gebhart/patrepeval huggingface dataset:
Parallel garbage collection for shared memory multiprocessors (2001)

We present a multiprocessor “stop-the-world” garbage collection framework that provides multiple forms of load balancing. Our parallel collectors use this framework to balance the work of root scanning, using static overpartitioning, andalsotobalance the work of tracing the object graph, using a form of dynamic load balancing called work stealing. We describe two collectors written using this framework: pSemispaces, a parallel semispace collector, and pMarkcompact, a parallel markcompact collector. 1
Performance Assessment of Three Commercial Assays for Direct Detection of Bacillus anthracis Spores (2003)

Bacillus anthracis , the cause of anthrax, has been used as a bioterrorism agent. Because the isolation and identification of B. anthracis by culture can take days, first response units (hazardous materials [HAZMAT], firemen, police, and hospital personnel) desire a quick and easy test that can be
Preparation of Completely 6-O-Desulfated Heparin and Its Ability to Enhance Activity of Basic Fibroblast Growth Factor (2000)

Although regioselective removal of 6-O-sulfate groups of heparin has been undertaken by several researchers, complete 6-O-desulfation with little side reaction has not been attained successfully. In this work, a modified method with a certain silylating reagent, N-methyl-N-(trimethylsilyl)trifluoroacetamide, has been established to produce completely 6-O-desulfated heparin with few other chemical changes. The degrees of 6-O-desulfation were estimated by means of chemical disaccharide analyses and/or (13)C NMR spectra. Although the completely 6-O-desulfated heparin lost about 20% of 2-O-sulfate groups, any other chemical changes and depolymerization were not detected. The completely 6-O-desulfated heparin displayed strong inhibition of COS-1 cell adhesion to basic fibroblast growth factor (bFGF)-coated well in a dose-dependent manner, as was clarified by the competitive cell-adhesion assay. Furthermore, the completely 6-O-desulfated heparin was shown to promote in vitro A31 fibroblast proliferation in a dose-dependent manner in the presence of bFGF. These results suggest that signal transduction through bFGF/bFGF receptor in A31 cells occurs in the absence of 6-O-sulfate groups in heparin. The involvement of 6-O-sulfate group(s) of heparin/heparan sulfate in the promotion of bFGF mitogenic activity was reported by several groups. This discrepancy between our results and those of other groups would be due to the differences in molecular size of heparin/heparan sulfate derivatives and/or cell species used for the assay.
New optical probes for the continuous monitoring of renal function (2008)

The ability to continuously monitor renal function via the glomerular filtration rate (GFR) in the clinic is currently an unmet medical need. To address this need we have developed a new series of hydrophilic fluorescent probes designed to clear via glomerular filtration for use as real time optical monitoring agents at the bedside. The ideal molecule should be freely filtered via the glomerular filtration barrier and be neither reabsorbed nor secreted by the renal tubule. In addition, we have hypothesized that a low volume of distribution into the interstitial space could also be advantageous. Our primary molecular design strategy employs a very small pyrazine-based fluorophore as the core unit. Modular chemistry for functionalizing these systems for optimal pharmacokinetics (PK) and photophysical properties have been developed. Structure-activity relationship (SAR) and pharmacokinetic (PK) studies involving hydrophilic pyrazine analogues incorporating polyethylene glycol (PEG), carbohydrate, amino acid and peptide functionality have been a focus of this work. Secondary design strategies for minimizing distribution into the interstitium while maintaining glomerular filtration include enhancing molecular volume through PEG substitution. <i>In vivo</i> optical monitoring experiments with advanced candidates have been correlated with plasma PK for measurement of clearance and hence GFR.
Incorporation of Exogenous Docosahexaenoic Acid into Triacylglycerols and Polar Lipids of <i>Chlorella vulgaris</i> (2005)

