gebhart/patrepeval huggingface dataset:
Synthesis of cyclic disulfide peptides: comparison of oxidation methods (1997)

Abstract: Seven cyclic disulfide peptides (oxytocin, salmon calcitonin 1-10, CTP, crustacean cardioactive peptide, somatostatin 3-14, [C2•6]-P-endorphin 1-6 and endothelin-P 3-11) were synthesized on soli&lt;:1 phase and cyclized either on the resin, simultaneously with the cleavage from the resin, or in solution after cleavage, using eight different oxidation methods. The purities of the crude peptides were compared in order to evaluate the efficacy of the different oxidation methods with respect to the peptide sequences.
Tissue engineering of cardiac valve prostheses II: biomechanical characterization of decellularized porcine aortic heart valves. (2002)

For both young patients with congenital heart disease and young, growing adults there is a need for replacement heart valves that will develop with the patient. Tissue-engineered heart valves coupled with in-vitro recellularization have this potential. One approach is to use acellular tissue matrices, but the decellularization treatment must not affect the biomechanical integrity of the valvular matrix. This study investigated the effect of 0.03% (w/v) and 0.1% (w/v) sodium dodecyl sulfate (SDS) on the mechanical integrity of porcine aortic valve leaflets.Left coronary porcine leaflets were treated with SDS (0.03% or 0.1%, w/v) in hypotonic or isotonic buffer and buffer alone. SDS in hypotonic buffer produced accellularity. Circumferential and radial specimens of treated leaflets were subjected to uniaxial tensile testing, and the effect of the buffer on leaflet morphology was assessed. Whole porcine aortic roots were also treated with 0.1% (w/v) SDS and subjected to function testing.SDS treatment significantly increased extensibility of the leaflet specimens, which was greater in the circumferential than radial direction. This was seen as a significantly decreased slope of both the elastic and collagen phases of the stress-strain behavior. The ultimate tensile strength and transition stress were not affected significantly; nor was there any significant difference between hypotonic buffer and hypotonic buffer + SDS treatments. Study of the leaflet morphology suggested that the increased extensibility was due to shrinkage as well as to increased hydration of the treated leaflets caused by the hypotonic buffer.SDS treatment produced a more extensible tissue with equal strength compared with the fresh aortic valve. Functionality experiments with SDS-treated whole aortic roots showed complete valve leaflet competence under physiological pressures (120 mmHg) as well as physiological leaflet kinematics.
Ambisense gene expression from recombinant rabies virus: random packaging of positive- and negative-strand ribonucleoprotein complexes into rabies virions (1997)

We have recovered from cDNA a rabies virus (RV) containing identical, transcriptionally active promoters at its genome (negative-strand) and antigenome RNA and directing efficient expression of a chloramphenicol acetyltransferase (CAT) reporter gene from the antigenome. Transcription of the antigenome CAT gene was terminated by a modified RV gene junction able to mediate transcription stop and polyadenylation but not reinitiation of downstream transcripts. While in standard RV-infected cells genome and antigenome RNAs were present in a 49:1 ratio, the ambisense virus directed synthesis of equal amounts of genome and antigenome RNA (1:1). Total replicative synthesis was reduced by a factor of less than 2, revealing an unexpectedly high level of replication activity of the transcriptionally active promoter in the absence of the parental antigenome promoter. Successful packaging of ambisense ribonucleoprotein complexes (RNPs) into virions demonstrated that the parental 5' end of the RV genome RNA does not contain putative signals required for incorporation into virions. As determined both for standard RV and ambisense RV, virus particles contained genome and antigenome RNPs in the same ratios as those present in infected cells (49:1 and 1:1, respectively), indicating indiscriminate incorporation of RNPs independent of signals in the RNA. Ambisense expression of multiple foreign genes from RV vectors may circumvent problems with transcriptional attenuation of rhabdovirus housekeeping genes.
A genetic and biochemical analysis of the bacteriophage [lambda] cro protein (1988)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1988.
Network-based approach to identify prognostic biomarkers for estrogen receptor–positive breast cancer treatment with tamoxifen (2015)

