gebhart/patrepeval huggingface dataset:
Detailed Studies of Molecular Conductance Using Atomic Resolution Scanning Tunneling Microscopy (2006)

Atomically resolved scanning tunneling microscopy and spectroscopy (STM/STS) have been used to carefully examine the relationship between molecular conductivity and the adsorption state of various organic molecules on silicon surfaces. We show that the particular configuration of styrene and cyclopentene molecules on silicon affects the conductivity of the molecules. Detailed correlation of STM images with point specific current-voltage spectroscopy reveal that observed negative peaks are due to random configuration changes driven by inelastically scattered electrons and not due to tuned alignment of molecule and electrode levels. These random processes, which include molecular rearrangement, desorption, and/or decomposition occur with increasing frequency at larger voltage and current settings.
An avian live attenuated master backbone for potential use in epidemic and pandemic influenza vaccines (2008)

The unprecedented emergence in Asia of multiple avian influenza virus (AIV) subtypes with a broad host range poses a major challenge in the design of vaccination strategies that are both effective and available in a timely manner. The present study focused on the protective effects of a genetically modified AIV as a source for the preparation of vaccines for epidemic and pandemic influenza. It has previously been demonstrated that a live attenuated AIV based on the internal backbone of influenza A/Guinea fowl/Hong Kong/WF10/99 (H9N2), called WF10att, is effective at protecting poultry species against low- and high-pathogenicity influenza strains. More importantly, this live attenuated virus provided effective protection when administered in ovo. In order to characterize the WF10att backbone further for use in epidemic and pandemic influenza vaccines, this study evaluated its protective effects in mice. Intranasal inoculation of modified attenuated viruses in mice provided adequate protective immunity against homologous lethal challenges with both the wild-type influenza A/WSN/33 (H1N1) and A/Vietnam/1203/04 (H5N1) viruses. Adequate heterotypic immunity was also observed in mice vaccinated with modified attenuated viruses carrying H7N2 surface proteins. The results presented in this report suggest that the internal genes of a genetically modified AIV confer similar protection in a mouse model and thus could be used as a master donor strain for the generation of live attenuated vaccines for epidemic and pandemic influenza.
Structural Properties of Group B Streptococcal Type III Polysaccharide Conjugate Vaccines That Influence Immunogenicity and Efficacy (1998)

In this study, we tested the hypothesis that the immunogenicity and protective efficacy of polysaccharide-protein conjugate vaccines are influenced by three variables: (i) molecular size of the conjugate, (ii) molecular size of the polysaccharide used for conjugation, and (iii) extent of polysaccharide-to-protein cross-linking. Type III group B Streptococcus capsular polysaccharide was linked by reductive amination at multiple sites to tetanus toxoid to create a polysaccharide-protein conjugate (III-TT). A single lot of III-TT was fractionated into small, medium, and large Mr pools. Whereas all three conferred protection in a maternal immunization-neonatal challenge model in mice, the smallest Mr conjugate evoked less polysaccharide-specific immunoglobulin G (IgG) than the two larger Mr conjugates. To test whether the molecular size of the polysaccharide used for conjugation also affected the immunogenicity of the conjugate, vaccines were synthesized using capsular polysaccharides with Mrs of 38,000, 105,000, and 349,000. Polysaccharide-specific IgG responses in mice increased with the Mr of the polysaccharides, and protective efficacy was lower for the smallest polysaccharide conjugate compared to the other two vaccines. Immunogenicity testing of a series of vaccines prepared with different degrees of polysaccharide-to-protein cross-linking demonstrated higher polysaccharide-specific antibody responses as the extent of cross-linking increased. However, opsonic activity was greatest in mouse antiserum raised to a moderately cross-linked conjugate, suggesting that some antibodies evoked by highly cross-linked conjugates were directed to a nonprotective epitope. We conclude that conjugate size, polysaccharide size, and degree of polysaccharide-protein cross-linking influence the immunogenicity and protective efficacy of III-TT conjugate vaccines.
Capturing natural hand articulation (2002)

