gebhart/patrepeval huggingface dataset:
Immunization of Macaques with Formalin-Inactivated Respiratory Syncytial Virus (RSV) Induces Interleukin-13-Associated Hypersensitivity to Subsequent RSV Infection (2002)

Respiratory syncytial virus (RSV) is a major cause of severe respiratory disease in infants and the elderly. RSV vaccine development has been hampered by results of clinical trials in the 1960s, when formalin-inactivated whole-RSV preparations adjuvated with alum (FI-RSV) were found to predispose infants for enhanced disease following subsequent natural RSV infection. We have reproduced this apparently immunopathological phenomenon in infant cynomolgus macaques and identified immunological and pathological correlates. Vaccination with FI-RSV induced specific virus-neutralizing antibody responses accompanied by strong lymphoproliferative responses. The vaccine-induced RSV-specific T cells predominantly produced the Th2 cytokines interleukin-13 (IL-13) and IL-5. Intratracheal challenge with a macaque-adapted wild-type RSV 3 months after the third vaccination elicited a hypersensitivity response associated with lung eosinophilia. The challenge resulted in a rapid boosting of IL-13-producing T cells in the FI-RSV-vaccinated animals but not in the FI-measles virus-vaccinated control animals. Two out of seven FI-RSV-vaccinated animals died 12 days after RSV challenge with pulmonary hyperinflation. Surprisingly, the lungs of these two animals did not show overt inflammatory lesions. However, upon vaccination the animals had shown the strongest lymphoproliferative responses associated with the most pronounced Th2 phenotype within their group. We hypothesize that an IL-13-associated asthma-like mechanism resulted in airway hyperreactivity in these animals. This nonhuman primate model will be an important tool to assess the safety of nonreplicating candidate RSV vaccines.
Studies on the solution- and solid-state structure of patellin 2 (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on the solution- and solid-state structure of patellin 2T. Mark Zabriskie, Mark P. Foster, Thomas J. Stout, Jon Clardy, and Chris M. IrelandCite this: J. Am. Chem. Soc. 1990, 112, 22, 8080–8084Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/ja00178a035https://doi.org/10.1021/ja00178a035research-articleACS PublicationsRequest reuse permissionsArticle Views212Altmetric-Citations47LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Coronary Artery Disease Detected by Coronary Computed Tomographic Angiography Is Associated With Intensification of Preventive Medical Therapy and Lower Low-Density Lipoprotein Cholesterol (2014)

Abnormal CCTA findings are associated with downstream intensification in statin and aspirin therapy. In particular, CCTA may lead to increased use of prognostically beneficial therapies in patients identified as having extensive, nonobstructive CAD.
A single-inductor dual-output switching converter with low ripples and improved cross regulation (2009)

This paper proposes a novel fly capacitor method for single-inductor dual-output (SIDO) switching converters to reduce the output ripples and spikes. An adaptive common-mode control is presented to suppress the cross regulation problem. The converter can automatically switch between pulse-width modulation (PWM) and pulse-frequency modulation (PFM) control to improve the efficiency. The SIDO converter is specified for one channel 1.2 V/400 mA and the other 1.8 V/200 mA with input voltage ranging from 2.7 V to 5 V. The chip has been fabricated on a 0.25 mum CMOS mixed signal process. The conversion efficiency is 82% at a total output power of 840 mW while the output ripples are about 20 mV and spikes less than 40 mV.
A 3D Face Model for Pose and Illumination Invariant Face Recognition (2009)

Generative 3D face models are a powerful tool in computer vision. They provide pose and illumination invariance by modeling the space of 3D faces and the imaging process. The power of these models comes at the cost of an expensive and tedious construction process, which has led the community to focus on more easily constructed but less powerful models. With this paper we publish a generative 3D shape and texture model, the Basel face model (BFM), and demonstrate its application to several face recognition task. We improve on previous models by offering higher shape and texture accuracy due to a better scanning device and less correspondence artifacts due to an improved registration algorithm. The same 3D face model can be fit to 2D or 3D images acquired under different situations and with different sensors using an analysis by synthesis method. The resulting model parameters separate pose, lighting, imaging and identity parameters, which facilitates invariant face recognition across sensors and data sets by comparing only the identity parameters. We hope that the availability of this registered face model will spur research in generative models. Together with the model we publish a set of detailed recognition and reconstruction results on standard databases to allow complete algorithm comparisons.
Perspective Correction Methods for Camera-Based Document Analysis (2005)

