gebhart/patrepeval huggingface dataset:
Activation of the Saccharomyces cerevisiae Heat Shock Transcription Factor Under Glucose Starvation Conditions by Snf1 Protein Kinase (2004)

Heat shock transcription factor (HSF) is an evolutionarily conserved protein that mediates eukaryotic transcriptional responses to stress. Although the mammalian stress-responsive HSF1 isoform is activated in response to a wide array of seemingly unrelated stresses, including heat shock, pharmacological agents, infection and inflammation, little is known about the precise mechanisms or pathways by which this factor is activated by many stressors. The baker's yeast Saccharomyces cerevisiae encodes a single HSF protein that responds to heat stress and glucose starvation and provides a simple model system to investigate how a single HSF is activated by multiple stresses. Although induction of the HSF target gene CUP1 by glucose starvation is dependent on the Snf1 kinase, HSF-dependent heat shock induction of CUP1 is Snf1-independent. Approximately 165 in vivo targets for HSF have been identified in S. cerevisiae using chromatin immunoprecipitation combined with DNA microarrays. Interestingly, approximately 30% of the HSF direct target genes are also induced by the diauxic shift, in which glucose levels begin to be depleted. We demonstrate that HSF and Snf1 kinase interact in vivo and that HSF is a direct substrate for phosphorylation by Snf1 kinase in vitro. Furthermore, glucose starvation-dependent, but not heat shock-dependent HSF phosphorylation, and enhanced chromosomal HSF DNA binding to low affinity target promoters such as SSA3 and HSP30, occurred in a Snf1-dependent manner. Consistent with a more global role for HSF and Snf1 in activating gene expression in response to changes in glucose availability, expression of a subset of HSF targets by glucose starvation was dependent on Snf1 and the HSF carboxyl-terminal activation domain.
Subtle gene modification in mouse ES cells: evidence for incorporation of unmodified oligonucleotides without induction of DNA damage (2010)

Gene targeting by single-stranded oligodeoxyribonucleotides (ssODNs) is a promising tool for site-specific gene modification in mouse embryonic stem cells (ESCs). We have developed an ESC line carrying a mutant EGFP reporter gene to monitor gene correction events shortly after exposure to ssODNs. We used this system to compare the appearance and fate of cells corrected by sense or anti-sense ssODNs. The slower appearance of green fluorescent cells with sense ssODNs as compared to anti-sense ssODNs is consistent with physical incorporation of the ssODN into the genome. Thus, the supremacy of anti-sense ssODNs, previously reported by others, may be an artefact of early readout of the EGFP reporter. Importantly, gene correction by unmodified ssODNs only mildly affected the viability of targeted cells and did not induce genomic DNA double-stranded breaks (DSBs). In contrast, ssODNs that were end-protected by phosphorothioate (PTO) linkages caused increased H2AX phosphorylation and impaired cell cycle progression in both corrected and non-corrected cells due to induction of genomic DSBs. Our results demonstrate that the use of unmodified rather than PTO end-protected ssODNs allows stable gene modification without compromising the genomic integrity of the cell, which is crucial for application of ssODN-mediated gene targeting in (embryonic) stem cells.
Inhibition of Inflammation and iNOS Improves Lymphatic Function in Obesity (2016)

Although recent studies have shown that obesity decreases lymphatic function, the cellular mechanisms regulating this response remain unknown. In the current study, we show that obesity results in perilymphatic accumulation of inflammatory cells and that local inhibition of this response with topical tacrolimus, an inhibitor of T cell differentiation, increases lymphatic vessel density, decreases perilymphatic iNOS expression, increases lymphatic vessel pumping frequency, and restores lymphatic clearance of interstitial fluid to normal levels. Although treatment of obese mice with 1400W, a selective inhibitor of iNOS, also improved lymphatic collecting vessel contractile function, it did not completely reverse lymphatic defects. Mice deficient in CD4(+) cells fed a high fat diet also gained weight relative to controls but were protected from lymphatic dysfunction. Taken together, our findings suggest that obesity-mediated lymphatic dysfunction is regulated by perilymphatic accumulation of inflammatory cells and that T cell inflammatory responses are necessary to initiate this effect.
Design and Implementation of an Open, Interoperable Automated Demand Response Infrastructure (2007)

demand This paper describes the concept for and lessons from the development and field-testing of an open, interoperable communications infrastructure to support automating demand response (DR). Automating DR allows greater levels of participation and improved reliability and repeatability of the demand response and customer facilities. Automated DR systems have been deployed for critical peak pricing and demand bidding and are being designed for real time pricing. The system is designed to generate, manage, and track DR signals between utilities and Independent System Operators (ISOs) to aggregators and end-use customers and their control systems. 1.
The retired breeder rat as a new model for antiplatelet drug discovery. (1977)

