gebhart/patrepeval huggingface dataset:
A monoclonal antibody that recognizes phosphatidylinositol inhibits induction of tumor necrosis factor alpha by different strains of Plasmodium falciparum (1994)

The clinical symptoms of human malaria are mediated, at least in part, by the release of tumor necrosis factor alpha (TNF) by monocytes and macrophages. We have found that lysates of Plasmodium falciparum-infected erythrocytes stimulate the secretion of TNF from human mononuclear cells, and we have generated several immunoglobulin M monoclonal antibodies (MAbs) that inhibit the induction of TNF by such lysates. Here we describe the properties of MAb 5AB3-11, which causes dose-dependent inhibition of the TNF-inducing factors derived from P. falciparum-infected erythrocytes, with a 50% reduction in TNF secretion at nanomolar concentrations (1 to 2 micrograms/ml). The inhibitory effect appears to be malaria specific in that the induction of TNF by either lipopolysaccharide or lipoteichoic acid is not affected. MAb 5AB3-11 binds to liposomes containing phosphatidylinositol but not to other phospholipid liposomes, showing that it recognizes a phosphatidylinositol-like epitope. MAb 5AB3-11 inhibits the induction of TNF by whole lysates from several strains of P. falciparum which originated from different parts of the tropics, indicating that all of the major TNF-inducing factors derived from Plasmodium-infected erythrocytes contain a common epitope. A phosphatidylinositol-like epitope expressed by Plasmodium-infected erythrocytes may be a suitable immunological target for the prevention or treatment of severe malaria.
On the utility of graphics cards to perform massively parallel\nsimulation with advanced Monte Carlo methods. (2009)

We present a case-study on the utility of graphics cards to perform massively parallel sim ulation with advanced Monte Carlo methods. Graphics cards, containing multiple Graphics\nProcessing Units (GPUs), are self-contained parallel computational devices that can be housed in conventional desktop and laptop computers. For certain classes of Monte Carlo algorithms they offer massively parallel simulation, with the added advantage over conventional distributed multi-core processors that they are cheap, easily accessible, easy to maintain, easy to code, dedicated local devices with low power consumption. On a canonical set of stochastic simulation examples including population-based Markov chain Monte Carlo methods and Sequential Monte Carlo methods, we find speedups from 35 to 500 fold over conventional single-threaded computer code. Our findings suggest that GPUs have the potential to facilitate the growth of statistical modelling into complex data rich domains through the availability of cheap and accessible many-core computation. We believe the speedup we observe should motivate wider use of parallelizable simulation methods and greater methodological attention to their design.
Rapid urease test provides specific identification of Campylobacter pylori in antral mucosal biopsies (1988)

In a prospective study, three antral biopsies were taken from 175 dyspeptic patients during routine endoscopy. One biopsy was inserted immediately into a gel-containing well of a CLOtest slide and two biopsies were sent to histopathology. Using the CLOtest, 84 of the 175 samples (48%) detected urease activity in the gastric biopsy, suggesting infection with Campylobacter pylori. Histopathological examination by two independent observers reported that 93 (52%) of the biopsies contained Campylobacter-like organisms. The CLOtest was found to have a specificity of 1.0 and sensitivity of 0.91, providing a rapid identification of most patients harbouring the organism in their gastric mucus.
Ciguatera fish poisoning. A southern California epidemic. (1995)

Ciguatera fish poisoning results from the bioconcentration of a variety of toxins produced by marine dinoflagellates. Signs and symptoms vary widely, but it usually presents as gastrointestinal and neurologic complaints beginning shortly after the ingestion of fish containing the toxins. Symptoms may persist for months and sometimes even years. Although cases have been reported throughout the United States, epidemics are most common along tropical and subtropical coasts and usually involve the ingestion of large carnivorous fish. We review the literature and report the first epidemic of 25 cases of ciguatera fish poisoning presenting to area hospitals in Southern California that were successfully tracked by the Department of Health Services and isolated to fish caught off the coast of Baja California, Mexico.
Thermodynamic modeling and optimization of multi-pressure heat recovery steam generator in combined power cycle (2008)

