gebhart/patrepeval huggingface dataset:
A Caries Vaccine? (2004)

Studies performed in numerous laboratories over several decades have demonstrated the feasibility of immunizing experimental rodents or primates with protein antigens derived from Streptococcus mutans or Streptococcus sobrinus against oral colonization by mutans streptococci and the development of dental caries. Protection has been attributed to salivary IgA antibodies which can inhibit sucrose-independent or sucrose-dependent mechanisms of streptococcal accumulation on tooth surfaces according to the choice of vaccine antigen. Strategies of mucosal immunization have been developed to induce high levels of salivary antibodies that can persist for prolonged periods and to establish immune memory. Studies in humans show that salivary antibodies to mutans streptococci can be induced by similar approaches, and that passively applied antibodies can also suppress oral re-colonization by mutans streptococci. Progress towards practical vaccine development requires evaluation of candidate vaccines in clinical trials. Promising strategies of passive immunization also require further clinical evaluation.
Mutations in the consensus helicase domains of the Werner syndrome gene. Werner's Syndrome Collaborative Group. (1997)

Werner syndrome (WS) is an autosomal recessive disease with a complex phenotype that is suggestive of accelerated aging. WS is caused by mutations in a gene, WRN, that encodes a predicted 1,432-amino-acid protein with homology to DNA and RNA helicases. Previous work identified four WS mutations in the 3' end of the gene, which resulted in predicted truncated protein products of 1,060-1,247 amino acids but did not disrupt the helicase domain region (amino acids 569-859). Here, additional WS subjects were screened for mutations, and the intron-exon structure of the gene was determined. A total of 35 exons were defined, with the coding sequences beginning in the second exon. Five new WS mutations were identified: two nonsense mutations at codons 369 and 889; a mutation at a splice-junction site, resulting in a predicted truncated protein of 760 amino acids; a 1-bp deletion causing a frameshift; and a predicted truncated protein of 391 amino acids. Another deletion is >15 kb of genomic DNA, including exons 19-23; the predicted protein is 1,186 amino acids long. Four of these new mutations either partially disrupt the helicase domain region or result in predicted protein products completely missing the helicase region. These results confirm that mutations in the WRN gene are responsible for WS. Also, the location of the mutations indicates that the presence or absence of the helicase domain does not influence the WS phenotype and suggests that WS is the result of complete loss of function of the WRN gene product.
Modulating the Therapeutic Activity of Nanoparticle Delivered Paclitaxel by Manipulating the Hydrophobicity of Prodrug Conjugates (2008)

A series of paclitaxel prodrugs designed for formulation in lipophilic nanoparticles are described. The hydrophobicity of paclitaxel was increased by conjugating a succession of increasingly hydrophobic lipid anchors to the drug using succinate or diglycolate cross-linkers. The prodrugs were formulated in well defined block copolymer-stabilized nanoparticles. These nanoparticles were shown to have an elimination half-life of approximately 24 h in vivo. The rate at which the prodrug was released from the nanoparticles could be controlled by adjusting the hydrophobicity of the lipid anchor, resulting in release half-lives ranging from 1 to 24 h. The diglycolate and succinate cross-linked prodrugs were 1-2 orders of magnitude less potent than paclitaxel in vitro. Nanoparticle formulations of the succinate prodrugs showed no evidence of efficacy in HT29 human colorectal tumor xenograph models. Efficacy of diglycolate prodrug nanoparticles increased as the anchor hydrophobicity increased. Long circulating diglycolate prodrug nanoparticles provided significantly enhanced therapeutic activity over commercially formulated paclitaxel at the maximum tolerated dose.
Significance of the O-Helix Residues of <i>Escherichia </i><i>coli</i> DNA Polymerase I in DNA Synthesis:  Dynamics of the dNTP Binding Pocket (1996)

