gebhart/patrepeval huggingface dataset:
Laser-Induced Fluorescence Detection of a Single Molecule in a Capillary (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLaser-Induced Fluorescence Detection of a Single Molecule in a CapillaryYuan-Hsiang. Lee, Russell G. Maus, Ben W. Smith, and James D. WinefordnerCite this: Anal. Chem. 1994, 66, 23, 4142–4149Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/ac00095a005https://doi.org/10.1021/ac00095a005research-articleACS PublicationsRequest reuse permissionsArticle Views529Altmetric-Citations89LEARN 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
Neoplastic Transformation by Truncated Alleles of Human NOTCH1/TAN1 and NOTCH2 (1997)

The Notch genes of Drosophila melanogaster and vertebrates encode transmembrane receptors that help determine cell fate during development. Although ligands for Notch proteins have been identified, the signaling cascade downstream of the receptors remains poorly understood. In human acute lymphoblastic T-cell leukemia, a chromosomal translocation damages the NOTCH1 gene. The damage apparently gives rise to a constitutively activated version of NOTCH protein. Here we show that a truncated version of NOTCH1 protein resembling that found in the leukemic cells can transform rat kidney cells in vitro. The transformation required cooperation with the E1A oncogene of adenovirus. The transforming version of NOTCH protein was located in the nucleus. In contrast, neither wild-type NOTCH protein nor a form of the truncated protein permanently anchored to the plasma membrane produced transformation in vitro. We conclude that constitutive activation of NOTCH similar to that found in human leukemia can contribute to neoplastic transformation. Transformation may require that the NOTCH protein be translocated to the nucleus. These results sustain a current view of how Notch transduces a signal from the surface of the cell to the nucleus.
Crystal Structure and Amino Acid Sequence of Wolinella Succinogenesl‐Asparaginase (1996)

The amino acid sequence and tertiary structure of Wolinella succinogenes L-asparaginase were determined, and were compared with the structures of other type-II bacterial L-asparaginases. Each chain of this homotetrameric enzyme consists of 330 residues. The amino acid sequence is 40-50% identical to the sequences of related proteins from other bacterial sources, and all residues previously shown to be crucial for the catalytic action of these enzymes are identical. Differences between the amino acid sequence of W. succinogenes L-asparaginase and that of related enzymes are discussed in terms of the possible influence on the substrate specificity. The overall fold of the protein subunit is almost identical to that observed for other L-asparaginases. Two fragments in each subunit, a very highly flexible loop (approximately 20 amino acids) that forms part of the active site, and the N-terminus (two amino acids), are not defined in the structure. The orientation of Thr14, a residue probably involved in the catalytic activity, indicates the absence of ligand in the active-site pocket. The rigid part of the active site, which includes the asparaginase triad Thr93-Lys 166-Asp94, is structurally very highly conserved with equivalent regions found in other type-II bacterial L-asparaginases.
Orally Administered Targeted Recombinant Beta-Lactamase Prevents Ampicillin-Induced Selective Pressure on the Gut Microbiota: a Novel Approach to Reducing Antimicrobial Resistance (2003)

Antibiotics that are excreted into the intestinal tract promote antibiotic resistance by exerting selective pressure on the gut microbiota. Using a beagle dog model, we show that an orally administered targeted recombinant beta-lactamase enzyme eliminates the portion of parenteral ampicillin that is excreted into the small intestine, preventing ampicillin-induced changes to the fecal microbiota without affecting ampicillin levels in serum. In dogs receiving ampicillin, significant disruption of the fecal microbiota and the emergence of ampicillin-resistant Escherichia coli and TEM genes were observed, whereas in dogs treated with ampicillin in combination with an oral beta-lactamase, these did not occur. These results suggest a new strategy for reducing antimicrobial resistance in humans.
Phosphatidylserine-Mediated Phagocytosis of Influenza A Virus-Infected Cells by Mouse Peritoneal Macrophages (2000)

Influenza virus induces apoptosis in cultured cell lines as well as in animal tissues. HeLa cells were infected with influenza virus A/Udon/72 (H3N2) under conditions resulting in almost 100% infection. Such cells underwent typical caspase-dependent apoptosis and were efficiently phagocytosed by macrophages prepared from peritoneal fluids of thioglycolate-treated mice. The membrane phospholipid phosphatidylserine appeared on the surfaces of virus-infected cells at around the time efficient phagocytosis became detectable. In fact, the phagocytosis was almost completely inhibited in the presence of liposomes containing phosphatidylserine, which did not influence the antibody-dependent uptake of zymosan particles by the same macrophages. These results indicate that macrophages phagocytose influenza virus-infected HeLa cells in a manner mediated by phosphatidylserine that appears on the surfaces of infected cells during the process of apoptosis.
Redundant filterbank precoders and equalizers. II. Blind channel estimation, synchronization, and direct equalization (1999)

