gebhart/patrepeval huggingface dataset:
Complete sequence of the genes encoding the VH and VL regions of low- and high- affinity monoclonal lgM and lgA1 rheumatoid factors produced by CD5+ B cells from a rheumatoid arthritis patient (1991)

We have characterized the VH and VL genes of three low-affinity polyreactive and two high-affinity monoreactive IgM and IgA1 rheumatoid factor (RF) mAb generated using circulating CD5+ B cells from a single rheumatoid arthritis patient. We found that four and one RF mAb utilized genes of the VHIV and VHIII families, respectively. The VHIV gene usage by these RF mAb differs from the preferential VHIII, VHI, and, to a lesser extent, VHII gene usage by the IgM with RF activity found in patients with mixed cryoglobulinemia, Waldenstrom's macroglobulinemia, and other monoclonal gammopathies. In addition, in contrast to the preponderant kappa L chain usage by the RF in these patients, a lambda L chain was utilized by all RF mAb from our rheumatoid arthritis patient. Two RF mAbs utilized V lambda I, two V lambda IV, and one V lambda III L chains. The VH genes of the two low-affinity polyreactive IgM RF mAb were in germline configuration. When compared with the deduced amino acid sequence of the putatively corresponding genomic segment, the VH gene of the high-affinity monoreactive IgM RF mAb displayed five amino acid differences, all of which are in the complementarity determining regions (CDR), possibly the result of a process of somatic point mutation and clonal selection driven by Ag. The unavailability of the corresponding genomic VH segment sequences made it impossible to infer whether the VH genes utilized by the two IgA1 RF were in a germline or somatically mutated configuration. Sequencing of the genes encoding the H chain CDR3 (D segments) revealed that all three low-affinity polyreactive RF mAb displayed a much longer D segment (36-45 bases) than their high-affinity monoreactive counterparts (15-24 bases), raising the possibility that a long D segment may be one of the factors involved in antibody polyreactivity.
Partial characterization of a C5a-inhibitor in peritoneal fluid. (1990)

We have recently described a 40-kDa protein in peritoneal fluid that neutralized the chemotactic activity of the C fraction C5a. It was deficient in peritoneal fluids of patients suffering from familial Mediterranean fever. Further characterization of the inhibitor with the use of 125I-rC5a binding to dibutyryl cAMP-induced U937 cells revealed dependence on the peritoneal fluid concentration, on the time of incubation and on temperature and pH. Fractionation of 125I-C5a on Sephadex G-50 column, before and after incubation with peritoneal fluid, revealed similar fractionation patterns despite loss of biologic activity of the treated C5a (but not its binding to polyclonal anti-C5a antibody). Analysis of rC5a by SDS-PAGE before and after treatment with partially purified C5a inhibitor, revealed slight modification of the inhibitor-treated C5a. Using various protease inhibitors (i.e., PMSF) suggested that the C5a inhibitor is a serine protease. It neutralized C5a by means of limited proteolysis which did not change C5a immunologic properties and changed only slightly its m.w. but abolished its receptor binding and chemotactic functions. It is suggested that the C5a inhibitor plays a role in the regulation of inflammation in serosal tissues and that its deficiency in familial Mediterranean fever may explain the attacks of sterile inflammation characteristic of this disease.
Compilation Techniques for Real-Time Java Programs (2007)

In this paper, we introduce the IBMreg WebSpherereg real time product, which incorporates a virtual machine that is fully Javatrade compliant as well as compliant with the Real-Time Specification for Java (RTSJ). We describe IBM's real-time Java enhancements, particularly in the area of our Testarossa (TR) ahead-of-time (AOT) compiler, our TR just-in-time (JIT) compiler, and our Metronome (Bacon, et al., 2003) deterministic garbage collector (GC). The main focus of this paper is on the various techniques employed by the TR compilers to optimize and regulate the performance of code running in a real-time Java environment through a simple Java source code example. Through the example, we highlight the additional checks required to provide a conformant RTSJ implementation as well as the performance issues with ahead-of-time code generation and the overheads required to support Metronome. We show how these checks are implemented in a production JVM, and then report the cost of the real-time changes in practice for the example as well as the SPECjvm98 benchmark suite, SPECjbb2000, and SPECjbb2005
Pyruvate carboxylase from Rhizobium etli: mutant characterization, nucleotide sequence, and physiological role (1996)

