gebhart/patrepeval huggingface dataset:
Aberrations of <i>ERBB2</i> and <i>TOP2A</i> genes in breast cancer (2009)

Copy number changes in TOP2A have frequently been linked to ERBB2 (HER2) amplified breast cancers. To study this relationship, copy number changes of ERBB2 and TOP2A were investigated by fluorescence in situ hybridization (FISH) in two cell lines; one characterized by having amplification of both genes and the other by having amplification of ERBB2 and deletion of TOP2A. The characteristics are compared to findings on paired ERBB2 and TOP2A data from 649 patients with invasive breast cancer from a previously published biomarker study. The physical localization of FISH signals in metaphase spreads from cell lines showed that simultaneous amplification is not a simple co-amplification of a whole amplicon containing both genes. Most gene signals are translocated to abnormal marker chromosomes. ERBB2 genes but not TOP2A genes are present in tandem amplicons, leading to a higher ERBB2 ratio. This observation was confirmed by patient FISH data: among 276 (43% of all patients) abnormal tumors, 67% had different ERBB2 and TOP2A status. ERBB2 amplification with normal TOP2A status was found in 36% of the abnormal tumors (15% of all patients). Simultaneous amplification of both genes was found in 28% of the abnormal tumors (12% of all patients) while TOP2A deletion and ERBB2 amplification was observed in 16% of the abnormal cases (8% of all patients). A small number of tumors had TOP2A amplification (4%) or deletion (6%) without simultaneous changes of the ERBB2 gene. ERBB2 deletion was also observed (5%) but only in tumors with simultaneous TOP2A deletion. The average gene/reference ratio was significantly different: 5.0 for TOP2A but 7.2 for ERBB2 in the amplified tumors (P<0.01). Amplification of the two genes may be caused by different mechanisms, leading to higher level of amplification for ERBB2 compared to TOP2A. In the majority of breast cancer patients, simultaneous aberration of ERBB2 and TOP2A is not explained by simple co-amplification.
Arrangement of sequences in the inverted terminal repetition of adenovirus 18 DNA. (1975)

In contrast to the single-stranded circular molecules produced with denatured DNA from other adenoviruses, there was associated with nearly all circular molecules of adenovirus type 18 a visible, duplex projection. These projections had a mean contour length of 0.31 +/- 0.12 mum, equivalent to approximately 3% of genome length. Individual projections ranged in size from 0.1 to 2 mum. Alkaline sucrose gradient purification of single-stranded molecules did not affect formation of these projections, and treatment of a preparation of circular molecules with Neurospora crassa single-strand specific nucleases yielded 0.34 +/- 0.09 mum duplex fragments. Single-stranded circles did not form if a limited number of nucleotides were removed from the 3' ends of native molecules by Escherichia coli exonuclease III digestion prior to denaturation and annealing. In addition, preformed single-stranded circles could be converted to linear molecules by similar treatment. Based on the formation of specific heteroduplex structures when preparations of native DNA were denatured and reannealed and the absence of branches on linear, single-stranded molecules, we conclude that projections are generated by unusually long, inverted terminal repetitions. The repetitious sequences occur in place of rather than in addition to regular sequences. These data provide direct, visual evidence for the arrangement of bases in the inverted terminal repetition of adenovirus DNA.
Modeling Tumor Treating fields (TTFields) application within a realistic human head model (2015)

Tumor Treating Fields (TTFields) are an antimitotic treatment against brain and other tumors. They are applied regionally and non-invasively by inducing intermediate frequency (100-300 kHz) alternating electric field of intensities between 1 to 3 V/cm through transducer arrays placed on the patient's skin close to the tumor. All TTFields studies predicted variability in treatment response among patients, whereas in vitro experiments indicate that the magnitude and direction of the electric field in the tumor might be crucial determinants of efficacy. Differences in the field might arise from varying tumor positions or array placement. By investigating different scenarios within a realistic human head model we hope to advance our understanding of TTFields therapy in clinical practice. We constructed a model from MRI data to calculate the electric field distribution in the brain using the Finite Element Method. An anisotropic electrical conductivity tensor was estimated using diffusion tensor imaging data. The head model contained different tissue types: scalp, skull, cerebrospinal fluid, gray and white matter. Additionally a virtual spherical tumor was included, two positions for the tumor were considered. Transducer arrays were placed on the scalp to model the commonly used device for TTFields delivery. One additional setup of the two transducer pairs was specifically adapted to the second tumor position. The results predict that the electric field strength exceeds the assumed therapeutic threshold value of 1 V/cm in both tumors for both active array pairs. For the second tumor the adapted transducer layout improved field delivery. The average field strength in the tumor further depends on tumor electrical properties. Yet a cystic and a solid tumor experience the same average field strength when treated with TTFields. As a next step towards personalized TTFields therapy, we will explore possible benefits of individualized treatment planning.
Improved lossless intra coding for next generation video coding (2016)

