gebhart/patrepeval huggingface dataset:
Distribution and origin of the basement membrane component perlecan in rat liver and primary hepatocyte culture. (1993)

Basement membranes contain three major components (ie collagen IV, laminin, and the heparan sulfate proteoglycan termed perlecan). Although the distribution and origin of both collagen IV and laminin have been well documented in the liver, perlecan has been poorly investigated, so far. We have studied the distribution and cellular origin of perlecan in rat livers in various conditions as well as in hepatocyte primary culture. By immunolocalization in both adult and 18-day-old fetal liver, perlecan was found in portal spaces, around central veins, and throughout the lobule. Immunoelectron microscopy revealed its presence at the level of basement membranes surrounding bile ducts and blood vessels, and in the space of Disse discontinuously interacting with hepatocyte microvilli. Precursors of perlecan were detected in the rough endoplasmic reticulum of bile duct cells and both vascular and sinusoidal endothelial cells. Both hepatocytes and Ito cells were negative. Northern-blot analysis confirmed the lack of appreciable expression of perlecan in hepatocytes isolated from either fetal or adult livers. In 18-month-diethylnitrosamine-treated rat liver, perlecan was abundant in neoplastic nodules. Electron microscopic investigation revealed an almost continuous layer of perlecan in the space of Disse and intracellular staining in sinusoidal endothelial cells, only. Perlecan mRNAs were detectable in malignant nodules, and absent in hepatocytes from nontumorous areas. Hepatocytes expressed high levels of perlecan mRNAs only when put in culture. This expression was reduced in conditions that allow improvement of hepatocyte survival and function (ie addition of corticoids, dimethylsulfoxide or nicotinamide to the medium, or in coculture with liver epithelial cells from biliary origin). Immunolocalization by light and electron microscopy showed that deposition of the proteoglycan occurred in coculture, in basement membranelike structures located around hepatocyte cords. In vitro attachment assay of hepatocytes on purified perlecan substrate indicated that these cells may interact with the proteoglycan through integrins which belong to the beta 1 family. These data suggest that deposition of perlecan in the space of Disse requires cellular cooperation. This article on perlecan, the third major component of hepatic basement membranes, shows a unique cellular origin in the liver and, as found for both collagen IV and laminin, an expression in adult hepatocytes when place in culture.
Global Haplotype Diversity in the Human Insulin Gene Region (2003)

The insulin minisatellite (INS VNTR) has been intensively analyzed due to its associations with diseases including diabetes. We have previously used patterns of variant repeat distribution in the minisatellite to demonstrate that genetic diversity is unusually great in Africans compared to non-Africans. Here we analyzed variation at 56 single nucleotide polymorphisms (SNPs) flanking the minisatellite in individuals from six populations, and we show that over 40% of the total genetic variance near the minisatellite is due to differences between Africans and non-Africans, far higher than seen in most genomic regions and consistent with differential selection acting on the insulin gene region, most likely in the non-African ancestral population. Linkage disequilibrium was lower in African populations, with evidence of clustering of historical recombination events. Analysis of haplotypes from the relatively nonrecombining region around the minisatellite revealed a star-shaped phylogeny with lineages radiating from an ancestral African-specific haplotype. These haplotypes confirmed that minisatellite lineages defined by variant repeat distributions are monophyletic in origin. These analyses provide a framework for a cladistic approach to future disease association studies of the insulin region within both African and non-African populations, and they identify SNPs which can be rapidly analyzed as surrogate markers for minisatellite lineage.
Prediction Models for Debonding Failure Loads of Carbon Fiber Reinforced Polymer Retrofitted Reinforced Concrete Beams (2006)

This study focuses on debonding failure in reinforced concrete beams with carbon fiber reinforced polymer composite bonded on the soffit using the wet lay-up method. An experimental study, which involved 26 tests, was carried out. The experiments showed two failure modes: Intermediate span debond and end debond. The first failure is the result of the high bond stress near the tip of a flexure-shear crack, whereas the second type of failure is due to the high shear stress developed in the weakest concrete layer at the tension reinforcement level. The experiments have shown that U-straps can be effective in preventing intermediate span and end debond. Based on experimental observations, two simple and practical theoretical models were developed and verified with the experimental data, together with a large database of other existing tests.
A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines (2014)

