gebhart/patrepeval huggingface dataset:
Electric Field-Induced Modification of Magnetism in Thin-Film Ferromagnets (2007)

A large electric field at the surface of a ferromagnetic metal is expected to appreciably change its electron density. In particular, the metal's intrinsic magnetic properties, which are commonly regarded as fixed material constants, will be affected. This requires, however, that the surface has a strong influence on the material's properties, as is the case with ultrathin films. We demonstrated that the magnetocrystalline anisotropy of ordered iron-platinum (FePt) and iron-palladium (FePd) intermetallic compounds can be reversibly modified by an applied electric field when immersed in an electrolyte. A voltage change of -0.6 volts on 2-nanometer-thick films altered the coercivity by -4.5 and +1% in FePt and FePd, respectively. The modification of the magnetic parameters was attributed to a change in the number of unpaired d electrons in response to the applied electric field. Our device structure is general and should be applicable for characterization of other thin-film magnetic systems.
An efficient approach to identify ilvA mutations reveals an amino-terminal catalytic domain in biosynthetic threonine deaminase from Escherichia coli (1993)

High-level expression of the regulatory enzyme threonine deaminase in Escherichia coli strains grown on minimal medium that are deficient in the activities of enzymes needed for branched-chain amino acid biosynthesis result in growth inhibition, possibly because of the accumulation of toxic levels of alpha-ketobutyrate, the product of the committed step in isoleucine biosynthesis. This condition affords a means for selecting genetic variants of threonine deaminase that are deficient in catalysis by suppression of growth inhibition. Strains harboring mutations in ilvA that decreased the catalytic activity of threonine deaminase were found to grow more rapidly than isogenic strains containing wild-type ilvA. Modification of the ilvA gene to introduce additional unique, evenly spaced restriction enzyme sites facilitated the identification of suppressor mutations by enabling small DNA fragments to be subcloned for sequencing. The 10 mutations identified in ilvA code for enzymes with significantly reduced activity relative to that of wild-type threonine deaminase. Values for their specific activities range from 40% of that displayed by wild-type enzyme to complete inactivation as evidenced by failure to complement an ilvA deletion strain to isoleucine prototrophy. Moreover, some mutant enzymes showed altered allosteric properties with respect to valine activation and isoleucine inhibition. The location of the 10 mutations in the 5' two-thirds of the ilvA gene is consistent with suggestions that threonine deaminase is organized functionally with an amino-terminal domain that is involved in catalysis and a carboxy-terminal domain that is important for regulation.
Spectrophotometric Determination of Aqueous Sulfide on a Pneumatically Enhanced Centrifugal Microfluidic Platform (2012)

A pneumatically enhanced centrifugal microfluidic platform was developed for rapid spectrophotometric determination of aqueous sulfide. This platform performs an automated analysis based on the reaction between hydrogen sulfide and N,N-dimethyl-p-phenylenediamine in the presence of iron(III) chloride to form Methylene Blue. The platform design minimizes the number of integrated valves required, compared to other centrifugal systems, significantly improving the ease of fabrication. The sequential analytical procedure and spectrophotometric analyses were performed directly on-disk, demonstrating significant advantages in portability and cost over conventional analytical methods. This method allows for rapid and precise determination of aqueous sulfide in the concentration range of 0.4-2.0 mg L(-1), which can be extended by a pneumatically induced, on-disk serial dilution to 6.0 mg L(-1). A detection limit of 0.4 mg L(-1) was calculated for this pneumatically enhanced method.
Synthesis of Yttrium Aluminum Garnet by the Glycothermal Method (1991)

The reaction of a stoichiometric mixture of aluminum isopropoxide and yttrium acetate in 1,4‐butanediol at 300°C yielded crystalline yttrium aluminum garnet having an approximate particle size of 30 nm. No other phases were detected. The use of ethylene glycol in place of 1,4‐butanediol afforded an amorphous product.
Fidelity of Mutant HIV-1 Reverse Transcriptases:  Interaction with the Single-Stranded Template Influences the Accuracy of DNA Synthesis (1998)