In order to identify functionally important residues in the O and O1 helices of Escherichia coli DNA polymerase I, we mutated 9 residues of this region to alanine. The alanine substitutions result in moderate to severe effects on the polymerase activity of the individual mutant enzymes. Severe loss of activity is associated with R754A, K758A, F762A, and Y766A. However, the loss of polymerase activity with different template primers exhibited a rather unique pattern implying differential participation of the individual residue in the synthesis directed by poly(rA), poly(dA), and poly(dC) templates. The ability of all mutants to form E-DNA binary complex was found to be unaffected with the exception of Y766A and F771A, where significant reduction in the cross-linking of both the template and the primer strand was noted. Most interestingly, the catalytic activity of all inactive mutant enzymes, with the exception of K758A, could be restored by substituting Mn2+ in place of Mg2+ as a divalent cation. Based on these results and associated changes in the kinetic parameters and other properties of the individual mutant enzyme, we conclude the following: (a) Tyr 766 and Phe 771 are either involved in the binding of template-primer or are in the vicinity of the DNA binding track. (b) Residues Arg 754, Lys 758, Phe 762, and Tyr 766 appear to be required for the binding of Mg.dTTP, while only Arg 754 and Lys 758 are utilized in the polymerization of Mn.dTTP. (c) In the polymerization of dGTP, only Lys 758 appears essential regardless of the type of divalent cation. (d) Phe 762 participates only in the binding of Mg.dTTP. Finally, (e) based on the analysis of the time course of nucleotide incorporation, processivity, and pyrophosphorolysis reaction, we suggest that Lys 758 is probably involved in a conformational change of the ternary complexes preceding and following the chemical step. In summary, our results suggest that the formation of the dNTP binding pocket is a dynamic process which requires the participation of different residues depending on the type of dNTP and the divalent cation.
FURTHER STUDIES OF SUPERCOOLED LIQUIDS. (1907)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFURTHER STUDIES OF SUPERCOOLED LIQUIDS.S. W. Young and W. E. BurkeCite this: J. Am. Chem. Soc. 1907, 29, 3, 329–339Publication Date (Print):March 1, 1907Publication History Published online1 May 2002Published inissue 1 March 1907https://pubs.acs.org/doi/10.1021/ja01957a015https://doi.org/10.1021/ja01957a015research-articleACS PublicationsRequest reuse permissionsArticle Views48Altmetric-Citations1LEARN 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
High-<i>Q</i> AlN photonic crystal nanobeam cavities fabricated by layer transfer (2012)

High-quality-factor one-dimensional photonic crystal nanobeam cavities embedding GaN/AlN quantum dots are fabricated by an epilayer transfer method. The GaN/AlN quantum dots are first grown on SiC before being transferred to a Si substrate using a hydrogen silsesquioxane bonding layer and highly selective back-etching of the SiC. Nanobeam cavities are then fabricated by electron-beam lithography, dry etching, and HF underetching of the bonding layer. The resulting nanocavity exhibits quality factors larger than 6.3 × 103, the highest quality factor reported to date for an optically active group-III nitride photonic crystal nanocavity.
Synthetic approaches to pseudopterosin G aglycone dimethyl ether (1998)

Three successive reactions of a dimethoxy arene with allylic cation equivalents were used to convert 2,3-dimethoxy-4-methyl-1-iodobenzene to the hexahydro-1H-phenalene system of the potent marine antiinflammatory pseudopterosins G–J.
BrainK for Structural Image Processing: Creating Electrical Models of the Human Head (2016)

BrainK is a set of automated procedures for characterizing the tissues of the human head from MRI, CT, and photogrammetry images. The tissue segmentation and cortical surface extraction support the primary goal of modeling the propagation of electrical currents through head tissues with a finite difference model (FDM) or finite element model (FEM) created from the BrainK geometries. The electrical head model is necessary for accurate source localization of dense array electroencephalographic (dEEG) measures from head surface electrodes. It is also necessary for accurate targeting of cerebral structures with transcranial current injection from those surface electrodes. BrainK must achieve five major tasks: image segmentation, registration of the MRI, CT, and sensor photogrammetry images, cortical surface reconstruction, dipole tessellation of the cortical surface, and Talairach transformation. We describe the approach to each task, and we compare the accuracies for the key tasks of tissue segmentation and cortical surface extraction in relation to existing research tools (FreeSurfer, FSL, SPM, and BrainVisa). BrainK achieves good accuracy with minimal or no user intervention, it deals well with poor quality MR images and tissue abnormalities, and it provides improved computational efficiency over existing research packages.
Impact of <i>KRAS</i> and <i>BRAF</i> Gene Mutation Status on Outcomes From the Phase III AGITG MAX Trial of Capecitabine Alone or in Combination With Bevacizumab and Mitomycin in Advanced Colorectal Cancer (2011)

KRAS gene mutation status was neither prognostic for OS nor predictive of bevacizumab outcome in patients with advanced CRC. BRAF gene mutation status was prognostic for OS but was not predictive of outcome with bevacizumab.
Effects of Leucine on Insulin Secretion and Beta Cell Membrane Potential in Mouse Islets of Langerhans (1991)

