gebhart/patrepeval huggingface dataset:
Molecular-Docking-Guided Design, Synthesis, and Biologic Evaluation of Radioiodinated Quinazolinone Prodrugs (2007)

Enzyme-mediated cancer imaging and therapy (EMCIT) is a novel approach in which radioactive water-soluble molecules are precipitated in vivo following their hydrolysis by extracellular enzymes overexpressed by cancer cells. AutoDock 3.0 was used to model the interaction-binding between a series of iodinated quinazolinone derivatives and human placental alkaline phosphatase (PLAP, crystal structure in the Protein Data Bank) and to assess the effects of structural modification of the derivatives. Ammonium 2-(2',4'-diphosphoryloxyphenyl)-6-iodo-4-(3H)-quinazolinone (IQ2-P,4-P), having the most favorable calculated inhibition constant, was synthesized and characterized. Concentration-dependent, PLAP-mediated conversion of IQ2-P,4-P (4)/125IQ2-P,4-P (6) to water-insoluble 2-(2',4'-dihydroxyphenyl)-6-[127I/125I]iodo-4-(3H)-quinazolinone (127IQ2-OH,4-OH (2)/125IQ2-OH,4-OH (7)) was observed in solution. Autoradiography indicated that 6 is hydrolyzed by human cancer cells and the resulting 7 precipitates on exterior cell surfaces. Biodistribution studies in mice demonstrated that 6 is minimally retained by normal tissues. The findings support the validity of the EMCIT approach.
Seamless Soft Handoff in Mobile Ad Hoc Networks (2007)

In our MILCOM 2006 paper [1], we have presented an integrated architecture for seamless soft handoff in mobile ad hoc networks, where various managers residing on multiple layers are proposed to tackle handoff issues in a cross-layer and cooperative manner. In this paper, we first demonstrate the handoff performance under nontrivial node mobility. Simulations show that our handoff scheme provides practically equivalent results as the benchmark with no handoff, which indicates that our scheme is quite resistant to node mobility. Next we investigate the general handoff problems where each node can possess multiple radios and nodes are randomly dispersed in some region. In this case, the network topology forms a multi-linked graph (multigraph). By converting the multigraph to simple graphs, our extensive simulations show that our scheme can render low latency, low overhead handoff with minimum packet loss. Finally, we study the synergies with IEEE 802.21 and describe how to integrate IEEE 802.21 into our multi-layer architecture.
PBA–PMMA 3‐Arm Star Block Copolymer Thermoplastic Elastomers (2008)

Abstract A series of well‐defined poly(methyl methacrylate)‐ block ‐poly(butyl acrylate) 3‐arm star block copolymers have been synthesized by ATRP. The incorporation of polar hard segment of PMMA was made possible with the aid of halogen exchange technique. Phase‐separated morphology of cylindrical PMMA domains hexagonally arranged in the pBA matrix was observed by small angle X‐ray scattering in all studied materials. The mechanical and thermal properties of the PBA–PMMA 3‐arm star block copolymers have been thoroughly characterized and their thermoplastic elastomer behavior was studied. It was found that the tensile properties of these materials are comparable with those of their linear ABA type block copolymer counterparts with similar compositions. magnified image
Biochemical Evidence for the Presence of a Single CD3δ and CD3γ Chain in the Surface T Cell Receptor/CD3 Complex (2004)

The T cell antigen receptor (TCR) consists of an alphabeta heterodimer and associated invariant CD3gamma, delta, epsilon, and zeta chains (TCR/CD3 complex). The general stoichiometry of the receptor complex, which is believed to be one molecule each of TCRalpha, TCRbeta, CD3gamma, and CD3delta and two molecules each of CD3epsilon and CD3zeta, is not clearly understood. Although it has been shown that there are two chains of CD3epsilon and CD3zeta, the stoichiometry of CD3gamma or CD3delta chains in the surface antigen receptor complex has not been determined. In the present study, transgenic mice expressing an altered form of mouse CD3delta and CD3gamma were employed to show that the surface TCR complexes contain one molecule each of CD3delta and CD3gamma. Thymocytes from wild type and CD3 chain transgenic mice on the appropriate knockout background were surface-biotinylated and immunoprecipitated using a specific antibody. The immunoprecipitates were resolved in two dimensions under nonreducing/reducing conditions to determine the stoichiometry of CD3delta and CD3gamma in the surface antigen receptor complex. Our data clearly show the presence of one molecule each of CD3delta and CD3gamma in the surface TCR/CD3 complex.
Hospital Preparedness for Weapons of Mass Destruction Incidents: An Initial Assessment (2004)

