gebhart/patrepeval huggingface dataset:
Dependence of the Enhanced Optical Scattering Efficiency Relative to That of Absorption for Gold Metal Nanorods on Aspect Ratio, Size, End-Cap Shape, and Medium Refractive Index (2005)

The current intense interest in the properties of plasmonic nanostructures for their applications in chemical and biochemical sensors, medical diagnostics and therapeutics, and biological imaging is fundamentally based on their enhanced optical absorption and scattering properties. In this study, the optical extinction, absorption, and scattering efficiencies were calculated as a function of shape definition, aspect ratio, surrounding medium, and material selection. The discrete dipole approximation method was used, which is known to be a very useful and versatile computational tool for particles with any arbitrary shape. Relative contribution of scattering to the total extinction for the longitudinal mode was found to be significantly dependent on the aspect ratio of the nanorod in a somewhat complex manner, different from a typical linear relationship for the resonance wavelength. A slight elongation of Au nanosphere gives rise to a drastic increase in the relative scattering efficiency, which eventually reaches a maximum and begins to decrease with further increase in the aspect ratio. This is ascribed to the increasing absorptive contribution from the larger imaginary dielectric function of the metal particle in the longer wavelength region where the red-shifted excitation of the longitudinal resonance mode occurs. For transverse mode exhibiting the blue-shift in the resonance peak, on the contrary, the absorption efficiency is relatively enhanced compared to the scattering efficiency with increasing aspect ratio. This is thought to result from the dominant effect of the interband transition present in this wavelength region. Besides the dependence of plasmonic characteristics on the aspect ratio of nanorod, the DDA results for a small change of the end-cap shape and the index of the surrounding medium lead us to conclude that there exist two competing key factors: a weighting factor assigned to the shape parameter and the dielectric function of the metal particle, which control the relative enhancement in the scattering and absorption as well as the linearity of resonance wavelength with regard to the aspect ratio.
Targeted Imaging of the Spatial and Temporal Variation of Matrix Metalloproteinase Activity in a Porcine Model of Postinfarct Remodeling (2011)

A novel, multimodality, noninvasive hybrid SPECT/CT imaging approach was validated and applied for in vivo evaluation of MMP activation in combination with cine MR analysis of LV deformation. Increased (99m)Tc-RP805 retention was seen throughout the heart early post-MI and was not purely a reciprocal of thallium-201 perfusion. The (99m)Tc-RP805 SPECT/CT imaging may provide unique information regarding regional myocardial MMP activation and predict late post-MI LV remodeling.
Cellular Internalization and Degradation of Antithrombin III-Thrombin, Heparin Cofactor II-Thrombin, and α1-Antitrypsin-Trypsin Complexes Is Mediated by the Low Density Lipoprotein Receptor-related Protein (1996)

The inhibition of proteinase activity by members of the serine proteinase inhibitor (serpin) family is a critical regulatory mechanism for a variety of biological processes. Once formed, the serpin enzyme complexes (SECs) are removed from the circulation by a hepatic receptor. The present study suggests that this receptor is very likely the low density lipoprotein receptor-related protein (LRP), a prominent liver receptor. In vitro binding studies revealed that antithrombin III (ATIII)-thrombin, heparin cofactor II (HCII)-thrombin, and alpha1-antitrypsin (alpha1AT)-trypsin bound to purified LRP, and their binding was inhibited by the 39-kDa receptor-associated protein (RAP), an antagonist of LRP-ligand binding activity. In contrast, native or modified forms of the inhibitors were unable to bind to LRP. Mouse embryonic fibroblasts, which express LRP, mediate the cellular internalization leading to degradation of these SECs, while mouse fibroblasts genetically deficient in LRP showed no capacity to internalize and degrade these complexes. SECs were also degraded by HepG2 cells, and this process was inhibited by LRP antibodies, RAP, and chloroquine. The cellular-mediated uptake and degradation was specific for SECs; native or modified forms of the inhibitors were not internalized and degraded. Finally, in vivo clearance studies in rats demonstrated that RAP inhibited the clearance of ATIII-125I-thrombin complexes from the circulation. Together, these results indicate that LRP functions as a liver receptor responsible for the plasma clearance of SECs.
Cannabinoid CB2 Receptor Activation Decreases Cerebral Infarction in a Mouse Focal Ischemia/Reperfusion Model (2007)

