gebhart/patrepeval huggingface dataset:
Antigenic Drift in the Influenza A Virus (H3N2) Nucleoprotein and Escape from Recognition by Cytotoxic T Lymphocytes (2000)

Viruses exploit different strategies to escape immune surveillance, including the introduction of mutations in cytotoxic T-lymphocyte (CTL) epitopes. The sequence of these epitopes is critical for their binding to major histocompatibility complex (MHC) class I molecules and recognition by specific CTLs, both of which interactions may be lost by mutation. Sequence analysis of the nucleoprotein gene of influenza A viruses (H3N2) isolated in The Netherlands from 1989 to 1999 revealed two independent amino acid mutations at the anchor residue of the HLA-B27-specific CTL epitope SRYWAIRTR (383 to 391). A R384K mutation was found in influenza A viruses isolated during the influenza season 1989-1990 but not in subsequent seasons. In the influenza season 1993-1994, a novel mutation in the same CTL epitope at the same position was introduced. This R384G mutation proved to be conserved in all influenza A viruses isolated from 1993 onwards. Both mutations R384K and R384G abrogated MHC class I presentation and allowed escape from recognition by specific CTLs.
CONFIRMING ANTHRAX (2006)

RETURN TO ISSUEPREVNewsNEXTCONFIRMING ANTHRAXAntibody-based technique might provide advantages over PCR procedureSTU BORMANCite this: Chem. Eng. News 2006, 84, 35, 10Publication Date (Print):August 28, 2006Publication History Published online14 November 2010Published inissue 28 August 2006https://pubs.acs.org/doi/10.1021/cen-v084n035.p010https://doi.org/10.1021/cen-v084n035.p010newsACS PublicationsCopyright © 2006 American Chemical SocietyArticle Views11Altmetric-Citations-LEARN 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 SUBJECTS:Biopolymers,Genetics,Immunology,Peptides and proteins Get e-Alerts
The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix (1975)

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed.
The JAK kinase inhibitor CP‐690,550 supresses the growth of human polycythemia vera cells carrying the JAK2V617F mutation (2008)

The somatic activating janus kinase 2 mutation (JAK2)(V617F) is detectable in most patients with polycythemia vera (PV). Here we report that CP-690,550 exerts greater antiproliferative and pro-apoptotic activity against cells harboring JAK2(V617F) compared with JAK2(WT). CP-690,550 treatment of murine factor-dependent cell Patersen-erythropoietin receptor (FDCP-EpoR) cells harboring human wild-type or V617F JAK2 resulted in inhibition of cell proliferation with a 50% inhibitory concentration (IC(50)) of 2.1 microM and 0.25 microM, respectively. Moreover, CP-690,550 induced a significant pro-apoptotic effect on murine FDCP-EpoR cells carrying JAK2(V617F), whereas a lesser effect was observed for cells carrying wild-type JAK2. This activity was coupled with inhibition of phosphorylation of the key JAK2(V617F)-dependent downstream signaling effectors signal transducer and activator of transcription (STAT)3, STAT5, and v-akt murine thymoma viral oncogene homolog (AKT). Furthermore, CP-690,550 treatment of ex-vivo-expanded erythroid progenitors from JAK2(V617F)-positive PV patients resulted in specific, antiproliferative (IC(50) = 0.2 microM) and pro-apoptotic activity. In contrast, expanded progenitors from healthy controls were less sensitive to CP-690,550 in proliferation (IC(50) > 1.0 microM), and apoptosis assays. The antiproliferative effect on expanded patient progenitors was paralleled by a decrease in JAK2(V617F) mutant allele frequency, particularly in a patient homozygous for JAK2(V617F). Flow cytometric analysis of expanded PV progenitor cells treated with CP-690,550 suggests a possible transition towards a pattern of erythroid differentiation resembling expanded cells from normal healthy controls.
Generating parallel code for SIMD machines (1992)