To elucidate hospital preparedness for weapons of mass destruction (WMD), we performed an initial assessment in the emergency response hospitals in Taipei. Interviews of hospital personnel were performed in 10 hospitals. Data collected included level of preparedness, mass decontamination capabilities, training of hospital staff, and facility security capabilities. No respondents believed their sites were fully prepared to handle a biologic incident, 70% (7/10) believed they were not prepared to manage a chemical weapons incident, and 80% believed they were unprepared for a radio-nuclear incident. Were a WMD incident to occur, 50% of respondents stated a single-room decontamination process would be set up. WMD preparedness had been incorporated into hospital response plans by 40% (4/10) of the institutions. Fifty percent (5/10) believed their emergency department could manage 20 to 50 casualties at once. No facility had stockpiled any medications for WMD treatment. All facilities had established networks of communication. No hospital has prepared media statements specific to WMD. Thirty percent (3/10) stated that their hospital staff had some training in WMD event management. All reported need for WMD-specific training but identified obstacles to achieving this. Sixty percent (6/10) of hospitals had a facility security plan, and 20% were able to perform a so-called isolation plan. None had awareness regarding the threat of a secondary device. Hospitals in this sample do not appear to be prepared to handle WMD events, especially in areas such as mass decontamination, mass medical response, and awareness among health care professionals, health communications, and facility security.(Ann Disaster Med.
Electronic structure of the alkaline-earth silicon nitrides M<sub>2</sub>Si<sub>5</sub>N<sub>8</sub>(M = Ca and Sr) obtained from first-principles calculations and optical reflectance spectra (2000)

Results of first-principles band-structure calculations for the ternary alkalineearth silicon nitrides M 2 Si 5 N 8 (M = Ca and Sr) are presented. In the structures of M 2 Si 5 N 8 (M = Ca, Sr and Ba), the N atoms show connections to two (N [2] ) and three (N [3] ) neighbouring silicon tetrahedral centres. Calculations show that the local electronic structure is strongly dependent on the local chemical bonding. The valence band is dominated by N 2p hybridized with the s, p states of the alkaline-earth-metal and silicon atoms. The upper part of the valence band is dominated by the 2p states of N [2] atoms, while the N [3] 2p states lie about 2 eV below the Fermi level. The bottom of the conduction band consists of the N 3s characters hybridized with s orbitals of the alkaline-earth metals, while the s character of Si atoms is higher in energy. Sr 2 Si 5 N 8 is a semiconductor with a direct energy gap at , while Ca 2 Si 5 N 8 is an indirect semiconductor. Optical diffuse reflectance spectra show an energy gap of 4.9 eV for Ca 2 Si 5 N 8 , 4.5 eV for Sr 2 Si 5 N 8 , as well as 4.1 eV for Ba 2 Si 5 N 8 , in fair agreement with the calculated values.
Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data (2003)

This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website.
Stable Modification of PDMS Surface Properties by Plasma Polymerization:  Application to the Formation of Double Emulsions in Microfluidic Systems (2006)

We describe a method based on plasma polymerization for the modification and control of the surface properties of poly(dimethylsiloxane) (PDMS) surfaces. By depositing plasma polymerized acrylic acid coatings on PDMS, we succeeded to fabricate stable (several days) hydrophilic and patterned hydrophobic/hydrophilic surfaces. We used this approach to generate direct and (for the first time in this material) double emulsions in PDMS microchannels.
Effect of Short‐Chain Fatty Acids on the Human Colonic Mucosa in Vitro (1992)

