gebhart/patrepeval huggingface dataset:
Membrane Pores Induced by Magainin (1996)

Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data.
Application-embedded retrieval from distributed free-text collections (1999)

A framework is presented for application-embedded information retrieval from distributed free-text collections. An application’s usage is sampled by an embedded information retrieval system. Samples are converted into queries to dis-tributed collections. Retrieval is adjusted through sample size and structure, anydata indexing, and dual space feedback. The framework is investi-gated with a retrieval system embedded in a text processor. The Problem The integration of query generation and feedback challenges information retrieval (IR) technologies. Rel-evance feedback (Aalbersberg 1992; Robertson and Walker 1997), while useful to information science pro-fessionals (Spink and Saracevic 1997), is frequently in-appropriate for lay users. Many users are unable to ade-quately state their information needs in queries (Burke, Hammond, and Young 1996). The constant, explicit so-licitation of relevance judgments interferes with many users ’ information-seeking behaviors (Kulyukin 1998c). Feedback utilization in the query space alone prohibits retrieval adjustments over multiple interactions (Ku-lyukin 1998a; Kulyukin, Hammond, and Burke 1998). The focus on maximizing the number of relevant docu-ments in every retrieval is inconsistent with many users’ information needs (Jansen et al. 1998). The approach to the integration of query generation and feedback henceforth presented is called application-embedded distributed IR. The approach is implemented in an embedded IR (EMIR) system for text proces-sors. The objective is a technology for building non-intrusive, feedback-sensitive IR tools that users embed into their applications to tap into and monitor informa-tion sources, while engaged in routine usages of those applications. The technology is motivated by a growing number of sources with a wealth of data, but few tools to timely put it to use.
Polymer nanocomposites exhibiting magnetically tunable microwave properties (2011)

Polymer nanocomposites (PNCs) have been synthesized using Rogers polymer and CoFe₂O₄ nanoparticles (CFO NPs). X-ray diffraction (XRD) confirms the inverse spinel crystal structure of CFO NPs and transmission electron microscopy (TEM) images show the uniform dispersion of nanoparticles (10 nm ± 1) into the polymer matrix. Magnetic measurements indicate superparamagnetic response near room temperature for all PNCs. A blocking temperature T(B)~298 K was observed and does not vary for different loading fractions of CFO NPs for the PNCs. The saturation magnetization (M(s)) was found to be 11 emu g⁻¹ for 30 wt% CFO, increasing to 32 emu g⁻¹ for the 80 wt% CFO loaded PNC. A large value of coercivity (H(c) = 19 kOe) is also observed at 10 K and is not affected by varying CFO loading. Microwave measurements show significant absorption in the 80 wt% CFO loading PNC and the quality factor shows a strong enhancement with applied magnetic field.
Gene Locater: Genetic linkage analysis software using three point testcross (2012)

The database is available for free at http://www.moperandib.com.
Short protocols in protein science : a compendium of methods from Current protocols in protein science (2003)

Strategies of Protein Purification & Characterization.Computational Analysis.Detection and Assay Methods.Extraction, Stabilization, and Concentration.Production of Recombinant Proteins.Purification of Recombinant Proteins.Characterization of Recombinant Proteins.Conventional Chromatographic Separations.Affinity Purification.Electrophoresis.Chemical Analysis.Post-Translational Modification: Glycosylation.Post-Translational Modification: Phosphorylation and Phosphatases.Post-Translational Modification: Specialized Applications.Chemical Modification of Proteins.Mass Spectrometry.Preparation and Handling of Peptides.Identification of Protein Interactions.Quantitation of Protein Interactions.Peptidases.Appendix 1: Reagents and Solutions.Appendix 2: Useful Measurements.Appendix 3: Commonly Used Techinques.Appendix 4: Suppliers.References.
Reproducibility of dynamic contrast‐enhanced MRI in human muscle and tumours: comparison of quantitative and semi‐quantitative analysis (2002)

