gebhart/patrepeval huggingface dataset:
Isolation and Characterization of “ <i>Dehalococcoides</i> ” sp. Strain MB, Which Dechlorinates Tetrachloroethene to <i>trans</i> -1,2-Dichloroethene (2009)

In an attempt to understand the microorganisms involved in the generation of trans-1,2-dichloroethene (trans-DCE), pure-culture "Dehalococcoides" sp. strain MB was isolated from environmental sediments. In contrast to currently known tetrachloroethene (PCE)- or trichloroethene (TCE)-dechlorinating pure cultures, which generate cis-DCE as the predominant product, Dehalococcoides sp. strain MB reductively dechlorinates PCE to trans-DCE and cis-DCE at a ratio of 7.3 (+/-0.4):1. It utilizes H2 as the sole electron donor and PCE or TCE as the electron acceptor during anaerobic respiration. Strain MB is a disc-shaped, nonmotile bacterium. Under an atomic force microscope, the cells appear singly or in pairs and are 1.0 microm in diameter and approximately 150 nm in depth. The purity was confirmed by culture-based approaches and 16S rRNA gene-based analysis and was corroborated further by putative reductive dehalogenase (RDase) gene-based, quantitative real-time PCR. Although strain MB shares 100% 16S rRNA gene sequence identity with Dehalococcoides ethenogenes strain 195, these two strains possess different dechlorinating pathways. Microarray analysis revealed that 10 putative RDase genes present in strain 195 were also detected in strain MB. Successful cultivation of strain MB indicates that the biotic process could contribute significantly to the generation of trans-DCE in chloroethene-contaminated sites. It also enhances our understanding of the evolution of this unusual microbial group, Dehalococcoides species.
INACTIVATION OF BACTERIA BY DECAY OF INCORPORATED RADIOACTIVE PHOSPHORUS (1956)

Cultures of Escherichia coli will not grow in media containing very high specific activities of radiophosphorus P(32), the inhibition of growth being due to the decay of assimilated P(32) atoms. Experiments with a differentially labeled thymineless strain of E. coli show that the P(32) disintegrations which occur in the bacterial deoxyribonucleic acid, i.e. in the nucleus, are mainly responsible for the inactivation of the cell. The kinetics with which radioactive bacterial populations are inactivated indicate that the function of several nuclei per bacterial cell must be eliminated by P(32) decay before the ability to generate a colony is lost. The efficiency with which each P(32) disintegration inactivates the nucleus in which it has occurred is calculated to be 0.02 (at -196 degrees ), i.e., similar in magnitude to the killing efficiency of P(32) decay in bacteriophages. P(32) decay and thymine starvation cooperate in bringing about the death of individuals of the thymineless strain, from which observation it is inferred that "thymineless death" is likewise a nuclear inactivation. The descendants of a non-radioactive bacterial culture grown for several generations in the presence of P(32) and the descendants of a radioactive culture grown in the absence of P(32) are inactivated by P(32) decay in a manner which indicates that the phosphorus atoms of bacterial nuclei are dispersed among the progeny nuclei in their line of descendance.
Toward Information Privacy for the Internet of Things: A Nonparametric Learning Approach (2018)

In an Internet of things network, multiple sensors send information to a fusion center for it to infer a public hypothesis of interest. However, the same sensor information may be used by the fusion center to make inferences of a private nature that the sensors wish to protect. To model this, we adopt a decentralized hypothesis testing framework with binary public and private hypotheses. Each sensor makes a private observation and utilizes a local sensor decision rule or privacy mapping to summarize that observation independently of the other sensors. The local decision made by a sensor is then sent to the fusion center. Without assuming knowledge of the joint distribution of the sensor observations and hypotheses, we adopt a nonparametric learning approach to design local privacy mappings. We introduce the concept of an empirical normalized risk, which provides a theoretical guarantee for the network to achieve information privacy for the private hypothesis with high probability when the number of training samples is large. We develop iterative optimization algorithms to determine an appropriate privacy threshold and the best sensor privacy mappings, and show that they converge. Finally, we extend our approach to the case of a private multiple hypothesis. Numerical results on both synthetic and real data sets suggest that our proposed approach yields low error rates for inferring the public hypothesis, but high error rates for detecting the private hypothesis.
Implementing Intelligent Network Services with the Session Initiation Protocol (1999)

