gebhart/patrepeval huggingface dataset:
An entry to chiral cyclohexenes from carbohydrates: a short, efficient, and enantiospecific synthesis of (–)-shikimic acid fromD-mannose (1983)

G. W. J. Fleet and T. K. M. Shing, J. Chem. Soc., Chem. Commun., 1983, 849 DOI: 10.1039/C39830000849
Generation of T Lineage Cells from Human Embryonic Stem Cells in a Feeder Free System (2008)

Human embryonic stem cells (hESC) have the potential to revolutionize certain medical treatments, including T-cell-based therapies. However, optimal approaches to develop T cells from hESC are lacking. In this report, we show that T-cell progenitors can be derived from hESC cultured as embryoid bodies (EBs). These EB-derived T-cell progenitors give rise to phenotypically and functionally normal cells of the T lineage when transferred into human thymic tissue implanted in immunocompromised mice, suggesting that introduction of these progenitors into patients may also yield functional T cells. Moreover, hematopoietic progenitors demonstrating T-cell potential appeared to be CD45+/CD34+, resembling those found in normal bone marrow. In contrast to T cells developed from hESC cocultured on murine stromal cells, the EB-derived T cells also expressed normal levels of CD45. Importantly, the EB system eliminates the previous need for murine cocultures, a key impediment to developing a protocol for T-cell progenitor derivation suitable for clinical use. Furthermore, following lentiviral-mediated introduction of a vector expressing enhanced green fluorescent protein into hESC, stable transgene expression was maintained throughout differentiation, suggesting a potential for gene therapy approaches aimed at the augmentation of T-cell function or treatment of T-cell disorders.
Pyruvate carboxylase from Thiobacillus novellus: properties and possible function (1984)

Pyruvate carboxylase (EC 6.4.1.1) from Thiobacillus novellus (ATCC 8093) was highly purified and found to have a pH optimum of 7.6, a temperature optimum of 25–35 °C, and a requirement for a monovalent and a divalent cation, as well as a CoA derivative, for maximum activity. These were best served by K + , Mg 2+ , and acetyl-CoA. K m values for pyruvate, ATP, HCO 3 − and Mg 2+ were 0.25, 0.04, 0.27, and 0.44 mM, respectively. Initial velocity plots of increasing acetyl-CoA concentrations gave a sigmoidal curve with K a of 4.2 μM, and Hill coefficients of 2.2. Plots of fixed acetyl-CoA concentrations against varying concentrations of pyruvate, ATP, or CO 2 all gave rectangular hyperbolae. Apart from end products, only hydroxypyruvic acid was found to be inhibitory. The enzyme was very sensitive to mercurials. This enzyme is not believed to serve an anaplerotic function, because of the simultaneous presence of the highly regulated phosphoenolpyruvate carboxylase in the organism. Instead, it may function either to supply oxaloacetate to the citrate cycle or as part of the system that provides reduced NADP + .
<title>Influence of temperature of the luminescence decay time on the behavior of a luminescence quenching oxygen sensor</title> (1995)

The temperature dependence of the luminescence lifetime is mainly used for temperature monitoring. But for luminescence quenching based chemical sensors it presents the major disturbance. We have investigated the temperature dependence of the luminescence decay times of the Ru[4.7 Ph<SUB>2</SUB>phen]<SUB>3</SUB> <SUP>2+</SUP>-complex, used as oxygen concentration monitor within the temperature range between 15 and 80 degree(s)C. The primal decay times (tau) <SUB>0</SUB> without quencher and (tau) with quencher are temperature dependent. The sensitivity of the sensor, expressed on the base of the STERN-VOLMER coefficient K<SUB>SV</SUB> is not temperature dependent.
Macrocyclic Peptidomimetics Forcing Peptides into Bioactive Conformations (1995)

