gebhart/patrepeval huggingface dataset:
Characterization and enrichment of murine hemopoietic stem cells by fluorescence activated cell sorting. (1981)

Several methods for supravital staining of mouse bone marrow cells are described. These methods were employed to sort fractions of bone marrow cells by a light activated cell sorter and to determine cytochemical properties of hemopoietic stem cells. Labelling with fluoresceinated wheat germ lectin confirmed that the stem cells are among the bone marrow cells with the highest surface density of N-acetylneuraminic acid. Staining with tetracycline revealed that the stem cells contain relatively active or relatively many mitochondria. Staining with the bisbenzimide H33342, a supravital DNA stain, indicated that most pluripotent stem cells are in a G0/G1 state of the cell cycle. Using these and other measurements, separation protocols can be devised to concentrate stem cells. Some of these are discussed.
Autologous Peritoneal Mesothelial Cell Implant in Rabbits and Peritoneal Dialysis Patients (1991)

Human and rabbit peritoneal mesothelial cells have been successfully cultured and autoimplanted. An original biopsy technique was used to take samples of peritoneal mesothelial cells and after culture they were characterized from the structural and caryological points of view. Staphylococcal peritonitis was induced in 12 rabbits with indwelling peritoneal catheters and after 4 days of antibiotics 6 of them were autoimplanted with cultured autologous mesothelial cells previously marked in 3 cases with thymidine (H3TdR). Direct morphological observation and autoradiography were used to compare the mesothelium of control rabbits and implanted rabbits sacrificed on days 3 and 6 and showed that the cell implants had taken. Four uremic CAPD patients recovering from severe peritonitis were implanted with about 300 million autologous peritoneal mesothelial cells, previously cultured and frozen. Morphological signs of taking were evident from peritoneal laparoscopy biopsies performed 3 and 6 days after implant. The aim of the study was merely to demonstrate that such implants are possible; however, the techniques may have interesting applications not only in peritoneal dialysis, but also in the vaster fields of medicine and surgery.
On improving the accuracy of structured light systems (2006)

We propose a nonlinear calibration method for improving the accuracy of structured light systems that use cameras and projectors. Previously we have developed a systematic method for the calibration of projectors as well as structured light systems for 3-D shape measurement. However, we used only a linear model and did not consider lens distortions of the camera and the projector. As a result, measurement accuracy was limited. In this paper, we develop nonlinear models for both the camera and the projector and apply them to develop a nonlinear algorithm for 3-D shape measurement. The aim is to improve system accuracy by reducing the nonlinear error caused by lens distortion. Experimental results on nonlinear camera and projector calibration, comparison of 3-D measurement errors with linear and nonlinear camera and projector models, as well as 3-D shape measurement of some sample objects are presented.
Differential regulation of inducible nitric oxide synthase by fibroblast growth factors and transforming growth factor beta in bovine retinal pigmented epithelial cells: inverse correlation with cellular proliferation. (1993)

Bovine retinal pigmented epithelial (RPE) cells express, after activation with interferon gamma (IFN-gamma) and lipopolysaccharide (LPS), an inducible nitric oxide synthase (NOS). Experiments were done to investigate the effects of the transforming growth factor beta 1, epidermal growth factor, and fibroblast growth factors (FGFs), which are abundant in the retina, on NOS activity. Transforming growth factor beta 1 slightly increases the production of nitrite, an oxidation product of NO, induced by LPS plus IFN-gamma, whereas acidic and basic FGFs markedly inhibit the nitrite release due to LPS/IFN-gamma in a concentration-dependent manner, and epidermal growth factor did not modify LPS/IFN-gamma-induced NOS activity. The growth factors alone did not stimulate nitrite release. We have attempted to elucidate the mechanism of FGF inhibition. Results with heparin, suramin, and tyrphostin suggest involvement of the high-affinity receptor for FGF in its inhibition of LPS/IFN-gamma-stimulated NOS activity. Continued stimulation of RPE cells with LPS/IFN-gamma was essential for the induction of NO synthesis, and maximal inhibition was obtained when FGF was present during stimulation with LPS/IFN-gamma, suggesting that FGF inhibits NOS induction. Furthermore, an antiproliferative action of NO was demonstrated by an inverse correlation between the amounts of nitrite or citrulline produced in response to different stimuli (LPS/IFN-gamma or LPS/IFN-gamma with growth factors) and the level of cellular proliferation. Similar inhibition of growth was obtained when RPE cells were incubated with an NO donor, sydnonimide. Because NO acts as a cytotoxic compound in the retina, FGF, by inhibiting the induction of NOS in RPE cells, may have beneficial effects in protecting the retina from cytokine and endotoxin-mediated tissue damage.
A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic β‐oxidation pathway (2003)