Docosahexaenoic acid (DHA)-enriched Chlorella vulgaris is commonly used as a feed in fisheries and as a dietary supplement. The time course DHA uptake into the Chlorella cells and incorporation of DHA into the triacylglycerols (TAG) and polar lipids (PL) were examined. After the addition of DHA into the Chlorella culture, DHA was rapidly taken up by the Chlorella cells and was mainly incorporated into TAG. However, some DHA was also incorporated into PL molecules. Although the percentage of DHA in the total fatty acids of total cellular lipids reached at 67%, the percentage in the total fatty acids of PL was 27.5%. As for the effects of pH, exogenous DHA was mainly incorporated into TAG molecules at pH 5-7. At pH 3-4 and 8, the DHA accumulated as free fatty acid in the cells. The exogenous DHA was rapidly incorporated into TAG molecules within 24 hours at pH 5-8. The findings should contribute profitably to production of better fishery feed and food supplement by using DHA-enriched Chlorella.
Pubic Bone Suburethral Stabilization Sling: Laparoscopic Assessment of a Transvaginal Operation for the Treatment of Stress Urinary Incontinence (1999)

The objective was to examine laparoscopically the mechanism and precision of a new transvaginal method for fixation of a suburethral stabilization sling prosthesis designed for the treatment of recurrent stress urinary incontinence. Nine patients with recurrent stress urinary incontinence after previous anti-incontinence surgery underwent transvaginal placement of a pretrimmed 2.0 x 5.5 cm synthetic pubic bone suburethral stabilization sling prosthesis with pubic bone anchors. Before the sling fixation sutures were tied, the space of Retzius was opened laparoscopically with an operative laparoscope, and sling placement was assessed. Patients were followed up postoperatively at routine intervals. All nine procedures were accomplished uneventfully and as planned. Laparoscopic surveillance demonstrated that bone anchor placement by palpation was accurate and that low-tension sling fixation necessitated 2.0- to 2.5-cm suture bridges between the lateral sling edges and the pubic bone anchors in all cases. Continence was restored in all cases; two patients experienced mild, transient urinary retention; one patient experienced transient detrusor instability. No significant postoperative complications were noted. Low-tension pubic bone suburethral sling placement requires suture bridging of approximately 2.0 to 2.5 cm per side when a prosthesis 5.5 cm long is employed.
Carbohydrate analysis : high performance liquid chromatography and capillary electrophoresis (1995)

Part 1. The Solute. 1. Preparation of carbohydrates for analysis by HPLC and HPCE (A.J. Mort, M.L. Pierce). Part 11. Analytical and Preparative Separations. 2. Reversed-phase and hydrophobic interaction chromatography of carbohydrates and glycoconjugates (Z. El Rassi). 3. High performance hydrophilic interaction chromatography of carbohydrates with polar solvents (S.C. Churms). 4. HPLC of carbohydrates with cation- and anion-exchange silica and resin-based stationary phases (C.G. Huber, G.K. Bonn). 5. Analysis of glycoconjugates using high-pH anionexchange chromatography (R.R. Townsend). 6. Basic studies on carbohydrate - protein interaction by high performance affinity chromatography and high performance capillary affinity electrophoresis using lectins as protein models (S. Honda). 7. Modem size exclusion chromatography of carbohydrates and glycoconjugates (S.C. Churms). 8. High performance capillary electrophoresis of carbohydrates and glycoconjugates (Z. El Rassi, W. Nashabeh). 9. Preparative HPLC of carbohydrates (K.B. Hicks). Part III. The Detection. 10. Pulsed electrochemical detection of carbohydrates at gold electrodes following liquid chromatographic separation (D.C. Johnson, W.R. LaCourse). I 1. On-column refractive index detection of carbohydrates separated by HPLC and CE (A.E. Bruno, B. Krattiger). 12. Mass spectrometry of carbohydrates and glycoconjugates (C.A. Settineri, A.L. Burlingame). 13. Evaporative light scattering detection of carbohydrates in HPLC (M. Dreux, M. Lafosse). 14. Chiroptical detectors for HPLC of carbohydrates (N. Purdie). 15. Pre- and post-column detection-oriented derivatization techniques in HPLC of carbohydrates (S. Hase). 16. Post-column enzyme reactors for the HPLC determination of carbohydrates -(L.J. Nagels, P.C. Maes). 17. Other direct and indirect detection methods of carbohydrates in HPLC and HPCE (Z. El Rassi, J.T. Smith).
Brain biocompatibility of a biodegradable, controlled‐release polymer in rats (1989)

