gebhart/patrepeval huggingface dataset:
Effects of High Frequency Chest Compression on Respiratory System Mechanics in Normal Subjects and Cystic Fibrosis Patients (1995)

OBJECTIVE: To investigate the short term effects of high frequency chest compression (HFCC) on several indices of respiratory system mechanics in normal subjects and patients with cystic fibrosis (CF). DESIGN: Comparative physiological approach. Subjects were blinded to 10 randomized HFCC settings (5, 10, 15, 20 and 25 Hz) with each applied at the lowest and at the highest background vest pressure. SETTING: Pulmonary function and lung mechanics laboratory, University of Alberta. PARTICIPANTS: Ten normal male volunteers (24.2±3.8 years) and 11 clinically stable CF patients (23.4±6.7 years). Normal subjects were nonsmokers who had normal lung function. The CF patients had a wide range of airway obstruction. INTERVENTIONS: HFCC was supplied by oscillating a pneumatic vest that covered the entire torso. Balloon tipped catheters were used to measure esophageal (Pes) and external chest wall (Pew) pressures. Changes in end‐expiratory lung volume (EELV) during HFCC were measured from a spirogram and were compared with baseline functional residual capacity (FRC). The HFCC induced air movement al the mouth, oscillated tidal volume (Vosc), was measured by reverse plethysmography. RESULTS: Both normals and CF patients had similar changes in Pes and EELV. At the highest background vest pressure and at the higher oscillation frequencies, EELV decreased approximately 30% from the no‐HFCC baseline FRC. Vosc decreased with increasing oscillation frequency but normals had higher Vosc than CF patients at each frequency. Conversion of Vose to flow () revealed that the highest occurred between 10 and 15 Hz for both normals and CF patients. Also, was dependent on the overall airway function. Low forced expired volume in 1 s resulted in low , especially when was measured during spontaneous expiration. CONCLUSIONS: CF patients with moderate or severe airway obstruction may gain maximal benefit from HFCC therapy when low vest pressure is used at an oscillation frequency of 10 to 15 Hz. The low vest pressure minimizes the decrease in EELV and 10 to 15 Hz maximizes .
Segmentation by surface-to-image registration (2006)

This paper presents a new image segmentation algorithm using surface-to-image registration. The algorithm employs multi-level transformations and multi-resolution image representations to progressively register atlas surfaces (modeling anatomical structures) to subject images based on weighted external forces in which weights and forces are determined by gradients and local intensity profiles obtained from images. The algorithm is designed to prevent atlas surfaces converging to unintended strong edges or leaking out of structures of interest through weak edges where the image contrast is low. Segmentation of bone structures on MR images of rat knees analyzed in this manner performs comparably to technical experts using a semi-automatic tool.
Greenhouse Gas Emissions from New Petrochemical Plants Background Information Paper for the Elaboration of Technical Notes and Guidelines for IDB Projects (2013)

The study encompasses background information on the relevant processing and "value chains" in the petrochemical industry within LAC, the current GHG emission control technologies available, and recommendations and relevant steps for the IDB, including the criteria to help evaluate the potential GHG emissions from the petrochemical sector and the criteria to help determine the minimal acceptable potential GHG emissions from petrochemical projects.
Human Immunodeficiency Virus Type 1 Env Trimer Immunization of Macaques and Impact of Priming with Viral Vector or Stabilized Core Protein (2008)

Currently there is limited information about the quality of immune responses elicited by candidate human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env)-based immunogens in primates. Here we describe a comprehensive analysis of neutralizing antibody and T-cell responses obtained in cynomolgus macaques by three selected immunization regimens. We used the previously described YU2-based gp140 protein trimers administered in an adjuvant, preceded by two distinct priming strategies: either alphavirus replicon particles expressing matched gp140 trimers or gp120 core proteins stabilized in the CD4-bound conformation. The rationale for priming with replicon particles was to evaluate the impact of the expression platform on trimer immunogenicity. The stable core proteins were chosen in an attempt to expand selectively lymphocytes recognizing common determinants between the core and trimers to broaden the immune response. The results presented here demonstrate that the platform by which Env trimers were delivered in the priming (either protein or replicon vector) had little impact on the overall immune response. In contrast, priming with stable core proteins followed by a trimer boost strikingly focused the T-cell response on the core sequences of HIV-1 Env. The specificity of the T-cell response was distinctly different from that of the responses obtained in animals immunized with trimers alone and was shown to be mediated by CD4(+) T cells. However, this regimen showed limited or no improvement in the neutralizing antibody responses, suggesting that further immunogen design efforts are required to successfully focus the B-cell response on conserved neutralizing determinants of HIV-1 Env.
Biochemical Characterization of the Catalytic Domain of Membrane-Type 4 Matrix Metalloproteinase (1999)

