gebhart/patrepeval huggingface dataset:
Femoral vein thrombosis and total hip replacement. (1977)

Of 160 patients who underwent total hip replacement, 81 developed venographic evidence of thrombi in the operated leg. In 46 cases (57%) the thrombus originated from the femoral vein, and in 43 of these the exact site of origin was defined by venography. In 34 cases (74%) the thrombus arose from the wall of the femoral vein at the level of the lesser trochanter. This region was studied by intraoperative venography in eight patients undergoing total hip replacement, and in every case severe distortion of the common femoral vein was observed, producing almost total occlusion. We suggest that intraoperative damage to the femoral vein results from manipulation of the leg, and that this is one reason why the operation is followed by a high incidence of deep vein thrombosis in the upper femoral region.
Real-time 3D image registration for functional MRI (1999)

Subject head movements are one of the main practical difficulties with brain functional MRI. A fast, accurate method for rotating and shifting a three-dimensional (3D) image using a shear factorization of the rotation matrix is described. Combined with gradient descent (repeated linearization) on a least squares objective function, 3D image realignment for small movements can be computed as rapidly as whole brain images can be acquired on current scanners. Magn Reson Med 42:1014-1018, 1999.
Tumor imaging by means of proteolytic activation of cell-penetrating peptides (2004)

We have devised and tested a new strategy for selectively delivering molecules to tumor cells. Cellular association of polyarginine-based, cell-penetrating peptides (CPPs) is effectively blocked when they are fused to an inhibitory domain made up of negatively charged residues. We call these fusions activatable CPPs (ACPPs) because cleavage of the linker between the polycationic and polyanionic domains, typically by a protease, releases the CPP portion and its attached cargo to bind to and enter cells. Association with cultured cells typically increases 10-fold or more upon linker cleavage. In mice xenografted with human tumor cells secreting matrix metalloproteinases 2 and 9, ACPPs bearing a far-red-fluorescent cargo show in vivo contrast ratios of 2-3 and a 3.1-fold increase in standard uptake value for tumors relative to contralateral normal tissue or control peptides with scrambled linkers. Ex vivo slices of freshly resected human squamous cell carcinomas give similar or better contrast ratios. Because CPPs are known to import a wide variety of nonoptical contrast and therapeutic agents, ACPPs offer a general strategy toward imaging and treating disease processes associated with linker-cleaving activities such as extracellular proteases.
Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae (2013)

RNA contains various chemical modifications that expand its otherwise limited repertoire to mediate complex processes like translation and gene regulation. 25S rRNA of the large subunit of ribosome contains eight base methylations. Except for the methylation of uridine residues, methyltransferases for all other known base methylations have been recently identified. Here we report the identification of BMT5 (YIL096C) and BMT6 (YLR063W), two previously uncharacterized genes, to be responsible for m3U2634 and m3U2843 methylation of the 25S rRNA, respectively. These genes were identified by RP-HPLC screening of all deletion mutants of putative RNA methyltransferases and were confirmed by gene complementation and phenotypic characterization. Both proteins belong to Rossmann-fold-like methyltransferases and the point mutations in the S-adenosyl-L-methionine binding pocket abolish the methylation reaction. Bmt5 localizes in the nucleolus, whereas Bmt6 is localized predominantly in the cytoplasm. Furthermore, we showed that 25S rRNA of yeast does not contain any m5U residues as previously predicted. With Bmt5 and Bmt6, all base methyltransferases of the 25S rRNA have been identified. This will facilitate the analyses of the significance of these modifications in ribosome function and cellular physiology.
Magnitude and economic effect of overuse of antisecretory therapy in the ambulatory care setting. (2010)

Proton pump inhibitors are often overused in the ambulatory care setting without documented valid indications. Inappropriate use of PPIs is associated with substantial cost expenditure and with the potential for adverse events.
Robust Protein Profiling with Complex Antibody Microarrays in a Dual-Colour Mode (2011)