For pt.I see ibid., vol.47, no.7, p.1988-2006 (1999). Transmitter redundancy introduced using finite impulse response (FIR) filterbank precoders offers a unifying framework for single- and multiuser transmissions. With minimal rate reduction, FIR filterbank transmitters with trailing zeros allow for perfect (in the absence of noise) equalization of FIR channels with FIR zero-forcing equalizer filterbanks, irrespective of the input color and the channel zero locations. Exploiting this simple form of redundancy, blind channel estimators, block synchronizers, and direct self-recovering equalizing filterbanks are derived in this paper. The resulting algorithms are computationally simple, require small data sizes, can be implemented online, and remain consistent (after appropriate modifications), even at low SNR colored noise. Simulations illustrate applications to blind equalization of downlink CDMA transmissions, multicarrier modulations through channels with deep fades, and superior performance relative to CMA and existing output diversity techniques relying on multiple antennas and fractional sampling.
More than Just Territorial: The 8th Circuit Establishment a Resourceful Precedent in Claiming Jurisdiction over Denials to Compel Arbitration (2010)

This note argues that the Eighth Circuit's decision to claim jurisdiction in Industrial Wire Products, Inc. v. Costco Wholesale Corp. was practical and resourceful, as that court is better suited to decide matters of contract interpretation. The highly specialized Federal Circuit should devote its time and expertise to governing cases in particular areas of law, like patent litigation and administrative law. This note further argues that the Eighth Circuit preserved judicial resources and adhered to the parties' intentions in holding that the patent infringement claims were required to proceed through arbitration.
Transglutaminase-Based Chemo-Enzymatic Conjugation Approach Yields Homogeneous Antibody–Drug Conjugates (2014)

Most chemical techniques used to produce antibody-drug conjugates (ADCs) result in a heterogeneous mixture of species with variable drug-to-antibody ratios (DAR) which will potentially display different pharmacokinetics, stability, and safety profiles. Here we investigated two strategies to obtain homogeneous ADCs based on site-specific modification of deglycosylated antibodies by microbial transglutaminase (MTGase), which forms isopeptidic bonds between Gln and Lys residues. We have previously shown that MTGase solely recognizes Gln295 within the heavy chain of IgGs as a substrate and can therefore be exploited to generate ADCs with an exact DAR of 2. The first strategy included the direct, one-step attachment of the antimitotic toxin monomethyl auristatin E (MMAE) to the antibody via different spacer entities with a primary amine functionality that is recognized as a substrate by MTGase. The second strategy was a chemo-enzymatic, two-step approach whereby a reactive spacer entity comprising a bio-orthogonal thiol or azide function was attached to the antibody by MTGase and subsequently reacted with a suitable MMAE-derivative. To this aim, we investigated two different chemical approaches, namely, thiol-maleimide and strain-promoted azide-alkyne cycloaddition (SPAAC). Direct enzymatic attachment of MMAE-spacer derivatives at an 80 molar excess of drug yielded heterogeneous ADCs with a DAR of between 1.0 to 1.6. In contrast to this, the chemo-enzymatic approach only required a 2.5 molar excess of toxin to yield homogeneous ADCs with a DAR of 2.0 in the case of SPAAC and 1.8 for the thiol-maleimide approach. As a proof-of-concept, trastuzumab (Herceptin) was armed with the MMAE via the chemo-enzymatic approach using SPAAC and tested in vitro. Trastuzumab-MMAE efficiently killed BT-474 and SK-BR-3 cells with an IC50 of 89.0 pM and 21.7 pM, respectively. Thus, the chemo-enzymatic approach using MTGase is an elegant strategy to form ADCs with a defined DAR of 2. Furthermore, the approach is directly applicable to a broad variety of antibodies as it does not require prior genetic modifications of the antibody sequence.
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data (2009)

The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).
Lossless watermarking technique for copyright protection of high resolution images (2014)

With the revolution of E-commerce websites, there is a great need for development of copyright protection techniques, which are able to detect ownership from the Intellectual Property. In this paper, a novel watermarking method, is proposed as a solution for copyright protection of very high resolution images. Application of the concept of Visual Cryptography and Central Limit Theorem, on a Correlation Matrix obtained from the image to be protected is the key approach used in this paper, so as to satisfy the requirements. The proposed method have merits such as 100 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">%</sup> imperceptibility and unrestricted watermark image size, without compromising robustness.
Discovering Rhetoric Agreement between a Request and Response (2017)

