gebhart/patrepeval huggingface dataset:
Combining Multi-Material Rapid Prototyping and Pseudo-Rigid Body Modeling for a new compliant mechanism (2014)

Multi-Material Rapid Prototyping (MM-RP) is a promising fabrication process for compliant mechanisms, for instance when compactness is a concern. The Pseudo-Rigid Body Model (PRBM) approach is well-known for the synthesis of compliant mechanisms. It is usually based on the use of compliant joints to provide the mechanism mobilities. In this paper, we propose the HSC joint as a new type of revolute compliant joint that is well adapted to MM-RP, and that offers interesting properties in terms of stiffness and range of motion. Based on the HSC joint, a new compliant mechanism, suitable for interventional MRI, is introduced with assessment of a first prototype that is entirely made out of a single polymer part. The interest is twofold. First, the device constitutes a promising solution in this medical context. Second, the impact of the use of MM-RP in combination with PRBM can be evaluated, and their use is discussed as a conclusion.
World Vaccine Congress Lyon - Terrapinn's 11th Annual Congress. (2009)

The 11th Annual World Vaccine Congress, held in Lyon, included topics covering new therapeutic developments in the field of vaccines. This conference report highlights selected presentations on the role of big pharma in vaccine development, the future direction of vaccine R&D, influenza preparedness in Europe, and vaccines for Staphylococcus aureus, CMV and cancer. Investigational drugs discussed include an H5N1 influenza vaccine program from Baxter International Inc/DynPort Vaccine Co LLC, FP-01 (Immune Targeting Systems Ltd), FluGEM (Mucosis BV), a nonstructural protein-1-altered live-attenuated influenza vaccine candidate from Vivaldi Biosciences Inc, PentaStaph (GlaxoSmithKline plc) and StaphVAX (Nabi Biopharmaceuticals), VCL-CB01 (Vical Inc) and astuprotimut-r (GlaxoSmithKline).
Preprocessing of tandem mass spectrometric data to support automatic protein identification (2003)

Liquid chromatography tandem mass spectrometry is a major tool for identifying proteins. The fragment spectra of peptides can be interpreted automatically in conjunction with a sequence database search. With the development of powerful automatic search engines, research now focuses on optimizing the result returned from database searches. We present a series of preprocessing steps for fragment spectra to increase the accuracy and specificity of automatic database searches. After processing, the correct amino acid sequences from the database can be related better to the fragment spectra. This increases the sensitivity and reliability of protein identifications, especially with very large genomic databanks, and can be important for the systematic characterization of post-translational modifications.
A novel threshold voltage defined switch for circuit camouflaging (2016)

Semiconductor supply chain is increasingly getting exposed to variety of security attacks such as Trojan insertion, cloning, counterfeiting, reverse engineering (RE), piracy of Intellectual Property (IP) or Integrated Circuit (IC) and side-channel analysis due to involvement of untrusted parties. In this paper, we propose threshold voltage-defined switches that will camouflage the logic gate both logically and physically to resist RE and IP piracy. The proposed gate can function as NAND, AND, NOR, OR, XOR, and XNOR robustly using threshold defined switches. We also propose a flavor of camouflaged gate that represents reduced functionality (NAND, NOR and NOT) at much lower overhead. The camouflaged design operates at nominal voltage and obeys conventional reliability limits. A small fraction of gates can be camouflaged to increase the RE effort extremely high. Simulation results indicate 46-53% area, 59-68% delay and 52-76% power overhead when 5-15% gates are identified and camouflaged using the proposed gate. A significant higher RE effort is achieved when the proposed gate is employed in the netlist using controllability, observability and hamming distance sensitivity based gate selection metrics.
Characterization of a Protein Kinase C-δ (PKC-δ) ATP Binding Mutant (1995)

