gebhart/patrepeval huggingface dataset:
Global variation in the genetic and biochemical basis of diamondback moth resistance to <i>Bacillus thuringiensis</i> (1997)

Insecticidal proteins from the soil bacterium Bacillus thuringiensis (Bt) are becoming a cornerstone of ecologically sound pest management. However, if pests quickly adapt, the benefits of environmentally benign Bt toxins in sprays and genetically engineered crops will be short-lived. The diamondback moth (Plutella xylostella) is the first insect to evolve resistance to Bt in open-field populations. Here we report that populations from Hawaii and Pennsylvania share a genetic locus at which a recessive mutation associated with reduced toxin binding confers extremely high resistance to four Bt toxins. In contrast, resistance in a population from the Philippines shows multilocus control, a narrower spectrum, and for some Bt toxins, inheritance that is not recessive and not associated with reduced binding. The observed variation in the genetic and biochemical basis of resistance to Bt, which is unlike patterns documented for some synthetic insecticides, profoundly affects the choice of strategies for combating resistance.
Nonlinear Adjustment towards Purchasing Power Parity in ASEAN Exchange Rates (2004)

The major finding of this study is that the long run purchasing power parity (PPP) deviations of the major ASEAN exchange rates exhibit nonlinear adjustment which may be characterised by the Smooth Transition Autoregressive (STAR) model. This finding warrants us that policy decision based on inappropriate linear studies may not be effectiveness. Besides, exchange rates with deviations with higher speed of adjustment are found to be more pruned to currency crisis.
Tabulation of dose equivalent per microcurie-day for source and target organs of an adult for various radionuclides (1974)

Data are tabulated on the radiation dose equivalent per microcurie-day for source and target organs of a human adult for 100 radionuclides. These are listed at the end of the volume. Included are several radionuclides where the parent has a daughter radionuclide of physical half-life less than five minutes. In such cases separate S tables are given for the parent and for the daughter as well as a composite table which contains S values for the parent plus S values for the daughter weighted according to the percent decay via the daughter. (CH)
Agonistic Anti-TIGIT Treatment Inhibits T Cell Responses in LDLr Deficient Mice without Affecting Atherosclerotic Lesion Development (2013)

Despite the inhibition of splenic T cell responses, agonistic anti-TIGIT treatment does not affect initial atherosclerosis development, possibly due to increased activity of dendritic cells.
High levels of chronic immune activation in both CD8 and CD4 T cell compartments negatively influences HCV treatment outcome in HCV/HIV-1 co-infection (128.17) (2009)

Abstract Chronic immune activation is strongly associated with Human Immunodeficiency virus 1 (HIV-1) disease progression. Here, we have investigated the state of T cell immune activation, as well as T cell responses to hepatitis C virus (HCV), in patients with HCV/HIV-1 co-infection on effective anti-retroviral therapy (ART). Co-infected subjects displayed elevated immune activation as determined by CD38 expression in both CD4 and CD8 T cells, as compared to mono-infected control groups. HCV-specific T cells in response to HCV antigens tended to be stronger in the co-infected patients with a more pronounced IFNγ profile by CD8 T cells and this group also had higher HCV loads at baseline. Patients who reached a sustained virological response to peg-interferon-α and ribavirin treatment displayed significantly lower pre-treatment levels of chronic T cell activation and a trend towards stronger HCV-specific T cell responses, as compared to patients who failed to clear. Data suggest a link between high levels of chronic immune activation, poor adaptive immune responses and HCV treatment failure in HCV/HIV-1 co-infected subjects. We suggest that the high level of chronic immune activation may provide a clue as to why patients co-infected with these viruses in general display faster viral disease progression. This work was supported by the Swedish Research Council, SIDA and the Swedish National Board of Health and Welfare.
Application of high‐resolution ESI and MALDI mass spectrometry to metabolite profiling of small interfering RNA duplex (2012)