Pyruvate carboxylase (PYC), a biotin-dependent enzyme which catalyzes the conversion of pyruvate to oxaloacetate, was hypothesized to play an important anaplerotic role in the growth of Rhizobium etli during serial subcultivation in minimal media containing succinate (S. Encarnación, M. Dunn, K. Willms, and J. Mora, J. Bacteriol. 177:3058-3066, 1995). R. etli and R. tropici pyc::Tn5-mob mutants were selected for their inability to grow in minimal medium with pyruvate as a sole carbon source. During serial subcultivation in minimal medium containing 30 mM succinate, the R. etli parent and pyc mutant strains exhibited similar decreases in growth rate with each subculture. Supplementation of the medium with biotin prevented the growth decrease of the parent but not the mutant strain, indicating that PYC was necessary for the growth of R. etli under these conditions. The R. tropici pyc mutant grew normally in subcultures regardless of biotin supplementation. The symbiotic phenotypes of the pyc mutants from both species were similar to those of the parent strains. The R. etli pyc was cloned, sequenced, and found to encode a 126-kDa protein of 1,154 amino acids. The deduced amino acid sequence is highly homologous to other PYC sequences, and the catalytic domains involved in carboxylation, pyruvate binding, and biotinylation are conserved. The sequence and biochemical data show that the R. etli PYC is a member of the alpha4, homotetrameric, acetyl coenzyme A-activated class of PYCs.
Safety, tolerance and pharmacokinetics of a humanized monoclonal antibody to respiratory syncytial virus in premature infants and infants with bronchopulmonary dysplasia (1998)

MEDI-493 was safe and well-tolerated in this high risk pediatric population. Mean serum concentrations of MEDI-493 that have been shown to produce a 2-log reduction in pulmonary RSV titer in cotton rats were maintained when 10 or 15 mg/kg MEDI-493 was given every 30 days to pediatric patients at high risk for serious RSV disease. Monthly doses of 15 mg/kg maintained concentrations of > 40 microg/ml for the majority of patients.
Germ-Line Mutations in Nonsyndromic Pheochromocytoma (2002)

Almost one fourth of patients with apparently sporadic pheochromocytoma may be carriers of mutations; routine analysis for mutations of RET, VHL, SDHD, and SDHB is indicated to identify pheochromocytoma-associated syndromes that would otherwise be missed.
Bonding interface materials evolution of intermediate In/Ag layers for low temperature fluxless solder based MEMS wafer level packaging (2008)

In this paper, we proposed new intermediate bonding layers (IBLs) of Ag-rich composition in In-Ag solder systems in contrast to previous studies mainly based on eutectic composition. The intermetallic compounds (IMCs) at the bonding interface were investigated with respect to the bonding condition, post-bonding room temperature storage and post-bonding heat treatment. The IMCs of Ag <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> In and Ag <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sub> In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> with high temperature resist to post-bonding process are derived under process condition of wafer bonding at 180degC, 40 mins and subsequent 120degC~130degC annealing for 24 hours. Based on our results, we can design proper packaging process flow so as to get reliable wafer level packaged MEMS devices.
HEALING OF NONUNION OF THE MEDIAL MALLEOLUS BY MEANS OF DIRECT CURRENT (1971)

FRIEDENBERG, Z. B. M.D. F.A.C.S.; HARLOW, M. C. M.D.; BRIGHTON, C. T. M.D., PH.D., F.A.C.S. Author Information
Impact of Soluble Epoxide Hydrolase and Epoxyeicosanoids on Human Health (2012)

The presence of epoxyeicosatrienoic acids (EETs) in tissues and their metabolism by soluble epoxide hydrolase (sEH) to 1,2-diols were first reported 30 years ago. However, appreciation of their importance in cell biology and physiology has greatly accelerated over the past decade with the discovery of metabolically stable inhibitors of sEH, the commercial availability of EETs, and the development of analytical methods for the quantification of EETs and their diols. Numerous roles of EETs in regulatory biology now are clear, and the value of sEH inhibition in various animal models of disease has been demonstrated. Here, we review these results and discuss how the pharmacological stabilization of EETs and other natural epoxy-fatty acids could lead to possible disease therapies.
Nicotine: A Unique Psychoactive Drug (1991)