This study aims to identify effective gene networks and prognostic biomarkers associated with estrogen receptor positive (ER+) breast cancer using human mRNA studies. Weighted gene coexpression network analysis was performed with a complex ER+ breast cancer transcriptome to investigate the function of networks and key genes in the prognosis of breast cancer. We found a significant correlation of an expression module with distant metastasis-free survival (HR = 2.25; 95% CI .21.03-4.88 in discovery set; HR = 1.78; 95% CI = 1.07-2.93 in validation set). This module contained genes enriched in the biological process of the M phase. From this module, we further identified and validated 5 hub genes (CDK1, DLGAP5, MELK, NUSAP1, and RRM2), the expression levels of which were strongly associated with poor survival. Highly expressed MELK indicated poor survival in luminal A and luminal B breast cancer molecular subtypes. This gene was also found to be associated with tamoxifen resistance. Results indicated that a network-based approach may facilitate the discovery of biomarkers for the prognosis of ER+ breast cancer and may also be used as a basis for establishing personalized therapies. Nevertheless, before the application of this approach in clinical settings, in vivo and in vitro experiments and multi-center randomized controlled clinical trials are still needed.
Regio- and Stereospecific Syntheses and Nitric Oxide Donor Properties of (E)-9- and (E)-10-Nitrooctadec-9-enoic Acids (2006)

[reaction: see text] Nitrated fatty acids act as endogenous peroxisome proliferator-activated receptor gamma (PPARgamma) ligands and nitric oxide (NO) donors. We describe the first specific preparation of the two regioisomers of nitrooleic acid, (E)-9-nitrooctadec-9-enoic acid (1) and (E)-10-nitrooctadec-9-enoic acid (2), from cis-cyclooctene and monomethyl azelate, respectively. These syntheses rely upon a Henry condensation between a nine-carbon nitro component and a nine-carbon aldehyde. Preliminary chemiluminescence NO detection studies reveal the ability of these nitrated fatty acids to release NO.
β‐Alanine but not taurine can function as an organic osmolyte in preimplantation mouse embryos cultured from fertilized eggs (2003)

Early preimplantation mouse embryos are susceptible to the detrimental effects of increased osmolarity and, paradoxically, their in vitro development is significantly compromised by osmolarities near that of oviductal fluid. In vitro development can be restored, however, by several compounds that are accumulated by 1-cell embryos to act as organic osmolytes, providing intracellular osmotic support and cell volume regulation. Taurine, a substrate of the beta-amino acid transporter that functions as an organic osmolyte transporter in other cells, had been proposed to function as an organic osmolyte in mouse embryos. Here, however, we found that taurine is neither able to provide protection for in vitro embryo development against increased osmolarity nor is it accumulated to higher intracellular levels as osmolarity is increased, indicating that it cannot function as an organic osmolyte in early preimplantation embryos. In contrast, beta-alanine, the other major substrate of the beta-amino acid transporter, both protects against increased osmolarity and is accumulated to somewhat higher levels as osmolarity is increased, indicating that it is able to function as an organic osmolyte in embryos. However, we also found that beta-alanine is displaced from embryos by glycine-the most effective organic osmolyte in embryos previously identified-and beta-alanine does not increase protection above that afforded by glycine at concentrations near those in vivo. Thus, the beta-amino acid transporter is likely present in early preimplantation embryos to supply beta-amino acids such as taurine for purposes other than to serve as organic osmolytes.
Exploiting weak connectivity for mobile file access (1995)

Weak corrrrecdvi~, in the form of intermittent, low-bandwidth, or expensive networks is a fact of life in mobile computing. In this paper, we describe how the Coda File System has evolved to exploit such networks.
Calorie Restriction in Biosphere 2: Alterations in Physiologic, Hematologic, Hormonal, and Biochemical Parameters in Humans Restricted for a 2-Year Period (2002)