Optimum configuration for single pressure (SP), dual pressure (DP) and triple pressure (TP) heat recovery steam generator (HRSG) is presented to improve heat recovery and thereby exergy efficiency of combined cycle. Deaerator was added to enhance efficiency and remove dissolved gases in feed water. A new method was introduced to evaluate low pressure (LP) and intermediate pressure (IP) in HRSG from local flue gas temperature to get minimum possible temperature difference in heaters instead of a usual fixation of pressures. Optimum location for deaerator was found at 1, 3 and 5 bar respectively for SP, DP and TP,in heat recovery at a high pressure (HP) of 200 bar. Results also showed optimum pressure for air compression and steam reheater by means of three categories of heat recovery.
Synthesis of compounds related to antitumor agents. III. On the additions of acyl halide, dialkyl acetylenedicarboxylate and N-substituted maleimides to 2,4-diamino-5-hydroxy-6-methylpyrimidine. (1976)

2, 4-Diamino-5-hydroxy-6-methylpyrimidine (I) was reacted with acyl halides to give pyrimido [5, 4-b] [1, 4] oxazin-6 (8H)-ones (IIIa, b). Dialkyl acetylenedicarboxylate was made addition with I to afford alkoxycarbonylmethylene-pyrimido [5, 4-b] [1, 4] oxazines (VI, VII). The configuration of this compound was assumed to be cis from the evidence of building pyridazino or furano ring. Similarly, with maleimide, the adduct (XIV) was obtained and converted to pyrimido [5, 4-b] [1, 4] oxazines (XV, XXIa-f).
Characterization of a Urinary Bufodienolide Na<sup>+</sup>,K<sup>+</sup>-ATPase Inhibitor in Patients After Acute Myocardial Infarction (1998)

Recent evidence suggests the existence of several endogenous Na+,K+-ATPase inhibitors in mammals. Previously, we have shown that the amphibian Na+,K+-ATPase inhibitor marinobufagenin (3,5-dihydroxy-14,15-epoxy bufodienolide) acts as a vasoconstrictor in isolated rat and human arteries. Mammalian plasma was shown to contain marinobufagenin-like immunoreactive material, which is responsive to saline volume expansion. The present study describes purification of a bufodienolide, which is similar to marinobufagenin, from the urine of patients after acute myocardial infarction with the use of thin-layer chromatography and reverse-phase high-performance liquid chromatography (HPLC). The purified substance cross-reacted with marinobufagenin antibody, demonstrated maximal UV absorbance at 300 nm characteristic of bufodienolides, and eluted from HPLC columns with the same retention time as marinobufagenin. Mass spectrometry of purified material revealed the presence of a substance indistinguishable from amphibian marinobufagenin and having molecular mass of 400 D. The present studies show that one of the human digitalis-like factors may have a bufodienolide structure and is likely to represent marinobufagenin or its isomer, and they suggest a role for this substance in the pathogenesis of myocardial ischemia.
Diffusion imaging of the in vivo heart using spin echoes–considerations on bulk motion sensitivity (2007)

Cardiac diffusion MRI based on stimulated-echo acquisition mode (STEAM) techniques is hampered by its inherent low signal-to-noise ratio (SNR) efficiency. Diffusion imaging using standard spin-echo (SE) techniques, on the other hand, offers higher SNRs but has been considered impractical for the beating heart due to excessive signal attenuation from cardiac bulk motion. In this work the effect of systolic cardiac motion on different diffusion-encoding schemes was studied in detail. Numerical simulations based on in vivo motion data (acquired by MRI tagging techniques) demonstrate an up to 10-fold decrease in bulk motion sensitivity of the diffusion encoding if the first-order moment of the diffusion-encoding gradients is nullified. It is shown that the remaining systolic phase pattern on the myocardium does not influence the magnitude images if the spatial resolution is chosen to be higher than 4 mm. Given these relatively low resolution requirements, we obtained in vivo diffusion-weighted (DW) short-axis images from four healthy volunteers using an SE-based diffusion-encoding sequence with excitation and refocusing in orthogonal planes for field of view (FOV) reduction. The results showed no significant signal loss due to cardiac motion, and the direction of the principal eigenvalues was found to be in good agreement with known myocardial fiber orientation.
An overview of solvent extraction treatment technologies (1990)