Cannabinoid CB(2) Receptor (CB(2)) activation has been shown to have immunomodulatory properties without psychotropic effects. The hypothesis of this study is that selective CB(2) agonist treatment can attenuate cerebral ischemia/reperfusion injury. Selective CB(2) agonists (O-3853, O-1966) were administered intravenously 1 h before transient middle cerebral artery occlusion (MCAO) or 10 mins after reperfusion in male mice. Leukocyte/endothelial interactions were evaluated before MCAO, 1 h after MCAO, and 24 h after MCAO via a closed cranial window. Cerebral infarct volume and motor function were determined 24 h after MCAO. Administration of the selective CB(2) agonists significantly decreased cerebral infarction (30%) and improved motor function (P<0.05) after 1 h MCAO followed by 23 h reperfusion in mice. Transient ischemia in untreated animals was associated with a significant increase in leukocyte rolling and adhesion on both venules and arterioles (P<0.05), whereas the enhanced rolling and adhesion were attenuated by both selective CB(2) agonists administered either at 1 h before or after MCAO (P<0.05). CB(2) activation is associated with a reduction in white blood cell rolling and adhesion along cerebral vascular endothelial cells, a reduction in infarct size, and improved motor function after transient focal ischemia.
Metal chelates as probes of biological systems (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal chelates as probes of biological systemsClaude F. Meares and Theodore G. WenselCite this: Acc. Chem. Res. 1984, 17, 6, 202–209Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/ar00102a001https://doi.org/10.1021/ar00102a001research-articleACS PublicationsRequest reuse permissionsArticle Views568Altmetric-Citations148LEARN 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
N-Hydroxypyridine-2-thione esters as radical precursors in kinetic studies. Measurements of rate constants for hydrogen-atom-abstraction reactions (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTN-Hydroxypyridine-2-thione esters as radical precursors in kinetic studies. Measurements of rate constants for hydrogen-atom-abstraction reactionsMartin. Newcomb and Seung Un. ParkCite this: J. Am. Chem. Soc. 1986, 108, 14, 4132–4134Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/ja00274a046https://doi.org/10.1021/ja00274a046research-articleACS PublicationsRequest reuse permissionsArticle Views580Altmetric-Citations80LEARN 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
Modeling RNA−Ligand Interactions:  The Rev-Binding Element RNA−Aminoglycoside Complex (1998)

An approach to the modeling of ligand-RNA complexes has been developed by combining three-dimensional structure-activity relationship (3D-SAR) computations with a docking protocol. The ability of 3D-SAR to predict bound conformations of flexible ligands was first assessed by attempting to reconstruct the known, bound conformations of phenyloxazolines complexed with human rhinovirus 14 (HRV14) RNA. Subsequently, the same 3D-SAR analysis was applied to the identification of bound conformations of aminoglycosides which associate with the Rev-binding element (RBE) RNA. Bound conformations were identified by parsing ligand conformational data sets with pharmacophores determined by the 3D-SAR analysis. These "bioactive" structures were docked to the receptor RNA, and optimization of the complex was undertaken by extensive searching of ligand conformational space coupled with molecular dynamics computations. The similarity between the bound conformations of the ligand from the 3D-SAR analysis and those found in the docking protocol suggests that this methodology is valid for the prediction of bound ligand conformations and the modeling of the structure of the ligand-RNA complexes.
Cd[sub x]Hg[sub 1−x]Te Films by Cathodic Sputtering (1967)

Films of ranging from to were deposited by cathodic sputtering on single crystal substrates of , Ge, and sapphire. The resulting films were amorphous, but became crystalline on annealing. Optical transmission and electron probe analysis showed a slightly lower Hg concentration in the film than was present in the source material. Although can be sputtered to give a polycrystalline film, it was not possible to obtain a film by sputtering .
The myelotoxicity of chloramphenicol: in vitro and in vivo studies: I. In vitro effects on cells in culture (1997)

1 Chloramphenicol is used extensively in non-industrialized countries for the treatment of life-threatening infections because it is cheap and effective, despite its known hemotoxicity and linkage to fatal aplastic anaemia. It is important to define the mechanism of toxicity so that means can be devised to ameliorate the toxic effects in order to produce safer usage. 2 Chloramphenicol, at concentrations from 5 mM to 2 mM initiated apoptosis in dividing cells from a monkey kidney-derived cell line and in haematopoietic progenitor cells from human neonatal cord blood. 3 Growth of progenitor cells was suppressed at concentrations of chloramphenicol which would be considered less than therapeutic during patient treatment. 4 These effects could be ameliorated in progenitor cells by co-culture with the antioxidant mercaptoethylamine and in monkey kidney cells by co-culture with vitamin C. 5 This is the first report of apoptosis in chloramphenicol toxicity and suggests a possible link between a metabolic event i.e. the production of free radicals; a morphological effect, apoptosis; and a clinical effect, bone marrow suppression and aplastic anaemia.
Immunotherapy for Alzheimer's disease (2004)

