gebhart/patrepeval huggingface dataset:
Higher-Order Cellular Information Processing with Synthetic RNA Devices (2008)

The engineering of biological systems is anticipated to provide effective solutions to challenges that include energy and food production, environmental quality, and health and medicine. Our ability to transmit information to and from living systems, and to process and act on information inside cells, is critical to advancing the scale and complexity at which we can engineer, manipulate, and probe biological systems. We developed a general approach for assembling RNA devices that can execute higher-order cellular information processing operations from standard components. The engineered devices can function as logic gates (AND, NOR, NAND, or OR gates) and signal filters, and exhibit cooperativity. RNA devices process and transmit molecular inputs to targeted protein outputs, linking computation to gene expression and thus the potential to control cellular function.
Using PCR to extend the limit of oligonucleotide synthesis. (1992)

A method has been developed to allow one to extend the practical limit of oligonucleotide synthesis by coupling the synthesis reaction to a subsequent PCR. Given that DNA synthesizers are capable of producing reasonable yields of oligonucleotides that are 125-150 bases in length, this method could be used to recover the minute amount of full-length product present in mixtures extended well beyond the established limits. This technology could be applied to gene synthesis and mutagenesis.
The Current Status of Breast MR Imaging Part I. Choice of Technique, Image Interpretation, Diagnostic Accuracy, and Transfer to Clinical Practice (2007)

Compared with mammography and breast ultrasonography, contrast material-enhanced magnetic resonance (MR) imaging is a breast imaging technique that offers not only information on lesion cross-sectional morphology but also on functional lesion features such as tissue perfusion and enhancement kinetics. After an enthusiastic start to clinical breast MR imaging in the early 1990s, a variety of difficulties and obstacles were identified that hampered the transfer of the modality into clinical practice, including a lack of standardization regarding image acquisition and interpretation guidelines, a lack of MR-compatible interventional materials, and a lack of evidence regarding its diagnostic accuracy--particularly specificity and positive predictive value, as well as sensitivity for ductal carcinoma in situ. This article is the first of two on the current status of breast MR imaging. The pathophysiologic basis of breast MR and the effects on acquisition technique and diagnostic accuracy, the diverging demands of high spatial and temporal resolution, and the different approaches that exist for image acquisition are reviewed. Advantages and disadvantages of different pulse sequence parameters are discussed to help radiologists make a balanced and informed decision regarding choice of image acquisition protocol. Imaging findings in common benign and malignant changes are described, and current concepts for differential diagnosis, including the MR Breast Imaging Reporting and Data System lexicon, are discussed. Furthermore, obstacles that impeded the technique's transfer into clinical practice are discussed, and the progress made in recent years, especially regarding the development of guidelines, procedural standardization, and MR-guided interventions are outlined.
<title>High-resolution scanning laser projection display with diode-pumped solid state lasers</title> (2000)

We demonstrate bright pictures in the pixel format of HDTV and XGA with a current power consumption lower than 2.5 kW and a RGB laser output power of 15 W with the wavelengths 446 nm, 532 nm and 629 nm. The laser projection system consists of a scanning unit with a rotating polygon scanner (rotational frequency up to 2 kHz) to write the lines and a galvanometer scanner for the vertical deflection of the lines. The system allows the separation of the RGB-laser with the video modulation part from the free moving scanning unit with an optical fiber. The optical fiber provides the video modulated RGB-laser power in a collinear beam to the scanner. We explain detailed the requirements for RGB--laser beams. The main demands for high resolution and sharp scanned pictures are near diffraction limited laser beams, but at least with an optical beam product of &lt; 0.75 mm mrad. Furthermore we give an outlook for an increase of pixel resolution.
Oncogenic Stress Induced by Acute Hyper-Activation of Bcr-Abl Leads to Cell Death upon Induction of Excessive Aerobic Glycolysis (2011)