Internet telephony is receiving increasing interest as an alternative to traditional telephone networks. This article shows how the IETF's Session Initiation Protocol (SIP) can be used to perform the services of traditional Intelligent Network protocols, as well as additional services.
A Graphene Nanoprobe for Rapid, Sensitive, and Multicolor Fluorescent DNA Analysis (2010)

Abstract Coupling nanomaterials with biomolecular recognition events represents a new direction in nanotechnology toward the development of novel molecular diagnostic tools. Here a graphene oxide (GO)‐based multicolor fluorescent DNA nanoprobe that allows rapid, sensitive, and selective detection of DNA targets in homogeneous solution by exploiting interactions between GO and DNA molecules is reported. Because of the extraordinarily high quenching efficiency of GO, the fluorescent ssDNA probe exhibits minimal background fluorescence, while strong emission is observed when it forms a double helix with the specific targets, leading to a high signal‐to‐background ratio. Importantly, the large planar surface of GO allows simultaneous quenching of multiple DNA probes labeled with different dyes, leading to a multicolor sensor for the detection of multiple DNA targets in the same solution. It is also demonstrated that this GO‐based sensing platform is suitable for the detection of a range of analytes when complemented with the use of functional DNA structures.
Flavanones inhibit the clonogenicity of HCT116 cololectal cancer cells (2011)

Naringenin has been shown to display various biological effects such as antioxidant, anticancer, anti-inflammatory, and antiviral activities. Taxifolin inhibits the production of lipopolysaccharide-induced prostaglandin E, and fustin suppresses the activity of acetylcholinesterase. They all belong to flavanone which is a class of flavonoids with a C6-C3-C6 skeleton. Since the anticancer activities of flavanone derivatives have rarely been reported, we examined the effects of 26 flavanone derivatives on HCT116 colorectal cancer cells. Our results suggest that flavanone derivatives control the expression of cell cycle regulatory proteins, which blocks G1 cell cycle progression and inhibits the clonogenicity of HCT116 cells. In addition, in order to design flavanone derivatives that show better anticancer activity, structure-activity relationships were examined.
Structural Optimization of a Wearable Deep Body Thermometer: From Theoretical Simulation to Experimental Verification (2015)

Deep body temperature (DBT) has yet to be measured continuously in everyday life, even though it is useful in physiological monitoring and chronobiology studies. We tried to address this issue by developing a transcutaneous thermometer based on the dual-heat-flux method (DHFM) invoking the principle of heat transfer, for which measurement error was mitigated by elaborate design. First, a structural modification based on the original design of the DHFM was implemented by the finite element method. Based on the results of the simulations, prototypes were then implemented and tested with an experimental system that mimicked the thermometer being applied to skin. The simulation phase proposed the adoption of an aluminum cover to boost measurement accuracy and suggested that thermometers of different height be chosen according to specified requirements. The results of the mock-up experiments support the modification put forward in the simulation phase: the standard type (15 mm in height) achieved the accuracy with error below 0.3°C while the thin type (9 mm in height) attained accuracy with error less than 0.5°C under normal ambient temperature ranging from 20 to 30°C. Even though the design should also be examined in vivo , it is believed that this study is an important step in developing a practical noninvasive deep body thermometer.
Biostatistics without the mathematics. Part 2 - Inferential statistics (2013)