Cancer cell lines are a tremendous resource for cancer biology and therapy development. These multipurpose tools are commonly used to examine the genetic origin of cancers, to identify potential novel tumor targets, such as tumor antigens for vaccine devel-opment, and utilized to screen potential therapies in preclinical studies. Mutations, gene expression, and drug sensitivity have been determined for many cell lines using next-generation sequencing (NGS). However, the human leukocyte antigen (HLA) type and HLA expression of tumor cell lines, characterizations necessary for the development of cancer vaccines, have remained largely incomplete and, such information, when available, has been distributed in many publications. Here, we determine the 4-digit HLA type and HLA expression of 167 cancer and 10 non-cancer cell lines from publically available RNA-Seq data. We use standard NGS RNA-Seq short reads from "whole transcriptome" sequencing, map reads to known HLA types, and statistically determine HLA type, heterozygosity, and expression. First, we present previously unreported HLA Class I and II genotypes. Second, we determine HLA expression levels in each cancer cell line, providing insights into HLA downregulation and loss in cancer. Third, using these results, we provide a fundamental cell line "barcode" to track samples and prevent sample annotation swaps and contamination. Fourth, we integrate the cancer cell-line specific HLA types and HLA expression with available cell-line specific mutation information and existing HLA binding prediction algorithms to make a catalog of predicted antigenic mutations in each cell line. The compilation of our results are a fundamental resource for all researchers selecting specific cancer cell lines based on the HLA type and HLA expression, as well as for the development of immunotherapeutic tools for novel cancer treatment modalities.
Identifying and tracking suspicious activities through IP gray space analysis (2007)

Campus or enterprise networks often have many unassigned IP addresses that collectively form IP gray space within the address blocks of such networks. Using one-month traffic data collected in a large campus network, we have monitored a significant amount of unwanted traffic towards IP gray space in various forms, such as worms, port scanning, and denial of service attacks. In this paper, we apply a heuristic algorithm to extract the IP gray space in our campus network. Subsequently, we analyze the behavioral patterns such as dominant activities and target randomness, of the gray space traffic for individual outside hosts. By correlating and contrasting the traffic towards IP gray addresses and live end hosts, we find the gray space traffic provides unique insight for uncovering the behavior, and intention,of anomalous traffic towards live end hosts. Finally, we demonstrate the applications of gray space traffic for identifying SPAM behavior, detecting malicious scanning and worm activities that successfully compromise end hosts.
Integrated optical amplifier for fast phase modulated signals (1989)

The amplifier is based on the optical Kerr effect in waveguides with large third-order nonlinear susceptibility. The short response time of the Kerr effect gives the device an extremely large bandwidth, exceeding that of any laser amplifier. Also, for binary signals, the amplifier is shown to have a phase regenerative effect. Examples of signal and pump powers are given for polydiacetylene waveguides.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Atrophy and growth failure of rat hindlimb muscles in tail-cast suspension (1984)

Atrophy and growth failure of muscle in a tail-cast suspension model were evaluated in hindlimbs of female Sprague-Dawley rats. Based on measurements of food consumption, animal growth rate, urinary excretion of urea and ammonia, and muscle size, 6 days seemed to be the optimum duration of suspension for studying muscle unloading. After 6 days, the soleus, plantaris, and gastrocnemius muscles from suspended animals were 27, 10, and 11% smaller (P less than 0.05), respectively, than those from tail-casted weight-bearing animals. The extensor digitorum longus and tibialis anterior muscles were unaffected by suspension (less than or equal to 6 days) while the triceps brachii hypertrophied (8%, P less than 0.05). Wet weight-to-dry weight ratios were smaller in the plantaris (-0.19, P less than 0.05) and gastrocnemius (-0.19, P less than 0.05) muscles from suspended rats. In the plantaris, this difference coincided with a higher protein concentration (+12 mg/g, P less than 0.001). In vitro measurements of protein metabolism in the soleus muscles of suspended rats showed both slower protein synthesis (P less than 0.05) and faster protein degradation (P less than 0.05), whereas these processes were unaltered in the extensor digitorum longus muscles.
Optimizing wound treatment through health care structuring and professional education (2004)

Considerable developments have occurred in wound healing and care over the last few decades. Innovative technologies such as use of growth factors, bioengineered skin, topical negative pressure, heat, oxygen, and others have entered the clinic. These techniques have been advantageous, but even the most advanced and sophisticated product requires proper wound care and wound bed preparation in order to function optimally. It has been shown that the organization of a wound team, not the change in products, increases the healing of problem wounds (MTV Report, Denmark, 2003). Efficacy studies are generally performed in a few centers with investigators already experienced in the field. This probably leads to an optimal efficacy of the product. Problems arise when the product is marketed and is used by clinicians not specially educated in wound care. If no treatment plan and education is performed, product efficacy and cost-effectiveness decrease dramatically. This is clearly a major problem for patients, but also for communities and, in the end, for companies' sale of the product. Structuring of treatment and education is for these reasons the largest present challenge in the area of wound healing. The optimal way to treat nonhealing wounds is based on a multidisciplinary concept that has been implemented in a national health care system as a recognized expert function. It should consist of a specific treatment plan including modern wound care products and well-educated personnel. This structure is similar to other areas of the medical profession, but has to a lesser degree been established in the treatment of problem wounds. A growing understanding of the importance of this area is, however, shown by the increasing number of working groups focusing on organization and education in wound care. Presently the European Wound Management Association, the World Union of Wound Healing Societies, and The Danish Wound Healing Society have created such types of working groups.
Linear and non-linear transient patterns in the splay Freedericksz transition of nematics (1992)

