gebhart/patrepeval huggingface dataset:
Linker-scanning mutational analysis of the transcriptional activity of the human immunodeficiency virus type 1 long terminal repeat (1991)

We have compared the relative importance of transcription regulatory regions in the U3 and R regions of the human immunodeficiency virus type 1 long terminal repeat (LTR) by using linker-scanning mutational analysis. Twenty-six mutant LTR-chloramphenicol acetyltransferase (CAT) transient expression plasmids were prepared in which consecutive 18-bp regions of wild-type LTR were replaced with an NdeI-XhoI-SalI (NXS) polylinker. The mutant LTR-CAT plasmids were transfected into unstimulated Jurkat cells, Jurkat cells stimulated with phytohemagglutinin and tetradecanoylphorbol acetate, and Jurkat cells which constitutively express the human immunodeficiency virus type 1 trans-activator protein, Tat. Transcriptional activity was measured by analysis of CAT activity. The activities of these mutants identified one major and several minor transcription control elements in addition to previously identified elements. In addition, this fine-structure analysis identified differences in utilization of regulatory regions between unstimulated, stimulated, and Tat-expressing Jurkat cells. A significant regulatory region was indicated by linker-scanning mutations between nucleotides -183 and -130 (relative to the transcription start site, +1). These mutations caused marked decreases in activity of the LTR in unstimulated and especially in stimulated Jurkat cells but had no effect in Tat-expressing Jurkat cells. DNA mobility shift studies comparing probes of wild-type and mutant sequences in the -183 to -130 region indicated that alterations in specific DNA binding correspond to the altered transcriptional activity of the mutants. The effects of mutations in several regulatory regions, in addition to the -183 to -130 region described above, differ between Tat-expressing and -nonexpressing Jurkat cells. For example, the NF-kB sites are necessary for transcription in both Tat-expressing and -nonexpressing cells. However, Tat-expressing Jurkat cells primarily require only the 3'-proximal site, while both stimulated and unstimulated Jurkat cells appear to require both sites. Mutants downstream of the TATA element cause a more significant decrease in activity in Tat-expressing Jurkat cells than in the others. Finally, several mutations in the 5' half of the LTR (-453 to -184) show modest increases in transcription (1.5-fold or less) in unstimulated Jurkat cells only, suggesting possible negative regulatory sites. In summary, our studies have identified a control region (-183 to -130) upstream of the NF-kB sites and have more precisely defined significant differences in the utilization of regulatory regions between unstimulated, stimulated, and Tat-expressing Jurkat cells.
Distribution of Hepatitis C Virus Genotypes Determined by Line Probe Assay in Patients with Chronic Hepatitis C Seen at Tertiary Referral Centers in the United States (1996)

The line probe assay can be used in patients with chronic HCV infection in the United States. In patients with chronic hepatitis C referred to tertiary centers in the United States, type 1 is the most common HCV genotype. Disease activity and viremia levels do not differ among patients chronically infected with HCV types 1, 2, or 3.
Promyelocytic Leukemia Protein (Pml) and Daxx Participate in a Novel Nuclear Pathway for Apoptosis (2000)

The promyelocytic leukemia protein (PML) gene of acute promyelocytic leukemia (APL) encodes a cell growth and tumor suppressor essential for multiple apoptotic signals. Daxx was identified as a molecule important for the cytoplasmic transduction of the Fas proapoptotic stimulus. Here, we show that upon mitogenic activation of mature splenic lymphocytes, Daxx is dramatically upregulated and accumulates in the PML nuclear body (NB) where PML and Daxx physically interact. In the absence of PML, Daxx acquires a dispersed nuclear pattern, and activation-induced cell death of splenocytes is profoundly impaired. PML inactivation results in the complete abrogation of the Daxx proapoptotic ability. In APL cells, Daxx is delocalized from the NB. Upon retinoic acid treatment, which induces disease remission in APL, Daxx relocalizes to the PML NBs. These results indicate that PML and Daxx cooperate in a novel NB-dependent pathway for apoptosis and shed new light in the role of PML in tumor suppression.
Stromal cell‐derived factor‐1α improves infarcted heart function through angiogenesis in mice (2007)