Massively parallel SIMD machines rely on data parallelism usually achieved by a careful hand coding to support program efficiency. This paper describes parallelization of code generated for SIMD machines by the compiler for the Equational Programming Language, EPL. The language supports architecture-independent scientific programming by recurrent equations. The EPL compiler serves as a programming aid for users of parallel machines by automating data partitioning and computation parallelization based on inherent data dependencies. In support of a Connection Machine architecture, the EPL compiler performs horizontal partitioning of the program, a process that selects a dimension of each data structure to be projected along the processor array. Each processor then holds a single instance of that structure and operations along the projected dimension are done in parallel. The paper describes horizontal partitioning, code generation in MPL and efficiency of programs generated for Maspar SIMD machine.
Theory of semiconductor heterojunctions: The role of quantum dipoles (1984)

At any semiconductor heterojunction there is an interface dipole associated with quantum-mechanical tunneling, which depends on the band "lineup" between the two semiconductors. When the interface dipolar response dominates, the actual band discontinuity must be close to that unique value which would give a zero interface dipole. A simple criterion is proposed for this zero-dipole lineup, which gives excellent agreement with experimental band lineups. The close connection between heterojunction band lineups and Schottky barrier formation is emphasized.
Phase II, Randomized Trial Comparing Bevacizumab Plus Fluorouracil (FU)/Leucovorin (LV) With FU/LV Alone in Patients With Metastatic Colorectal Cancer (2002)

The encouraging results of this randomized trial support further study of bevacizumab 5 mg/kg plus chemotherapy as first-line therapy for metastatic colorectal cancer.
Programmed cell death: a way of life for plants. (1996)

Cell death in higher plants has been widely observed in predictable patterns throughout development and in response to pathogenic infection. Genetic, biochemical, and morphological evidence suggests that these cell deaths occur as active processes and can be defined formally as examples of programmed cell death (PCD). Intriguingly, plants have at least two types of PCD, an observation that is also true of PCD in animals [Schwartz, L. M., Smith, W.W., Jones, M. E. E. & Osborne, B. A. (1993) Proc. Natl. Acad. Sci. USA 90, 980-984]. Thus, in plants, PCD resembles either a common form of PCD seen in animals called apoptosis or it resembles a morphologically distinct form of cell death. The ubiquitous occurrence and necessity of PCD for plant development and defense suggest that the underlying mechanisms of regulation and execution of these processes merit further examination.
Production of an Extracellular Polysaccharide by Haloferax mediterranei (1988)

The extremely halophilic archaebacterium Haloferax mediterranei produces an exocellular polymeric substance that gives the colonies a typical mucous character and is responsible for the appearance of a superficial layer in unshaken liquid medium. This exocellular polymeric substance can be obtained from the supernatant of shaken liquid cultures by cold ethanol precipitation, and yields as high as 3 mg/ml have been detected. The substance was produced under all the conditions tested and with all substrates assayed, although higher yields were obtained with sugars, particularly glucose, as carbon and energy source. The total exocellular polymeric substance produced was proportional to the total biomass. The polymer is a heteropolysaccharide containing mannose as the major component. Glucose, galactose, and another unidentified sugar were also present, as well as amino sugars, uronic acids, and a considerable amount of sulfate, which accounts for the acidic nature of the polymer. The infrared spectrum and specific assays showed the absence of acyl groups. The rheological properties of polymer solutions were studied, showing a pseudoplastic behavior and a high apparent viscosity at relatively low concentrations. Viscosity was remarkably resistant to extremes of pH, temperature, or salinity. These characteristics make this polymer interesting for enhanced oil recovery and other applications for which a very resistant thickening agent is required.
Development of Technologies Aiding Large-Tissue Engineering (1998)

