gebhart/patrepeval huggingface dataset:
Combinatorial and High-Throughput Screening of Materials Libraries: Review of State of the Art (2011)

Rational materials design based on prior knowledge is attractive because it promises to avoid time-consuming synthesis and testing of numerous materials candidates. However with the increase of complexity of materials, the scientific ability for the rational materials design becomes progressively limited. As a result of this complexity, combinatorial and high-throughput (CHT) experimentation in materials science has been recognized as a new scientific approach to generate new knowledge. This review demonstrates the broad applicability of CHT experimentation technologies in discovery and optimization of new materials. We discuss general principles of CHT materials screening, followed by the detailed discussion of high-throughput materials characterization approaches, advances in data analysis/mining, and new materials developments facilitated by CHT experimentation. We critically analyze results of materials development in the areas most impacted by the CHT approaches, such as catalysis, electronic and functional materials, polymer-based industrial coatings, sensing materials, and biomaterials.
Interferon immunogenicity: technical evaluation of interferon-alpha 2a. (1997)

Observations from some studies with interferon-alpha 2a (IFN-alpha 2a) have shown the presence of neutralizing antibodies in a proportion of patients. As a result, an investigation into the production of antibodies to IFN-alpha 2a was undertaken. A number of technical aspects of its production and storage were investigated, including the possibility of an incorrect structure, which could affect the immunogenicity of the IFN-alpha 2a molecule. These investigations demonstrated the presence, in vials of IFN-alpha 2a, of both interferon-interferon (IFN-IFN) aggregates and aggregates of interferon with human serum albumin (HSA), the excipient of the galenical form of IFN-alpha 2a (IFN-HSA) aggregates. The amount of aggregates is temperature dependent, there being very little increase in aggregate content over time when vials are stored at 4 degrees C. The relative immunogenicity of IFN-alpha 2a increased when the vials were stored at ambient temperature but not when stored at 4 degrees C. These findings demonstrate that the immunogenicity of IFN-alpha 2a is likely to be related to the storage temperature. Storage of IFN-alpha 2a vials at 2-8 degrees C is now recommended. A new formulation has been introduced that does not contain HSA as an excipient, removing the possibility of IFN-HSA aggregation.
Improved performance in protein secondary structure prediction by inhomogeneous score combination. (1999)

The prediction is freely available over the Internet on the Network Protein Sequence Analysis (NPS@) WWW server at http://pbil.ibcp.fr/NPSA/npsa_server.ht ml. The source code of the combiner can be obtained on request for academic use.
Spacing of the -10 and -35 regions in the tac promoter. Effect on its in vivo activity. (1985)

In the tac promoter (deBoer, H. A., Comstock, L. J., and Vasser, M. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 21-25) the spacing between the -35 and -10 consensus sequences is 16 base pairs. Between these two regions we inserted 1 or 2 base pairs to increase the distance to 17 base pairs (trc promoter) or 18 base pairs (tic promoter). The activities of the three promoters were compared in vivo by fusion to the chloramphenicol acetyltransferase or to the Escherichia coli 4.5 S RNA gene. Both measurements gave consistent results. The trc and tic promoters are on average about 90% and 65% as active as the tac promoter, respectively.
The Role of the Fecal Stream in Crohnʼs Disease: An Historical and Analytic Review (1998)

Since 1939, a series of clinical reports and laboratory investigations have suggested that the intestinal fecal stream may play a significant part in the pathogenesis of Crohn's disease (CD). The beneficial effect of exclusion of the stream by ileostomy was followed by improvement in patients with CD of the ileum and colon despite little change in the histopathology of the excluded loop, even to the point of allowing restoration of intestinal continuity in some patients. End ileostomy lowers the risk of recurrence of CD compared with anastomotic operations. Ileostomy effluent can reactivate the clinical activity of quiescent bypassed bowel and some of its biochemical processes, and may be related to an ultrafilterable constituent > 5 microns. Experimental models of inflammatory bowel disorders in immunologically altered rodents (transgenic, knockout, or spontaneous) require the presence of normal luminal bacteria, especially of the Bacteroides species, and respond to antibiotic (metronidazole) therapy. Thus, many but not all of the well-recognized clinical features of CD are compatible with a pathogenetic role of the fecal stream. Although difficult to quantitate, this concept opens the way to a variety of testable research lines, and allows some speculation regarding its clinical implications.
Interaction of human apohemoglobin with inositol hexaphosphate. (1979)

