gebhart/patrepeval huggingface dataset:
Asynchronous Expression of the Immediate-Early Protein of Herpesvirus Saimiri in Populations of Productively Infected Cells (1985)

The time course of virus replication in cultures of permissive cells infected with high multiplicities of herpesvirus saimiri (HVS), a gammaherpesvirus, is protracted relative to the replication of herpes simplex virus (HSV), an alphaherpesvirus, under similar conditions. The basis for this difference was investigated by quantitative immunofluorescence microscopy exploiting monoclonal antibodies specific to the HVS 52 000 mol. wt. immediate-early polypeptide (IE 52K) and to delayed-early (DE 51K, DE 110K) and late (130K and capsid proteins) gene products to measure the timing of gene expression in individual cells of infected cultures. The timing of the transitions from IE to DE and from DE to late protein synthesis occurred at proportionately different intervals in the growth cycle of HVS, relative to that of HSV. In particular, the DE to late transition occurred relatively later in HVS infections. However, asynchrony in the events leading to the expression of the first class of virus proteins (IE 52K) was the main source of the extended course of HVS replication in populations of infected cells. This asynchrony was not modified significantly by infection at different stages of the host cell-cycle and was reduced, but not overcome, by very high applied multiplicities of infection. Double-antibody staining revealed a positive correlation between the accumulation of high concentrations of parental virus particles at perinuclear sites and early detection of HVS IE 52K gene expression. Both of these events remained sensitive to a microtubule poison (colcemid) for many hours after infection with HVS, whereas the rapid and synchronous expression of the IE 175K protein (ICP4) in HSV-1-infected cells was insensitive to post-infection exposures to this drug. We conclude that significant differences in early stages of virus entry and intracellular processing which precede immediate-early gene expression are largely responsible for differences between the replicative cycles of these representatives of gamma- and alphaherpesviruses in cultures of permissive cells.
“On Water”, Phosphine‐Free Palladium‐Catalyzed Room Temperature CH Arylation of Indoles (2013)

Get on top of your chemistry! An “on water”, palladium-catalyzed, phosphine-free direct CH arylation of indoles, with iodoarenes at 25–30 °C, is disclosed (see scheme; TBDMS=N-tert-butyldimethylsilyl ether; SEM=N-2-(trimethylsilyl)ethoxymethyl; Bn=benzyl, Piv=pivabyl). The mildness of the reaction conditions permits the tolerance of a variety of N1-protected indoles. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Gene profiling of scleroderma skin reveals robust signatures of disease that are imperfectly reflected in the transcript profiles of explanted fibroblasts (2006)

SSc has a distinct gene profile that is not confounded by geographic location, indicating that extended multicenter studies may be worthwhile to identify distinct subsets of disease by transcript profiling. Explanted SSc fibroblasts show an incomplete reflection of the SSc phenotype.
A Toll-Like Receptor 2 Ligand Stimulates Th2 Responses In Vivo, via Induction of Extracellular Signal-Regulated Kinase Mitogen-Activated Protein Kinase and c-Fos in Dendritic Cells (2004)

The adaptive immune system can generate distinct classes of responses, but the mechanisms that determine this are poorly understood. In this study, we demonstrate that different Toll-like receptor (TLR) ligands induce distinct dendritic cell (DC) activation and immune responses in vivo. Thus, Escherichia coli LPS (TLR-4 stimulus), activates DCs to produce abundant IL-12(p70), but little IL-10, and stimulates Th1 and Tc1 responses. In contrast, Pam-3-cys (TLR-2 stimulus) elicits less IL-12(p70), but abundant IL-10, and favors Th2 and T cytotoxic 2 (Tc2) responses. These distinct responses likely occur via differences in extracellular signal-regulated kinase signaling in DCs. Thus, Pam-3-cys induces enhanced extracellular signal-regulated kinase signaling, compared with LPS, resulting in suppressed IL-12(p70) and enhanced IL-10 production, as well as enhanced induction of the transcription factor, c-Fos. Interestingly, DCs from c-fos(-/-) mice produce more IL-12(p70), but less IL-10, compared with control DCs. Therefore, different TLR ligands induce distinct cytokines and signaling in DCs, and differentially bias Th responses in vivo.
The Genome of Simian Virus 40 (1978)