Abstract In the course of evaluating potential technologies for treatment of contaminated soils at a regulated site in the upper Midwest, solvent extraction technology was reviewd and appeared to be a viable alternative to incineration and land disposal. Because of stringent federal and state land disposal rules, liability issues, and rising disposal costs, technologies that will treat and detoxify hazardous wastes effectively are preferred over other less aggressive technologies. Industry is actively seeking and evaluating options, and the regulatory community is encouraging development and application of new treatment technologies as alternatives to land disposal. To advance this effort, the U.S. Environmental Protection Agency (EPA) established the Superfund Innovative Technology Evaluation (SITE) program to promote the development of innovative technologies and to demonstrate such technologies at Superfund sites. Solvent extration technology is being evaluated in the SITE program. This paper was prepared because of the lack of a compiled source of existing information on the alternative use of solvent extraction technology for treating soils contaminated with hazardous substances in a manner other than incineration.
Association Test Algorithm Between a Qualitative Phenotype and a Haplotype or Haplotype Set Using Simultaneous Estimation of Haplotype Frequencies, Diplotype Configurations and Diplotype-Based Penetrances (2004)

Analysis of the association between haplotypes and phenotypes is becoming increasingly important. We have devised an expectation-maximization (EM)-based algorithm to test the association between a phenotype and a haplotype or a haplotype set and to estimate diplotype-based penetrance using individual genotype and phenotype data from cohort studies and clinical trials. The algorithm estimates, in addition to haplotype frequencies, penetrances for subjects with a given haplotype and those without it (dominant mode). Relative risk can thus also be estimated. In the dominant mode, the maximum likelihood under the assumption of no association between the phenotype and presence of the haplotype (L(0max)) and the maximum likelihood under the assumption of association (L(max)) were calculated. The statistic -2 log(L(0max)/L(max)) was used to test the association. The present algorithm along with the analyses in recessive and genotype modes was implemented in the computer program PENHAPLO. Results of analysis of simulated data indicated that the test had considerable power under certain conditions. Analyses of two real data sets from cohort studies, one concerning the MTHFR gene and the other the NAT2 gene, revealed significant associations between the presence of haplotypes and occurrence of side effects. Our algorithm may be especially useful for analyzing data concerning the association between genetic information and individual responses to drugs.
Real-time phase microscopy using a phase-lock interferometer (1978)

A phase-lock interference microscope (PLIM) has been designed and constructed. The instrument measures optical phase in real time with analog output voltages proportional to phase and position. The PLIM has been used to measure gradient index profiles in optical fibers, wall thicknesses of microballoons for laser induced fusion, the phase of biological specimens, and the surface finish of optical surfaces. The peak-to-peak noise of the instrument is lambda/50.
Fast Defogging and Restoration Assessment Approach to Road Scene Images (2016)

Single image defogging has received increased attention recently. However, most existing methods are generic restoration methods which may cause partial over-enhancing to the image at a short distance. This certainly makes these defogging methods may be not suitable for road images. In this paper, we propose a new image defogging algorithm that divides the original foggy image into three regions and different enhancement processes are performed for the different region. As the results, the far-away region image that is most concerned by a car driver can be moderately enhanced, and over-enhancement of the bottom region image can be also limited effectively. To effectively measure the defogging effects of various algorithms, the assessment methods based on image feature and visibility distance are proposed for road scene image. The comparative study and quantitative evaluation show that the proposed method can obtain very good defogging image with relatively fast speed.
Capacity of Multi-service CDMA Cellular Networks with Best-Effort Applications (2002)

In this paper we compute the uplink capacity of power-control CDMA mobile networks with an idealized power control, that contain best-effort type applications, i.e. applications whose transmission rate can be controlled. An arriving best-effort call is assumed to have a fixed amount of traffic to send, so the transmission rate assigned to it determines the duration of the call. We allow for multi-services (so that mobile stations have different quality of service requirements). Unlike some previous published work where soft blocking was considered (and the system was thus allowed to operate beyond capacity), we assume that a call admission mechanism is implemented in order to prevent a new call to arrive when the system is already saturated. This guarantees the quality of service of ongoing calls.
Genetic and biochemical characterization of the Lactobacillus delbrueckii subsp. lactis bacteriophage LL-H lysin (1995)