In response to deregulated oncogene activation, mammalian cells activate disposal programs such as programmed cell death. To investigate the mechanisms behind this oncogenic stress response we used Bcr-Abl over-expressing cells cultivated in presence of imatinib. Imatinib deprivation led to rapid induction of Bcr-Abl activity and over-stimulation of PI3K/Akt-, Ras/MAPK-, and JAK/STAT pathways. This resulted in a delayed necrosis-like cell death starting not before 48 hours after imatinib withdrawal. Cell death was preceded by enhanced glycolysis, glutaminolysis, and amino acid metabolism leading to elevated ATP and protein levels. This enhanced metabolism could be linked to induction of cell death as inhibition of glycolysis or glutaminolysis was sufficient to sustain cell viability. Therefore, these data provide first evidence that metabolic changes induced by Bcr-Abl hyper-activation are important mediators of oncogenic stress-induced cell death.During the first 30 hours after imatinib deprivation, Bcr-Abl hyper-activation did not affect proliferation but resulted in cellular swelling, vacuolization, and induction of eIF2α phosphorylation, CHOP expression, as well as alternative splicing of XPB, indicating endoplasmic reticulum stress response. Cell death was dependent on p38 and RIP1 signaling, whereas classical death effectors of ER stress, namely CHOP-BIM were antagonized by concomitant up-regulation of Bcl-xL.Screening of 1,120 compounds for their potential effects on oncogenic stress-induced cell death uncovered that corticosteroids antagonize cell death upon Bcr-Abl hyper-activation by normalizing cellular metabolism. This protective effect is further demonstrated by the finding that corticosteroids rendered lymphocytes permissive to the transforming activity of Bcr-Abl. As corticosteroids are used together with imatinib for treatment of Bcr-Abl positive acute lymphoblastic leukemia these data could have important implications for the design of combination therapy protocols.In conclusion, excessive induction of Warburg type metabolic alterations can cause cell death. Our data indicate that these metabolic changes are major mediators of oncogenic stress induced by Bcr-Abl.
How common is complex regional pain syndrome-Type I? (2007)

Department of Anesthesiology, Vanderbilt University School of Medicine, 701 Medical Arts Building, 1211, 21st Avenue South, Nashville, TN 37212, USA *Corresponding author. Tel.: +1 615 936 1821. E-mail: [email protected]
Inhibition of CD47 Effectively Targets Pancreatic Cancer Stem Cells via Dual Mechanisms (2015)

These data are consistent with efficient in vivo targeting of CSCs, and strongly suggest that CD47 inhibition could be a novel adjuvant treatment strategy for PDAC independent of underlying and highly variable driver mutations.
Temporal regulation of murine cytomegalovirus transcription and mapping of viral RNA synthesized at immediate early times after infection (1984)

The replication of murine cytomegalovirus strain Smith in murine embryonic fibroblasts was investigated at immediate early, early, and late times after infection. Cloned subgenomic HindIII fragments of murine cytomegalovirus DNA served to define the regions of transcription. At immediate early times viral RNA classes ranging in size from 5.1 to 1.05 kilobases (kb) were transcribed mainly from the fragments HindIII-K and -L, whereas low levels of transcription were detected from the two termini HindIII-E and HindIII-N. A characteristic pattern of proteins could be translated from immediate early RNA in vitro. At early and late times after infection transcription from all HindIII fragments occurred, but different patterns of transcripts and proteins could be identified. Inhibitors of DNA synthesis induced differences in the late transcription pattern, located in the HindIII-F fragment. The coding region for abundant immediate early transcription could be located at between 0.769 and 0.817 map units. A plasmic clone containing the main part (0.769 to 0.815 map units) of this region was constructed. This region coded for six polyadenylated immediate early RNA species of 5.1, 2.75, 2.0, 1.75, 1.65, and 1.05 kb in size. Only the 1.75-kb RNA originated entirely from the HindIII-L fragment. The 5.1- and 2.75-kb RNA species were encoded by both the HindIII-L and HindIII-K fragments, and the 2.0-, 1.65-, and 1.05-kb RNA species were entirely transcribed within HindIII-K.
Endoplasmic Reticulum Stress Triggers Autophagy (2006)

