gebhart/patrepeval huggingface dataset:
Regenerative Potential of Embryonic Renal Multipotent Progenitors in Acute Renal Failure (2007)

Bone marrow-and adult kidney-derived stem/progenitor cells hold promise in the development of therapies for renal failure. Here is reported the identification and characterization of renal multipotent progenitors in human embryonic kidneys that share CD24 and CD133 surface expression with adult renal progenitors and have the capacity for self-renewal and multilineage differentiation. It was found that these CD24+CD133+ cells constitute the early primordial nephron but progressively disappear during nephron development until they become selectively localized to the urinary pole of Bowman's capsule. When isolated and injected into SCID mice with acute renal failure from glycerol-induced rhabdomyolysis, these cells regenerated different portions of the nephron, reduced tissue necrosis and fibrosis, and significantly improved renal function. No tumorigenic potential was observed. It is concluded that CD24+CD133+ cells represent a subset of multipotent embryonic progenitors that persist in human kidneys from early stages of nephrogenesis. The ability of these cells to repair renal damage, together with their apparent lack of tumorigenicity, suggests their potential in the treatment of renal failure.
Binding of human respiratory syncytial virus to cells: implication of sulfated cell surface proteoglycans (2000)

Binding of human respiratory syncytial virus (HRSV) to cultured cells was measured by flow cytometry. Using this assay and influenza virus as a control virus with a well-characterized receptor, a systematic search of cell surface molecules that might be implicated in HRSV binding was carried out. Treatment of cells with different enzymes or with other reagents suggested that heparin-like glycosaminoglycans (GAGs) were involved in attachment of HRSV, but not influenza virus, to host cells. This was further confirmed by a lack of binding of HRSV to CHO-K1 mutant cell lines deficient in glycosylation or GAGs biosynthesis and by an inhibition of binding after preincubation of virus with heparin and other GAGs. The degree of sulfation, more than the polysaccharide backbone of GAGs, seems to be critical for virus binding.
A general method for comparing the expected performance of tracking and motion capture systems (2005)

We introduce a general method for evaluating and comparing the expected performance of sensing systems for interactive computer graphics. Example applications include head tracking systems for virtual environments, motion capture systems for movies, and even multi-camera 3D vision systems for image-based visual hulls.Our approach is to estimate the asymptotic position and/or orientation uncertainty at many points throughout the desired working volume, and to visualize the results graphically. This global performance estimation can provide both a quantitative assessment of the expected performance, and intuition about the type and arrangement of sources and sensors, in the context of the desired working volume and expected scene dynamics.
Biochemical markers of bone turnover: part I: biochemistry and variability. (2005)

With the ageing population in most countries, disorders of bone and mineral metabolism are becoming increasingly relevant to every day clinical practice. Consequently, the interest in, and the need for effective measures to be used in the screening, diagnosis and follow-up of such pathologies has markedly grown. Together with clinical and imaging techniques, biochemical tests play an important role in the assessment and differential diagnosis of metabolic bone disease. In recent years, the isolation and characterisation of cellular and extracellular components of the skeletal matrix have resulted in the development of molecular markers that are considered to reflect either bone formation or bone resorption. These biochemical indices are non-invasive, comparatively inexpensive and, when applied and interpreted correctly, helpful tools in the diagnostic and therapeutic assessment of metabolic bone disease. Part I of this article provides an overview of the basic biochemistry of bone markers, and sources of non-specific variability. Part II (to be published in a subsequent issue of this journal) will review the current evidence regarding the clinical use of biochemical markers of bone remodelling in metabolic and metastatic bone disease.
Positive inotropic and lusitropic effects of HNO/NO − in failing hearts: Independence from β-adrenergic signaling (2003)