To investigate the function of protein kinase C (PKC)-delta, we mutated its ATP binding site by converting the invariant lysine in the catalytic domain (amino acid 376) to an arginine. Expression vectors containing wild type and mutant PKC-delta cDNAs were generated either with or without an influenza virus hemagglutinin epitope tag. After expression in 32D cells by transfection, the PKC-delta ATP binding mutant (PKC-delta K376R) was not able to phosphorylate itself or the PKC-delta pseudosubstrate region-derived substrate, indicating that PKC-delta K376R was an inactive enzyme. PKC activity was inhibited by 67% in 32D cells coexpressing both PKC-delta wild type (PKC-delta WT) and PKC-delta K376R when compared to 32D cells expressing only PKC-delta WT. Mixture of PKC-delta WT and PKC-delta K376R kinase sources in vitro also reduced the enzymatic activity of PKC-delta WT. These results suggest that PKC-delta K376R competes with PKC-delta WT and inhibits PKC-delta WT phosphorylation of its in vitro substrate. While PKC-delta WT overexpressed in 32D cells demonstrated 12-O-tetradecanoylphorbol-13-acetate (TPA)-dependent translocation from the cytosolic to the membrane fraction, PKC-delta K376R was exclusively localized in the membrane fraction even prior to TPA stimulation. Unlike PKC-delta WT which was phosphorylated on tyrosine residue(s) only after TPA treatment, PKC-delta K376R was constitutively phosphorylated on tyrosine residue(s). Although exposure of PKC-delta WT transfectants to TPA induced 32D monocytic differentiation, the 32D/PKC-delta K376R transfectants were resistant to TPA-induced differentiation. Thus, expression of active PKC-delta is required to mediate 32D monocytic differentiation in response to TPA stimulation.
HPV Pseudovirions As DNA Delivery Vehicles (2011)

"The ability of HPV pseudovirions to efficiently deliver DNA into cells suggests several potential applications in basic biology, including the characterization of virion biology and measurement of protective neutralizing antibody titers in vitro and in vivo, as well as their employment for more direct medical applications".
BCR/ABL activates Rap1 and B-Raf to stimulate the MEK/Erk signaling pathway in hematopoietic cells (2004)

The BCR/ABL fusion tyrosine kinase activates various intracellular signaling pathways, thus causing chronic myeloid leukemia (CML). Here we demonstrate that the inducible expression of BCR/ABL in a murine hematopoietic cell line, TonB210, leads to the activation of the Ras family small GTPase Rap1, which is inhibited by the ABL kinase inhibitor imatinib. The Rap1 activity in a CML cell line, K562, was also inhibited by imatinib. Inhibition of Rap1 activation by a dominant negative mutant of Rap1, Rap1-N17, or SPA-1 inhibited the BCR/ABL-induced activation of Elk-1. BCR/ABL also activated in a kinase activity-dependent manner the B-Raf kinase, which is an effector molecule of Rap1 and a potent activator of the MEK/Erk/Elk-1 signaling pathway. Together, these data suggest that, in addition to the well-established Ras/Raf-1 pathway, BCR/ABL activates the alternative signaling pathway involving Rap1 and B-Raf to activate Erk, which may play important roles in leukemogenesis.
The use of a triple nucleoside‐nucleotide regimen for nonoccupational HIV post‐exposure prophylaxis (2005)

TDF-3TC-d4T is significantly better tolerated than ZDV-3TC or ZDV-3TC-NFV as NPEP and results in greater numbers of individuals completing 28 days of treatment.
Analytical Methods for Resistant Starch (1999)

Resistant starch has recently been defined as “…the sum of starch and products of starch degradation not absorbed in the small intestine of healthy individuals” (1). An analytical method for RS should then take into account all the starch and α-dextrins covering this physiological definition. Furthermore, it should be validated using in vivo data from human healthy subjects. The general principle of the method is the following: 1) the samples are digested by a pancreatic α-amylase then 2) resistant starch content is determined by direct analysis of the residual starch after hydrolysis or by substracting to the total starch of the sample, the amount of starch which has been digested. None of the “European methods” (Englyst et al., 1992, Bjôrck et al., 1986, Champ, 1992, Faisant et al., 1995) are exempt of criticism. Moreover, none of them are able to analyze resistant starch as defined because they do not consider potentially digestible starch arriving at the end of the ileum. The last two methods appeared to be more quickly and easily reproduced than Englyst’s method. However Englyst’s method is the only one which has been validated in vivo on humans. Besides these European meth-ods, Muir and O’Dea (1992, 1993) developed another procedure, validated in vivo, that is supposed to mimic physiological conditions for starch digestion.
Diffusion and Partitioning of Solutes in Agarose Hydrogels:  The Relative Influence of Electrostatic and Specific Interactions (2003)