LL-H, a virulent phage of Lactobacillus delbrueckii subsp. lactis, produces a peptidoglycan-degrading enzyme, Mur, that is effective on L. delbrueckii, Lactobacillus acidophilus, Lactobacillus helveticus, and Pediococcus damnosus cell walls. In this study, the LL-H gene mur was cloned into Escherichia coli, its nucleotide sequence was determined, and the enzyme produced in E. coli was purified and biochemically characterized. Mur was purified 112-fold by means of ammonium sulfate precipitation and cation-exchange chromatography. The cell wall-hydrolyzing activity was found to be associated with a 34-kDa protein. The C-terminal domain of Mur is not essential for catalytic activity since it can be removed without destroying the lytic activity. The N-terminal sequence of the purified lysin was identical to that deduced from the nucleotide sequence, but the first methionine is absent from the mature protein. The N-terminal part of this 297-amino-acid protein had homology with several Chalaropsis-type lysozymes. Reduction of purified and Mur-digested L. delbrueckii cell wall material with labeled NaB3H4 indicated that the enzyme is a muramidase. The temperature optimum of purified Mur is between 30 and 40 degrees C, and the pH optimum is around 5.0. The LL-H lysin Mur is stable at temperatures below 60 degrees C.
A method of decoupling of radio frequency coils in magnetic resonance imaging : application to MRI with ultra short echo time concurrent excitation and acquisition (2013)

Ankara : The Department of Electrical and Electronics Engineering and the Graduate School of Engineering and Science of Bilkent University, 2013.
Molecular Typing of <i>Salmonella enterica</i> Serovar Typhi Isolates from Various Countries in Asia by a Multiplex PCR Assay on Variable-Number Tandem Repeats (2003)

A multiplex PCR method incorporating primers flanking three variable-number tandem repeat (VNTR) loci (arbitrarily labeled TR1, TR2, and TR3) in the CT18 strain of Salmonella enterica serovar Typhi has been developed for molecular typing of S. enterica serovar Typhi clinical isolates from several Asian countries, including Singapore, Indonesia, India, Bangladesh, Malaysia, and Nepal. We have demonstrated that the multiplex PCR could be performed on crude cell lysates and that the VNTR banding profiles produced could be easily analyzed by visual inspection after conventional agarose gel electrophoresis. The assay was highly discriminative in identifying 49 distinct VNTR profiles among 59 individual isolates. A high level of VNTR profile heterogeneity was observed in isolates from within the same country and among countries. These VNTR profiles remained stable after the strains were passaged extensively under routine laboratory culture conditions. In contrast to the S. enterica serovar Typhi isolates, an absence of TR3 amplicons and a lack of length polymorphisms in TR1 and TR2 amplicons were observed for other S. enterica serovars, such as Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Enteritidis, and Salmonella enterica serovar Paratyphi A, B, and C. DNA sequencing of the amplified VNTR regions substantiated these results, suggesting the high stability of the multiplex PCR assay. The multiplex-PCR-based VNTR profiling developed in this study provides a simple, rapid, reproducible, and high-resolution molecular tool for the epidemiological analysis of S. enterica serovar Typhi strains.
The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity (2000)

An explosive epidemic of human immunodeficiency virus type 1 (HIV-1) has been documented among the injecting drug user population of Kathmandu, Nepal, whose seropositivity rate has risen from 0 to 40% between 1995 and 1997. By using Catrimox to preserve whole-blood RNA at ambient temperature for transportation, HIV-1 envelope V3-V4 sequences were obtained from 36 patients in this group. Analysis of the sequences indicated a homogenous epidemic of subtype C virus, with at least two independent introductions of the virus into the population. Viral diversity was restricted within two transmission subclusters, with the majority of variation occurring in V4. Calculation of the synonymous-to-nonsynonymous mutation ratio (Ks:Ka) across this region showed that significant evolutionary pressure had been experienced during the rapid horizontal spread of the virus in this population, most strongly directed to the region between V3 and V4.
The ESAT-6 Protein of Mycobacterium tuberculosis Interacts with Beta-2-Microglobulin (β2M) Affecting Antigen Presentation Function of Macrophage (2014)