We investigated the application of a high-resolution Orbitrap mass spectrometer equipped with an electrospray ionization (ESI) source and a matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometer to the metabolite profiling of a model small interfering RNA (siRNA) duplex TSR#34 and compared their functions and capabilities. TSR#34 duplex was incubated in human serum in vitro, and the duplex and its metabolites were then purified by ion exchange chromatography in order to remove the biological matrices. The fraction containing the siRNA duplex and its metabolites was collected and desalted and then subjected to high-performance liquid chromatography (HPLC) equipped with a reversed phase column. The siRNA and its metabolites were separated into single strands by elevated chromatographic temperature and analyzed using the ESI-Orbitrap or the MALDI-TOF mass spectrometer. Using this method, the 5' and/or 3' truncated metabolites of each strand were detected in the human serum samples. The ESI-Orbitrap mass spectrometer enabled differentiation between two possible RNA-based sequences, a monoisotopic molecular mass difference which was less than 2 Da, with an intrinsic mass resolving power. In-source decay (ISD) analysis using a MALDI-TOF mass spectrometer allowed the sequencing of the RNA metabolite with characteristic fragment ions, using 2,4-dihydroxyacetophenone (2,4-DHAP) as a matrix. The ESI-Orbitrap mass spectrometer provided the highest mass accuracy and the benefit of on-line coupling with HPLC for metabolite profiling. Meanwhile, the MALDI-TOF mass spectrometer, in combination with 2,4-DHAP, has the potential for the sequencing of RNA by ISD analysis. The combined use of these methods will be beneficial to characterize the metabolites of therapeutic siRNA compounds.
P‐111: Voltage and Rubbing Angle Dependent Behavior of the Single Cell Gap Transflective Fringe Field Switching (FFS) Mode (2005)

Abstract Rubbing angle‐dependent electro‐optic characteristics in the single cell gap transflective FFS mode have been studied. The adjustment of the rubbing angle reduces the difference in voltage‐dependent reflectance and transmittance curves.
Fast, Ultrasensitive Virus Detection Using a Young Interferometer Sensor (2006)

We report the application of an integrated optical Young interferometer sensor for ultrasensitive, real-time, direct detection of viruses. We have validated the sensor by detecting herpes simplex virus type 1 (HSV-1), but the principle is generally applicable. Detection of HSV-1 virus particles was performed by applying the virus sample onto a sensor surface coated with a specific antibody against HSV-1. The performance of the sensor was tested by monitoring virus samples at clinically relevant concentrations. We show that the Young interferometer sensor can specifically and sensitively detect HSV-1 at very low concentrations (850 particles/mL). We have further demonstrated that the sensor can specifically detect HSV-1 suspended in serum. Extrapolation of the results indicates that the sensitivity of the sensor approaches the detection of a single virus particle binding, yielding a sensor of unprecedented sensitivity with wide applications for viral diagnostics.
CEA monitoring in colorectal cancer. What you should know. (2006)

Carcinoembryonic antigen (CEA) monitoring in patients with stage I-IV colorectal cancer has been, and remains, a controversial issue in oncology practice. Recommendations vary from bimonthly monitoring to no monitoring in the surveillance setting (for stage I-III disease). In the metastatic setting, there are no clear guidelines for CEA follow-up, although continued monitoring in such patients is common in the oncology community. This manuscript reviews the accuracy of CEA testing, its value as a prognostic indicator, and its role in surveillance and response assessment. The limitations of the test in the adjuvant and metastatic settings are illustrated through several case reports from the Colorectal Oncology Clinic at Roswell Park Cancer Institute. Guidelines for CEA monitoring are provided, based on a detailed literature review and institutional experience.
Carbamoylmethylphosphoryl Derivatives as Actinide Extractants (1983)

