gebhart/patrepeval huggingface dataset:
Characterization of Effector and Memory T Cell Subsets in the Immune Response to Bovine Tuberculosis in Cattle (2015)

Cultured IFN-γ ELISPOT assays are primarily a measure of central memory T cell (Tcm) responses with humans; however, this important subset of lymphocytes is poorly characterized in cattle. Vaccine-elicited cultured IFN-γ ELISPOT responses correlate with protection against bovine tuberculosis in cattle. However, whether this assay measures cattle Tcm responses or not is uncertain. The objective of the present study was to characterize the relative contribution of Tcm (CCR7+, CD62Lhi, CD45RO+), T effector memory (Tem, defined as: CCR7-, CD62Llow/int, CD45RO+), and T effector cells (CCR7-, CD62L-/low, CD45RO-), in the immune response to Mycobacterium bovis. Peripheral blood mononuclear cells (PBMC) from infected cattle were stimulated with a cocktail of M. bovis purified protein derivative, rTb10.4 and rAg85A for 13 days with periodic addition of fresh media and rIL-2. On day 13, cultured PBMC were re-stimulated with medium alone, rESAT-6:CFP10 or PPDb with fresh autologous adherent cells for antigen presentation. Cultured cells (13 days) or fresh PBMCs (ex vivo response) from the same calves were analyzed for IFN-γ production, proliferation, and CD4, CD45RO, CD62L, CD44, and CCR7 expression via flow cytometry after overnight stimulation. In response to mycobacterial antigens, ~75% of CD4+ IFN-γ+ cells in long-term cultures expressed a Tcm phenotype while less than 10% of the ex vivo response consisted of Tcm cells. Upon re-exposure to antigen, long-term cultured cells were highly proliferative, a distinctive characteristic of Tcm, and the predominant phenotype within the long-term cultures switched from Tcm to Tem. These findings suggest that proliferative responses of Tcm cells to some extent occurs simultaneously with reversion to effector phenotypes (mostly Tem). The present study characterizes Tcm cells of cattle and their participation in the response to M. bovis infection.
Two-photon fluorescence excitation cross sections of biomolecular probes from 690 to 960 nm (1998)

We report on two-photon fluorescence excitation (TPE) action cross sections for five widely used molecular fluorophores. Measurements were performed by use of ultrashort (~100-fs) Ti:sapphire pulsed excitation over the range 690-960 nm. TPE spectra were obtained by comparison with a fluorescein calibration standard. Large cross sections were found for the cyanine reagent Cy 3 (~140 GM) and for Rhodamine 6G (~150 GM), both at 700 nm [1 GM = 10(-50) (cm(4) s)/photon]. Several fluorophores show interesting and desirable blue shifts with respect to twice the one-photon absorption wavelength. Fluorophore fluorescence intensities showed no significant departure (?4%) from quadratic illumination power dependence, indicating genuine two-photon processes. Implications of these measurements for two-photon laser-scanning microscopy are discussed.
Contrast agent‐enhanced magnetic resonance imaging of skeletal muscle damage in animal models of muscular dystrophy (2000)

Membrane lesions play an early role in the pathogenesis of muscular dystrophy. Using a new albumin-targeted contrast agent (MS-325), sarcolemmal integrity of two animal models for muscular dystrophy was studied by MRI. Intravenously injected MS-325 does not enter skeletal muscle of normal mice. However, mdx and Sgca-null mutant mice, animal models for Duchenne and sarcoglycan-deficient limb-girdle muscular dystrophy, respectively, showed significant accumulation of MS-325 in skeletal muscle. The results suggest that contrast agent-enhanced MRI could serve as a common, noninvasive imaging procedure for evaluating the localization, extent, and mechanisms of skeletal muscle damage in muscular dystrophy. Furthermore, this method is expected to facilitate assessment of therapeutic approaches in these diseases. Magn Reson Med 44:655–659, 2000. © 2000 Wiley-Liss, Inc.
Engineering of Ralstonia eutropha for Production of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from Fructose and Solid-State Properties of the Copolymer (2002)

