gebhart/patrepeval huggingface dataset:
Comparison of visual inspection, radiographic examination, laser fluorescence and their combinations on treatment decisions for occlusal surfaces. (2008)

VI and L provided on average the greatest intra- and inter-examiner reproducibility, respectively. Although the combination of diagnostic methods may decrease both intra- and inter examiners reproducibility, combination of VI, L and RX resulted in the greatest sensitivity, being statistically superior to RX and L. There was more inter-examiner agreement for the option of restorative treatment, while the use of sealants as a treatment option yielded the lowest values. Negative predictive values were numerically inferior to positive predictive values, indicating that the examiners preferred not to restore a carious tooth than to proceed operatively in an intact tooth. The combination of the three methods studied showed the best results in determining treatment plans for occlusal surfaces, when compared to the other types of exams. On the other hand, radiographic examination and laser fluorescence were less efficient when used alone.
Solution structures of .alpha.-conotoxin G1 determined by two-dimensional NMR spectroscopy (1989)

Two-dimensional NMR data have been used to generate solution structures of alpha-conotoxin G1, a potent peptide antagonist of the acetylcholine receptor. Structural information was obtained in the form of proton-proton internuclear distance constraints, and initial structures were produced with a distance geometry algorithm. Energetically more favorable structures were generated by using the distance geometry structures as input for a constrained energy minimization program. The results of both of these calculations indicate that the overall backbone conformation of the molecule is well-defined by the NMR data whereas the side-chain conformations are generally less well-defined. The main structural features derived from the NMR data were the presence of tight turns centered on residues Pro5 and Arg9. The solution structures are compared with previous proposed models of conotoxin G1, and the NMR data are interpreted in conjunction with chemical modification studies and structural properties of other antagonists of the acetylcholine receptor to gain insight into structure-activity relationships in these peptide toxins.
Refining procedures for the administration of substances (2001)

3 Re®nement for individual routes and procedures 13 3.1 Intra-art icular 13 3.2 Intracerebral (intracerebroventricular) 14 3.3 Intradermal 16 3.4 Intramuscular 16 3.5 Intranasal 18 3.6 Intraperitoneal 19 3.7 Intratracheal 20 3.8 Intravaginal 20 3.9 Intravenous and intra-arterial 21 3.10 Oral routes 25 3.10.1 Inclusion in an animal’s food or water 25 3.10.2 Dosing directly into the pharynx 27 3.10.3 Oral gavage 28 3.11 Osmotic minipumps 30 3.12 Respiratory routes 31 3.12.1 Whole body exposure 31 3.12.2 Nose only=Snout only exposure 32 3.12.3 Mask exposure 33 3.13 Subcutaneous 34 3.14 TopicalÐdermal 35 3.15 TopicalÐocular 36 3.16 Footpad 37 3.17 Uncommon routes 38 4 Special considerations for wild animals 38 References 39 WORKING PARTY REPORT
Clathrin polymerization is not required for bulk-phase endocytosis in rat fetal fibroblasts. (1994)

To assess the role of clathrin in the bulk endocytic flow of rat foetal fibroblasts, the rate of internalization of fluid-phase and membrane-lipid tracers were compared, under control conditions and after inhibition of endocytic clathrin-coated pit formation. After intracellular potassium depletion or upon cell transfer into 0.35 M NaCl, the rate of internalization of receptor-bound transferrin and the residual membrane area of plasmalemmal clathrin-coated pits and vesicles were similarly decreased by approximately 90%. In contrast, the initial rate (< 5 min) of intracellular accumulation of the fluid-phase tracer HRP was not affected. Both in control and treated cells, the rate of HRP accumulation declined after approximately 5 min, and was twofold lower in treated cells, due to enhanced regurgitation. After correction for regurgitation, the endocytic rate constant was similar to measurements at shorter intervals and identical in control and treated cells. Similarly, the rate of internalization and the steady-state level of intracellular accumulation of two fluorescent lipid derivatives, 6-[N-(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]hexanoylglucosylsp hingosine (C6-NBD-GlcCer) and 1-[4-(trimethylamino)phenyl]-6-phenylhexa-1,3,5-triene (TMA-DPH), were not affected by potassium depletion, indicating that the endocytic membrane traffic was equally preserved. Finally, the size distribution of primary endocytic particles that were accessible to HRP within 15 s before glutaraldehyde fixation was also indistinguishable in control and potassium-depleted cells. The simplest explanation is that clathrin polymerization is necessary to concentrate receptor-bound ligands in primary endocytic vesicles, but superfluous to the basic endocytic machinery in rat foetal fibroblasts.
The B Subunit ofEscherichia coliHeat-Labile Enterotoxin Inhibits Th1 but Not Th17 Cell Responses in Established Experimental Autoimmune Uveoretinitis (2008)