We have used random sequence mutagenesis and complementation in a bacterial selection system to establish a large library of immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) mutants with amino acid substitutions in the beta3-beta4 region of the fingers subdomain [Kim, B., Hathaway, T. R., and Loeb, L. A. (1996) J. Biol. Chem. 271, 4872-4878]. We show here that one of these mutants, D76V, exhibits increased accuracy of copying both DNA and RNA templates in a primer extension assay with biased dNTP pools. More detailed analysis of DNA-dependent polymerization showed that the D76V mutation conferred an up to 14-fold increase in fidelity of nucleotide insertion and a 9-fold reduced mutation rate in an M13mp2 lacZalpha forward mutation assay. Substitution at D76 with positively charged (D76R) and nonpolar (D76V and D76I) residues increased replicational accuracy, while substitutions with negatively charged (D76E) and polar residues (D76S and D76C) had little effect on fidelity. We propose that D76 affects replicational accuracy by mediating interaction between the fingers subdomain and the single-stranded template. Our work shows that the Escherichia coli complementation system can yield HIV RT mutants with increased fidelity that have not been isolated from the natural host and that are valuable in understanding the molecular bases of replicational accuracy.
L ‐Aspartase: New Tricks from an Old Enzyme (2000)

The enzyme L-aspartate ammonia-lyase (aspartase) catalyzes the reversible deamination of the amino acid L-aspartic acid, using a carbanion mechanism to produce fumaric acid and ammonium ion. Aspartase is among the most specific enzymes known with extensive studies failing, until recently, to identify any alternative amino acid substrates that can replace L-aspartic acid. Aspartases from different organisms show high sequence homology, and this homology extends to functionally related enzymes such as the class II fumarases, the argininosuccinate and adenylosuccinate lyases. The high-resolution structure of aspartase reveals a monomer that is composed of three domains oriented in an elongated S-shape. The central domain, comprised of five-helices, provides the subunit contacts in the functionally active tetramer. The active sites are located in clefts between the subunits and structural and mutagenic studies have identified several of the active site functional groups. While the catalytic activity of this enzyme has been known for nearly 100 years, a number of recent studies have revealed some interesting and unexpected new properties of this reasonably well-characterized enzyme. The non-linear kinetics that are seen under certain conditions have been shown to be caused by the presence of a separate regulatory site. The substrate, aspartic acid, can also play the role of an activator, binding at this site along with a required divalent metal ion. Truncation of the carboxyl terminus of aspartase at specific positions leads to an enhancement of the catalytic activity of the enzyme. Truncations in this region also have been found to introduce a new, non-enzymatic biological activity into aspartase, the ability to specifically enhance the activation of plasminogen to plasmin by tissue plasminogen activator. Even after a century of investigation there are clearly a number of aspects of this multifaceted enzyme that remain to be explored.
Cytokines ‐ killers in the brain? (1999)

Given at the Meeting of the Physiological Society held at the University of Southampton on 10 September 1998
Three-Dimensional Computed Tomography in Maxillofacial Surgical Planning (1988)

Fifty-four maxillofacial three-dimensional computed tomographic examinations were performed during a 12-month period for the purpose of surgical planning. Pathologic entities in the series included trauma, neoplasia, cleft palate, and other developmental anomalies. Computer-assisted mandibular disarticulation was performed routinely after each study to permit direct viewing of the mandible or maxilla in isolation. Three-dimensional computed tomography is a useful technique for maxillofacial surgical planning.
Vagal afferent innervation of the atria of the rat heart reconstructed with confocal microscopy (1997)