Fermentable dietary fiber components are known to stimulate colonic crypt proliferation. As these compounds are rapidly degraded to short-chain fatty acids (SCFAs) by the anaerobic microflora, the hypothesis was tested that this trophic effect of fiber may be mediated by SCFAs. Biopsies were taken from normal cecal mucosa of 45 individuals during routine colonoscopy. They were incubated for 3 hours with sodium salts of SCFAs at physiological concentrations (three SCFAs = acetate 60 mmol/L + propionate 25 mmol/L + butyrate 10 mmol/L; acetate 60 mmol/L; propionate 25 mmol/L; butyrate 10 mmol/L) or equimolar NaCl (control). Cell proliferation was measured autoradiographically by subsequent pulse labeling with [3H]thymidine (1 hour). The labeling index (number of labeled cells divided by the total number of cells) was computed for the crypt as a whole and for five equal crypt compartments (compartment 1 = crypt base, compartment 5 = crypt surface). Cecal crypt proliferation was raised significantly in all incubation experiments with SCFAs. Butyrate (10 mmol/L, increase + 89%) and propionate (25 mmol/L, + 70%) were as effective in stimulating proliferation as the combination of three SCFAs (+103%), although the effect of acetate (+31%) was minor. Increasing the butyrate concentration to 25 mmol/L or 60 mmol/L did not result in a further increase of cell labeling. SCFAs stimulated proliferation in the basal three crypt compartments only. An expansion of the proliferative zone to compartments 4 and 5 was not observed. SCFAs, especially butyrate and propionate, are luminal trophic factors for the cecal epithelium.(ABSTRACT TRUNCATED AT 250 WORDS)
Comparing top k lists (2003)

Motivated by several applications, we introduce various distance measures between k lists. Some of these distance measures are metrics, while others are not. For each of these latter distance measures: we show that it is a metric in the following two seemingly unrelated aspects:step-(i) it satisfies a relaxed version of the polygonal (hence, triangle) inequality, andstep-(ii) there is a metric with positive constant multiples that bounds our measure above and below.This is not a coincidence---we show that these two notions of almost being a metric are the same. Based on the second notion, we define two distance measures to be equivalent if they are bounded above and below by constant multiples of each other. We thereby identify a large and robust equivalence class of distance measures.Besides the applications to the task of identifying good notions of (dis-)similarity between two top k lists, our results imply polynomial-time constant-factor approximation algorithms for the rank aggregation problem with respect to a large class of distance measures.
Genetic engineering (1996)

Knowing the structure of DNA – and how it works – has created many exciting new possibilities in the world of biotechnology (the use of biological processes to make useful products). Probably the most important technology to flow from Crick and Watson's discovery is genetic engineering.
Adversarial Deep Learning for Robust Detection of Binary Encoded Malware (2018)

Malware is constantly adapting in order to avoid detection. Model-based malware detectors, such as SVM and neural networks, are vulnerable to so-called adversarial examples which are modest changes to detectable malware that allows the resulting malware to evade detection. Continuous-valued methods that are robust to adversarial examples of images have been developed using saddle-point optimization formulations. We are inspired by them to develop similar methods for the discrete, e.g. binary, domain which characterizes the features of malware. A specific extra challenge of malware is that the adversarial examples must be generated in a way that preserves their malicious functionality. We introduce methods capable of generating functionally preserved adversarial malware examples in the binary domain. Using the saddle-point formulation, we incorporate the adversarial examples into the training of models that are robust to them. We evaluate the effectiveness of the methods and others in the literature on a set of Portable Execution (PE) files. Comparison prompts our introduction of an online measure computed during training to assess general expectation of robustness.
Recombination and absorption in n-type gallium arsenide (1992)

