gebhart/patrepeval huggingface dataset:
CELLULAR AND SUBCELLULAR MECHANISMS OF PHOTODYNAMIC ACTION: THE 1O2 HYPOTHESIS AS A DRIVING FORCE IN RECENT RESEARCH (1978)

Abstract— Since 1972 the protective (quenching) effect of N 3 ‐ and the enhancing effect of D 2 O have been used in combination to demonstrate 1 O 2 ( 1 Δ g ) as the major reactive intermediate in the dye‐sensitized photooxygenation of biomolecules in in vitro systems. Extended application to in vivo systems has recently begun, producing some results which generally support the involvement of 1 O 2 pathways in the photosensitization processes. The use of other 1 O 2 quenchers and acceptors has also been increasing. In the application of these techniques as diagnostic tests for 1 O 2 participation in in vivo systems, careful examination of the experimental conditions should be made with respect to the quenching capability and accessibility of D 2 O in the specified cellular environment. Furthermore, the diffusive nature of 1 O 2 , generation sites, generation efficiencies, the location and type of sensitizers, and the reactivity of 1 O 2 with presumed target structures in the cell should also be taken into account in the interpretation. Recent studies illustrating the importance of these factors are discussed. Finally, a tentative picture of the mode of in vivo photodynamic activity of common dye sensitizers is outlined.
Thrombin Activity Associated with Neuronal Damage during Acute Focal Ischemia (2012)

Mechanisms of ischemic neuronal and vascular injury remain obscure. Here we test the hypothesis that thrombin, a blood-borne coagulation factor, contributes to neurovascular injury during acute focal ischemia. Stroke was induced in adult Sprague Dawley rats by occluding the middle cerebral artery. Intra-arterial thrombin infusion during ischemia significantly increased vascular disruption and cellular injury. Intravenous infusion of argatroban, a direct thrombin inhibitor, alleviated neurovascular injury. Immunostaining showed thrombin on neurons in the ischemic core. Using an activatable cell-penetrating peptide engineered to detect thrombin activity, we discovered that thrombin proteolytic activity was specifically associated with neuronal damage during ischemia. Protease activated receptor-1, the presumptive thrombin receptor, appeared to mediate ischemic neurovascular injury. Furthermore, rats receiving thrombin during ischemia showed cognitive deficit, whereas rats receiving argatroban retained intact learning and memory. These results suggest a potential role for thrombin contributing to neurovascular injury and several potential avenues for neuroprotection.
A Controlled Clinical Trial of E5 Murine Monoclonal IgM Antibody to Endotoxin in the Treatment of Gram-Negative Sepsis (1991)

Treatment with E5 antiendotoxin antibody appears safe. It reduces mortality and enhances the resolution of organ failure among patients with gram-negative sepsis who are not in shock when treated.
Cumulative Voting Consensus Method for Partitions with Variable Number of Clusters (2007)

Over the past few years, there has been a renewed interest in the consensus clustering problem. Several new methods have been proposed for finding a consensus partition for a set of n data objects that optimally summarizes an ensemble. In this paper, we propose new consensus clustering algorithms with linear computational complexity in n. We consider clusterings generated with random number of clusters, which we describe by categorical random variables. We introduce the idea of cumulative voting as a solution for the problem of cluster label alignment, where, unlike the common one-to-one voting scheme, a probabilistic mapping is computed. We seek a first summary of the ensemble that minimizes the average squared distance between the mapped partitions and the optimal representation of the ensemble, where the selection criterion of the reference clustering is defined based on maximizing the information content as measured by the entropy. We describe cumulative vote weighting schemes and corresponding algorithms to compute an empirical probability distribution summarizing the ensemble. Given the arbitrary number of clusters of the input partitions, we formulate the problem of extracting the optimal consensus as that of finding a compressed summary of the estimated distribution that preserves maximum relevant information. An efficient solution is obtained using an agglomerative algorithm that minimizes the average generalized Jensen-Shannon divergence within the cluster. The empirical study demonstrates significant gains in accuracy and superior performance compared to several recent consensus clustering algorithms.
Expression pattern of T-cell–associated chemokine receptors and their chemokines correlates with specific subtypes of T-cell non-Hodgkin lymphoma (2000)

