gebhart/patrepeval huggingface dataset:
Single Nucleotide Polymorphisms in Genes Associated with Isoniazid Resistance in <i>Mycobacterium tuberculosis</i> (2003)

Isoniazid (INH) is a central component of drug regimens used worldwide to treat tuberculosis. Previous studies have identified resistance-associated mutations in katG, inhA, kasA, ndh, and the oxyR-ahpC intergenic region. DNA microarray-based experiments have shown that INH induces several genes in Mycobacterium tuberculosis that encode proteins physiologically relevant to the drug's mode of action. To gain further insight into the molecular genetic basis of INH resistance, 20 genes implicated in INH resistance were sequenced for INH resistance-associated mutations. Thirty-eight INH-monoresistant clinical isolates and 86 INH-susceptible isolates of M. tuberculosis were obtained from the Texas Department of Health and the Houston Tuberculosis Initiative. Epidemiologic independence was established for all isolates by IS6110 restriction fragment length polymorphism analysis. Susceptible isolates were matched with resistant isolates by molecular genetic group and IS6110 profiles. Spoligotyping was done with isolates with five or fewer IS6110 copies. A major genetic group was established on the basis of the polymorphisms in katG codon 463 and gyrA codon 95. MICs were determined by the E-test. Semiquantitative catalase assays were performed with isolates with mutations in the katG gene. When the 20 genes were sequenced, it was found that 17 (44.7%) INH-resistant isolates had a single-locus, resistance-associated mutation in the katG, mabA, or Rv1772 gene. Seventeen (44.7%) INH-resistant isolates had resistance-associated mutations in two or more genes, and 76% of all INH-resistant isolates had a mutation in the katG gene. Mutations were also identified in the fadE24, Rv1592c, Rv1772, Rv0340, and iniBAC genes, recently shown by DNA-based microarray experiments to be upregulated in response to INH. In general, the MICs were higher for isolates with mutations in katG and the isolates had reduced catalase activities. The results show that a variety of single nucleotide polymorphisms in multiple genes are found exclusively in INH-resistant clinical isolates. These genes either are involved in mycolic acid biosynthesis or are overexpressed as a response to the buildup or cellular toxicity of INH.
Metal-ammonia reduction of cycloalkanones. A revised mechanism (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal-ammonia reduction of cycloalkanones. A revised mechanismJohn W. Huffman, Ranjit C. Desai, and Joseph E. LaPradeCite this: J. Org. Chem. 1983, 48, 9, 1474–1479Publication Date (Print):May 1, 1983Publication History Published online1 May 2002Published inissue 1 May 1983https://pubs.acs.org/doi/10.1021/jo00157a018https://doi.org/10.1021/jo00157a018research-articleACS PublicationsRequest reuse permissionsArticle Views200Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
General noise processes in hybrid infrared focal plane arrays (1991)

The noise limitations of IR imaging systems are often described as arising from predominantly temporal sources, such as background, thermal, and readout noise. Actual systems can also be limited by structured pattern) noises and drift. This is especially true with the advent of highly integrated hybrid focal plane arrays, which consist of an infrared detector array, usually photovoltaic, mated to a silicon CMOS VLSI readout device. In these arrays the large detector count, high density, and complexity create new susceptibilities for image noise. Low natural backgrounds in some systems, and the need to save aperture area in others, often force the designer to work at low background levels and high quanturn efficiencies, eliminating options for simpler FPA architectures and making control of focal plane elements more challenging. The desire to dc couple the array output and use an infrequent detector equalization update further complicates the issue. We discuss several noise processes in low-background hybrid arrays, both observed and anticipated. These processes are described through example circuits, typical of proposed and assembled lR focal plane arrays.
A photolithographic process for fabrication of devices with isolated single-walled carbon nanotubes (2004)