Recently, there have been efforts by the ITU-T VCEG and ISO/IEC MPEG to further improve the compression performance of the High Efficiency Video Coding (HEVC) standard for developing a potential next generation video coding standard. The exploratory codec software of this potential standard includes new coding tools for inter and intra coding. In this paper, we present a new intra prediction mode for lossless intra coding. Our new intra mode derives a prediction filter for each input pixel using its neighboring reconstructed pixels, and applies this filter to the nearest neighboring reconstructed pixels to generate a prediction pixel. The proposed intra mode is demonstrated to improve the performance of the exploratory software for lossless intra coding, yielding a maximum and average bitrate savings of 4.4% and 2.11%, respectively.
Private-by-Design Advertising and Analytics: From Theory to Practice (2014)

how to operate the auctions that are critical to current advertising systems.Without this component, these systems leave unanswered what revenue the broker (i.e. an ad network like Google) can earn, thereby reducing the likelihood that a private-by-design advertising system will be of commercial interest.In this thesis, we address the challenge of running auctions that leverage a user profile for ad ranking while keeping the user profile private.Each of the systems cited above claims to be practical in that they provide both good privacy and good utility at reasonable cost.However, none of the proposed designs have been deployed and evaluated in real-life settings.This thesis attempts to fill this gap and answer a number of fundamental questions:"Is private-by-design advertising really practical?","Can relevant ads be delivered?","Is it possible to adequately measure the systems without infringing on user privacy?", "Will unforeseen devils in the details kill the system?"To do so, we built, deployed, and evaluated a fully functional prototype of a private-by-design ad system based on the Privad design [33].Our deployment delivered functional ads in the sense that the ads were targeted to user interests, displayed on publisher webpages, linked to real shopping websites, and in fact led to actual purchases.Side-by-side with Privad, we also deployed a distributed differentially-private user analytics system, PDDP [19], that served as our primary means of gathering experimental data. ContributionsAltogether, this thesis makes the following contributions towards transforming private-by-design advertising from a theoretical abstraction to a practical sys-
The Mechanism of Addition of Grignard Reagents to Ketones (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Mechanism of Addition of Grignard Reagents to KetonesC. Gardner Swain and Henry B. BoylesCite this: J. Am. Chem. Soc. 1951, 73, 2, 870–872Publication Date (Print):February 1, 1951Publication History Published online1 May 2002Published inissue 1 February 1951https://pubs.acs.org/doi/10.1021/ja01146a531https://doi.org/10.1021/ja01146a531research-articleACS PublicationsRequest reuse permissionsArticle Views1003Altmetric-Citations57LEARN 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
Genetic system for analyzing Escherichia coli thymidylate synthase (1984)

Random in vitro mutagenesis of the thyA gene is being used to delineate its regulatory elements as well as the functional domains of its product, thymidylate synthase (EC 2.1.1.45). Streamlined procedures have been developed for the isolation and characterization of the mutants. Positive selection for synthase-deficient thyA Escherichia coli permitted the isolation of 400 mutants, which are being categorized by phenotypic and genetic criteria. An in situ 5-fluorodeoxyuridylate binding assay was devised to rapidly probe the substrate binding domain, whereas facile mapping procedures, based on pBR322- or M13-borne thyA deletion derivatives, were developed to localize mutations. The sequence changes of one amber mutation and another mutation that abolishes catalysis while maintaining substrate binding activity are presented. The orientation of the thyA gene on the E. coli chromosome was established.
GENERALIZED MENINGITIS OF OTITIC ORIGIN; USE OF FORCED SPINAL DRAINAGE IN TREATMENT: Report of a Case (1935)

By generalized meningitis I refer to that form in which organisms are obtained in culture from the spinal fluid. Such a condition is often met and, except in the epidemic type, the outcome is unfortunately almost invariably fatal. Cases of meningitis in which the organisms are obtained only from the spinal fluid in smears offer a very different prognosis from those in which the organisms are grown in culture. The case reported here is of interest because of recovery following an attack of generalized meningitis. REPORT OF CASE In M. P., a girl of 13 years, acute otitis media on the right side developed on Feb. 10, 1934, at which time a myringotomy was performed. There had been no previous trouble with the ears or other serious illness. The ear continued to discharge, and the patient was admitted to the Manhattan Eye, Ear and Throat Hospital. Eight days later a
Novel Macromolecular Self-organization of Poly(ethylene glycol)- block-poly(L-histidine): pH-induced Formation of Core-shell Nanoparticles in Aqueous Media (2001)