SDF-1 protects against deterioration of cardiac function after acute myocardial infarction by promoting angiogenesis. The safety and long-term prognosis of this treatment remains to be determined.
Ustekinumab and Marked Clinical Responses in Patients with Moderate to Severe Psoriasis (2010)

Background Ustekinumab has demonstrated significant efficacy and favorable safety in patients with moderate to severe psoriasis. Objective Characterization of patients achieving marked clinical responses (Psoriasis Area and Severity Index [PASI] 90 or Physician's Global Assessment [PGA] of cleared) in two double-blind, placebo-controlled, phase III studies. Methods PHOENIX 1 (n=766) and PHOENIX 2 (n=1,230) patients were randomized to receive placebo or ustekinumab 45 or 90 mg at weeks 0 and 4, then every 12 weeks. At week 12, placebo patients crossed over to ustekinumab. Marked responses, defined as PASI 90 or PGA of cleared, are reported. Results A significantly higher proportion of ustekinumab-treated patients in PHOENIX 1 (39.9%) and PHOENIX 2 (47.0%) achieved marked responses at week 12, compared with placebo-treated patients (p&lt;0.001 each). At week 28, approximately 50% of ustekinumab-treated patients achieved marked responses. Conclusion Significant proportions of ustekinumab-treated patients with moderate to severe psoriasis achieved marked clinical responses through week 28. Ustekinumab had a favorable risk-benefit profile through up to 18 months of follow-up.
How will Deep Learning Change Internet Video Delivery? (2017)

research-article Share on How will Deep Learning Change Internet Video Delivery? Authors: Hyunho Yeo KAIST KAISTView Profile , Sunghyun Do KAIST KAISTView Profile , Dongsu Han KAIST KAISTView Profile Authors Info & Claims HotNets-XVI: Proceedings of the 16th ACM Workshop on Hot Topics in NetworksNovember 2017 Pages 57–64https://doi.org/10.1145/3152434.3152440Published:30 November 2017Publication History 18citation950DownloadsMetricsTotal Citations18Total Downloads950Last 12 Months83Last 6 weeks12 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Role of the Escherichia coli DnaK and DnaJ heat shock proteins in the initiation of bacteriophage lambda DNA replication. (1988)

We examined the role of two Escherichia coli heat shock proteins, the dnaK and dnaJ gene products, during the initiation of lambda dv DNA replication in vitro. Using 14C-labeled lambda P protein we showed that the DnaK and DnaJ heat shock proteins function together to release lambda P protein from the preprimosomal complex consisting of lambda origin of replication-lambda O-lambda P-DnaB protein. Hydrolysis of ATP, catalyzed presumably by DnaK, is required during this reaction. Substitution of DnaK protein with that of the mutant DnaK756 protein blocks lambda P release. After DnaK and DnaJ action, the preprimosomal complex, isolated on Sepharose 4B, can support lambda dv DNA replication without any additional prepriming proteins. Using DnaK-affinity chromatography we showed that both lambda O and lambda P proteins bind to DnaK protein. The lambda P protein interacts with DnaK protein in a salt-resistant, hydrophobic manner, and ATP hydrolysis is necessary to elute at least part of lambda P protein from the DnaK-affinity column. The proposed mechanism of action of the prokaryotic DnaK and DnaJ heat shock proteins agrees with the hypothesis that Hsp70, the DnaK analogue of eukaryotes, uses ATP to disrupt hydrophobic aggregates [Pelham, H. R. B. (1986) Cell 46, 959-961].
Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice (2008)

DNA vaccines offer a generic approach to influenza virus immunization applicable to multiple animal species. In addition, the ability to substitute plasmids encoding different strains enables rapid adaptation of the vaccine to newly evolving field isolates.
Cascading Failures in Power Grids - Analysis and Algorithms (2014)