Escherichia coli uses fatty acids as a sole carbon and energy source during aerobic growth by means of the enzymes encoded by the fad regulon. We report that this bacterium can also grow on fatty acids under anaerobic conditions provided that a terminal respiratory electron acceptor such as nitrate is available. This anaerobic utilization pathway is distinct from the well-studied aerobic pathway in that (i). it proceeds normally in mutant strains lacking various enzymes of the aerobic pathway; (ii). it functions with fatty acids (octanoate and decanoate) that cannot be used by wild-type E. coli strains under aerobic conditions; and (iii). super-repressor mutants of the fadR regulatory locus that block aerobic growth on fatty acids fail to block the anaerobic pathway. We have identified homologues of the FadA, FadB and FadD proteins required for aerobic fatty acid utilization called YfcY, YfcX and YdiD, respectively, which are involved in anaerobic growth on fatty acids. A strong FadR binding site was detected upstream of the yfcY gene consistent with microarray analyses, indicating that yfcYX expression is negatively regulated by FadR under aerobic growth conditions. In contrast, transcriptional regulation of ydiD appears to be independent of FadR, and anaerobic growth on fatty acids is not under FadR control. These three genes are conserved in the available genome sequences of pathogenic E. coli, Shigella and Salmonella strains.
Candidate odorant receptors from the malaria vector mosquito Anopheles gambiae and evidence of down-regulation in response to blood feeding (2001)

Olfaction plays a major role in host preference and blood feeding, integral behaviors for disease transmission by the malaria vector mosquito Anopheles gambiae sensu stricto (henceforth A. gambiae). We have identified four genes encoding candidate odorant receptors from A. gambiae that are selectively expressed in olfactory organs, contain approximately seven transmembrane domains, and show significant similarity to several putative odorant receptors in Drosophila melanogaster. Furthermore, one of the putative A. gambiae odorant receptors exhibits female-specific antennal expression and is down-regulated 12 h after blood feeding, a period during which substantial reduction in olfactory responses to human odorants has been observed. Taken together, these data suggest these genes encode a family of odorant receptors in A. gambiae, whose further study may aid in the design of novel antimalarial programs.
Bezafibrate reduces heart rate and blood pressure in patients with hypertriglyceridemia (2001)

Bezafibrate reduces heart rate, blood pressure, insulin and FFA in hypertriglyceridemic patients. The hemodynamic effects cannot be attributed to changes in sympathetic activity or renal sodium absorption. Instead, based on the increase in plasma cGMP levels, the bezafibrate-induced hemodynamic effects are most likely to be caused by bezafibrate-induced improvement of endothelial function.
PARIS: Probabilistic Alignment of Relations, Instances, and Schema (2011)

One of the main challenges that the Semantic Web faces is the integration of a growing number of independently designed ontologies. In this work, we present PARIS, an approach for the automatic alignment of ontologies. PARIS aligns not only instances, but also relations and classes. Alignments at the instance level cross-fertilize with alignments at the schema level. Thereby, our system provides a truly holistic solution to the problem of ontology alignment. The heart of the approach is probabilistic, i.e., we measure degrees of matchings based on probability estimates. This allows PARIS to run without any parameter tuning. We demonstrate the efficiency of the algorithm and its precision through extensive experiments. In particular, we obtain a precision of around 90% in experiments with some of the world's largest ontologies.
Synthesis and micellization of thermoresponsive galactose‐based diblock copolymers (2011)