We have successfully fabricated devices with isolated single-walled carbon nanotubes (SWNTs) using exclusively standard i-line (365 nm) photolithography. Catalyst islands were patterned with an SU-8-photoresist-based process. This method provides well-defined islands, down to 1 µm in size. The islands are clearly visible with an optical microscope and are used as alignment marks for optical alignment of subsequent layers. SWNTs were grown by chemical vapour deposition (CVD). Contacts to the nanotubes were fabricated by standard photolithography.
A Protein Interaction Map of <i>Drosophila melanogaster</i> (2003)

Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.
Aggrecanase versus matrix metalloproteinases in the catabolism of the interglobular domain of aggrecan <i>in vitro</i> (1999)

The importance of aggrecanase versus matrix metalloproteinase (MMP) enzymic activities in the degradation of aggrecan in normal and osteoarthritic (OA) articular cartilage in vitro was studied in order to further our understanding of the potential role of these two enzyme activities in aggrecan catabolism during the pathogenesis of cartilage degeneration. Porcine and bovine articular cartilage was maintained in explant culture for up to 20 days in the presence or absence of the catabolic stimuli retinoic acid, interleukin-1 or tumour necrosis factor-alpha. Release of proteoglycan from cartilage was measured as glycosaminoglycan (GAG) release using a colorimetric assay. Analysis of proteoglycan degradation products, both released into culture media and retained within the cartilage matrix, was performed by Western blotting using antibodies specific for the N- and C-terminal neoepitopes generated by aggrecanase- and MMP-related catabolism of the interglobular domain of the aggrecan core protein (IGD). In addition, studies determining the mRNA expression for MMP-3 and MMP-13 in these same cultures were undertaken. These analyses indicated that all three catabolic agents stimulated the release of >80% of the GAG from the articular cartilage over 4 days. The degree of GAG release corresponded to an increase in aggrecanase-generated aggrecan catabolites released into the media and retained within the cartilage. Importantly, there was no evidence for the release of MMP-generated aggrecan metabolites into the medium, nor the accumulation of MMP-generated catabolites within the tissue in these same cultures. Expression of the mRNAs for two MMPs known to be capable of degrading the aggrecan IGD, MMP-3 and MMP-13, was detected. However, increased expression of these MMPs was not correlated with aggrecan degradation. Analyses using porcine cartilage, cultured with or without catabolic stimulation for 12 h to 20 days, indicated that primary cleavage of the IGD by aggrecanase was responsible for release of aggrecan metabolites at both the early and late time points of culture. Cultures of late-stage OA human articular cartilage samples indicated that aggrecanase activity was upregulated in the absence of catabolic stimulation when compared with normal porcine or bovine cartilage. In addition, even in this late-stage degenerate cartilage, aggrecanase and not MMP activity was responsible for the release of the majority of aggrecan from the cartilage. This study demonstrates that the release of aggrecan from both normal and OA cartilage in response to catabolic stimulation in vitro involves a primary cleavage by aggrecanase and not MMPs.
Construction and Characterization of a Quadruplex DNA Selective Single-Chain Autoantibody from a Viable Motheaten Mouse Hybridoma with Homology to Telomeric DNA Binding Proteins (1998)

An autoantibody produced by a hybridoma derived from a viable motheaten mouse was isolated and found to have moderately high binding affinity for nucleic acids and specific preference for quadruplex DNAs. Polymerase chain reaction primers were designed to link the cloned parental antibody variable region fragments together in a subcloning vector. This single-chain variable fragment construct was then subcloned into the T7 promoter-driven expression vector pET22b(+). The construct contains (N- to C-terminal) a pelB leader sequence, variable heavy chain, glycine-serine polylinker, variable light chain, and biotin mimic peptide "strep-tag" sequence (pelB-VH-linker-VL-strep-tag). The ca. 29 kDa protein was expressed, exported to the periplasmic space of NovaBlue (DE) Escherichia coli, and purified by streptavidin affinity chromatography by binding the fused strep-tag peptide. The specificity of the purified single-chain variable fragment (scFv) for quadruplex and duplex DNAs was evaluated by a radioimmunofilterbinding assay. It retained about 10-fold higher affinity for quadruplexes relative to duplex DNA, a reduction of ca. 4-fold from the relative preferences of the parent IgG. The complementary-determining regions contain sequences that are homologous to or conservatively divergent from the key DNA-binding helix-turn-helix-forming motifs of Myb/RAP1 family telomeric DNA-binding proteins (1-3). The presence of this antibody in the autoimmune repertoire suggests a possible linkage between autoimmunity, telomeric DNA binding proteins, and aging.
Development Study on A Micro-Solid Propellant Rocket Array Thruster (2002)