Nicotine is a unique psychoactive drug which produces arousal, relaxation, promotion of REM sleep and skeletal muscle relaxation in both animals and humans in tobacco smoking concentrations. Normal tobacco smokers, deprived of tobacco for 12 hr show a decrease in alpha 1, an increase in alpha 2 EEG power, and a decrease in the recovery cycle of the Hoffmann reflex after smoking cigarettes containing nicotine.
Antisense RNA (1991)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Dimethoxyphenol oxidase activity of different microbial blue multicopper proteins (2001)

2,6-Dimethoxyphenol is a versatile substrate for Pyricularia oryzae laccase, PpoA from Marinomonas mediterranea, phenoxazinone synthase from Streptomyces antibioticus and mammalian ceruloplasmin. In addition, in cellular extracts of microorganisms expressing other blue multicopper proteins with no enzymatic activity previously described, such as Escherichia coli (copper resistance CueO), Pseudomonas syringae and Xanthomonas campestris (copper resistance CopA), Bacillus subtilis (sporulation protein CotA) and Saccharomyces cerevisiae (iron transporter Fet3p), laccase activity is detected under appropriate conditions. This oxidase activity can be spectrophotometrically followed by the oxidation of 2,6-dimethoxyphenol. Specific staining after SDS-PAGE is also possible for some of these proteins. This detection assay can facilitate the study of the multiple functions that such proteins seem to carry out in a variety of microorganisms.
Effects of Recombinant Human Soluble Thrombomodulin (rhs-TM) on a Rat Model of Disseminated Intravascular Coagulation with Decreased Levels of Plasma Antithrombin III (1994)

We reported that recombinant human soluble thrombomodulin (rhs-TM) is effective for disseminated intravascular coagulation (DIC) in vivo, in mice and rats. In the present work, we investigated the effects of decreased plasma antithrombin III (ATIII) levels on anticoagulant effects of rhs-TM, as compared to findings with heparin, of which effect is lowered by the decreased plasma ATIII levels in patients with DIC. Rat plasma ATIII levels decreased when we mixed plasma with anti-rat ATIII antibody and the potential of heparin to prolong APTT or PT was markedly diminished. The potential of rhs-TM to prolong APTT and PT was not affected. In rats injected with anti-rat ATIII antibody, plasma ATIII levels decreased immediately. When the rats were infused with tissue factor (TF), DIC was induced. At doses of rhs-TM and heparin which were equally effective at inhibiting the decrease in platelet count and fibrinogen level in control rats treated with TF, only rhs-TM remained effective in preventing DIC in rats with reduced ATIII levels. Heparin was not effective when administered to these rats with reduced ATIII levels. Therefore, rhs-TM effectively inhibits coagulation independent of ATIII levels, in contrast to heparin, which depends on the ATIII level.
Wireless Information-Theoretic Security (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper considers the transmission of confidential data over wireless channels. Based on an information-theoretic formulation of the problem, in which two legitimates partners communicate over a quasi-static fading channel and an eavesdropper observes their transmissions through a second independent quasi-static fading channel, the important role of fading is characterized in terms of average secure communication rates and outage probability. Based on the insights from this analysis, a practical secure communication protocol is developed, which uses a four-step procedure to ensure wireless information-theoretic security: (i) common randomness via opportunistic transmission, (ii) message reconciliation, (iii) common key generation via privacy amplification, and (iv) message protection with a secret key. A reconciliation procedure based on multilevel coding and optimized low-density parity-check (LDPC) codes is introduced, which allows to achieve communication rates close to the fundamental security limits in several relevant instances. Finally, a set of metrics for assessing average secure key generation rates is established, and it is shown that the protocol is effective in secure key renewal—even in the presence of imperfect channel state information. </para>
Detection and Characterization of Rickettsia tsutsugamushi (Rickettsiales: Rickettsiaceae) in Infected Leptotrombidium (Leptotrombidium) fletcheri Chiggers (Acari: Trombiculidae) with the Polymerase Chain Reaction (1994)