Abstract: Cyclic peptides that are potent regulators of biological processes are rapidly emerging as important mechanistic probes and drug leads. Nature clearly uses macrocycles to. constrain peptides into conformations that can selectively bind proteins or. small molecules. Therapeutic effects of such macrocycles, often containing additional conformational constraints that fine­ tune structure (e.g. D-amino acids, N-methyl substituents, aromatic rings, to name a few), have so far been mainly discovered by accident. However it is now becoming possible to rationally design synthetic macrocycles to selectively recognize and inhibit a specific protein. A receptor-binding struc­ ture is more easily adopted by macrocyclic peptidomimetics than more flexible acyclic peptides because the former have less conformational entropy. Macrocycles are often stable to hydrolysis by peptidases that degrade acyclic peptides and hydrophobic side chains can protect peptide bonds in macrocycles from hydrolysis, as well as enhance lipophilicity, cell permeability and bioavailability. Synthetic efforts to obtain bioactive conformations of short peptides have so far been substrate-based, guided by molecular modelling predictions and structure-activity data for modified amino acid sequences of substrates. However, dramatic advances in molecular biology, X-ray crystallography, NMR spectroscopy and computing are rapidly producing three dimensional structures of proteins, promising direct observation of protein-bound conformations of small molecules and receptor-based design of peptidomimetics with surface complementarity for proteins. This perspective review highlights examples of both natural and synthetic bioactive macrocyclic peptides containing constraints that fix conformation, and briefly illustrates the promise that receptor-based design holds for structural and functional mimicry of peptides by macrocycles.
Rapid procedure for detecting enterohemorrhagic Escherichia coli O157:H7 in food (1991)

A sensitive, specific procedure was developed for detecting Escherichia coli O157:H7 in food in less than 20 h. The procedure involves enrichment of 25 g of food in 225 ml of a selective enrichment medium for 16 to 18 h at 37 degrees C with agitation (150 rpm). The enrichment culture is applied to a sandwich enzyme-linked immunosorbent assay (ELISA) with a polyclonal antibody specific for E. coli O157 antigen as the capture antibody and a monoclonal antibody specific for enterohemorrhagic E. coli of serotypes O157:H7 and O26:H11 as the detection antibody. The ELISA can be completed within 3 h. The sensitivity of the procedure, determined by using E. coli O157:H7-inoculated ground beef and dairy products, including different varieties of cheese, was 0.2 to 0.9 cell per g of food. A survey of retail fresh ground beef and farm raw milk samples with this procedure revealed that 3 (2.8%) of 107 ground beef samples and 11 (10%) of 115 raw milk samples were positive for E. coli O157:H7. Most-probable-number determinations revealed E. coli O157:H7 populations of 0.4 to 1.5 cells per g in the three ground beef samples. In addition to being highly specific, sensitive, and rapid, this procedure is easy to perform and is amenable to use by laboratories performing routine microbiological testing.
A novel SOI CBiCMOS compatible device structure for analog and mixed-mode circuits (1995)

A novel SOI CBiCMOS compatible structure has been developed which can be operated as both an MOS and lateral bipolar transistor. During the MOS operation, the new structure provides a very effective body contact to eliminate the floating-body effects such as I-V kink, low breakdown voltage and the anomalous subthreshold characteristics. In the bipolar mode, the structure provides a very efficient base contact with low base resistance compared to most existing base contact schemes.
92-kD gelatinase is produced by eosinophils at the site of blister formation in bullous pemphigoid and cleaves the extracellular domain of recombinant 180-kD bullous pemphigoid autoantigen. (1994)

Eosinophils are prominent in bullous pemphigoid (BP), and proteases secreted from these and other inflammatory cells may induce disruption of the basement membrane. We used in situ hybridization and immunohistochemistry to localize the sites of 92-kD gelatinase expression in BP lesions. In all samples (20/20), a strong signal for gelatinase mRNA was detected only in eosinophils and was most pronounced where these cells accumulated at the floor of forming blisters. No other cells were positive for enzyme mRNA. Both eosinophils and neutrophils, however, contained immunoreactive 92-kD gelatinase indicating that active expression occurred only in eosinophils. Degranulated eosinophils were also seen near blisters, and as demonstrated by gelatin zymography, immunoblotting, and ELISA, 92-kD gelatinase protein was prominent in BP blister fluid. No other gelatinolytic activity was specifically detected in BP fluid, and only small amounts of 92-kD gelatinase were present in suction blister fluids. As demonstrated in vitro, 92-kD gelatinase cleaved the extracellular, collagenous domain of recombinant 180-kD BP autoantigen (BP180, BPAG2, HD4, type XVII collagen), a transmembrane molecule of the epidermal hemidesmosome. Our results suggest that production and release 92-kD gelatinase by eosinophils contributes significantly to tissue damage in BP.
Effects of Engine Oil Residues on Asphalt Cement Quality (2011)