Chemokine receptors mediate the migration of lymphocytes through the binding of soluble ligands, and their expression is differentially regulated in lymphocyte subsets. The pattern of chemokine receptor expression in T-cell non-Hodgkin lymphoma has not been previously studied. Using a panel of mouse monoclonal antibodies, we studied the immunohistochemical expression of the Th1-associated chemokine receptor CXCR3 in 141 patients with T-cell lymphoma, and we studied the receptors CCR4 and CCR5 and some of their ligands in a subset of these tumors. Expression of CXCR3 was typical of the smaller T cells in angioimmunoblastic lymphoma (15 of 18 patients), angiocentric lymphoma (3 of 3 patients), histiocyte-rich tumors (4 of 5 patients), and unspecified T-cell lymphomas (17 of 39 patients). CXCR3 expression was seen in only 1 of 15 patients with anaplastic lymphoma kinase (ALK)-positive anaplastic large-cell lymphoma. In contrast, all ALK-positive tumors showed diffuse reactivity for the Th2-associated receptor CCR4 (5 of 5 patients). CCR4 expression was also a consistent feature of the large-cell transformation of mycosis fungoides. CCR5 expression showed no consistent association with any T-cell tumor type. The chemokines Mig (CXCR3 ligand), TARC (CCR4 ligand), and MCP-2 (CCR5 ligand) were detected in intratumoral blood vessels and histiocytes. Mig was also coexpressed by a subset of CXCR3-positive tumor cells in 6 of 20 lymphomas. MCP-2 was highly expressed in stromal cells in 3 patients with nodal involvement by cutaneous T-cell lymphoma. As with normal T-cell subsets, we demonstrated that there is frequent differential expression of chemokine receptors in T-cell tumors, which may explain, in part, the distinctive patterns of spread in different tumor subtypes. (Blood. 2000;96:685-690)
Effects of $\hbox {Ca}^{2+}$ Co-Doping on the Scintillation Properties of LSO:Ce (2008)

In addition to desirable physical properties including a density of 7.4 g/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , an effective atomic number of 66, and no hygroscopicity, Lu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> :Ce has well-known scintillation properties of ~30 900 photons/MeV, an emission peak near 420 nm, and a decay time of ~43 ns. These scintillation properties are achieved with Ce doping concentrations roughly in the range of 0.05 to 0.5 atomic percent relative to Lu. These properties make Lu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> :Ce a widely used scintillator in positron emission tomography, in particular. We have found that both the light output and decay time may be improved by a combination of optimized crystal growth atmosphere and co-doping with divalent cations such as Ca. Scintillation light output of ~38 800 photons/MeV has been achieved as well as scintillation decay time as short as 31 ns with no long components. The relationship between growth conditions, dopant concentration, decay time, and light output is well defined, thus allowing one to reliably "tune" the crystal to the desired combination of light output and decay time. Possible explanations of the underlying mechanism are being explored and include compensation of oxygen vacancies, alteration of the relative occupancies of the cerium lattice sites, and suppression of trapping centers. In addition to higher count-rate capability and better coincidence timing, the improved decay time is expected to be particularly advantageous for time-of-flight positron emission tomography. Also, phoswich detectors comprising "standard" LSO (~43 ns decay time) and "fast" LSO (~31 ns decay time) become an attractive alternative to typical phoswich designs that often suffer from problems of mismatched light outputs and indices of refraction or the absorption of one scintillator's light by the other.
Self-Assembled Fmoc-Peptides as a Platform for the Formation of Nanostructures and Hydrogels (2009)