Recombinant Ralstonia eutropha capable of producing poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) copolymer [P(3HB-co-3HHx)] from fructose was engineered by introduction of genes for crotonyl-CoA reductase (CCR) from Streptomyces cinnamonensis (ccrSc) and for PHA synthase and (R)-specific enoyl-CoA hydratase from Aeromonas caviae (phaC-JAc). In this recombinant strain, C6-acyl-CoA intermediates were provided via beta-ketothiolase-mediated elongation of butyryl-CoA, which was generated from crotonyl-CoA by the function of CCR. The recombinant strain could accumulate the copolyester up to 48 wt % of dry cell weight with 1.5 mol % of 3HHx fraction from fructose, when the expression of ccrSc under the control of the PBAD promoter was induced with 0.01% L-arabinose. The absence of L-arabinose or the deletion of ccrSc from the plasmid resulted in accumulation of poly(3-hydroxybutyrate) homopolymer, indicating the critical role of CCR in the formation of the 3-hydroxyhexanoate unit. Higher CCR activity obtained by the addition of a larger amount of L-arabinose did not affect the composition but reduced the intracellular content of the copolyester. The P(3HB-co-1.5 mol % 3HHx) copolyester produced from fructose by the recombinant R. eutropha showed relatively lower melting temperatures (150 degrees C and 161 degrees C) and lower crystallinity (48 +/- 5%) compared to those (175 degrees C and 60 +/- 5%) of P(3HB) homopolymer. It has been found that the incorporation of a small amount (1.5 mol %) of 3HHx units into P(3HB) sequences leads to a remarkable change in the solid-state properties of P(3HB) crystals. The present study demonstrates the potential of the engineered pathway for the production of copolyesters having favorable characteristics from inexpensive carbon resources.
Security architecture for a virtual heterogeneous machine (2002)

We describe security for a virtual heterogeneous machine (VHM). Our security architecture is based upon separation of services into four distinct domains. It is designed to take advantage of operating system support for domains, where available. We have chosen to use emerging public key technology as an interim solution to provide domain separation. A prototype demonstration of our architecture has been developed.
Energy and Quality Evaluation for Compressive Sensing of Fetal Electrocardiogram Signals (2016)

This manuscript addresses the problem of non-invasive fetal Electrocardiogram (ECG) signal acquisition with low power/low complexity sensors. A sensor architecture using the Compressive Sensing (CS) paradigm is compared to a standard compression scheme using wavelets in terms of energy consumption vs. reconstruction quality, and, more importantly, vs. performance of fetal heart beat detection in the reconstructed signals. We show in this paper that a CS scheme based on reconstruction with an over-complete dictionary has similar reconstruction quality to one based on wavelet compression. We also consider, as a more important figure of merit, the accuracy of fetal beat detection after reconstruction as a function of the sensor power consumption. Experimental results with an actual implementation in a commercial device show that CS allows significant reduction of energy consumption in the sensor node, and that the detection performance is comparable to that obtained from original signals for compression ratios up to about 75%.
Intestinal alkaline phosphatase has beneficial effects in mouse models of chronic colitis (2010)

Endogenous IAP appears to play a role in protecting the host against chronic colitis. Orally administered cIAP exerts a protective effect in two independent mouse models of chronic colitis and may represent a novel therapy for human IBD.
Conducting and transparent single-wall carbon nanotube electrodes for polymer-fullerene solar cells (2005)

We describe the use of single-wall carbon nanotube (SWNT) thin films as transparent and conducting electrodes for hole collection in poly(hexyl)thiophene-[6-6]phenyl-C61-butyric acid methyl ester (P3HT-PCBM) organic photovoltaics. We report a power conversion efficiency of 1%, with a fill factor of 0.3 and a short-circuit current of 6.5mA∕cm2 under 100mW∕cm2 polychromatic white light illumination measured in air. These values are comparatively higher than reference cells of similar thickness made on indium tin oxide (ITO) glass substrates. This is attributed to the three-dimensional nature of the interface between the SWNTs and the P3HT-PCBM nanocomposite. Our results indicate that solution processed SWNT thin films are a viable alternative to ITO for photovoltaic devices, eliminating an expensive vacuum deposition step in the fabrication of organic solar cells.
Definition of the Mycobacterial SOS Box and Use To Identify LexA-Regulated Genes inMycobacterium tuberculosis (2002)