This paper discusses and documents an investigation of chemical aging in asphalt cement modified with Engine Oil Residue (EOR). EOR is produced during the recycling of used motor oils collected from vehicles. It has been reported that a significant fraction of the asphalt cement used in parts of Canada is blended with EOR to meet certain low temperature Superpave grades. Such material can provide a low-cost method of increasing the grade span when blended with asphalt high in asphaltenes. However, concerns exist that such modifiers may negatively affect asphalt quality in several ways. First, the paraffinic nature of the EOR and possible presence of engine detergents can reduce the adhesion to the aggregate and thereby increase moisture damage. Second, metals such as iron, copper, and chromium, abundantly present in EOR, can act as catalysts in the oxidation of asphalt cement. Finally, paraffin can precipitate asphaltenes, which may accelerate further chemical and physical hardening. This paper presents results of aging tests on straight and EOR-modified asphalt cements. We found that EOR significantly increased oxidation rates and the tendency for asphaltenes to precipitate, leading to a less ductile material with higher stress at low temperatures, which typically results in early and increased cracking. // Cet article discute et documente une enquete sur le vieillissement chimique du bitume modifie avec moteur un residu petrolier de moteur (RPM). Le RPM est produit pendant le recyclage des huiles a moteur utilisees recueillies sur les vehicules. Il a ete signale qu'une fraction significative du bitume utilise dans certaines regions du Canada est melangee a du RPM pour repondre a certains grades de Superpave a basse temperature. Ce materiel peut fournir une methode a bas cout pour augmenter l'etendue du grade lorsque melange avec un bitume a forte teneur en asphaltenes. Cependant, des preoccupations existent que de tels modificateurs peuvent nuire a la qualite du bitume de plusieurs facons. Tout d'abord, la nature du solvant du RPM et la presence eventuelle de detergents moteur peuvent reduire l'adherence a l'agregat et augmenter ainsi les dommages de l'humidite. Deuxiemement, les metaux comme le fer, le cuivre et le chrome, abondamment presents dans le RPM, peuvent agir comme catalyseurs dans l'oxydation du ciment bitume. Enfin, la paraffine peut precipiter les asphaltenes, ce qui peut accelerer davantage le durcissement chimique et physique. Cet article presente les resultats de tests de vieillissement sur le bitume pur et celui modifie au RPM. Nous avons constate que le RPM augmente significativement les taux d'oxydation et la tendance des asphaltenes a precipiter, conduisant a un materiau moins ductile avec des contraintes plus elevees a basses temperatures, ce qui generalement entraine une fissuration precoce et plus grande.
Tumor antigens for cancer immunotherapy: therapeutic potential of xenogeneic DNA vaccines (2004)

Preclinical animal studies have convincingly demonstrated that tumor immunity to self antigens can be actively induced and can translate into an effective anti-tumor response. Several of these observations are being tested in clinical trials. Immunization with xenogeneic DNA is an attractive approach to treat cancer since it generates T cell and antibody responses. When working in concert, these mechanisms may improve the efficacy of vaccines. The use of xenogeneic DNA in overcoming immune tolerance has been promising not only in inbred mice with transplanted tumors but also in outbred canines, which present with spontaneous tumors, as in the case of human. Use of this strategy also overcomes limitations seen in other types of cancer vaccines. Immunization against defined tumor antigens using a xenogeneic DNA vaccine is currently being tested in early phase clinical trials for the treatment of melanoma and prostate cancers, with proposed trials for breast cancer and Non-Hodgkin's Lymphoma.
Aberrant temporal and spatial brain activity during rest in patients with chronic pain (2010)

In the absence of external stimuli, human hemodynamic brain activity displays slow intrinsic variations. To find out whether such fluctuations would be altered by persistent pain, we asked 10 patients with unrelenting chronic pain of different etiologies and 10 sex- and age-matched control subjects to rest with eyes open during 3-T functional MRI. Independent component analysis was used to identify functionally coupled brain networks. Time courses of an independent component comprising the insular cortices of both hemispheres showed stronger spectral power at 0.12 to 0.25 Hz in patients than in control subjects, with the largest difference at 0.16 Hz. A similar but weaker effect was seen in the anterior cingulate cortex, whereas activity of the precuneus and early visual cortex, used as a control site, did not differ between the groups. In the patient group, seed point-based correlation analysis revealed altered spatial connectivity between insulae and anterior cingulate cortex. The results imply both temporally and spatially aberrant activity of the affective pain-processing areas in patients suffering from chronic pain. The accentuated 0.12- to 0.25-Hz fluctuations in the patient group might be related to altered activity of the autonomic nervous system.
Listeria Intracellular Growth and Virulence Require Host-Derived Lipoic Acid (2003)