The nature and density of charged sites in an agarose gel have been studied. Diffusion and partition coefficients of various organic and inorganic ions have been measured as a function of ionic strength, μ, and pH to investigate the solute−gel interactions resulting from charge effects and specific complexation. The majority of binding sites in the gel are pyruvate groups, with an intrinsic protonation constant of log Kaint = 3.9. We measured the charge density of the gel as a function of added salt and pH and evaluated the Donnan potential. The partition coefficients of cations decrease and those of anions increase with increasing ionic strength because of progressive screening of the anionic sites in the gel, as predicted by the Boltzmann and Poisson−Boltzmann equations. The charges in the gel become completely screened at μ ≈ 10-2. As predicted with the Smoluchowski−Poisson−Boltzmann theory, the diffusion coefficient of cationic species is reduced at low ionic strength. We tested both cylindrical and spherical symmetries of Poisson−Boltzmann cell models to describe these variations and obtained better results with the former. In addition to electrostatic effects, we detected specific interactions between metal ions and the gel, and we determined the intrinsic association constants. General models are presented for the partitioning and diffusion of solutes in the gel, which consider steric, electrostatic, and chemical interactions.
Parenteral Fish Oil as Monotherapy Improves Lipid Profiles in Children With Parenteral Nutrition–Associated Liver Disease (2010)

A fish oil-based lipid emulsion used as monotherapy in children who exclusively depended on PN for survival was associated with significant improvement in all major lipid panels as well as improvement of hyperbilirubinemia. Parenteral fish oil may be the preferred lipid source in children with dyslipidemia.
Detection of Single-Electron Charging in an Individual InAs Quantum Dot by Noncontact Atomic-Force Microscopy (2005)

Single-electron charging in an individual InAs quantum dot was observed by electrostatic force measurements with an atomic-force microscope (AFM). The resonant frequency shift and the dissipated energy of an oscillating AFM cantilever were measured as a function of the tip-back electrode voltage, and the resulting spectra show distinct jumps when the tip was positioned above the dot. The observed jumps in the frequency shift, with corresponding peaks in dissipation, are attributed to a single-electron tunneling between the dot and the back electrode governed by the Coulomb blockade effect, and are consistent with a model based on the free energy of the system. The observed phenomenon may be regarded as the "force version" of the Coulomb blockade effect.
Effects of various liquid organic solvents on solvent‐induced crystallization of amorphous poly(lactic acid) film (2012)

Abstract The effects of 60 organic solvent on poly(lactic acid) (PLA) were systematically investigated using the Hansen solubility parameter (HSP). The hydrogen bonding solubility parameter accurately reflects the solubility of PLA films using HSP but it depends on hydrogen bonding, as well as dispersion and polar parameters. The PLA films immersed in organic solvent became cloudy and showed no changes in chemical structure. However, solvent‐induced crystallization of the PLA films was observed. Crystalline structures do not dependent on the organic solvent but on the degree of swelling. The organic solvent‐induced crystallization formed a crystallized mixture of a‐ and β‐forms. The density of the crystalline PLA films was lower than that of amorphous PLA films. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Distance-from-boundary as a metric for texture image retrieval (2002)

A new metric is proposed for texture image retrieval, which is based on the signed distance of the images in the database to a boundary chosen by the query. This novel metric has three advantages: (1) the boundary distance measures are relatively insensitive to the sample distributions; (2) the same retrieval results can be obtained with respect to different (but visually similar) queries; (3) retrieval performance can be improved. The boundaries are obtained by using a statistical learning algorithm called support vector machine (SVM), and hence the boundaries can be simply represented by some vectors and their combination coefficients. Experimental results on the Brodatz texture database indicate that a significantly better retrieval performance can be achieved as compared to the traditional Euclidean distance-based approach. This technique can be further developed to learn pattern similarities among different texture classes and used in relevance feedback.
Switched time-delay elements based on AlGaAs/GaAs optical waveguide technology at 1.32 μm for optically controlled phased-array antennas (1992)

