gebhart/patrepeval huggingface dataset:
Towards a Safer Interaction with Transactional Memory by Tracking Object Visibility (2005)

Lately there has been an increasing interest in Transactional Memory (TM), a programming API that helps programmers writing scalable concurrent programs using sequential code. It is well known that writing concurrent programs using locks is a difficult task: coarse grained locking results in poor performance, and fine grained locking introduces the risk of deadlocking, and makes program's maintenance difficult. With TM, the programmer only specifies what is required to be executed atomically, without worrying about the synchronization required to achieve this task. There are suggested implementations for TM both in hardware (HTM) and software (STM). While HTM is much faster than STM, it also has more limitations than STM does, and therefore it is not likely that we will have a widely available TM that is implemented purely in hardware in the near future. While STM can compensate for most of the HTM limitations, it imposes a new difficulty on the programmer: STM does not allow concurrent access to an object by transactional and non-transactional code: that is, if an object is accessed using regular read and write operations while it is also being accessed by a transaction, the atomicity of the transaction involving this object might break. Requiring the programmer to keep track of which objects may be involved in transactions will only result in more error-prone concurrent programs. On the other hand, accessing all objects by only transactional code would be safe, but probably not practical as long as we do not have an efficient and robust pure HTM solution. We therefore introduce a new scheme that implicitly tracks object visibility: with our new scheme, objects that might be accessed by multiple threads are automatically guarded by transactions, and therefore are guaranteed not to be accessed by non-transactional code. Moreover, the scheme is transparent to the programmer, and can work with many different implementations of TM, including the lately suggested hybrid TM (HyTM) that uses STM only when HTM fails (or when HTM is not available).
Improved transfer of the leukocyte integrin CD18 subunit into hematopoietic cell lines by using retroviral vectors having a gibbon ape leukemia virus envelope (1995)

Leukocyte adherence deficiency (LAD) is an inherited immunodeficiency disease caused by defects in the CD18 leukocyte integrin subunit. Transduction of CD18 into hematopoietic cells from children with LAD represents a potential therapy for this disorder. In an attempt to maximize transfer and expression of CD18, we evaluated retroviral vectors with and without the neomycin selectable marker, with a modified tRNA primer binding site designed to prevent inhibition of gene expression, and with two different viral envelope proteins produced by using the amphotropic retrovirus packaging cell line PA317 or the gibbon ape leukemia virus packaging cell line PG13. The vectors were tested using transducing K562/CD11b cells and LAD Epstein-Barr virus (EBV) B cells and measuring levels of cell-surface CD11/CD18 expression by fluorescence-activated cell sorter analysis. The best results were obtained with vectors made using PG13 packaging cells, for which about 25% of the K562 cells exposed once to the vectors expressed surface CD11b/CD18 and about 25% of the LAD EBV B cells exposed three times over a 3-day period to the vectors expressed surface CD11a/CD18. In contrast, transduction of cells under similar conditions with retroviral vectors produced using PA317 producer cells yielded less than 2% of the K562 cells and less than 4% of the LAD EBV B cells expressing the CD11/CD18 heterodimer on the cell surface. The presence or absence of the neomycin resistance gene or the modified tRNA primer had no effect on CD18 gene transfer rate or expression level. The increase in transduction with PG13 vectors correlated with Northern blotting and reverse transcription-polymerase chain reaction studies that indicated that both K562 cells and the LAD EBV B cells express transcripts for the gibbon ape leukemia virus receptor at higher levels than for the amphotropic virus receptor. These findings indicate that the transduction efficiency of retroviral packaging cell lines correlates with receptor gene expression in the target cells and that vectors made using PG13 cells may be efficacious for gene therapy for LAD and other diseases in which gene transfer to hematopoietic cells is required.
Receptor-Mediated Recognition and Uptake of Iron from Human Transferrin by Staphylococcus aureus and Staphylococcus epidermidis (1998)