There are many clinical situations in which a large tissue mass is required to replace tissue lost to surgical resection (e.g., mastectomy). It is possible that autologous cell transplantation on biodegradable polymer matrices may provide a new therapy to engineer large tissue which can be used to treat these patients. A number of challenges must be met to engineer a large soft tissue mass. These include the design of (1) a structural framework to maintain a space for tissue development, (2) a space-filling matrix which provides for localization of transplanted cells, and (3) a strategy to enhance vascularization of the forming tissue. In this paper we provide an overview of several technologies which are under development to address these issues. Specifically, support matrices to maintain a space for tissue development have been fabricated from polymers of lactide and glycolide. The ability of these structures to resist compressive forces was regulated by the ratio of lactide to glycolide in the polymer. Smooth muscle cell seeding onto polyglycolide fiber-based matrices has been optimized to allow formation of new tissues in vitro and in vivo. Finally, polymer microsphere drug delivery technology is being developed to release vascular endothelial growth factor (VEGF), a potent angiogenic molecule, at the site of tissue formation. This strategy, which combines several different technologies, may ultimately allow for the engineering of large soft tissues.
A Tandem Approach to Photoactivated Olefin Metathesis: Combining a Photoacid Generator with an Acid Activated Catalyst (2009)

Combining an acid activated precatalyst with a photoacid generator (PAG) in the presence of ultraviolet light resulted in a highly efficient catalyst for olefin metathesis. The tandem system of precatalyst and PAG was capable of both ring closing metathesis (RCM) and ring opening metathesis polymerization (ROMP) in good to excellent conversion. Mechanistic investigations revealed that the catalytically active species is very similar to that of other well-known Ru-based catalysts.
Protein phosphorylation and regulation of adaptive responses in bacteria (1989)

Bacteria continuously adapt to changes in their environment. Responses are largely controlled by signal transduction systems that contain two central enzymatic components, a protein kinase that uses adenosine triphosphate to phosphorylate itself at a histidine residue and a response regulator that accepts phosphoryl groups from the kinase. This conserved phosphotransfer chemistry is found in a wide range of bacterial species and operates in diverse systems to provide different regulatory outputs. The histidine kinases are frequently membrane receptor proteins that respond to environmental signals and phosphorylate response regulators that control transcription. Four specific regulatory systems are discussed in detail: chemotaxis in response to attractant and repellent stimuli (Che), regulation of gene expression in response to nitrogen deprivation (Ntr), control of the expression of enzymes and transport systems that assimilate phosphorus (Pho), and regulation of outer membrane porin expression in response to osmolarity and other culture conditions (Omp). Several additional systems are also examined, including systems that control complex developmental processes such as sporulation and fruiting-body formation, systems required for virulent infections of plant or animal host tissues, and systems that regulate transport and metabolism. Finally, an attempt is made to understand how cross-talk between parallel phosphotransfer pathways can provide a global regulatory curcuitry.
Molecular and polymeric precursors to boron carbide nanofibers, nanocylinders, and nanoporous ceramics (2003)

Abstract New decaborane-based, single-source molecular and polymeric precursors to boron carbide have been developed that enable the formation of boron carbide in processed forms, including nanofibers, nanocylinders, and nanoporous materials.
Family size, infection and atopy: the first decade of the 'hygiene hypothesis' (2000)

Declining family size is one factor that has been proposed to contribute to increasing asthma and hay fever prevalence, but its relative importance has not been quantified. Objective. Our purpose was to determine the change in asthma and hay fever prevalence that would be expected from the reduction in family size that has occurred in England/Wales and New Zealand over recent decades. Methods. The relative change in family size between 1961 and 1991 in England/Wales and New Zealand was determined from census data for these years. Summary weighted odds ratios were calculated for the associations among birth order, family size, and asthma and hay fever prevalence. The expected increase in the prevalence of asthma and hay fever between 1961 and 1991 resulting from changes in family size was then calculated. Results. The expected relative increase in the prevalence of asthma between 1961 and 1991 as a result of the smaller family size was 1% and 5% for England/ Wales and New Zealand, respectively; smaller family size would be expected to increase the prevalence of hay fever prevalence in England/Wales by 4%. Conclusions. Changes in family size over the last 30 years do not appear to explain much of the reported increase in asthma or hay fever prevalence. The contribution that other risk factors have made to these increases could be assessed with use of a similar approach. (
The development of probiotic treatment in obesity: a review (2013)