Vision-based motion capturing of hand articulation is a challenging task, since the hand presents a motion of high degrees of freedom. Model-based approaches could be taken to approach this problem by searching in a high dimensional hand state space, and matching projections of a hand model and image observations. However, it is highly inefficient due to the curse of dimensionality. Fortunately, natural hand articulation is highly constrained, which largely reduces the dimensionality of hand state space. This paper presents a model-based method to capture hand articulation by learning hand natural constraints. Our study shows that natural hand articulation lies in a lower dimensional configurations space characterized by a union of liner manifolds spanned by a set of basis configurations. By integrating hand motion constraints, an efficient articulated motion-capturing algorithm is proposed based on sequential Monte Carlo techniques. Our experiments show that this algorithm is robust and accurate for tracking natural hand movements. This algorithm is easy to extend to other articulated motion capturing tasks.
Phase I Trial of Pazopanib in Patients with Advanced Cancer (2009)

Pazopanib was generally well tolerated and showed antitumor activity across various tumor types. A monotherapy dose of 800 mg once daily was selected for phase II studies.
The role of MNK proteins and eIF4E phosphorylation in breast cancer cell proliferation and survival (2010)

eIF4E is over-expressed in many tumours, including a high proportion of breast cancers. eIF4E is an oncogene, and signalling pathways which promote eIF4E activity represent potential targets for therapeutic intervention in cancer. MNKs phosphorylate eIF4E on serine 209, a modification that can be required for eIF4E-dependent cell transformation. There is therefore a clear requirement to determine the role of MNKs in the proliferation and survival of cells from the major human tumours, such as breast cancer. Phosphorylated eIF4E protein was readily detectable in some breast tumour samples, but was below the limits of detection in others. Of 6 breast cancer cell lines representing the major sub-types of breast cancer, phosphorylated eIF4E was readily detectable in 5 of them, with MCF-7 cells displaying markedly lower levels. Long term colony forming assays demonstrated that all the five lines with high levels of phosphorylated eIF4E were highly sensitive to a MNK inhibitor. In short term assays, a range of responses was revealed. MCF-7 cells were insensitive in both assays. The anti-proliferative effects of the MNK inhibitor in breast cancer cells are primarily cytostatic, rather than cytotoxic, and are potentially due to the inhibition of cyclin D1 synthesis. Our data provide evidence that the sensitivity of breast cancer cells to MNK inhibition may correlate with baseline levels of eIF4E phosphorylation, and suggest that a proportion of breast cancers could be sensitive to inhibiting MNK kinase activity, and that the presence of phosphorylated eIF4E could provide a biomarker for the identification of responsive tumours.
Facile Synthesis of meso-Tetrakis(perfluoroalkyl)porphyrins: Spectroscopic Properties and X-ray Crystal Structure of Highly Electron-Deficient 5,10,15,20-Tetrakis(heptafluoropropyl)porphyrin (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFacile Synthesis of meso-Tetrakis(perfluoroalkyl)porphyrins: Spectroscopic Properties and X-ray Crystal Structure of Highly Electron-Deficient 5,10,15,20-Tetrakis(heptafluoropropyl)porphyrinStephen G. DiMagno, R. Allen Williams, and Michael J. TherienCite this: J. Org. Chem. 1994, 59, 23, 6943–6948Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/jo00102a017https://doi.org/10.1021/jo00102a017research-articleACS PublicationsRequest reuse permissionsArticle Views1005Altmetric-Citations96LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Structure-Guided Design of Antibodies (2010)

Monoclonal antibodies capable of recognizing antigens with high affinity and specificity represent a wellestablished class of biological agents. Since the development of hybridoma technology in 1975, advances in recombinant DNA technologies and computational and biophysical methods have allowed us to develop a better understanding of the relationships between antibody sequence, structure, and function. These advances enable us to manipulate antibody sequences with the goal of improving upon, or creating new biological or biophysical properties. In this review we will focus on recent successes in using structure-guided computational methods to design antibodies and antibody-like molecules with optimized affinity and specificity to antigen and for enhancing protein stability.
Cancer gene detection using surface‐enhanced Raman scattering (SERS) (2002)

Abstract We describe the development of a surface‐enhanced Raman scattering (SERS) method for cancer gene detection. The technology uses DNA gene probes based on SERS labels for gene detection. The detection method uses nanostructured metallic substrates as SERS‐active platforms. The surface‐enhanced Raman gene (SERGen) probes can be used to detect DNA targets via hybridization to DNA sequences complementary to these probes. The probes do not require the use of radioactive labels and have great potential to provide both sensitivity and selectivity. The usefulness of the SERGen approach and its applications in cancer gene diagnostics (e.g. BRCA1 breast cancer gene and BAX gene) is discussed. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Cloning of a polycistronic cDNA from tomato encoding γ-glutamyl kinase and γ-glutamyl phosphate reductase (1997)