The authors have developed the practical prototype of a micro-solid propellant rocket array thruster for attitude control of a 10kg class micro-spacecraft. a target of this activity is to build the array thruster with 10000 of solid propellant micro-rockets arrayed on a 100×100mm substrate. The prototype with the Φ0.8 micro-rockets arrayed at a pitch of 1.2mm on a 20×30mm substrate has built and tested so far. Boron/potassium nitrate (NAB) propellant is used with/without initiator of lead rhodanide/potassium chlorate/nitrocellulose (RK). Impulse thrust was measured by means of a pendulum method. The experimental results show that the prototype has proper ignition characteristics and further experimental studies are needed to evaluate and to control the impulse thrust with accuracy. We are planning to conduct the thrust measurement test under vacuum condition.
Duplex Generative Adversarial Network for Unsupervised Domain Adaptation (2018)

Domain adaptation attempts to transfer the knowledge obtained from the source domain to the target domain, i.e., the domain where the testing data are. The main challenge lies in the distribution discrepancy between source and target domain. Most existing works endeavor to learn domain invariant representation usually by minimizing a distribution distance, e.g., MMD and the discriminator in the recently proposed generative adversarial network (GAN). Following the similar idea of GAN, this work proposes a novel GAN architecture with duplex adversarial discriminators (referred to as DupGAN), which can achieve domain-invariant representation and domain transformation. Specifically, our proposed network consists of three parts, an encoder, a generator and two discriminators. The encoder embeds samples from both domains into the latent representation, and the generator decodes the latent representation to both source and target domains respectively conditioned on a domain code, i.e., achieves domain transformation. The generator is pitted against duplex discriminators, one for source domain and the other for target, to ensure the reality of domain transformation, the latent representation domain invariant and the category information of it preserved as well. Our proposed work achieves the state-of-the-art performance on unsupervised domain adaptation of digit classification and object recognition.
Immunogene therapy by adenovirus vector expressing CD40 ligand for metastatic liver cancer in rats. (2008)

Adenovirus vector-mediated CD40L gene therapy is an effective therapeutic method for metastatic liver cancer.
Enantioselective Syntheses of (-)-(<i>R</i>)-Rolipram, (-)-(<i>R</i>)-Baclofen and Other GABA Analogues via Rhodium-Catalyzed Conjugate Addition of Arylboronic Acids (2003)

Highly enantioselective syntheses of two important γ-aminobutyric acid (GABA) analogues, the antispastic drug (-)-(R)-Baclofen and the antidepressant agent (-)-(R)-Rolipram, are reported. Key-steps in both syntheses are the Rh-catalyzed asymmetric 1,4-additions of arylboronic acids to 4-aminobut-2,3-enoic acid derivatives.
Design, Synthesis, and Structural Characterization of Molecular and Supramolecular Heterobimetallic Metallamacrocycles Based on the 1,1‘-Bis(4-pyridyl)ferrocene (Fe(η<sup>5</sup>-C<sub>5</sub>H<sub>4</sub>-1-C<sub>5</sub>H<sub>4</sub>N)<sub>2</sub>) Ligand (2003)