Three classes of carbamoylmethylphosphoryl extractants were studied for their ability to extract selected tri-, tetra-, and hexavalent actinides from nitric acid. The three extractants are dihexyl-N,N-diethylcarbamoylmethylphosphonate (DHDECMP), hexyl hexyl-N,N-diethylcarbamoylmethylphosphinate (HHDECMP), and octyl(phenyl)-N,N-diisobutylcarbamoylmethylphosphine oxide OφD[IB]CMPO. The above three extractrants were compared on the basis of nitric acid and extractant dependencies for Am(III), solubility of complexes on loading with Nd(III) and U(VI), and selectivity of actinide(III) over fission products. The influence of temperature on DAm from LiNO3 (10-2M HNO3) and from 3 M HNO3 using dilute solutions of DHDECMP, HHDECMP, OφD[IB]CMPO in o-xylene showed that the increase in DAm in the series phosphone-phosphinate-phosphine oxide was due primarily to an increase in the enthalpy of extraction. The above information was used to develop conceptual flowsheets for the extraction of all of the actinides (U, Np, Pu, Am, and Cm) from high-level liquid waste from PUREX processing using 0.4 M 0φD[IB]CMP0 in DEB and for the extraction of all of the actinides from dissolved spent LWR fuel using 0.8 M DHDECMP in DEB. In both flowsheets, no oxidation state of Pu is necessary since the III, IV, and VI state extract into the organic phase.
hi<scp>PSC</scp>‐derived <scp>iMSC</scp>s: NextGen <scp>MSC</scp>s as an advanced therapeutically active cell resource for regenerative medicine (2016)

Mesenchymal stem cells (MSCs) are being assessed for ameliorating the severity of graft-versus-host disease, autoimmune conditions, musculoskeletal injuries and cardiovascular diseases. While most of these clinical therapeutic applications require substantial cell quantities, the number of MSCs that can be obtained initially from a single donor remains limited. The utility of MSCs derived from human-induced pluripotent stem cells (hiPSCs) has been shown in recent pre-clinical studies. Since adult MSCs have limited capability regarding proliferation, the quantum of bioactive factor secretion and immunomodulation ability may be constrained. Hence, the alternate source of MSCs is being considered to replace the commonly used adult tissue-derived MSCs. The MSCs have been obtained from various adult and foetal tissues. The hiPSC-derived MSCs (iMSCs) are transpiring as an attractive source of MSCs because during reprogramming process, cells undergo rejuvination, exhibiting better cellular vitality such as survival, proliferation and differentiations potentials. The autologous iMSCs could be considered as an inexhaustible source of MSCs that could be used to meet the unmet clinical needs. Human-induced PSC-derived MSCs are reported to be superior when compared to the adult MSCs regarding cell proliferation, immunomodulation, cytokines profiles, microenvironment modulating exosomes and bioactive paracrine factors secretion. Strategies such as derivation and propagation of iMSCs in chemically defined culture conditions and use of footprint-free safer reprogramming strategies have contributed towards the development of clinically relevant cell types. In this review, the role of iPSC-derived mesenchymal stromal cells (iMSCs) as an alternate source of therapeutically active MSCs has been described. Additionally, we also describe the role of iMSCs in regenerative medical applications, the necessary strategies, and the regulatory policies that have to be enforced to render iMSC's effectiveness in translational medicine.
Determination of (13C)urea enrichment by gas chromatography/mass spectrometry and gas chromatography/isotope ratio mass spectrometry (1994)

We present gas chromatographic/mass spectrometric and gas chromatographic/isotope ratio mass spectrometric assays of the 13C enrichment of plasma urea converted to its dimethylaminomethylene derivative. The limits of sensitivity of the two techniques are 0.2% and 0.02%, respectively. The techniques were tested in rats and humans infused with (13C)urea or (3-13C)lactate. (13C)Urea enrichment during the infusion of (3-13 C)lactate in humans was not detectable by gas chromatography/mass spectrometry but was easily measured by gas chromatography/isotope ratio mass spectrometry. These assays should be useful for clinical investigations, in which the incorporation of a (13C)gluconeogenic substrate into glucose must be corrected for the incorporation of 13CO2 derived from the oxidation of the substrate. This correction involves measuring the low-level 13C enrichment of urea.
Structure and Mechanical Properties of (CrAl)N and (CrAlSiY)N Coatings Prepared by Asymmetrical Bipolar DC Magnetron Sputtering (2016)