Nitroxyl anion (HNONO(-)), the one-electron reduced form of nitric oxide (NO), induces positive cardiac inotropy and selective venodilation in the normal in vivo circulation. Here we tested whether HNO/NO(-) augments systolic and diastolic function of failing hearts, and whether contrary to NO/nitrates such modulation enhances rather than blunts beta-adrenergic stimulation and is accompanied by increased plasma calcitonin gene-related peptide (CGRP). HNO/NO(-) generated by Angelis' salt (AS) was infused (10 microg/kg per min, i.v.) to conscious dogs with cardiac failure induced by chronic tachycardia pacing. AS nearly doubled contractility, enhanced relaxation, and lowered cardiac preload and afterload (all P < 0.001) without altering plasma cGMP. This contrasted to modest systolic depression induced by an NO donor diethylamine(DEA)NO or nitroglycerin (NTG). Cardiotropic changes from AS were similar in failing hearts as in controls despite depressed beta-adrenergic and calcium signaling in the former. Inotropic effects of AS were additive to dobutamine, whereas DEA/NO blunted beta-stimulation and NTG was neutral. Administration of propranolol to nonfailing hearts fully blocked isoproterenol stimulation but had minimal effect on AS inotropy and enhanced lusitropy. Arterial plasma CGRP rose 3-fold with AS but was unaltered by DEA/NO or NTG, supporting a proposed role of this peptide to HNO/NO(-) cardiotropic action. Thus, HNO/NO(-) has positive inotropic and lusitropic action, which unlike NO/nitrates is independent and additive to beta-adrenergic stimulation and stimulates CGRP release. This suggests potential of HNO/NO(-) donors for the treatment of heart failure.
The ICSI Meeting Project: Resources and Research (2004)

This paper provides a progress report on ICSI’s Meeting Project, including both the data collected and annotated as part of the project, as well as the research lines such materials support. We include a general description of the official “ICSI Meeting Corpus”, as currently available through the Linguistic Data Consortium, discuss some of the existing and planned annotations which augment the basic transcripts provided there, and describe several research efforts that make use of these materials. The corpus supports wideranging efforts, from low-level processing of the audio signal (including automatic speech transcription, speaker tracking, and work on far-field acoustics) to higher-level analyses of meeting structure, content, and interactions (such as topic and sentence segmentation, and automatic detection of dialogue acts and meeting “hot spots”). 1.
Finite-length unequal error protection rateless codes: design and analysis (2005)

A generalization of rateless codes (LT and Raptor codes) to provide unequal error protection (UEP) property is proposed in this paper. The proposed codes (UEP-LT and UEP-Raptor codes) are analyzed for the best possible performance over the binary erasure channel (BEC) in finite-length cases. We derive upper and lower bounds on the bit error probabilities under the maximum-likelihood (ML) decoding. We further verify our work with simulations. Simulation results indicate that the bounds are tight for small error rates, and the proposed codes have strong UEP property.
A soluble activity from adherent marrow cells cooperates with IL 3 in stimulating growth of pluripotential hematopoietic precursors (1988)

Marrow cells from 5-fluorouracil (5-FU)-treated mice formed few or no mixed erythroid colonies when plated in semisolid medium with interleukin 3 (IL 3) and erythropoietin (Ep) alone. When conditioned medium (CM) from plastic-adherent marrow or thymus cells was also included, however, growth of mixed erythroid colonies was strongly stimulated. Both IL 3 and the accessory activity (AA) had to be present at the initiation of the cultures for growth to occur. AA was also produced by a cloned immortalized line (95/1.7) of fibroblastoid marrow cells that lacked macrophage-specific cell surface markers. Colony- stimulating factor-1 (CSF-1) was also released, but not granulocyte colony-stimulating activity. When 95/1.7 CM was analyzed by gel filtration, AA eluted with an apparent size of 35 kd and separated completely from the CSF-1. Biologic assays failed to detect IL 1 or IL 3 activity in 95/1.7 CM. Growth of mixed erythroid colonies from 5-FU- treated marrow is thus stimulated by adherent marrow cell-derived factors that appear distinct not only from the known CSFs including IL 3, but also from IL 1.
Handbook of Indices of Food Quality and Authenticity (1997)

Food quality and authenticity indicators Cereal grains Fruit and vegetables Dairy products Meat, fish and poultry Oils and fats Spices, flavourants and condiments Tea, coffee and cocoa Quality indicators for processed foods.
Single-electron charging and periodic conductance resonances in GaAs nanostructures (1990)