Staphylococcus aureus and Staphylococcus epidermidis both recognize and bind the human iron-transporting glycoprotein, transferrin, via a 42-kDa cell surface protein receptor. In an iron-deficient medium, staphylococcal growth can be promoted by the addition of human diferric transferrin but not human apotransferrin. To determine whether the staphylococcal transferrin receptor is involved in the removal of iron from transferrin, we employed 6 M urea-polyacrylamide gel electrophoresis, which separates human transferrin into four forms (diferric, monoferric N-lobe, and monoferric C-lobe transferrin and apotransferrin). S. aureus and S. epidermidis but not Staphylococcus saprophyticus (which lacks the transferrin receptor) converted diferric human transferrin into its apotransferrin form within 30 min. During conversion, iron was removed sequentially from the N lobe and then from the C lobe. Metabolic poisons such as sodium azide and nigericin inhibited the release of iron from human transferrin, indicating that it is an energy-requiring process. To demonstrate that this process is receptor rather than siderophore mediated, we incubated (i) washed staphylococcal cells and (ii) the staphylococcal siderophore, staphyloferrin A, with porcine transferrin, a transferrin species which does not bind to the staphylococcal receptor. While staphyloferrin A removed iron from both human and porcine transferrins, neither S. aureus nor S. epidermidis cells could promote the release of iron from porcine transferrin. In competition binding assays, both native and recombinant N-lobe fragments of human transferrin as well as a naturally occurring human transferrin variant with a mutation in the C-lobe blocked binding of 125I-labelled transferrin. Furthermore, the staphylococci removed iron efficiently from the iron-loaded N-lobe fragment of human transferrin. These data demonstrate that the staphylococci efficiently remove iron from transferrin via a receptor-mediated process and provide evidence to suggest that there is a primary receptor recognition site on the N-lobe of human transferrin.
A silicon-based, three-dimensional neural interface: manufacturing processes for an intracortical electrode array (1991)

A method has been developed for the manufacture of a "three-dimensional" electrode array geometry for chronic intracortical stimulation. This silicon based array consists of a 4.2 x 4.2 x 0.12 mm thick monocrystalline substrate, from which project 100 conductive, silicon needles sharpened to facilitate cortical penetration. Each needle is electrically isolated from the other needles, and is about 0.09 mm thick at its base and 1.5 mm long. The sharpened end of each needle is coated with platinum to facilitate charge transfer into neural tissue. The following manufacturing processes were used to create this array. 1) Thermomigration of 100 aluminum pads through an n-type silicon block. This creates trails of highly conductive p+ silicon isolated from each other by opposing pn junctions. 2) A combination of mechanical and chemical micromachining which creates individual penetrating needles of the p+ silicon trails. 3) Metal deposition to create active electrode areas and electrical contact pads. 4) Array encapsulation with polyimide. The geometrical, mechanical, and electrical properties of these arrays should make them well suited as interfaces to cortical tissue.
DNA Microarray Analysis of Chimpanzee Liver during Acute Resolving Hepatitis C Virus Infection (2001)

Hepatitis C virus (HCV) poses a worldwide health problem in that the majority of individuals exposed to HCV become chronically infected and are predisposed for developing significant liver disease. DNA microarray technology provides an opportunity to survey transcription modulation in the context of an infectious disease and is a particularly attractive approach in characterizing HCV-host interactions, since the mechanisms underlying viral persistence and disease progression are not understood and are difficult to study. Here, we describe the changes in liver gene expression during the course of an acute-resolving HCV infection in a chimpanzee. Clearance of viremia in this animal occurred between weeks 6 and 8, while clearance of residual infected hepatocytes did not occur until 14 weeks postinfection. The most notable changes in gene expression occurred in numerous interferon response genes (including all three classical interferon antiviral pathways) that increased dramatically, some as early as day 2 postinfection. The data suggest a biphasic mechanism of viral clearance dependent on both the innate and adaptive immune responses and provide insight into the response of the liver to a hepatotropic viral infection.
Isolation and Analysis of metA, a Methionine Biosynthetic Gene Encoding Homoserine Acetyltransferase in Corynebacterium glutamicum (1998)