School of Chemistry & Molecular Engineering, Seoul National University, San 56-1,Shillim-dong, Kwanak-ku, Seoul 151-742, KoreaReceived December 1, 2000Keywords : Block copolymer, Poly(ethylene glycol), Poly(L-histidine), Self-assembly.Block copolymers composed of hydrophilic groups andhydrophobic segments can sometimes self-assemble in aselective solvent forming a supramolecular structure. Manystudies have been concentrated on block copolymers thatform polymeric micelles in an organic solvent.
Effect of medium composition on results of macrobroth dilution antifungal susceptibility testing of yeasts (1986)

A total of 62 different clinical yeast isolates were examined for susceptibility to four antifungal agents, amphotericin B, 5-fluorocytosine (5-FC), ketoconazole, and miconazole, using synthetic amino acid medium-fungi (SAAM-F), buffered yeast nitrogen broth (BYNB), Kimmig broth, casein-yeast-glucose broth (CYG), antibiotic medium 3-FDA (ANTI-3), and tryptic soy broth (TSB). A macrobroth dilution format was used with MICs determined after incubation for 24 and 48 h. All analyses were performed in duplicate. In general, MICs were more reproducible after 48 h of incubation. Furthermore, with certain medium-antifungal agent combinations, MICs determined after incubation for 48 h were significantly higher than those determined after 24 h. For instance, with 5-FC irrespective of the medium used, greater than 25% of all 48-h MICs were more than one twofold dilution higher than the corresponding MICs determined after incubation for 24 h. Similar observations were made with amphotericin B when tested with BYNB and CYG and with the imidazoles when tested in all of the media except CYG. The actual MICs obtained with the different antifungal agents were clearly influenced by the test medium used. The rank order of amphotericin B MICs according to test medium was as follows: BYNB greater than SAAM-F = Kimmig = CYG = ANTI-3 = TSB. With 5-FC, the following pattern was observed: Kimmig = ANTI-3 greater than SAAM-F = CYG = TSB greater than BYNB. For both imidazoles, ketoconazole and miconazole, the rank order of MICs according to test medium was BYNB = Kimmig = CYG = ANTI-3 = TSB greater than SAAM-F. The results of this investigation suggested that broth dilution susceptibility testing of yeasts is best performed with an incubation period of 48 h. Furthermore, medium composition can significantly influence the results of such testing.
Application of the Polanyi adsorption potential theory to adsorption from solution on activated carbon. IV. Steric factors, as illustrated by the adsorption of planar and octahedral metal acetylacetonates (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplication of the Polanyi adsorption potential theory to adsorption from solution on activated carbon. IV. Steric factors, as illustrated by the adsorption of planar and octahedral metal acetylacetonatesCary C. T. Chiou and Milton ManesCite this: J. Phys. Chem. 1973, 77, 6, 809–813Publication Date (Print):March 1, 1973Publication History Published online1 May 2002Published inissue 1 March 1973https://pubs.acs.org/doi/10.1021/j100625a015https://doi.org/10.1021/j100625a015research-articleACS PublicationsRequest reuse permissionsArticle Views170Altmetric-Citations23LEARN 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 options Get e-Alerts
Benzo[b]thiophene. III.<sup>1</sup> Synthesis of Hydroxylated Diphenylalkanes from Anisyl Derivatives of Benzo[b]thiophene (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBenzo[b]thiophene. III.1 Synthesis of Hydroxylated Diphenylalkanes from Anisyl Derivatives of Benzo[b]thiopheneRené Royer, Pierre Demerseman, Jean-Pierre Lechartier, and Andrée CheutinCite this: J. Org. Chem. 1962, 27, 11, 3808–3814Publication Date (Print):November 1, 1962Publication History Published online1 May 2002Published inissue 1 November 1962https://pubs.acs.org/doi/10.1021/jo01058a013https://doi.org/10.1021/jo01058a013research-articleACS PublicationsRequest reuse permissionsArticle Views115Altmetric-Citations11LEARN 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
Enhanced Activity of Enzymes Immobilized in Thermoresponsive Core−Shell Microgels (2009)