Spontaneous circulating platelet aggregates were observed in male retired breeder rats but in nonbred males of the same age and strain. Fasting serum lipid, platelet serotonin, and platelet rich plasma cyclic guanosine monophosphate levels were similar in retired breeders and nonbred rats. The in vitro response of platelets from retired breeder and nonbred rats to adenosine diphosphate and collagen were also similar. Administration of prostaglandin E1 and antiplatelet drugs (acetylsalicylic acid, sulfinpyrazone, and dipyridamole) reduced the number of circulating platelet aggregates in the breeder rats. It was concluded that the retired breeder rat may be a useful model for identification of new anti-platelet drugs.
Use of plasma arc welding process to combat hydrogen metallic disbonding of austenitic stainless steel claddings (1993)

A separation type crack, metallic disbonding, occurred between austenitic stainless steel weld metal cladding and 2 1/4Cr-1Mo base metal in the hydrodesulfurizing reactor of an oil refining plant. For stainless steel cladding, the submerged arc welding (SAW) process with a strip electrode is usually applied, but the authors experimented with the plasma arc welding (PAW) process with hot wire electrode for the cladding. The metallic disbonding is considered to be attributed to hydrogen accumulation at the transition zone and has been generally studied on a laboratory scale using an autoclave. The authors used a electrolytic hydrogen charging technique for the sake of experimental simplicity and made a comparison with the results for gaseous hydrogen charging. The main conclusions obtained were follows: The PAW stainless steel weld metal cladding is more resistant to metallic disbonding with the PAW process is explained by the desirable microstructure and properties of the first layer of weld metal at the transition zone. Electrolytic hydrogen charging pretty well reproduces the results of autoclave gas phase charging.
Modelling quest data for game designers (2006)

As Massively Multiplayer Online Games gain popularity, there has been a concomitant increase in size and complexity, both technically and in terms of player usage. To understand the structures and dynamics of these complex environments, game designers need detailed visualisations that expose usage patterns from gameplay data. This paper presents a quest data model devised to provide database support for evaluation tasks performed by designers of online role playing games.
Fighting online click-fraud using bluff ads (2010)

Online advertising is currently the richest source of revenue for many Internet giants. The increased number of online businesses, specialized websites and modern profiling techniques have all contributed to an explosion of the income of ad brokers from online advertising. The single biggest threat to this growth, is however, click-fraud. Trained botnets and individuals are hired by click-fraud specialists in order to maximize the revenue of certain users from the ads they publish on their websites, or to launch an attack between competing businesses. In this note we wish to raise the awareness of the networking research community on potential research areas within the online advertising field. As an example strategy, we present Bluff ads; a class of ads that join forces in order to increase the effort level for click-fraud spammers. Bluff ads are either targeted ads, with irrelevant display text, or highly relevant display text, with irrelevant targeting information. They act as a litmus test for the legitimacy of the individual clicking on the ads. Together with standard threshold-based methods, fake ads help to decrease click-fraud levels.
FMS's scheduling by colored Petri net model and Hopfield neural network algorithm (2002)

Multiprocessor multitask scheduling is very important in running FMS and is usually one of combinatorial optimization problem which are NP complete. This paper intend to develop an optimization scheme based on colored Petri net model and Hopfield neural network algorithm. At first, the FMS scheduling problem is analyzed and a colored Petri net model for FMS scheduling system is presented. Then, by introducing a special energy function, Hopfield neural network which is suitable to solve the scheduling problem is presented. Finally, the simulation result is discussed.
Efficient Generation of A9 Midbrain Dopaminergic Neurons by Lentiviral Delivery of LMX1A in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells (2011)

Human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC) offer great hope for in vitro modeling of Parkinson's disease (PD), as well as for designing cell-replacement therapies. To realize these opportunities, there is an urgent need to develop efficient protocols for the directed differentiation of hESC/iPSC into dopamine (DA) neurons with the specific characteristics of the cell population lost to PD, i.e., A9-subtype ventral midbrain DA neurons. Here we use lentiviral vectors to drive the expression of LMX1A, which encodes a transcription factor critical for ventral midbrain identity, specifically in neural progenitor cells. We show that clonal lines of hESC engineered to contain one or two copies of this lentiviral vector retain long-term self-renewing ability and pluripotent differentiation capacity. Greater than 60% of all neurons generated from LMX1A-engineered hESC were ventral midbrain DA neurons of the A9 subtype, compared with ∼10% in green fluorescent protein-engineered controls, as judged by specific marker expression and functional analyses. Moreover, DA neuron precursors differentiated from LMX1A-engineered hESC were able to survive and differentiate when grafted into the brain of adult mice. Finally, we provide evidence that LMX1A overexpression similarly increases the yield of DA neuron differentiation from human iPSC. Taken together, our data show that stable genetic engineering of hESC/iPSC with lentiviral vectors driving controlled expression of LMX1A is an efficient way to generate enriched populations of human A9-subtype ventral midbrain DA neurons, which should prove useful for modeling PD and may be helpful for designing future cell-replacement strategies.
Modified Vaccinia virus Ankara-based vaccines in the era of personalized immunotherapy of cancer (2017)