Recent studies suggested that manipulation of the composition of the microbial ecosystem in the gut might be a novel approach in the treatment of obesity. Such treatment might consist of altering the composition of the microbial communities of an obese individual by administration of beneficial microorganisms, commonly known as probiotics. Here, we intend to contribute to the developmental process of probiotic treatment of human obesity. The aim is to review the evidence regarding the potential effect of probiotic strains on reduction of weight and body fat. A literature study was conducted focusing on clinical trials that examined the effect of specific microorganisms on body weight control. Analysis of the eligible articles pointed out that Lactobacillus gasseri SBT 2055, Lactobacillus rhamnosus ATCC 53103, and the combination of L. rhamnosus ATCC 53102 and Bifidobacterium lactis Bb12 may reduce adiposity, body weight, and weight gain. This suggests that these microbial strains can be applied in the treatment of obesity. Furthermore, short chain fatty acid production and low grade inflammation were found as the underlying mechanisms of action that influence metabolism and affect body weight. These findings might contribute to the development of probiotic treatment of obesity. Further research should be directed to the most effective combination and dosage rate of probiotic microorganisms.
Detection and Clinical Significance of Intratumoral EGFR Mutational Heterogeneity in Chinese Patients with Advanced Non-Small Cell Lung Cancer (2013)

Approximately 30% of patients presented intratumoral EGFR mutational heterogeneity, accompanying with relatively low EGFR copy number. EGFR mutant content was correlated with the response and prognosis of EGFR-TKIs.
Organization of the major and minor capsid proteins in human papillomavirus type 33 virus-like particles (1995)

The organization of the major (L1) and minor (L2) proteins in the human papillomavirus capsid is still largely unknown. In this study we analysed the disulphide bonding between L1 proteins and the association of L2 proteins with capsomers using virus-like particles obtained in insect cells by co-expression of the L1 and L2 genes of human papillomavirus type 33. About 50% of the L1 protein molecules in these particles (1.29 g/cm3) formed disulphide-bonded trimers. Reduction of the intermolecular disulphide bonds by dithiotreitol (DTT) treatment caused disassembly of virus-like particles into capsomers. This indicates that disulphide bonds between capsomers at the threefold symmetry positions of the capsid are essential for the assembly of the papillomavirus capsid. In contrast, the L2 protein was not engaged in intermolecular disulphide bonding. The L2 protein remained associated with capsomers on disassembly by treatment with DTT. When the disassembly was carried out in 0.65 M-NaCl, complete L2 protein molecules bound preferentially to capsomer oligomers, whereas truncated L2 protein molecules bound only to monomers. In 0.15 M-NaCl only complete L2 protein molecules remained bound to capsomers. This indicates that different regions of the L2 protein molecule are differentially involved in the association of the papillomavirus capsid.
p53 nuclear protein expression is an independent prognostic marker in clinically localized prostate cancer patients undergoing radical prostatectomy. (1995)

Immunohistochemical (IHC) staining for p53 protein nuclear expression was evaluated in archival paraffin-embedded radical prostatectomy specimens from 139 patients with clinically localized prostate cancer followed up from 1 to 8 (mean, 4) years. Elevated nuclear p53 protein expression was detected in 85 (61%) of 139 patients, being heterogeneous and focal in the majority of specimens. Only four specimens displayed homogeneous nuclear accumulation of p53 protein. Disease progression, most commonly prostate-specific antigen elevation, was noted in 46 (33%) patients, with 39 (85%) having positive p53 protein IHC stains. Conversely, 93 (67%) of 139 have not recurred, with 46 (49%) having positive p53. Of all 54 p53-negative patients, 47 (87%) have had no disease recurrence. An increased p53 protein IHC stain was associated with a higher pathological stage (T1 and T2, 51% versus >/=T3, 69%) and Gleason score 2-4, 17%; 5-7, 72%; and 8-10, 87.5%). Despite these associations, p53 IHC staining was an independent predictor of disease-free survival in a multivariate analysis of p53, age, race, stage, and grade. This study revealed that a majority of clinically localized prostate cancers heterogeneously express elevated nuclear levels of p53 protein in at least a subset of malignant cells, and that this expression is an independent predictor of disease progression in prostate cancer patients after radical prostatectomy.
Progesterone and its Metabolite Allopregnanolone Differentially Regulate Hemostatic Proteins after Traumatic Brain Injury (2008)