Eukaryotic cells have evolved strategies to respond to stress conditions. For example, autophagy in yeast is primarily a response to the stress of nutrient limitation. Autophagy is a catabolic process for the degradation and recycling of cytosolic, long lived, or aggregated proteins and excess or defective organelles. In this study, we demonstrate a new pathway for the induction of autophagy. In the endoplasmic reticulum (ER), accumulation of misfolded proteins causes stress and activates the unfolded protein response to induce the expression of chaperones and proteins involved in the recovery process. ER stress stimulated the assembly of the pre-autophagosomal structure. In addition, autophagosome formation and transport to the vacuole were stimulated in an Atg protein-dependent manner. Finally, Atg1 kinase activity reflects both the nutritional status and autophagic state of the cell; starvation-induced autophagy results in increased Atg1 kinase activity. We found that Atg1 had high kinase activity during ER stress-induced autophagy. Together, these results indicate that ER stress can induce an autophagic response.
Incremental Basis Construction from Temporal Difference Error (2011)

In many reinforcement learning (RL) systems, the value function is approximated as a linear combination of a fixed set of basis functions. Performance can be improved by adding to this set. Previous approaches construct a series of basis functions that in sufficient number can eventually represent the value function. In contrast, we show that there is a single, ideal basis function, which can directly represent the value function. Its addition to the set immediately reduces the error to zero—without changing existing weights. Moreover, this ideal basis function is simply the value function that results from replacing the MDP’s reward function with its Bellman error. This result suggests a novel method for improving value-function estimation: a primary reinforcement learner estimates its value function using its present basis functions; it then sends its TD error to a secondary learner, which interprets that error as a reward function and estimates the corresponding value function; the resulting value function then becomes the primary learner’s new basis function. We present both batch and online versions in combination with incremental basis projection, and demonstrate that the performance is superior to existing methods, especially in the case of large discount factors. 1.
Dynamic Formation of a Hot Field Reversed Configuration with Improved Confinement by Supersonic Merging of Two Colliding High-βCompact Toroids (2010)

A hot stable field-reversed configuration (FRC) has been produced in the C-2 experiment by colliding and merging two high-$\ensuremath{\beta}$ plasmoids preformed by the dynamic version of field-reversed $\ensuremath{\theta}$-pinch technology. The merging process exhibits the highest poloidal flux amplification obtained in a magnetic confinement system (over tenfold increase). Most of the kinetic energy is converted into thermal energy with total temperature (${T}_{i}+{T}_{e}$) exceeding 0.5 keV. The final FRC state exhibits a record FRC lifetime with flux confinement approaching classical values. These findings should have significant implications for fusion research and the physics of magnetic reconnection.
Oxygen sensors based on luminescence quenching: interactions of pyrene with the polymer supports (1995)

Oxygen quenching of pyrene has been studied in a diverse series of polymers. Most measurements were made using homo- or copolymers containing a poly(dimethylsiloxane) region. Systematic variations in the polymer properties have been made in order to delineate the structural features important for satisfactory use as supports for oxygen sensors. In particular, quenching behavior was examined as a function of the type and amount of copolymer cross-linkers; these were added to produce domains of different polarity and rigidity that would segregate the sensor molecule. A domain model (Xu, W.; et al. Anal. Chem. 1994, 66, 4133-4141) was used to explain the variations in oxygen-quenching properties as a function of additives and cross-linkers. The relative affinity of the different domains for the pyrene and the efficacy of the domains for oxygen quenching controls the overall behavior of the sensing response.
Serum Bactericidal Antibody Responses to Meningococcal Polysaccharide Vaccination as a Basis for Clinical Classification of Common Variable Immunodeficiency (2008)