While interest in immunotherapies is renewed by the successful introduction of immune checkpoint blocking agent in the clinic, advances in genome sequencing are opening new possibilities in the design of increasingly personalized vaccines. Personalization of medicine can now be realistically contemplated at the single patient level. Unlike the previous generation of cancer vaccines, neoantigen directed vaccines would target truly specific tumor antigens resulting from acquired tumor genome mutations. Immune response induced by this next generation vaccine would not be subject to self-tolerance and will likely result to enhanced efficacy. Nevertheless, this new technologies can hold to their promises only if sponsors manage to meet several scientific, technical, logistical and regulatory challenges. In particular manufacturers will have to design, manufacture, and deliver to the patient a new pharmaceutical grade in a matters of weeks. In this paper, we briefly review current technologies currently tried at the translation of personalized vaccines and explore the possibilities offered by the Modified Vaccinia virus Ankara in this next wave of cancer vaccines.
Activated neu Induces Rapid Tumor Progression (1996)

Expression of the activated neu oncogene in transgenic mice has been associated with both the synchronous (single-step) and the stochastic (multistep) transformation of the mammary epithelium. To determine the basis for these conflicting observations, additional strains of transgenic mice carrying the activated neu oncogene under the transcriptional control of the mouse mammary tumor virus promoter/enhancer were produced. Activated neu transgene expression, as measured by in situ hybridization and ribonuclease protection assays, resulted in rapid conversion of the normal mammary epithelium to malignant phenotype in three independent strains of mice. Expression of the transgene in male mice led to epithelial hyperplasia of the epididymis and male infertility but not malignancy. These results indicate that tissue context is an important parameter in malignant progression and that expression of appropriate levels of activated neu is sufficient for rapid production of mammary tumors in transgenic mice.
PSİKİYATRİ HEMŞİRELİĞİ UYGULAMASININ ÖĞRENCİLERİN PROBLEM ÇÖZME BECERİSİ, DEPRESYON DÜZEYİ VE KENDİLİK ALGISI ÜZERİNDEKİ ETKİLERİNİN İNCELENMESİ (1998)

Bu arastirina: lisans egitimi alan hemsirelik ogrencilerinin psikiyatri hemsireligi dersinin uygulamalarindan sonra problem cozme becerileri, depresyon duzeyleri ve baskalariyla karsilastirildiginda kendilik algilarinda bir degisiklik olup olmadigini saplamak amaciyla yapilmistir, Arastirma Ege Universitesi Hemsirelik Yuksek Okulunda. 1997-1998 ogretim yilinda psikiyatri hemsireligi dersinin uygulamalarinaka llan son sinif ogrencileriyle yurutulmustur N— 1 13 . Arastirmada veriler, anket lormu ve standardize edilmis olcekler kullanilarak toplanmistir. Anket formunda sosyo-demografik ozelliklere iliskin soru formu ile birlikte, Problem Cozme Envanteri PCE . Beck Depresyon Envanteri BDE ve Sosyal Karsilastirma Olcegi SKO kullanilmistir. Verilerin degerlendirilmcsi icin. sayisal ve yuzdelik dagilimlar. iki es arasindaki farkin onemlilik tes i ve korelasyon katsayilari hesaplanmistir. Ogrencilerin uygulama oncesine gore uygulama sonrasinda problem cozme becerilerinde gelisme oldugu ancak bu gelismenin istatistiksel anlamlilik duzeyinde olmadigi saptanmistir Uz 0,84. Ogrencilerdeki bu gelisme problem cozme envanterinin kendine guvenli yaklasimla problemi cozme alt olcegi ile ilgili olarak istatistiksel anlamlilik duzeyinde olmustur l— 2.08. Ogrencilerin depresyon puanlari uygulama sonrasinda dusmustur
Multiscale analysis of shapes applied to thermal infrared sea surface images (2002)

The paper describes a new technique for segmentation of infrared sea surface images applied to detection of bi-dimensional oceanic structures. The method is based on a multiscale analysis of isotherms curvature and a characterization through the phase portraits technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An optical sectioning programmable array microscope implemented with a digital micromirror device (1999)