A C-terminal truncated form of membrane-type 4 matrix metalloproteinase (MT4-MMP; MMP 17), lacking the hemopexin-like and transmembrane domain, was expressed in Escherichia coli. The catalytic domain was produced by tryptic activation of the recombinant proenzyme and proved to be catalytically active towards the fluorogenic substrate for matrix metalloproteinases (7-methoxycoumarin-4-yl) acetyl-Pro-Leu-Gly-Leu(3-(2,4-dinitrophenyl)-L-2,3-diaminopro-p ionyl)-Ala-Arg-NH2. In contrast to the other three MT-MMPs (MT1-, MT2-, and MT3-MMP), the catalytic domain of MT4-MMP does not activate progelatinase A, nor does it hydrolyze one of the offered extracellular matrix (ECM) proteins, such as collagen types I, II, III, IV, and V, gelatin, fibronectin, laminin or decorin. TIMP-1, a poor inhibitor of MT1-, MT2- and MT3-MMP, suppresses MT4-MMP activity effectively. The progelatinase A/TIMP-2 complex that usually reacts like TIMP-2 also inhibits MT4-MMP. TIMP-2, a strong inhibitor of other MT-MMPS, inhibits MT4-MMP at low concentrations. With increasing TIMP-2 concentration, however, activity passes through a minimum and then increases until at high TIMP-2 concentration the activity is the same as in the absence of TIMP-2. TIMP-1 or the progelatinase A/TIMP-2 complex do not prevent reactivation of MT4-MMP catalytic domain at high TIMP-2 concentrations.
DIOS-MSEED: A Chip-Based Method for Measurement of Enantiomeric Excess by Kinetic Resolution/Mass Spectrometry (2001)

The determination of enantiomeric excess by kinetic resolution mass spectrometry has been implemented with the Desorption/Ionization On Silicon (DIOS) MS technique. Measurements can thereby be made much more rapidly than was previously possible, bringing this general methodology for screening asymmetric catalysts closer to true high-throughput status.
Bead-linked Proteoliposomes:  A Reconstitution Method for NMR Analyses of Membrane Protein−Ligand Interactions (2005)

Structural information about the interactions between membrane proteins and their ligands provides insights into the membrane protein functions. A variety of surfactants have been used for structural analyses of membrane proteins, and in some cases, they yielded successful results. However, the use of surfactants frequently increases the conformational instability of membrane proteins and distorts their normal function. Here, we propose a new strategy of membrane protein reconstitution into lipid bilayers on affinity beads, which maintains the native conformation and function of the protein for NMR studies. The reconstituted membrane proteins are suitable for NMR analyses of interactions, by using the transferred cross-saturation method. The strategy was successfully applied to the interaction between a potassium ion channel, KcsA, and a pore-blocker, agitoxin2 (AgTx2). This strategy would be useful for analyzing the interactions between various membrane proteins and their ligands.
P1‐096: TOMM40, APOE, and age of onset of Alzheimer's disease (2010)