The nucleotide sequence of SV40 DNA was determined, and the sequence was correlated with known genes of the virus and with the structure of viral messenger RNA's. There is a limited overlap of the coding regions for structural proteins and a complex pattern of leader sequences at the 5' end of late messenger RNA. The sequence of the early region is consistent with recent proposals that the large early polypeptide of SV40 is encoded in noncontinguous segments of DNA.
Protein kinase A‐dependent and ‐independent stimulation of exocytosis by cAMP in mouse pancreatic B‐cells (1997)

1. The mechanisms by which cAMP stimulates Ca(2+)-dependent insulin secretion were investigated by combining measurements of whole-cell Ca2+ currents, the cytoplasmic free Ca2+ concentration ([Ca2+]i) and membrane capacitance in single mouse B-cells maintained in tissue culture. 2. Cyclic AMP stimulated exocytosis > 4-fold in whole-cell experiments in which secretion was evoked by intracellular dialysis with a Ca(2+)-EGTA buffer with a [Ca2+]i of 1.5 microM. This effect was antagonized by inhibitors of protein kinase A (PKA). 3. Photorelease of cAMP from a caged precursor potentiated exocytosis at Ca2+ concentrations which were themselves stimulatory (> or = 60 nM), but was without effect in the complete absence of Ca2+. 4. Elevation of intracellular cAMP (by exposure to forskolin) evoked a 6-fold PKA-dependent enhancement of the maximal exocytotic response (determined as the maximum increase in cell capacitance that could be elicited by a train of depolarizations) in perforated-patch whole-cell recordings. 5. Exocytosis triggered by single depolarizations in standard whole-cell recordings was strongly potentiated by cAMP, but in this case the effect was unaffected by PKA inhibition. 6. When exocytosis was triggered by Ca2+ released from Ca(2+)-NP-EGTA ('caged Ca2+'), cAMP exerted a dual stimulatory effect on secretion: a rapid (initiated within 80 ms) PKA-independent phase and a late PKA-dependent component. 7. We conclude that cAMP stimulates insulin secretion both by increasing the release probability of secretory granules already in the readily releasable pool and by accelerating the refilling of this pool.
Antiviral Activity of 10-Carboxymethyl-9-Acridanone (1976)

Intraperitoneal administration of 10-carboxymethyl-9-acridanone sodium salt (CMA) protected at least 50% of mice tested from otherwise lethal infections with Semliki forest, coxsackie B1, Columbia SK, Western equine encephalitis, herpes simplex, and pseudorabies viruses. The protective effect against influenza A2/Asian/J305 and coxsackie A21 viruses was less but was statistically significant. When administered either subcutaneously or orally, CMA protected at least 50% of mice against Semliki forest and pseudorabies viruses; the effect against coxsackie B1 and herpes simplex viruses was less but was statistically significant. Initiation of treatment could be delayed from 2 to 24 h after infection of mice with coxsackie B1, herpes simplex, Semliki forest, and Western equine encephalitis viruses without loss of an antiviral effect. CMA did not inactivate Semliki forest or coxsackie B1 viruses on contact and was without effect against any of the viruses tested in tissue culture by the tube dilution assay. The humoral antibody response in mice to both influenza virus and sheep erythrocytes was unaffected by CMA. After administration of CMA, an interferon-like substance was induced in mice or mouse cell culture but not in rabbits or rabbit cell culture.
Flexible Persistence Framework for Object-Oriented Middleware (2001)

The ability to store object states persistently in a convenient and flexible way is an important requirement for middleware environments. In this paper we propose a language independent framework for flexible and extensible persistent storage services for object-oriented middleware. The framework is specified by interface definitions and the rationale of their interplay. To support application-specific requirements like particular data repositories and distribution aspects, different persistence services are feasible within the proposed framework. These services are easy to use, since objects are stored persistently by inheriting from a single class; additional auxiliary classes–like, for instance, factory or session classes in related approaches–are not required. We remark that inter-object transactional behavior is not in the scope of a persistent storage service; these issues are addressed by transactional services. To show the open design of the proposed framework, we sketch how the framework can be integrated with the Transaction Service proposed by the
Molecular recognition of mono- and di-saccharides by phenylboronic acids in solvent extraction and as a monolayer (1991)

m- and p-Hexadecyloxyphenylboronic acids (m-1 and p-1, respectively) selectively extract saccharides; the monolayer of m-1 at the air–water interface selectively responds to these saccharides, the order of the change in π–A isotherms being similar to that of the extractability.
Primary Fibril Nucleation of Aggregation Prone Tau Fragments PHF6 and PHF6* (2016)