The purpose of this study was to determine the reproducibility of dynamic contrast-enhanced (DCE)-MRI and compare quantitative kinetic parameters with semi-quantitative methods, and whole region-of-interest (ROI) with pixel analysis. Twenty-one patients with a range of tumour types underwent paired MRI examinations within a week, of which 16 pairs were evaluable. A proton density-weighted image was obtained prior to a dynamic series of 30 T(1)-weighted spoiled gradient echo images every 11.9 s with an intravenous bolus of gadopentetate dimeglumine given after the third baseline data point. Identical ROIs around the whole tumour and in skeletal muscle were drawn by the same observer on each pair of examinations and used for the reproducibility analysis. Semi-quantitative parameters, gradient, enhancement and AUC (area under the curve) were derived from tissue enhancement curves. Quantitative parameters (K(trans), k(ep), v(e)) were obtained by the application of the Tofts' model. Analysis was performed on data averaged across the whole ROI and on the median value from individual pixels within the ROI. No parameter showed a significant change between examinations. For all parameters except K(trans), the variability was not dependent on the parameter value, so the absolute values for the size of changes needed for significance should be used for future reference rather than percentages. The size of change needed for significance in a group of 16 in tumours for K(trans), k(ep) and v(e) was -14 to +16%, -0.20 ml/ml/min (15%) and -1.9[?]ml/ml (6%), respectively (pixel analysis), and -16 to +19%, -0.23 ml/ml/min (16%) and +/- 1.9[?]ml/ml (6%) (whole ROI analysis). For a single tumour, changes greater than -45 to +83%, +/- 0.78 ml/ml/min (60%) and +/- 7.6 ml/ml (24%), respectively, would be significant (pixel analysis). For gradient, enhancement and AUC the size of change needed for significance in tumours was -0.24 (17%), -0.05 (6%) and -0.06 (8%), respectively for a group of 16 (pixel analysis), and +/- 0.96 (68%), +/- 0.20 (25%) and +/- 0.22 (32%) for individuals. In muscle, the size of change needed for significance in a group of 16 for K(trans), k(ep) and v(e) was -30 to +44%, +/- 0.81 ml/ml/min (61%) and +/- 1.7 ml/ml (13%). For gradient, enhancement and AUC it was +/- 0.09 (20%), +/- 0.02 (8%) and +/- 0.03 (12%). v(e), enhancement and AUC are highly reproducible DCE-MRI parameters. K(trans), k(ep) and gradient have greater variability, with larger changes in individuals required to be statistically significant, but are nevertheless sufficiently reproducible to detect changes greater than 14-17% in a cohort of 16 patients. Pixel analyses slightly improve reproducibility estimates and retain information about spatial heterogeneity. Reproducibility studies are recommended when treatment effects are being monitored.
The 16-kDa Proteolytic Fragment of Insulin-Like Growth Factor (IGF) Binding Protein-3 Inhibits the Mitogenic Action of Fibroblast Growth Factor on Mouse Fibroblasts with a Targeted Disruption of the Type 1 IGF Receptor Gene (1997)

We previously reported that a 16-kDa proteolytic fragment of IGF Binding Protein-3 (IGFBP-3), which is devoid of affinity for IGFs, inhibits the mitogenic effects of IGF-I on chick embryo fibroblasts. Here, we set out to determine if the fragment had biological effects on fibroblasts from mouse embryos homozygous for a targeted disruption of the Type 1 IGF receptor gene. In the cell clone used, bFGF (but not IGF, EGF or PDGF) was mitogenic in serum-free medium, increasing 14C-thymidine uptake by a factor of 10-15 within 24 hours and doubling cell proliferation. The 16-kDa fragment, isolated by HPLC following limited proteolysis of recombinant human (rh) IGFBP-3 by plasmin, in both assays dose-dependently (20 to 100 ng/ml) inhibited (up to 100%) maximal stimulation induced by 25 ng/ml bFGF, whereas intact IGFBP-3 had virtually no effect. Similar results were obtained with control wild-type cells. In the latter, the mitogenic activity of 1% fetal calf serum (equal to that of 25 ng/ml bFGF) was inhibited by only 25-30% by 100 ng/ml 16-kDa fragment or 200 ng/ml rhIGFBP-3. This agrees with an antagonistic action, affecting the mitogenic activity of serum that is attributable to IGFs. The 16-kDa IGFBP-3 fragment therefore appears to be a potent inhibitor of mitogenic signals resulting from activation of both the type 1 IGF and FGF receptors.
Image registration for image-based rendering (2005)

