gebhart/patrepeval huggingface dataset:
Efficient and Convenient Heterogeneous Palladium‐Catalyzed Regioselective Deuteration at the Benzylic Position (2007)

The Pd/C-catalyzed efficient and regioselective hydrogen-deuterium (H-D) exchange reaction on the benzylic site proceeded in D2O in the presence of a small amount of H2 gas. The use of the Pd/C-ethylenediamine complex [Pd/C(en)] as a catalyst instead of Pd/C led to the efficient deuterium incorporation into the benzylic site of O-benzyl protective groups without hydrogenolysis. These H-D exchange reactions provide a post synthetic and D(2)-gas-free deuterium-labeling method on a wide variety of benzylic sites using D2O as the deuterium source and heterogeneous Pd/C or Pd/C(en) as a reusable heterogeneous palladium catalyst under mild and neutral conditions.
Novel Flavivirus or New Lineage of West Nile Virus, Central Europe (2005)

A flavivirus (strain 97-103) was isolated from Culex pipens mosquitoes in 1997 following floods in South Moravia, Czech Republic. The strain exhibited close antigenic relationship to West Nile virus (WNV) prototype strain Eg-101 in a cross-neutralization test. In this study, mouse pathogenicity characteristics and the complete nucleotide and putative amino acid sequences of isolate 97-103, named Rabensburg virus (RabV) after a nearby Austrian city, were determined. RabV shares only 75%-77% nucleotide identity and 89%-90% amino acid identity with representative strains of WNV lineages 1 and 2. Another RabV strain (99-222) was isolated in the same location 2 years later; it showed >99% nucleotide identity to strain 97-103. Phylogenetic analyses of RabV, WNV strains, and other members of the Japanese encephalitis virus (JEV) complex clearly demonstrated that RabV is either a new (third) lineage of WNV or a novel flavivirus of the JEV group.
Transgenic studies with a keratin promoter-driven growth hormone transgene: Prospects for gene therapy (1997)

Keratinocytes are potentially appealing vehicles for the delivery of secreted gene products because they can be transferred to human skin by the relatively simple procedure of grafting. Adult human keratinocytes can be efficiently propagated in culture with sufficient proliferative capacity to produce enough epidermis to cover the body surface of an average adult. However, the feasibility of delivering secreted proteins through skin grafting rests upon (i) the strength of the promoter in keratinocytes and (ii) the efficiency of protein transport through the basement membrane of the stratified epithelium and into the bloodstream. In this paper, we use transgenic technology to demonstrate that the activity of the human keratin 14 promoter remains high in adult skin and that keratinocyte-derived human growth hormone (hGH) can be produced, secreted, and transported to the bloodstream of mice with efficiency that is sufficient to exceed by an order of magnitude the circulating hGH concentration in growing children. Transgenic skin grafts from these adults continue to produce and secrete hGH stably, at approximately 1/10 physiological levels in the bloodstream of nontransgenic recipient mice. These studies underscore the utility of the keratin 14 promoter for expressing foreign transgenes in keratinocytes and demonstrate that keratinocytes can be used as effective vehicles for transporting factors to the bloodstream and for eliciting metabolic changes. These findings have important implications for considering the keratinocyte as a possible vehicle for gene therapy.
Production of Monoclonal Antibodies Specific for the i and 1,2 Flagellar Antigens of Salmonella typhimurium and Characterization of Their Respective Epitopes (1998)

Salmonella typhimurium expresses two antigenically distinct flagellins, each containing a different H antigen (i and 1,2), the combination of which is highly specific for this serotype. In this study, overlapping recombinant flagellin fragments were constructed from the fliC (H:i) and fljB (H:1,2) flagellin genes, and the expression products were tested for binding to H antigen-specific monoclonal and polyclonal antibodies. A minimal area, 86 amino acids for H:i and 102 amino acids for H:1,2, located in the central variable domain of each flagellin was required for the binding of serotype-specific antibodies, providing further evidence for the presence of a discontinuous H epitope. Two peptides comprising these areas were shown to be highly suitable for application as antigens in an enzyme-linked immunosorbent assay detecting S. typhimurium-specific antibody.
Isolation and identification of 4-hydroxy- and 4-oxoretinoic acid. In vitro metabolites of all-trans-retinoic acid in hamster trachea and liver (1979)

