gebhart/patrepeval huggingface dataset:
Establishment of a human cell line after transformation by a plasmid containing the early region of the SV40 genome (1983)

A human clonal cell line, designated TAH9, has been established from cells of adipose tissue by fusion with E. coli protoplasts containing a recombinant plasmid carrying the early genes of Simian virus 40. The establishment of the cell line is preceeded by a delayed growth crisis. The results indicate that, after cell transformation, another event(s) of low frequency is required for cell immortalization. Some biological properties of TAH9 cells are also described.
Quantitative study of atomic ordering in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ga</mml:mi></mml:mrow><mml:mrow><mml:mn>0.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">In</mml:mi></mml:mrow><mml:mrow><mml:mn>0.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>P thin films by<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">P</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>31</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math>nuclear magnetic resonance (1992)

We use $^{31}\mathrm{P}$ nuclear-magnetic-resonance (NMR) spectra to measure the degree of cation ordering in thin films of the semiconductor alloy ${\mathrm{Ga}}_{0.5}$${\mathrm{In}}_{0.5}$P grown by organometallic vapor-phase epitaxy. We show that the five possible ${\mathrm{Ga}}_{\mathit{n}}$${\mathrm{In}}_{4\mathrm{\ensuremath{-}}\mathit{n}}$P clusters in ${\mathrm{Ga}}_{\mathit{x}}$${\mathrm{In}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$P give rise to resolved NMR lines under magic-angle spinning, allowing a determination of the degree of cation ordering from the relative areas of the five lines. The ordering is shown to be weak (order parameter \ensuremath{\le}0.6) even in films that appear highly ordered in transmission electron microscopy.
Changing R&D models in research-based pharmaceutical companies (2016)

New drugs serving unmet medical needs are one of the key value drivers of research-based pharmaceutical companies. The efficiency of research and development (R&D), defined as the successful approval and launch of new medicines (output) in the rate of the monetary investments required for R&D (input), has declined since decades. We aimed to identify, analyze and describe the factors that impact the R&D efficiency. Based on publicly available information, we reviewed the R&D models of major research-based pharmaceutical companies and analyzed the key challenges and success factors of a sustainable R&D output. We calculated that the R&D efficiencies of major research-based pharmaceutical companies were in the range of USD 3.2-32.3 billion (2006-2014). As these numbers challenge the model of an innovation-driven pharmaceutical industry, we analyzed the concepts that companies are following to increase their R&D efficiencies: (A) Activities to reduce portfolio and project risk, (B) activities to reduce R&D costs, and (C) activities to increase the innovation potential. While category A comprises measures such as portfolio management and licensing, measures grouped in category B are outsourcing and risk-sharing in late-stage development. Companies made diverse steps to increase their innovation potential and open innovation, exemplified by open source, innovation centers, or crowdsourcing, plays a key role in doing so. In conclusion, research-based pharmaceutical companies need to be aware of the key factors, which impact the rate of innovation, R&D cost and probability of success. Depending on their company strategy and their R&D set-up they can opt for one of the following open innovators: knowledge creator, knowledge integrator or knowledge leverager.
Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. (1992)

In this work, we have predicted and mapped the potential Z-DNA-forming sequences in over one million base pairs of human DNA, containing 137 complete genes. The computer program (Z-Hunt-II) developed for this study uses a rigorous thermodynamic search strategy to map the occurrence of left-handed Z-DNA in genomic sequences. The search algorithm has been optimized to search large sequences for the potential occurrence of Z-DNA, taking into account sequence type, length, and cooperativity for a given stretch of potential Z-DNA-forming nucleotides. In this extensive data set we have identified 329 potential Z-DNA-forming sequences. The exact locations of the potential Z-DNA-forming sequences in the data set have been mapped with respect to the location of structural features of the genes. This analysis reveals a distinctly nonrandom distribution of potential Z-DNA-forming sequences across human genes and, most notably, that strong Z-DNA-forming sequences are more commonly found near the 5' ends of genes. We find that 35% of the Z-DNA-forming sequences are located upstream of the first expressed exon, while only 3% of the sequences are located downstream of the last expressed exon. The remaining 62% of the Z-DNA-forming sequences, which are located either in introns (47.1%) or exons (14.9%), are also nonrandomly distributed, with a strong bias toward locations near the site of transcription initiation. We interpret this distribution of potential Z-DNA-forming sequences toward the 5' end of human genes in terms of the well established "twin-domain model" of transcription-induced supercoiling and the effect of this topological strain on Z-DNA formation in eukaryotic cells.
Relationship between photosynthetic radiation‐use efficiency of barley canopies and the photochemical reflectance index (PRI) (1996)