Image-based rendering (IBR) has received much attention in recent years for its ability to synthesize photo-realistic novel views. To support translational motion, existing IBR methods either require a large amount of reference images or assume that some geometric information is available. However, rendering with a large amount of images is very expensive in terms of image acquisition, data storage, and memory costs. As IBR accepts various kinds of geometric proxy, we may use image registration techniques, such as stereo matching and structure and motion recognition, to obtain geometric information to help reduce the number of images required. Unfortunately, existing image registration techniques only support a small search range and require closely sampled reference images. This results in a high spatial sampling rate, making IBR impractical for use in scalable walkthrough environments. Our primary objective of this project is to develop an image registration technique that would recover the geometric proxy for IBR while, at the same time, reducing the number of reference images required. In this paper, we analyze the roles and requirements of an image registration technique for reducing the spatial sampling rate. Based on these requirements, we present a novel image registration technique to automatically recover the geometric proxy from reference images. With the distinguishing feature of supporting a large search range, the new method can accurately identify correspondences even though the reference images may only be sparsely sampled. This can significantly reduce the acquisition effort, the model size, and the memory cost.
A dynamic prognostic model to predict survival in primary myelofibrosis: a study by the IWG-MRT (International Working Group for Myeloproliferative Neoplasms Research and Treatment) (2009)

Age older than 65 years, hemoglobin level lower than 100 g/L (10 g/dL), white blood cell count greater than 25 x 10(9)/L, peripheral blood blasts 1% or higher, and constitutional symptoms have been shown to predict poor survival in primary myelofibrosis (PMF) at diagnosis. To investigate whether the acquisition of these factors during follow-up predicts survival, we studied 525 PMF patients regularly followed. All 5 variables had a significant impact on survival when analyzed as time-dependent covariates in a multivariate Cox proportional hazard model and were included in 2 separate models, 1 for all patients (Dynamic International Prognostic Scoring System [DIPSS]) and 1 for patients younger than 65 years (age-adjusted DIPSS). Risk factors were assigned score values based on hazard ratios (HRs). Risk categories were low, intermediate-1, intermediate-2, and high in both models. Survival was estimated by the HR. When shifting to the next risk category, the HR was 4.13 for low risk, 4.61 for intermediate-1, and 2.54 for intermediate-2 according to DIPSS; 3.97 for low risk, 2.84 for intermediate-1, and 1.81 for intermediate-2 according to the age-adjusted DIPSS. The novelty of these models is the prognostic assessment of patients with PMF anytime during their clinical course, which may be useful for treatment decision-making.
<title>Local annealing of shape memory alloys using laser scanning and computer vision</title> (2000)

A complete set-up for local annealing of Shape Memory Alloys (SMA) is proposed. Such alloys, when plastically deformed at a given low temperature, have the ability to recover a previously memorized shape simply by heating up to a higher temperature. They find more and more applications in the fields of robotics and micro engineering. There is a tremendous advantage in using local annealing because this process can produce monolithic parts, which have different mechanical behavior at different location of the same body. Using this approach, it is possible to integrate all the functionality of a device within one piece of material. The set-up is based on a 2W-laser diode emitting at 805nm and a scanner head. The laser beam is coupled into an optical fiber of 60(mu) in diameter. The fiber output is focused on the SMA work-piece using a relay lens system with a 1:1 magnification, resulting in a spot diameter of 60(mu) . An imaging system is used to control the position of the laser spot on the sample. In order to displace the spot on the surface a tip/tilt laser scanner is used. The scanner is positioned in a pre-objective configuration and allows a scan field size of more than 10 x 10 mm<SUP>2</SUP>. A graphical user interface of the scan field allows the user to quickly set up marks and alter their placement and power density. This is achieved by computer controlling X and Y positions of the scanner as well as the laser diode power. A SMA micro-gripper with a surface area less than 1 mm<SUP>2</SUP> and an opening of the jaws of 200(mu) has been realized using this set-up. It is electrically actuated and a controlled force of 16mN can be applied to hold and release small objects such as graded index micro-lenses at a cycle time of typically 1s.
Test Methods for Measuring Material Properties of Composite Materials in all Three Material Axes (2012)