Antibody microarrays are a multiplexing technique for the analyses of hundreds of different analytes in parallel from small sample volumes of few microlitres only. With sensitivities in the picomolar to femtomolar range, they are gaining importance in proteomic analyses. These sensitivities can be obtained for complex protein samples without any pre-fractionation or signal amplification. Also, no expensive or elaborate protein depletion steps are needed. As with custom DNA-microarrays, the implementation of a dual-colour assay adds to assay robustness and reproducibility and was therefore a focus of our technical implementation. In order to perform antibody microarray experiments for large sets of samples and analytes in a robust manner, it was essential to optimise the experimental layout, the protein extraction, labelling and incubation as well as data processing steps. Here, we present our current protocol, which is used for the simultaneous analysis of the abundance of more than 800 proteins in plasma, urine, and tissue samples.
Genetic and expressional alterations of CHD genes in gastric and colorectal cancers (2011)

Frameshift mutation and loss of expression of CHD genes are common in GCs and CRCs with MSI-H.These alterations might contribute to cancer pathogenesis by deregulating CHD-mediated chromatin remodelling.
Pluripotent hematopoietic stem cells of low and high density can repopulate W/Wv mice. (1992)

We have studied several features of pluripotent hematopoietic stem cells (PHSC) and day-12 spleen colony-forming units (CFU-S12) in murine bone marrow. C57BL/6J marrow cell suspensions were separated by elutriation and fractions were obtained at flow rates (FR) of 25 ml/min, 29/30 ml/min, 35 ml/min, and with the rotor off. All four fractions contained PHSC that could repopulate W/Wv mice, but significant numbers of CFU-S12 were found only in the three higher FR fractions. Cells in the FR29/30 fraction were shown to have almost three-fold more repopulating activity than fresh marrow in a competitive repopulation assay. The PHSC in fractions separated by elutriation were enriched by depleting cells expressing specific lineage markers with monoclonal antibodies and magnetic immunobeads. As few as 10(4) lineage negative (lin-) cells from FR35 or 10(5) lin--cells from FR25 conferred long-term multilineage repopulation in W/Wv mice, as demonstrated by Southern blot analysis of DNA from recipient thymus and bone marrow. We conclude that PHSC are heterogeneous for cell size and density and that the highest concentration of PHSC resides in the subset of intermediate density present in the FR29/30 fraction.
Set-Membership Acoustic Tracking of Autonomous Underwater Vehicles (2002)

Summary A set-membership algorithm is presented for tracking of Autonomous Underwater Vehicles (AUVs) from acoustic time-of-flight measurements received by a field of surface floating buoys. The algorithm assumes that measurement errors and AUV dynamics uncertainties are of unknown but bounded magnitude, with known bounds, and produces as output the set of admissible AUV positions. The proposed procedure has been validaied by srmulations in which uncertainty models have been obtained from field data at sea. Tracking performance is shown superior than that of the Extended Kalman Filter (EKF) in presence of biased disturbances.
Functional expression of indoleamine 2,3-dioxygenase by murine CD8α+ dendritic cells (2002)

Immunoregulatory antigen-presenting cells (APC) play an important role in maintaining T cell homeostasis and self-tolerance. In particular, recent evidence demonstrates a role for inhibition of T cell proliferation by macrophage tryptophan catabolism involving the activity of the enzyme indoleamine 2,3-dioxygenase (IDO). Dendritic cells (DC) have also been shown to exert immunoregulatory effects mediated by tryptophan catabolism and to cause T cell apoptosis. In the present study, we have comparatively analyzed the expression of IDO activity by murine macrophages and splenic DC. By means of PCR, Western blotting and measurements of enzyme functional activity, we obtained evidence that, different from macrophages, DC constitutively express IDO. Following activation by IFN-gamma, the latter cells, in particular the CD8 alpha(+) subset, exhibit high functional activity and, unlike macrophages, mediate apoptosis of T(h) cells in vitro. Therefore, in the mouse, CD8 alpha(+) DC may be unique APC capable of fully expressing the IDO mechanism functionally.
Defining cytolytic T lymphocyte recognition of chemically modified self. I. Response to trinitrophenyl-H-2Kk. (1985)

We used purified class I antigen incorporated into liposomes to examine the response of secondary cytolytic T lymphocytes (CTL) to chemically modified self. By generating the secondary response in the presence of T cell helper factor, the level of CTL response was limited by CTL recognition of added antigen rather than by helper cell generation of lymphokines. We found a strong secondary response against chemically modified self when spleen cells from trinitrophenyl (TNP)-primed C3H/HeJ mice were stimulated with a) TNP-modified liposomes containing H-2Kk, b) liposomes containing H-2Kk purified from TNP-modified RDM-4 (H-2k) cells, or c) liposomes containing the limited trypsin proteolysis product of H-2Kk that had been directly modified with TNP. In contrast, we were not able to generate a significant CTL response with unmodified H-2Kk incorporated into vesicles along with TNP-modified membrane components lacking H-2Kk. These results suggest that TNP-modified H-2Kk is a major antigenic site recognized by CTL from C3H/HeJ mice after priming against TNP-modified self.
Clearance of Pseudomonas aeruginosa from the murine gastrointestinal tract is effectively mediated by O-antigen-specific circulating antibodies (1995)

