitudinal, demographic, and contextual data is that researchers have no way to answer the 'why' behind the 'what'. We have combined the collection and analysis of behavioral instrumentation with other HCI methods to develop a system for Tracking Real-Time User Experience (TRUE). Using two case studies as examples, we demonstrate how we have evolved instrumentation methodology and analysis to extensively improve the design of video games. It is our hope that TRUE is adopted and adapted by the broader HCI community, becoming a useful tool for gaining deep insights into user behavior and improvement of design for other complex systems.
Image analysis can be used to detect spatial changes in the histopathology of pancreatic tumours (2003)

Pancreatic cancer is frequently associated with intense growth of fibrous tissue at the periphery of tumours, but the histopathological quantification of this stromal reaction has not yet been used as a prognostic factor because of the difficulty of obtaining quantitative measures using manual methods. Manual histological grading is a poor indicator of outcome in this type of cancer and there is a clinical need to establish a more sensitive indicator. Recent pancreatic tumour biology research has focused upon the stromal reaction and there is an indication that its histopathological quantification may lead to a new prognostic indicator. Histological samples from 21 cases of pancreatic carcinoma were stained using the sirius red, light-green method. Multiple images from the centre and periphery of each tumour were automatically segmented using colour cluster analysis to subdivide each image into representative colours. These were classified manually as stroma, cell cytoplasm or lumen in order to measure the area of each component in each image. Measured areas were analysed to determine whether the technique could detect spatial differences in the area of each tissue component over all samples, and within individual samples. Over all 21 cases, the area of stromal tissue at the periphery of the tumours exceeded that at the centre by an average of 10.0 percentage points (P < 0.001). Within individual tumours, the algorithm was able to detect significantly more stroma (P < 0.05) at the periphery than the centre in 11 cases, whilst none of the remaining cases had significantly more stromal tissue at the centre than the periphery. The results demonstrate that semi-automated analysis can be used to detect spatial differences in the area of fibrous tissue in routinely stained sections of pancreatic cancer.
A single amino acid insertion in the WRKY domain of the Arabidopsis TIR–NBS–LRR–WRKY‐type disease resistance protein SLH1 (sensitive to low humidity 1) causes activation of defense responses and hypersensitive cell death (2005)

In this study we characterized the sensitive to low humidity 1 (slh1) mutant of Arabidopsis ecotype No-0 which exhibits normal growth on agar plate medium but which on transfer to soil shows growth arrest and development of necrotic lesions. cDNA microarray hybridization and RNA gel blot analysis revealed that genes associated with activation of disease resistance were upregulated in the slh1 mutants in response to conditions of low humidity. Furthermore, the slh1 mutants accumulate callose, autofluorescent compounds and salicylic acid (SA). We demonstrate that SA is required for the slh1 phenotype but not PAD4 or NPR1. SLH1 was isolated by map-based cloning and it encodes a resistance (R)-like protein consisting of a domain with Toll and interleukin-1 receptor homology (TIR), a nucleotide-binding domain (NB), leucine-rich repeats (LRR) and a carboxy-terminal WRKY domain. SLH1 is identical to the R gene RRS1-R of the Arabidopsis ecotype Nd-1, a gene which confers resistance to the bacterial pathogen Ralstonia solanacearum GMI1000 and also functions as an R gene to this pathogen in No-0. We identified a 3 bp insertion mutation in slh1 that results in the addition of a single amino acid in the WRKY domain; thereby impairing its DNA-binding activity. Our data suggest that SLH1 disease resistance signaling may be negatively regulated by its WRKY domain in the R protein and that the constitutive defense activation conferred by the slh1 mutation is inhibited by conditions of high humidity.