gebhart/patrepeval huggingface dataset:
Irreversible inhibitors of the HIV protease (1993)

HIV protease is an important chemotherapeutic target for an anti-AIDS drug. Recently, haloperidol was identified as a non-peptide inhibitor of the protease by a computer-based structural search. The synthesis and biological characterization of a number of derivatives of haloperidol that irreversibly inactivate both the HIV-1 and HIV-2 proteases is reported. The inactivation is due to the presence of either an electrophilic epoxide or an {alpha}, {beta}-unsaturated ketone in the analog.
A 7.86 mW +12.5 dBm in-band IIP3 8-to-320 MHz capacitive harmonic rejection mixer in 65nm CMOS (2014)

We present a low-power high-linearity capacitive harmonic rejection mixer for cognitive radio applications. A passive mixer first receiver with capacitive 16-phase sinusoidal weighting implements harmonic rejection down-conversion, and an AC-coupled fully differential capacitor feedback transimpedance amplifier provides baseband linear voltage gain and band-pass filtering achieving an in-band IIP3 of +12.5 dBm at 320 MHz LO over 3 MHz baseband. The 1.62mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> mixer in 65nm CMOS consumes 40 μW per I/Q complex output channel, and 7.82 mW for 16-phase PLL clock generation and distribution.
Color mutants of Aspergillus flavus and Aspergillus parasiticus in a study of preharvest invasion of peanuts (1986)

A comparison of the invasion of flowers, aerial pegs, and kernels by wild-type and mutant strains of Aspergillus flavus or A. parasiticus along with aflatoxin analyses of kernels from different drought treatments have supported the hypothesis that preharvest contamination with aflatoxin originates mainly from the soil. Evidence in support of soil invasion as opposed to aerial invasion was the following. A greater percentage of invasion of kernels rather than flower or aerial pegs by either wild-type A. flavus or mutants. Significant invasion by an A. parasiticus color mutant occurred only in peanuts from soil supplemented with the mutant, whereas adjacent plants in close proximity but in untreated soil were only invaded by wild-type A. flavus or A. parasiticus. Aflatoxin data from drought-stressed, visibly undamaged peanut kernels showed that samples from soil not supplemented with a mutant strain contained a preponderance of aflatoxin B's (from wild-type A. flavus) whereas adjacent samples from mutant-supplemented soil contained a preponderance of B's plus G's (from wild-type and mutant A. parasiticus). Preliminary data from two air samplings showed an absence of propagules of A. flavus or A. parasiticus in air around the experimental facility.
The 2.6 Angstrom Crystal Structure of a Human A <sub>2A</sub> Adenosine Receptor Bound to an Antagonist (2008)

The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.
A Terahertz Two-wire Waveguide with Low Bending Loss (2010)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. K. Mbonye, R. Mendis, and D. M. Mittleman, "A Terahertz Two-wire Waveguide with Low Bending Loss," in Conference on Lasers and Electro-Optics 2010, OSA Technical Digest (CD) (Optical Society of America, 2010), paper CTuQ7. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Synthesis and characterization of new polyamides and polyimides prepared from 2,2-bis[4-(4-aminophenoxy)phenyl]adamantane (1999)

In this work, we synthesized a new diamine containing a pendant adamantane group and a flexible aryl ether unit, 2,2-bis[4-(4-aminophenoxy)phenyl]adamantane (BAPA) in three steps starting from 2-adamantanone. A series of new polyamides having inherent viscosities of 0.72–0.90 dL·g–1 were prepared by direct polycondensation with aromatic dicarboxylic acids using triphenyl phosphite and pyridine as condensing agents. All polymers revealed an amorphous nature and were almost readily soluble in a variety of polar solvents. The glass transition temperature of these polyamides range from 254–294°C. The polyamides remain fairly stable up to a temperature around 450°C and lose 10% weight between 490 and 524°C in nitrogen atmosphere. A series of new polyimides were also synthesized from BAPA and various aromatic tetracarboxylic dianhydrides by the conventional two-step method. The inherent viscosities of polyimides were in the range of 0.66–0.77 dL·g–1. The polyimides are amorphous and have glass transition temperatures between 276 and 310°C. Thermogravimetric analyses demonstrated that almost all polymers are stable up to 450°C, and the 10% weight loss temperatures were recorded in the range of 515 to 541°C in nitrogen.
Machine Learning Harnesses Molecular Dynamics to Discover New $\mu$ Opioid Chemotypes (2018)