Abstract Thermoresponsive double hydrophilic diblock copolymers poly(2‐(2′‐methoxyethoxy)ethyl methacrylate‐ co ‐oligo(ethylene glycol) methacrylate)‐ b ‐poly(6‐ O ‐methacryloyl‐ D ‐galactopyranose) (P(MEO 2 MA‐ co ‐OEGMA)‐ b ‐PMAGP) with various compositions and molecular weights were obtained by deprotection of amphiphilic diblock copolymers P(MEO 2 MA‐ co ‐OEGMA)‐ b ‐poly(6‐ O ‐methacryloyl‐1,2:3,4‐di‐ O ‐isopropylidene‐ D ‐galactopyranose) (P(MEO 2 MA‐ co ‐OEGMA)‐ b ‐PMAlpGP), which were prepared via reversible addition‐fragmentation chain transfer (RAFT) polymerization using P(MEO 2 MA‐ co ‐OEGMA) as macro‐RAFT agent. Dynamic light scattering and UV–vis studies showed that the micelles self‐assembled from P(MEO 2 MA‐ co ‐OEGMA)‐ b ‐PMAlpGP were thermoresponsive. A hydrophobic dye Nile Red could be encapsulated by block copolymers P(MEO 2 MA‐ co ‐OEGMA)‐ b ‐PMAGP upon micellization and released upon dissociation of the formed micelles under different temperatures. The galactose functional groups in the PMAGP block have specific interaction with HepG2 cells, and P(MEO 2 MA‐ co ‐OEGMA)‐ b ‐PMAGP has potential applications in hepatoma‐targeting drug delivery and biodetection. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Ketone body therapy: from the ketogenic diet to the oral administration of ketone ester (2014)

Ketone bodies (KBs), acetoacetate and β-hydroxybutyrate (βHB), were considered harmful metabolic by-products when discovered in the mid-19th century in the urine of patients with diabetic ketoacidosis. It took physicians many years to realize that KBs are normal metabolites synthesized by the liver and exported into the systemic circulation to serve as an energy source for most extrahepatic tissues. Studies have shown that the brain (which normally uses glucose for energy) can readily utilize KBs as an alternative fuel. Even when there is diminished glucose utilization in cognition-critical brain areas, as may occur early in Alzheimer's disease (AD), there is preliminary evidence that these same areas remain capable of metabolizing KBs. Because the ketogenic diet (KD) is difficult to prepare and follow, and effectiveness of KB treatment in certain patients may be enhanced by raising plasma KB levels to ≥2 mM, KB esters, such as 1,3-butanediol monoester of βHB and glyceryl-tris-3-hydroxybutyrate, have been devised. When administered orally in controlled dosages, these esters can produce plasma KB levels comparable to those achieved by the most rigorous KD, thus providing a safe, convenient, and versatile new approach to the study and potential treatment of a variety of diseases, including epilepsy, AD, and Parkinson's disease.
Gustatory responses of pigs to sixty compounds tasting sweet to humans (2002)

The gustatory responses of pigs to 60 compounds perceived as sweet by humans were studied via a semi-quantitative behavioural method derived from the Richter two-bottle preference test. Among the 60 compounds tested 35 are effective in pigs, but with an effectiveness much lower in pigs than in humans. Lugduname and carrelame, which are the two most potent sweeteners in humans, are also the most effective compounds in pigs.
Mass and charge distributions of amyloid fibers involved in neurodegenerative diseases: mapping heterogeneity and polymorphism (2018)

Heterogeneity and polymorphism are generic features of amyloid fibers with some important effects on the related disease development. We report here the characterization, by charge detection mass spectrometry, of amyloid fibers made of three polypeptides involved in neurodegenerative diseases: Aβ<sub>1-42</sub> peptide, tau and α-synuclein. Beside the mass of individual fibers, this technique enables to characterize the heterogeneity and the polymorphism of the population. In the case of Aβ<sub>1-42</sub> peptide and tau protein, several coexisting species could be distinguished and characterized. In the case of α-synuclein, we show how the polymorphism affects the mass and charge distributions.
Reliability and validity of body composition measures in female athletes (1999)

The purpose of this investigation was to determine the reliability and validity of bioelectrical impedance (BIA) and near-infrared interactance (NIR) for estimating body composition in female athletes. Dual-energy X-ray absorptiometry was used as the criterion measure for fat-free mass (FFM). Studies were performed in 132 athletes [age = 20.4 +/- 1.5 (SD) yr]. Intraclass reliabilities (repeat and single trial) were 0.987-0.997 for BIA (resistance and reactance) and 0.957-0.980 for NIR (optical densities). Validity of BIA and NIR was assessed by double cross-validation. Because correlations were high (r = 0.969-0.983) and prediction errors low, a single equation was developed by using all 132 subjects for both BIA and NIR. Also, an equation was developed for all subjects by using height and weight only. Results from dual-energy X-ray absorptiometry analysis showed FFM = 49.5 +/- 6.0 kg, which corresponded to %body fat (%BF) of 20.4 +/- 3.1%. BIA predicted FFM at 49.4 +/- 5.9 kg (r = 0.981, SEE = 1.1), and NIR prediction was 49. 5 +/- 5.8 kg (r = 0.975, SEE = 1.2). Height and weight alone predicted FFM at 49.4 +/- 5.7 kg (r = 0.961, SEE = 1.6). When converted to %BF, prediction errors were approximately 1.8% for BIA and NIR and 2.9% for height and weight. Results showed BIA and NIR to be extremely reliable and valid techniques for estimating body composition in college-age female athletes.
Simian virus 40 agnoprotein facilitates perinuclear-nuclear localization of VP1, the major capsid protein (1986)