We investigate the electron transport through a graphene p-n junction under a perpendicular magnetic field. By using the Landauer-Büttiker formalism combined with the nonequilibrium Green function method, the conductance is studied for clean and disordered samples. For the clean p-n junction, the conductance is quite small. In the presence of disorders, it is strongly enhanced and exhibits a plateau structure at a suitable range of disorders. Our numerical results show that the lowest plateau can survive for a very broad range of disorder strength, but the existence of high plateaus depends on system parameters and sometimes cannot be formed at all. When the disorder is slightly outside of this disorder range, some conductance plateaus can still emerge with its value lower than the ideal value. These results are in excellent agreement with a recent experiment.
A human intermediate conductance calcium-activated potassium channel (1997)

An intermediate conductance calcium-activated potassium channel, hIK1, was cloned from human pancreas. The predicted amino acid sequence is related to, but distinct from, the small conductance calcium-activated potassium channel subfamily, which is approximately 50% conserved. hIK1 mRNA was detected in peripheral tissues but not in brain. Expression of hIK1 in Xenopus oocytes gave rise to inwardly rectifying potassium currents, which were activated by submicromolar concentrations of intracellular calcium (K0.5 = 0.3 microM). Although the K0.5 for calcium was similar to that of small conductance calcium-activated potassium channels, the slope factor derived from the Hill equation was significantly reduced (1.7 vs. 3. 5). Single-channel current amplitudes reflected the macroscopic inward rectification and revealed a conductance level of 39 pS in the inward direction. hIK1 currents were reversibly blocked by charybdotoxin (Ki = 2.5 nM) and clotrimazole (Ki = 24.8 nM) but were minimally affected by apamin (100 nM), iberiotoxin (50 nM), or ketoconazole (10 microM). These biophysical and pharmacological properties are consistent with native intermediate conductance calcium-activated potassium channels, including the erythrocyte Gardos channel.
Cell-Free Transcription at 95°: Thermostability of Transcriptional Components and DNA Topology Requirements of Pyrococcus Transcription (1999)

Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100 degrees. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100 degrees. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg(2+) ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95 degrees was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70 degrees and 90 degrees. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.
Survival function of ERK1/2 as IL-3-activated, staurosporine-resistant Bcl2 kinases (2000)

Bcl2 phosphorylation at Ser-70 may be required for the full and potent suppression of apoptosis in IL-3-dependent myeloid cells and can result from agonist activation of mitochondrial protein kinase C (PKC). Paradoxically, expression of exogenous Bcl2 can protect parental cells from apoptosis induced by the potent PKC inhibitor, staurosporine (stauro). High concentrations of stauro of up to 1 microM only partially inhibit IL-3-stimulated Bcl2 phosphorylation but completely block PKC-mediated Bcl2 phosphorylation in vitro. These data indicate a role for a stauro-resistant Bcl2 kinase (SRK). We show that aurintricarboxylic acid (ATA), a nonpeptide activator of cellular MEK/mitogen-activated protein kinase (MAPK) kinase, can induce Ser-70 phosphorylation of Bcl2 and support survival of cells expressing wild-type but not the phosphorylation-incompetent S70A mutant Bcl2. A role for a MEK/MAPK as a responsible SRK was implicated because the highly specific MEK/MAPK inhibitor, PD98059, also can only partially inhibit IL-3-induced Bcl2 phosphorylation, whereas the combination of PD98059 and stauro completely blocks phosphorylation and synergistically enhances apoptosis. p44MAPK/extracellular signal-regulated kinase 1 (ERK1) and p42 MAPK/ERK2 are activated by IL-3, colocalize with mitochondrial Bcl2, and can directly phosphorylate Bcl2 on Ser-70 in a stauro-resistant manner both in vitro and in vivo. These findings suggest a role for the ERK1/2 kinases as SRKs. Thus, the SRKs can serve to functionally link the IL-3-stimulated proliferative and survival signaling pathways and, in a novel capacity, may explain how Bcl2 can suppress stauro-induced apoptosis. In addition, although the mechanism of regulation of Bcl2 by phosphorylation is not yet clear, our results indicate that phosphorylation may functionally stabilize the Bcl2-Bax heterodimerization.
Alcohol and the developing fetus--a review. (2001)

Fetal alcohol syndrome (FAS) is a collection of signs and symptoms seen in some children exposed to alcohol in the prenatal period. It is characterized mainly by physical and mental retardation, craniofacial anomalies and minor joint abnormalities. However, with the increasing incidence of FAS, there is a great variation in the clinical features of FAS. This article describes in detail these clinical features. Due to ethical reasons it is not possible to perform experiments on pregnant women. Hence to study the effects of alcohol, various animal and avian experimental models have been chosen. The various experimental findings and human correlation are described. The exact mechanism by which alcohol induces its teratogenic effects is not known. The possible mechanisms are discussed. Measures to prevent the occurrence of FAS have been suggested.
Convolutional Neural Network Based Approach to In Silico Non-Anticipating Prediction of Antigenic Distance for Influenza Virus (2020)