Listeria monocytogenes is a Gram-positive intracytosolic pathogen that causes severe disease in pregnant and immunocompromised individuals. We found that L. monocytogenes lacking the lipoate protein ligase LplA1 was defective for growth specifically in the host cytosol and was less virulent in animals by a factor of 300. A major target for LplA1, the E2 subunit of pyruvate dehydrogenase (PDH), lacked a critical lipoyl modification when the DeltalplA1 strain was grown intracellularly, which suggests that abortive growth was due to loss of PDH function. Thus, the use of host-derived lipoic acid may be a critical process for in vivo replication of bacterial pathogens.
Clinical application of two computerized diabetes management systems: comparison with the log-book method. (1992)

In two consecutive studies the clinical application and suitability of two computer-assisted data management systems (Camit and Cadmo) were evaluated in a prospective manner. In each study nineteen long-standing, stable insulin-dependent patients were randomly assigned to one of two groups. In study I assessment of metabolic control and insulin dose adjustments were based either on the Camit S1 data analysis or on the conventional log-book method, whereas in study II the Camit S2 and the Cadmo simulation programs were evaluated. HbA1c values decreased significantly in both studies (p < 0.05). A clear decline in hypoglycemic events as well as a significant reduction of the percentage of glucose values below 4.0 mmol/l (p < 0.005) and a marked increase (p < 0.05) in the percentage of glucose levels in the target range (4.0-10.0 mmol/l) were observed. We found both computerized assessment systems to be reliable and suitable for the assessment of blood glucose control and for insulin dose finding. The graphical and statistical presentation of the numerous glucose and insulin data allowed a better summary of blood glucose control and metabolic trends. More time could be spent for problem solving, which proved to be much less exhausting with the computer for the attending physician. Further studies should address the educational potential of computerized systems for the patient as well as for the physician.
Phagocytic killing of Neisseria gonorrhoeae by human monocytes (1983)

The ability of human monocytes to phagocytize and kill nonpiliated opaque (T3) and transparent (T4) gonococci was investigated in a tumbling tube suspension assay. A serum-sensitive strain, F62, and a serum-resistant strain, FA19, were studied. CFU remaining after incubation with monocytes were used to assess the extent of killing. The data show that 50% of T3 and T4 gonococci of both strains were killed by monocytes over a 2-h period. Serum was necessary for the killing of transparent gonococci of both strains as well as for FA19 T3. Concentrations of serum ranging from 0.5 to 10% were equally effective, and heat-labile components were required. Killing of F62 T3, however, occurred in the absence of serum. An increased ratio of bacteria to monocytes decreased the rate of killing. A 30-min preopsonization of gonococci in 10% serum resulted in an enhanced rate of killing. Monocytes were able to kill plate-grown, but not log-phase, organisms. Disruption of the monocytes by sonication to release internalized bacteria did not increase the number of viable organisms. The addition of 10 micrograms of cytochalasin B per ml completely inhibited the reduction in colony numbers over time. These data indicate that freshly isolated human monocytes are capable of phagocytizing and killing nonpiliated gonococci.
DETECTION OF CYTOMEGALOVIRUS, EPSTEIN–BARR VIRUS AND HERPES VIRUS-6 IN PATIENTS WITH RHEUMATOID ARTHRITIS WITH OR WITHOUT SJÖGREN'S SYNDROME (1994)

The frequency of latent viral infection by cytomegalovirus (CMV), Epstein-Barr virus (EBV) and herpes virus-6 (HHV-6) was investigated in patients with RA with or without Sjögren's syndrome (SS) and in normal controls. Virus presence was determined by polymerase chain amplification of DNA isolated from peripheral blood mononuclear or polymorphonuclear cells and/or saliva-derived mononuclear/epithelial cells. Anti-viral antibodies and autoantibodies were also assayed. Patients with RA both with and without SS were found to have a significantly increased frequency of latent viral infection (two-fold higher, P = 0.035 for EBV and seven-fold higher, P = 0.018 for HHV-6) compared to normal controls but only in cells isolated from saliva. The increased frequency of virally infected cells from the saliva of patients with RA, regardless of the SS status, when compared to normal controls may reflect the ongoing inflammatory process, the impact of therapy and/or a less effective local immune responsiveness.
Immunotoxins and Anticancer Drug Conjugate Assemblies: The Role of the Linkage between Components (2011)