A three-dimensional linear analysis of transient patterns occuring during the splay Freedericksz transition is presented including contributions relevant for the electrically driven case. The most rapidly growing modes have a wave vector predominantly along the initial directore alignment. The onset of the pattern formation is compared with the results of a nonlinear calculation carried out previously for the wave vector in the perpendicular direction. This shows that the nonlinear effect is the relevant mechanism for large dielectric anisotropy whereas for low anisotropy the linear pattern is favored. Preliminary experiments have been carried out with electric and magnetic fields using two materials with high and low dielectric anisotropy. Both, linear and nonlinear structures were found. A transition between the two types of patterns induced by changing the frequency of the applied electric field is presented.
Breast cancer cell migration is regulated through junctional adhesion molecule-A-mediated activation of Rap1 GTPase (2011)

Our findings provide compelling evidence of a novel role for JAM-A in driving breast cancer cell migration via activation of Rap1 GTPase and β1-integrin. We speculate that JAM-A over-expression in some breast cancer patients may represent a novel therapeutic target to reduce the likelihood of metastasis.
Design of Potent, Selective, and Orally Bioavailable Inhibitors of Cysteine Protease Cathepsin K (2003)

Osteoclast-mediated bone matrix resorption has been attributed to cathepsin K, a cysteine protease of the papain family that is abundantly and selectively expressed in osteoclast. Inhibition of cathepsin K could potentially be an effective method to prevent osteoporosis. Structure-activity studies on a series of reversible ketoamides based inhibitors of cathepsin K have led to identification of potent and selective compounds. Crystallographic studies have given insights into the mode of binding of these inhibitors. A series of ketoamides with varying P1 moieties were first synthesized to find an optimum group that would fit into the S1 subsite of the cysteine protease, cathepsin K. With a desired P1 group in place a variety of heterocyclic analogues in the P' region were synthesized to study their steric and electronic effects. In the process of exploring these P' heterocyclic variations, excellent selectivity was gained over other highly homologous cysteine proteases, including cathepsins L, S, and V. The favorable pharmacokinetic properties of some of these cathepsin K inhibitors in rats make them suitable for evaluation in rodent osteoporosis models. A representative cathepsin K inhibitor was shown to attenuate PTH-stimulated hypercalcemia in the TPTX rat model. These inhibitors provide a viable lead series in the discovery of new therapies for the prevention and treatment of osteoporosis
4,4′-Dimethoxytrityl and 4,4′,4″-trimethoxytrityl as protecting groups for amino functions; selectivity for primary amino groups and application in 15N-labelling (1997)

4,4′-Dimethoxytrityl tetrafluoroborate (DMT+ BF4–) and 4,4′,4″-trimethoxytrityl tetrafluoroborate (TMT+ BF4–) are useful reagents for protecting primary and some secondary amines. Protected amines are obtained either by reaction of DMT+ BF4– or TMT+ BF4– with the amine or by alkylating DMT- or TMT-amine (available from DMT+ BF4– and TMT+ BF4– by treatment with ammonia). Alkylation of DMT- or TMT-amine stops after monoalkylation. Deprotection of the alkylated DMT- and TMT-amine is achieved by treatment with an acid of appropriate molarity (e.g. 0.1 M HCl in 1∶1 tetrahydrofuran–water for TMT-amines). The value of the methodology described is illustrated by a synthesis of (15NH2) adenosine. X-Ray molecular structures of one DMT and two TMT derivatives are reported.
Water-soluble antioxidants in human tears: effect of the collection method. (2001)

The conflict in published data on tear antioxidants is caused by differences in collection methods. With the exception of urate, antioxidants accumulate to very high levels in corneal cells. Spuriously high antioxidant levels in tears collected using Schirmer strips, therefore, are most probably caused by contamination with intracellular constituents. The capillary tube collection method is proposed as the method of choice for reflex tear collection for biochemical studies. This less-invasive method facilitates the evaluation of tear antioxidant levels as a biomonitoring tool for corneal health. Although moderately increased antioxidant levels may be beneficial, the authors hypothesize that marked increases may indicate damage to the ocular surface.
Centromeric index versus DNA content flow karyotypes of human chromosomes measured by means of slit‐scan flow cytometry (1987)