The colonization of mucosal surfaces by Pseudomonas aeruginosa can lead to local or disseminated disease. Secretory immunoglobulin A (IgA) has been assumed to be responsible for preventing mucosal colonization by interfering with the binding of bacterial ligands to epithelial surface receptors. However, the efficacy of this mechanism of immunity derives little actual support from in vivo experiments. In an investigation of the role of local and systemic immunization strategies in reducing colonization of the gastrointestinal tract of mice by P. aeruginosa, the bacterial antigens that were potential targets for immune effectors promoting mucosal clearance were identified. Levels of gastrointestinal colonization were reduced when immunity to homologous O antigens, but not that to pili or flagella, was elicited. Oral vaccination with attenuated Salmonella typhimurium expressing P. aeruginosa serogroup O11 antigen elicited mucosal and serum IgA antibodies and serum IgG antibodies specific for the recombinant antigen. Oral challenge of immunized mice with P. aeruginosa serogroup O11 demonstrated protection against gastrointestinal colonization. Intraperitoneal immunization with a serogroup O11 high-molecular-weight O-polysaccharide antigen elicited only serum IgG and IgM antibodies yet was as effective as oral vaccination in protecting mice against gastrointestinal colonization. This finding was confirmed by the demonstration that intraperitoneal immunization with purified lipopolysaccharide was also protective against mucosal surface colonization. These results call into question the need for local immune effectors, particularly secretory IgA, directed at bacterial ligands for epithelial surface components, in protecting a mucosal surface from bacterial challenge.
High Expression of FAP in Colorectal Cancer Is Associated With Angiogenesis and Immunoregulation Processes (2020)

Fibroblast activation protein α (FAP) plays an important role in tissue remodeling and helps tumor cells invade surrounding tissue. We sought to investigate FAP as a prognostic molecular marker in colorectal cancer (CRC) using immunohistochemical and transcriptomic data. <i>FAP</i> expression and clinicopathological information were obtained from The Cancer Genome Atlas data set. The association of <i>FAP</i> expression and tissue cellular heterogeneity landscape was explored using the xCell method. We evaluated FAP protein expression in a cohort of 92 CRCs and 19 non-tumoral tissues. We observed that <i>FAP</i> was upregulated in tumors both at the mRNA and protein levels, and its expression was associated with advanced stages, poor survival, and consensus molecular subtype 4. <i>FAP</i> expression was also associated with angiogenesis and collagen degradation. We observed an enrichment in immune-cell process-related genes associated with <i>FAP</i> overexpression. Colorectal cancers with high <i>FAP</i> expression display an inflamed phenotype enriched for macrophages and monocytes. Those tumors showed enrichment for regulatory T cell populations and depletion of T<sub>H</sub>1 and natural killer T cells, pointing to an immunosuppressive environment. Colorectal cancers with high levels of stromal FAP are associated with aggressive disease progression and survival. Our results suggest that FAP plays additional roles in tumor progression such as modulation of angiogenesis and immunoregulation in the tumor microenvironment.
Antenna engineering handbook (1961)

Introduction to Antennas.Fundamentals of Antennas.Arrays of Discrete Elements.Dipoles and Monopoles.Loop Antennas.Small Antennas.Microstrip Antennas.Slot Antennas.Slot-Antenna Arrays.Leaky-Wave Antennas.Long-Wire Antennas.Surface-Wave Antennas and Surface-Wave Excited Arrays.Helical Antennas.Frequency-Independent Antennas.Horn Antennas.Lens Antennas.Reflector Antennas.Feeds for Lenses and Reflectors.Electromechanical Scanning Antennas.Frequency-Scan Antennas.Phased Arrays.Conformal and Low-Profile Arrays.Adaptive Antennas.Methods of Polarization Synthesis.Low-Frequency Antennas.Medium-Frequency Broadcast Antennas.High-Frequency Antennas.VHF and UHF Communications Antennas.TV and FM Transmitting Antennas.TV Receiving Antennas.Microwave-Relay Antennas, Radiometer Antennas.Radar Antennas.Microwave Beacon Antennas.Tracking Antennas.Satellite Antennas.Earth Station Antennas.Aircraft Antennas.Seeker Antennas.Direction-Finding Antennas and Systems.ECM and ESM Antennas.Radio-Telescope Antennas.Transmission Lines and Waveguide.Impedance Matching and Broadbanding.Radomes.Microwave Propagation.Antenna Measurements.Materials and Design Data.
Design and accuracy evaluation of high-speed and high precision parallel mechanism (2002)

