gebhart/patrepeval huggingface dataset:
Distinct combinations of NF-kappa B subunits determine the specificity of transcriptional activation. (1992)

The nuclear factor that binds to the kappa light-chain enhancer of B cells (NF-kappa B) is a transcription factor that regulates the expression of a variety of cellular and viral genes. NF-kappa B is composed of distinct subunits, and at least four independent genes (p105, p100, p65, and c-rel) have been isolated that encode related proteins that bind kappa B sites. Because it is possible that specific interactions of different subunits can allow selective gene activation, we have characterized the specificity of transcriptional activation by various combinations of these subunits. When tested alone, an approximately 49-kDa form (p49) of the p100 protein bound weakly to kappa B, but p49 associated with p65 to bind efficiently to this site. Furthermore, p49 acted in combination with either p65 or a Rel/VP16 fusion protein to activate kappa B-dependent transcription in Jurkat T leukemia cells. The p49/p65 or p49/Rel combination stimulated transcription mediated by the canonical kappa B site but did not stimulate reporter genes containing interleukin 2 receptor alpha or major histocompatibility complex kappa B elements, despite its ability to bind to these sites. Transactivation mediated by the p49/p100 and p65 NF-kappa B proteins is therefore sensitive to minor changes in the sequence of the kappa B site. Specificity determined by the association of NF-kappa B subunits provides a mechanism to selectively regulate variant kappa B sites associated with different cellular and viral genes.
Detailed Calculations of the Number of Distinct Sites Visited in Random Walk on Several Two-Dimensional Substrate Lattices (1971)

Calculations of the number of distinct sites visited in random walk on six physically different substrate lattices are carried out with exact, Monte Carlo and approximate analytical techniques. The fraction, λ, of the total possible sites, m, which are distinct is tabulated and plotted for all useful m for four lattice geometries and for 10≤m≤1000 for two more. The validity of this single valued characterization is examined and found to be very good, especially for larger m. Plots of parameters for functional application of the results are given.
Prostate cancer therapy: standard management, new options and experimental approaches. (2005)

The management of prostate cancer is one of the core tasks for urologists today. This review focuses on therapeutic options for the curative and palliative treatment of prostate cancer. Within the area of urological competence, radical prostatectomy remains the standard procedure for the curative treatment of localised prostate cancer. Recently, interest in minimally-invasive procedures such as brachytherapy, focused ultrasound and cryotherapy has increased considerably. Established palliative treatment strategies include hormonal treatment schemes as the gold standard. Chemotherapeutic regimes are used for the hormone refractory disease. In addition to both the standard and new urological therapeutic options, promising experimental systemic strategies for the generalised disease are presented in this review.
Congruence-Association Model and Experiments in Film Music: Toward Interdisciplinary Collaboration (2015)

Abstract The article draws attention to the value of objective measurement of both human responses and soundtracks for validating conjectures about the role of film music. Based on empirical research on film music as well as ideas from film theory and cognitive science, the author’s Congruence-Association Model with Working Narrative (CAM-WN) is introduced as a means for organizing ideas about the role of music in film. The application of CAM-WN to the problem of unattended film music is reviewed, and the notion of subjective silence is examined in the context of spectrographic representation of film music. While empirical research with human participants is also encouraged, the complexity of the enterprise is highlighted by a list of questions to consider in advance. Interdisciplinary collaboration is suggested as a means for overcoming the complexity of film-music behavioral research, though it is not a panacea. The Lund University Film Studies Department offers an important example in this direction.
PHOTODYNAMIC THERAPY OF SUBFOVEAL CHOROIDAL NEOVASCULARIZATION IN AGE-RELATED MACULAR DEGENERATION WITH VERTEPORFIN (2000)

Treatment of Age-Related Macular Degeneration with Photodynamic Therapy (TAP) Study Group Author Information
Receptor analogs and monoclonal antibodies that inhibit adherence of Bordetella pertussis to human ciliated respiratory epithelial cells. (1988)

The adherence of Bordetella pertussis to human respiratory cilia is critical to the pathogenesis of whooping cough. To explore the development of agents that could interrupt adherence, the structure of the receptor on the ciliary surface was investigated. Using an in vitro adherence assay to human ciliated epithelial cells, galactose, lactose, and complex carbohydrates containing lactose eliminated adherence when preincubated with the bacteria. 10(-2) M galactose eluted adherent bacteria from cilia. B. pertussis and its two purified adhesins bound specifically to natural lactose-containing glycolipids in a TLC assay. mAbs to eukaryotic glycoconjugates with specificity for substituted galactose-glucose moieties blocked adherence when preincubated with ciliated cells. The carbohydrates that serve as receptors for B. pertussis on human cilia are galactose-glucose-containing glycolipids. Receptor analogs and anti-receptor antibodies effectively block adherence of B. pertussis to cilia and thus should be considered candidates for therapeutic intervention against disease.
The UV absorption spectrum of C60 (buckminsterfullerene): A narrow band at 3860 Å (1987)