Common variable immunodeficiency (CVID) is a heterogeneous group of disorders characterized by hypogammaglobulinemia and increased susceptibility to recurrent pyogenic infections. This study was performed to subclassify CVID on the basis of the bactericidal antibody responses of patients to polysaccharide meningococcal vaccine. Twenty-five patients with CVID (18 male and 7 female) and 25 healthy volunteers received meningococcal polysaccharide vaccine A + C. Serum bactericidal antibody (SBA) titers were measured at baseline and after 3 weeks. Response was correlated with clinical and immunological manifestations of CVID. Twenty-four (96%) of the 25 normal controls had a protective SBA titer of > or = 8 postvaccination, whereas only 16 (64%) of the 25 CVID patients had a protective titer (P value = 0.013). Among the patients with CVID who were nonresponders, there were significantly increased rates of bronchiectasis (P = 0.008), splenomegaly (P = 0.016), and autoimmunity (P = 0.034) in comparison with patients who had protective SBA titers. A reversed CD4/CD8 ratio was more common in the nonresponder group of patients (P = 0.053). We conclude that individuals with CVID who cannot produce protective postvaccination titers after receiving meningococcal polysaccharide vaccine are more likely to exhibit bronchiectasis, splenomegaly, and autoimmune diseases. Vaccination response may define subgroups of patients with CVID, enabling more effective monitoring and therapeutic strategies.
Pornographies (2000)

To be radical about pornography used to mean that one favored less censorship; now it often means that one favors more. That political change reflects a shift in the dominant paradigm of pornography and its putative evils. Until quite recently, most people who believed pornography wrong thought that it offended against decency and propriety and was therefore obscene . That was certainly the view of the law. English judges first created the crime of obscene libel in 1727 on the basis that such expression tended to corrupt the morals of the King's subjects, a thought that inspired most subsequent legislation in the common‐law world. Sometimes the underlying concern really was paternalistic: pornography degrades and corrupts its producers and consumers; the law forces them to become better people. More often, however, it was just moralism of the familiar sorts: the view that a majority of a community is entitled to enforce its moral views on the rest, either because that is democratic or because that is just what it means to be a community. The obscenity paradigm thus had two features. First, it was illiberal: it ranked personal autonomy below realizing the good, enforcing the majority will, or embodying communitarian values. Second, it was gender neutral: to understand the nature of pornography did not require theorizing relations between men and women. On the obscenity paradigm, pornography was a matter of virtue versus vice, majorities versus minorities.
Genetic and pharmacological inhibition of GITR‐GITRL interaction reduces chronic lung injury induced by bleomycin instillation (2006)

We have recently identified a gene named GITR (glucocorticoid-induced TNF receptor related gene). GITR is expressed in different cells and tissues such as T lymphocytes from thymus and spleen and lymph nodes, and also in the lung. GITR ligand (GITRL) is expressed in several cells including macrophages, B cells, dendritic cells, and endothelial cells. In the present study, by comparing the responses in wild-type (WT) mice (GITR+/+) and GITR-deficient mice (GITR-/-), we investigated the role played by GITR-GITRL interaction in the development of chronic lung injury caused by bleomycin instillation. When compared with bleomycin-treated GITR+/+ mice, bleomycin-treated GITR-/- mice exhibited a reduced degree of i) lung infiltration with polymorphonuclear neutrophils (MPO activity); ii) edema formation; iii) histological evidence of lung injury; iv) TNF-alpha and interleukin (IL)-1beta production; v) nitrotyrosine formation; and vi) NF-kappaB activation. The cotreatment of GITR+/+ mice with Fc-GITR fusion protein (6.25 microg/mouse) also significantly attenuated all of the above indicators of lung damage and inflammation. Our results clearly demonstrate that GITR-GITRL interaction plays an important role in the chronic lung injury induced by bleomycin in the mice.
Cloning of Two Distinct cDNAs Encoding Parvalbumin, the Major Allergen of Atlantic Salmon (Salmo salar) (1996)