The central maxim of inferential statistics is generalization from the sample to the population. Descriptive statistics describes a sample data set (which is an organized collection of data on a common theme), depicting its central tendency and dispersion, while inferential statistics focuses on drawing inferences regarding the population by analyzing the sample data. To do this it resorts largely to the hypothesis testing approach whose goal is to reject the null hypothesis. The result is usually returned as a p value that denotes the maximum probability of getting the observed result assuming the null hypothesis to be true. A large number of hypothesis tests are available and the one to be applied depends upon the research question, the nature of the variables of interest and the number of groups that are to be compared. The standard Student’s t-test is used for comparing the means of two independent or paired data sets that are normally distributed. One-way analysis of variance (ANOVA) and its counterpart in repeated measures extends the comparison of means to more than two populations. There are non-parametric counterparts of each of these tests that compare medians of data sets that are not normally distributed. Categorical variables can be compared between independent groups by chi-square test or Fisher’s exact test, while McNemar’s chi-square test and Cochran’s Q test can be employed for comparing paired proportions. Strength of association between two numerical variables can be quantified by a correlation coefficient, such as Pearson’s product moment coefficient of correlation r or Spearman’s rank-correlation coefficient r, and Kendall’s tau. The relative risk and odds ratio are used to quantify association between two binary categorical variables. The intraclass correlation coefficient can be calculated as a measure of the agreement between related sets of numerical data. The Bland-Altman plot is a graphical method for doing the same. Cohen’s kappa statistic measures agreement between categorical variables. With the increasing availability and user-friendly nature of statistical software, the drudgery associated with statistical computation is now gone, leaving the researcher free to concentrate on the correct application of techniques rather than worry about the calculation. Key words: hypothesis testing, p value, type I error, type II error, parametric tests, non-parametric tests
Adhesive Behavior of Single Carbon Nanotubes (2010)

We examined the adhesion of a carbon nanotube (CNT) tip using a manipulation technique with a transmission electron microscope. In addition, we estimated the maximum normal adhesion possibility of a CNT-based gecko tape. The adhesive behavior of a single isolated CNT to Au solid surfaces has high normal strength (6.84 nN), which has a linear relation to the cross section of a CNT, indicating the mechanism: van der Waals force was inferred from the contact of two flat surfaces. Adhesion measurements conducted on several surface materials verify that the surface chemistry affects adhesive properties of CNT tips.
Dual estimators for position and current sensorless SRM drives based on the decomposed model (2005)

Although development of position sensorless switched reluctance motor drives has gained lots of considerations during the past decade, removing current sensors from the drive, or implementation of a back up system in case of a current sensor failure, has never been discussed in the literature. Based on the decomposed SR model, phase current and rotor position can be referred to as dual variables. This means that using this model and measuring phase voltage, phase current can be estimated from the rotor position and vice versa; however, both cannot be unknown at the same time. This paper proposes, for the first time, dual estimators for rotor position and phase current. These estimators may be utilized to remove sensors for cost reduction as well as back up virtual sensors in a fault resilient drive. The validation results show the effectiveness of the proposed estimators
Epilogue to Part Two (2009)

Our brief look at the historical record has revealed that democracy has been quite rare over the course of human history. Indeed, by modern definitions of democracy it only came into existence at the start of the twentieth century. We do not adopt such a narrow definition of democracy and thus regard Ancient Athens, the Republics of Venice and the Netherlands, and the United States from the time of the country's founding as all democracies of one form or another but with limited voting franchises.
The Effect of Journal Roughness and Foil Coatings on the Performance of Heavily Loaded Foil Air Bearings (2002)

Foil air bearing load capacity tests were conducted to investigate if a solid lubricant coating applied to the surface of the bearing's top foil can function as a break-in coating. Two foil coating materials, a conventional soft polymer film (polyimide) and a hard ceramic (alumina), were independently evaluated against as-ground and worn (run-in) journals coated with NASA PS304, a high-temperature solid lubricant composite coating. The foil coatings were evaluated at journal rotational speeds of 30,000 rpm and at 25 °C. Tests were also performed on a foil bearing with a bare (uncoated) nickel-based superalloy top foil to establish a baseline for comparison. The test results indicate that the presence of a top foil solid lubricant coating is effective at increasing the load capacity performance of the foil bearing. Compared to the uncoated baseline, the addition of the soft polymer coating on the top foil increased the bearing load coefficient by 120 percent when operating against an as-ground journal surface and 85% against a run-in journal surface. The alumina coating increased the load coefficient by 40 percent against the as-ground journal but did not have any effect when the bearing was operated with the run-in journal. The results suggest that the addition of solid lubricant films provide added lubrication when the air film is marginal, indicating that as the load capacity is approached foil air bearings transition from hydrodynamic to mixed and boundary lubrication.
Monoclonal antibodies against the human mannose receptor as a specific marker in flow cytometry and immunohistochemistry for macrophages (1997)