Integrated optical time-shift networks consisting of cascaded pairs of 2 x 2 linear electrooptic switches and optical delay lines in GaAs waveguides at 1.32 micron are investigated for true-time optical beam forming in phased array antennas. We report new state-of-the-art results in curved waveguide and corner bend insertion loss, and preliminary results from 2-bit time delay generators (TDGs) constructed in the form of GaAs-based photonic integrated circuits utilizing these components. These results represent significant progress in our longer-term goal of demonstrating a 7-bit TDG with a loss matching monolithic microwave integrated circuit (MMIC) delay line techniques, while providing very wide bandwidth unmatched by MMIC technology.
Olfactory Receptor Database: a database of the largest eukaryotic gene family (1999)

The Olfactory Receptor Database (ORDB) is a WWW-accessible database that stores data on Olfactory Receptor-like molecules (ORs) and has been open to the public since June 1996. It contains a public and a private area. The public area includes published DNA and protein sequence data for ORs, links to OR models and data on their expression, chromosomal localization and source organism, as well as (i) links to bibliography through PubMed and (ii) interactive WWW-based tools, such as BLAST homology searching. The private area functions as a service to laboratories that are actively cloning receptors. Source laboratories enter the sequences of the receptor clones they have characterized to the private database and can search for identical or near identical OR sequences in both public and private databases. If another laboratory has cloned and deposited an identical or closely matching sequence there are means for communication between the laboratories to help avoid duplication of work. ORDB is available via the WWW at http://crepe.med.yale.edu/ORDB/HTML
Microsoft Windows server 2012 : pocket consultant (2012)

* Introduction * Part I: Windows Server 2012 Administration Fundamentals * Chapter 1: Windows Server 2012 Administration Overview * Chapter 2: Managing Servers Running Windows Server 2012 * Chapter 3: Monitoring Processes, Services, and Events * Chapter 4: Automating Administrative Tasks, Policies, and Procedures * Chapter 5: Enhancing Computer Security * Part II: Windows Server 2012 Directory Services Administration * Chapter 6: Using Active Directory * Chapter 7: Core Active Directory Administration * Chapter 8: Creating User and Group Accounts * Chapter 9: Managing User and Group Accounts * Part III: Windows Server 2012 Data Administration * Chapter 10: Managing File Systems and Drives * Chapter 11: Configuring Volumes and RAID Arrays * Chapter 12: Data Sharing, Security, and Auditing * Chapter 13: Data Backup and Recovery * Part IV: Windows Server 2012 Network Administration * Chapter 14: Managing TCP/IP Networking * Chapter 15: Running DHCP Clients and Servers * Chapter 16: Optimizing DNS
Application of Computer-Aided Drug Repurposing in the Search of New Cruzipain Inhibitors: Discovery of Amiodarone and Bromocriptine Inhibitory Effects (2013)

Cruzipain (Cz) is the major cystein protease of the protozoan Trypanosoma cruzi , etiological agent of Chagas disease. From a 163 compound data set, a 2D-classifier capable of identifying Cz inhibitors was obtained and applied in a virtual screening campaign on the DrugBank database, which compiles FDA-approved and investigational drugs. Fifty-four approved drugs were selected as candidates, four of which were acquired and tested on Cz and T. cruzi epimastigotes. Among them, the antiparkinsonian and antidiabetic drug bromocriptine and the antiarrhythmic amiodarone showed dose-dependent inhibition of Cz and antiproliferative activity on the parasite.
Epidithiodiketopiperazines Block the Interaction between Hypoxia-inducible Factor-1α (HIF-1α) and p300 by a Zinc Ejection Mechanism (2009)