To support a natural flow of a conversation between humans and automated agents, rhetoric structures of each message has to be analyzed. We classify a pair of paragraphs of text as appropriate for one to follow another, or inappropriate, based on both topic and communicative discourse considerations. To represent a multi-sentence message with respect to how it should follow a previous message in a conversation or dialogue, we build an extension of a discourse tree for it. Extended discourse tree is based on a discourse tree for RST relations with labels for communicative actions, and also additional arcs for anaphora and ontology-based relations for entities. We refer to such trees as Communicative Discourse Trees (CDTs). We explore syntactic and discourse features that are indicative of correct vs incorrect request-response or question-answer pairs. Two learning frameworks are used to recognize such correct pairs: deterministic, nearest-neighbor learning of CDTs as graphs, and a tree kernel learning of CDTs, where a feature space of all CDT sub-trees is subject to SVM learning. We form the positive training set from the correct pairs obtained from Yahoo Answers, social network, corporate conversations including Enron emails, customer complaints and interviews by journalists. The corresponding negative training set is artificially created by attaching responses for different, inappropriate requests that include relevant keywords. The evaluation showed that it is possible to recognize valid pairs in 70% of cases in the domains of weak request-response agreement and 80% of cases in the domains of strong agreement, which is essential to support automated conversations. These accuracies are comparable with the benchmark task of classification of discourse trees themselves as valid or invalid, and also with classification of multi-sentence answers in factoid question-answering systems. The applicability of proposed machinery to the problem of chatbots, social chats and programming via NL is demonstrated. We conclude that learning rhetoric structures in the form of CDTs is the key source of data to support answering complex questions, chatbots and dialogue management.
Purification and properties of a lipase fromPenicillium chrysogenum isolated from industrial wastes (2000)

A fungal lipase was isolated from the wastes of industrial cultures of Penicillium chrysogenum employed in antibiotics production. Lipase activity was only detected in solid aggregates present in the protein concentrates. To extract the lipase, Triton X-100 was the most suitable surfactant. The lipase was further purified by hydrophobic interaction and anion exchange chromatography. A molecular mass of approx 40 kDa and a pI of approx 3.8 were estimated. Optimum pH and temperature were 7.9–8.1 and 45 °C respectively. Although its activity in the hydrolysis of lipids and esters is not very high, the lipase from P chrysogenum proved to be notably efficient in several synthetic reactions in non-aqueous media. © 2000 Society of Chemical Industry
Identification of an activating transcription factor (ATF) binding site in the human transforming growth factor-beta 2 promoter. (1992)

Transforming growth factor TGF-beta 2 is encoded by multiple mRNA transcripts of 5.8, 5.1, 4.0, 3.8, and 2.8 kilobase pairs (kb) that are expressed in various human and monkey cells. Northern blot analysis using genomic fragments of DNA was used to demonstrate that some of this size heterogeneity is due to differences in the length of the 5'-untranslated region. Probes that were colinear with the first 600 nucleotides of the 5'-untranslated region detected only the 5.8-, 4.0-, and 3.8-kb transcripts. In order to identify DNA elements that regulate the transcription of these mRNA transcripts, deletion constructs of 5'-flanking DNA were ligated to the coding region for chloramphenicol acetyltransferase (CAT) and analyzed for promoter activity in several cell lines. Sequences responsible for putative enhancer and silencer regions were identified between -778 and -40 relative to the transcription initiation site. Addition of a cyclic AMP-responsive element/activating transcription factor-like element at -74 resulted in a 5-10-fold increase in CAT activity over that expressed with a construct that contained only the TATA box. This increase in CAT activity was suppressed by the addition of DNA sequences between -257 and -187, whereas sequences between -778 and -257 stimulated CAT activity. Point mutations within the ATF binding site at -74 resulted in a marked decrease in CAT expression. Cotransfection with ATF-1 or ATF-2 expression plasmids resulted in both dose-dependent stimulatory and inhibitory activities that were cell type-dependent. These studies identify multiple transcription initiation sites for TGF-beta 2 and demonstrate that transcription from one of these promoters is dependent upon an ATF binding site located 5' of the TATA box.
Le Haut-Atlas central (Maroc). Stratigraphie et paléontologie du Lias supérieur et du Dogger inférieur. Dynamique du bassin et des peuplements (1992)

Sadki Driss. Le Haut-Atlas central (Maroc). Stratigraphie et paléontologie du Lias supérieur et du Dogger inférieur. Dynamique du bassin et des peuplements. In: Documents des Laboratoires de Géologie, Lyon, n°142, 1996. Le Haut-Atlas central (Maroc). Stratigraphie et paléontologie du Lias supérieur et du Dogger inférieur. Dynamique du bassin et des peuplements. pp. 3-245.
Neutralizing B-Cell–Activating Factor Antibody Improves Survival and Inhibits Osteoclastogenesis in a Severe Combined Immunodeficient Human Multiple Myeloma Model (2007)