The bidentate ferrocenyl sandwich [Fe(η5-C5H4-1-C5H4N)2] (1) has been used as a coordination ligand in reactions with AgNO3, Cd(NO3)2, Cu(CH3COO)2, Zn(CH3COO)2, and ZnCl2 to obtain the heterobimetallic metallamacrocyclic derivatives [Fe(η5-C5H4-1-C5H4N)2]2Ag2(NO3)2·1.5H2O, [Fe(η5-C5H4-1-C5H4N)2]2 Cu2(CH3COO)4·3H2O, [Fe(η5-C5H4-1-C5H4N)2]2Cd2(NO3)4·CH3OH·0.5C6H6, [Fe(η5-C5H4-1-C5H4N)2]2Zn2(CH3COO)4, and [Fe(η5-C5H4-1-C5H4N)2]2Zn2Cl4 (abbreviated in the following as (1AgI)22+, (1CdII)24+, (1CuII)24+, (1ZnIIacetate)24+, and (1ZnIIchloride)24+). The reaction with the ferrocenedicarboxylic acid complex [Fe(η5-C5H4COOH)2] has led to the supramolecular adduct [Fe(η5-C5H4-1-C5H4N)2][Fe(η5-C5H4COOH)2] (1[Fe(η5-C5H4COOH)2]). All compounds have been structurally characterized by single-crystal X-ray diffraction.
Radiation-hard 16K CMOS/SOS clocked static RAM (1981)

A low-temperature, radiation-hard, 2.21µM channel length, CMOS/SOS process has been developed for a 5V power-supply, 16K clocked static RAM, with a standard six-transistor cell configuration. The well-known edge leakage problem in mesa-isolated N-channel SOS transistors has been eliminated. At V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</inf> of 5V, the 16K RAM has typical access times of 150 nsecs and 110 nsecs with phosphorus doped polysilicon and tantalum silicide gates, respectively; the static power dissipation is 35µW and the operating power is 20 mW at 3 MHz.
Synthesis of Arachidonic Acid in the Human Placenta <i>in vitro</i> (1979)

The syntheses of arachidonic acid and total fatty acids were measured in human placentas at the end of the first trimester and at term using 14C-acetate in in vitro incorporation experiments. The rates of arachidonic acid synthesis were determined to be 0.70 (first trimester) and 0.64 (term) mumol/h/100 g of placental tissue. The calculated rates of total fatty acid synthesis amount to 0.5 (first trimester) and 0.6 (term) mumol palmitate-equivalents/h/100 g. The results suggest that the human placenta seems to be not dependent on maternal arachidonic acid. Near term the placenta even could be source of arachidonic acid.
Towards uncovering BGP hijacking attacks (2015)

Internet est constitué de milliers de systèmes autonomes (Autonomous Systems, AS) qui échangent des informations de routage grâce au protocole BGP (Border Gateway Protocol). Chaque AS attend des autres qu'il lui donne des informations de routage correctes, et leur accorde donc une confiance totale. Le détournement de préfixe (prefix hijacking) exploite cette confiance afin d'introduire des routes falsifiées. Les techniques qui détectent cette attaque génèrent un nombre important d'alertes, composé de faux positifs résultant d'opérations de routage courantes. Dans cette dissertation, nous cherchons à trouver la cause principale de ces alertes, de manière indubitable. A cette fin, d'une part, nous réduisons le nombre d'alertes en analysant en profondeur ces réseaux, dont nous dérivons une série de structures qui reflètent les pratiques standard de routage du monde réel, et en considérant le risque associé à ces structures lors une attaque par détournement. D'autre part, nous utilisons des bases de données auxiliaires qui nous permettent de connaître la raison derrière un évènement de routage, qui n'est, en général, connue que du propriétaire du réseau. Précisément, nous regardons les préfixes à origines multiples (Multiple Origin AS, MOAS), et mettons en évidence une classification nous permettant d'éliminer 80% des alertes. Nous présentons un cas réel où un MOAS coïncide avec du spam et des sites d'arnaque en ligne. Nous étudions les préfixes non-disjoints, et présentons un prototype permettant d'éliminer 50% des alertes sub-MOAS.Nous explorons l'espace IP non assigné, cherchons des adresses IP joignables, et localisons une grande quantité de spam et des sites d'arnaques en ligne.
Fast computation of discrete Fourier transforms using polynomial transforms (1979)