EtxB preimmunization protects mice from EAU induction by inhibiting Th1 responses, but the resultant reduction in IFN-gamma responses by EtxB does not effect infiltration or structural damage in established EAU, where Th17 responses predominate. These data highlight the critical importance of the dynamics of T-cell phenotype and infiltration during EAU when considering immunomodulatory therapy.
Adapting concepts from systems biology to develop systems exposure event networks for exposure science research (2010)

Systems exposure science has emerged from the traditional environmental exposure assessment framework and incorporates new concepts that link sources of human exposure to internal dose and metabolic processes. Because many human environmental studies are designed for retrospective exposure evaluations they often do not provide practical toxicological outcome parameters. Our goal was to examine concepts from systems biology research and adapt them to a network approach that maps forward to a perturbation event using two hypothetical examples. The article proposes that environmental exposure studies should not only retrospectively document exposure levels, but also measure biological parameters that can be used to inform relevant systemic changes.
Prostate Stem Cell Antigen Is Overexpressed in Prostate Cancer Metastases (2005)

Prostate cancer metastases express PSCA. However, greater PSCA staining intensity and level of PSCA mRNA expression was associated with bone metastases compared with lymph node metastases. This study suggests that PSCA is a promising tumor marker and potential therapeutic target for patients with metastatic prostate cancer.
RAG-dependent peripheral T cell receptor diversification in CD8+T lymphocytes (2002)

Rearrangement of T cell receptor (TCR) genes is driven by transient expression of V(D)J recombination-activating genes (RAGs) during lymphocyte development. Immunological dogma holds that T cells irreversibly terminate RAG expression before exiting the thymus, and that all of the progeny arising from mature T cells express the parental TCRs. When single pancreatic islet-derived, NRP-A7 peptide-reactive CD8(+) T cells from nonobese diabetic (NOD) mice were repeatedly stimulated with peptide-pulsed dendritic cells, daughter T cells reexpressed RAGs, lost their ability to bind to NRP-A7K(d) tetramers, ceased to transcribe tetramer-specific TCR genes, and, instead, expressed a vast array of other TCR rearrangements. Pancreatic lymph node (PLN) CD8(+) T cells from animals expressing a transgenic NRP-A7-reactive TCR transcribed and translated RAGs in vivo and displayed endogenous TCRs on their surface. RAG reexpression also occurred in the PLN CD8(+) T cells of wild-type NOD mice and could be induced in the peripheral CD8(+) T cells of nondiabetes-prone TCR-transgenic B10.H2(g7) mice by stimulation with peptide-pulsed dendritic cells. In contrast, reexpression of RAGs could not be induced in the CD8(+) T cells of B6 mice expressing an ovalbumin-specific, K(b)-restricted TCR, or in the CD8(+) T cells of NOD mice expressing a lymphocytic choriomeningitis virus-specific, D(b)-restricted TCR. Extra-thymic reexpression of the V(D)J recombination machinery in certain CD8(+) T cell subpopulations, therefore, enables further diversification of the peripheral T cell repertoire.
Dynamic Near-Infrared Optical Imaging of 2-Deoxyglucose Uptake by Intracranial Glioma of Athymic Mice (2009)

Our results suggest that the near-infrared dye labeled 2-DG may serve as a useful fluorescence imaging probe to noninvasively assess intracranial tumor burden in preclinical animal models.
Tree rebalancing in optimal time and space (1986)