Experiments of sedimentation velocity and equilibrium indicate that in the presence of inositol hexaphosphate the degree of polymerization of apohemoglobin is shifted in favor of the formation of tetramers, with a maximum effect when the concentration of the polyphosphate is 1 mM. Above this concentration, a redissociation of the system into dimers is promoted. This phenomenon is probably due to the binding of inositol hexaphosphate to apohemoglobin with a stoichiometry higher than 1 mol of polyphosphate/4 subunits. The optical rotatory dispersion spectrum of apohemoglobin is also modified by its interaction with inositol hexaphosphate suggesting a small increase in the helical content of the protein. Measurements of circular dichroism in the near-UV region of the spectrum indicate that the environment of the aromatic chromophores of the protein such as tyrosine, phenyalanine, and tryptophan is not affected by the interaction. The presence of inositol hexaphosphate decreases the rate of reaction of the beta-93 cysteinyl residues of apohemoglobin with both p-mercuribenzoate and N-ethylmaleimide, suggesting a conformational change of the protein also at the level of its tertiary structure.
Security issues for the semantic Web (2004)

This paper first describes the developments in semantic Web and then provides an overview of secure semantic Web. In particular XML security, RDF security, and secure information integration and trust on the semantic Seb are discussed. Finally directions for research on secure semantic Web are provided.
Induction of incomplete autophagic response by hepatitis C virus via the unfolded protein response† (2008)

Our studies delineate the molecular pathway by which HCV induces autophagic vacuoles and also demonstrate the perturbation of the autophagic response by HCV. These unexpected effects of HCV on the host cell likely play an important role in HCV pathogenesis.
Chemical Ligation Approach To Form a Peptide Bond between Unprotected Peptide Segments. Concept and Model Study (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Ligation Approach To Form a Peptide Bond between Unprotected Peptide Segments. Concept and Model StudyChuan-Fa Liu and James P. TamCite this: J. Am. Chem. Soc. 1994, 116, 10, 4149–4153Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/ja00089a001https://doi.org/10.1021/ja00089a001research-articleACS PublicationsRequest reuse permissionsArticle Views1496Altmetric-Citations160LEARN 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
Fitting New Speakers Based on a Short Untranscribed Sample (2018)

Learning-based Text To Speech systems have the potential to generalize from one speaker to the next and thus require a relatively short sample of any new voice. However, this promise is currently largely unrealized. We present a method that is designed to capture a new speaker from a short untranscribed audio sample. This is done by employing an additional network that given an audio sample, places the speaker in the embedding space. This network is trained as part of the speech synthesis system using various consistency losses. Our results demonstrate a greatly improved performance on both the dataset speakers, and, more importantly, when fitting new voices, even from very short samples.
The Contract Net Protocol: High-Level Communication and Control in a Distributed Problem Solver (1980)

The contract net protocol has been developed to specify problem-solving communication and control for nodes in a distributed problem solver. Task distribution is affected by a negotiation process, a discussion carried on between nodes with tasks to be executed and nodes that may be able to execute those tasks.
Shortened Telomere Length Is Associated with Increased Risk of Cancer: A Meta-Analysis (2011)

The results of this meta-analysis suggest that the presence of shortened telomeres may be a marker for susceptibility to human cancer, but single larger, well-design prospective studies are warranted to confirm these findings.
Construction and Characterization of Hexon-Chimeric Adenoviruses: Specification of Adenovirus Serotype (1998)

This study has used the strategy of gene replacement to characterize the contribution of the adenovirus (Ad) capsid protein hexon to serotype definition. By replacing the Ad type 5 (Ad5) hexon gene with sequences from Ad2, we have changed the type specificity of the chimeric virus. The type-determining epitopes are primarily associated with loop 1 of hexon and, to a much lesser degree, with loop 2. In spite of the serotype distinctiveness of the chimeric hexon viruses, epitope similarity between the vectors resulted in a low level of cross-reactive neutralizing antibody, which in combination with activated cellular and innate arms of the immune system is sufficient to suppress gene transduction following readministration in vivo.
Lanthanide-doped LiYF4 nanoparticles: Synthesis and multicolor upconversion tuning (2010)

We report the synthesis of tetragonal-phase LiYF 4 nanoparticles doped with upconverting lanthanide ions. The nanoparticles have been characterized by XRD, TEM, and luminescence decay studies. The size of the as-synthesized LiYF 4 nanoparticles can be tuned by varying the precursor ratio of F to lanthanide ions. Passivated by oleic acid ligands, the LiYF 4 nanoparticles can be readily dispersed in a wide range of nonpolar solvents including hexane, cyclohexane, dichloromethane, and toluene. The lanthanide-doped (Yb 3+ , Er 3+ , Tm 3+ , Ho 3+ ) LiYF 4 nanoparticles show intense upconversion emissions upon near infrared excitation at 980 nm. By varying composition and concentration of the dopant ions, the color output can be precisely modulated under single wavelength excitation with a diode laser.
Human Immunodeficiency Virus–Induced Apoptosis of Human Hepatocytes via CXCR4 (2003)