Leucine is known to enhance insulin secretion from islets of Langerhans, and insulin promotes leucine uptake in peripheral tissues. The present studies were designed to elucidate the effects of leucine on glucose responsiveness and stimulus secretion coupling in mouse islets of Langerhans. The effects of 20 mM leucine on insulin secretion and membrane potential were studied over a range of glucose concentrations (0-27.7 mM). Microdissected, perifused pancreatic islets from normal adult mice were used for both studies of insulin secretion and electrophysiology in order to make a close comparison between these measurements. Leucine enhanced the insulin secretion in the presence of 5.6, 11.1, and 22.2 mM glucose. In the presence of leucine, 27 mM glucose inhibited insulin secretion. In the absence of glucose-leucine did not induce electrical activity of the beta cell membrane, whereas in the presence of 5.6, 11.1, and 22.2 mM glucose leucine increased spike frequency. Thus, leucine shifts both the glucose-dependent insulin secretion and electrical activity toward lower glucose concentrations. It is concluded that leucine and glucose share a common metabolic pathway (citric acid cycle) for stimulatory effects. Leucine is deaminated to form 2-ketoisocaproic acid (KIC) and produce NH4+. We propose that in the absence of glucose this increases cytosolic pH, which in turn increases K+ permeability, and inhibits electrical activity and insulin secretion.
Novel Insights into the Roles of Rho Kinase in Cancer (2016)

Rho-associated coiled-coil kinase (ROCK) is a major downstream effector of the small GTPase RhoA. The ROCK family, consisting of ROCK1 and ROCK2, plays a central role in the organization of the actin cytoskeleton, and is involved in a wide range of fundamental cellular functions such as contraction, adhesion, migration, proliferation, and apoptosis. Since the discovery of effective inhibitors such as fasudil and Y27632, the biological roles of ROCK have been extensively explored in numerous diseases, including cancer. Accumulating evidence supports the concept that ROCK plays important roles in tumor development and progression through regulating many key cellular functions associated with malignancy, including tumorigenicity, tumor growth, metastasis, angiogenesis, tumor cell apoptosis/survival and chemoresistance as well. This review focuses on the new advances of the most recent 5 years from the studies on the roles of ROCK in cancer development and progression; the discussion is mainly focused on the potential value of ROCK inhibitors in cancer therapy.
Approaches to the Synthesis of Cytochalasans. Part 2. Pyrrolinone derivatives as basic units (1980)

Abstract Several attempts to prepare 3‐acetyl‐5‐benzyl‐3‐pyrrolin‐2‐one ( 7 ) from phenylalanine are described. This goal was only reached formally, because compound 7 exists in the tautomeric form of (Z)‐5‐benzyl‐3‐(1′‐hydroxyethylidene)‐4‐pyrrolin‐2‐one ( 17 ) according to the spectral data. The problem of tautomerism in pyrrolinone systems is discussed.
The importance of lactobacilli in maintaining normal microbial balance in the crop (1977)

1. The effect of lactobacilli on Escherichia ccli has been examined in vitro and in chicken crop in vivo. 2. Inhibition of E. coli was dependent on the presence of sufficient numbers of lactobacilli. 3. In a standard test some lactobacilli were bacteriostatic and one was bactericidal. The bacteriostasis was due to the low pH produced by these strains but bactericidal activity could not be accounted for by pH alone. 4. In gnotobiotic animals the bactericidal strain was no more inhibitory for E. coli than was a bacteriostatic strain.
WR75 junction circulator using 90° and 180° ridge UEs (2002)

The gain–bandwidth product of a practical junction circulator is fixed by the quality factor of its junction and the topology of its matching circuit. One difficulty with the design of a large mean power circulator or a millimetre one is that its quality factor may not be compatible with the use of 30° and 90° UEs. A method of overcoming these difficulties is to employ a 180° UE at each so-called characteristic plane of the junction. The purpose of the paper is to describe one arrangement in a WR75 waveguide. The device has a return loss of 20 dB and an insertion loss of 0.17 dB over a 16% frequency band. The quality factor of its complex gyrator circuit is 4.0.
How to get rid of the noise in the corpus : cleaning large samples of digital newspaper texts (2011)

Large digital text samples are promising sources for text-analytical research in the social sciences. However, they may turn out to be very troublesome when not cleaned of the 'noise' of doublets and sampling errors that induce biases and distort the reliability of content-analytical results. This paper claims that these problems can be remedied by making innovative use of computational and corpus-linguistic procedures. Automatic pairwise document comparison based on a vector space model will bring doublets to light, while sampling errors can be discerned with the help of textmining procedures that measure the 'keyness' of a document, i.e. the degree to which it contains or does not contain keywords representing research topic.
Framework for monitoring and testing web application scalability on the cloud (2012)

By allowing resources to be acquired on-demand and in variable amounts, cloud computing provides an appealing environment for deploying pilot projects and for performance testing of Web applications and services. However, setting up cloud environments for performance testing still requires a significant amount of manual effort. To aid performance engineers in this task, we developed a framework that integrates several common benchmarking and monitoring tools. The framework helps performance engineers to test applications under various configurations and loads. Furthermore, the framework supports dynamic server allocation based on incoming load using a response-time-aware heuristics. We validated the framework by deploying and stress-testing the MediaWiki application. An experimental evaluation was conducted aimed at comparing the response-time-aware heuristics against Amazon Auto-Scale.
Deformable mirror using the PMN electrostrictor (1981)