This work recounts the efforts to completely characterize recombination, absorption and luminescence in n-type GaAs grown by metal-organic chemical vapor deposition (MOCVD) and doped with selenium to create electron concentrations, n$\sb{\rm o}$, from 1.3 $\times$ 10$\sp{17}$ cm$\sp{-3}$ to 3.8 $\times$ 10$\sp{18}$ cm$\sp{-3}$. To investigate recombination, photoluminescence (PL) decay was observed on double heterostructures (DH's) with thicknesses ranging from 0.25 to 10 $\mu$m. For n$\sb{\rm o}$ $<$ 10$\sp{18}$ cm$\sp{-3}$, recombination is dominated by radiative transitions with no evidence of Shockley-Read-Hall (SRH) recombination. For higher electron concentrations, samples show evidence of SRH recombination as reflected in the intensity dependence of PL decay. Even so, radiative recombination and photon recycling are important for all n$\sb{\rm o}$ studied. No evidence for Auger recombination is found, but an upper limit on the Auger coefficient is determined. Transmission measurements on thin-film DH's were used to deduce the near band edge absorption coefficient, $\alpha$(h$\nu$), over the photon energy range of 1.35 $\le$ h nu $\le$ 1.7 eV. A strong dependence of $\alpha$(h$\nu$) on the electron concentration was found as expected, based on previous work. Differences in the absorption tail, which increase with increasing n$\sb{\rm o}$, were attributed to compensation in the material studied previously. PL decay on thin-film membranes (for which the substrate is removed) yielded lifetimes greater than 1 $\mu$s for n$\sb{\rm o}$ = 1.3 $\times$ 10$\sp{17}$ cm$\sp{-3}$. This lifetime was enhanced three times over that observed with the substrate intact, because of enhanced photon recycling. By suppressing bulk recombination in this manner, it is found that the AlGaAs/GaAs interface recombination velocity, S, has an absolute upper limit of 25 cm/s. A more reasonable value is estimated as S $\le$ 11 cm/s. The absorption and recombination measurements are used to compute B, the radiative recombination coefficient, with self-consistent results. It is found that B decreases significantly with increasing n$\sb{\rm o}$. This is qualitatively in agreement with previous work, but the results differ quantitatively. This work describes completely the near band edge absorption properties and the recombination characteristics of high-quality n-GaAs grown by MOCVD. The results fill a void of understanding of intrinsic recombination in moderately doped n-GaAs and should be of value for the characterization and modeling of GaAs devices.
From under a Green Eyeshade (1995)

Journal Article From under a Green Eyeshade Get access THE EDITOR THE EDITOR Search for other works by this author on: Oxford Academic Google Scholar The Opera Quarterly, Volume 11, Issue 3, 1995, Pages 1–2, https://doi.org/10.1093/oq/11.3.1 Published: 01 September 1995
Normally on photomultiplier gating circuit with reduced post-gate artifacts for use in transient luminescence measurements (1992)

A normally on gating circuit with reduced gate-associated artifacts and improved extinction has been developed for focusing electrode-equipped photomultiplier tubes (PMTs) such as the Thorn EMI, Inc. model 9816. Unlike previous gating methods where the focusing electrode is pulsed negative with respect to the photocathode (PC) to gate the tube off, this method holds the focusing electrode at a constant potential of +80 V with respect to the PC and pulses the first dynode from +80 to −246 V. This technique effectively eliminates post-gate signals induced by PC irradiation during the gating period, though at the cost of lower extinction efficiencies. By also pulsing the fifth dynode capacitatively with −326 V, attenuation is restored to greater than 107:1. The circuit assembly is compact enough to fit within a standard PMT housing and operates from the PMT dynode current. Turn-off and turn-on times of 55 and 40 ns, respectively, are obtained. The gate is thus suitable for exciting light pulse rejection in low level, submicrosecond time-resolved fluorescence, and phosphorescence measurements.
On using CAD models to compute the pose of curved 3D objects (2002)

A new approach is presented for explicitly relating image observables to models of curved three-dimensional objects. This relationship is used for object recognition and positioning. Object models consist of collections of parametric surface patches. The image observables considered are raw range data, surface normals and Gaussian curvature, raw image contours, contour orientation and curvature, raw image intensity, and intensity gradient. Elimination theory provides a method for constructing an implicit equation that relates these observables to the three-dimensional position and orientation of object models. Determining the unknown parameters is reduced to a fitting problem between the implicit equation and served data points. A preliminary implementation is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Treatment of Recurrent Aborters by Immunization With Paternal Cells—Controlled Trial (1991)