The agnoprotein of simian virus 40 (SV40) is a 61-amino-acid protein encoded in the leader of some late mRNAs. In indirect immunofluorescence studies with antisera against SV40 capsid proteins, we show that mutants which make no agnoprotein display abnormal perinuclear-nuclear localization of VP1, the major capsid protein, but not VP2 or VP3, the minor capsid proteins. In wild-type (WT) SV40-infected CV-1P cells, VP1 was found predominantly in the cytoplasm until 36 h postinfection (p.i.), approximately the time that high levels of agnoprotein became detectable under our infection conditions. Thereafter, VP1 localized rapidly to the perinuclear region and to the nucleus. In contrast, in agnoprotein-minus mutant-infected CV-1P cells, perinuclear-nuclear accumulation of VP1 occurred much less efficiently; a significantly greater fraction of cells with predominantly cytoplasmic fluorescence was observed up to 48 h p.i. At 48 and 60 h p.i., more cells with largely perinuclear and little nuclear staining were seen than in WT-infected controls. In similar analyses with stably transfected cell lines constitutively expressing the agnoprotein, VP1 localized to the nucleus before 30 h p.i., regardless of the infecting virus. Delayed nuclear entry of VP1 in a mutant which makes no agnoprotein was also overcome in a revertant which has a second site point mutation in VP1. This suggests that an alteration of VP1 can partially overcome the defect of the agnogene mutation by enhancement of the rate of its own nuclear localization. Taken together, these results indicate that at least one function of the agnoprotein is to enhance the efficiency of perinuclear-nuclear localization of VP1.
Comparison of the Quantum II, API Yeast Ident, and AutoMicrobic systems for identification of clinical yeast isolates (1988)

The Quantum II Yeast Identification System (Abbott Laboratories) is a microprocessor-based spectrophotometric system for identification of clinical yeast isolates within 24 h. We compared the Quantum II system with the API Yeast Ident (Analytab Products) and the AutoMicrobic System Yeast Biochemical Card (AMS-YBC; Vitek Systems, Inc.) for the identification of 221 clinical yeast isolates, including 120 common clinical isolates (Candida albicans, C. tropicalis, C. parapsilosis, Torulopsis glabrata, and Cryptococcus neoformans) and 101 relatively uncommon clinical isolates. The API 20C (Analytab) was used as the reference system. The Quantum II and AMS-YBC systems correctly identified 181 (82%) and 184 (83%) isolates, respectively, whereas the Yeast Ident system correctly identified 132 (60%) isolates. Of the 120 common clinical isolates, 113 (94%) were correctly identified by Quantum II, 103 (86%) were correctly identified by AMS-YBC, and 83 (69%) were correctly identified by Yeast Ident. Of the 101 uncommon clinical isolates tested, 68 (67%) were correctly identified by Quantum II, 81 (80%) were correctly identified by AMS-YBC, and 49 (49%) were correctly identified by Yeast Ident. The overall accuracy of the Quantum II, AMS-YBC, and API Yeast Ident was not sufficient to recommend any of these systems for routine use in the clinical microbiology laboratory without substantial expansion of the respective data bases.
Controlled Clinical Trial of Dichloroacetate for Treatment of Congenital Lactic Acidosis in Children (2006)

In this highly heterogeneous population of children with congenital lactic acidosis, oral DCA for 6 months was well tolerated and blunted the postprandial increase in circulating lactate. However, it did not improve neurologic or other measures of clinical outcome.
CD28 interaction with B7 costimulates primary allogeneic proliferative responses and cytotoxicity mediated by small, resting T lymphocytes. (1992)