The utility of vaccine strategies to treat neurodegenerative diseases such as Alzheimer's disease (AD) may still hold promise. Both active and passive immunization strategies reduced AD-like pathology and restored cognitive deficits in transgenic mice. These results were initially met with considerable optimism; however, phase IIa clinical trials were halted because of a small but significant occurrence of meningoencephalitis. Knowledge gained from studies on amyloid-beta peptide (A beta) immunotherapy will allow optimization of new-generation vaccines, targeting highly specific epitopes while reducing undesired side effects. In harnessing and steering the immune system, an effective response can be generated against A beta. If this proves successful, A beta vaccination could provide the first definitive treatment for AD.
The Placenta Harbors a Unique Microbiome (2014)

Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA-based and whole-genome shotgun (WGS) metagenomic studies. Identified taxa and their gene carriage patterns were compared to other human body site niches, including the oral, skin, airway (nasal), vaginal, and gut microbiomes from nonpregnant controls. We characterized a unique placental microbiome niche, composed of nonpathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. In aggregate, the placental microbiome profiles were most akin (Bray-Curtis dissimilarity <0.3) to the human oral microbiome. 16S-based operational taxonomic unit analyses revealed associations of the placental microbiome with a remote history of antenatal infection (permutational multivariate analysis of variance, P = 0.006), such as urinary tract infection in the first trimester, as well as with preterm birth <37 weeks (P = 0.001).
Detection of Cyclic Volatile Organic Compounds Using Single-Step Anodized Nanoporous Alumina Sensors (2009)

Conventional methods of fabricating anodic aluminum oxide (AAO) materials have utilized a multistep anodization process to manufacture sensor substrates and templates for nanostructured materials. The multistep anodization produces structured, highly ordered hexagonal nanopores. In this paper, it is demonstrated that a single-step anodization process employed in the manufacturing of moisture sensors produces a nanoporous AAO material suitable for the detection and discrimination of low molecular weight volatile organic compounds. Electrical impedance methods have been employed to analyze the electrical response of the single-step anodized AAO materials in the presence of cyclic organic vapors. The sensor exhibits an impedance response that discriminates cyclohexane, cyclohexene, benzene, toluene, and the three isomers of xylene. The impedance measurements have a direct correlation with the relative permittivity, polarizability, and dipole moments of the organic analytes.
Synergetic anticancer effect of combined gemcitabine and photodynamic therapy on pancreatic cancer in vivo (2009)

PDT has a significant anti-tumor effect, which is maintained for a short time and can be significantly enhanced by small doses of gemcitabine.
Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications (1990)

Although mobility of the phylogenetically widespread group I introns appears to be mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of the td and sunY introns are different from their eukaryotic counterparts. Most notably, they cleave at a distance from the intron insertion sites. The td enzyme was shown to cleave 23-26 nt 5' and the sunY endonuclease 13-15 nt 3' to the intron insertion site to generate 3-nt or 2-nt 3'-OH extensions, respectively. The absolute coconversion of exon markers between the distant cleavage and insertion sites is consistent with the double-strand-break repair model for intron mobility. As a further critical test of the model we have demonstrated that the mobility event is independent of DNA sequences that encode the catalytic intron core structure. Thus, in derivatives in which the lacZ or kanR coding sequences replace the intron, these marker genes are efficiently inserted into intron-minus alleles when the cognate endonuclease is provided in trans. The process is therefore endonuclease-dependent, rather than dependent on the intron per se. These findings, which imply that the endonucleases rather than the introns themselves were the primordial mobile elements, are incorporated into a model for the evolution of mobile introns.
Ice nanotube: What does the unit cell look like? (2000)

It is discovered that for an n-gonal ice nanotube built from stacking a single type of n-gonal rings of water, the unit cell consists of two stacked n-gonal rings. In one ring the O–H bonds of water molecules line up clockwise whereas in the other ring the O-H bonds line up counterclockwise. Among the n-gonal ice nanotubes examined, the pentagonal or hexagonal ice nanotube appears to be the most stable.
Mesenchymal stem cells reside in virtually all post-natal organs and tissues (2006)