Hydrogels are of great interest as a class of materials for tissue engineering, axonal regeneration, and controlled drug delivery, as they offer 3D interwoven scaffolds to support the growth of cells. Herein, we extend the family of the aromatic Fmoc-dipeptides with a library of new Fmoc-peptides, which include natural and synthetic amino acids with an aromatic nature. We describe the self-assembly of these Fmoc-peptides into various structures and characterize their distinctive molecular and physical properties. Moreover, we describe the fabrication of the bioactive RGD sequence into a hydrogel. This unique material offers new opportunities for developing cell-adhesive biomedical hydrogel scaffolds, as well as for establishing strategies to modify surfaces with bioactive materials.
Activity-centric scene synthesis for functional 3D scene modeling (2015)

We present a novel method to generate 3D scenes that allow the same activities as real environments captured through noisy and incomplete 3D scans. As robust object detection and instance retrieval from low-quality depth data is challenging, our algorithm aims to model semantically-correct rather than geometrically-accurate object arrangements. Our core contribution is a new scene synthesis technique which, conditioned on a coarse geometric scene representation, models functionally similar scenes using prior knowledge learned from a scene database. The key insight underlying our scene synthesis approach is that many real-world environments are structured to facilitate specific human activities, such as sleeping or eating. We represent scene functionalities through virtual agents that associate object arrangements with the activities for which they are typically used. When modeling a scene, we first identify the activities supported by a scanned environment. We then determine semantically-plausible arrangements of virtual objects -- retrieved from a shape database -- constrained by the observed scene geometry. For a given 3D scan, our algorithm produces a variety of synthesized scenes which support the activities of the captured real environments. In a perceptual evaluation study, we demonstrate that our results are judged to be visually appealing and functionally comparable to manually designed scenes.
EXPRESSION OF HUMAN CD59 IN TRANSGENIC PIG ORGANS ENHANCES ORGAN SURVIVAL IN AN EX VIVO XENOGENEIC PERFUSION MODEL1,2 (1996)

The serious shortage of available donor organs for patients with end stage organ failure who are in need of solid organ transplantation has led to a heightened interest in xenotransplantation. The major barrier to successful discordant xenotransplantation is hyperacute rejection. Hyperacute rejection results from the deposition of preformed antibodies that activate complement on the luminal surface of the vascular endothelium, leading to vessel occlusion and graft failure within minutes to hours. Endogenous membrane-associated complement inhibitors normally protect endothelial cells from autologous complement -- however, these molecules are species-restricted and therefore are ineffective at inhibiting activated xenogeneic complement. To address the pathogenesis of hyperacute rejection in the pig-to-human combination, F1 offspring were generated from a transgenic founder animal that was engineered to express the human terminal complement inhibitor hCD59. High-level cell surface expression of hCD59 was detected in the hearts and kidneys of these transgenic F1 animals, similar to expression levels in human kidney tissue. The hCD59 was expressed on both large vessel and capillary endothelium. Ex vivo perfusion experiments, using human blood as the perfusate, were performed with transgenic porcine hearts and kidneys to evaluate the ability of hCD59 to inhibit hyperacute rejection. These experiments demonstrated that transgenic organs expressing hCD69 resisted hyperacute rejection, as measured by increased organ function for both the hearts and the kidneys, as compared with control pig organs. Hearts from hCD59-expressing animals demonstrated a five-fold prolongation in function compared with controls, 109.8 +/- 20.7 min versus 21.2 +/- 2.9 min (P = 0.164). The hCD59-expressing kidneys also demonstrated significantly prolonged function at 157.8 +/- 27.0 min compared with 60.0 +/- 6.1 min for controls (P = 0.0174). Deposition of C9 neoantigen In the vasculature of porcine organs perfused with human blood was markedly reduced in organs expressing hCD59. These studies demonstrate that C5b-9 plays an important role in hyperacute rejection of a porcine organ perfused with human blood and suggest that donor pigs transgenic for hCD59 may be an integral component of successful clinical xenotransplantation.
Urban adaptation can roll back warming of emerging megapolitan regions (2014)