Narrow channels interrupted by two controlled potential barriers and having a tunable electron density were made in GaAs, and their conductance was measured at low temperatures. Reproducible and accurately periodic oscillations of the conductance with changing density are found to correspond to the sequential addition of single electrons to the segment of the channel between the barriers. Detailed examination of the line shape of the conductance versus density provides a new insight into the transport mechanism.
Implications of fundamental threshold voltage variations for high-density SRAM and logic circuits (2002)

As the number of transistors integrated on a circuit continues to increase, roughly doubling every 18 months, the impact of transistor variations on circuit performance becomes more significant. Even in the absence of systematic variations (implant nonuniformities, Leff and Weff variations), there exists a fundamental variability in the threshold voltage V/sub T/ due to the finite number of dopant atoms in the extremely small MOSFET channel area. This work presents for the first time the impact of these fundamental V/sub T/ variations on SRAM cell stability and CMOS logic performance. We also analyze the impact of device scaling on these V/sub T/ variations and propose guidelines for future SRAM cell design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lysosomal Phospholipase A2 Is Selectively Expressed in Alveolar Macrophages (2004)

Lung surfactant is the surface-active agent comprised of phospholipids and proteins that lines pulmonary alveoli. Surfactant stabilizes the alveolar volume by reducing surface tension. Previously, we identified a lysosomal phospholipase A2, termed LPLA2, with specificity toward phosphatidylcholine and phosphatidylethanolamine. The phospholipase is localized to lysosomes, is calcium-independent, has an acidic pH optimum, and transacylates ceramide. Here, we demonstrate that LPLA2 is selectively expressed in alveolar macrophages but not in peritoneal macrophages, peripheral blood monocytes, or other tissues. Other macrophage-associated phospholipase A2s do not show a comparable distribution. LPLA2 is of high specific activity and recognizes disaturated phosphatidylcholine as a substrate. The lysosomal phospholipase A2 activity is six times lower in alveolar macrophages from mice with a targeted deletion of the granulocyte macrophage colony-stimulating factor (GM-CSF), a model of impaired surfactant catabolism, compared with those from wild-type mice. However, LPLA2 activity and protein levels are measured in GM-CSF null mice in which GM-CSF is expressed as a transgene under the control of the surfactant protein C promoter. Thus LPLA2 may be a major enzyme of pulmonary surfactant phospholipid degradation by alveolar macrophages and may be deficient in disorders of surfactant metabolism.
Cavity quantum electrodynamics for superconducting electrical circuits: An architecture for quantum computation (2004)

We propose a realizable architecture using one-dimensional transmission line resonators to reach the strong-coupling limit of cavity quantum electrodynamics in superconducting electrical circuits. The vacuum Rabi frequency for the coupling of cavity photons to quantized excitations of an adjacent electrical circuit (qubit) can easily exceed the damping rates of both the cavity and qubit. This architecture is attractive both as a macroscopic analog of atomic physics experiments and for quantum computing and control, since it provides strong inhibition of spontaneous emission, potentially leading to greatly enhanced qubit lifetimes, allows high-fidelity quantum nondemolition measurements of the state of multiple qubits, and has a natural mechanism for entanglement of qubits separated by centimeter distances. In addition it would allow production of microwave photon states of fundamental importance for quantum communication.
Critical factors in the design of growth factor releasing scaffolds for cartilage tissue engineering (2008)

Engineering defined scaffolds that deliver growth factors in a controlled way is a task seldom attained. If growth factor delivery appears to be beneficial overall, the optimal delivery conditions for cartilage reconstruction should be more thoroughly investigated.
An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi (2005)