Computational chemists typically assay drug candidates by virtually screening compounds against crystal structures of a protein despite the fact that some targets, like the $\mu$ Opioid Receptor and other members of the GPCR family, traverse many non-crystallographic states. We discover new conformational states of $\mu OR$ with molecular dynamics simulation and then machine learn ligand-structure relationships to predict opioid ligand function. These artificial intelligence models identified a novel $\mu$ opioid chemotype.
Cloning and molecular characterization of a soluble epoxide hydrolase from Aspergillus niger that is related to mammalian microsomal epoxide hydrolase (1999)

Aspergillus niger strain LCP521 harbours a highly processive epoxide hydrolase (EH) that is of particular interest for the enantioselective bio-organic synthesis of fine chemicals. In the present work, we report the isolation of the gene and cDNA for this EH by use of inverse PCR. The gene is composed of nine exons, the first of which is apparently non-coding. The deduced protein of the A. niger EH shares significant sequence similarity with the mammalian microsomal EHs (mEH). In contrast to these, however, the protein from A. niger lacks the common N-terminal membrane anchor, in line with the fact that this enzyme is, indeed, soluble in its native environment. Recombinant expression of the isolated cDNA in Escherichia coli yielded a fully active EH with similar characteristics to the fungal enzyme. Sequence comparison with mammalian EHs suggested that Asp(192), Asp(348) and His(374) constituted the catalytic triad of the fungal EH. This was subsequently substantiated by the analysis of respective mutants constructed by site-directed mutagenesis. The presence of an aspartic acid residue in the charge-relay system of the A. niger enzyme, in contrast to a glutamic acid residue in the respective position of all mEHs analysed to date, may be one important contributor to the exceptionally high turnover number of the fungal enzyme when compared with its mammalian relatives. Recombinant expression of the enzyme in E. coli offers a versatile tool for the bio-organic chemist for the chiral synthesis of a variety of fine chemicals.
Superchiral Light Generation on Degenerate Achiral Surfaces (2018)

A novel route of superchiral near-field generation is demonstrated based on geometrically achiral systems supporting degenerate and spatially superimposed plasmonic modes. Such systems generate a single-handed chiral near field with simultaneous zero far-field circular dichroism. The phenomenon is theoretically elucidated with a rotating dipole model, which predicts a uniform single-handed chiral near field that flips handedness solely by reversing the handedness of the source. This property allows detection of pure background free molecular chirality through near-field light-matter interaction, which is experimentally demonstrated in the precise identification of both handedness of a chiral molecule on a single substrate with about four orders of magnitude enhancement in detection sensitivity compared to its conventional volumetric counterpart.
<i>TAENIA SOLIUM</i>: MOLECULAR CLONING AND SEROLOGIC EVALUATION OF 14- AND 18-KDA RELATED, DIAGNOSTIC ANTIGENS (2000)