The defining feature of a programmable array microscope (PAM) is the presence of a spatial light modulator in the image plane. A spatial light modulator used singly or as a matched pair for both illumination and detection can be used to generate an optical section. Under most conditions, the basic optical properties of an optically sectioning PAM are similar to those of rotating Nipkow discs. The method of pattern generation, however, is fundamentally different and allows arbitrary illumination patterns to be generated under programmable control, and sectioning strategies to be changed rapidly in response to specific experimental conditions. We report the features of a PAM incorporating a digital micromirror device, including the axial sectioning response to fluorescent thin films and the imaging of biological specimens. Three axial sectioning strategies were compared: line scans, dot lattice scans and pseudo-random sequence scans. The three strategies varied widely in light throughput, sectioning strength and robustness when used on real biological samples. The axial response to thin fluorescent films demonstrated a consistent decrease in the full width at half maximum (FWHM), accompanied by an increase in offset, as the unit cells defining the patterns grew smaller. Experimental axial response curves represent the sum of the response from a given point of illumination and cross-talk from neighbouring points. Cross-talk is minimized in the plane of best focus and when measured together with the single point response produces a decrease in FWHM. In patterns having constant throughput, there appears to be tradeoff between the FWHM and the size of the offset. The PAM was compared to a confocal laser scanning microscope using biological samples. The PAM demonstrated higher signal levels and dynamic range despite a shorter acquisition time. It also revealed more structures in x-z sections and less intensity drop-off with scanning depth.
Solvent effects on emission yield and lifetime for coumarin laser dyes. Requirements for a rotatory decay mechanism (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolvent effects on emission yield and lifetime for coumarin laser dyes. Requirements for a rotatory decay mechanismGuilford Jones II, William R. Jackson, Chol Yoo Choi, and William R. BergmarkCite this: J. Phys. Chem. 1985, 89, 2, 294–300Publication Date (Print):January 1, 1985Publication History Published online1 May 2002Published inissue 1 January 1985https://pubs.acs.org/doi/10.1021/j100248a024https://doi.org/10.1021/j100248a024research-articleACS PublicationsRequest reuse permissionsArticle Views8031Altmetric-Citations1039LEARN 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 optionsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Epitaxial Aluminum‐Doped Zinc Oxide Thin Films on Sapphire: II, Defect Equilibria and Electrical Properties (1995)

The electrical transport properties of epitaxial ZnO films grown on different orientations of sapphire substrates have been measured as a function of partial pressure of oxygen. After equilibration, the carrier concentration is found to change from a p ‐1/4 O2 to a p ‐3/8 O2 dependence with increasing oxygen partial pressure. The partial pressure dependence is shown to be consistent with zinc vacancies being the rate‐controlling diffusive species. In addition, the carrier concentration in ZnO films grown on A‐, C‐, and M‐plane sapphire are the same but that of R‐plane sapphire is systematically lower. Electron Hall mobility measurements as a function of carrier concentration for all the substrate orientations exhibit a transition from “single‐crystal” behavior at high carrier concentrations to “polycrystalline” behavior at low carrier concentrations. This behavior is attributed to the effective height of potential barriers formed at the low‐angle grain boundaries in the epitaxial ZnO films. The trap density at the grain boundaries is deduced to be 7 × 10 12 /cm 2 . The electron mobility, at constant carrier concentration, varies with the substrate orientation on which the ZnO films were grown. The difference is attributed to the difference in dislocation density in the films produced as a result of lattice mismatch with the different sapphire orientations.
Adsorption of water from aqueous ethanol using 3-.ANG. molecular sieves (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdsorption of water from aqueous ethanol using 3-.ANG. molecular sievesWah Koon Teo and Douglas M. RuthvenCite this: Ind. Eng. Chem. Process Des. Dev. 1986, 25, 1, 17–21Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/i200032a003https://doi.org/10.1021/i200032a003research-articleACS PublicationsRequest reuse permissionsArticle Views1826Altmetric-Citations107LEARN 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
Identification and typing of herpes simplex viruses with monoclonal antibodies (1982)

Monoclonal antibodies which reacted with type-specific antigens of herpes simplex virus type 2 or with antigens shared by herpes simplex virus types 1 and 2 were used in an indirect immunofluorescence assay to type virus isolates and to detect viral antigens in cells obtained from herpetic lesions. Complete concordance was obtained for 42 isolates typed by endonuclease restriction analysis of viral DNA and by indirect immunofluorescence with monoclonal antibodies. Examination of a limited number of ulcerative lesions revealed that indirect immunofluorescence and virus isolation were comparable in detecting herpes simplex virus. The results indicate that monoclonal antibodies can be used to accurately identify and type isolates of herpes simplex virus.
8. The climatic sequence in cores from the Mediterranean Sea, Indian Ocean and Antarctic Ocean (1971)

Summary Among the earliest cores examined by Emiliani (1955B) was the Swedish core 189 taken in the western Mediterranean. Radiometric evidence in limited to a single radiocarbon date, but correlation with Atlantic cores is clear (Emiliani 1958, fig. 2). The