We have developed a precise and high-speed arm applied to assembly processes in electrical product and machine industries. The arm is designed based on the requirement from Japanese major industries. The paper addresses the background of the development, the required specification for the robot arm, and the brief introduction of the prototype arm and evaluations of accuracy. We test the repeatability of parallel mechanism. Then we calibrate the kinematic model of parallel mechanism to improve its absolute accuracy using laser tracking coordinate measuring system.
Synthesis of Linear, β-Cyclodextrin-Based Polymers and Their Camptothecin Conjugates (2003)

6(A),6(D)-Bis-(2-amino-2-carboxylethylthio)-6(A),6(D)-dideoxy-beta-cyclodextrin 1, a diamino acid derivative of beta-cyclodextrin, is synthesized and condensed with difunctionalized PEG comonomers to give linear, high molecular weight (M(w) over 50 kDa) beta-cyclodextrin-based polymers (2-4) with pendant functionality (carboxylate). 2-4 are all highly soluble in aqueous solutions (over 200 mg/mL). 20-O-trifluoroglycinylcamptothecin, 5a, and 20-O-trifluoroglycinylglycinylglycinylcamptothecin, 5b, are synthesized and conjugated to 2 to give polymer-camptothecin (CPT) prodrugs. The solubility of CPT is increased by more than three orders of magnitude when it is conjugated to 2. The rates of CPT release from the conjugates HGGG6 (high molecular weight polymer (M(w) 97 kDa), glyglygly linker and 6 wt % CPT loading) and HG6 (high MW polymer (M(w) 97 kDa), gly linker and 6 wt % CPT loading) in either mouse or human plasma are dramatically accelerated over the rates of pure hydrolysis at pH = 7.4, indicating the presence of enzymatic cleavage as a rate-determining step at this pH in the release of the CPT. The pH of aqueous solution has a large effect on hydrolysis rate of CPT from HGGG6 and HG6; the lower the pH, the slower the rate in the range at 4.1 <or= pH <or= 13.1. The IC(50)'s of polymer 2e, CPT, and the CPT conjugates HG6 and HGGG6 are found to be cell-line dependent with LS174T, HT29, A2780, and PC3 cells using in vitro MTT assays. The parent polymer 2e has very low toxicity to all cultured cells tested.
Kynurenine Pathway Measurements in Huntington's Disease Striatum: Evidence for Reduced Formation of Kynurenic Acid (1990)

Recent evidence suggests that there may be overactivation of the N-methyl-D-aspartate (NMDA) subtype of excitatory amino acid receptors in Huntington's disease (HD). Tryptophan metabolism by the kynurenine pathway produces both quinolinic acid, an NMDA receptor agonist, and kynurenic acid, an NMDA receptor antagonist. In the present study, multiple components of the tyrosine and tryptophan metabolic pathways were quantified in postmortem putamen of 35 control and 30 HD patients, using HPLC with 16-sensor electrochemical detection. Consistent with previous reports in HD putamen, there were significant increases in 5-hydroxyindoleacetic acid, 5-hydroxytryptophan, and serotonin concentrations. Within the kynurenine pathway, the ratio of kynurenine to kynurenic acid was significantly (p less than 0.01) increased twofold in HD patients as compared with controls, consistent with reduced formation of kynurenic acid in HD. CSF concentrations of kynurenic acid were significantly reduced in HD patients as compared with controls and patients with other neurologic diseases. Because kynurenic acid is an endogenous inhibitor of excitatory neurotransmission and can block excitotoxic degeneration in vivo, a relative deficiency of this compound could directly contribute to neuronal degeneration in HD.
Genome-wide copy-number variation analysis identifies common genetic variants at 20p13 associated with aggressiveness of prostate cancer (2011)