Human immunodeficiency virus (HIV) infection is commonly associated with liver dysfunction. The X4 HIV glycoprotein 120 envelope (env) induces apoptosis in T cells and neurons via the HIV coreceptor CXCR4. Therefore, we investigated whether hepatocyte death could result from the HIV env signaling through CXCR4 on the hepatocyte. We demonstrated that hepatocytes in humans express CXCR4 on the cell surface. Furthermore, we established that the X4 HIV env and the entire HIV virion signal hepatocyte apoptosis through CXCR4. The apoptotic process is dependent on G(ialpha) protein signaling, yet it is independent of caspase cascade activation. Thus, HIV can directly cause hepatocyte death in humans by signaling through CXCR4, without infecting the cell.
Molecular Cloning and Functional Expression of the Gene Encoding the Human Proteinase‐Activated Receptor 2 (1995)

We previously reported the molecular cloning of a mouse guanosine-nucleotide-binding-protein-coupled receptor similar to the thrombin receptor. Since the physiological agonist was unknown, the receptor was named proteinase-activated receptor 2. We describe here the cloning and functional expression of the gene encoding the corresponding human receptor. The gene is divided into two exons separated by about 14 kb intronic DNA. The deduced protein sequence is 397 amino acids long and 83% identical to the mouse receptor sequence. Within the extracellular amino terminus, the residues predicted to form the tethered agonist ligand differ between the two receptors; of the first six residues only four are conserved. At positions five and six, a lysine residue and a valine residue, respectively, have replaced arginine and leucine residues found in the mouse sequence. When the human receptor is expressed in Chinese hamster ovary cells, it can be activated by low nanomolar concentrations of the serine proteinase trypsin and by peptides made from the receptor sequence. Northern-blot analysis of receptor expression showed that the receptor transcript is widely expressed in human tissues with especially high levels in pancreas, liver, kidney, small intestine and colon. Moderate expression was detected in many organs but none in brain or skeletal muscle. By fluorescence in situ hybridization, the human proteinase-activated receptor 2 gene was mapped to chromosomal region 5q13, where, previously, the related thrombin receptor gene has been located.
Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity (2000)

Single-chain antibody mutants have been evolved in vitro with antigen-binding equilibrium dissociation constant K(d) = 48 fM and slower dissociation kinetics (half-time > 5 days) than those for the streptavidin-biotin complex. These mutants possess the highest monovalent ligand-binding affinity yet reported for an engineered protein by over two orders of magnitude. Optimal kinetic screening of randomly mutagenized libraries of 10(5)-10(7) yeast surface-displayed antibodies enabled a >1,000-fold decrease in the rate of dissociation after four cycles of affinity mutagenesis and screening. The consensus mutations are generally nonconservative by comparison with naturally occurring mouse Fv sequences and with residues that do not contact the fluorescein antigen in the wild-type complex. The existence of these mutants demonstrates that the antibody Fv architecture is not intrinsically responsible for an antigen-binding affinity ceiling during in vivo affinity maturation.
External Regulation of Controlled Polymerizations (2012)

Polymer chemists, through advances in controlled polymerization techniques and reliable post-functionalization methods, now have the tools to create materials of almost infinite variety and architecture. Many relevant challenges in materials science, however, require not only functional polymers but also on-demand access to the properties and performance they provide. The power of such temporal and spatial control of polymerization can be found in nature, where the production of proteins, nucleic acids, and polysaccharides helps regulate multicomponent systems and maintain homeostasis. Here we review existing strategies for temporal control of polymerizations through external stimuli including chemical reagents, applied voltage, light, and mechanical force. Recent work illustrates the considerable potential for this emerging field and provides a coherent vision and set of criteria for pursuing future strategies for regulating controlled polymerizations.
Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products (2005)

In this paper we report that the inclusion of heat-resistant RecA protein from a thermophilic bacteria, Thermus thermophilus, and its cofactor (ATP) in PCR effectively eliminates non-specific PCR products. The effect of RecA protein, which catalyzes pairing between homologous DNA molecules with great fidelity in genetic recombination, is due to its promotion of precise priming in PCR (i.e. priming at sites where the primer sequence is completely complementary to that of the target sequence). In addition, the RecA protein substantially reduces the primer concentration required for PCR. These experimental results have led to the realization of multiplex PCR, which involves PCR for multiple sites in the same reaction mixture. We were able to successfully perform multiplex PCR with over a dozen reactions without affecting the amplification pattern of the PCR products.
The molecular mechanism of sensitization to Fas‐mediated apoptosis by 2‐methoxyestradiol in PC3 prostate cancer cells (2003)