A simple deformable bimorphous mirror using the PMN electrostrictor has been made for refocusing a light beam. Parabolic deformation of the mirror has been measured by an interferometric technique on a cycle with rising and falling electric fields. In comparison with the hard PZT piezostrictor, the electrostrictor is found to be promising for practical mirror control applications because of a large strain with neither hysteresis nor aging effects.
Nucleotide sequence: the β-hemolysin gene of<i>Staphylococcus aureus</i> (1989)

Journal Article Nucleotide sequence: the β-hemolysin gene of Staphylococcus aureus Get access Steven J. Projan, Steven J. Projan The Departments of Applied Genetics and Plasmid Biology, The Public Health Research Institute455 First Avenue, New York, NY 10016, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar John Kornblum, John Kornblum The Departments of Applied Genetics and Plasmid Biology, The Public Health Research Institute455 First Avenue, New York, NY 10016, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Barry Kreiswirth, Barry Kreiswirth The Departments of Applied Genetics and Plasmid Biology, The Public Health Research Institute455 First Avenue, New York, NY 10016, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Soraya L. Moghazeh, Soraya L. Moghazeh The Departments of Applied Genetics and Plasmid Biology, The Public Health Research Institute455 First Avenue, New York, NY 10016, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar William Eisner, William Eisner The Departments of Applied Genetics and Plasmid Biology, The Public Health Research Institute455 First Avenue, New York, NY 10016, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard P. Novick Richard P. Novick The Departments of Applied Genetics and Plasmid Biology, The Public Health Research Institute455 First Avenue, New York, NY 10016, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 8, 25 April 1989, Page 3305, https://doi.org/10.1093/nar/17.8.3305 Published: 25 April 1989 Article history Received: 24 January 1989 Published: 25 April 1989
Humoral Immune Response in Acquired Immunity to Chlamydial Genital Infection of Female Guinea Pigs (1983)

Immunity to reinfection in the genital tract of female guinea pigs with the agent of guinea pig inclusion conjunctivitis was found to be dependent upon an intact humoral immune response. Cell-mediated immunity in the absence of humoral immunity had no apparent role in resistance to challenge infection.
Effectiveness of Warning Signals in Semi-Autonomous Vehicles (2019)

<div class="section abstract"><div class="htmlview paragraph">The rise of automation in the automotive industry has ensured significant progress in vehicle safety and infrastructure. During the transition to full autonomy, the driver is often the redundancy and safety feature in the event of a hazard or automation error. Understanding driver behavior in the transition from non-driver to driver is important for safety. Proper handling of transitions will be more critical as these events become less common and users trust automated driving systems. This research investigates the case of SAE level-3 automated driving systems, where the driver need not constantly pay attention but is responsible for reaction during hazards. Findings include quantitative and qualitative assessment of various warning modes for a distracted driver responding to an automated driving failure situation. Driver response time and behavior for these events are compared to instances with minimal warning systems. The results offer insight into human-vehicle interfaces during the transition towards full autonomy.</div></div>
Go-sha-jinki-Gan (GJG) ameliorates allodynia in chronic constriction injury model mice via suppression of TNF-α expression in the spinal cord (2016)

Our data suggest that GJG ameliorates allodynia in chronic constriction injury model mice via suppression of tumor necrosis factor-a expression derived from activated microglia. GJG is a promising drug for the treatment of neuropathic pain induced by neuro-inflammation.
I‐TASSER: Fully automated protein structure prediction in CASP8 (2009)

The I-TASSER algorithm for 3D protein structure prediction was tested in CASP8, with the procedure fully automated in both the Server and Human sections. The quality of the server models is close to that of human ones but the human predictions incorporate more diverse templates from other servers which improve the human predictions in some of the distant homology targets. For the first time, the sequence-based contact predictions from machine learning techniques are found helpful for both template-based modeling (TBM) and template-free modeling (FM). In TBM, although the accuracy of the sequence based contact predictions is on average lower than that from template-based ones, the novel contacts in the sequence-based predictions, which are complementary to the threading templates in the weakly or unaligned regions, are important to improve the global and local packing in these regions. Moreover, the newly developed atomic structural refinement algorithm was tested in CASP8 and found to improve the hydrogen-bonding networks and the overall TM-score, which is mainly due to its ability of removing steric clashes so that the models can be generated from cluster centroids. Nevertheless, one of the major issues of the I-TASSER pipeline is the model selection where the best models could not be appropriately recognized when the correct templates are detected only by the minority of the threading algorithms. There are also problems related with domain-splitting and mirror image recognition which mainly influences the performance of I-TASSER modeling in the FM-based structure predictions.