Incubation of [3H]retinoic acid in the presence of hamster liver 10000g supernatant produces several metabolites that are more polar than the parent compound. Two of these metabolites are identical with synthetic all-trans-4-hydroxyretinoic acid and all-trans-4-oxoretinoic acid both in ultraviolet absorption and mass spectral characteristics and in migration rates on two different reverse-phase high-pressure liquid chromatographic systems. The metabolites produced in a cell-free liver incubation reaction also migrate on a high-pressure liquid chromatography column together with metabolites isolated from a tracheal organ culture system. Both the metabolites and the synthetic standards show less biological activity than the parent all-trans-retinoic acid in a tracheal organ culture assay.
Odd–even effect and metal induced structural convergence in self-assembled monolayers of bipyridine derivatives (2007)

Scanning tunneling microscopy (STM) observations reveal that bipyridine derivatives which exhibit various two-dimensional structures due to the odd-even chain length effect are converged into a lamellar structure upon metal coordination.
Using Noninvasive Prenatal Testing for Aneuploidies in a Developing Country: Lessons Learnt (2014)

Abstract The objective of the present study was to analyze the utility of noninvasive prenatal testing (NIPT) for aneuploidies in a developing country like India. NIPT was offered to 500 pregnant women, after review of data of the ongoing pregnancy. Pre-test counseling included the different methodologies of testing, their benefits, limitations, turnaround time and interpretation of the result and was offered to all. Different vendors were used for the test. The results were explained in a post-test counseling session. The indications of NIPT were positive second (36.6 %) or first (22 %) trimester screen, advanced maternal age with or without positive biochemical screen (24.6 %), ultrasound soft markers (10.8 %), previous history of Down syndrome (4.6 %) and anxious couple (0.1 %). No aneuploidy was detected in 484 samples. In 1 case, no result was available. Fifteen (3 %) cases showed positive results. These included 8 cases of trisomy 21, 3 cases of trisomy 18, 3 cases of monosomy X, and 1 case of triploidy. Confirmatory testing revealed 6 cases (40 %) to be false positive—1 case of trisomy 21, 1 case of trisomy 18, 3 cases of monosomy X, and 1 case of triploidy. Of 484 cases, 230 have delivered healthy neonates, while the rest have yet to deliver. Four cases had to discontinue pregnancy due to complications in later pregnancy but unrelated to the NIPT results. Noninvasive prenatal test qualifies as an ‘advanced’ screening test, and requires invasive diagnostic tests for confirmation of the positive results. The pre- and post-test counseling is essential to appropriately explain the limitations, benefits, and the results to the couple. Recommendations are made for the appropriate deployment of this new technology in developing countries.
Identification of Multiple Protective Epitopes (Protectopes) in the Central Conserved Domain of a Prototype Human Respiratory Syncytial Virus G Protein (1999)

A recombinant fusion protein (BBG2Na) comprising the central conserved domain of the respiratory syncytial virus subgroup A (RSV-A) (Long) G protein (residues 130 to 230) and an albumin binding domain of streptococcal protein G was shown previously to protect mouse upper (URT) and lower (LRT) respiratory tracts against intranasal RSV challenge (U. F. Power, H. Plotnicky-Gilquin, T. Huss, A. Robert, M. Trudel, S. Stahl, M. Uhlén, T. N. Nguyen, and H. Binz, Virology 230:155-166, 1997). Panels of monoclonal antibodies (MAbs) and synthetic peptides were generated to facilitate dissection of the structural elements of this domain implicated in protective efficacy. All MAbs recognized native RSV-A antigens, and five linear B-cell epitopes were identified; these mapped to residues 152 to 163, 165 to 172, 171 to 187 (two overlapping epitopes), and 196 to 204, thereby covering the highly conserved cysteine noose domain. Antibody passive-transfer and peptide immunization studies revealed that all epitopes were implicated in protection of the LRT, but not likely the URT, against RSV-A challenge. Pepscan analyses of anti-RSV-A and anti-BBG2Na murine polyclonal sera revealed lower-level epitope usage within the central conserved region in the former, suggesting diminished immunogenicity of the implicated epitopes in the context of the whole virus. However, Pepscan analyses of RSV-seropositive human sera revealed that all of the murine B-cell protective epitopes (protectopes) that mapped to the central conserved domain were recognized in man. Should these murine protectopes also be implicated in human LRT protection, their clustering around the highly conserved cysteine noose region will have important implications for the development of RSV vaccines.
Adapting software pipelining for reconfigurable computing (2000)