The genetic determinants for aggressiveness of prostate cancer (PCa) are poorly understood. Copy-number variations (CNVs) are one of the major sources for genetic diversity and critically modulate cellular biology and human diseases. We hypothesized that CNVs may be associated with PCa aggressiveness. To test this hypothesis, we conducted a genome-wide common CNVs analysis in 448 aggressive and 500 nonaggressive PCa cases recruited from Johns Hopkins Hospital (JHH1) using Affymetrix 6.0 arrays. Suggestive associations were further confirmed using single-nucleotide polymorphisms (SNPs) that tagged the CNVs of interest in an additional 2895 aggressive and 3094 nonaggressive cases, including those from the remaining case subjects of the JHH study (JHH2), the NCI Cancer Genetic Markers of Susceptibility (CGEMS) Study, and the CAncer of the Prostate in Sweden (CAPS) Study. We found that CNP2454, a 32.3 kb deletion polymorphism at 20p13, was significantly associated with aggressiveness of PCa in JHH1 [odds ratio (OR) = 1.30, 95% confidence interval (CI): 1.01-1.68; P = 0.045]. The best-tagging SNP for CNP2454, rs2209313, was used to confirm this finding in both JHH1 (P = 0.045) and all confirmation study populations combined (P = 1.77 × 10(-3)). Pooled analysis using all 3353 aggressive and 3584 nonaggressive cases showed the T allele of rs2209313 was significantly associated with an increased risk of aggressive PCa (OR = 1.17, 95% CI: 1.07-1.27; P = 2.75 × 10(-4)). Our results indicate that genetic variations at 20p13 may be responsible for the progression of PCa.
Regioselective oxidation of phospho‐NSAIDs by human cytochrome P450 and flavin monooxygenase isoforms: implications for their pharmacokinetic properties and safety (2012)

CYPs and FMOs play an important role in the metabolism of phospho-NSAIDs, resulting in differential pharmacokinetic profiles between phospho-NSAIDs and NSAIDs in vivo. The consequently more rapid detoxification of phospho-NSAIDs is likely to contribute to their greater safety.
Fast mode decision algorithm for Residual Quadtree coding in HEVC (2011)

High Efficiency Video Coding (HEVC) is an in- progress next generation video coding standard. It has a similar basic structure to the ITU/MPEG H.264/AVC coder but with further enhancement on each coding tool to increase compression efficiency. Thus, a Residual Quadtree (RQT) coding scheme is adopted in the conventional transform coding procedure. The cost is the additional computation complexity when compared to the fixed-size transform. In this paper, we design a fast algorithm for Residual Quadtree mode decision. Considering the Rate-Distortion efficiency, we replace the original depth-first mode decision process by a Merge-and-Split decision process. Furthermore, because a substantial numbers of zero-blocks are produced after quantization and mode decision, we reduce the unnecessary computation by using the inheritance property of zero-blocks. In addition, for nonzero-blocks, two early termination schemes are developed for both TU Merge and TU Split procedures, respectively. Comparing to HM 2.0, our method saves the RQT encoding time from 42% to 55% for a number of test videos with negligible coding loss.
Development of photocrosslinkable hyaluronic acid‐polyethylene glycol‐peptide composite hydrogels for soft tissue engineering (2004)

Hyaluronic acid (HA; also called hyaluronan) is a naturally derived, nonimmunogenic, nonadhesive glycosaminoglycan that has important roles in several wound-healing processes. In previous work, we created photocrosslinkable glycidyl methacrylate-HA (GMHA) hydrogel biomaterials that were cytocompatible, biologically active, and had a decreased rate of hyaluronidase degradation compared with native HA. The goal of the studies presented herein was to explore peptide conjugation techniques to further adjust the material and biological properties of the GMHA hydrogels. We conjugated GMHA with acrylated forms of polyethylene glycol (PEG) and PEG-peptides to yield GMHA-PEG-peptide composite hydrogels. By varying the reactant concentrations, we created stable hydrogels with high peptide conjugation efficiencies (up to 80%), controllable peptide concentrations (in the range of 1-6 micromol peptide per milliliter of hydrogel), and defined physicochemical properties (e.g., swelling ratio, enzymatic degradation rate). These composite hydrogels may prove to be a promising scaffolding biomaterial for a variety of soft tissue engineering applications.