Material properties were determined for fiber-reinforced polymers (FRPs) with respect to all three material orientations using existing ASTM standards when applicable. Determining strength and stiffness properties both in-plane (load applied parallel to fiber orientation) and out-of-plane (load applied perpendicular to fiber orientation) is important in designing for ballistic protection. Shear strength, shear modulus, compressive strength, compressive modulus, tension strength, tensile modulus, and Poisson’s ratio were all measured in the plane of the fibers and out-of-plane. In order to measure certain out-of-plane material properties, unique testing standards were developed. Test standards that are available for obtaining out-of-plane properties are tedious to perform particularly since premature failures occur at bonds between the composites and fixtures. In addition, there are currently no existing standards intended for measuring out-of-plane compressive properties and Poisson’s ratio. Finally, materials tested in this research had a defined thickness ranging from 1.91 cm to 3.81 cm which caused conflicts with existing standards meant to be performed with longer specimens. This paper provides solutions for measuring each material property by summarizing all testing and fabrication procedures required.
Toxicology and pharmacokinetics of intravesical gemcitabine: a preclinical study in dogs. (1999)

More active and well-tolerated agents are needed for the treatment of superficial bladder cancer. This study investigated intravesical gemcitabine to establish the toxicology and pharmacokinetics necessary for clinical trials. Beagle dogs (in groups of 2; n = 6) received 100 mg, 350 mg, or 1 g of drug by intravesical administration on alternate days three times/week for 4 weeks. Animals were observed for clinical signs of toxicity; gemcitabine levels and peripheral blood counts were taken three times weekly. The dogs were euthanized, and a full necropsy was performed at days 1 and 14 after the last dose. Intravesical gemcitabine was given at 100 mg (n = 2), 350 mg (equivalent to the 1000 mg/m2 human dose; n = 3), and 3.5 g (n = 1). i.v. gemcitabine was given at 350 mg (n = 2). Plasma samples drawn at time points up to 8 h were analyzed for systemic absorption and clearance of drug. Doses of 100 and 350 mg were well tolerated with no clinical side effects. Necropsies revealed normal bone marrow cellularity and normal bladder histology. At 1 g, signs of severe clinical toxicity were evident, and after only three doses, necropsies demonstrated severe bone marrow hypoplasia, cystitis, and intestinal necrosis. At all intravesical doses, significant systemic absorption was seen. The T1/2 (+/- SD) for intravesical and i.v. administration of 350 mg was 328 (+/-6.8) min and 99.3 (+/-5.2) min, respectively (P<0.001). Intravesical gemcitabine is well tolerated and has no direct bladder toxicity at doses up to 1000 mg/m2. Higher doses result in gastrointestinal, bladder, and bone marrow toxicity.
NOD/LtSz- Rag1 null Mice: An Immunodeficient and Radioresistant Model for Engraftment of Human Hematolymphoid Cells, HIV Infection, and Adoptive Transfer of NOD Mouse Diabetogenic T Cells (2000)