Some processes of excess radiation dissipation have been associated with changes in leaf reflectance near 531 nm. We aimed to study the relations between the photochemical reflectance index (PRI) derived from this signal, and photosynthetic radiation‐use efficiency (defined as net CO 2 assimilation rate/incident photon flux density) in a cereal canopy. Measurements of reflectance, fluorescence, gas exchange and xanthophyll cycle pigments were made in the morning, midday and afternoon in barley canopies with two levels of nitrogen fertilization. The photosynthetic radiation‐use efficiency decreased at midday, mainly in the third leaf, in both treatments, with lower values for the nitrogen deficient leaves. The zeaxanthin content showed the inverse pattern, increasing at midday and in the nitrogen deficient treatment. The photosynthetic radiation‐use efficiency was well correlated with the epoxidation state, EPS (violaxanthin + 0.5 antheraxanthin)/(violaxanthin + antheraxanthin + zeaxanthin). The PRI [here defined as (R 539 ‐ R 570 )/(R 539 + R 570 )] was significantly correlated with epoxidation state and zeaxanthin and with photosynthetic radiation‐use efficiency. These results validate the utility of PRI in the assessment of radiation‐use efficiency at canopy level.
Crosslinking transcription factors to their recognition sequences with Pt<sup>II</sup>complexes (1992)

We have prepared phosphorothioate-containing cyclic oligodeoxynucleotides that fold into 'dumbbells' containing CRE and TRE sequences, the binding sequences for the CREB and JUN proteins, respectively. Six phosphorothioate residues were introduced into each of the recognition sequences. K2PtCl4 crosslinks CRE to CREB and TRE to JUN. The extent of crosslinking is about eight times greater than that observed with standard oligodeoxynucleotides and amounts to 30-50% of the efficiency of non-covalent association as estimated by gel-shift assays. Crosslinking is reversed by incubation with NaCN. The crosslinking reaction is specific--a dumbbell oligonucleotide with six phosphorothioate groups introduced into the Sp1 recognition sequence could not be crosslinked efficiently to CREB or JUN proteins with K2PtCl4. The binding of TRE to CREB is not strong enough for effective detection by gel-shift assays, but the TRE-CREB complex is crosslinked efficiently by K2PtCl4 and can then readily be detected.
Image recognition with an analog neural net chip (2003)

The authors applied an analog neural net chip to several machine vision tasks, among them: locate the address blocks on mail pieces, find handwritten text on checks, and discriminate between handwritten and machine printed characters. The chip, operating as a co-processor of a workstation, provides a speed-up of about a factor of 1000, compared with the workstation. The computation speed achieved lies between one and ten billion multiply-accumulates per second. The neural net chip is based on building blocks, 'neurons', that can be arranged in various network architectures. The data flow is optimized for implementing large, structured neural nets, and is also suited for any task where signals are to be convolved with many kernels. Some of the networks are trained on the neural net chip with a weight-perturbation learning algorithm that was adapted to work with the coarse quantization of the weights and the states in the chip.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Titration of Fluorine in Aqueous Solutions (1937)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTTitration of Fluorine in Aqueous SolutionsR. J. Rowley and H. V. ChurchillCite this: Ind. Eng. Chem. Anal. Ed. 1937, 9, 12, 551–552Publication Date (Print):December 1, 1937Publication History Published online1 May 2002Published inissue 1 December 1937https://pubs.acs.org/doi/10.1021/ac50116a001https://doi.org/10.1021/ac50116a001research-articleACS PublicationsRequest reuse permissionsArticle Views119Altmetric-Citations26LEARN 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
New Catalyst Systems for the Catalytic Conversion of Methane into Methanol (2002)

Palladium complexes with N-heterocyclic carbenes, such as in the biscarbene chelate ligands shown (R=tBu, Me; X=Br, I), have proved to be stable in strongly acidic media and were tested in the catalytic conversion of methane into methanol. The prominent influence of the halogenide ligand is shown since, in contrast to the bromo complex, the iodo complex does not catalyze the reaction. The steric bulk of the substituents R also influences the catalytic activity.
A new regioselective synthesis of pterocarpans (1989)

T. A. Engler, K. D. Combrink and J. P. Reddy, J. Chem. Soc., Chem. Commun., 1989, 454 DOI: 10.1039/C39890000454
Predictors of Adherence With Antihypertensive and Lipid-Lowering Therapy (2005)

Adherence with concomitant AH and LL therapy is poor, with only 1 in 3 patients adherent with both medications at 6 months. Physicians may be able to significantly improve adherence by initiating AH and LL therapy concomitantly and by reducing pill burden.
Continuous-tone gray-scale photomasks based on photosensitive spin-on-glass technology for deep-UV lithography applications (2003)