Modeling results incorporating several distinct urban expansion futures for the United States in 2100 show that, in the absence of any adaptive urban design, megapolitan expansion, alone and separate from greenhouse gas-induced forcing, can be expected to raise near-surface temperatures 1-2 °C not just at the scale of individual cities but over large regional swaths of the country. This warming is a significant fraction of the 21st century greenhouse gas-induced climate change simulated by global climate models. Using a suite of regional climate simulations, we assessed the efficacy of commonly proposed urban adaptation strategies, such as green, cool roof, and hybrid approaches, to ameliorate the warming. Our results quantify how judicious choices in urban planning and design cannot only counteract the climatological impacts of the urban expansion itself but also, can, in fact, even offset a significant percentage of future greenhouse warming over large scales. Our results also reveal tradeoffs among different adaptation options for some regions, showing the need for geographically appropriate strategies rather than one size fits all solutions.
Sufentanil pharmacokinetics in neurosurgical patients. (1989)

The effects of respiratory alkalosis and dehydration on the pharmacokinetics of sufentanil have been determined. Forty neurosurgical patients entered the study: group I (n = 20) had spinal surgery while group II (n = 20) had elective craniotomies. All patients received a single intravenous bolus of sufentanil (2 micrograms/kg) during induction of anesthesia. Patients in group II received furosemide (40 mg) and mannitol (1 g/kg) prior to surgery and were hyperventilated to a PaCO2 below 30 mmHg. The anesthetic management was identical in both groups. Arterial blood samples were collected to determine sufentanil concentrations (RIA), blood gases, pH, hematocrit and electrolytes. Patients in group II had significantly higher blood pH and urinary output when compared to group I (p less than 0.05). Plasma sufentanil concentrations were best fitted to a bi-exponential curve and the pharmacokinetic variables calculated using a curve stripping program (STRIPE). No significant differences were observed between groups regarding plasma sufentanil concentrations or pharmacokinetic parameters. Our results demonstrate that respiratory alkalosis and dehydration do not alter the pharmacokinetics of sufentanil after intravenous bolus administration.
Mutual Transcriptional Interference between RelA and Androgen Receptor (1996)

Cross-modulation between androgen receptor (AR) and NF-kappaB/Rel proteins was studied using various androgen- and NF-kappaB-regulated reporter genes under transient transfection conditions. In COS-1 cells, elevated expression of RelA (p65) repressed AR-mediated transactivation in a dose-dependent manner, whereas NFkappaB1 (p50), another major member of the NF-kappaB family, did not influence transactivation. The repression of AR appeared to involve the N-terminal region of the protein between residue 297 and the DNA-binding domain. RelA-mediated transrepression could not be overcome by increasing the amount of AR. Transcriptional interference between RelA and AR was mutual in that cotransfected AR was able to attenuate transactivation by RelA in a dose- and steroid-dependent fashion. An excess of RelA was able to rescue the repression to some extent. Immunological analyses of RelA and AR protein levels indicated that transrepression was not due to reciprocal decrease in their amounts. Neither did AR increase the concentration of IkappaBalpha, which can sequester and inactivate RelA. Electrophoretic mobility shift assays using extracts from cotransfected cells and purified recombinant proteins showed that AR and RelA did not significantly influence each other's DNA binding activity. Nevertheless, protein-protein interaction experiments demonstrated a weak association between AR and RelA. Collectively, these data suggest that the mutual repression in intact cells is due to formation of AR-RelA complexes that are held together by another partner or to competition for a coactivator required for transcription.
Cloning and expression of a rabbit cDNA encoding a serum-activated ethylisopropylamiloride-resistant epithelial Na+/H+ exchanger isoform (NHE-2) (1993)