Recently we developed mouse monoclonal antibodies (mAb) against the isolated human 175-kDa mannose receptor. In the present study we tested whether these mAb are suitable for the detection of the mannose receptor on cultured macrophages using flow cytometry and on cells in human tissues using immunohistochemistry. Human monocytes did not react with the mAb in flow cytometry. Mannose receptor expression became detectable on monocytes cultured for 3 days (macrophages), and was maximal from 4 days onward. The mannose receptor was up-regulated on dexamethasone-treated (immunosuppressed) macrophages, and down-regulated on lipopolysaccharide-treated (activated) macrophages. Immunohistochemically the staining pattern of our mAb was compared with the marker of monocytes/macrophages KP1. In a bone marrow smear, only macrophages were stained with our mAb, whereas all myeloid cells were stained with KP1. In the thymus and lymph node, mannose receptor-positive branched cells (macrophages and dendritic cells) were detected in connective tissue, thymus cortex (not medulla), and in the T cell area (not the B cell area) of lymph nodes, whereas KP1 stained branched cells in all areas. It was concluded that the mAb are useful tools in flow cytometry and immunohistochemistry for the specific detection of cells expressing mannose receptor.
N-Channel MOSFET field protection by nonmasked boron ion implantation (1973)

A boron ion implant protects the thick-oxide field regions of n-channel MOSFETs by penetrating the thick oxide and increasing the doping at the silicon interface. Active devices, with thin oxide in their gate regions, are not greatly affected because the implant lies buried beneath their channels. The method is compatible with standard four-mask FET processing, adding no new masking steps. Measurements of field properties were made on FET devices with thick oxides in their gate regions. Measurements are also reported for normal thin-oxide devices. The implant effect is characterized by the difference in properties between implanted and unimplanted devices on the same wafers. the degree of protection as a function of both implant dose and energy is reported over a wide range. The results are compared with calculations that accurately account for the nonuniform profile, with good agreement. Field protection, as measured by the thick-oxide threshold voltage, has a sharp peak at a well-defined energy. At energies below the peak, too many ions stop in the oxide; above the peak, they lie too deep in the silicon. Threshold voltages and transconductance of thin-oxide devices are unaffected, but the threshold voltage sensitivity to substrate bias is increased somewhat.
Meniscal Measurements of T1<sub>ρ</sub>and T2 at MR Imaging in Healthy Subjects and Patients with Osteoarthritis (2008)

Meniscal T1(rho) and T2 values correlate with clinical findings of OA and can be used to differentiate healthy subjects from patients with mild or severe OA.
Protection of Woodchucks from Infection with Woodchuck Hepatitis Virus by Immunization with Recombinant Core Protein (1989)

Woodchucks were immunized with recombinant woodchuck hepatitis virus (WHV) core antigen (WHcAg) to investigate whether such immunization protects against WHV infection. The C gene was cloned into a pUC12 vector and expressed in Escherichia coli. Core particles purified by sucrose and CsCl gradient centrifugation had a buoyant density of 1.37 g/ml which corresponded to the density of WHcAg particles present in chronically infected liver. Two animals immunized with the recombinant antigen developed high antibody titres and were protected against infection after challenge with WHV. The surface antigen (WHsAg) and WHV DNA were not detected in the sera of immunized animals after challenge and these animals did not develop anti-WHs. Three control animals developed a typical WHV infection. The protection from WHV infection may depend not on the presence of antibodies against the core protein but on a cellular immune response to WHcAg.
Lipopolysaccharide (LPS)-binding Protein Inhibits Responses to Cell-bound LPS (2003)