This paper focuses on cascading line failures in the transmission system of the power grid. Recent large-scale power outages demonstrated the limitations of percolation- and epid- emic-based tools in modeling cascades. Hence, we study cascades by using computational tools and a linearized power flow model. We first obtain results regarding the Moore-Penrose pseudo-inverse of the power grid admittance matrix. Based on these results, we study the impact of a single line failure on the flows on other lines. We also illustrate via simulation the impact of the distance and resistance distance on the flow increase following a failure, and discuss the difference from the epidemic models. We then study the cascade properties, considering metrics such as the distance between failures and the fraction of demand (load) satisfied after the cascade (yield). We use the pseudo-inverse of admittance matrix to develop an efficient algorithm to identify the cascading failure evolution, which can be a building block for cascade mitigation. Finally, we show that finding the set of lines whose removal has the most significant impact (under various metrics) is NP-Hard and introduce a simple heuristic for the minimum yield problem. Overall, the results demonstrate that using the resistance distance and the pseudo-inverse of admittance matrix provides important insights and can support the development of efficient algorithms.
Advances in manganese-oxide ‘composite’ electrodes for lithium-ion batteries (2005)

Recent advances to develop manganese-rich electrodes derived from ‘composite’ structures in which a Li2MnO3 (layered) component is structurally integrated with either a layered LiMO2 component or a spinel LiM2O4 component, in which M is predominantly Mn and Ni, are reviewed. The electrodes, which can be represented in two-component notation as xLi2MnO3·(1 − x)LiMO2 and xLi2MnO3·(1 − x)LiM2O4, are activated by lithia (Li2O) and/or lithium removal from the Li2MnO3, LiMO2 and LiM2O4 components. The electrodes provide an initial capacity >250 mAh g−1 when discharged between 5 and 2.0 V vs. Li0 and a rechargeable capacity up to 250 mAh g−1 over the same potential window. Electrochemical charge and discharge reactions are followed on compositional phase diagrams. The data bode well for the development and exploitation of high capacity electrodes for the next generation of lithium-ion batteries.
Adeno-Associated Virus Vector Mediated Delivery of the HBV Genome Induces Chronic Hepatitis B Virus Infection and Liver Fibrosis in Mice (2015)

Liver cirrhosis and hepatocellular carcinomas are major health problems of chronic hepatitis B virus (HBV) infection. To date, rare model has reproduced liver fibrosis associated with long-term HBV infection which in turn has hindered both the understanding of HBV biology and the development of new treatment options. Here, using adeno-associated virus serotype 8 (AAV8) mediated delivery of a 1.2-kb HBV genome, we successfully generated a chronic HBV infectious mouse model that presents the associated liver fibrosis observed following human infection. After AAV8/HBV1.2 vector administration, mice demonstrated effective HBV replication and transcription which resulted in HBV antigen expression and viremia over 6 months. Although no obvious acute inflammatory response was noted, these mice still developed chronic liver disease and hepatic fibrogenesis as demonstrated by increased ground glass-like hepatocytes, an increasing trend of collagen deposition and upregulated fibrosis markers, including type I collagen, type III collagen, tissue inhibitor of metalloproteinase (TIMP), and transforming growth factor-β1(TGF-β1). Taken together, AAV-mediated HBV gene delivery to the mouse liver, induced HBV persistent infection accompanied by liver fibrosis which can serve as a model for investigating the precise mechanisms underlying liver fibrosis following chronic HBV infection as well as for the potential development of novel therapeutics.
Development and Optimization of a TiO2-Coated Fiber-Optic Cable Reactor: Photocatalytic Degradation of 4-Chlorophenol (1995)