We have used confocal microscopy to analyze the vagal afferent innervation of the rat heart. Afferents were labeled by injecting 1,1'-dioleyl-3,3,3',3'-tetramethylindocarbocyanine methanesulfonate (DiI) into the nodose ganglia of animals with prior supranodose de-efferentations, autonomic ganglia were stained with Fluoro-gold, and tissues were examined in whole mounts. Distinctively different fiber specializations were observed in the epi-, myo-, and endocardium: Afferents to the epicardium formed complexes associated with cardiac ganglia. These ganglia consisted of four major ganglionated plexuses, two on each atrium, at junctions of the major vessels with the atria. Ganglionic locations and sizes (left > right) were consistent across animals. In addition to principal neurons (PNs), significant numbers of small intensely fluorescent (SIF) cells were located in each of these plexuses, and vagal afferents provided dense pericellular varicose endings around the SIF cells in each ganglionic plexus, with few if any terminations on PNs. In the myocardium, vagal afferents formed close contacts with cardiac muscles, including conduction fibers. In the endocardium, vagal fibers formed "flower-spray" and "end-net" terminals in connective tissue. With three-dimensional reconstruction of confocal optical sections, a novel polymorphism was seen: Some fibers had one or more collaterals ending as endocardial flower sprays and other collaterals ending as myocardial intramuscular endings. Some unipolar or pseudounipolar neurons within each cardiac ganglionic plexus were retrogradely labeled from the nodose ganglia. In conclusion, vagal afferents form a heterogeneity of differentiated endings in the heart, including structured elements which may mediate chemoreceptor function, stretch reception, and local cardiac reflexes.
Matrix eQTL: ultra fast eQTL analysis via large matrix operations (2012)

We have developed a new software for computationally efficient eQTL analysis called Matrix eQTL. In tests on large datasets, it was 2-3 orders of magnitude faster than existing popular tools for QTL/eQTL analysis, while finding the same eQTLs. The fast performance is achieved by special preprocessing and expressing the most computationally intensive part of the algorithm in terms of large matrix operations. Matrix eQTL supports additive linear and ANOVA models with covariates, including models with correlated and heteroskedastic errors. The issue of multiple testing is addressed by calculating false discovery rate; this can be done separately for cis- and trans-eQTLs.
Serum and Urine Metabolite Profiling Reveals Potential Biomarkers of Human Hepatocellular Carcinoma (2011)

Hepatocellular carcinoma (HCC) is a common malignancy in the world with high morbidity and mortality rate. Identification of novel biomarkers in HCC remains impeded primarily because of the heterogeneity of the disease in clinical presentations as well as the pathophysiological variations derived from underlying conditions such as cirrhosis and steatohepatitis. The aim of this study is to search for potential metabolite biomarkers of human HCC using serum and urine metabolomics approach. Sera and urine samples were collected from patients with HCC (n = 82), benign liver tumor patients (n = 24), and healthy controls (n = 71). Metabolite profiling was performed by gas chromatography time-of-flight mass spectrometry and ultra performance liquid chromatography-quadrupole time of flight mass spectrometry in conjunction with univariate and multivariate statistical analyses. Forty three serum metabolites and 31 urinary metabolites were identified in HCC patients involving several key metabolic pathways such as bile acids, free fatty acids, glycolysis, urea cycle, and methionine metabolism. Differentially expressed metabolites in HCC subjects, such as bile acids, histidine, and inosine are of great statistical significance and high fold changes, which warrant further validation as potential biomarkers for HCC. However, alterations of several bile acids seem to be affected by the condition of liver cirrhosis and hepatitis. Quantitative measurement and comparison of seven bile acids among benign liver tumor patients with liver cirrhosis and hepatitis, HCC patients with liver cirrhosis and hepatitis, HCC patients without liver cirrhosis and hepatitis, and healthy controls revealed that the abnormal levels of glycochenodeoxycholic acid, glycocholic acid, taurocholic acid, and chenodeoxycholic acid are associated with liver cirrhosis and hepatitis. HCC patients with alpha fetoprotein values lower than 20 ng/ml was successfully differentiated from healthy controls with an accuracy of 100% using a panel of metabolite markers. Our work shows that metabolomic profiling approach is a promising screening tool for the diagnosis and stratification of HCC patients.
Supernatants from dengue virus type‐2 infected macrophages induce permeability changes in endothelial cell monolayers (2003)