We report the biocompatibility in the rat brain of a controlled-release, biodegradable polymer, the polyanhydride poly-[bis(p-carboxyphenoxy)propane-sebacic acid] copolymer (PCPP-SA) in a 20:80 formulation. The biodegradable polyanhydride can be used for drug delivery directly into the brain, circumventing the difficulties posed by the blood-brain barrier and avoiding the consequences of having to administer toxic doses systematically to reach therapeutic doses in the central nervous system. The tissue reaction in the presence of PCPP-SA was compared to that seen with other standard neurosurgical implants. Fifty-six adult Sprague-Dawley rats were assigned to one of seven groups and underwent bilateral frontal lobe implantation of PCPP-SA (42 hemispheres), Surgicel (oxidized regenerated cellulose) (35 hemispheres), or Gelfoam (absorbable gelatin sponge) (35 hemispheres). None of the animals showed any behavioral changes or neurological deficits suggestive of either systemic or localized toxicity from the biodegradable polyanhydride, all surviving to the scheduled data of sacrifice. PCPP-SA evoked a well localized inflammatory reaction, comparable to that of Surgicel, which resolved as the PCPP-SA polymer degraded over five weeks. The biodegradable polyanhydride has been shown in this study to be nontoxic and biocompatible in the rat brain, when compared to standard neurosurgical implants.
Consistent Patterns in the Development and Immunodominance of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific CD8+T-Cell Responses following Acute HIV-1 Infection (2002)

Human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T-cell responses generated during acute infection play a critical role in the initial control of viremia. However, little is known about the viral T-cell epitopes targeted during acute infection or about their hierarchy in appearance and relative immunodominance over time. In this study, HIV-1-specific CD8+ T-cell responses in 18 acutely infected individuals expressing HLA-A3 and/or -B7 were characterized. Detailed analysis of CD8 responses in one such person who underwent treatment of acute infection followed by reexposure to HIV-1 through supervised treatment interruptions (STI) revealed recognition of only two cytotoxic T-lymphocyte (CTL) epitopes during symptomatic acute infection. HIV-1-specific CD8+ T-cell responses broadened significantly during subsequent exposure to the virus, ultimately targeting 27 distinct CTL epitopes, including 15 different CTL epitopes restricted by a single HLA class I allele (HLA-A3). The same few peptides were consistently targeted in an additional 17 persons expressing HLA-A3 and/or -B7 during acute infection. These studies demonstrate a consistent pattern in the development of epitope-specific responses restricted by a single HLA allele during acute HIV-1 infection, as well as persistence of the initial pattern of immunodominance during subsequent STI. In addition, they demonstrate that HIV-1-specific CD8+ T-cell responses can ultimately target a previously unexpected and unprecedented number of epitopes in a single infected individual, even though these are not detectable during the initial exposure to virus. These studies have important implications for vaccine design and evaluation.
Loading of MHC Class I and II Presentation Pathways by Exogenous Antigens: A Quantitative In Vivo Comparison (2004)

The MHC class I pathway is usually fueled by endogenous Ags, while exogenous Ags reach the MHC class II pathway. Although exogenous epitopes may also enter the MHC class I pathway, quantification of the efficiency of the process has remained a difficult task. In an attempt of such a quantification, we directly compared the amount of exogenous virus-like particles required for induction of cytotoxic T cell responses by cross-priming with the amount of virus-like particles required for induction of Th cell responses by the conventional route of MHC class II loading as an internal standard. Surprisingly, we found that cross-presentation of peptides derived from exogenous Ags on MHC class I molecules is of only marginally lower efficiency ( approximately 1- to 10-fold) than the classical MHC class II pathway in vitro and in vivo. Thus, Ag quantities required for cross-presentation and cross-priming are similar to those required for fueling the MHC class II pathway.
Risk factors for N2 metastasis in patients with non-small-cell lung cancer (2014)

SUV(max) and tumor cell grade are independent risk factors for N(2) metastasis.
Nuglets: a Virtual Currency to Stimulate Cooperation in Self-Organized Mobile Ad Hoc Networks (2001)