We have developed, characterized, and utilized a photochemical reactor system that employs an optical fiber cable as a means of light transmission to solid supported TiO_2. Light energy is transmitted to TiO_2 particles, which are chemically anchored onto quartz fiber cores, via radial refraction of light out of the fiber. Operational factors that influence the efficiency of the bundled-array optical fiber reactor are as follows: the uniformity and extent of light propagation down the fiber, the degree of light absorption by the TiO_2 coating of the refracted light, and the ability of the chemical substrates to diffuse into the TiO_2 coating. A TiO_2 coating layer that minimizes the interfacial surface area of the quartz core and TiO_2 particles and operation with incident irradiation angles near 90" enhance light propagation down the fibers. A maximum quantum efficiency of Φ = 0.011 for the oxidation of 4-chlorophenol was achieved. This can be compared to a maximum quantum efficiency of Φ = 0.0065 for 4-chlorophenol oxidation in a TiO_2 slurry reactor operated under similar conditions.
Sapogenin Structure: Analysis of the 13C- and 1H-nmr Spectra of Soyasapogenol B (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSapogenin Structure: Analysis of the 13C- and 1H-nmr Spectra of Soyasapogenol BRobert L. Baxter, Keith R. Price, and G. Roger FenwickCite this: J. Nat. Prod. 1990, 53, 2, 298–302Publication Date (Print):March 1, 1990Publication History Published online1 July 2004Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/np50068a004https://doi.org/10.1021/np50068a004research-articleACS PublicationsRequest reuse permissionsArticle Views333Altmetric-Citations21LEARN 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
Using SVMs for Text Categorization (1998)

In summary, inductive learning methods offer great potential to support flexible, dynamic, and personalized information access and management in a wide variety of tasks.
The cloned platelet thrombin receptor couples to at least two distinct effectors to stimulate phosphoinositide hydrolysis and inhibit adenylyl cyclase. (1992)

Thrombin both stimulates phosphoinositide hydrolysis and inhibits adenylyl cyclase in a variety of cell types. Whether the cloned human platelet thrombin receptor accounts for both of these signaling events is unknown. We report that thrombin receptor agonist peptide causes both phosphoinositide hydrolysis and inhibition of adenylyl cyclase in naturally thrombin-responsive CCL-39 cells. To exclude the possibility that the agonist peptide or thrombin itself may activate these pathways via distinct receptors and to circumvent a lack of suitable thrombin receptor-null cells, we utilized a designed "enterokinase receptor," a thrombin receptor with its thrombin cleavage recognition sequence LDPR replaced by DDDDK, the enterokinase cleavage recognition sequence. Transfection of enterokinase-unresponsive cells with this construct conferred both enterokinase-sensitive phosphoinositide hydrolysis and inhibition of adenylyl cyclase. The phosphoinositide hydrolysis response was largely insensitive to pertussis toxin, whereas the adenylyl cyclase response was completely blocked by pertussis toxin. These data show that the cloned thrombin receptor can effect both phosphoinositide hydrolysis and inhibition of adenylyl cyclase via at least two distinct effectors, most likely Gq-like and Gi-like G-proteins.
Design Recommendations for Self-Monitoring in the Workplace (2017)

One way to improve the productivity of knowledge workers is to increase their self-awareness about productivity at work through self-monitoring. Yet, little is known about expectations of, the experience with, and the impact of self-monitoring in the workplace. To address this gap, we studied software developers, as one community of knowledge workers. We used an iterative, user-feedback-driven development approach (N=20) and a survey (N=413) to infer design elements for workplace self-monitoring, which we then implemented as a technology probe called WorkAnalytics. We field-tested these design elements during a three-week study with software development professionals (N=43). Based on the results of the field study, we present design recommendations for self-monitoring in the workplace, such as using experience sampling to increase the awareness about work and to create richer insights, the need for a large variety of different metrics to retrospect about work, and that actionable insights, enriched with benchmarking data from co-workers, are likely needed to foster productive behavior change and improve collaboration at work. Our work can serve as a starting point for researchers and practitioners to build self-monitoring tools for the workplace.
Intracellular Delivery of Peptidyl Ligands by Reversible Cyclization: Discovery of a PDZ Domain Inhibitor that Rescues CFTR Activity (2015)