We performed replica exchange molecular dynamics and forward flux sampling simulations of hexapeptide VQIINK and VQIVYK systems, also known as, respectively, fragments PHF6* and PHF6 from the tau protein. Being a part of the microtubule binding region, these fragments are known to be aggregation prone, and at least one of them is a prerequisite for fibril formation of the tau protein. Using a coarse-grained force field, we establish the phase behavior of both fragments, and investigate the nucleation kinetics for the conversion into a β-sheet fibril. As the conversion is, in principle, a reversible process, we predict the rate constants for both the fibril formation and melting, and examine the corresponding mechanisms. Our simulations indicate that, while both fragments form disordered aggregates, only PHF6 is able to form β-sheet fibrils. This observation provides a possible explanation for the lack of available steric zipper crystal structures for PHF6*.
A comparison of the effects of botulinum toxin A and steroid injection on nasal allergy (2008)

BTX-A may provide better AR symptom relief in terms of duration and degree than a steroid injection.
A robust methodology for in vivo T1 mapping (2010)

In this article, a robust methodology for in vivo T(1) mapping is presented. The approach combines a gold standard scanning procedure with a novel fitting procedure. Fitting complex data to a five-parameter model ensures accuracy and precision of the T(1) estimation. A reduced-dimension nonlinear least squares method is proposed. This method turns the complicated multi-parameter minimization into a straightforward one-dimensional search. As the range of possible T(1) values is known, a global grid search can be used, ensuring that a global optimal solution is found. When only magnitude data are available, the algorithm is adapted to concurrently restore polarity. The performance of the new algorithm is demonstrated in simulations and phantom experiments. The new algorithm is as accurate and precise as the conventionally used Levenberg-Marquardt algorithm but much faster. This gain in speed makes the use of the five-parameter model viable. In addition, the new algorithm does not require initialization of the search parameters. Finally, the methodology is applied in vivo to conventional brain imaging and to skin imaging. T(1) values are estimated for white matter and gray matter at 1.5 T and for dermis, hypodermis, and muscle at 1.5 T, 3 T, and 7 T.
CATRA (2011)

We introduce an interactive method to assess cataracts in the human eye by crafting an optical solution that measures the perceptual impact of forward scattering on the foveal region. Current solutions rely on highly-trained clinicians to check the back scattering in the crystallin lens and test their predictions on visual acuity tests. Close-range parallax barriers create collimated beams of light to scan through sub-apertures, scattering light as it strikes a cataract. User feedback generates maps for opacity, attenuation, contrast and sub-aperture point-spread functions. The goal is to allow a general audience to operate a portable high-contrast light-field display to gain a meaningful understanding of their own visual conditions. User evaluations and validation with modified camera optics are performed. Compiled data is used to reconstruct the individual's cataract-affected view, offering a novel approach for capturing information for screening, diagnostic, and clinical analysis.
Degrading PCBs through composting (1998)

Michigan State University tests efficacy of composting for bioremediation of soil contaminated by a packaging plant.
Coded apertures for efficient pyroelectric motion tracking (2003)

Coded apertures may be designed to modulate the visibility between source and measurement spaces such that the position of a source among N resolution cells may be discriminated using logarithm of N measurements. We use coded apertures as reference structures in a pyroelectric motion tracking system. This sensor system is capable of detecting source motion in one of the 15 cells uniformly distributed over a 1.6m x 1.6m domain using 4 pyroelectric detectors.
Toward Automated Dynamic Malware Analysis Using CWSandbox (2007)

Malware is notoriously difficult to combat because it appears and spreads so quickly. In this article, we describe the design and implementation of CWSandbox, a malware analysis tool that fulfills our three design criteria of automation, effectiveness, and correctness for the Win32 family of operating systems
Growth of Thick ${\rm BaZrO}_{3}$-Doped ${\rm YBa}_{2}{\rm Cu}_{3}{\rm O}_{7-\delta}$ Films With High Critical Currents in High Applied Magnetic Fields (2009)