A simple algorithm is given which takes an arbitrary binary search tree and rebalances it to form another of optimal shape, using time linear in the number of nodes and only a constant amount of space (beyond that used to store the initial tree). This algorithm is therefore optimal in its use of both time and space. Previous algorithms were optimal in at most one of these two measures, or were not applicable to all binary search trees. When the nodes of the tree are stored in an array, a simple addition to this algorithm results in the nodes being stored in sorted order in the initial portion of the array, again using linear time and constant space.
A General Technique To Rank Protein−Ligand Binding Affinities and Determine Allosteric versus Direct Binding Site Competition in Compound Mixtures (2004)

To realize the full potential of combinatorial chemistry-based drug discovery, generic and efficient tools must be developed that apply the strengths of diversity-oriented chemical synthesis to the identification and optimization of lead compounds for disease-associated protein targets. We report an affinity selection-mass spectrometry (AS-MS) method for protein-ligand affinity ranking and the classification of ligands by binding site. The method incorporates the following steps: (1) an affinity selection stage, where protein-binding compounds are selected from pools of ligands in the presence of varying concentrations of a competitor ligand, (2) a first chromatography stage to separate unbound ligands from protein-ligand complexes, and (3) a second chromatography stage to dissociate the ligands from the complexes for identification and quantification by MS. The ability of the competitor ligand to displace a target-bound library member, as measured by MS, reveals the binding site classification and affinity ranking of the mixture components. The technique requires no radiolabel incorporation or direct biochemical assay, no modification or immobilization of the compounds or target protein, and all reaction components, including any buffers or cofactors required for protein stability, are free in solution. We demonstrate the method for several compounds of wide structural variety against representatives of the most important protein classes in contemporary drug discovery, including novel ATP-competitive and allosteric inhibitors of the Akt-1 (PKB) and Zap-70 kinases, and previously undisclosed antagonists of the M(2) muscarinic acetylcholine receptor, a G-protein coupled receptor (GPCR). The theoretical basis of the technique is analyzed mathematically, allowing quantitative estimation of binding affinities and, in the case of allosteric interaction, absolute determination of binding cooperativity. The method is readily applicable to high-throughput screening hit triage, combinatorial library-based affinity optimization, and developing structure-activity relationships among multiple ligands to a given receptor.
Mutations in a Dominant Nef Epitope of Simian Immunodeficiency Virus Diminish TCR:Epitope Peptide Affinity but not Epitope Peptide:MHC Class I Binding (2011)

Viruses like HIV and SIV escape from containment by CD8(+) T lymphocytes through generating mutations that interfere with epitope peptide:MHC class I binding. However, mutations in some viral epitopes are selected for that have no impact on this binding. We explored the mechanism underlying the evolution of such epitopes by studying CD8(+) T lymphocyte recognition of a dominant Nef epitope of SIVmac251 in infected Mamu-A*02(+) rhesus monkeys. Clonal analysis of the p199RY-specific CD8(+) T lymphocyte repertoire in these monkeys indicated that identical T cell clones were capable of recognizing wild-type (WT) and mutant epitope sequences. However, we found that the functional avidity of these CD8(+) T lymphocytes for the mutant peptide:Mamu-A*02 complex was diminished. Using surface plasmon resonance to measure the binding affinity of the p199RY-specific TCR repertoire for WT and mutant p199RY peptide:Mamu-A*02 monomeric complexes, we found that the mutant p199RY peptide:Mamu-A*02 complexes had a lower affinity for TCRs purified from CD8(+) T lymphocytes than did the WT p199RY peptide:Mamu-A*02 complexes. These studies demonstrated that differences in TCR affinity for peptide:MHC class I ligands can alter functional p199RY-specific CD8(+) T lymphocyte responses to mutated epitopes, decreasing the capacity of these cells to contain SIVmac251 replication.
Catalytic Deoxygenation of Stearic Acid in a Continuous Reactor over a Mesoporous Carbon-Supported Pd Catalyst (2009)