Our laboratory has shown in numerous experiments that the neurosteroids progesterone (PROG) and allopregnanolone (ALLO) improve molecular and functional outcomes after traumatic brain injury (TBI). As coagulopathy is an important contributor to the secondary destruction of nervous tissue, we hypothesized that PROG and ALLO administration may also have a beneficial effect on coagulation protein expression after TBI. Adult male Sprague-Dawley rats were given bilateral contusions of the medial frontal cortex followed by treatments with PROG (16 mg/kg), ALLO (8 mg/kg), or vehicle (22.5% hydroxypropyl-beta-cyclodextrin). Controls received no injury or injections. Progesterone generally maintained procoagulant (thrombin, fibrinogen, and coagulation factor XIII), whereas ALLO increased anticoagulant protein expression (tissue-type plasminogen activator, tPA). In addition, PROG significantly increased the ratio of tPA bound to neuroserpin, a serine protease inhibitor that can reduce the activity of tPA. Our findings suggest that in a model of TBI, where blood loss may exacerbate injury, it may be preferable to treat patients with PROG, whereas it might be more appropriate to use ALLO as a treatment for thrombotic stroke, where a reduction in coagulation would be more beneficial.
Identification of cell surface receptors for murine macrophage inflammatory protein-1 alpha (1991)

We have produced recombinant proteins for a cytokine, L2G25BP (macrophage inflammatory protein-1 alpha) (MIP-1 alpha). By using the recombinant protein (rMIP-1 alpha), receptors for MIP-1 alpha were identified on Con A-stimulated and unstimulated CTLL-R8, a T cell line, and LPS-stimulated RAW 264.7, a macrophage cell line. The 125I-rMIP-1 alpha binds to the receptor in a specific and saturable manner. Scatchard analysis indicated a single class of high affinity receptor, with a Kd of approximately 1.5 x 10(-9) M and approximately 1200 binding sites/Con A-stimulated CTLL-R8 cell and a Kd of 0.9 x 10(-9) M and approximately 380 binding sites/RAW 264.7 cell. 125I-rMIP-1 alpha binding was inhibited by unlabeled rMIP-1 alpha in a dose-dependent manner, but not by IL-1 alpha or IL-2. rMIP-1 alpha inhibited the proliferation of unstimulated CTLL-R8 cells. Rabbit anti-rMIP-1 alpha antibodies blocked the growth-inhibitory effect of the rMIP-1 alpha on CTLL-R8 cells.
Nucleic Acid Therapeutics: State of the Art and Future Prospects (1998)

AS WE APPROACH the new millennium, a quick glance backwards reveals that truly astounding progress has been made in the identification of genes responsible for cell growth, development, and neoplastic transformation. With this knowledge has come a natural desire to “translate” this information
Rosiglitazone induces interleukin‐1 receptor antagonist in interleukin‐1β–stimulated rat synovial fibroblasts via a peroxisome proliferator–activated receptor β/δ–dependent mechanism (2005)

Rosiglitazone stimulates IL-1Ra production by a PPARbeta/delta mechanism in activated rat synovial fibroblasts, further contributing to its potential antiarthritic properties and opening new perspectives for the modulation of inflammatory genes by specific PPAR agonists in articular cells.