The metA gene encoding homoserine acetyltransferase, the first enzyme of the methionine biosynthetic pathway, was isolated from a pMT1-based corynebacterium glutamicum gene library via complementation of an Escherichia coli metA mutant. A DNA-sequence analysis of the cloned DNA is identified an open-reading frame of 1,137 bp which encodes a protein with the molecular weight of 41,380 comprising 379 amino acids. The putative protein product showed good amino acid-sequence homology to its counterpart in other organisms. The internal fragment of the cloned DNA was successfully used to disrupt chromosomal metA, demonstrating the identity of the cloned gene. The C. glutamicum metA mutant lost the ability to grow on glucose minimal medium supplemented with homoserine. However, the mutant could grow on a minimal medium supplemented with cystathionine, demonstrating that C. glutamicum uses the cystathionine route to synthesize methionine. Introduction of a plasmid carrying cloned metA into C. glutamicum resulted in a 10-fold increase in enzyme activities and expression of a protein product of M(r) 41,000, which agrees with the sequence data and is similar in size to those of other homoserine acetyltransferases. Unlike E. coli whose metA product uses succinyl coenzyme A as a substrate, the cloned metA gene produced homoserine acetyltransferase which uses only acetyl coenzyme A as the acyl donor.
Protective efficacy of mycobacterial 71-kDa cell wall associated protein using poly (dl-lactide-co-glycolide) microparticles as carrier vehicles (1998)

Microparticles composed of poly (DL-lactide-co-glycolide) (DL-PLG) were used as delivery vehicles for evaluating the immunoreactive and immunoprotective properties of 71-kDa cell wall associated protein of Mycobacterium tuberculosis H37Ra. Mice immunized with 71-kDa microparticles entrapped in DL-PLG (PLG-MPs) exhibited significantly higher T-cell stimulation and cytokine release in comparison to 71-kDa emulsified in Freund's incomplete adjuvant (FIA) as well as a BCG vaccinated group throughout the post-immunization (p.im.) period. Further, the protective efficacy of 71-kDa was evaluated on the basis of survival rates and viable bacilli load in different organs at 30 days post challenge (p.c.), with the median lethal dose (LD50) of M. tuberculosis H37Rv at weeks 8 and 16 p.im. Both 71-kDa-PLG and 71-kDa-FIA immunized groups exhibited a comparable protection (90%) which was significantly higher (P < 0.5) than in the BCG group (70%) at week 8 p.im. and it was consistent with the decreased bacterial load in the target organs. However, on increasing the interval of challenge to 16 weeks p.im., the protective efficacy of 71-kDa-PLG was sustained (85%) while that of 71-kDa-FIA began to wane (70%). Further. the 71-kDa-PLG immunized group exhibited a significantly higher (P < 0.001) clearance of bacterial load from the lungs and livers in comparison to the 71-kDa-FIA immunized group. The results suggest the long-term protective potential of a PLG-microparticle based antigen delivery system for tuberculosis.
Quantitative basic residue requirements in the cleavage-activation site of the fusion glycoprotein as a determinant of virulence for Newcastle disease virus (1988)

Newcastle disease virus exhibits a wide range of pathogenicity and virulence which, as with all paramyxoviruses, is directly related to the cleavability of a precursor (F0) of the fusion glycoprotein by cellular proteases. Sequence analyses of the cleavage site of several virulent and avirulent isolates of the Newcastle disease virus serotype reveal a correlation between virulence or pathogenicity and a high content of basic amino acid residues at the cleavage site. A similar correlation has been seen for other paramyxoviruses.
Blood compatibility of SUUU‐PEO‐heparin graft copolymers (1992)

Biological responses to heparinized segmented polyurethaneurea (SPUU-PEO-Heparin) were evaluated in vitro and ex vivo. In vitro assays involved plasma protein adsorption, platelet adhesion, and release reaction studies. In addition, an ex vivo rabbit arterio-artery (A-A) shunt experiment was also performed to measure occlusion times of the heparinized surfaces. All SPUU-PEO-Heparin surfaces demonstrated less protein adsorption than Biomer and protein adsorption patterns similar to SPUU-PEO surfaces. Platelet adhesion and release studies demonstrated that both SPUU-PEO-Heparin and SPUU-PEO surfaces adsorbed less platelets and inhibited platelet release, as compared to Biomer. These findings correlated with reduction in protein adsorption observed for the modified surfaces. In low flow rate ex-vivo A-A shunt experiments, all heparinized surfaces prolonged occlusion time longer than controls. However, SPUU-PEO surfaces did not prolong occlusion time when compared to Biomer, although these surfaces suppressed protein adsorption and platelet interaction in vitro. The improved blood compatibility of SPUU-PEO-Heparin surfaces attest to the usefulness of this approach in improving the blood compatibility of blood contacting surfaces.
Marrow transplantation for acute lymphoblastic leukemia: factors affecting relapse and survival (1989)