The ability of dengue virus-infected human monocyte-derived macrophages to induce permeability changes in primary human umbilical vein endothelial cells was investigated. Supernatants from dengue virus type 2-infected monocyte-derived macrophages increased permeability in human umbilical vein endothelial cell monolayers without inducing endothelial cell infection. Production of permeabilising activity from monocyte-derived macrophages occurred after the peak of progeny virus release. TNF-alpha, a known inducer of endothelial cell permeability, was released from dengue virus infected monocyte-derived macrophages but its release did not coincide with release of endothelial cell permeabilising activity. Permeability induction was enhanced by pre-incubation with supernatants from infected monocyte-derived macrophages harvested at the time of peak release of TNF-alpha and infectious virus. Thus, supernatants from dengue virus-infected monocyte-derived macrophages contain factors that increase human umbilical vein endothelial cell permeability, but this is not accompanied by endothelial cell infection or directly correlated with release of dengue virus or TNF-alpha from monocyte-derived macrophages. This model system can be used for further in vitro analysis of mechanisms that may relate to capillary leakage and the development of dengue haemorrhagic fever/dengue shock syndrome.
Activation of AKT and Enhanced Resistance to Apoptosis Induced by Surface IgM Ligation in ZAP-70-Positive Chronic Lymphocytic Leukemia B Cells. (2005)

Abstract Signaling through the B-cell receptor (BCR) for antigen has been implicated to play a role in the pathogenesis and/or progression of chronic lymphocytic leukemia (CLL). Previously we found that BCR ligation on CLL cells that expressed ZAP-70 induced significantly higher levels of phosphorylation in p72Syk, BLNK, and phospholipase C-gamma than did BCR ligation on CLL cells that lacked expression of this protein tyrosine kinase. We hypothesized that CLL B cells that express ZAP-70 also may have enhanced levels of AKT activation following BCR ligation that is associated with increased resistance to apoptosis. CLL B cells were stimulated via surface IgM ligation and monitored at various time points for phosphorylation of cytoplasmic signaling molecules via immunoblot analyses and for viability by flow cytometry after staining with propidium iodide and DiOC6 to detect changes in mitochondrial membrane potential associated with apoptosis. We found that CLL cells that expressed ZAP-70 experienced significantly higher levels of AKT phosphorylation within 10 minutes following BCR-ligation than did ZAP-70-negative CLL cells. Over time a significantly higher proportion of ZAP-70-negative CLL cells were induced to undergo apoptosis by BCR-ligation than similarly treated CLL cells that were ZAP-70 positive. The differences between these two groups in leukemia cell viability over time after BCR ligation could be abrogated by addition of LY294002, a PI3-K inhibitor, to the CLL cell cultures 30 minutes prior to surface IgM ligation. We conclude that ZAP-70-positive CLL cells are relatively resistant to apoptosis induced by surface IgM ligation under the experimental conditions used, a characteristic that is associated with enhanced phosphorylation of AKT and activation of AKT-dependent pathways following BCR ligation. These studies support a model proposing that BCR ligation induces signaling that results in enhanced growth and/or survival of CLL cells that express ZAP-70 relative to that of leukemia cells that lack expression of this tyrosine kinase. Because expression of ZAP-70 typically is associated with expression of unmutated Ig V genes in CLL, the improved signaling afforded by expression of this tyrosine kinase may account in part for the greater tendency for disease progression observed in patients with CLL cells that use unmutated Ig V genes.
Capsular polysaccharides and lipopolysaccharides from two Bacteroides fragilis reference strains: chemical and immunochemical characterization (1983)