Mesenchymal stem cells (MSCs) are multipotent cells which can give rise to mesenchymal and non-mesenchymal tissues in vitro and in vivo. Whereas in vitro properties such as (trans)differentiation capabilities are well known, there is little information regarding natural distribution and biology in the living organism. To investigate the subject further, we generated long-term cultures of cells with mesenchymal stem cell characteristics from different organs and tissues from adult mice. These populations have morphology, immunophenotype and growth properties similar to bone marrow-derived MSCs. The differentiation potential was related to the tissue of origin. The results indicate that (1) cells with mesenchymal stem characteristics can be derived and propagated in vitro from different organs and tissues (brain, spleen, liver, kidney, lung, bone marrow, muscle, thymus, pancreas); (2) MSC long-term cultures can be generated from large blood vessels such as the aorta artery and the vena cava, as well as from small vessels such as those from kidney glomeruli; (3) MSCs are not detected in peripheral blood. Taken together, these results suggest that the distribution of MSCs throughout the post-natal organism is related to their existence in a perivascular niche. These findings have implications for understanding MSC biology, and for clinical and pharmacological purposes.
Choosing Near-Linear Parameters in the Four-Parameter Logistic Model for Radioligand and Related Assays (1986)

Ten parameters extracted from six currently used parametrizations of the four-parameter logistic model, and one new proposal, were examined for their statistical behavior in nonlinear least-squares estimation in combination with ELISA and RIA data. Those which are adequately near-linear on the basis of the Lowry-Morton lambda statistic were identified and can be recommended for use in practice.
Crystal growth, electro-optic and electrostrictive properties of yttrium and erbium formate dihydrates, Y(HCOO)3 · 2H2O (YFD) and Er(HCOO)3 · 2H2O (ErFD) (1991)

Article Crystal growth, electro-optic and electrostrictive properties of yttrium and erbium formate dihydrates, Y(HCOO)3 · 2H2O (YFD) and Er(HCOO)3 · 2H2O (ErFD) was published on August 1, 1991 in the journal Zeitschrift für Kristallographie - Crystalline Materials (volume 194, issue 1-4).
Determination of a Statistically Valid Neutralization Titer in Plasma That Confers Protection against Simian-Human Immunodeficiency Virus Challenge following Passive Transfer of High-Titered Neutralizing Antibodies (2002)

We previously reported that high-titered neutralizing antibodies directed against the human immunodeficiency virus type 1 (HIV-1) envelope can block the establishment of a simian immunodeficiency virus (SIV)/HIV chimeric virus (SHIV) infection in two monkeys following passive transfer (R. Shibata et al., Nat. Med. 5:204-210, 1999). In the present study, increasing amounts of neutralizing immunoglobulin G (IgG) were administered to 15 pig-tailed macaques in order to obtain a statistically valid protective neutralization endpoint titer in plasma. Using an in vitro assay which measures complete neutralization of the challenge SHIV, we correlated the titers of neutralizing antibodies in plasma at the time of virus inoculation (which ranged from 1:3 to 1:123) with the establishment of infection in virus-challenged animals. Ten of 15 monkeys in the present experiment were virus free as a result of neutralizing IgG administration as monitored by DNA PCR (peripheral blood mononuclear cells and lymph node cells), RNA PCR (plasma), virus isolation, and the transfer of lymph node cell suspensions (10(8) cells) plus 8 ml of whole blood from protected animals to naïve macaques. The titer of neutralizing antibodies in the plasma calculated to protect 99% of virus-challenged monkeys was 1:38.
Patient-Reported Utilization Patterns of Fentanyl Transdermal System and Oxycodone Hydrochloride Controlled-Release Among Patients With Chronic Nonmalignant Pain (2003)

Transdermal fentanyl and oxycodone HCl controlled-release both appear to be used by patients in a manner that is inconsistent with the standard recommendation in the manufacturers' PI;however, the difference between patient-reported utilization and the PI recommendation is more pronounced with oxycodone HCl controlled-release.
540 MHz 21 mW MDFE equalizer and detector in 0.25 μm CMOS (2002)

The distinguishing parts of an multilevel decision feedback equalization (MDFE) channel compared to a PRML channel are the forward equalizer and the feedback detector. These two blocks are also known as the feedforward filter (FFF) and feedback filter (FBF). Both analog and mixed/digital implementations are possible for these functions. The present work describes an all-digital approach that is based on a simplified digital equalizer function and a RAM-based detector.