Our data show a role for BAFF as a survival factor in MM. Importantly, the in vivo antitumor activity of neutralizing anti-BAFF antibody provide the preclinical rationale for its evaluation in the treatment of MM.
Total Synthesis of (±)-Communesin F via a Cycloaddition with Indol-2-one (2012)

A concise total synthesis of (±)-communesin F has been completed in 15 linear steps from 4-bromotryptophol in an overall yield of 6.7%. A key step features the cycloaddition of indol-2-one with 3-(2-azidoethyl)-4-bromoindole and facilitates the rapid construction of the lower aminal-containing tetracyclic core of the natural product.
Bioinformatics and functional genomics (2004)

The bestselling introduction to bioinformatics and functional genomicsnow in an updated editionWidely received in its previous edition, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded Second Edition, it continues to be the go-to source for students and professionals involved in biomedical research.This edition provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include:Several fundamentally important proteins, such as globins, histones, insulin, and albumins, are included to better show how to apply bioinformatics tools to basic biological questions.A completely updated companion web site, which will be updated as new information becomes available - visit www.wiley.com/go/pevsnerbioinformaticsDescriptions of genome sequencing projects spanning the tree of life.A stronger focus on how bioinformatics tools are used to understand human disease.The book is complemented by lavish illustrations and more than 500 figures and tablesfifty of which are entirely new to this edition. Each chapter includes a Problem Set, Pitfalls, Boxes explaining key techniques and mathematics/statistics principles, Summary, Recommended Reading, and a list of freely available software. Readers may visit a related Web page for supplemental information at www.wiley.com/go/pevsnerbioinformatics.Bioinformatics and Functional Genomics, Second Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.Praise for the first edition:...ideal both for biologists who want to master the application of bioinformatics to real-world problems and for computer scientists who need to understand the biological questions that motivate algorithms. Quarterly Review of Biology an excellent textbook for graduate students and upper level undergraduate students. Annals of Biomedical Engineeringhighly recommended for academic and medical libraries, and for researchers as an introduction and reference E-Streams
A METHOD FOR THE DETERMINATION OF FAT IN MILK (NEPHELOMETRIC METHOD). (1914)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA METHOD FOR THE DETERMINATION OF FAT IN MILK (NEPHELOMETRIC METHOD).W. R. BloorCite this: J. Am. Chem. Soc. 1914, 36, 6, 1300–1304Publication Date (Print):June 1, 1914Publication History Published online1 May 2002Published inissue 1 June 1914https://pubs.acs.org/doi/10.1021/ja02183a019https://doi.org/10.1021/ja02183a019research-articleACS PublicationsRequest reuse permissionsArticle Views141Altmetric-Citations5LEARN 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
Low-temperature Ar/N2 remote plasma nitridation of SiO2 thin films (2002)

Low-temperature nitridation of SiO2 thin films by Ar/N2 remote plasma processing was investigated using on-line Auger electron spectroscopy, angle-resolved x-ray photoelectron spectroscopy (ARXPS), and optical emission spectroscopy (OES). Nitridation experiments were performed at 300 °C using 30 W Ar/N2 remote plasmas at 0.1 and 0.3 Torr. Ar/N2 remote plasma exposure of 5 nm SiO2 films for 30 min results in nitrogen incorporation throughout the films, independent of process pressure and plasma reactor configuration (i.e., upstream versus downstream N2 injection). ARXPS indicates a N–Si3 local bonding configuration with second nearest neighbor oxygen atoms. Ar/N2 remote plasma exposure at 0.1 Torr results in higher nitrogen concentrations (8–10 at. %). Reactor configuration has a negligible effect at 0.1 Torr; conversely, downstream N2 injection results in higher nitrogen concentrations (5–6 at. %) than upstream injection (3–4 at. %) at 0.3 Torr. OES indicates that the Ar/N2 remote plasmas contain N2 triplet excited states and ground-state N atoms. The Ar emission intensities and the saturation N concentrations in the resultant films follow similar trends with processing pressure and reactor configuration; the N2 first positive emission intensities run counter to these trends. We infer that low-temperature SiO2 nitridation by Ar/N2 remote plasmas is a two-step process: O removal by Ar+ ion bombardment and N insertion by plasma-generated active N species. Moreover, the first step appears to be rate limiting under the conditions employed in this study. Annealing the oxynitride films in N2 at 900 °C decreases the N concentration and results in a more uniform nitrogen distribution.