Composite (CrAl)N and (CrAlSiY)N hard coatings were deposited on 1Cr11Ni2W2MoV steel substrates by arc ion plating system under negative bias of 0 V, 100 V and 200V respectively. Pulsed bias gave rise to the deviation of elements, the decreased deposition rate, and the change of the preferred orientation, the crystalline refining, the dense structure and improved hardness. The doping with small amount of Si and Y did not change the phase structure, but (CrAlSiY)N coatings possessed higher hardness value than (CrAl)N coatings in case of the same deposition parameters. The harder coatings exhibited the lower toughness and the lower scratch critical load (Lc).
Morphological and physical property effects for solvent cast films of poly‐2, 5(6) benzimidazole (1978)

Abstract A polybenzimidazole having the structural repeat unit magnified image and designated AB‐PBI was formed into films by casting or precipitating from dilute solutions. Selected films were swollen in a plasticizing medium arid drawn about 2X. All films were dried in a vacuum oven to aid in the removal of residual solvent and moisture. Wide angle X‐ray scattering (WAXS) was used to show the type of ordering found in this material and to indicate the extent of molecular orientation. Neither a glass transition nor a crystalline melting point has been observed for this polymer, A Perkin‐Elmer DSC was used to scan the temperature range from −150 to H‐400°C in search of secondary transitions. The rheovibron proved more sensitive and a transition was located in the vicinity of −60°C. An activation energy‐was determined. The morphology of this polymer is subject to speculation. The ability of the chain to adopt a linear conformation leads to the possibility of a liquid‐crystalline nature in solution. A model based on the data in hand is suggested. Stress‐strain data was used to compare the mechanical properties of films prepared by several methods as well as to demonstrate the effect of orientation on strength.
Population Structure of the<i>Bacillus cereus</i>Group as Determined by Sequence Analysis of Six Housekeeping Genes and the<i>plcR</i>Gene (2004)

The population structure of the Bacillus cereus group (52 strains of B. anthracis, B. cereus, and B. thuringiensis) was investigated by sequencing seven gene fragments (rpoB, gyrB, pycA, mdh, mbl, mutS, and plcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in the plcR tree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. The plcR gene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of the plcR gene may be frequent. The homogeneity of B. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.
Experimental investigation of the combustive sound source (1995)

In this paper, we describe a unique low frequency underwater sound source called the combustive sound source (CSS). In this device, a combustible gas mixture is captured in a combustion chamber and ignited with a spark. The ensuing combustion produces expanding gases which in turn produce high intensity, low frequency acoustic pulses. With high-speed motion pictures of the CSS event, we relate the motion of the bubble to the acoustic waveform. We also compare the measured first bubble period in the CSS pressure signature with the predictions of the Rayleigh-Willis equation, including the dependence of the radiated acoustic waveform on the volume and depth of the bubble. Measurements of the first bubble period agree with Rayleigh-Willis theory in trend, but not in absolute value. In addition, we discuss the variation of the acoustic output with the fuel/oxygen mixture. Finally, several other factors that affect the acoustic output of CSS are discussed. These include the shape of the CSS combustion chamber, the type of oxidizer and fuel, and the ignition source.
Transactive Energy Auction with Hidden User Information in Microgrid (2016)

This research proposes a novel auction mechanism for transactive energy exchange between buyers and sellers, modeled as agents in a microgrid. The mechanism is implemented by a separate microgrid controller (MC) agent, and requires big data flow with the other agents through an iterative bidding process. Although private user information remains hidden to the MC, a theoretical analysis shows that under the assumption of convexity of the agents utilities, the proposed auction is still able to maximize the social welfare (SW), i.e. the aggregate utilities of the agents. In addition, it is shown that the mechanism exhibits the key desirable features of individual rationality and weak budget balance, guaranteeing that neither the payoff to any agent nor the net monetary revenue after termination, is negative. The proposed approach also incorporates a mechanism to redistribute the sellers shares in a fair manner. As an example, a maximum entropy based fair redistribution scheme is addressed. The theoretical analysis reported here is accompanied by extensive set of simulations that illustrate the various aspects of the proposed mechanism.
A skill refinement learning model for rule-based expert systems (1990)