We have applied slit-scan flow cytometry (SSFCM) to classify human chromosomes according to their centromeric index (CI) and relative DNA content. The resulting bivariate--CI vs. DNA content--distributions shows 14 peaks for normal human chromosomes. Distinct peaks are produced by chromosomes 1, 2, 3, 4 + 5, 6 + 7 + X, 8, 13 + 14 + 15, 16, 17 + 18, 19 + 20, and 21 + 22 + Y. In addition, chromosomes 9 through 12 are resolved into three peaks. The identity of the chromosomes comprising each peak was determined by comparing CI vs. DNA content distributions measured for normal human chromosomes by means of SSFCM with CI and DNA content values measured for human chromosomes with image analysis. The accuracy of CI measurement by SSFCM was verified by measuring CIs for human chromosomes isolated from human/rodent hybrid cell lines containing only a few known human chromosomes. These studies showed CIs measured for human chromosomes 1-19 and 21 to be in close agreement with the CIs calculated by means of image analysis. We further confirmed the chromosome assignments for each peak by showing that the relative volumes of the peaks in the CI vs. DNA content distributions for chromosomes from normal cells are similar to the relative frequencies of chromosomes expected for these peaks based on the peak assignments.
Artificial Vision for the Blind: Electrical Stimulation of Visual Cortex Offers Hope for a Functional Prosthesis (1974)

Electrical stimulation of the occipital cortex resulted in discrete photic sensations or "phosphenes" in two volunteers who had been totally blind for 7 and 28 years, respectively. Stimulation of multiple electrodes allowed one patient to recognize simple patterns, including letters. Both patients made an uneventful recovery, and the success of these experiments reinforces the hope that a functional visual prosthesis can be developed, although many problems remain to be solved.
Purinergic Modulation of Interleukin-1β Release from Microglial Cells Stimulated with Bacterial Endotoxin (1997)

Microglial cells express a peculiar plasma membrane receptor for extracellular ATP, named P2Z/P2X7 purinergic receptor, that triggers massive transmembrane ion fluxes and a reversible permeabilization of the plasma membrane to hydrophylic molecules of up to 900 dalton molecule weight and eventual cell death (Di Virgilio, F. 1995. Immunol. Today, 16:524-528). The physiological role of this newly cloned (Surprenant, A., F. Rassendren, E. Kawashima, R. A. North and G. Buell, 1996. Science (Wash. DC). 272:735-737) cytolytic receptor is unknown. In vitro and in vivo activation of the macrophage and microglial cell P2Z/P2X7 receptor by exogenous ATP causes a large and rapid release of mature IL-1 beta. In the present report we investigated the role of microglial P2Z/P2X7 receptor in IL-1 beta release triggered by LPS. Our data suggest that LPS-dependent IL-1 beta release involves activation of this purinergic receptor as it is inhibited by the selective P2Z/P2X7 blocker oxidized ATP and modulated by ATP-hydrolyzing enzymes such as apyrase or hexokinase. Furthermore, microglial cells release ATP when stimulated with LPS. LPS-dependent release of ATP is also observed in monocyte-derived human macrophages. It is suggested that bacterial endotoxin activates an autocrine/paracrine loop that drives ATP-dependent IL-1 beta secretion.
Reactions in supercritical fluids - a review (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions in supercritical fluids - a reviewBala Subramaniam and Mark A. McHughCite this: Ind. Eng. Chem. Process Des. Dev. 1986, 25, 1, 1–12Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/i200032a001https://doi.org/10.1021/i200032a001research-articleACS PublicationsRequest reuse permissionsArticle Views1500Altmetric-Citations210LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Lattice-mismatched approaches for high-performance, III-V photovoltaic energy converters (2005)

We discuss lattice-mismatched (LMM) approaches utilizing compositionally step-graded layers and buffer layers that yield III-V photovoltaic devices with performance parameters equaling those of similar lattice-matched (LM) devices. Our progress in developing high-performance, LMM, InP-based GaInAs/InAsP materials and devices for thermophotovoltaic (TPV) energy conversion is highlighted. A novel, monolithic, multi-bandgap, tandem device for solar PV (SPV) conversion involving LMM materials is also presented along with promising preliminary performance results.
Bandgap shifted InGaAsP/InP quantum well waveguidesusing MeV ion implantation (1995)

A large blue shift of the bandgap 90 nm, in an 1nGaAsP/InP quantum well (QW) pin laser structure using a single-step MeV phosphorous ion implantation is reported. The absorption constant at the original band-edge was reduced from 110 cm-1 to only 4 cm-1. No excess loss in the waveguide due to the QW intermixing process was observed. Current/voltage measurements indicate that junction characteristics are well maintained, providing a means of producing side-by-side active and passive sections using a simple, single processing step on laser structures fabricated using standard growth techniques.