Catalytic deoxygenation of neat stearic acid was studied at 360 °C under 10 bar argon or 5 vol % hydrogen in argon in a fixed-bed reactor (down flow) using mesoporous-supported Pd/C (Sibunit) beads as a catalyst. The results showed stable catalyst performance, giving about 15% conversion level of stearic acid. The main liquid-phase product was heptadecane, while the main gaseous products were CO and CO2.
Myeloma Cell-Osteoclast Interaction Enhances Angiogenesis Together with Bone Resorption: A Role for Vascular Endothelial Cell Growth Factor and Osteopontin (2007)

Osteoclast-derived osteopontin and VEGF from myeloma cells cooperatively enhance angiogenesis and also induce osteoclastogenic activity by vascular endothelial cells. These observations suggest the presence of a close link between myeloma cells, osteoclasts, and vascular endothelial cells to form a vicious cycle between bone destruction, angiogenesis, and myeloma expansion.
Activities of daily living and cognitive levels of function in dementia (1993)

The number of progressive dementia patients being caredfor in long term institutions is increasing. As medical science continues to search for answers to treatment and cure, caregivers continue to struggle with managing cares and promoting patient dignity. Evaluation and identification of individual patient cognitive assets and limitations is essential in planning patient cares. The purpose of this study is to describe two tools, used in a team aproach, to facilitate managing basic daily cares. The study compares the scoring of the two tools indicating a substantial relationship between the two instruments and suggests that the Cognitive Performance Test (CPT) and the Self Care Performance Test (SCPT) rate behavior and task performance in a consistently similar manner. The results suggest that the scales are an accurate predictor of demented patients cognitive abilities and limitations and can facilitate designing nursng care plans. The CPT(which can be given in about 20 minutes) can be completed upon admission, the test score shared with nursing and the SCPT can guide plans of care. Cares planned in this manner are likely to allow the patients independence in performing those cares they are capable of and not frustrating them by expecting them to perform skills they have lost. This study focuses on patients in the later stages of progressive dementia. Fifty-eight subjects were rated using the two tools. Fifty-one of the 58 subjects in the study received a rating level offour or lower. (Allen 's levels of rating progressive dementia with level six being normalfunctioning.) Patient scores for both the CPT and the SCPT are based on observance of performance and do not require verbal responses and therefore lower level dementia patients can be more reliably rated.
Purification of Laboratory Chemicals, Fourth Edition. By W. L. F. (1997)

Purification of Laboratory Chemicals, Fourth Edition. By W. L. F.Armarego (Australian National University, The John Curtin School ofMedical Research). and D.D. Perrin (Australian National University,Formerly of the Medical Chemistry Group). Butterworth Heinemann Press:Oxford. 1996. v + 529 pp. ARP $195.00. ISBN 0-7506-2839-1.
Recent advances in microstrip filters for communications and other applications (1997)

Modern microwave communication systems require, especially in satellite and mobile communications, high-performance narrow-band bandpass filters having low insertion loss and high selectivity together with linear phase or flat group delay in the passband. Usually, these criteria are fulfilled using waveguide cavity or dielectric resonator loaded cavity filters because of their low loss. However, in order to reduce size, weight and cost, there has been a growing interest in planar structures. The disadvantage of high conductor loss of the planar filters using conventional conducting thin films can be overcome by replacing them with high-temperature superconducting (HTS) thin films. These can have a very low conductor loss. An alternative is by combining with active MMIC devices to compensate the loss. Under those driving forces many novel types of microstrip filters have recently been developed. This paper is intended to address this development. Different types of newly developed microstrip filters, particularly those developed at the University of Birmingham, such as slow-wave microstrip filters, cross-coupled microstrip filters and miniature dual-mode microstrip filters are presented.
Opioid Peptide Drug Development: Transport of Opioid Chimeric Peptides Through the Blood-Brain Barrier (1992)