Allergy to fish is common in Northern Europe. Variable reactions to different fish species are usually experienced among fish allergic patients. The allergens of cod fish and particularly the major allergen parvalbumin β ( Gadus callarias ) have been extensively studied in Norway. In the present communication, the white muscle parvalbumin was similarly found to be a major allergen in Atlantic salmon ( Salmo salar , Sal s1 ). A purified salmon parvalbumin was obtained by anion exchange chromatography, gel filtration chromatography (GFC) and high‐performance liquid chromatography (HPLC) of the muscle extracts. The antigenicity and allergenicity of salmon parvalbumin were confirmed using various immunologic and electrophoretic techniques. The protein is representative for several isoallergens judged by the amino acid (AA) sequence variance at certain sites in the AA sequence of CNBr cleavage peptides. Using sera from patients with cod and salmon allergy Sal s1 was demonstrated to be the major allergen of Atlantic salmon, as judged by RAST‐ and ELISA‐inhibitions and crossed radioimmunoelectrophoresis (CRIE) techniques. The protein was also demonstrated to be antigenic by the use of polyclonal cod and salmon antibodies in IgG ELISA and immunoelectrophoretic methods. Cloning of parvalbumin cDNA from Atlantic salmon was performed based on an alignment of parvalbumin AA sequences from other species. A probe was generated by PCR and used for screening a salmon muscle cDNA‐library. Subcloning and sequencing of two hybridizing clones revealed transcripts from two different parvalbumin genes. The translated sequences of both clones belong to the β‐lineage of parvalbumins and include the entire coding region.
Lymphocyte function-associated antigen-1 (LFA-1) interaction with intercellular adhesion molecule-1 (ICAM-1) is one of at least three mechanisms for lymphocyte adhesion to cultured endothelial cells. (1988)

Intercellular adhesion molecule-1 (ICAM-1) on the surface of cultured umbilical vein and saphenous vein endothelial cells was upregulated between 2.5- and 40-fold by rIL-1, rTNF, LPS and rIFN gamma corresponding to up to 5 X 10(6) sites/cell. Endothelial cell ICAM-1 was a single band of 90 kD in SDS-PAGE. Purified endothelial cell ICAM-1 reconstituted into liposomes and bound to plastic was an excellent substrate for both JY B lymphoblastoid cell and T lymphoblast adhesion. Adhesion to endothelial cell ICAM-1 in planar membranes was blocked completely by monoclonal antibodies to lymphocyte function associated antigen-1 (LFA-1) or ICAM-1. Adhesion to artificial membranes was most sensitive to ICAM-1 density within the physiological range found on resting and stimulated endothelial cells. Adhesion of JY B lymphoblastoid cells, normal and genetically LFA-1 deficient T lymphoblasts and resting peripheral blood lymphocytes to endothelial cell monolayers was also assayed. In summary, LFA-1 dependent (60-90% of total adhesion) and LFA-1-independent basal adhesion was observed and the use of both adhesion pathways by different interacting cell pairs was increased by monokine or lipopolysaccharide stimulation of endothelial cells. The LFA-1-dependent adhesion could be further subdivided into an LFA-1/ICAM-1-dependent component which was increased by cytokines and a basal LFA-1-dependent, ICAM-1-independent component which did not appear to be affected by cytokines. We conclude that ICAM-1 is a regulated ligand for lymphocyte-endothelial cell adhesion, but at least two other major adhesion pathways exist.
Structure of monolayers formed by coadsorption of two n-alkanethiols of different chain lengths on gold and its relation to wetting (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of monolayers formed by coadsorption of two n-alkanethiols of different chain lengths on gold and its relation to wettingPaul E. Laibinis, Ralph G. Nuzzo, and George M. WhitesidesCite this: J. Phys. Chem. 1992, 96, 12, 5097–5105Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://pubs.acs.org/doi/10.1021/j100191a065https://doi.org/10.1021/j100191a065research-articleACS PublicationsRequest reuse permissionsArticle Views1221Altmetric-Citations281LEARN 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