The bases of the mycobacterial SOS box important for LexA binding were determined by replacing each base with every other and examining the effect on the induction of a reporter gene following DNA damage. This analysis revealed that the SOS box was longer than originally thought by 2 bp in each half of the palindromic site. A search of the Mycobacterium tuberculosis genome sequence with the new consensus, TCGAAC(N)(4)GTTCGA, identified 4 sites which were perfect matches and 12 sites with a single mismatch which were predicted to bind LexA. Genes which could potentially be regulated by these SOS boxes were ascertained from their positions relative to the sites. Examination of expression data for these genes following DNA damage identified 12 new genes which are most likely regulated by LexA as well as the known M. tuberculosis DNA damage-inducible genes recA, lexA, and ruvC. Of these 12 genes, only 2 have a predicted function: dnaE2, a component of DNA polymerase III, and linB, which is similar to 1,3,4,6-tetrachloro-1,4-cylcohexadiene hydrolase. Curiously, of the remaining 10 genes predicted to be LexA regulated, 7 are members of the M. tuberculosis 13E12 repeat family, which has some of the characteristics of mobile elements.
Overexpression of Protein Disulfide Isomerase DsbC Stabilizes Multiple-Disulfide-Bonded Recombinant Protein Produced and Transported to the Periplasm in Escherichia coli (2000)

Dsb proteins (DsbA, DsbB, DsbC, and DsbD) catalyze formation and isomerization of protein disulfide bonds in the periplasm of Escherichia coli. By using a set of Dsb coexpression plasmids constructed recently, we analyzed the effects of Dsb overexpression on production of horseradish peroxidase (HRP) isozyme C that contains complex disulfide bonds and tends to aggregate when produced in E. coli. When transported to the periplasm, HRP was unstable but was markedly stabilized upon simultaneous overexpression of the set of Dsb proteins (DsbABCD). Whereas total HRP production increased severalfold upon overexpression of at least disulfide-bonded isomerase DsbC, maximum transport of HRP to the periplasm seemed to require overexpression of all DsbABCD proteins, suggesting that excess Dsb proteins exert synergistic effects in assisting folding and transport of HRP. Periplasmic production of HRP also increased when calcium, thought to play an essential role in folding of nascent HRP polypeptide, was added to the medium with or without Dsb overexpression. These results suggest that Dsb proteins and calcium play distinct roles in periplasmic production of HRP, presumably through facilitating correct folding. The present Dsb expression plasmids should be useful in assessing and dissecting periplasmic production of proteins that contain multiple disulfide bonds in E. coli.
Specific binding of murine leukemia inhibitory factor to normal and leukemic monocytic cells. (1988)

Leukemia inhibitory factor (LIF), a glycoprotein capable of suppressing the clonogenicity and inducing the differentiation of the murine myeloid leukemia cell line M1, was radioiodinated to a high specific radioactivity with retention of full biological activity. Binding of 125I-labeled LIF to M1 cells reached a steady state at 37 degrees C after approximately equal to 40 min and was in competition with unlabeled LIF but not granulocyte colony-stimulating factor or a range of other cytokines or differentiation-inducing agents. Specific binding was demonstrable to cells from a range of murine hemopoietic tissues including the bone marrow, the spleen, and the peritoneal cavity. Autoradiography revealed macrophages, monocytes, and their precursors to be the major cell types responsible for 125I-labeled LIF binding within these tissues. Receptors on M1 cells were of high affinity (apparent Kd, 100-200 pM) and few in number (300-500 per cell).
Arabidopsis AtcwINV3 and 6 are not invertases but are fructan exohydrolases (FEHs) with different substrate specificities (2004)

ABSTRACT The genome of Arabidopsis thaliana contains six putative cell‐wall type invertase genes ( AtcwINV1‐6 ). Heterologous expression of AtcwINV1, 3 and 6 cDNAs in Pichia pastoris revealed that the enzymes encoded by AtcwINV3 and 6 did not show invertase activity. Instead, AtcwINV3 is a 6‐FEH and AtcwINV6 is a fructan exohydrolase (FEH) that can degrade both inulin and levan‐type fructans. For AtcwINV6 it is proposed to use the term (6&amp;1) FEH. In contrast, AtcwINV1 is a typical invertase. FEH activity was also detected in crude extracts of different parts of Arabidopsis . To verify that the FEH activity of AtcwINV3 and 6 were not artefacts of the heterologous expression system, the protein corresponding to AtcwINV3 was isolated from whole Arabidopsis plants and indeed showed only 6‐FEH activity and no invertase activity. Although no fructans can be detected in Arabidopsis plants, it is shown that kestoses (trimers) can be synthesized in crude leaf extracts. The putative physiological significance of FEH in so‐called non‐fructan plants is discussed.
Different Effects of Surfactant Proteins B and C – Implications for Development of Synthetic Surfactants (2010)