Fermentor growth of Bacteroides fragilis under controlled conditions in a complex medium containing 1% glucose and 10% fetal calf serum resulted in high yields of bacteria. After hot phenol-water extraction of the organisms, capsular polysaccharide was isolated from the aqueous phase and purified by Sephacryl S-300 chromatography in a buffer with 3% sodium deoxycholate. Lipopolysaccharide was isolated by phenol-chloroform-light petroleum ether extraction. The capsular polysaccharide from B. fragilis strain NCTC 9343 contained six sugars: L-fucose, D-galactose, D- and L-quinovosamine, D-glucosamine, and galacturonic acid. The capsule of strain ATCC 23745 also contained D-glucose, L-fucosamine, L-rhamnosamine, and a 3-amino-3,6-dideoxyhexose but lacked D-quinovosamine. The latter capsule also contained alanine (4%). The capsular polysaccharides were different immunochemically by ELISA inhibition. The lipopolysaccharide of both strains contained the same sugars (L-rhamnose, D-glucose, D-galactose, and D-glucosamine) and fatty acids (13-methyl-tetradecanoic and 3-hydroxy-hexadecanoic and 3-hydroxy-15 methyl-hexadecanoic as major constituents) and were identical by ELISA inhibition.
The perioperative use of corticosteroids and bupivacaine in the management of lumbar disc disease (1993)

The introduction of microdiscectomy to lumbar spine surgery has resulted in a significant decrease in postoperative pain and length of hospital stay. Intraoperative application of long-acting local anesthetic agents has been used for many general and neurosurgical procedures for the management of postoperative pain. In addition, many surgeons routinely use intraoperative corticosteroids during lumbar discectomy to reduce traumatic nerve root inflammation. However, the efficacy of intraoperative long-acting local anesthetic agents and corticosteroids for reduction of postoperative discomfort has not been reported for lumbar discectomy. This study evaluated 32 patients at a university-based Veterans Administration hospital undergoing lumbar microdiscectomy. All 32 patients presented with radicular symptoms and had radiographic confirmation of a herniated nucleus pulposus. These patients were divided into three groups. Group 1 (12 patients) received 160 mg intramuscular Depo-Medrol (methylprednisolone acetate) and 250 mg intravenous Solu-Medrol (methyl-prednisolone sodium succinate) at the start of the operation. A macerated fat graft soaked in 80 mg Depo-Medrol was placed over the affected nerve root following discectomy. In addition, 30 ml of 0.25% bupivacaine was infiltrated into the paraspinal musculature at skin incision and during closure. Group 2 (10 patients) received 30 ml of 0.25% bupivacaine infiltrated into the paraspinal musculature at skin incision and at closure. In this group of patients, a saline-soaked fat graft was placed over the affected nerve root. Group 3 (10 patients) acted as a control group, undergoing lumbar microdiscectomy without corticosteroids or bupivacaine. Patients receiving bupivacaine and corticosteroids (Group 1) had a statistically significantly shorter hospital stay (1.4 days) compared to the control group (4.0 days) (p = 0.0004, Mann-Whitney U-test). Patients in Group 1 required less postoperative narcotic analgesia than the other groups. Finally, a larger percentage of patients in Group 1 reported complete relief of back and radicular pain on postoperative Day 1 compared to other groups. Postoperative complications and functional outcome were not different between the groups. These results indicate that the combination of long-acting anesthetic agents and corticosteroids can reduce postoperative discomfort and subsequently the length of postoperative hospital stay.
Dye-mediated photosensitization of murine neuroblastoma cells. (1986)

The purpose of this study was to determine if photosensitization mediated by the fluorescent dye, merocyanine 540, could be used to preferentially kill murine neuroblastoma cells in simulated autologous remission marrow grafts. Simultaneous exposure of Neuro 2a or NB41A3 neuroblastoma cells to merocyanine 540 and white light reduced the concentration of in vitro-clonogenic tumor cells 50,000-fold. By contrast, the same treatment had little effect on the graft's ability to rescue lethally irradiated syngeneic hosts. Lethally irradiated C57BL/6J X A/J F1 mice transplanted with photosensitized mixtures of neuroblastoma cells and normal marrow cells (1:100 or 1:10) survived without developing neuroblastomas. It is conceivable that merocyanine 540-mediated photosensitization will prove useful for the extracorporeal purging of residual neuroblastoma cells from human autologous remission marrow grafts.