A unique Na+/H+ exchanger isoform, NHE-2, was cloned and characterized. NHE-2 is a protein of 809 amino acids with a calculated size of 90,787. It exhibits overall amino acid identity of 50, 44, and 60% with other cloned mammalian Na+/H+ exchangers NHE-1, NHE-3, and NHE-4, respectively. Northern blot analysis of poly(A+) RNA isolated from rabbit ileum, kidney cortex, and kidney medulla using NHE-2 cDNA as a probe revealed messages of 5.2, 4.2, and 3.2 kilobases with relative abundance (in descending order) kidney medulla > kidney cortex > ileum. More detailed tissue distribution of message was performed by ribonuclease protection assay. NHE-2 was predominantly expressed in kidney, intestine, and adrenal gland with a small amount in skeletal muscle and trachea. Stable expression of NHE-2 in PS120 fibroblasts confirmed that NHE-2 is a functional Na+/H+ exchanger which is defined by amiloride-sensitive Na+-dependent alkalinization of acid-loaded cells. NHE-2 has the same Ki for amiloride inhibition as NHE-1 (1 microM) but is 25-fold more resistant to ethylisopropylamiloride inhibition than is NHE-1 (500 versus 20 nM). Like NHE-1, NHE-2 can be activated by serum. Expression of NHE-2 in a polarized human intestinal epithelial cell line, Caco-2 cells, results in functional expression of NHE-2 in the apical membrane. Thus, we conclude that NHE-2 is a candidate to be an apical membrane Na+/H+ exchanger in intestinal and renal epithelial cells.
Identification of two distinct regions of deletion at 6q in gastric carcinoma (1995)

Loss of heterozygosity (LOH) affecting the long arm of chromosome 6 has been found repeatedly in human cancers. Recently, our group reported that del(6)(q21-22-->qter) was the most consistent structural cytogenetic abnormality in gastric carcinomas. To determine more precisely the deleted region, we studied 51 tumors with 9 polymorphic markers on this chromosome arm. LOH of one or more markers was found in 39% of the tumors. LOH at region 6q22.3 was detected in 50% of informative tumors and at 6q26-q27 in 37% of informative tumors. By comparative analysis of LOH regions, we identified two separate regions of overlapped deletions at 6q, one between 6q16.3-q21 and 6q22.3-q23.1, another distal to 6q23-q24. A comparison of clinicopathologic features of gastric carcinomas with and without LOH at 6q revealed statistically significant or suggestive differences between LOH and young age of the patients and proximal location of the tumors. The two informative early gastric carcinomas both showed LOH at 6q. The occurrence of LOH at 6q was similar in all histological types. We conclude that two distinct regions at 6q appear to be involved in the early stages of gastric carcinogenesis.
A Road Map to Stable, Soluble, Easily Crystallized Pentacene Derivatives (2001)

[structure: see text] A series of 6,13-disubstituted pentacenes, in which the substituents are functionalized ethyne units, were synthesized and analyzed by X-ray crystallography. The resulting pentacene derivatives were highly soluble and oxidatively stable and exhibited a significant amount of pi-stacking in the crystal.
Stable Aqueous Dispersions of Noncovalently Functionalized Graphene from Graphite and their Multifunctional High-Performance Applications (2010)

We present a scalable and facile technique for noncovalent functionalization of graphene with 1-pyrenecarboxylic acid that exfoliates single-, few-, and multilayered graphene flakes into stable aqueous dispersions. The exfoliation mechanism is established using stringent control experiments and detailed characterization steps. Using the exfoliated graphene, we demonstrate highly sensitive and selective conductometric sensors (whose resistance rapidly changes >10,000% in saturated ethanol vapor), and ultracapacitors with extremely high specific capacitance (∼ 120 F/g), power density (∼ 105 kW/kg), and energy density (∼ 9.2 Wh/kg).
A Formal Total Synthesis of Epothilone A:  Enantioselective Preparation of the C1−C6 and C7−C12 Fragments1 (1998)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTA Formal Total Synthesis of Epothilone A: Enantioselective Preparation of the C1−C6 and C7−C12 Fragments1Richard E. Taylor, Gabriel M. Galvin, Kerry A. Hilfiker, and Yue ChenView Author Information Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 Cite this: J. Org. Chem. 1998, 63, 25, 9580–9583Publication Date (Web):November 18, 1998Publication History Received24 July 1998Published online18 November 1998Published inissue 1 December 1998https://pubs.acs.org/doi/10.1021/jo981461uhttps://doi.org/10.1021/jo981461ubrief-reportACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views780Altmetric-Citations29LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Anions,Ketones,Organic synthesis,Oxidation Get e-Alerts