Four female and four male crew members, including two of the present authors (R. Walford and T. MacCallum)--seven of the crew being ages 27 to 42 years, and one aged 67 years--were sealed inside Biosphere 2 for two years. During seven eighths of that period they consumed a low-calorie (1750-2100 kcal/d) nutrient-dense diet of vegetables, fruits, nuts, grains, and legumes, with small amounts of dairy, eggs, and meat (approximately 12% calories from protein, approximately 11% from fat, and approximately 77% from complex carbohydrates). They experienced a marked and sustained weight loss of 17 +/- 5%, mostly in the first 8 months. Blood was drawn before entry into Biosphere 2, at many time-points inside it, and four times during the 30 months following exit from it and return to an ad libitum diet. Longitudinal studies of 50 variables on each crew member compared outside and inside values by means of a Bayesian statistical analysis. The data show that physiologic (e.g., body mass index, with a decrease of 19% for men and 13% for women; blood pressure, with a systolic decrease of 25% and a diastolic decrease of 22%), hematologic (e.g., white blood cell count, decreased 31%), hormonal (e.g., insulin, decreased 42%; T3, decreased 19%), biochemical (e.g., blood sugar, decreased 21%; cholesterol, decreased 30%), and a number of additional changes, including values for rT3, cortisol, glycated hemoglobin, plus others, resembled those of rodents or monkeys maintained on a calorie-restricted regime. Significant variations in several substances not hitherto studied in calorie-restricted animals are also reported (e.g., androstenedione, thyroid binding globulin, renin, and transferrin). We conclude that healthy nonobese humans on a low-calorie, nutrient-dense diet show physiologic, hematologic, hormonal, and biochemical changes resembling those of rodents and monkeys on such diets. With regard to the health of humans on such a diet, we observed that despite the selective restriction in calories and marked weight loss, all crew members remained in excellent health and sustained a high level of physical and mental activity throughout the entire 2 years.
Tissue Cytokine Patterns in Patients with Polymyalgia Rheumatica and Giant Cell Arteritis (1994)

Patients with polymyalgia rheumatica have vascular involvement. Patients with polymyalgia rheumatica and giant cell arteritis share in situ production of mRNA specific for macrophage-derived cytokines. T cells recruited to vasculitic lesions in patients with giant cell arteritis predominantly produce interleukin-2 and interferon-gamma. Patients with polymyalgia rheumatica do not have interferon-gamma production, suggesting that interferon-gamma may be involved in the progression to overt arteritis.
Mechanisms of Pancreatic β-Cell Death in Type 1 and Type 2 Diabetes (2005)

Type 1 and type 2 diabetes are characterized by progressive beta-cell failure. Apoptosis is probably the main form of beta-cell death in both forms of the disease. It has been suggested that the mechanisms leading to nutrient- and cytokine-induced beta-cell death in type 2 and type 1 diabetes, respectively, share the activation of a final common pathway involving interleukin (IL)-1beta, nuclear factor (NF)-kappaB, and Fas. We review herein the similarities and differences between the mechanisms of beta-cell death in type 1 and type 2 diabetes. In the insulitis lesion in type 1 diabetes, invading immune cells produce cytokines, such as IL-1beta, tumor necrosis factor (TNF)-alpha, and interferon (IFN)-gamma. IL-1beta and/or TNF-alpha plus IFN-gamma induce beta-cell apoptosis via the activation of beta-cell gene networks under the control of the transcription factors NF-kappaB and STAT-1. NF-kappaB activation leads to production of nitric oxide (NO) and chemokines and depletion of endoplasmic reticulum (ER) calcium. The execution of beta-cell death occurs through activation of mitogen-activated protein kinases, via triggering of ER stress and by the release of mitochondrial death signals. Chronic exposure to elevated levels of glucose and free fatty acids (FFAs) causes beta-cell dysfunction and may induce beta-cell apoptosis in type 2 diabetes. Exposure to high glucose has dual effects, triggering initially "glucose hypersensitization" and later apoptosis, via different mechanisms. High glucose, however, does not induce or activate IL-1beta, NF-kappaB, or inducible nitric oxide synthase in rat or human beta-cells in vitro or in vivo in Psammomys obesus. FFAs may cause beta-cell apoptosis via ER stress, which is NF-kappaB and NO independent. Thus, cytokines and nutrients trigger beta-cell death by fundamentally different mechanisms, namely an NF-kappaB-dependent mechanism that culminates in caspase-3 activation for cytokines and an NF-kappaB-independent mechanism for nutrients. This argues against a unifying hypothesis for the mechanisms of beta-cell death in type 1 and type 2 diabetes and suggests that different approaches will be required to prevent beta-cell death in type 1 and type 2 diabetes.
Toxic Effects of Acute Glutathione Depletion by Buthionine Sulfoximine and Dimethylfumarate on Murine Mammary Carcinoma Cells (1988)