It is widely known that death receptor Fas-dependent apoptotic signals are associated with development of prostate cancer, but the key pathways involved in sensitivity to the apoptosis remain unclear. Here we investigated the molecular mechanism by which 2-methoxyestradiol (2-ME) effectively sensitizes a human prostate cancer cell line, PC3, to Fas-mediated apoptosis. 2-ME significantly inhibited nuclear factor-kappaB (NF-kappaB) activation and downregulated Fas-associated death domain (FADD) protein interluekin-1beta-converting enzyme inhibitory protein (FLIP). Overexpression of the dominant negative mutant form of IkappaBalpha (d/n IkappaBalpha) or treatment with Ikappa kinase-specific inhibitor Bay117082 gave the same results, although the sensitizing effect was not as pronounced. A selective inhibitor of Akt phosphorylation, LY294002, accelerated formation of the death-inducing signaling complex (DISC) not only by FLIP reduction but also by enhancement of recruitment of the FADD to Fas, thereby sensitizing PC3 cells to apoptosis similar to the case with 2-ME stimulation. Moreover, we found that inhibition of 2-ME-induced extracellular signal-regulated kinase (ERK) activation by the upstream kinase inhibitor PD98059 significantly enhanced 2-ME-mediated suppression of Akt activation, resulting in much greater sensitization to apoptosis. Taken together, the present findings indicate that 2-ME suppresses NF-kappaB/FLIP signaling and enhances DISC formation through inhibition of Akt, and that PC3 cells thereby are being sensitized to Fas-mediated apoptosis and by a process closely associated with ERK.
Doping of graphene: Density functional calculations of charge transfer between GaAs and carbon nanostructures (2008)

Density functional theory is used to show that charge transfer occurs between chemical dopants in GaAs and adsorbates composed of ${\text{C}}_{60}$ or graphene lying on the (110) surface of GaAs. In the case of ${\text{C}}_{60}$, charge transfer only occurs for $n$-type GaAs, in agreement with previous experimental results. However, the calculations show that transfer between graphene and both $n$- and $p$-type GaAs can occur, which offers a simple way of doping graphene.
Preparation and properties of inclusion complexes of polyethylene glycol with .alpha.-cyclodextrin (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and properties of inclusion complexes of polyethylene glycol with .alpha.-cyclodextrinAkira Harada, Jun Li, and Mikiharu KamachiCite this: Macromolecules 1993, 26, 21, 5698–5703Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ma00073a026https://doi.org/10.1021/ma00073a026research-articleACS PublicationsRequest reuse permissionsArticle Views4117Altmetric-Citations413LEARN 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
Immersive 3D Holoscopic Video System (2012)

We demonstrated a 3D holoscopic video system for 3DTV application. We showed that using a field lens and a square aperture significantly reduces the vignetting problem associated with a relay system and achieves over 95 percent fill factor. The main problem for such a relay system is the nonlinear distortion during the 3D image capturing, which can seriously affect the reconstruction process for a 3D display. The nonlinear distortion mainly includes lens radial distortion (intrinsic) and microlens array perspective distortion (extrinsic). This is the task of future work. Our results also show that the SS coding approach performs better than the standard HEVC scheme. Furthermore, we show that search and retrieval performance relies on the depth map's quality and that the multimodal fusion boosts the retrieval performance.
Association of Nitrotyrosine Levels With Cardiovascular Disease and Modulation by Statin Therapy (2003)

The findings from this preliminary study indicate that nitrotyrosine levels are associated with the presence of CAD and appear to be modulated by statin therapy. These results suggest a potential role for nitric oxide-derived oxidants as inflammatory mediators in CAD and may have implications for atherosclerosis risk assessment and monitoring of anti-inflammatory actions of statins.
Identification of two oligodeoxyribonucleotide binding proteins on plasma membranes of human cell lines (1996)

Two oligodeoxyribonucleotide (oligodN) binding proteins of approximately 100-110 kDa were identified in the plasma membranes of human HL-60, HepG2, H1, and KB cells by a photolabeling technique. Solubilization of cellular membranes with a nonionic detergent did not interfere with the binding of these two proteins to oligodNs, and both proteins were susceptible to serine protease action. The binding affinities of these two proteins to oligodNs were found to be similar; Scatchard plot analysis revealed the Kd for phosphodiester (PO) 21-mer oligodeoxycytidine to be 60 nM and binding sites numbered approximately 1.2 x 10(6)/cell for HepG2 cells. Both phosphorothioate (PS) and PO oligodNs could bind to these two proteins with the binding affinity for PS oligodNs being much stronger than that for PO oligodNs. The binding to oligodNs was affected by the ionic strength of the reaction. Dextran sulfate, tRNA, and double-stranded DNA inhibited the binding of oligodNs, whereas ATP, ADP, AMP, and TTP had no effect. Given their high affinity for oligodNs, these membranes proteins may play an important role in the action of oligodNs.