We present a quantitative study of the catalytic activity of beta-d-glucosidase from almonds adsorbed on thermosensitive microgels. The core-shell particles used as a carrier system consist of a solid polystyrene core onto which a poly(N-isopropylacrylamide) (PNiPA) network is grafted. In the swollen state of this microgel, i.e., below the critical solution temperature (LCST) of PNiPA, high amounts of enzyme can be immobilized into the PNiPA network without loss of colloidal stability. The enzymatic activity of beta-d-glucosidase in its native form and in the adsorbed state was analyzed in terms of Michaelis-Menten kinetics. Moreover, the dependence of the enzymatic activity on temperature was investigated. We demonstrate that the enzymatic activity of beta-d-glucosidase adsorbed on such a core-shell microgel is increased by a factor of more than three compared to its activity in solution. This is in marked contrast to other carrier systems that usually lead to a strong decrease of enzymatic activity. Both the high loading capacity of the carrier observed and the increase of the catalytic activity of immobilized beta-d-glucosidase are traced back to the formation of strong interactions between the enzyme and microgel. Studies by Fourier-transform infrared (FT-IR) spectroscopy identify the formation of hydrogen bonds as driving forces for the adsorption. Hydrogen bonding may also be the reason for the enhanced activity.
Deep transfer metric learning (2015)

Conventional metric learning methods usually assume that the training and test samples are captured in similar scenarios so that their distributions are assumed to be the same. This assumption doesn't hold in many real visual recognition applications, especially when samples are captured across different datasets. In this paper, we propose a new deep transfer metric learning (DTML) method to learn a set of hierarchical nonlinear transformations for cross-domain visual recognition by transferring discriminative knowledge from the labeled source domain to the unlabeled target domain. Specifically, our DTML learns a deep metric network by maximizing the inter-class variations and minimizing the intra-class variations, and minimizing the distribution divergence between the source domain and the target domain at the top layer of the network. To better exploit the discriminative information from the source domain, we further develop a deeply supervised transfer metric learning (DSTML) method by including an additional objective on DTML where the output of both the hidden layers and the top layer are optimized jointly. Experimental results on cross-dataset face verification and person re-identification validate the effectiveness of the proposed methods.
Clavulanic acid biosynthesis; the final steps (2001)

The chemically unstable anabolite (3R,5R)-clavulanate-9-aldehyde 1 and an NADPH dependent dehydrogenase have been detected in the broth of Streptomyces clavuligerus. The purified enzyme was shown to make clavulanic acid by reduction of the aldehydic moiety of synthetic 1 to the allylic alcohol of clavulanic acid 2. A DNA sequence corresponding to the enzyme’s N-terminal amino acid sequence was located within the clavulanic acid biosynthetic gene cluster. We have named this novel enzyme clavulanic acid dehydrogenase (CAD). In an attempt to determine the origin of 1, fermentations of S. clavuligerus were fed ornithine labelled with stable isotopes in the carboxy group. The results of these experiments are discussed.
Neurosteroid Prolongs GABA<sub>A</sub>Channel Deactivation by Altering Kinetics of Desensitized States (1997)

Fast applications of GABA (1 mM) to nucleated and outside-out patches excised from granule neurons in cerebellar slices from developing rats evoked currents with a double exponential time course reminiscent of that of IPSCs. A neurosteroid 3alpha, 21dihydroxy-5alpha-pregnan-20-one (THDOC) remarkably increased the slow deactivation time constant and slowed down recovery from desensitization, as estimated by paired-pulse GABA applications. THDOC also reduced the amplitude of GABA currents, whereas it failed to affect the fast deactivation component and its relative contribution to peak amplitude. The effects of THDOC on slow deactivation were greater in rats younger than postnatal day 13 (P13) as compared with rats at P30-P35. THDOC failed to alter deactivation of short responses induced by a less-potent agonist taurine at saturating doses. These responses had deactivation kinetics described by a fast single exponential decay, little desensitization, and quick recovery. However, THDOC slowed deactivation if taurine responses were long enough to allow consistent desensitization, suggesting that desensitized states are required for the neurosteroid to modulate GABA responses. In outside-out patches, just as desensitized states prolonged GABA responses by producing reopening of channels activated by brief GABA pulses, THDOC increased the channel open probability by further increasing the number of late channel openings, resulting in a prolongation of the slow deactivation. Our data suggest that neurosteroid potentiates the inhibitory postsynaptic transmission via the prolongation of the slow deactivation and that the alteration of kinetics of entry and exit from desensitized states underlies the allosteric modification of GABAA receptors by neurosteroids.
Socially grounded engineering for digital libraries (1995)

Our work embodies one approach to developing theories of use that can be embedded in programs and new ways of working. We argue that building digital libraries that work will require that systems design, development and deployment be grounded in use and done collaboratively with users, and we will describe our approach to accomplishing this as well as the issues and questions it raises.