Glutathione (GSH) depletion to approximately equal to 5% of control for 48 h or longer by 0.05 mM L-buthionine sulfoximine (BSO) led to appreciable toxicity for the 66 murine mammary carcinoma cells growing in vitro [L.A. Dethlefsen et al., Int. J. Radiat. Oncol. Biol. Phys. 12, 1157-1160 (1986)]. Such toxicity in normal, proliferating cells in vivo would be undesirable. Thus the toxic effects after acute GSH depletion to approximately equal to 5% of control by BSO plus dimethylfumarate (DMF) were evaluated in these same 66 cells to determine if this anti-proliferative effect could be minimized. Two hours of 0.025 mM DMF reduced GSH to 45% of control, while 6 h of 0.05 mM BSO reduced it to 16%. However, BSO (6 h) plus DMF (2 h) and BSO (24 h) plus DMF (2 h) reduced GSH to 4 and 2%, respectively. The incorporation (15-min pulses) of radioactive precursors into protein and RNA were unaffected by these treatment protocols. In contrast, cell growth was only modestly affected, but the incorporation of [3H]thymidine into DNA was reduced to 64% of control by the BSO (24 h) plus DMF (2 h) protocol even though it was unaffected by the BSO (6 h) plus DMF (2 h) treatment. The cellular plating efficiencies from both protocols were reduced to approximately equal to 75% of control cells. However, the aerobic radiation response, as measured by cell survival, was not modified at doses of either 4.0 or 8.0 Gy. The growth rates of treated cultures, after drug removal, quickly returned to control rates and the resynthesis of GSH in cells from both protocols was also rapid. The GSH levels after either protocol were slightly above control by 12 h after drug removal, dramatically over control (approximately equal to 200%) by 24 h, and back to normal by 48 h. Thus even a relatively short treatment with BSO and DMF resulting in a GSH depletion to 2-5% of control had a marked effect on DNA synthesis and plating efficiency and a modest effect on cellular growth. One cannot rule out a direct effect of the drugs, but presumably the antiproliferative effects are due to a depletion of nuclear GSH with the subsequent inhibition of the GSH/glutaredoxin-mediated conversion of ribonucleotides to deoxyribonucleotides. However, even after extended treatment, upon drug removal, GSH was rapidly resynthesized and cellular DNA synthesis and growth quickly resumed.
Ultrasonic Imaging of Tumor Angiogenesis Using Contrast Microbubbles Targeted via the Tumor-Binding Peptide Arginine-Arginine-Leucine (2005)

Abstract Endothelial cells (EC) of angiogenic tumor vasculature are characterized by altered expression of molecular markers on their surface. Numerous peptides have been identified that specifically bind tumor angiogenic endothelium, including the tripeptide arginine-arginine-leucine (RRL). We hypothesized that ultrasound contrast microbubbles (MB) targeted via linkage with RRL would specifically adhere to tumor angiogenic endothelium versus normal myocardium, and that this selective adhesion could be detected ultrasonically. Microbubbles were conjugated to cyclic peptides containing either RRL (RRL-MB) or a glycine control sequence (control-MB). As measured in a parallel plate flow chamber, in vitro adhesion of RRL-MBs was three times greater to cultured tumor–derived ECs than to normal ECs (P &amp;lt; 0.01), demonstrating selective binding of RRL-MBs to tumor endothelium. Mice bearing s.c. Clone C or PC3 tumors were given i.v. injections of fluorescent RRL to show in vivo localization to tumor vasculature or were ultrasonically imaged following i.v. injections of targeted contrast MBs. Ultrasound images showed strong RRL-MB contrast enhancement within the tumors but not the control tissue myocardium. Control-MBs caused minimal enhancement in either tissue. Quantitative acoustic videointensity was significantly greater for the tumors than the hearts (5 ± 1 versus 0.5 ± 1 intensity units; P = 0.001). These data show that ultrasound contrast MBs targeted to tumor vasculature via RRL preferentially adhere to tumor versus normal vasculature and that this selective adherence can be detected with ultrasound. Targeted microbubbles may thus offer a noninvasive contrast-enhanced ultrasound imaging technique for the functional imaging of tumor neovascularization, and may have further implications for therapeutic tumor targeting.
Modified Infusion Procedures Affect Recombinant Adeno-Associated Virus Vector Type 2 Transduction in the Liver (2005)