High quality, thick YBa <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7-delta</sub> (YBCO) films with splayed, self-assembled BaZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> insulating nanodot columns were epitaxially grown by pulsed laser deposition on short pieces of ion-beam-assisted deposition (IBAD) MgO substrate. Variations in superconducting and microstructural properties were observed for samples grown at different substrate temperatures between 790 and 810 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deg</sup> C. At substrate temperatures between 790 and 800 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deg</sup> C, samples were measured to have large self-field <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> of 670-787 A/cm at 77 K and minimum <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> of 353-392 A/cm for all angles at 65 K, 3 T.
Pulse-Quench Catalytic Reactor Studies Reveal a Carbon-Pool Mechanism in Methanol-to-Gasoline Chemistry on Zeolite HZSM-5 (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPulse-Quench Catalytic Reactor Studies Reveal a Carbon-Pool Mechanism in Methanol-to-Gasoline Chemistry on Zeolite HZSM-5Patrick W. Goguen, Teng Xu, Dewey H. Barich, Timothy W. Skloss, Weiguo Song, Zhike Wang, John B. Nicholas, and James F. HawView Author Information The Laboratory for Magnetic Resonance and Molecular Science, Department of Chemistry Texas A&M University, College Station, Texas 77843 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland, Washington 99352 Cite this: J. Am. Chem. Soc. 1998, 120, 11, 2650–2651Publication Date (Web):March 4, 1998Publication History Received17 November 1997Published online4 March 1998Published inissue 1 March 1998https://pubs.acs.org/doi/10.1021/ja973920zhttps://doi.org/10.1021/ja973920zrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1355Altmetric-Citations164LEARN 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 SUBJECTS:Alkyls,Cations,Hydrocarbons,Nuclear magnetic resonance spectroscopy,Reagents Get e-Alerts
The Biosynthesis of Collagen and Its Disorders (1979)

(Second of Two Parts)How Do Defects in Biosynthesis Explain Genetic Diseases of Collagen?There are many rare genetic diseases that involve connective tissues, such as skin and bone.As the information reviewed above about collagen structure and biosynthesis accumulated, biochemical data were quickly obtained to explain a number of genetic diseases in man on the basis of molecular defects in collagen biosynthesis. The biochemical data helped to define specific subtypes of some of these diseases. At the same time, study of several of these genetic diseases provided new information about the biosynthetic process itself. For example, shortly after lysyl . . .
An Ecosystem for Learning and Using Sensor-Driven IM Status Messages (2009)

The Nomatic prototype system and communications ecosystem automatically infers users' place, activity, and availability from sensors on their handheld devices or laptop computers and then reports this information to their instant-messaging contacts.In our system, Nomatic (nomad and automatic), we explore a way to amplify and leverage this passive style of content creation by focusing on status messages. These short bits of text are usually created by users in the context of small communities of people who monitor each other for playor work-related distributed coordination. Status messages appear in instant-messaging (IM) clients as short customizable phrases such as "at lunch" or "out of the office." Commercial services also provide facilities for communicating status without IM (for example, Facebook, Twitter, and Jaiku). By simply attaching sensor data to the status information that users enter in IM, we can create a rich ecosystem of context-aware applications that benefit users. At the most basic level, keeping status content up to date helps mitigate the increasing problem of interruptions in mobile communications, but there are many other potential uses of such data. To be effective, we must keep this ecosystem in balance by supporting the user's ability to provide status information, supporting other users' ability to understand that data, and effectively motivating both types of users to keep their status information accurate.
A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity (2007)

Large interindividual variance has been observed in sensitivity to drugs. To comprehensively decipher the genetic contribution to these variations in drug susceptibility, we present a genome-wide model using human lymphoblastoid cell lines from the International HapMap consortium, of which extensive genotypic information is available, to identify genetic variants that contribute to chemotherapeutic agent-induced cytotoxicity. Our model integrated genotype, gene expression, and sensitivity of HapMap cell lines to drugs. Cell lines derived from 30 trios of European descent (Center d'Etude du Polymorphisme Humain population) and 30 trios of African descent (Yoruban population) were used. Cell growth inhibition at increasing concentrations of etoposide for 72 h was determined by using alamarBlue assay. Gene expression on 176 HapMap cell lines (87 Center d'Etude du Polymorphisme Humain population and 89 Yoruban population) was determined by using the Affymetrix GeneChip Human Exon 1.0ST Array. We evaluated associations between genotype and cytotoxicity, genotype and gene expression and correlated gene expression of the identified candidates with cytotoxicity. The analysis identified 63 genetic variants that contribute to etoposide-induced toxicity through their effect on gene expression. These include genes that may play a role in cancer (AGPAT2, IL1B, and WNT5B) and genes not yet known to be associated with sensitivity to etoposide. This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes induced by chemotherapeutic agents.