The hypoxic response in humans is regulated by the hypoxia-inducible transcription factor system; inhibition of hypoxia-inducible factor (HIF) activity has potential for the treatment of cancer. Chetomin, a member of the epidithiodiketopiperazine (ETP) family of natural products, inhibits the interaction between HIF-alpha and the transcriptional coactivator p300. Structure-activity studies employing both natural and synthetic ETP derivatives reveal that only the structurally unique ETP core is required and sufficient to block the interaction of HIF-1alpha and p300. In support of both cell-based and animal work showing that the cytotoxic effect of ETPs is reduced by the addition of Zn(2+) through an unknown mechanism, our mechanistic studies reveal that ETPs react with p300, causing zinc ion ejection. Cell studies with both natural and synthetic ETPs demonstrated a decrease in vascular endothelial growth factor and antiproliferative effects that were abrogated by zinc supplementation. The results have implications for the design of selective ETPs and for the interaction of ETPs with other zinc ion-binding protein targets involved in gene expression.
AESOP: an outline-oriented authoring system (2002)

Because a hypermedia document is more complex than conventional text, it requires preparation with respect to two key aspects. First, the author begins to develop a "vision" of the document-usually based on some outline level description of his objectives. At the same time as this outline is being developed, the author begins to extract useful segments from his resource materials and prepares his first version of the logic of a system of hyperlinks among those segments. We present a system named "Authoring Environment for the Desktop" (AESOP) with two different types of "outlining" tools to handle these aspects. Planning the "vision" consists in defining a "logical" tree structure of the document. The plan for the link structure is based on a primitive unit called the view area, and AESOP provides a construct named Bento-Box for crating and manipulating view areas. Authors specify spatial and temporal layout within a single Bento-Box and define hyperlinks among the Bento-Boxes.
Synthesis and in Vitro Hydroxyapatite Binding of Peptides Conjugated to Calcium-Binding Moieties (2007)

To confer bone-binding properties to proteins and other biological agents that lack specific targeting capacity, model peptide-based molecules were synthesized containing poly(aspartic acid), poly(glutamic acid), or a bisphosphonate (pamidronate). These motifs have well-documented affinities to hydroxyapatite, a property desirable for the targeting of molecules to bone for drug delivery and tissue engineering applications. Model peptides of increasing molecular mass (5-33 amino acids) were directly conjugated to eight aspartic acids (Asp8), eight glutamic acids (Glu8), or pamidronate, purified by high-performance liquid chromatography, and characterized by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectroscopy. The modified peptides were incubated with hydroxyapatite in phosphate-buffered saline at physiological conditions over 24 h. This study revealed a significant amount (>90%) of conjugated peptides adsorbed to the hydroxyapatite as compared to unmodified peptides (<5%). It was found that while there were significant differences between the different hydroxyapatite-binding and control groups for all time points, the size of the peptide had no statistical effect on peptide-hydroxyapatite binding. These results demonstrate that bisphosphonate and oligopeptide conjugates hold great promise for the development of new bioactive molecules for bone-specific applications.
GaN substrates by HVPE (2008)

The availability of GaN substrates is crucial for GaN-based laser diodes. Also high performance LEDs ask for high quality substrates. Methods for growth of bulk GaN are reviewed with a focus on hydride vapour phase epitaxy (HVPE), which currently is the method used for the production of GaN substrates. Also the ammonothermal approach is briefly discussed. Both approaches still have to overcome limitations before mass-production at affordable prices is feasible. These limitations are related to the maximum growth rate yielding high quality material as well as the boule length that can be achieved together with high material quality.
Wireless capsule endoscopy (2003)

Gastroscopy, small bowel endoscopy, and colonoscopy are uncomfortable because they require comparatively large diameter flexible cables to be pushed into the bowel, which carry light by fibreoptic bundles, power, and video signals. Small bowel endoscopy is currently especially limited by problems of discomfort and failure to advance enteroscopes far into the small bowel. There is a clinical need for better methods to examine the small bowel especially in patients with recurrent gastrointestinal bleeding from this site.
Wafer bonding for MEMS and CMOS integration (2011)

Wafer bonding became during past decade an important technology for MEMS manufacturing and wafer-level 3D integration applications. The increased complexity of the MEMS devices brings new challenges to the processing techniques. In MEMS manufacturing wafer bonding can be used for integration of the electronic components (e.g. CMOS circuitries) with the mechanical (e.g. resonators) or optical components (e.g. waveguides, mirrors) in a single, wafer-level process step. However, wafer bonding with CMOS wafers brings additional challenges due to very strict requirements in terms of process temperature and contamination. These challenges were identified and wafer bonding process solutions will be presented illustrated with examples.