A paired sequential trial was undertaken to establish whether paternal mononuclear cells improved the prognosis in couples with recurrent abortions. For this purpose, 10(7)-10(8) cells obtained from the blood of partners were injected intravenously, subcutaneously, and intra-dermally into women who had had three or more consecutive miscarriages with the same partner. Control women were given normal saline, injected in the same manner. The result of the sequential analysis showed that there was no significant beneficial effect of the cells compared to control. The overall success rate was 70% (32/46 couples). The success rate in patients given cells was 62% (13/21), while in those given saline it was 76% (19/25). While the overall success rate in this study compares with a number of other studies, we find an equally high success rate with non-immunized patients. We conclude that the value of immunization for the prevention of recurrent miscarriage has not been established.
Defining the Antigenic Diversity of Plasmodium falciparum Apical Membrane Antigen 1 and the Requirements for a Multi-Allele Vaccine against Malaria (2012)

Apical Membrane Antigen 1 (AMA1) is a leading malaria vaccine candidate and a target of naturally-acquired human immunity. Plasmodium falciparum AMA1 is polymorphic and in vaccine trials it induces strain-specific protection. This antigenic diversity is a major roadblock to development of AMA1 as a malaria vaccine and understanding how to overcome it is essential. To assess how AMA1 antigenic diversity limits cross-strain growth inhibition, we assembled a panel of 18 different P. falciparum isolates which are broadly representative of global AMA1 sequence diversity. Antibodies raised against four well studied AMA1 alleles (W2Mef, 3D7, HB3 and FVO) were tested for growth inhibition of the 18 different P. falciparum isolates in growth inhibition assays (GIA). All antibodies demonstrated substantial cross-inhibitory activity against different isolates and a mixture of the four different AMA1 antibodies inhibited all 18 isolates tested, suggesting significant antigenic overlap between AMA1 alleles and limited antigenic diversity of AMA1. Cross-strain inhibition by antibodies was only moderately and inconsistently correlated with the level of sequence diversity between AMA1 alleles, suggesting that sequence differences are not a strong predictor of antigenic differences or the cross-inhibitory activity of anti-allele antibodies. The importance of the highly polymorphic C1-L region for inhibitory antibodies and potential vaccine escape was assessed by generating novel transgenic P. falciparum lines for testing in GIA. While the polymorphic C1-L epitope was identified as a significant target of some growth-inhibitory antibodies, these antibodies only constituted a minor proportion of the total inhibitory antibody repertoire, suggesting that the antigenic diversity of inhibitory epitopes is limited. Our findings support the concept that a multi-allele AMA1 vaccine would give broad coverage against the diversity of AMA1 alleles and establish new tools to define polymorphisms important for vaccine escape.
Sequence of events in natural infection of Pekin duck embryos with duck hepatitis B virus (1985)

The major mode of natural infection of duck hepatitis B virus (DHBV) in Pekin ducks is vertical transmission, with 95 to 100% of the embryos from DHBV-infected dams eventually becoming infected. Maternally transmitted virus is present in large quantities in the yolk of unincubated eggs and is taken up by the embryo during early development. Synthesis of DHBV DNA in the embryo begins at about 6 days of incubation and coincides with the formation of the liver. DHBV DNA synthesis is incomplete, however, until 8 to 10 days of incubation, as shown by comparing the electrophoretic patterns of DHBV-specific nucleic acid species from embryonic livers at successive stages of development. From 8 days of incubation and continuing throughout embryonic development, subviral particles, which resemble viral replication intermediates isolated from infected livers of post-hatch ducklings, appear in the circulation. These particles contain a polymerase activity that utilizes an RNA template to synthesize viral DNA. Our results suggest that certain host functions, which appear during embryonic development, may be required for DHBV replication and assembly. It is possible that in mammals a similar developmental process occurs. The failure to find human hepatitis B virus in the circulation of most babies, born to hepatitis B virus carrier women, in the first few weeks after birth may reflect such a process.