Research in equipping rule-based expert systems with skill refinement behavior by utilizing the recognize-act control mechanism is described. An overview of expert system skill refinement is provided. A skill refinement model for generating plans is then presented. Two closely coupled and mutually supportive mechanisms characterize this model: a rule-selecting mechanism (corresponding to a buyer-selecting procedure) that dynamically incorporates the concept of multiple selection/preference criteria into the conflict resolution process, and an economics-based credit assignment mechanism (corresponding to a capital reallocation procedure) that uses an inference engine's experiences to update the potentiality of each rule participating in the problem-solving process. A mathematical description of the model is given. An example is provided to illustrate the inference engine's skill refinement and the applicability of the model is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Radioimmunoassay of Follicle-Stimulating Hormone (FSH)-Suppressing Protein (FSP): Stimulation of Bovine Granulosa Cell FSP Secretion by FSH* (1991)

A RIA for bovine (b) FSH-suppressing protein (FSP) was developed using an antiserum raised in a rabbit to purified 39-kDa bFSP, iodinated 35-kDa FSP as tracer, and purified 35-kDa bFSP as standard. Purified 35-kDa FSP was iodinated using the iodogen procedure, and the iodinated FSP was purified by dye affinity chromatography. After a logit log-dose transformation of the dose-response curves, parallel displacement lines were observed between 31-, 35-, and 39-kDa FSP, bovine follicular fluid, bovine granulosa cell culture medium, and medium from bovine granulosa cells stimulated with bFSH. The specificity of the assay was investigated by comparing the immunoassay levels of FSP with in vitro bioassay levels based on the ability of FSP/inhibin to suppress FSH in rat anterior pituitary cell cultures in fractions obtained throughout the purification procedure of FSP from bovine follicular fluid. This demonstrated that 1) the FSP immunoactivity was associated with in vitro bioactivity in all fractions of the purification procedure; 2) a number of inhibin-related and other proteins showed low (less than 0.5%) or nondetectable cross-reactivity in the RIA; and 3) the in vitro biological to immunological ratios for 31-, 35-, and 39-kDa FSP were similar, indicating that the RIA detects all forms of purified bFSP. The secretion of FSP by bovine granulosa cells in culture was investigated in the presence and absence of bFSH and bLH, respectively. FSP production was proportional to granulosa cell number and decreased from highest levels at 24 h to lowest levels at 96 h of culture. The addition of either bFSH or 8-bromo-cAMP to the culture medium stimulated FSP production by a factor of 2-3 at 48 and 72 h of culture, while the addition of bLH had no effect on FSP production. Theca interna tissue cultured under the same conditions did not produce FSP. In contrast to FSP, stimulation of bovine granulosa cells with bFSH or bLH had no effect on inhibin production during the 96 h of culture, while the addition of bFSH and bLH caused a stimulation of progesterone production at 48 and 72 h of culture. It is concluded that 1) the RIA described here is specific for all mol wt forms of bFSP; 2) FSP was secreted by bovine granulosa cells and not thecal cells in vitro; and 3) FSP secretion by bovine granulosa cells in vitro is regulated by bFSH and not bLH.
Antibody humanization by molecular dynamics simulations—<i>in‐silico</i> guided selection of critical backmutations (2016)

Monoclonal antibodies represent the fastest growing class of biotherapeutic proteins. However, as they are often initially derived from rodent organisms, there is a severe risk of immunogenic reactions, hampering their applicability. The humanization of these antibodies remains a challenging task in the context of rational drug design. "Superhumanization" describes the direct transfer of the complementarity determining regions to a human germline framework, but this humanization approach often results in loss of binding affinity. In this study, we present a new approach for predicting promising backmutation sites using molecular dynamics simulations of the model antibody Ab2/3H6. The simulation method was developed in close conjunction with novel specificity experiments. Binding properties of mAb variants were evaluated directly from crude supernatants and confirmed using established binding affinity assays for purified antibodies. Our approach provides access to the dynamical features of the actual binding sites of an antibody, based solely on the antibody sequence. Thus we do not need structural data on the antibody-antigen complex and circumvent cumbersome methods to assess binding affinities. © 2016 The Authors Journal of Molecular Recognition Published by John Wiley & Sons Ltd.