Treatment of premature newborn rabbits with synthetic surfactants containing a surfactant protein C analogue in a simple phospholipid mixture gives similar tidal volumes as treatment with poractant alfa (Curosurf(R)) but ventilation with a positive end-expiratory pressure (PEEP) is needed for this synthetic surfactant to stabilize the alveoli at end-expiration. The effect on lung gas volumes seems to depend on the structure of the peptide since treatment with a synthetic surfactant containing the 21-residue peptide (LysLeu(4))(4)Lys (KL(4)) gives low lung gas volumes in experiments also performed with PEEP. Surfactant preparations containing both surfactant proteins B and C or their analogues prevent alveolar collapse at end-expiration even if ventilated without PEEP. Treatment of premature newborn rabbits with different natural surfactants indicates that both the lipid composition and the proteins are important in order to stabilize the alveoli at end-expiration. Synthetic surfactants containing two peptides may be able to replace natural surfactants within the near future but more trials need to be performed before any conclusion can be drawn about the ideal composition of this new generation of synthetic surfactants.
Soluble Complement Receptor Type 1 Protects Rats from Lethal Shock Induced by Anti-Crry Antibody following Lipopolysaccharide Priming (2002)

sCR1 may be an effective treatment for acute shock involving complement activation.
Total Synthesis of (–)‐Epothilone B: An Extension of the Suzuki Coupling Method and Insights into Structure–Activity Relationships of the Epothilones (1997)

The highest biological activities displayed by epothilone-related compounds have been found for epothilone B (1) and a derivative that was prepared en route to the natural product. Key steps in the total synthesis were a Suzuki coupling providing a trisubstituted double bond in the macrocycle and its subsequent stereoselective epoxidation with dimethyldioxirane.
Direct amination of ethylene by zeolite catalysis (1987)

M. Deeba, M. E. Ford and T. A. Johnson, J. Chem. Soc., Chem. Commun., 1987, 562 DOI: 10.1039/C39870000562
Drug Transport across the Blood–Brain Barrier (2012)

The blood-brain barrier (BBB) prevents the brain uptake of most pharmaceuticals. This property arises from the epithelial-like tight junctions within the brain capillary endothelium. The BBB is anatomically and functionally distinct from the blood-cerebrospinal fluid barrier at the choroid plexus. Certain small molecule drugs may cross the BBB via lipid-mediated free diffusion, providing the drug has a molecular weight <400 Da and forms <8 hydrogen bonds. These chemical properties are lacking in the majority of small molecule drugs, and all large molecule drugs. Nevertheless, drugs can be reengineered for BBB transport, based on the knowledge of the endogenous transport systems within the BBB. Small molecule drugs can be synthesized that access carrier-mediated transport (CMT) systems within the BBB. Large molecule drugs can be reengineered with molecular Trojan horse delivery systems to access receptor-mediated transport (RMT) systems within the BBB. Peptide and antisense radiopharmaceuticals are made brain-penetrating with the combined use of RMT-based delivery systems and avidin-biotin technology. Knowledge on the endogenous CMT and RMT systems expressed at the BBB enable new solutions to the problem of BBB drug transport.
Generation of Prothrombin‐Converting Activity and the Exposure of Phosphatidylserine at the Outer Surface of Platelets (1982)