We are attempting to design a simpler assay based on synthetic or recombinant antigens to replace the labor-intensive enzyme-linked immunoelectrotransfer blot (EITB-C), which is currently used to diagnose Taenia solium cysticercosis. From the lentil lectin-bound fraction of cyst glycoproteins (the LLGP fraction used in the EITB-C), we previously identified and purified 2 related polypeptides of 14- and 18-kDa that demonstrated diagnostic usefulness. Using degenerate oligonucleotide primers corresponding to amino acid sequences of these polypeptides and a cDNA library prepared from T. solium cysticerci, we amplified cDNA clones that represent the 14- and 18-kDa polypeptides. These clones share sequence homology at the nucleotide and amino acid levels. Synthetic polypeptides that represented the full-length, mature proteins (sTS14 and sTS18) were assessed for serologic potential using an ELISA. sTS14, but not sTS18, demonstrated utility as a diagnostic antigen. sTS14 was recognized by antibodies in a majority of the sera from patients with cysticercosis and none of the sera from persons with other helminth infections or uninfected human sera. Furthermore, polyclonal antibodies to sTS14 reacted with 6 discrete proteins present in the LLGP cyst fraction, suggesting that TS14 is a subunit of other previously described antigens used for diagnosing cysticercosis.
Communication—Electrocatalytic Coupling of Methane at Platinum Oxide Electrodes in Superacids (2020)

Electrochemical oxidation of methane in the absence of chemical oxidants offers the potential to directly synthesize high value hydrocarbons at low temperatures. Experimental results demonstrate methane oxidization at oxidized Pt electrodes in liquid superacid electrolytes. Ethane and ethylene are observed as products under chronoamperometric experiments at room temperature. Faradaic efficiencies for C 2 products range from 5% to 25% at anodic potentials between 0.8 to 1.4 V vs RHE. A generalized Lewis-acid Pt 2+ mechanism including methylidene coupling is proposed.
POSTER: Design Space Exploration for Performance Optimization of Deep Neural Networks on Shared Memory Accelerators (2017)

The growing prominence and computational challenges imposed by Deep Neural Networks (DNNs) has fueled the design of specialized accelerator architectures and associated dataflows to improve their implementation efficiency. Each of these solutions serve as a datapoint on the throughput vs. energy trade-offs for a given DNN and a set of architectural constraints. In this paper, we set out to explore whether it is possible to systematically explore the design space so as to estimate a given DNN's (both inference and training) performance on an shared memory architecture specification using a variety of data-flows. To this end, we have developed a framework, DEEPMATRIX, which given a description of a DNN and a hardware architecture, automatically identifies how the computations of the DNN's layers need to partitioned and mapped on to the architecture such that the overall performance is maximized, while meeting the constraints imposed by the hardware (processing power, memory capacity, bandwidth etc.) We demonstrate DEEPMATRIX's effectiveness for the VGG DNN benchmark, showing the trade-offs and sensitivity of utilization based on different architecture constraints.
A virtual design environment using evolutionary agents (2002)

The virtual design environment is an information architecture to support design-manufacturing-supplier planning decisions in a distributed, heterogeneous environment. The approach utilizes evolutionary intelligent agents as program entities which generate and execute queries among distributed computing applications and databases. The evolutionary agents support a global evolutionary optimization process in which successive populations systematically select planning alternatives which reduce cost and increase throughput. A prototype of the virtual design environment has been implemented using CORBA as a principal distributed systems programming tool. The prototype has been used to examine design-manufacturing-supplier decisions for a real commercial electronic circuit board product (Pitney Bowes Inc.) and to explore plans in controlled experiments with alternative manufacturing facilities.
Imaging CDMAM phantom with tomosynthesis (2008)

We studied the use of the mammography contrast detail phantom (CDMAM) with tomosynthesis to evaluate the performance of our system as well as to explore the application of CDMAM in 3D breast imaging. The system was Hologic's 1st generation tomosynthesis machine. CDMAM phantom plus PMMA slabs were imaged at 3 cm, 5 cm, 7 cm, and 9 cm PMMA-equivalent thickness with 11 projections per scan and the scan angle selected from 0, 15 and 28 degrees. CDMAM images were reconstructed using the back projection method, and were scored with the CDCOM automatic analysis program. The threshold thickness of each disk size was obtained with psychometric curve fitting. We first studied errors and variability associated with the results when different numbers of images were used in contrast detail analysis, then studied factors that affected CDMAM results in tomosynthesis, including the x-ray dose, the scan angle, the in-plane reconstruction pixel size, the slice-to-slice step size, the location of the CDMAM inside the PMMA slabs, and the scatter effect. This paper will present results of CDMAM performance of our tomosynthesis system, as well as their dependence on the various factors, and the comparison with 2D mammography. Additionally we will discuss the novel processing and analysis methods developed during this study, and make proposals to modify the CDMAM phantom and the CDCOM analysis program to optimize the method for 3D tomosynthesis.
Expression of cytoplasmic CD3 ε proteins in activated human adult natural killer (NK) cells and CD3 γ, δ, ε complexes in fetal NK cells. Implications for the relationship of NK and T lymphocytes (1992)