In mobile ad hoc networks, it is usually assumed that all the nodes belong to the same authority; therefore, they are expected to cooperate in order to support the basic functions of the network such as routing. In this paper, we consider the case in which each node is its own authority and tries to maximize the benefits it gets from the network. In order to stimulate cooperation, we introduce a virtual currency and detail the way it can be protected against theft and forgery. We show that this mechanism fulfills our expectations without significantly decreasing the performance of the network.
Transcranial current stimulation focality using disc and ring electrode configurations: FEM analysis (2008)

We calculated the electric fields induced in the brain during transcranial current stimulation (TCS) using a finite-element concentric spheres human head model. A range of disc electrode configurations were simulated: (1) distant-bipolar; (2) adjacent-bipolar; (3) tripolar; and three ring designs, (4) belt, (5) concentric ring, and (6) double concentric ring. We compared the focality of each configuration targeting cortical structures oriented normal to the surface ('surface-radial' and 'cross-section radial'), cortical structures oriented along the brain surface ('surface-tangential' and 'cross-section tangential') and non-oriented cortical surface structures ('surface-magnitude' and 'cross-section magnitude'). For surface-radial fields, we further considered the 'polarity' of modulation (e.g. superficial cortical neuron soma hyper/depolarizing). The distant-bipolar configuration, which is comparable with commonly used TCS protocols, resulted in diffuse (un-focal) modulation with bi-directional radial modulation under each electrode and tangential modulation between electrodes. Increasing the proximity of the two electrodes (adjacent-bipolar electrode configuration) increased focality, at the cost of more surface current. At similar electrode distances, the tripolar-electrodes configuration produced comparable peak focality, but reduced radial bi-directionality. The concentric-ring configuration resulted in the highest spatial focality and uni-directional radial modulation, at the expense of increased total surface current. Changing ring dimensions, or use of two concentric rings, allow titration of this balance. The concentric-ring design may thus provide an optimized configuration for targeted modulation of superficial cortical neurons.
Genotype Specification Language (2016)

We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.
In Situ Cross-Linkable Hydrogel of Hyaluronan Produced via Copper-Free Click Chemistry (2013)

Injectable hydrogels are useful in biomedical applications. We have synthesized hyaluronic acids chemically modified with azide groups (HA-A) and cyclooctyne groups (HA-C), respectively. Aqueous HA-A and HA-C solutions were mixed using a double-barreled syringe to form a hydrogel via strain-promoted [3 + 2] cycloaddition without any catalyst at physiological conditions. The hydrogel slowly degraded in PBS over 2 weeks, which was accelerated to 9 days by hyaluronidase, while it rapidly degraded in a cell culture media with fetal bovine serum within 4 days. Both HA-A and HA-C showed good biocompatibility with fibroblast cells in vitro. They were administered using the double-barreled syringe into mice subcutaneously and intraperitoneally. Residue of the hydrogel was cleared 21 days after subcutaneous administration, while it was cleared 7 days after intraperitoneal administration. This injectable HA hydrogel is expected to be useful for tissue engineering and drug delivery systems utilizing its orthogonality.
Enantioselective Synthesis of (−)‐β‐Santalol by a Copper‐Catalyzed Enynol Cyclization–Fragmentation Reaction (2009)

The right cat for the desired odor: The key step in an enantioselective synthesis of the prized fragrance (−)-β-santalol was a highly selective copper-catalyzed cyclization–fragmentation reaction of an enynol (see scheme). When a platinum catalyst was used for the cyclization step, the desired fragmentation did not take place; instead, a product containing a cyclopropane ring was formed with 100 % selectivity.
XPS and SPR Analysis of Glycoarray Surface Density (2009)