We isolated from a tomato cDNA library the tomPRO1 locus, which encodes gamma-glutamyl kinase (GK) and gamma-glutamyl phosphate reductase (GPR). This locus is unusual among eukaryotic genetic elements because it contains two open reading frames, and thus resembles prokaryotic polycistronic operons. The first open reading frame, specifying GK, is terminated by a TAA codon, which is followed by five nucleotides, an ATG translation initiation codon, and the second open reading frame, encoding GPR. DNA sequence analysis of fragments obtained by PCR amplification confirmed that the internal TAA and neighboring sequences are present in the endogenous tomPRO1 sequence in tomato. We demonstrated with RNase protection assays that the tomPRO1 locus is transcribed in tomato tissue culture cells, into a product that contains the internal stop codon. In Escherichia coli, tomPRO1 directed the synthesis of two proteins, a 33-kDa GK and a 44-kDa GPR. Antibodies against the 44-kDa GPR purified from E. coli recognized a 70-kDa product in tomato tissue culture cells and a 60-kDa product in leaves and roots. These results suggest that in tomato tissues, GPR is made as part of a longer polypeptide by some translational mechanism that enables bypass of the internal stop codon, such as frameshifting or ribosome hopping. The tomPRO1 locus may be the first example of a nuclear genetic element in plants that encodes two functional enzymes in two distinct open reading frames.
Adaptive RBF neural network in signal detection (2002)

This paper addresses the application of locally optimum (LO) signal detection techniques to environments in which the noise density is not known a-priori. For small signal levels, the LO detection rule is shown to involve a nonlinearity which depends on the noise density. The estimation of the noise density is a major part of the computational burden of LO detection rules. In this paper, adaptive estimation of the noise density is implemented using a radial basis function neural network. The technique places few assumptions on the properties of the noise, and performs well under a wide variety of circumstances. Experimental results illustrate the system performance as a variety of noise densities are encountered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A theoretical study of hole induced desorption (1999)

A two-dimensional quantum mechanical model describing hole induced desorption is developed and discussed. The model is used for a detailed study of hole induced molecular oxygen desorption and dissociation dynamics on a silver surface. The O2–substrate interaction is described by four diabatic semiempirical potential energy surfaces. These potentials describe physisorption of O2 on the substrate together with two molecular ion states (superoxide and peroxide) and a dissociative adsorption state. The model is used to correlate desorption and dissociation yields with various parameters of the system such as: excitation scheme, substrate work function (φm) and isotope used (Mad). In all cases examined, both desorption and dissociation channels were found to be active. It is demonstrated that experimental measurements of the branching ratio between these two channels and the variation of this ratio as a function of φm and Mad allows determination of the excitation route induced by the hole.
Host DNases prevent vascular occlusion by neutrophil extracellular traps (2017)

Platelet and fibrin clots occlude blood vessels in hemostasis and thrombosis. Here we report a noncanonical mechanism for vascular occlusion based on neutrophil extracellular traps (NETs), DNA fibers released by neutrophils during inflammation. We investigated which host factors control NETs in vivo and found that two deoxyribonucleases (DNases), DNase1 and DNase1-like 3, degraded NETs in circulation during sterile neutrophilia and septicemia. In the absence of both DNases, intravascular NETs formed clots that obstructed blood vessels and caused organ damage. Vascular occlusions in patients with severe bacterial infections were associated with a defect to degrade NETs ex vivo and the formation of intravascular NET clots. DNase1 and DNase1-like 3 are independently expressed and thus provide dual host protection against deleterious effects of intravascular NETs.
Dimethyl- and Diethyldithiocarbamate Complexes of Some Metal Carbonyl Compounds (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDimethyl- and Diethyldithiocarbamate Complexes of Some Metal Carbonyl CompoundsF. A. Cotton and J. A. McClevertyCite this: Inorg. Chem. 1964, 3, 10, 1398–1402Publication Date (Print):October 1, 1964Publication History Published online1 May 2002Published inissue 1 October 1964https://pubs.acs.org/doi/10.1021/ic50020a012https://doi.org/10.1021/ic50020a012research-articleACS PublicationsRequest reuse permissionsArticle Views615Altmetric-Citations119LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
FGF signaling pathways in endochondral and intramembranous bone development and human genetic disease (2002)