Immunotoxins and antibody-drug conjugates are protein-based drugs combining a target-specific binding domain with a cytotoxic domain. Such compounds are potentially therapeutic against diseases including cancer, and several clinical trials have shown encouraging results. Although the targeted elimination of malignant cells is an elegant concept, there are numerous practical challenges that limit conjugates' therapeutic use, including inefficient cellular uptake, low cytotoxicity, and off-target effects. During the preparation of immunoconjugates by chemical synthesis, the choice of the hinge component joining the two building blocks is of paramount importance: the conjugate must remain stable in vivo but must afford efficient release of the toxic moiety when the target is reached. Vast efforts have been made, and the present article reviews strategies employed in developing immunoconjugates, focusing on the evolution of chemical linkers.
Synthesis, Structure, Assembly, and Modulation of the CO2 Adsorption Properties of a Zinc-Adeninate Macrocycle (2009)

The preparation and self-assembly of zinc adeninate macrocycles [Zn(6)(adeninate)(6)(pyridine)(6)(dimethylcarbamate)(6)] is described. The macrocycles self-assemble through adenine-adenine hydrogen bonding interactions into a 3-D porous crystalline material that maintains its structural integrity after removal of guest molecules and coordinated pyridine molecules. By adjusting the activation temperature prior to gas adsorption measurements, the size of the pore aperture can be modulated to afford unique gas sorption properties including selective gas adsorption and CO(2) sequestration.
Long Running Jobs in an Authenticated Environment (1993)

Current authentication systems require that a user have a valid token or ticket for a job to run. These tickets are issued with limited lifetimes, and their renewal requires a user to enter her password. We have developed a system called lat with which a user may schedule a batch job to be run at a later date in the current environment. The batch job is stored on a secure machine, and sent and received only in encrypted form. When it is time for the job to run, the server generates a ticket for the original user and sends it (encrypted) to the machine on which the job will run. The user is given an option to specify that tickets should be continually generated for the job until its execution has completed. March 29, 1993 Center for Information Technology Integration University of Michigan 519 West William Street Ann Arbor, MI 48103-4943 -- -- Long Running Jobs in an Authenticated Environment A. D. Rubin rubin@citi.umich.edu P. Honeyman honey@citi.umich.edu 1. Introduction Adapta...
Functional comparison of single- and double-stranded mdr1 antisense oligodeoxynucleotides in human ovarian cancer cell lines. (2005)

Novel findings from this study suggest that double-stranded antisense ODNs more effectively inhibit target protein expression and consequently enhance chemoresponsiveness through improvements in cellular uptake and distribution to the nucleus.
Discovery and Evaluation of 2-Anilino-5-aryloxazoles as a Novel Class of VEGFR2 Kinase Inhibitors (2005)

A series of derivatives of 2-anilino-5-phenyloxazole (5) has been identified as inhibitors of VEGFR2 kinase. Herein we describe the structure-activity relationship (SAR) of this novel template. Optimization of both aryl rings led to very potent inhibitors at both the enzymatic and cellular levels. Oxazole 39 had excellent solubility and good oral PK when dosed as the bis-mesylate salt and demonstrated moderate in vivo efficacy against HT29 human colon tumor xenografts. X-ray crystallography confirmed the proposed binding mode, and comparison of oxazoles 39 and 46 revealed interesting differences in orientation of 2-pyridyl and 3-pyridyl rings, respectively, attached at the meta position of the 5-phenyl ring.
Principles and practice of real-time visual tracking for navigation and mapping (2004)

We present examples of real-time mobile navigation systems and approaches to vision-based Simultaneous Localization and Mapping (SLAM) based on the second generation of our image processing library, XVision. Although the application-field of XVision is not limited to mobile navigation, the real-time requirements and limited computational resources on mobile systems provide a good testbed for it. We discuss the general architecture of the library and its modular processing pipeline, and we show how multiple tracking and low-level image processing primitives for color, texture and disparity can be combined to produce vision-guided navigation systems. The applications we discuss make use of XVision capabilities to solve the temporal correspondence problem by tracking an image feature in a given image domain.