A variable-length poly-T variant within intron 6 of the TOMM40 gene was found to correlate with the retrospectively determined age of Alzheimer's disease (AD) onset (Roses AD et al, 2009). TOMM40 encodes the translocase of the outer mitochondrial membrane pore subunit. Longer TOMM40 poly-T lengths (L) are associated with earlier age of AD onset than shorter TOMM40 (S) lengths. Because retrospective estimation of age of onset can be unreliable, we correlated TOMM40 genotype with prospectively determined age of onset of incident mild cognitive impairment (MCI) and AD to test the hypothesis that the TOMM40 L variant is associated with a younger age of symptomatic AD onset. Cognitively normal residents of Maricopa County age 21 years and older were recruited through local media ads into either the Arizona APOE cohort, a longitudinal study of cognitive aging or the Arizona Alzheimer's Disease Center cohort (Caselli RJ et al, 2009). The APOE-TOMM40 region was sequenced by Polymorphic DNA Technologies (Alameda, CA). TOMM40 poly-T lengths were converted to genotypes: short poly-T (14-20 T residues) = S, and long poly-T (≥21 T residues) = L. Symptom surveys, neurologic exams, and neuropsychological tests were repeated every 1-2 years. MCI and AD diagnoses met published diagnostic criteria. Of 37 incident cases of MCI and AD, DNA was available and sequenced in 30. Mean age of neuropsychologically confirmed symptomatic onset was 77.3 +/- 10.6 years that occurred 58.9 +/- 40.5 months after study entry. Incident MCI and AD subjects included 7 APOE e4/4's (all TOMM40 LL's, onset age 69 ± 6),10 APOE e3/4's (6 LL's, 4 SL's, onset ages 73 ± 9 and 84 ± 4), 11 APOE e3/3's (3 LL's, 8 SL's, onset ages 79 ± 18 and 83 ± 11 at clinical onset), and 2 APOE e2/3's (1 LL, 1 SL, onset ages 90 and 77). As predicted, LL's had a younger mean age at clinical onset than SL's in the overall group (73 ± 11 vs. 82 ± 9 years, p = 0.02). Additional cases are needed to test the association in APOE subgroups. The LL TOMM40 genotype was associated with younger age of incident MCI and AD onset compared to the SL genotype. A larger confirmatory study is underway.
Electrical impedance index in human skin: measurements after occlusion, in 5 anatomical regions and in mi Id irritant contact dermatitis (1993)

The electrical impedance in 23 healthy volunteers at 2-6 different skin sites was measured with a new impedance device, which makes possible non-invasive local measurements to a controlled depth. In 11 subjects, the test sites were occluded for 24 h using empty Finn Chambers and chambers with water, physiological saline, a paper disc or 0.002% sodium lauryl sulfate (SLS). In the normal skin of 10 subjects, the electrical impedance was measured from 5 different body areas for 5 consecutive days. In 3 subjects, daily measurements for 1 month were done, both from normal skin and from skin following the application of 2% SLS. The results show that the irritation index based on electrical skin impedance gives little day-to-day variation at one and the same test site, in comparison to the variations between different test sites on the same subject and the interindividual variations observed. Significant differences in impedance values between different anatomical regions of normal skin were found. Occlusion does not affect readings taken 24 h or later after removal, but increases variance for readings taken 1 h after removal. Effects on the skin of mild irritation and its recovery phase are easily monitored with the new device. Technology based on electrical impedance, in its newly presented form, with the advantages of improved geometrical definition and depth control, can be used as an objective tool to measure skin irritation. For detection of subclinical irritant contact dermatitis, repeated readings taken over several days may be needed.
Tourist Tour Planning Supported by Social Network Analysis (2012)

In line with the just recent "social machines" phenomena, this work proposes an extension based on social network analysis (SNA) to the tourist tour planning. It is able to estimate the tourist's satisfaction with individual Point of Interest (POI), and accordingly recommend or not that POI in the tour in view for that tourist. We first provide a model of developing a social network comprised of tourists and reviewers including their personal attributes (like age or gender in their social profile), preferences of reviewers for certain POIs, and tourists' preferences for certain types or categories of POIs (say archeology) in a given touristic destination. Then in the second part, an algorithm for grouping into "islands" of most similar reviewers to a certain tourist is defined. Additionally, a ranking algorithm based on authority centrality is adopted to identify the highest ranked reviewer within the island and recommend his preferred POI to a given tourist. The results of the evaluation tests prove our approach as feasible in estimating the tourist's satisfaction with individual POIs. Moreover, it is already promising since acting within a social network as opposed to its counterparts of less appreciation for the social dimension of user.
Independent domain folding of Pseudomonas exotoxin and single-chain immunotoxins: influence of interdomain connections. (1992)