ESAT-6, an abundantly secreted protein of Mycobacterium tuberculosis (M. tuberculosis) is an important virulence factor, inactivation of which leads to reduced virulence of M. tuberculosis. ESAT-6 alone, or in complex with its chaperone CFP-10 (ESAT-6:CFP-10), is known to modulate host immune responses; however, the detailed mechanisms are not well understood. The structure of ESAT-6 or ESAT-6:CFP-10 complex does not suggest presence of enzymatic or DNA-binding activities. Therefore, we hypothesized that the crucial role played by ESAT-6 in the virulence of mycobacteria could be due to its interaction with some host cellular factors. Using a yeast two-hybrid screening, we identified that ESAT-6 interacts with the host protein beta-2-microglobulin (β2M), which was further confirmed by other assays, like GST pull down, co-immunoprecipitation and surface plasmon resonance. The C-terminal six amino acid residues (90-95) of ESAT-6 were found to be essential for this interaction. ESAT-6, in complex with CFP-10, also interacts with β2M. We found that ESAT-6/ESAT-6:CFP-10 can enter into the endoplasmic reticulum where it sequesters β2M to inhibit cell surface expression of MHC-I-β2M complexes, resulting in downregulation of class I-mediated antigen presentation. Interestingly, the ESAT-6:β2M complex could be detected in pleural biopsies of individuals suffering from pleural tuberculosis. Our data highlight a novel mechanism by which M. tuberculosis may undermine the host adaptive immune responses to establish a successful infection. Identification of such novel interactions may help us in designing small molecule inhibitors as well as effective vaccine design against tuberculosis.
A native antigen “reverse capture” microarray platform for autoantibody profiling of prostate cancer sera (2007)

Cancer sera contain antibodies that react with autologous cellular antigens. Here, we report the use of a novel native antigen-based platform, the "reverse capture" autoantibody microarray, for identification of autoantigens against which autoantibody expression may be used to differentiate between patients with prostate cancer and benign prostate hyperplasia (BPH). Serum samples were collected at our institution from patients with BPH and patients with prostate carcinoma with similar blood prostate-specific antigen levels. IgG was purified from individual prostate cancer sera, differentially labeled with fluorescent dyes, and competitively hybridized against purified IgG from a group of well-characterized BPH control patients on our reverse capture microarray platform. For each experiment, we performed a two-slide dye-swap. Using this platform, we identified 28 unique antigen-autoantibody reactivities that have the potential to discriminate prostate cancer from BPH. These autoantigens, with p-values ≤0.01, can be placed into the following general categories: protein kinases, cell-cycle regulators, cancer-growth factors, apoptosis mediators, and transcription factors. In addition, only 1 of the 28 autoantigens remained differentially targeted by autoantibodies in post-surgical prostate cancer patients after a minimum 1-year follow-up. Autoantibody profiling using this platform may be a useful tool for differentiating between malignant and benign diseases of the prostate.
Targeted metabolomics for discrimination of systemic inflammatory disorders in critically ill patients (2012)

The occurrence of systemic inflammatory response syndrome (SIRS) remains a major problem in intensive care units with high morbidity and mortality. The differentiation between noninfectious and infectious etiologies of this disorder is challenging in routine clinical practice. Many biomarkers have been suggested for this purpose; however, sensitivity and specificity even of high-ranking biomarkers remain insufficient. Recently, metabolic profiling has attracted interest for biomarker discovery. The objective of this study was to identify metabolic biomarkers for differentiation of SIRS/sepsis. A total of 186 meta-bolites comprising six analyte classes were determined in 143 patients (74 SIRS, 69 sepsis) by LC-MS/MS. Two markers (C10:1 and PCaaC32:0) revealed significantly higher concentrations in sepsis. A classification model comprising these markers resulted in 80% and 70% correct classifications in a training set and a test set, respectively.This study demonstrates that acylcarnitines and glycerophosphatidylcholines may be helpful for differentiation of infectious from noninfectious systemic inflammation due to their significantly higher concentration in sepsis patients. Considering the well known pathophysiological relevance of lipid induction by bacterial components, metabolites as identified in this study are promising biomarker candidates in the differential diagnosis of SIRS and sepsis.