Article Adapting software pipelining for reconfigurable computing Share on Authors: Timothy J. Callahan University of California at Berkeley University of California at BerkeleyView Profile , John Wawrzynek University of California at Berkeley University of California at BerkeleyView Profile Authors Info & Claims CASES '00: Proceedings of the 2000 international conference on Compilers, architecture, and synthesis for embedded systemsNovember 2000 Pages 57–64https://doi.org/10.1145/354880.354889Published:01 November 2000 58citation437DownloadsMetricsTotal Citations58Total Downloads437Last 12 Months7Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Use of recombinant human granulocyte-macrophage colony-stimulating factor in autologous marrow transplantation for lymphoid malignancies (1988)

The use of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) following autologous marrow transplantation for lymphoid malignancies was explored in a phase I/II dose escalation study. rhGM-CSF given as a 2-hour infusion daily for 14 days was well tolerated at doses up to 240 micrograms/m2/day. When compared with 86 disease-matched and treatment-matched historical controls, patients receiving greater than or equal to 60 micrograms/m2/day rhGM-CSF recovered neutrophil and platelet counts more rapidly, had fewer days with fever, and were discharged from the hospital sooner.
SparseBeads data: benchmarking sparsity-regularized computed tomography (2017)

Sparsity regularization (SR) such as total variation (TV) minimization allows accurate image reconstruction in x-ray computed tomography (CT) from fewer projections than analytical methods. Exactly how few projections suffice and how this number may depend on the image remain poorly understood. Compressive sensing connects the critical number of projections to the image sparsity, but does not cover CT, however empirical results suggest a similar connection. The present work establishes for real CT data a connection between gradient sparsity and the sufficient number of projections for accurate TV-regularized reconstruction. A collection of 48 x-ray CT datasets called SparseBeads was designed for benchmarking SR reconstruction algorithms. Beadpacks comprising glass beads of five different sizes as well as mixtures were scanned in a micro-CT scanner to provide structured datasets with variable image sparsity levels, number of projections and noise levels to allow the systematic assessment of parameters affecting performance of SR reconstruction algorithms6. Using the SparseBeads data, TV-regularized reconstruction quality was assessed as a function of numbers of projections and gradient sparsity. The critical number of projections for satisfactory TV-regularized reconstruction increased almost linearly with the gradient sparsity. This establishes a quantitative guideline from which one may predict how few projections to acquire based on expected sample sparsity level as an aid in planning of dose- or time-critical experiments. The results are expected to hold for samples of similar characteristics, i.e. consisting of few, distinct phases with relatively simple structure. Such cases are plentiful in porous media, composite materials, foams, as well as non-destructive testing and metrology. For samples of other characteristics the proposed methodology may be used to investigate similar relations.
miR-221 and miR-155 regulate human dendritic cell development, apoptosis, and IL-12 production through targeting of p27kip1, KPC1, and SOCS-1 (2011)

Dendritic cells (DCs) are potent antigen-presenting cells derived from hematopoietic progenitor cells and circulating monocytes. To investigate the role of microRNAs (miRNAs) during DC differentiation, maturation, and function, we profiled miRNA expression in human monocytes, immature DCs (imDCs), and mature DCs (mDCs). Stage-specific, differential expression of 27 miRNAs was found during monocyte differentiation into imDCs and mDCs. Among them, decreased miR-221 and increased miR-155 expression correlated with p27(kip1) accumulation in DCs. Silencing of miR-221 or overexpressing of miR-155 in DCs resulted in p27(kip1) protein increase and DC apoptosis. Moreover, mDCs from miR-155(-/-) mice were less apoptotic than those from wild-type mice. Silencing of miR-155 expression had little effect on DC maturation but reduced IL-12p70 production, whereas miR-155 overexpression in mDCs enhanced IL-12p70 production. Kip1 ubiquitination-promoting complex 1, suppressor of cytokine signaling 1, and CD115 (M-CSFR) were functional targets of miR-155. Furthermore, we provide evidence that miR-155 indirectly regulated p27(kip1) protein level by targeting Kip1 ubiquitination-promoting complex 1. Thus, our study uncovered miRNA signatures during monocyte differentiation into DCs and the new regulatory role of miR-221 and miR-155 in DC apoptosis and IL-12p70 production.
Serum Procalcitonin and C-Reactive Protein Levels as Markers of Bacterial Infection: A Systematic Review and Meta-analysis (2004)