NK cells have been defined as CD3-, CD16+, and/or CD56+ lymphocytes that mediate MHC-unrestricted cytotoxicity against certain tumors and virus-infected cells. Although CD3 epsilon transcripts have been detected in some NK clones, it has generally been thought that NK cells do not express CD3 proteins other than zeta which is associated with CD16 (Fc gamma RIII). We demonstrate that adult peripheral blood NK cell lines and clones express cytoplasmic CD3 epsilon proteins, but not CD3 delta or gamma. CD3 epsilon proteins were detected by immunoprecipitation, Western blot analysis, and immunofluorescence using antiserum directed against the cytoplasmic domain of CD3 epsilon. Although resting, adult peripheral blood NK cells have essentially undetectable levels of CD3 epsilon protein, expression was increased substantially after activation. In contrast to adult NK cells, NK cell clones established from human fetal liver express CD3 gamma, delta, and epsilon protein subunits that associate and form CD3 epsilon, gamma and CD3 epsilon, delta complexes in the cytoplasm, but are apparently unable to be transported to the cell surface. These results indicate that expression of CD3 gamma delta epsilon subunits is not restricted to T lymphocytes and supports the possibility that NK and T cells may be derived from common origins.
Simplified procedure for correcting both errors and erasures of Reed-Solomon code using Euclidean algorithm (1988)

It is well known that the Euclidean algorithm or its equivalent, continued fractions, can be used to find the error locator polynomial and the error evaluator polynomial in Berlekamp's key equation that is needed to decode a Reed-Solomon (RS) code. In the paper, a simplified procedure is developed and proved to correct erasures as well as errors by replacing the initial condition of the Euclidean algorithm by the erasure locator polynomial and the Forney syndrome polynomial. By this means, the errata locator polynomial and the errata evaluator polynomial can be obtained simultaneously and simply, by the Euclidean algorithm only. With this improved technique, the complexity of time-domain Reed-Solomon decoders for correcting both errors and erasures is reduced substantially from previous approaches. As a consequence, decoders for correcting both errors and erasures of RS codes can be made more modular, regular, simple, and naturally suitable for both VLSI and software implementation. An example illustrating this modified decoding procedure is given for a (15, 9) RS code.
Na3[B20H17NH3]: synthesis and liposomal delivery to murine tumors. (1994)