Despite the fact that the carbohydrate microarray has seen increasing use within the field of glycobiology, the surface chemistry of the glycoarray remains largely unexplored. Motivated by the need to develop surface analytical techniques to characterize carbohydrate-modified surfaces, we developed a quantitative X-ray photoelectron spectroscopy (XPS) and surface plasmon resonance imaging (SPR imaging) method to study glycan biosensors. We performed a comparative analysis on the relative coverage of mixed self-assembled monolayers (SAMs) on gold, consisting of a thiol-functionalized trimannoside (Manalpha1,2Manalpha1,2Manalpha-OEG-SH) at varying concentrations (0-100%) mixed separately with two thiol-containing polyethylene glycol oligomers. XPS C1s core level analysis was used to identify the O-C-O functionality unique to the carbohydrate acetal moiety and to separate and quantify the relative coverage of sugar in carbohydrate/OEG mixed SAMs. XPS spectra of the mixed SAMs demonstrated a proportional increase in the acetal signature of the glycan with increasing sugar concentration. To relate surface glycan density with biological function, we carried out a kinetic analysis of Concanavalin A (ConA) binding to SAMs of varying densities of carbohydrate using SPR imaging. We observed protein binding that was highly dependent on both glycan density and the nature of the OEG-thiol used in the mixed self-assembly. These results illustrate the utility of surface analytical techniques such as XPS and SPR in carbohydrate biosensor characterization and optimization.
Epithelial Cell Repopulation and Preparation of Rodent Extracellular Matrix Scaffolds for Renal Tissue Development (2015)

This protocol details the generation of acellular, yet biofunctional, renal extracellular matrix (ECM) scaffolds that are useful as small-scale model substrates for organ-scale tissue development. Sprague Dawley rat kidneys are cannulated by inserting a catheter into the renal artery and perfused with a series of low-concentration detergents (Triton X-100 and sodium dodecyl sulfate (SDS)) over 26 hr to derive intact, whole-kidney scaffolds with intact perfusable vasculature, glomeruli, and renal tubules. Following decellularization, the renal scaffold is placed inside a custom-designed perfusion bioreactor vessel, and the catheterized renal artery is connected to a perfusion circuit consisting of: a peristaltic pump; tubing; and optional probes for pH, dissolved oxygen, and pressure. After sterilizing the scaffold with peracetic acid and ethanol, and balancing the pH (7.4), the kidney scaffold is prepared for seeding via perfusion of culture medium within a large-capacity incubator maintained at 37 °C and 5% CO2. Forty million renal cortical tubular epithelial (RCTE) cells are injected through the renal artery, and rapidly perfused through the scaffold under high flow (25 ml/min) and pressure (~230 mmHg) for 15 min before reducing the flow to a physiological rate (4 ml/min). RCTE cells primarily populate the tubular ECM niche within the renal cortex, proliferate, and form tubular epithelial structures over seven days of perfusion culture. A 44 µM resazurin solution in culture medium is perfused through the kidney for 1 hr during medium exchanges to provide a fluorometric, redox-based metabolic assessment of cell viability and proliferation during tubulogenesis. The kidney perfusion bioreactor permits non-invasive sampling of medium for biochemical assessment, and multiple inlet ports allow alternative retrograde seeding through the renal vein or ureter. These protocols can be used to recellularize kidney scaffolds with a variety of cell types, including vascular endothelial, tubular epithelial, and stromal fibroblasts, for rapid evaluation within this system.
Purification of Recombinant Glycosylated Human Gamma Interferon Expressed in Transformed Chinese Hamster Ovary Cells (1984)

Human IFN-gamma was produced in cultures of a Chinese hamster ovary (CHO) cell line transformed with a combination of plasmids encoding HuIFN-gamma cDNA and mouse DHFR cDNA and subsequently selected for growth in the presence of methotrexate. Confluent monolayers of these cells constitutively secrete HuIFN-gamma into the medium reaching a concentration of 2-5 micrograms/ml; the supernatant of the monolayer could be harvested daily for a period of more than 10 days. IFN-gamma was purified by passing the filtered CHO cell culture medium directly through a phosphocellulose column followed by elution and adsorption on a Con A-Sepharose column. Further concentration on an AMICON PM 10 filter and removal of high mw contaminating proteins with DEAE-Sephacel resulted in a IFN-gamma preparation of more than 99% purity (specific activity of about 10(8) International units per mg of protein). Each liter of CHO conditioned culture medium yielded 1-2 mg pure HuIFN-gamma. Its molecular weight, as determined by gel filtration, is about 50 kD and corresponds to a dimer structure. SDS-polyacrylamide gel electrophoresis indicated the presence of a 21 kD and a 25 kD polypeptide as compared with 17 kD for unglycosylated, bacterially made HuIFN-gamma and consistent with the two glycosylated forms of HuIFN-gamma produced in mitogen-stimulated human lymphocyte cultures.