A meta-analysis was performed to evaluate the accuracy of determination of procalcitonin (PCT) and C-reactive protein (CRP) levels for the diagnosis of bacterial infection. The analysis included published studies that evaluated these markers for the diagnosis of bacterial infections in hospitalized patients. PCT level was more sensitive (88% [95% confidence interval [CI], 80%-93%] vs. 75% [95% CI, 62%-84%]) and more specific (81% [95% CI, 67%-90%] vs. 67% [95% CI, 56%-77%]) than CRP level for differentiating bacterial from noninfective causes of inflammation. The Q value for PCT markers was higher (0.82 vs. 0.73). The sensitivity for differentiating bacterial from viral infections was also higher for PCT markers (92% [95% CI, 86%-95%] vs. 86% [95% CI, 65%-95%]); the specificities were comparable (73% [95% CI, 42%-91%] vs. 70% [95% CI, 19%-96%]). The Q value was higher for PCT markers (0.89 vs. 0.83). PCT markers also had a higher positive likelihood ratio and lower negative likelihood ratio than did CRP markers in both groups. On the basis of this analysis, the diagnostic accuracy of PCT markers was higher than that of CRP markers among patients hospitalized for suspected bacterial infections.
Cycling efficiency in humans is related to low UCP3 content and to type I fibres but not to mitochondrial efficiency (2006)

The purpose of this study was to investigate the hypothesis that cycling efficiency in vivo is related to mitochondrial efficiency measured in vitro and to investigate the effect of training status on these parameters. Nine endurance trained and nine untrained male subjects (V(O2peak) = 60.4 +/- 1.4 and 37.0 +/- 2.0 ml kg(-1) min(-1), respectively) completed an incremental submaximal efficiency test for determination of cycling efficiency (gross efficiency, work efficiency (WE) and delta efficiency). Muscle biopsies were taken from m. vastus lateralis and analysed for mitochondrial respiration, mitochondrial efficiency (MEff; i.e. P/O ratio), UCP3 protein content and fibre type composition (% MHC I). MEff was determined in isolated mitochondria during maximal (state 3) and submaximal (constant rate of ADP infusion) rates of respiration with pyruvate. The rates of mitochondrial respiration and oxidative phosphorylation per muscle mass were about 40% higher in trained subjects but were not different when expressed per unit citrate synthase (CS) activity (a marker of mitochondrial density). Training status had no influence on WE (trained 28.0 +/- 0.5, untrained 27.7 +/- 0.8%, N.S.). Muscle UCP3 was 52% higher in untrained subjects, when expressed per muscle mass (P < 0.05 versus trained). WE was inversely correlated to UCP3 (r = -0.57, P < 0.05) and positively correlated to percentage MHC I (r = 0.58, P < 0.05). MEff was lower (P < 0.05) at submaximal respiration rates (2.39 +/- 0.01 at 50% V(O2max)) than at state 3 (2.48 +/- 0.01) but was neither influenced by training status nor correlated to cycling efficiency. In conclusion cycling efficiency was not influenced by training status and not correlated to MEff, but was related to type I fibres and inversely related to UCP3. The inverse correlation between WE and UCP3 indicates that extrinsic factors may influence UCP3 activity and thus MEff in vivo.
Conditions for purification of proteins by free‐flow zone electrophoresis (1990)

The separation of proteins by free-flow zone electrophoresis is generally impaired by a number of secondary effects which cause spreading of the protein streams with resultant loss in resolution. A strategy is outlined, based on experimental observations and numerical modeling, which allows the operating conditions and separation chamber dimensions to be chosen so as to obtain complete separation of two proteins of known mobility. This approach takes into account some dispersive phenomena such as molecular diffusion, electroosmosis and residence time gradients. In some cases, the right operating conditions cannot be achieved on earth and electrophoresis separations in microgravity may then be justified.
Molecular Modeling of Covalently Attached Alkyl Monolayers on the Hydrogen-Terminated Si(111) Surface (2001)