The use of chimeric peptides and physiologic-based strategies for drug delivery through the BBB may be applied to opioid peptides (dynorphins, endorphin analogs, and enkephalin analogs), and these agents have considerable advantages in drug development with respect to drug addiction. Recent research has allowed for the development of efficacious BBB drug transport vectors, as well as the demonstration that these vectors allow for shuttling of opioid peptides through the BBB in vivo. The major challenge to future research is the development of coupling strategies that allow for the release of biologically active opioid peptide from the drug transport vector following its cleavage by disulfide reductase enzymes, which are abundant in brain. These coupling strategies must be developed in advance since the amino groups necessary for coupling are incorporated into the opioid peptide at the level of solid-state synthesis.
Model of a Ternary Complex between Activated Factor VII, Tissue Factor and Factor IX (2002)

Upon binding to tissue factor, FVIIa triggers coagulation by activating vitamin K-dependent zymogens, factor IX (FIX) and factor X (FX). To understand recognition mechanisms in the initiation step of the coagulation cascade, we present a three-dimensional model of the ternary complex between FVIIa:TF:FIX. This model was built using a full-space search algorithm in combination with computational graphics. With the known crystallographic complex FVIIa:TF kept fixed, the FIX docking was performed first with FIX Gla-EGF1 domains, followed by the FIX protease/EGF2 domains. Because the FIXa crystal structure lacks electron density for the Gla domain, we constructed a chimeric FIX molecule that contains the Gla-EGF1 domains of FVIIa and the EGF2-protease domains of FIXa. The FVIIa:TF:FIX complex has been extensively challenged against experimental data including site-directed mutagenesis, inhibitory peptide data, haemophilia B database mutations, inhibitor antibodies and a novel exosite binding inhibitor peptide. This FVIIa:TF:FIX complex provides a powerful tool to study the regulation of FVIIa production and presents new avenues for developing therapeutic inhibitory compounds of FVIIa:TF:substrate complex.
Affinity maturation of a Taq DNA polymerase specific affibody by helix shuffling (1999)

The possibility of increasing the affinity of a Taq DNA polymerase specific binding protein (affibody) was investigated by an alpha-helix shuffling strategy. The primary affibody was from a naive combinatorial library of the three-helix bundle Z domain derived from staphylococcal protein A. A hierarchical library was constructed through selective re-randomization of six amino acid positions in one of the two alpha-helices of the domain, making up the Taq DNA polymerase binding surface. After selections using monovalent phage display technology, second generation variants were identified having affinities (K(D)) for Taq DNA polymerase in the range of 30-50 nM as determined by biosensor technology. Analysis of binding data indicated that the increases in affinity were predominantly due to decreased dissociation rate kinetics. Interestingly, the affinities observed for the second generation Taq DNA polymerase specific affibodies are of similar strength as the affinity between the original protein A domain and the Fc domain of human immunoglobulin G. Further, the possibilities of increasing the apparent affinity through multimerization of affibodies was demonstrated for a dimeric version of one of the second generation affibodies, constructed by head-to-tail gene fusion. As compared with its monomeric counterpart, the binding to sensor chip immobilized Taq DNA polymerase was characterized by a threefold higher apparent affinity, due to slower off-rate kinetics. The results show that the binding specificity of the protein A domain can be re-directed to an entirely different target, without loss of binding strength.
Electrochemical Reduction of CO2 to CO Catalyzed by a Bimetallic Palladium Complex (2006)

The bis(triphosphine) ligand C6H4{P[CH2CH2P(C6H11)2]2}2, m-(triphos)2 (1), is synthesized by the reaction of m-bis(phosphino)benzene with 4 equiv of vinyldicyclohexylphosphine. Reaction of 1 with 2 equiv of [Pd(CH3CN)4](BF4)2 results in the formation of the bimetallic complex {m-(triphos)2[Pd(CH3CN)]2}(BF4)4 (2). A structural study of 2 confirms the presence of two [Pd(triphosphine)(CH3CN)]2+ substituents at the meta positions of a benzene ring. Complex 2 catalyzes the electrochemical reduction of CO2 to CO in acidic dimethylformamide solutions. The kinetics of this reaction have been studied, and the reaction is 0.5 order in catalyst and first order in CO2. This catalyst exhibits catalytic rates comparable to that of its monometallic analogues. Significantly higher turnover numbers are observed for 2 than observed previously for monometallic, bimetallic, and dendritic complexes of this class of catalysts.