Lipopolysaccharide (LPS)-binding protein (LBP) is an acute phase reactant that may play a dual role in vivo, both potentiating and decreasing cell responses to bacterial LPS. Whereas low concentrations of LBP potentiate cell stimulation by transferring LPS to CD14, high LBP concentrations inhibit cell responses to LPS. One inhibitory mechanism involves the ability of LBP to neutralize LPS by transferring it to plasma lipoproteins, whereas other inhibitory mechanisms, such as the one described here, do not require exogenous lipoproteins. Here we show that LBP can inhibit monocyte responses to LPS that has already bound to membrane-bound CD14 (mCD14) on the cell surface. LBP caused rapid dissociation of LPS from mCD14 as measured by the ability of LBP to inhibit cross-linking of a radioiodinated, photoactivatable LPS derivative to mCD14. Whereas LBP removed up to 75% of the mCD14-bound LPS in 10 min, this was not accompanied by extensive release of the LPS from the cells. The cross-linking data suggest that much of the LPS that remained bound to the cells was associated with LBP. The ability of LBP to inhibit cell responses could not be explained by its effect on LPS internalization, because LBP did not significantly increase the internalization of the cell-bound LPS. In cell-free LPS cross-linking experiments, LBP inhibited the transfer of LPS from soluble CD14 to soluble MD-2. Our data support the hypothesis that LBP can inhibit cell responses to LPS by inhibiting LPS transfer from mCD14 to the Toll-like receptor 4-MD-2 signaling receptor.
Local chain configuration dependence of the mechanisms of analogous reactions of PVC, 7. Nucleophilic substitution with potassium 2-ethylhexylthioglycolate and related effects on Tg (2000)

The nucleophilic substitution reaction of poly(vinyl chloride) (PVC) with potassium 2-ethylhexylthioglycolate (KEHTG) was performed in a cyclohexanone solution. The evolution of unreacted iso-, hetero- and syndiotactic triad contents with the degree of substitution was observed by means of 13C NMR spectroscopy. Due to steric hindrance the fraction of mmr tetrads which react occasionally by the central chlorine of the mr triad instead of the mm is smaller than that found previously for sodium benzenethiolate (NaBT) and sodium thiobenzoate (NaTB), but not nil as in the case of sodium 2-mercaptobenzothiazolate (NaMBT). Correspondingly, the increase in stereoselective character of the reaction as the result of the nucleophile bulkiness is found to approximate to that observed for NaMBT. This conclusion was confirmed on the basis of FTIR results and takes the molecular microstructure-based mechanisms of substitution of PVC, as discussed in previous work, an important step further. From the evolution of Tg with the degree of conversion it follows that Tg varies with the degree of substitution in a similar way to the ratio between the extent to which mmr and rrmr structures intervene in the substitution reaction, thereby providing valuable information regarding the Tg /microstructure relationship as discussed in recent papers.
Cytotoxic activity and lymphokine production of T cell receptor (TCR)-<i>alpha</i>  <i>beta</i>+ and TCR-gamma delta+ cytotoxic T lymphocyte (CTL) clones recognizing HLA-A2 and HLA-A2 mutants. Recognition of TCR-gamma delta+ CTL clones is affected by mutations at positions 152 and 156. (1990)

TCR-gamma delta+ CTL clones were generated from CD4-CD8- T cells that were stimulated twice with the cell line JY. Either IL-2 or IL-4 was used as growth factor. A number of TCR-gamma delta+ clones were found to lyse the stimulator cell line JY. Two of these clones secreted N alpha-benzyloxycarbonyl-L-lysine thiobenzyl ester serine esterase activity after stimulation with JY cells. The cytotoxic activity of these two clones was blocked by a mAb specific for HLA-A2. Moreover, these two TCR-gamma delta+ clones selectively lysed human fibroblast line M1 and murine P815 cells transfected with DNA fragments encoding HLA-A2 but not those transfected with HLA-B7 encoding DNA, indicating that these clones recognize HLA-A2. Analysis of the recognition of HLA-A2 by using target cells transfected with mutated HLA-A2 encoding genes revealed that the nature of the amino acid at position 152 of the molecule is critical for recognition of the TCR-alpha beta+ as well as the TCR-gamma delta+ CTL clones since replacement of Val for Ala at that position resulted in abrogation of recognition of one TCR-gamma delta+ and one TCR-alpha beta+ clone and substitution of Val for Glu affected recognition of all clones. Substitution of Leu for Trp at position 156 abrogated recognition by one TCR-gamma delta+ and one TCR-alpha beta+ T cell clone, but recognition by the other clones was not changed. All clones were able to secrete IL-2, IFN-gamma, and GM-CSF but not IL-4 after activation.