The structure of octadecyl monolayers on the H-terminated Si(111) surface is investigated by molecular modeling simulations, using substitution percentages from 33.3% to 100% of the Si−H moieties by Si−alkyl groups. In all calculations, two-dimensionally repeating boxes were used to mimic the modified surface. Calculations without this repeating box approach were shown to be unsuccessful. The results on the repeating boxes showed that only with a substitution percentage of ∼50% is there a good correlation between the structure of the monolayers as obtained from molecular modeling and the available experimental data. A variety of substitution patterns with a substitution percentage of 50% on the Si(111) surface were investigated, which showed that a zigzag-type pattern is most suitable to describe the structure of the layers. From the results of the investigations, an important conclusion for future experimental work is drawn. It is shown that the experimentally determined substitution percentage of 50−55% of the Si−H for Si−alkyl groups is close to the maximum value that can be reached on the H-terminated Si(111) surface.
Species- and Stage-Specific Antigens in Exoerythrocytic Stages of Plasmodium falciparum (1984)

Numerous exoerythrocytic forms of Plasmodium falciparum ( PFEEF ) were obtained from the liver of the South American monkey, Cebus apella, for analysis of the antigens on this stage. As antigen for the fluorescent assay, 5-micron sections of liver fragments collected on day 5 following sporozoite inoculation and fixed in Carnoy's solution or kept in liquid nitrogen were used. Two types of fluorescent labeling of the PFEEF were identified: diffuse and peripheral. Each of 23 sera from individuals with P. falciparum infection acquired naturally by mosquito bite showed the diffuse and peripheral patterns of fluorescence at low serum dilutions (i.e., 1:10-1:100), but only peripheral staining at higher serum dilutions (i.e., 1:200-1:1,600). All other polyclonal sera tested showed only the diffuse pattern of fluorescence whatever the serum dilution used; this was true for P. falciparum infections acquired accidentally by blood transfusion, heterologous human infections with P. vivax, P. ovale, P. malariae or P. cynomolgi, and experimental animal infections with P. berghei, P. gallinaceum, or P. cynomolgi. Fluorescent antibody titers on PFEEF were generally 1-4 dilutions lower than on blood stages. No age-dependent pattern of fluorescence titers was found in 30 sera from individuals ranging in age from 2-78 years living in a malaria-endemic area. Twenty-six monoclonal antibodies directed to P. falciparum blood stages which reacted at high titers with rings, schizonts, merozoites, and gametocytes did not react with PFEEF antigen even when using the undiluted ascitic fluid.(ABSTRACT TRUNCATED AT 250 WORDS)
Regulation ofPseudomonas aeruginosacorneal infection in IL-1ß converting enzyme (ICE, caspase-1) deficient mice (2004)

These data provide evidence that bacterial infection in the cornea of ICE(-/-) mice induces a reduced inflammatory response by: reduction in PMN and cytokines and chemokines that attract these cells to the cornea; enhanced apoptotic cell death in the infected epithelium; and increased IL-1Ra levels. The data also confirm the importance of IL-1 regulation in this model and suggest that ICE inhibition may be an attractive ancillary therapeutic strategy to control the host response to this pathogen.
Cardioprotective effects of morphine on rat heart suffering from ischemia and reperfusion. (2003)

To investigate the cardioprotective effects of morphine on ischemic reperfused rat heart in vitro and its mechanism.The isolated rat heart was perfused in a Langendorff apparatus. Infarct myocardium was determined by TTC. Coronary flow (CF), heart rate (HR), left ventricular pressure (LVP), the first derivative of ventricular pressure (LVP/dtmax) and infarct size after ischemia and reperfusion in rat heart given 0.3 micro mol/L morphine were observed. The effects of naloxone and glibenclamide on the cardioprotection of morphine were also measured.After ischemia and reperfusion, CF, HR, LVP and LVP/dtmax of isolated rat hearts decreased significantly (P < 0.01). After morphine preconditioning, HR, LVP and LVP/dtmax increased (P < 0.01) and infarct size was reduced significantly (P < 0.01), while no significant change in CF (P > 0.05). The cardioprotective effects of morphine were abolished by naloxone or glibenclamide completely.Morphine can reduce ischemia-reperfusion injuries in isolated rat heart. The cardioprotective effects of morphine are mediated by a local opioid receptor-K(ATP) channel linked mechanism in rat hearts.