Evaluation of the antigenic similarity degree between the strains of the influenza virus is highly important for vaccine production. The conventional method used to measure such a degree is related to performing the immunological assays of hemagglutinin inhibition. Namely, the antigenic distance between two strains is calculated on the basis of HI assays. Usually, such distances are visualized by using some kind of antigenic cartography method. The known drawback of the HI assay is that it is rather time-consuming and expensive. In this paper, we propose a novel approach for antigenic distance approximation based on deep learning in the feature spaces induced by hemagglutinin protein sequences and Convolutional Neural Networks (CNNs). To apply a CNN to compare the protein sequences, we utilize the encoding based on the physical and chemical characteristics of amino acids. By varying (hyper)parameters of the CNN architecture design, we find the most robust network. Further, we provide insight into the relationship between approximated antigenic distance and antigenicity by evaluating the network on the HI assay database for the H1N1 subtype. The results indicate that the best-trained network gives a high-precision approximation for the ground-truth antigenic distances, and can be used as a good exploratory tool in practical tasks.
A Chromosomal Locus Controlling Extracellular Agarase Production by Streptomyces coelicolor A 3(2), and its Inactivation by Chromosomal Integration of Plasmid SCP1 (1981)

The properties of various mutants showed that, in the presence of an inorganic nitrogen source, agar utilization by Streptomyces coelicolor requires the action of at least three groups of enzymes: a diffusible or cell-free extracellular agarase, some further degradative step(s), and the enzymes of galactose metabolism. Two unselected mutations (dag), both leading to loss of diffusible agarase and an undefined second agar utilization function, were detected among a small number of S. coelicolor derivatives from a culture collection, and mapped to the 9 o’clock ‘silent’ region of the genetic map. One of these mutations (dagA1) had apparently resulted, directly or indirectly, from the insertion of the plasmid SCP1 in this region during formation of the NF fertility type. The other (dag-2) was 100% linked to dagA1 and the integrated SCP1, but only 98% linked to the site of insertion of SCP1 in an ‘NF-like’ but Dag+ strain. SCP1-chromosome interactions in other regions of the genetic map had no effect on the agar-solubilizing phenotype, nor had three other unstable genetic phenomena in S. coelicolor.
Imatinib Plasma Levels Are Correlated With Clinical Benefit in Patients With Unresectable/Metastatic Gastrointestinal Stromal Tumors (2009)

PURPOSE To study the pharmacokinetics (PK) of imatinib (IM) in patients with advanced GI stromal tumors (GISTs) treated in a randomized phase II study and to explore the potential relationship between IM plasma levels and long-term clinical outcomes. PATIENTS AND METHODS Patients were randomly assigned to receive IM at 400 mg versus 600 mg daily. IM plasma levels were analyzed in a subset of patients (n = 73) for whom PK data on day 1 and at steady-state (SS, day 29) were available. IM PK was evaluated using a population PK approach. The relationship between IM plasma exposure and clinical outcome was explored by grouping patients into quartiles according to IM trough concentration (C(min)). The clinical outcome parameters evaluated include overall objective benefit rate (OOBR; complete response plus partial response plus stable disease) time to progression (TTP), and KIT genotyping. Results IM PK exposure showed a high inter-patient variability, and clinical outcomes were correlated with IM trough levels at SS. The median TTP was 11.3 months for patients in the lowest C(min) quartile (Q1, < 1,110 ng/mL) compared with more than 30 months for Q2 to Q4 (P = .0029). OOBR was also inferior in Q1 patients. In patients with GIST with KIT exon 11 mutations (n = 39), the OOBR was 67% for Q1 patients versus 100% for all others (P = .001). CONCLUSION In patients with advanced GIST, IM trough levels at SS were associated with clinical benefit. Patients with IM C(min) below 1,100 ng/mL showed a shorter TTP and lower rate of clinical benefit (OOBR). Further studies are justified to test whether monitoring IM plasma levels might optimize clinical outcomes for patients with GIST.
Low-pressure solubility of gases in liquid water (1977)

Aqueous solutions of gases reveal many peculiarities generally not observed in other liquids. For example, most gaseous solutes show a partial molar entropy and enthalpy of solution that are substantially lower than for other solvents, and the partial molar heat capacity is anomalously large. All these phenomena (and several other properties of aqueous solutions) have made water a particularly interesting liquid for studies in gas solubility. Furthermore, since water forms the basis of all biologically important systems, it is unique and thus deserves special attention. Indeed, the solubility of gases in this liquid has been the subject of innumerable investigations. Experimental data are so abundant, that in our preceding review on gas solubility, water was deliberately omitted.
Anti‐prostate specific membrane antigen designer T cells for prostate cancer therapy (2004)