Engagement of the CD3/T cell antigen receptor complex on small, resting T cells is insufficient to trigger cell-mediated cytotoxicity or to induce a proliferative response. In the present study, we have used genetic transfection to demonstrate that interaction of the B7-BB1 B cell activation antigen with the CD28 T cell differentiation antigen costimulates cell-mediated cytotoxicity and proliferation initiated by either anti-CD2 or anti-CD3 monoclonal antibody (mAb). Moreover, a B7-negative Burkitt's lymphoma cell line that fails to stimulate an allogeneic mixed lymphocyte response is rendered a potent stimulator after transfection with B7. The mixed leukocyte reaction proliferative response against the B7 transfectant is inhibited by either anti-CD28 or B7 mAb. We also demonstrate that freshly isolated small, resting human T cells can mediate anti-CD3 or anti-CD2 mAb-redirected cytotoxicity against a murine Fc receptor-bearing mastocytoma transfected with human B7. These preexisting cytotoxic T lymphocytes in peripheral blood are present in both the CD4 and CD8 subsets, but are preferentially within the CD45RO+ "memory" population. While small, resting T cells apparently require costimulation by CD28/B7 interactions, this requirement is lost after T cell activation. Anti-CD3 initiates a cytotoxic response mediated by in vitro cultured T cell clones in the absence of B7 ligand. The existence of functional cytolytic T cells in the small, resting T cell population may be advantageous in facilitating rapid responses to immune challenge.
Correlating Solution Binding and ESI-MS Stabilities by Incorporating Solvation Effects in a Confined Cucurbit[8]uril System (2010)

The high-throughput characterization of solution binding equilibria is essential in biomedical research such as drug design as well as in material applications of synthetic systems in which reversible binding interactions play critical roles. Although isothermal titration calorimetry (ITC) has been widely employed for describing such binding events, factors such as speed, concentration, and sample complexity would principally favor a mass spectrometry approach. Here, we show a link between ITC and electrospray ionization mass spectrometry (ESI-MS) by incorporating solvation free energies in the study of the ternary complexes of the macrocyclic host cucurbit[8]uril (CB[8]). The binding affinities of 32 aromatic reference complexes were studied by ITC and ESI-MS and combined with solvation data of the guests from an implicit solvation model (SM8) to obtain a correlation between aqueous and gas-phase measurements. The data illustrates the critical importance of solvation on the binding strength in CB[8]'s ternary complexes. Finally, this treatment enabled us to predict association constants that were in excellent agreement with measured values, including several highly insoluble guest compounds.
The Use of Virtual Reality Exposure in the Treatment of Anxiety Disorders (1999)

One possible alternative to standard in vivo exposure may be virtual reality exposure. Virtual reality integrates real-time computer graphics, body tracking devices, visual displays, and other sensory input devices to immerse a participant in a computer-generated virtual environment. Virtual reality exposure (VRE) is potentially an efficient and cost-effective treatment of anxiety disorders. VRE therapy has been successful in reducing the fear of heights in the first known controlled study of virtual reality in the treatment of a psychological disorder. Outcome was assessed on measures of anxiety, avoidance, attitudes, and distress. Significant group differences were found on all measures such that the VRE group was significantly improved at posttreatment but the control group was unchanged. The efficacy of virtual reality exposure therapy was also supported for the fear of flying in a case study. The potential for virtual reality exposure treatment for these and other disorders is explored.
Design, Construction, and Characterization of a Dual-Promoter Multigenic DNA Vaccine Directed Against an HIV-1 Subtype C/B′ Recombinant (2008)

An effective vaccine against HIV-1 is generally considered the best hope for controlling the raging AIDS pandemic. As a part of our AIDS vaccine development effort, we constructed a dual-promoter plasmid capable of high-level expression of 2 independent transgenes. HIV-1 gag, pol, env, nef, and tat from a primary subtype C/B' CCR5-tropic HIV-1 were "codon" optimized, modified to eliminate known functional activity, and assembled using an overlapping polymerase chain reaction into 2 plasmids: ADVAX-I (containing env and gag) and ADVAX-II (containing pol and nef-tat). These 2 dual-promoter candidate vaccines showed levels of HIV-1 gene expression comparable to those observed with single-gene plasmids in vitro. Importantly, immunization of mice with these vaccine constructs resulted in dose-dependent multigenic CD4 and CD8 T-cell responses equivalent to those provided by vaccination with single-gene plasmids. With input from the US Food and Drug Administration, ADVAX-I and ADVAX-II have since been combined as a single candidate DNA vaccine, ADVAX. A phase 1 clinical trial of this product has been successfully completed, and its use in prime-boost studies is now underway.