We have studied the refolding of completely unfolded and reduced Pseudomonas exotoxin (PE) and of recombinant single-chain immunotoxins made with monoclonal antibody B3 that are composed of a heavy-chain variable region connected by a flexible linker to the corresponding light-chain variable region (Fv), which is in turn fused to a truncated form of PE. We have found by direct activity assays that different functional domains of these multifunctional proteins fold independently with different kinetics. The ADP-ribosylation domain of PE and of the recombinant immunotoxin fold rapidly, whereas the assembly of the binding and/or translocation domains is regained more slowly. The complete refolding of native PE occurs more rapidly than the refolding of the recombinant immunotoxins. To determine the influence of the connector region between the B3(Fv) moiety and the toxin on the folding process of the recombinant immunotoxin B3(Fv)-PE38KDEL, we have made two different mutations in the peptide that connects the single-chain Fv domain to domain II of PE. These molecules show different folding kinetics, differences in their propensity to aggregate, and different yields of correctly folded molecules. A mutation that decreases aggregation increases the rate of formation and the yield of active immunotoxin molecules.
Biotin-avidin-amplified enzyme immunoassay for detection of herpes simplex virus antigen in clinical specimens (1983)

A biotin-avidin-amplified enzyme-linked immunosorbent assay (B-A ELISA) has been developed to detect herpes simplex virus type 1 (HSV-1) and HSV-2 antigens in clinical specimens. The test was designed as a solid-phase, double-antibody, sandwich assay in which plates were coated with a polyclonal rabbit immunoglobulin G anti-HSV reagent, and the sandwich antibody was a biotin-labeled mouse immunoglobulin M monoclonal antibody that reacts with a common antigen associated with HSV-1 and HSV-2. The test can be completed in 4 h if antibody-coated plates are available. The detection limit of the B-A ELISA, determined by titration of virus stocks, was found to be approximately 90 PFU or 6 X 10(3) physical particles of either HSV-1 or HSV-2 per 50 microliter of virus stock. The following results were obtained in a study in which swabs were taken from a variety of lesions and assayed for infectivity in tissue culture and by B-A ELISA. Of 421 suspected HSV lesions tested, 69 were positive by both tests and 159 were negative by both tests. A total of 122 were positive by B-A ELISA but negative for infectivity. Seventy-one were negative by B-A ELISA but contained infectious virus. The HSV specificity of the assay was substantiated by partial blocking of reactivity with rabbit immunoglobulin G anti-HSV and by the absence of reactivity with a nonspecific biotin-labeled mouse immunoglobulin M monoclonal antibody.
Protein transfer of glycosyl-phosphatidylinositol-B7-1 into tumor cell membranes: a novel approach to tumor immunotherapy. (1999)

Modification of tumor cells with one or more costimulatory adhesion molecules has been proposed as a means to develop therapeutic cancer vaccines for use in human immunotherapy. Expression of B7-1 (CD80) in tumors by gene transfer creates an immunogenic tumor cell that induces antitumor immunity and protects mice from further challenge with wild-type tumor cells. In this report, we demonstrate that protein transfer of glycosyl-phosphatidylinositol (GPI)-anchored costimulatory molecules into tumor cell membranes could be used as an alternative to gene transfer for tumor immunotherapy. Incubation of isolated tumor membranes with purified GPI-anchored B7-1 results in stable incorporation of B7-1 on tumor cell membranes within a few hours. Immunization of C57BL/6 mice with EG7 tumor membranes modified to express GPI-B7-1 by protein transfer induces tumor-specific T-cell proliferation and CTLs. In addition, immunization with these EG7 membranes protects mice from parental tumor challenge. The protein transfer approach used here does not require foreign vectors or live tumor cells and is completed within a matter of hours. Irradiated cells or membrane preparations from fresh or frozen tumor tissue can be used. Therefore, protein transfer of glycolipid-anchored molecules provides an efficient and novel approach to modify tumor membranes for human immunotherapy. This approach is not limited to costimulatory molecules because any cell surface protein can be converted to a GPI-anchored form by recombinant techniques.
[Studies on fingerprinting and identification of main species of Herba Epimedii]. (2008)