A general strategy was developed for the intracellular delivery of linear peptidyl ligands through fusion to a cell-penetrating peptide and cyclization of the fusion peptides via a disulfide bond. The resulting cyclic peptides are cell permeable and have improved proteolytic stability. Once inside the cell, the disulfide bond is reduced to produce linear biologically active peptides. This strategy was applied to generate a cell-permeable peptide substrate for real-time detection of intracellular caspase activities during apoptosis and an inhibitor for the CFTR-associated ligand (CAL) PDZ domain as a potential treatment for cystic fibrosis.
Enzymatic incorporation of a new base pair into DNA and RNA (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymatic incorporation of a new base pair into DNA and RNAChristopher Switzer, Simon E. Moroney, and Steven A. BennerCite this: J. Am. Chem. Soc. 1989, 111, 21, 8322–8323Publication Date (Print):October 1, 1989Publication History Published online1 May 2002Published inissue 1 October 1989https://pubs.acs.org/doi/10.1021/ja00203a067https://doi.org/10.1021/ja00203a067research-articleACS PublicationsRequest reuse permissionsArticle Views1596Altmetric-Citations295LEARN 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
An assessment of environmental conditions for control of downy brome by Pseudomonas fluorescens D7 (2009)

Purpose: We evaluated the conditions that favoured Pseudomonas fluorescens strain D7 (P.f. D7) growth and inhibition of downy brome. Design/methodology/approach: Tn5 mutagenesis and a competitive assay were used to isolate mutants of P.f. D7. Isolates were screened for polysaccharide production and toxin response. Seven mutants were tested under varying pH, temperature and water potential and characterised using Random Amplified Polymorphic DNA analysis. Findings: Temperature, pH, and water potential did not affect weed suppression in bioassays, except at 37°C and with NaCl. Originality and/value: Understanding the genetics of P.f. D7 will help in the development of successful weed biocontrol systems.
GRB2 Interaction with the Ecotropic Murine Leukemia Virus Receptor, mCAT-1, Controls Virus Entry and Is Stimulated by Virus Binding (2011)

For retroviruses such as HIV-1 and murine leukemia virus (MLV), active receptor recruitment and trafficking occur during viral entry. However, the underlying mechanisms and cellular factors involved in the process are largely uncharacterized. The viral receptor for ecotropic MLV (eMLV), a classical model for retrovirus infection mechanisms and pathogenesis, is mouse cationic amino acid transporter 1 (mCAT-1). Growth factor receptor-bound protein 2 (GRB2) is an adaptor protein that has been shown to couple cell surface receptors, such as epidermal growth factor receptor (EGFR) and hepatocyte growth factor receptor, to intracellular signaling events. Here we examined if GRB2 could also play a role in controlling infection by retroviruses by affecting receptor function. The GRB2 RNA interference (RNAi)-mediated suppression of endogenous GRB2 resulted in a consistent and significant reduction of virus binding and membrane fusion. The binding between eMLV and cells promoted increased GRB2-mCAT-1 interactions, as detected by immunoprecipitation. Consistently, the increased colocalization of GRB2 and mCAT-1 signals was detected by confocal microscopy. This association was time dependent and paralleled the kinetics of cell-virus membrane fusion. Interestingly, unlike the canonical binding pattern seen for GRB2 and growth factor receptors, GRB2-mCAT-1 binding does not depend on the GRB2-SH2 domain-mediated recognition of tyrosine phosphorylation on the receptor. The inhibition of endogenous GRB2 led to a reduction in surface levels of mCAT-1, which was detected by immunoprecipitation and by a direct binding assay using a recombinant MLV envelope protein receptor binding domain (RBD). Consistent with this observation, the expression of a dominant negative GRB2 mutant (R86K) resulted in the sequestration of mCAT-1 from the cell surface into intracellular vesicles. Taken together, these findings suggest a novel role for GRB2 in ecotropic MLV entry and infection by facilitating mCAT-1 trafficking.