Recombinant adeno-associated virus (rAAV) vectors have therapeutic potential for the treatment of several types of liver diseases including hepato-deficiency disorders. Most of the preclinical and clinical applications involve the use of adeno-associated vector serotype 2 (AAV-2). However, when this vector is delivered at high doses into the portal vein or hepatic artery, a relatively small number of hepatocytes are stably transduced. We elected to determine if the route of vector administration and altering the vascular delivery route within the liver influenced the relative level of transduction. First, we delivered an AAV vector expressing the human factor IX gene from a liver-specific promoter into the hepatic artery, portal vein, or general circulation of rats. Transgene expression was equal with hepatic artery and portal vein infusion, which was higher than vector administered via peripheral venous infusion. Next, we determined how localized perfusion or changing the vector dwell time affected AAV transduction in vivo. To do this, we infused an AAV vector lacking a functional expression and quantified transduction by quantifying the number of double-stranded vector DNA genomes. By increasing vector dwell time in the liver to 5 min, vector transduction was enhanced approximately 4- to 5- fold. To establish if gene transduction could be restricted to a specific anatomic location in the liver, we delivered vector into specific liver lobes by clamping the venous inflow to the middle and left liver lobes (noninfused lobes) and infusing vector into the right two liver lobes through the hepatic artery followed by vector circulation between the two right lobes and general circulation for 5 min. With this selective infusion, 40 to 120 times higher vector genome was observed in the perfused lobes than the nonperfused lobes. All the procedures described in this study were performed without detectable liver injury or toxicity. In all, the present study clearly demonstrated that hepatic arterial infusion of rAAV is effective for liver-directed gene therapy and that other parameters related to blood flow can be adjusted to further optimize gene transfer.
Protein binding to supported lipid membranes: investigation of the cholera toxin-ganglioside interaction by simultaneous impedance spectroscopy and surface plasmon resonance (1993)

The specific recognition reaction between cholera toxin (ChTo) and the ganglioside GM1 was investigated in situ on planar supported lipid layers using simultaneous surface plasmon resonance (SPR) and electrochem. impedance measurements. The lipid monolayers contg. different amts. of GM1 were formed on alkanethiol-coated gold surfaces by a new lipid/detergent diln. technique. The formation of the layers was investigated using both SPR and impedance measurements. While the optical properties of the different lipid layers remained unchanged, the layer capacitance was seen to depend on the GM1 to POPC molar ratio. The selective binding of ChTo to these layers was detected with high sensitivity by SPR. The comparatively small impedance changes assocd. with the protein adsorption suggest a high water content of the ChTo layers. The B5 subunit interacts similarly with these supported lipid layers. [on SciFinder (R)]
Evaluating the Experience of Children With Type 1 Diabetes and Their Parents Taking Part in an Artificial Pancreas Clinical Trial Over Multiple Days in a Diabetes Camp Setting (2016)

Participants manifested a positive attitude toward the AP. Further studies are required to explore participants' perceptions early in the AP development to individualize the new treatment as much as possible, and to tailor it to respond to their needs and values.
Preparation of acrylic copolymers and crosslinking agents and properties as a film (2009)

Abstract Copolymers of butyl acrylate (BA)‐methyl methacrylate (MMA)‐acrylic acid (AA) and intraparticle crosslinking agents containing N ‐methylol acrylamide (NMA) and ethylene glycol dimethacrylate (EGDMA) were prepared by emulsion copolymerization. After that, films were prepared from the mixture of copolymers and the interparticle crosslinking agents. The interparticle crosslinking agents were prepared from hexamethylene diisocyanate and aziridine ethanol. Mixtures of the copolymer and the interparticle crosslinking agent were cast to films and crosslinked in a convection oven. The effects of the contents of the intra/interparticle crosslinking agents were also evaluated. By increasing the contents of EGDMA, roughness of the films was increased because of the effects of EGDMA acting as an intraparticle crosslinking agent. By increasing the contents of the interparticle crosslinking agent, roughness was also increased by the reaction between the copolymers and interparticle crosslinking agent. Tensile strength and water and chemical resistance of the film were increased, whereas elongation of film was decreased by increasing the contents of interparticle crosslinking agents. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009