We developed a method for detecting and characterizing the DNA of Rickettsia tsutsugamushi in chiggers (larval trombiculid mites) by polymerase chain reaction (PCR). Three procedures for extracting DNA from frozen chiggers were compared by evaluating the yield of PCR amplicand obtained with nine oligonucleotide primer pairs derived from the rickettsial 22 kD, 47 kD, groESL, 56 kD, and 110 kD antigen genes. Although extracts and primer pairs differed in amplification efficiency, R. tsutsugamushi DNA was successfully detected in extracts of colonized infected Leptotrombidium (Leptotrombidium) fletcheri (Wormersley & Heaslip) chiggers and in uninfected chigger extracts seeded with known amounts of Karp-strain rickettsiae. The 22 kD gene restriction fragment length polymorphisms (RFLP) observed in PCR amplicands from five rickettsial isolates obtained from the infected chigger colony over a 26-yr period were identical to those of PCR amplicands derived directly from infected chiggers taken from the same colony. This suggests that stable transmission of R. tsutsugamushi occurs in mites (62 generations), and isolates encompass the full genetic heterogeneity found in the chigger. PCR/RFLP analysis is an important new tool for investigating the complex epidemiology of scrub typhus rickettsiae in their mite vectors.
Topological Requirements and Signaling Properties of T Cell–activating, Anti-CD28 Antibody Superagonists (2003)

Full activation of naive T cells requires both engagement of the T cell antigen receptor (TCR; signal 1) and costimulatory signaling by CD28 (signal 2). We previously identified two types of rat CD28-specific monoclonal antibodies (mAbs): "conventional," TCR signaling-dependent costimulatory mAbs and "superagonistic" mAbs capable of inducing the full activation of primary resting T cells in the absence of TCR ligation both in vitro and in vivo. Using chimeric rat/mouse CD28 molecules, we show that the superagonists bind exclusively to the laterally exposed C"D loop of the immunoglobulin-like domain of CD28 whereas conventional, costimulatory mAbs recognize an epitope close to the binding site for the natural CD80/CD86 ligands. Unexpectedly, the C"D loop reactivity of a panel of new antibodies raised against human CD28 could be predicted solely on the basis of their superagonistic properties. Moreover, mouse CD28 molecules engineered to express the rat or human C"D loop sequences activated T cell hybridomas without TCR ligation when cross-linked by superagonistic mAbs. Finally, biochemical analysis revealed that superagonistic CD28 signaling activates the nuclear factor kappaB pathway without inducing phosphorylation of either TCRzeta or ZAP70. Our findings indicate that the topologically constrained interactions of anti-CD28 superagonists bypass the requirement for signal 1 in T cell activation. Antibodies with this property may prove useful for the development of T cell stimulatory drugs.
Composite Medium with Simultaneously Negative Permeability and Permittivity (2000)

We demonstrate a composite medium, based on a periodic array of interspaced conducting nonmagnetic split ring resonators and continuous wires, that exhibits a frequency region in the microwave regime with simultaneously negative values of effective permeability &mgr;(eff)(omega) and permittivity varepsilon(eff)(omega). This structure forms a "left-handed" medium, for which it has been predicted that such phenomena as the Doppler effect, Cherenkov radiation, and even Snell's law are inverted. It is now possible through microwave experiments to test for these effects using this new metamaterial.
Effect of the Twin‐seeded Character on Sorghum Performance1 (1977)

The sorghum [ Sorghum bicolor (L.) Moench] sessile spikelet normally contains two flowers. Usually, only the upper develops into a seed, but the lower also develops into a seed in some cultivars, resulting in twin seededness. A study of the influence of the twin‐seeded character on sorghum performance was made by use of isogenic lines. Isogenic single‐ and twin‐seeded A‐ and B‐lines of the sorghum cultivars ‘Combine Kafir‐60’ and ‘Redlan’ were developed by backcrossing. The twin‐seeded allele ( Ts ) caused sterility in some instances, especially in A‐lines. Attempts to develop twin‐seeded lines of ‘KS 24’ resulted in much sterility and multiple seededness of up to five seeds per spikelet. Comparisons were made of isogenic single‐ and twinseeded counterparts of the sorghum hybrids ‘KS652’, ‘RS610’, ‘RS702’, ‘RS650’, 62MH248, and 55MH19 at Manhattan, Kans. and Mead, Neb. The percentage of spikelets with twin seed was influenced by genotype and environment. Twin seededness had no effect on days to 50% bloom, plant height, and panicles per plant. There was little evidence that twin seededness affected test weight, although it decreased seed weight and the number of seed‐bearing spikelets per panicle while increasing the number of seeds per panicle. Grain yields of the single‐ and twin‐seeded counterparts of RS610 and RS702 did not differ significantly, but twin‐seeded counterparts of the remaining hybrids yielded significantly less grain than the single‐seeded counterparts.
Use of In Vivo-Regulated Promoters To Deliver Antigens from Attenuated Salmonella enterica var. Typhimurium (1999)