Polynomial transforms, defined in rings of polynomials, have been introduced recently and have been shown to give efficient algorithms for the computation of two-dimensional convolutions. In this paper we present two methods for computing discrete Fourier transforms (DFT) by polynomial transforms. We show that these techniques are particularly well adapted to multidimensional DFT's as well as to some one-dimensional DFT's and yield algorithms that are, in many instances, more efficient than the fast Fourier transform (FFT) or the Winograd Fourier Transform (WFTA). We also describe new split nesting and split prime factor techniques for computing large DFT's from a small set of short DFT's with a minimum number of operations.
In hybridoma cultures, deprivation of any single amino acid leads to apoptotic death, which is suppressed by the expression of thebcl-2 gene (1998)

The transfection of murine hybridomas with the apoptosis suppressor gene bcl-2 has been reported to result in the extension of batch culture duration, leading to significant improvements in culture productivity. In the present study, the effect of deprivation, individually, of each amino acid found in culture medium was examined to characterize the chemical environment of the culture in terms of its propensity to induce apoptosis. When cells were deprived of each amino acid, individually for 48 h, the majority of cell deaths in each case occurred by apoptosis, with essential amino acids being clearly most effective. For nearly all the amino acids, the viability of the bcl-2 cell line cultures was greater than 70% after 48 h, representing a substantial improvement in viability over control cell line cultures. Time course studies revealed that the induction of death could be divided into two phases. Initially, following the deprivation of a single essential amino acid, there was a period of time during which all the control cell line cultures retained high viability. The duration of this phase varied from 15 h in the case of lysine deprivation, through to 40 h in the case methionine deprivation. In the second phase of deprivation, the cultures exhibited an abrupt and rapid collapse in viability. The time taken for the viability to fall to 50% was similar for each amino acid. In every case, the duration of both phases of the bcl-2 cultures was considerably extended. Specific utilization rates were increased during the control cultures relative to the bcl-2 cultures for both the growth phase (ranging between 2% and 57% higher than the bcl-2 cultures) and the death phase (ranging between 172% to 1900% higher than the bcl-2 culture).
Mining point-of-interest data from social networks for urban land use classification and disaggregation (2015)

Over the last few years, much online volunteered geographic information (VGI) has emerged and has been increasingly analyzed to understand places and cities, as well as human mobility and activity. However, there are concerns about the quality and usability of such VGI. In this study, we demonstrate a complete process that comprises the collection, unification, classification and validation of a type of VGI-online point-of-interest (POI) data-and develop methods to utilize such POI data to estimate disaggregated land use (i.e., employment size by category) at a very high spatial resolution (census block level) using part of the Boston metropolitan area as an example. With recent advances in activity-based land use, transportation, and environment (LUTE) models, such disaggregated land use data become important to allow LUTE models to analyze and simulate a person's choices of work location and activity destinations and to understand policy impacts on future cities. These data can also be used as alternatives to explore economic activities at the local level, especially as government-published census-based disaggregated employment data have become less available in the recent decade. Our new approach provides opportunities for cities to estimate land use at high resolution with low cost by utilizing VGI while ensuring its quality with a certain accuracy threshold. The automatic classification of POI can also be utilized for other types of analyses on cities.
Hierarchical Multimodal LSTM for Dense Visual-Semantic Embedding (2017)

We address the problem of dense visual-semantic embedding that maps not only full sentences and whole images but also phrases within sentences and salient regions within images into a multimodal embedding space. Such dense embeddings, when applied to the task of image captioning, enable us to produce several region-oriented and detailed phrases rather than just an overview sentence to describe an image. Specifically, we present a hierarchical structured recurrent neural network (RNN), namely Hierarchical Multimodal LSTM (HM-LSTM). Compared with chain structured RNN, our proposed model exploits the hierarchical relations between sentences and phrases, and between whole images and image regions, to jointly establish their representations. Without the need of any supervised labels, our proposed model automatically learns the fine-grained correspondences between phrases and image regions towards the dense embedding. Extensive experiments on several datasets validate the efficacy of our method, which compares favorably with the state-of-the-art methods.
Factors Associated With Acute Pain Estimation, Postoperative Pain Resolution, Opioid Cessation, and Recovery (2019)

ClinicalTrials.gov Identifier: NCT01067144.