Development of a small animal model for the in vivo study of human immunity and infectious disease remains an important goal, particularly for investigations of HIV vaccine development. NOD/Lt mice homozygous for the severe combined immunodeficiency (Prkdcscid) mutation readily support engraftment with high levels of human hematolymphoid cells. However, NOD/LtSz-scid mice are highly radiosensitive, have short life spans, and a small number develop functional lymphocytes with age. To overcome these limitations, we have backcrossed the null allele of the recombination-activating gene (Rag1) for 10 generations onto the NOD/LtSz strain background. Mice deficient in RAG1 activity are unable to initiate V(D)J recombination in Ig and TCR genes and lack functional T and B lymphocytes. NOD/LtSz-Rag1null mice have an increased mean life span compared with NOD/LtSz-scid mice due to a later onset of lymphoma development, are radioresistant, and lack serum Ig throughout life. NOD/LtSz-Rag1null mice were devoid of mature T or B cells. Cytotoxic assays demonstrated low NK cell activity. NOD/LtSz-Rag1null mice supported high levels of engraftment with human lymphoid cells and human hemopoietic stem cells. The engrafted human T cells were readily infected with HIV. Finally, NOD/LtSz-Rag1null recipients of adoptively transferred spleen cells from diabetic NOD/Lt+/+ mice rapidly developed diabetes. These data demonstrate the advantages of NOD/LtSz-Rag1null mice as a radiation and lymphoma-resistant model for long-term analyses of engrafted human hematolymphoid cells or diabetogenic NOD lymphoid cells.
Tyrosine phosphorylation of three cellular proteins correlates with transformation of rat 1 cells by pp60src (1991)

The analysis of phosphotyrosine-containing proteins in Rat 1 cells overexpressing either the tyrosine kinase pp60c-src or genetic variants containing alterations in functional and structural domains has led to the identification of three proteins whose tyrosine phosphorylation correlated with pp60src-induced cellular transformation. The tyrosine phosphorylation of one of these proteins, p120, has been previously shown by us and others to coincide with the presence of kinase-activated, membrane-associated pp60src in chicken embryo cells. The second protein was identified as the ras-associated GTPase-activating protein (GAP). The third protein whose tyrosine phosphorylation was markedly elevated in Rat 1 cells expressing activated, membrane-bound forms of pp60src had an apparent molecular mass of 64-67 kDa. The electrophoretic mobility of this protein varied in cells expressing different pp60src variants. The tyrosine-phosphorylated form of p64-67 was present in immune complexes containing GAP, suggesting a stable interaction between these two cellular proteins.
Image reconstruction from fan-beam projections on less than a short scan (2002)

This work is concerned with 2D image reconstruction from fan-beam projections. It is shown that exact and stable reconstruction of a given region-of-interest in the object does not require all lines passing through the object to be measured. Complete (non-truncated) fan-beam projections provide sufficient information for reconstruction when 'every line passing through the region-of-interest intersects the vertex path in a non-tangential way'. The practical implications of this condition are discussed and a new filtered-backprojection algorithm is derived for reconstruction. Experiments with computer-simulated data are performed to support the mathematical results.
Dataflow process networks (1995)

We review a model of computation used in industrial practice in signal processing software environments and experimentally and other contexts. We give this model the name "dataflow process networks," and study its formal properties as well as its utility as a basis for programming language design. Variants of this model are used in commercial visual programming systems such as SPW from the Alta Group of Cadence (formerly Comdisco Systems), COSSAP from Synopsys (formerly Cadis), the DSP Station from Mentor Graphics, and Hypersignal from Hyperception. They are also used in research software such as Khoros from the University of New Mexico and Ptolemy from the University of California at Berkeley, among many others. Dataflow process networks are shown to be a special case of Kahn process networks, a model of computation where a number of concurrent processes communicate through unidirectional FIFO channels, where writes to the channel are nonblocking, and reads are blocking. In dataflow process networks, each process consists of repeated "firings" of a dataflow "actor." An actor defines a (often functional) quantum of computation. By dividing processes into actor firings, the considerable overhead of context switching incurred in most implementations of Kahn process networks is avoided. We relate dataflow process networks to other dataflow models, including those used in dataflow machines, such as static dataflow and the tagged-token model. We also relate dataflow process networks to functional languages such as Haskell, and show that modern language concepts such as higher-order functions and polymorphism can be used effectively in dataflow process networks. A number of programming examples using a visual syntax are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>