RNA interference (RNAi) mediates gene silencing in many eukaryotes and has been widely used to investigate gene functions. A common method to induce sustained RNAi is introducing plasmids that synthesize short hairpin RNAs (shRNAs) using Pol III promoters. While these promoters synthesize shRNAs and elicit RNAi efficiently, they lack cell specificity. Monitoring shRNA expression levels in individual cells by Pol III promoters is also difficult. An alternative way to deliver RNAi is to use Pol II-directed synthesis of shRNA. Previous efforts in developing a Pol II system have been sparse and the results were conflicting, and the usefulness of those Pol II vectors has been limited due to low efficacy. Here we demonstrate a new Pol II system that directs efficient shRNA synthesis and mediates strong RNAi at levels that are comparable with the commonly used Pol III systems. In addition, this system synthesizes a marker protein under control of the same promoter as the shRNA, thus providing an unequivocal indicator, not only to the cells that express the shRNA, but also to the levels of the shRNA expression. This system may be adapted for in vivo shRNA expression and gene silencing.
Characterization of 2 Influenza A(H3N2) Clinical Isolates with Reduced Susceptibility to Neuraminidase Inhibitors Due to Mutations in the Hemagglutinin Gene (2002)

Previous studies have shown that amino acid changes in the hemagglutinin (HA) gene of influenza viruses may result in decreased susceptibility to neuraminidase inhibitors (NAIs) in vitro. However, the emergence and characteristics of such HA variants in the clinical setting remain poorly studied. Herein, we report 2 influenza A(H3N2) isolates, from untreated patients, harboring an Arg229-->Ile substitution in the HA1 gene. The Ile229 variants were as sensitive as the Arg229 viruses to zanamivir and oseltamivir in neuroaminidase inhibition assays but were significantly less susceptible (by 60-140-fold) in cell-based assays. Although the Ile229 variants adsorbed less efficiently to Madin-Darby canine kidney (MDCK) cells in kinetic binding assays, they remained very sensitive to zanamivir in ferrets. Our study shows the importance of the HA1 229 residue in virus binding to MDCK cells and confirms the unreliability of cell-based assays in predicting the in vivo susceptibility of HA variants to NAIs.
Prediction of irinotecan and 5-fluorouracil toxicity and response in patients with advanced colorectal cancer (2010)

Irinotecan and 5-fluorouracil (5-FU) are used to treat metastatic colorectal cancer. Irinotecan's active metabolite is inactivated by UDP-glucuronosyltransferase 1A1 (UGT1A1), which is deficient in Gilbert's syndrome. Irinotecan and metabolites are transported by P-glycoprotein, encoded by ABCB1. 5-FU targets folate metabolism through inhibition of thymidylate synthase (TYMS). Methylenetetrahydrofolate reductase (MTHFR) generates active folate necessary for haematopoiesis. We retrospectively genotyped 140 Swedish and Norwegian irinotecan and 5-FU-treated colorectal cancer patients from the Nordic VI clinical trial for selected variants of UGT1A1, ABCB1, TYMS and MTHFR. We found an increased risk of clinically relevant early toxicity in patients carrying the ABCB1 3435 T/T genotype, Odds ratio (OR)=3.79 (95% confidence interval (CI)=1.09-13.2), and in patients carrying the UGT1A1(*)28/(*)28 genotype, OR=4.43 (95% CI=1.30-15.2). Patients with UGT1A1(*)28/(*)28 had an especially high risk of neutropenia, OR=6.87 (95% CI=1.70-27.7). Patients who had reacted with toxicity during the first two cycles were in total treated with fewer cycles (P<0.001), and less often responded to treatment (P<0.001). Genetic variation in ABCB1 was associated with both early toxicity and lower response to treatment. Carriers of the ABCB1 1236T-2677T-3435T haplotype responded to treatment less frequently (43 vs 67%, P=0.027), and survived shorter time, OR=1.56 (95% CI=1.01-2.45).
Synthesis and Biological Evaluation of Tryptamines Found in Hallucinogenic Mushrooms: Norbaeocystin, Baeocystin, Norpsilocin, and Aeruginascin (2020)

A general synthetic method was developed to access known tryptamine natural products present in psilocybin-producing mushrooms. <i>In vitro</i> and <i>in vivo</i> experiments were then conducted to inform speculations on the psychoactive properties, or lack thereof, of the natural products. In animal models, psychedelic activity by baeocystin alone was not evident using the mouse head twitch response assay, despite its putative dephosphorylated metabolite, norpsilocin, possessing potent agonist activity at the 5-HT<sub>2A</sub> receptor.
Microarray-Based Detection of Protein Binding and Functionality by Gold Nanoparticle Probes (2005)