The polyhedral borane ion [n-B20H18]2- reacts with liquid ammonia in the presence of a suitable base to produce an apical-equatorial (ae) isomer of the [B20H17NH3]3- ion, [1-(2'-B10H9)-2-NH3B10H8]3-. The structure of this product has been confirmed by 11B NMR spectroscopy and x-ray crystallography. This species undergoes acid-catalyzed rearrangement to an apical-apical (a2) isomer, [1-(1'-B10H9)-2-NH3B10H8]3-, whose structure has been determined by 11B NMR spectroscopy. The sodium salts of both the ae and the a2 isomers of [B20H17NH3]3- have been encapsulated within small unilamellar liposomes, composed of distearoyl phosphatidylcholine/cholesterol (1:1), and investigated as boron-delivery agents for boron neutron capture therapy (BNCT) of cancer. The biodistribution of boron was determined after the injection of liposomal suspensions into BALB/c mice bearing EMT6 tumors. Both [B20H17NH3]3- isomers exhibited excellent tumor uptake and selectivity at very low injected doses, achieving peak tumor boron concentrations of 30-40 micrograms of B/g of tissue and tumor/blood boron ratios of approximately 5. The enhanced retention of the [B20H17NH3]3- isomers by EMT6 tumors may be attributed to their facile intracellular oxidation to an extremely reactive NH3-substituted [n-B20H18]2- ion, the electrophilic [B20H17NH3]- ion. Both isomers of [B20H17NH3]3- are at least 0.5 V more easily oxidized than other previously investigated species containing 20 boron atoms. In another experiment, [ae-B20H17NH3]3- was encapsulated in liposomes prepared with 5% PEG-2000-distearoyl phosphatidylethanolamine in the liposome membrane. As expected, these liposomes exhibited a longer circulation lifetime in the biodistribution experiment, resulting in the continued accumulation of boron in the tumor over the entire 48-hr experiment and reaching a maximum of 47 micrograms of B/g of tumor.
Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal (2010)

Host immunity to VAR2CSA influences the parasite dynamics during pregnancy, suggesting that the acquisition of protective immunity requires pre-exposure to a limited number of parasite variants. Presence of highly conserved residues in surface-exposed areas of the VAR2CSA immunodominant DBL5epsilon domain, suggest its potential in inducing antibodies with broad reactivity.
Incorporation of Vpr into Human Immunodeficiency Virus Type 1 (1995)

The 96-amino acid Vpr protein is the only virion-associated regulatory protein encoded by the human immunodeficiency virus type 1 (HIV-1). Vpr incorporation into the viral particle is most likely due to an interaction with a viral structural protein. Recent data have shown that DNA encoding for the p55 Gag precursor protein (Pr55gag) is the minimal viral genetic information necessary for Vpr incorporation. Other studies have suggested that the p6 portion of Pr55gag, which is unique to lentiviruses, is involved in Vpr incorporation. To investigate the mechanism of incorporation of Vpr into HIV-1 virions, COS-7 cells were cotransfected with ptrENV, an expression vector that encodes all of the HIV-1 regulatory proteins including Rev and Vpr, and different constructs of pIIIgagCAR, a rev-dependent Gag expression plasmid that encodes Pr55gag and the viral protease. Virions produced from gag constructs containing a premature p6 termination codon at positions Leu-1, Ser-17, Tyr-36, or Leu-44 lacked detectable Vpr. In contrast, gag constructs with double Pro-10-Pro-11 substitutions for Leu-10-Leu-11 or a premature termination codon at position Pro-49 of p6 were still able to incorporate Vpr, however, with lower efficiency than wild type. The mutations described in this study affected directly two short regions within the p6 domain, which are highly conserved among primate immunodeficiency viruses. Our results suggest that the conserved (P-T/S-A-P-P) and (L-X-S-L-F-G) motifs located near the N-terminus and C-terminus, respectively, of the p6 domain of Gag are critical for Vpr incorporation into HIV-1 virions.
Development of a Multiplex Reverse Transcription–Polymerase Chain Reaction Diagnostic Test Specific for Turkey Astrovirus and Coronavirus (2004)

A multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the simultaneous detection of two enteric viruses of poultry: turkey enteric coronavirus (TCV) and turkey astrovirus (TAstV). PCR primers were designed to conserved regions within the nucleocapsid gene of TCV and to the polymerase gene of TAstV-2. The primer pairs were successfully used in a multiplex RT-PCR to detect nucleic acid of TAstV-2 and TCV. The test was optimized for use with intestines/feces from naturally infected turkeys. The primers were specific and did not amplify other common RNA or DNA avian viruses. The detection limit was determined to be 10 ng of RNA used as starting template. The use of this specific test allows the rapid and early diagnosis of two financially costly viruses affecting the commercial turkey industry.