Transplant outcome was analyzed in 690 recipients of bone marrow transplants (BMTs) for acute lymphoblastic leukemia (ALL) in first (n = 299) or second remission (n = 391). Actuarial 5-year leukemia-free survival was 42% +/- 9% (95% confidence interval) and 26% +/- 6%, respectively; relapse rates were 29% +/- 9% and 52% +/- 8%, respectively. Five-year leukemia-free survival was 56% +/- 18% in children and 39% +/- 10% in adults (P less than .02) transplanted in first remission. In first-remission adults, non-T-cell phenotype, male to female donor-recipient sex-match and graft-v-host disease (GVHD) were associated with decreased leukemia-free survival; inclusion of corticosteroids in the regimen to prevent GVHD was associated with increased leukemia-free survival. Variables associated with decreased leukemia-free survival after second-remission transplants were age greater than or equal to 16 years and relapse occurring while on therapy. Variables associated with increased probability of relapse were similar for first- and second-remission transplants and included GVHD prophylaxis without methotrexate and absence of GVHD. In first-remission transplants, leukocyte count greater than or equal to 50 x 10(9)/L at diagnosis was also associated with increased relapse; in second remission, relapse while receiving chemotherapy was also associated with increased posttransplant relapse. These data emphasize the importance of both disease- and transplant-related variables in predicting outcome after BMT. They may be used to explain differences between studies, design future trials, and identify persons most likely to benefit from BMT.
CD1d-Based Combination Therapy Eradicates Established Tumors in Mice (2009)

The use of Abs that induce tumor cell death together with immunostimulatory reagents to activate innate and adaptive immune cells has emerged as a potent approach for the treatment of cancer. We have previously demonstrated that the use of three mAbs (anti-DR5, anti-CD40, anti-CD137) termed TriMab can induce rejection in a majority of mice with established experimental or carcinogen-induced tumors. However, given the potential toxicity of CD40 agonists in the clinic, we tested an alternative approach to directly activate/mature APCs using anti-CD1d mAbs. In this study, we used a combination of three mAbs (anti-DR5, anti-CD137, anti-CD1d) that we termed 1DMab and demonstrated that this approach suppressed and/or eradicated established experimental renal, breast, and colon carcinomas in mice. Tumor suppression induced by 1DMab therapy required CD8(+) T cells, IFN-gamma, and CD1d, while NK cells and IL-12 were partially required. Interestingly 1DMab therapy was more effective than TriMab in tumor models regulated by CD1d-restricted type II NKT cells, but less efficacious against tumors where T regulatory cells were critical. Anti-CD1d mAbs could also be relatively effective in combination with anti-CD137 and conventional chemotherapeutics. This is the first study to illustrate the antitumor activity of CD1d-reactive mAbs in combination and our results strongly suggest that rational combination chemoimmunotherapies based on tumor immunoregulation may improve the efficacy of treatment.
Search algorithms for biosequences using random projection (2001)

Thesis (Ph. D.)--University of Washington, 2001
Pyrometer at low radiation for measuring the forehead skin temperature (2006)

This paper presents the results of the design, construction, calibration and tests of a low radiation pyrometer for temperature measurement of the human body. The instrument is based on a low cost thermopile as detector and an optical system. It is specially designed to measure the forehead temperature of a person. It is useful in applications like: Measurement of temperature of people in the airports (to prevent contamination with contagious diseases infection) or applications in medicine as continuous monitoring of the temperature of patients in intensive care units at hospitals. The instrument has been calibrated using an on-purpose-built black body and its precision is of 0.19 °C.
Cloning and sequencing of a plasmid-borne gene (opd) encoding a phosphotriesterase (1988)