This study describes the construction and analysis of three in vivo-inducible promoter expression plasmids, containing pnirB, ppagC, and pkatG, for the delivery of foreign antigens in the DeltaaroAD mutant of Salmonella enterica var. Typhimurium (hereafter referred to as S. typhimurium). The reporter genes encoding beta-galactosidase and firefly luciferase were used to assess the comparative levels of promoter activity in S. typhimurium in vitro in response to different induction stimuli and in vivo in immunized mice. It was determined that the ppagC construct directed the expression of more beta-galactosidase and luciferase in S. typhimurium than the pnirB and pkatG constructs, both in vitro and in vivo. The gene encoding the C fragment of tetanus toxin was expressed in the aroAD mutant of S. typhimurium (BRD509) under the control of the three promoters. Mice orally immunized with attenuated S. typhimurium expressing C fragment under control of the pagC promoter [BRD509(pKK/ppagC/C frag)] mounted the highest tetanus toxoid-specific serum antibody response. Levels of luciferase expression in vivo and C-fragment expression in vitro from the pagC promoter appeared to be equivalent to if not lower than the levels of expression detected with the constitutive trc promoter. However, mice immunized with BRD509(pKK/ppagC/C frag) induced significantly higher levels of tetanus toxoid-specific antibody than BRD509(pKK/C frag)-immunized mice, suggesting that the specific location of foreign antigen expression may be important for immunogenicity. Mutagenesis of the ribosome binding sites (RBS) in the three promoter/C fragment expression plasmids was also performed. Despite optimization of the RBS in the three different promoter elements, the expression levels in vivo and overall immunogenicity of C fragment when delivered to mice by attenuated S. typhimurium were not affected. These studies suggest that in vivo-inducible promoters may give rise to enhanced immunogenicity and increase the efficacy of S. typhimurium as a vaccine vector.
Opinion spam and analysis (2008)

Evaluative texts on the Web have become a valuable source of opinions on products, services, events, individuals, etc. Recently, many researchers have studied such opinion sources as product reviews, forum posts, and blogs. However, existing research has been focused on classification and summarization of opinions using natural language processing and data mining techniques. An important issue that has been neglected so far is opinion spam or trustworthiness of online opinions. In this paper, we study this issue in the context of product reviews, which are opinion rich and are widely used by consumers and product manufacturers. In the past two years, several startup companies also appeared which aggregate opinions from product reviews. It is thus high time to study spam in reviews. To the best of our knowledge, there is still no published study on this topic, although Web spam and email spam have been investigated extensively. We will see that opinion spam is quite different from Web spam and email spam, and thus requires different detection techniques. Based on the analysis of 5.8 million reviews and 2.14 million reviewers from amazon.com, we show that opinion spam in reviews is widespread. This paper analyzes such spam activities and presents some novel techniques to detect them
Neural guidance molecules regulate vascular remodeling and vessel navigation (2005)

The development of the embryonic blood vascular and lymphatic systems requires the coordinated action of several transcription factors and growth factors that target endothelial and periendothelial cells. However, according to recent studies, the precise "wiring" of the vascular system does not occur without an ordered series of guidance decisions involving several molecules initially discovered for axons in the nervous system, including ephrins, netrins, slits, and semaphorins. Here, we summarize the new advances in our understanding of the roles of these axonal pathfinding molecules in vascular remodeling and vessel guidance, indicating that neuronal axons and vessel sprouts use common molecular mechanisms for navigation in the body.