We report a microarray format for the detection of proteins and protein functionality (kinase activity) based on marking either specific antibody-protein binding or peptide phosphorylation events by attachment of gold nanoparticles followed by silver deposition for signal enhancement. The attachment of the gold nanoparticles is achieved by standard avidin-biotin chemistry. The detection principle is resonance light scattering. Highly selective recognition of standard proteins (proteins A and G) down to 1 pg/mL for proteins in solution and 10 fg for proteins on the microarray spots is demonstrated. Enzyme activity of the kinase (PKA) is detected with high specificity down to a limit of 1 fg for an established peptide substrate (kemptide) on the microarray spots. Kinase inhibition by the inhibitor (H89) is shown, demonstrating the potential for high-throughput screening for inhibitors.
Multicolor Imaging of Endoplasmic Reticulum-Located Esterase As a Prodrug Activation Enzyme (2014)

The carboxylesterase families of enzymes are key participants in phase I drug metabolism processes. Carboxylesterase families 1 and 2 are of particular clinical relevance. These enzymes produce endoplasmic reticulum localization signals, are primarily localized in the endoplasmic reticulum, and hydrolyze a wide range of ester-containing prodrugs into an activated form. In order to detect enzymes belonging to both families, we developed an optical multicolor imaging technique, which provides a distinct color window for multicolor imaging. This technique required the design and synthesis of three new mechanistic colored probes that fluoresce red, green, or blue and are based on the quinone methide cleavage process. These activity-based probes allow rapid and clear visualization with high specificity against the endoplasmic reticulum in cultured cells based on endoplasmic reticulum localized esterases including both families of carboxylesterase enzymes.
Phase conjugate optics and real-time holography (1978)

Nonlinear optical mixing can be used to perform a variety of new optical functions, as well as real-time holography. The theory and some of the first experiments are described.
Comparative effects of plateletderived growth factor‐BB and insulin‐like growth factor‐I, individually and in combination, on periodontal regeneration in Macaca fascicularis (1996)

Platelet-derived growth factor (PDGF) and insulin-like growth factor I (IGF-I) in combination have previously been shown to enhance periodontal regeneration. The objective of this study was to further characterize the biological effects of this combination of growth factors in non-human primates and compare the effects to those of each growth factor individually. Ligature-induced periodontitis was initiated in 10 cynomolgus monkeys. After periodontal lesions were established, surgery was performed, and either a methylcellulose gel vehicle or vehicle containing 10 micrograms each of either PDGF-BB, IGF-I or both PDGF-BB and IGF-I was applied to exposed root surfaces. Biopsies were taken 4 and 12 wk after treatment and the extent of periodontal regeneration was assessed by histomorphometry. At both 4 and 12 wk vehicle-treated lesions generally revealed minimal osseous defect fill (ODF) (8.5 +/- 2.1% and 14.5 +/- 5.7%, respectively) and new attachment (NA) (34.1 +/- 5.2% and 26.6 +/- 10.5%, respectively). IGF-I treatment did not significantly alter healing compared to vehicle in any parameter at both 4 and 12 wk. PDGF-BB-treated sites exhibited significant (p < 0.05) regeneration of NA (69.6 + 12.0%) at 12 wk; trends for PDGF-BB treatment effect were also observed in other parameters at 4 and 12 wk, although these increases were not statistically significant. Treatment with PDGF-BB/IGF-I resulted in 21.6 +/- 5.1% and 42.5 +/- 8.3% ODF at 4 and 12 wk, respectively, and 64.1 +/- 7.7% and 74.6 +/- 7.4% NA at 4 and 12 wk, respectively (all significantly greater than vehicle, p < 0.05). The results from this study demonstrated that: 1) IGF-I alone at the dose tested did not significantly alter periodontal wound healing; 2) PDGF-BB alone significantly stimulated NA, with trends of effect on other parameters; and 3) the PDGF-BB/IGF-I combination resulted in significant increases in NA and ODF above vehicle at both 4 and 12 wk.