A technology for the low cost production of continuous tone gray scale photomasks for deep UV photolithography applications has been demonstrated. This technology is based on the use of a photosensitive spin-on-glass (SOG) thin film deposited onto a UV transparent substrate such as quartz. Different light exposure energies, from either a lithography setup or a laser pattern generator, onto the photosensitive SOG film changes the UV absorption spectrum at both H and I mercury emission lines. The amount of photo induced attenuation on the film is directly proportional to light exposure energy, hence allowing the formation of fully continuous tone patterns. Once the image pattern is photo-generated with a resolution of 0.1 to 1 micrometer, it is permanently fixed by a thermal treatment step without the need of an etching step. This new continuous tone deep UV photomask technology offers new cost effective opportunities for the production of micro-electro-mechanical systems (MEMS) structures, diffractive optical elements (DOEs), computer generated holograms (CGHs), and kinoform optics.
Understanding and managing the relationship between requirement changes and product constraints in component-based software projects (2002)

The recent surge of interest in component based software engineering (CBSE) represents a strong re emergence of systems integration within the software industry. This approach comprises the acquisition adaptation, and integration of reusable software components, often are purchased off the shelf to enable rapid deployment of complex systems with minimum development effort and resource cost. While the number of CBSE based projects continues to increase, small percentage can be claimed success. The paper asserts that the existence of a cyclical dependency between requirement change and reusable software component selection creates fundamental project management problems in component based software development. This is due to: (1) the high cost in effort and time required to re-evaluate, reselect, and reintegrate reusable software components to support new changes in the overall system requirements; and (2) the high cost in effort and time required to re-evaluate, renegotiate, and rewrite the system requirements to reflect the constraints of the underlying software components selected. We use our experience in building component based distributed network management systems to illustrate the problems with cyclical requirement component dependency in CBSE. We also present a set of effective risk mitigation strategies that have been adopted to minimize these problems in ongoing CBSE projects.
3D shape measurements for plano-convex lenses using fringe projection techniques (2014)

An approach using the fringe projection technique to perform the 3D profile measurement for a plano-convex lens is proposed. A fringe pattern is illuminated onto the lens object, and a CCD camera is employed to record the transmitted fringes on the screen. Fringes on the obtained image are deformed both by the refractive index and the topography of the object, and are analyzable to retrieve the 3D shape.
Correction: Pericytes Derived from Adipose-Derived Stem Cells Protect against Retinal Vasculopathy (2013)

Background: Retinal vasculopathies, including diabetic retinopathy (DR), threaten the vision of over 100 million people. Retinal pericytes are critical for microvascular control, supporting retinal endothelial cells via direct contact and paracrine mechanisms. With pericyte death or loss, endothelial dysfunction ensues, resulting in hypoxic insult, pathologic angiogenesis, and ultimately blindness. Adipose-derived stem cells (ASCs) differentiate into pericytes, suggesting they may be useful as a protective and regenerative cellular therapy for retinal vascular disease. In this study, we examine the ability of ASCs to differentiate into pericytes that can stabilize retinal vessels in multiple pre-clinical models of retinal vasculopathy.
Sum-frequency generation with a free-electron laser: A study of gallium phosphide (1994)

The use of a free-electron laser (FEL) allows the study of (non)linear optical properties of materials over unsurpassed large spectral intervals. Here we report on the application of a FEL as the IR source in spectroscopic infrared-visible sum-frequency generation (SFG). Using the extremely wide tunability and the high peak power of a FEL we have studied the frequency dependence of the nonlinear susceptibility for sum-frequency generation in gallium phosphide between 20 and 32 \ensuremath{\mu}m in great detail. It is shown that the SFG spectrum is heavily modified by linear optical effects.
Determination of minority carrier lifetimes in n-type GaAs and their implications for solar cells (2002)

A comprehensive study of n-type lifetimes versus doping concentration in selenium doped n-GaAs is detailed. By observing the photoluminescence delay of double heterostructure it is found that for N/sub D/<10/sup 18/ cm/sup -3/ the minority carrier lifetime is dominated by radiative recombination and photon recycling, and that both are also important for all doping concentrations studied. For N/sub D/>10/sup 18/ cm/sup -3/, the authors are able to set an upper limit on the Auger recombination coefficient. The B coefficient in n-GaAs is deduced to about 2.0*10/sup -10/ cm/sup 3//s for lowly doped material, but it decreases with increasing doping concentration. These results are used to project efficiencies of GaAs solar cells using analytical models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Towards a component-based middleware framework for configurable and reconfigurable grid computing (2005)