Plasmid pCMS1 was isolated from Pseudomonas diminuta MG, a strain which constitutively hydrolyzes a broad spectrum of organophosphorus compounds. The native plasmid was restricted with PstI, and individual DNA fragments were subcloned into pBR322. A recombinant plasmid transformed into Escherichia coli possessed weak hydrolytic activity, and Southern blotting with the native plasmid DNA verified that the DNA sequence originated from pCMS1. When the cloned 1.3-kilobase fragment was placed behind the lacZ' promoter of M13mp10 and retransformed into E. coli, clear-plaque isolates with correctly sized inserts exhibited isopropyl-beta-D-thiogalactopyranoside-inducible whole-cell activity. Sequence determination of the M13 constructions identified an open reading frame of 975 bases preceded by a putative ribosome-binding site appropriately positioned upstream of the first ATG codon in the open reading frame. An intragenic fusion of the opd gene with the lacZ gene produced a hybrid polypeptide which was purified by beta-galactosidase immunoaffinity chromatography and used to confirm the open reading frame of opd. The gene product, an organophosphorus phosphotriesterase, would have a molecular weight of 35,418 if the presumed start site is correct. Eighty to ninety percent of the enzymatic activity was associated with the pseudomonad membrane fractions. When dissociated by treatment with 0.1% Triton and 1 M NaCl, the enzymatic activity was associated with a molecular weight of approximately 65,000, suggesting that the active enzyme was dimeric.
Plasma Membrane-associated Sialidase as a Crucial Regulator of Transmembrane Signalling (2008)

Mammalian sialidases, glycosidases responsible for the removal of sialic acids from glycoproteins and glycolipids, has been implicated to participate in many biological processes as well as in lysosomal catabolism. Among those forms identified to date, plasma membrane-associated sialidase, Neu3, is a key enzyme in degradation of gangliosides, for which it exhibits a special substrate preference. This sialidase has been shown to control transmembrane signalling for many cellular processes, including cell differentiation, cell growth and apoptosis, and human orthologue NEU3 is markedly up-regulated in various cancers. It is known to suppress apoptosis in cancer cells. Furthermore, its overexpression causes impaired glucose tolerance and hyper-insulinaemia together with overproduction of insulin in enlarged islets in the transgenic mice. The present review primarily summarizes our recent results, focusing on Neu3 as a regulator of transmembrane signalling.
Development of Mobile Ad-Hoc Network for Collaborative Unmanned Aerial Vehicles (2013)

The purpose of this research was to develop a mobile ad-hoc network for collaborative Unmanned Aerial Vehicles (UAVs) based on a mesh networking standard called IEEE 802.11s. A low-cost, small form-factor, IEEE 802.11a based wireless modem was selected and integrated with the existing flight control system developed at Virginia Commonwealth University (VCU) UAV Laboratory. A self-configurable user-space application on the wireless modem was developed to provide functionality to collaborative algorithms, and to monitor the performance of the wireless network. The RAMS simulator, developed at VCU, was upgraded to support the simulation of advanced networking capabilities by integrating with a simulator called ns-3. The reconfigurability and performance of the IEEE 802.11s mesh network was validated and evaluated by conducting real-world flights. The results show that the IEEE 802.11s is a promising solution for collaborative UAV applications.
Effects of separation length and voltage on isoelectric focusing in a plastic microfluidic device (2006)

Abstract This paper describes the investigation on the effects of separation length and voltage on IEF in a plastic microfluidic device. A LIF, whole‐channel imaging detection (WCID) system was developed to monitor proteins while they were moving under an electric field. IEF was carried out in a separation medium consisting of carrier ampholytes and a mixture of linear polymers (hydroxyethylcellulose and hydroxypropylcellulose). We found that the IEF separation resolution is essentially independent of separation length when the same voltage is applied, which agrees with the theory. This result supports the notion that IEF in a microfabricated device leads to more rapid analysis without sacrificing the resolving power. A higher separation voltage also brought about more rapid analysis and superior separation resolution. IEF of two proteins (green fluorescence protein and R‐phycoerythrin) was achieved in 1.5 min when 500 V was applied across a 1.9‐cm channel. We found that a linear relationship exists between the focusing time and the inverse of the electrical field strength. In addition, we confirmed the phenomenon in which the pH gradient was compressed to the middle of a channel, and we found that the relative amount of the gradient compression decreased with the channel length.