The anti-PSMA designer T cells exhibit an antibody-type specificity that can recognize PSMA expressing tumor cells in a MHC-independent fashion, resulting in T-cell activation, target cell lysis in vitro and inhibition of tumor growth in vivo.
Discovery of novel hematopoietic cell adhesion molecules from human bone marrow stromal cell membrane protein extracts by a new cell- blotting technique (1994)

In an attempt to define the role of cell adhesion molecules (CAMs) within the bone marrow (BM) microenvironment in normal hematopoiesis and in leukemia development, a novel cell-blotting technique that involved cell adhesion to protein bands after separation by lithium dodecyl sulfate-polyacrylamide gel electrophoresis (LDS-PAGE) and blotting onto polyvinylidene difluoride (PVDF) membrane has been developed. Human BM stromal cell membrane fractions have been prepared from Dexter-type cultures after cell lysis by sonification and differential centrifugations of the sonification contents. The 20,000 g pellets representing membrane fractions have been solubilized by 2% Triton X-100, 0.575% LDS, and 8 mol/L urea in sequential order. The protein extracts are fractionated by LDS-PAGE and screened for CAMs by the new cell-blotting technique. This led to identification of nine protein bands in lanes containing LDS extracts showing adhesion of KG1a (CD34+ progenitor myeloid) cells. Evidence that the BM proteins exhibiting KG1a cell adhesion are novel CAMs is based on the observations that these proteins, in comparison with known CAMs, specifically VCAM-1, CD54, and CD44, show (1) contrasting detergent- solubility properties, (2) different temperature requirement for mediating cell adhesion function, and (3) markedly distinct electrophoretic mobilities. The various cell types tested, notably KG1a, NALM-6, WIL-2, Ramos, HS-Sultan, K562, JY B lymphoblastoid cells, and T lymphoblasts, showed distinctive patterns of binding to different subsets of BM CAMs. These results demonstrate a new approach to studies of molecular mechanisms that may determine specificity of hematopoietic cellular localization within BM microenvironment and may play an important role in controlling hematopoiesis.
Biomarkers for Sepsis: A Review with Special Attention to India (2014)

Sepsis is a serious infection and still a common cause of morbidity and mortality in resource-limited settings such as India. Even when microbiologic diagnostics are available, bacteremia is only identified in a proportion of patients who present with sepsis and bloodstream infections. Biomarkers have been used in a variety of disease processes and can help aid in diagnosing bacterial infections. There have been numerous biomarkers investigated to aid with diagnosis and prognostication in sepsis with the majority suffering from lack of sensitivity or specificity. Procalcitonin has been heralded as the biomarker that holds the most promise for bloodstream infections. Data are emerging in India, and in this review, we focus on the current data of biomarkers in sepsis with particular attention to how biomarkers could be used to augment diagnosis and treatment in India.
Carbon Nanotube Synthesis: A Review (2005)

Discovered in 1991, carbon nanotubes (CNTs) have reached the forefront of many industrial research projects. Carbon nanotubes are tubular carbon molecules with remarkable mechanical, chemical, thermal and electrical properties, which make them useful in various applications. This paper reviews three methods of synthesizing the nanomaterial, namely arc-discharge, laser-ablation and fixed bed/fluidized bed catalytic. These methods have generated a large interest in many industrial companies to date. At the moment, the most critical issue faced by industrial companies is determining the best synthesis method, which will give the most economical large-scale production of CNTs. Compared to the other two methods, the catalytic technique to synthesize CNTs is simple, inexpensive, energy-efficient and can produce large CNTs quantities of high yield and purity.
Introducing antigen-binding sites in structural loops of immunoglobulin constant domains: Fc fragments with engineered HER2/neu-binding sites and antibody properties (2010)

Yeast surface display libraries of human IgG1 Fc regions were prepared in which loop sequences at the C-terminal tip of the CH3 domain were randomized. A high percentage of these library members bound to soluble CD64 and Protein A indicating that the randomization step did not grossly interfere with the overall structure of the displayed Fc. Sorting these libraries by FACS for binders against HER2/neu yielded antigen-specific Fc binders (Fcab; Fc antigen binding) of which one was affinity matured, resulting in Fcab clone H10-03-6 which showed >10-fold improvement in antigen-binding activity versus the parental clone. Pre-equilibrium surface plasmon resonance experiments revealed a K(D) value of 69 nM. H10-03-6 did not react with other members of the HER family and specifically interacted with HER2-positive but not with HER2-negative cells. Importantly, Fcab H10-03-6 elicited potent antibody-dependent cellular cytotoxicity in vitro. Finally, the in vivo half-life in mice was similar to wild-type Fc indicating that the amino acid changes in the CH3 domain did not affect the pharmacokinetic behavior of the recombinant Fc. Our data demonstrate that the Fcab scaffold combines all features of normal antibodies in a small 50 kD homodimeric protein: antigen binding, effector functions and long half-life in vivo.