Significant progress has been made in the design and development of grid middleware which, in its present form, is founded on service-oriented architecture and Web services technologies. Nevertheless, grid middleware is still severely limited in key areas. In this paper we discuss work that aims to address some of these limitations. First, we consider how ideas and principles from the wider middleware research community can usefully be applied in a grid middleware context. Then we focus on our own current work on integration of the grid middleware platform with an extensible set of interaction types and advanced network services, and on an architectural framework for grid middleware internals. We believe that these areas, along with complexity management, become increasingly important as sophisticated e-science applications start to exploit the potential of service-oriented architecture-based middleware.
Effect of herbimycin A, an antagonist of tyrosine kinase, on bcr/abl oncoprotein-associated cell proliferations: abrogative effect on the transformation of murine hematopoietic cells by transfection of a retroviral vector expressing oncoprotein P210bcr/abl and preferential inhibition on Ph1-positive leukemia cell growth (1992)

Herbimycin A, a benzoquinoid ansamycin antibiotic, was demonstrated to decrease intracellular phosphorylation by protein tyrosine kinase (PTK). In Philadelphia chromosome (Ph1)-positive leukemias such as chronic myelogenous leukemia (CML) and Ph1-positive acute lymphoblastic leukemia (ALL), both of which express bcr-abl fused gene products (P210bcr-abl or P190bcr-abl protein kinase) with augmented tyrosine kinase activities, herbimycin A markedly inhibited the in vitro growth of the Ph1-positive ALL cells and the leukemic cells derived from CML blast crisis. However, the same dose of herbimycin A did not inhibit in vitro growth of a broad spectrum of Ph1-negative human leukemia cells, and several other protein kinase antagonists also displayed no preferential inhibition. Furthermore, we demonstrated that herbimycin A has an antagonizing effect on the growth of transformed cells by a transfection of retroviral amphotrophic vector expressing P210bcr/abl into a murine interleukin (IL)-3-dependent myeloid FDC-P2 cell line. This inhibition was abrogated by the addition of sulfhydryl compounds, similar to the reaction previously described for Rous sarcoma virus transformation. The inhibitory effect of herbimycin A on the growth of Ph1-positive cells was associated with decreased bcr/abl tyrosine kinase activity, but no decrease of bcr-abl mRNA and protein, suggesting that the inactivation of bcr-abl tyrosine kinase activity by herbimycin A may be induced by its binding to the bcr-abl protein portion that is rich with sulfhydryl groups. The present study indicates that herbimycin A is a beneficial agent for the investigation of the role of the bcr-abl gene in Ph1-positive leukemias and further suggests that the development of agents inhibiting the bcr-abl gene product may offer a new therapeutic potential for Ph1-positive leukemias.
Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of <i>EP300</i> and <i>CREBBP</i> (2016)

Chromosomal translocations are a genomic hallmark of many hematologic malignancies. Often as initiating events, these structural abnormalities result in fusion proteins involving transcription factors important for hematopoietic differentiation and/or signaling molecules regulating cell proliferation and cell cycle. In contrast, epigenetic regulator genes are more frequently targeted by somatic sequence mutations, possibly as secondary events to further potentiate leukemogenesis. Through comprehensive whole-transcriptome sequencing of 231 children with acute lymphoblastic leukemia (ALL), we identified 58 putative functional and predominant fusion genes in 54.1% of patients (n = 125), 31 of which have not been reported previously. In particular, we described a distinct ALL subtype with a characteristic gene expression signature predominantly driven by chromosomal rearrangements of the ZNF384 gene with histone acetyltransferases EP300 and CREBBP ZNF384-rearranged ALL showed significant up-regulation of CLCF1 and BTLA expression, and ZNF384 fusion proteins consistently showed higher activity to promote transcription of these target genes relative to wild-type ZNF384 in vitro. Ectopic expression of EP300-ZNF384 and CREBBP-ZNF384 fusion altered differentiation of mouse hematopoietic stem and progenitor cells and also potentiated oncogenic transformation in vitro. EP300- and CREBBP-ZNF384 fusions resulted in loss of histone lysine acetyltransferase activity in a dominant-negative fashion, with concomitant global reduction of histone acetylation and increased sensitivity of leukemia cells to histone deacetylase inhibitors. In conclusion, our results indicate that gene fusion is a common class of genomic abnormalities in childhood ALL and that recurrent translocations involving EP300 and CREBBP may cause epigenetic deregulation with potential for therapeutic targeting.
Identifying "best bet" web search results by mining past user behavior (2006)

The top web search result is crucial for user satisfaction with the web search experience. We argue that the importance of the relevance at the top position necessitates special handling of the top web search result for some queries. We propose an effective approach of leveraging millions of past user interactions with a web search engine to automatically detect "best bet" top results preferred by majority of users. Interestingly, this problem can be more effectively addressed with classification than using state-of-the-art general ranking methods. Furthermore, we show that our general machine learning approach achieves precision comparable to a heavily tuned, domain-specific algorithm, with significantly higher coverage. Our experiments over millions of user interactions for thousands of queries demonstrate the effectiveness and robustness of our techniques.