In the present paper we compare prothrombin‐converting activities of platelets non‐activated, or activated by collagen, thrombin or collagen plus thrombin in the absence and presence of added factor V a . In all experiments described, the rate of thrombin formation for platelets activated by the combined action of collagen and thrombin is greater than that of platelets stimulated by collagen or thrombin alone. The presence of added factor V a enhanced the rate of thrombin formation in all cases, but the higher activity observed with platelets stimulated by collagen plus thrombin remains. When platelets are activated by collagen plus thrombin in the presence factor X a and prothrombin, a lag period of approximately 10 min is observed before the rate of thrombin formation reaches a steady state. Addition of an excess of factor V a in this experiment reduces the lag time to 3 min. This lag period is interpreted as the time required to generate extra binding sites for the prothrombinase complex at the platelet surface. These extra sites explain the difference in thrombin formation rate between these platelets and platelets activated by either collagen or thrombin only. The exposure of phospholipids at the platelet outer surface was studied with phospholipases after various activations of the platelets. It is demonstrated that activation by collagen plus thrombin is accompanied by increased susceptibility of platelet phospholipids towards phospholipase A 2 . Among these degradable phospho‐ lipids are 25% of the phosphatidylserine and 30% of the phosphatidylethanolamine. On the other hand, little no phosphatidylserine is exposed at the membrane exterior of thrombin‐treated or control platelets. We propose that the exposure of phosphatidylserine at the outer surface of platelets activated with thrombin plus collagen essential for the rate enhancement of thrombin formation observed under these conditions. The possibility of transbilayer movement of phospholipids in the platelet membrane as a result of the activation process will be discussed.
Tunable infrared modulator and switch using Stark shift in step quantum wells (1990)

A tunable infrared modulator and/or switch using intersubband Stark shift in a step quantum well is discussed. The device utilizes the intersubband absorption and the large change of separation between energy levels in the step quantum well under an applied electric field. The incident infrared beam on the device is either absorbed or transmitted depending on the energy separation of the levels, and thus the modulation can be achieved by adjusting the energy levels with an applied electric field. The extremely short lifetime of the intersubband transition makes this modulator suitable for application in high-speed long-wavelength optical communications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interpreting the convergence of Lyman series absorption lines (1990)

Spectra of quasars at high z often show absorption at the Lyman limit from intervening gas systems at intermediate z having N(H) approx. greater than 10(exp 7) cm(-2). In some circumstances, N(H) can be determined by measuring the strength of the Lyman limit absorption or the damping wings of Lyman - alpha. With a spectrum taken at low wavelength resolution, say, lambda/delta lambda approx. 10(exp 3), it is usually not possible to distinguish individual Lyman series lines near the limit, yet one can still discern how rapidly the average intensity drops off as the limit is approached from the long wavelength side. The purpose here is to point out the information which is available from measurements of this series convergence.
Mitochondrial Targeting of HumanO6-Methylguanine DNA Methyltransferase Protects against Cell Killing by Chemotherapeutic Alkylating Agents (2005)

DNA repair capacity of eukaryotic cells has been studied extensively in recent years. Mammalian cells have been engineered to overexpress recombinant nuclear DNA repair proteins from ectopic genes to assess the impact of increased DNA repair capacity on genome stability. This approach has been used in this study to specifically target O(6)-methylguanine DNA methyltransferase (MGMT) to the mitochondria and examine its impact on cell survival after exposure to DNA alkylating agents. Survival of human hematopoietic cell lines and primary hematopoietic CD34(+) committed progenitor cells was monitored because the baseline repair capacity for alkylation-induced DNA damage is typically low due to insufficient expression of MGMT. Increased DNA repair capacity was observed when K562 cells were transfected with nuclear-targeted MGMT (nucl-MGMT) or mitochondrial-targeted MGMT (mito-MGMT). Furthermore, overexpression of mito-MGMT provided greater resistance to cell killing by 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU) than overexpression of nucl-MGMT. Simultaneous overexpression of mito-MGMT and nucl-MGMT did not enhance the resistance provided by mito-MGMT alone. Overexpression of either mito-MGMT or nucl-MGMT also conferred a similar level of resistance to methyl methanesulfonate (MMS) and temozolomide (TMZ) but simultaneous overexpression in both cellular compartments was neither additive nor synergistic. When human CD34(+) cells were infected with oncoretroviral vectors that targeted O(6)-benzylguanine (6BG)-resistant MGMT (MGMT(P140K)) to the nucleus or the mitochondria, committed progenitors derived from infected cells were resistant to 6BG/BCNU or 6BG/TMZ. These studies indicate that mitochondrial or nuclear targeting of MGMT protects hematopoietic cells against cell killing by BCNU, TMZ, and MMS, which is consistent with the possibility that mitochondrial DNA damage and nuclear DNA damage contribute equally to alkylating agent-induced cell killing during chemotherapy.