Over the last decade the identification of mutations in the receptors for fibroblast growth factors (FGFs) has defined essential roles for FGF signaling in both endochondral and intramembranous bone development. FGF signaling pathways are essential for the earliest stages of limb development and throughout skeletal development. In this review, we examine the role of FGF signaling in bone development and in human genetic diseases that affect bone development. We also explore what is presently known about how FGF signaling pathways interact with other major signaling pathways that regulate chondrogenesis and osteogenesis.
131. Specification of configuration about quadricovalent asymmetric atoms (1951)

R. S. Cahn and C. K. Ingold, J. Chem. Soc., 1951, 612 DOI: 10.1039/JR9510000612
Model reactions for the biosynthesis of thyroxine. XII. Nature of a thyroxine precursor formed in the synthesis of thyroxine from diiodotyrosine and its keto acid analog (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModel reactions for the biosynthesis of thyroxine. XII. Nature of a thyroxine precursor formed in the synthesis of thyroxine from diiodotyrosine and its keto acid analogAkira. Nishinaga, Hans J. Cahnmann, Hideo. Kon, and Teruo. MatsuuraCite this: Biochemistry 1968, 7, 1, 388–397Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/bi00841a049https://doi.org/10.1021/bi00841a049research-articleACS PublicationsRequest reuse permissionsArticle Views114Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Audio Bandwidth Extension by Frequency Scaling of Sinusoidal Partials (2008)

This paper describes a new technique of efficient coding of high-frequency signal components as an alternative to Spectral Band Replication. The main idea is to reconstruct the high frequency harmonic structure trajectories by using fundamental frequencies obtained at the encoder side. Audio signal is decomposed into narrow subbands by demodulation based on the local instantaneous frequency of individual partials. High frequency components are reconstructed by modulation of the baseband signals with appropriately scaled instantaneous frequencies. Such approach offers correct synthesis of rapidly changing sinusoids as well as proper reconstruction of harmonic structure in the high-frequency band. This technique performs also a correct energy adjustment of sinusoidal partials. High compression efficiency has been achieved and confirmed by listening tests.
Safety (toxicity), pharmacokinetics, immunogenicity, and impact on elements of the normal immune system of recombinant human IL-15 in rhesus macaques (2011)

IL-15 uses the heterotrimeric receptor IL-2/IL-15Rβ and the γ chain shared with IL-2 and the cytokine-specific IL-15Rα. Although IL-15 shares actions with IL-2 that include activation of natural killer (NK) and CD8 T cells, IL-15 is not associated with capillary leak syndrome, activation-induced cell death, or with a major effect on the number of functional regulatory T cells. To prepare for human trials to determine whether IL-15 is superior to IL-2 in cancer therapy, recombinant human IL-15 (rhIL-15) was produced under current good manufacturing practices. A safety study in rhesus macaques was performed in 4 groups of 6 animals each that received vehicle diluent control or rhIL-15 at 10, 20, or 50 μg/kg/d IV for 12 days. The major toxicity was grade 3/4 transient neutropenia. Bone marrow examinations demonstrated increased marrow cellularity, including cells of the neutrophil series. Furthermore, neutrophils were observed in sinusoids of enlarged livers and spleens, suggesting that IL-15 mediated neutrophil redistribution from the circulation to tissues. The observation that IL-15 administration was associated with increased numbers of circulating NK and CD8 central and effector-memory T cells, in conjunction with efficacy studies in murine tumor models, supports the use of multiple daily infusions of rhIL-15 in patients with metastatic malignancies.
Conformational studies of sequential polypeptides containing lysine and tyrosine (1978)

Abstract The conformation of three sequential copolypeptides, poly( L ‐tyrosyl‐ L ‐lysine), poly( L ‐tyrosyl‐ L ‐lysyl‐ L ‐lysine), and poly[ L ‐tyrosyl‐( L ‐lysyl) 2 ‐ L ‐lysine] have been studied by a variety of techniques, including CD, ir spectroscopy, analytical ultracentrifugation, and x‐ray diffraction. Depending upon the pH and sovent composition, poly( L ‐tyrosyl‐ L lysyl‐ L ‐lysine) and poly [ L ‐tyrosyl‐( L lysyl) 2 ‐ L ‐lysine] can adopt either the α‐helical or random‐coil conformation, while poly( L ‐tyrosyl‐ L ‐lysine) forms either inter‐ or intramolecular β‐structures.
Clinical trial: the effect and timing of food on the pharmacokinetics and pharmacodynamics of dexlansoprazole MR, a novel Dual Delayed Release formulation of a proton pump inhibitor – evidence for dosing flexibility (2009)

Dexlansoprazole MR can be administered without regard to food or the timing of food in most patients.