The fingerprinting features of E. koreanum are rather different from others and can be used for the species identification. There are some common fingerprinting features in the most samples of E. brevicornu, E. acuminatum and E. myrianthum, respectively, and these features are seldom found in the samples of other species. The HPLC fingerprints of E. pubescens and E. leptorrhizum appear steadily among all samples of the species respectively, but it is difficult to distinguish the spcecies from other species with the HPLC fingerprints only. The HPLC fingerprints of E. sagittatum and E. wushanense vary greatly within the species. It is also showed that the quality of Herba Epimedii varied significantly according to the HPLC features.
Cancer invasion and micrometastasis visualized in live tissue by green fluorescent protein expression. (1997)

We report the establishment of stable, high-level green fluorescent protein (GFP)-expressing cell lines in vitro that permit the detection and visualization of distant micrometastases when they are implanted orthotopically in nude mice. Chinese hamster ovary cells were transfected with the dicistronic expression vector containing the humanized GFP cDNA. A stable GFP-expressing clone was selected in 1.5 microM methotrexate in vitro and injected s.c. in nude mice. Stable high-level expression of GFP was maintained in the s.c. growing tumors. To use GFP expression for metastasis studies, fragments of s.c. growing tumor, which are comprised of GFP-expressing cells, were implanted by surgical orthotopic implantation in the ovary of nude mice. Subsequent micrometastases were detected in systemic organs and could be visualized by GFP fluorescence in the lung, liver, and other organs down to the single-cell level. With this fluorescent tool, we detected and visualized for the first time tumor cells at the microscopic level in fresh viable tissue in their normal host organ. Confocal microscopy further enabled us to study physiologically relevant patterns of invasion and micrometastasis.
Validation of housekeeping genes for normalizing RNA expression in real-time PCR (2004)

Analysis of RNA expression using techniques like real-time PCR has traditionally used reference or housekeeping genes to control for error between samples. This practice is being questioned as it becomes increasingly clear that some housekeeping genes may vary considerably in certain biological samples. We used real-time reverse transcription PCR (RT-PCR) to assess the levels of 13 housekeeping genes expressed in peripheral blood mononuclear cell culture and whole blood from healthy individuals and those with tuberculosis. Housekeeping genes were selected from conventionally used ones and from genes reported to be invariant in human T cell culture. None of the commonly used housekeeping genes [e.g., glyceraldehyde-phosphate-dehydrogenase (GAPDH)] were found to be suitable as internal references, as they were highly variable (>30-fold maximal variability). Furthermore, genes previously found to be invariant in human T cell culture also showed large variation in RNA expression (>34-fold maximal variability). Genes that were invariant in blood were highly variable in peripheral blood mononuclear cell culture. Our data show that RNA specifying human acidic ribosomal protein was the most suitable housekeeping gene for normalizing mRNA levels in human pulmonary tuberculosis. Validations of housekeeping genes are highly specific for a particular experimental model and are a crucial component in assessing any new model.
Mechanisms of Function of Neural Grafts In The Adult Mammalian Brain (1987)

Evidence for the survival, growth and function of grafted neural tissues in the adult mammalian brain is reviewed. In addition to considering the viability of grafts in the different model systems that have been investigated, consideration is given to alternative mechanisms by which the grafts might exert a functional influence over the host brain and the host animal's behaviour: (a) acute influence over spontaneous recovery of function, (b) chronic but diffuse secretion of neurochemicals into the host neuropile, (c) tonic reinnervation of the host brain, (d) bridging grafts, and (e) reciprocal reinnervation and full incorporation of graft tissue into host circuitry. It is concluded that no one mechanism is primary, but that different levels of reorganization can take place in different graft paradigms and neural systems.
[The roles of PPARs in digestive diseases]. (2005)

Peroxisome proliferator-activated receptor gamma (PPARgamma), one of the nuclear receptors, is expressed at high levels in adipose tissue and is related to adipocyte differentiation and insulin sensitivity. PPARgamma is also expressed at high levels in digestive organs, especially in the colon epithelium. The physiological and pathological roles of PPARgamma in the gastrointestinal tract have been investigated and recognized as an endogenous regulator of innate immunity, inflammation, and cell proliferation. PPARgamma ligands have recently been reported to improve the condition of patients with non-alcoholic steatohepatitis (NASH). Thus, PPARgamma ligands are indeed potential benefit candidates for various digestive diseases. In this review, we will focus on the current knowledge and new insights of the roles of PPARgamma in digestive diseases, especially in (1) inflammatory bowel disease (IBD), (2) colon cancer, and (3) NASH.