The absorption spectrum of the special C60 cluster buckminsterfullerene has been studied in a supersonic beam by laser depletion of the cold van der Waals complexes of C60 with benzene and methylene chloride. Both complexes were found to display a single, isolated absorption band in the near ultraviolet superimposed on a structureless absorption continuum. For the methylene chloride complex this feature is centered at 3860 Å, and is roughly 50 cm−1 wide. In the benzene van der Waals cluster, the corresponding feature is located at 3863 Å, and has a similar width. This spectrum is tentatively assigned to the 0–0 band of the lowest 1T1u←1Ag (LUMO+1←HOMO) transition of a truncated icosahedral carbon shell structure, broadened by coupling to the underlying quasicontinuum of ground state vibrational levels.
Incidence and Prevalence of Idiopathic Pulmonary Fibrosis (2006)

Our results suggest that idiopathic pulmonary fibrosis is probably more common in the United States than previously reported.
Rhabdomyolysis and acute renal failure resulting from alcohol and drug abuse (2000)

Rhabdomyolysis is a common cause of acute renal failure (ARF) associated with drug misuse. Abuse of the gel formulation of temazepam has been a particular problem in the West of Scotland. We performed a retrospective review of dialysis-dependent ARF from rhabdomyolysis and drug misuse in the West of Scotland, 1986-1997. We identified 76 patients, of whom 87% were male. Seventeen cases occurred in the first 6 years, compared with 59 in the subsequent 6 years. Median age was 32. Thirty cases followed intravenous drug misuse, 46 followed oral drug misuse. The substances most frequently misused were alcohol (54%), heroin (24%) and parenteral temazepam (17%). The temazepam cases all followed the introduction of the gel formulation. Three out of 4 patients requiring limb amputation had injected temazepam. Of intravenous drug misusers tested, 72% were hepatitis-C-positive. Some 43% of patients had deprivation scores in the worst category. ARF due to rhabdomyolysis from substance misuse is increasing in our area. Alcohol is frequently responsible. The introduction of the gel formulation of temazepam has contributed to the increase. Those at risk in this study were young, male, had a high incidence of hepatitis C and lived in the most deprived areas.
Direct delivery of exogenous MHC class I molecule-binding oligopeptides to the endoplasmic reticulum of viable cells (1997)

After brief incubation of cells with fluorescein-conjugated peptides that bind major histocompatibility complex (MHC) class I molecules, peptides were detected within the endoplasmic reticulum (ER) by microscopy or by binding to radiolabeled class I molecules. ER delivery of a nonfluorescent peptide was demonstrated using a mAb highly specific for the peptide-class I molecule complex. ER localization of peptides: (i) required expression of appropriate class I molecules in the ER but not on the cell surface, (ii) was diminished by expression of TAP, the MHC-encoded cytosol to ER peptide transporter, and (iii) was blocked by pinocytosis inhibitors but not by brefeldin A. These findings demonstrate the existence of a pathway, likely vesicular in nature, that conveys small extracellular substances to the ER without traversing the Golgi complex or the cytosol. This pathway contributes to the loading of exogenous peptides to MHC class I molecules, but its evolutionary significance may lie in other cellular processes, such as maintaining ER homeostasis or signaling by extracellular substances.
Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis (2004)

Summary The CBF cold response pathway has a prominent role in cold acclimation. The pathway includes action of three transcription factors, CBF1, 2 and 3 (also known as DREB1b, c and a, respectively), that are rapidly induced in response to low temperature followed by expression of the CBF-targeted genes (the CBF regulon) that act in concert to increase plant-freezing tolerance. The results of transcriptome profiling and mutagenesis experiments, however, indicate that additional cold response pathways exist and may have important roles in life at low temperature. To further understand the roles that the CBF proteins play in configuring the low temperature transcriptome and to identify additional transcription factors with roles in cold acclimation, we used the Affymetrix GeneChip containing probe sets for approximately 24,000 Arabidopsis genes to define a core set of cold-responsive genes and to determine which genes were targets of CBF2 and 6 other transcription factors that appeared to be coordinately regulated with CBF2. A total of 514 genes were placed in the core set of cold-responsive genes, 302 of which were upregulated and 212 downregulated. Hierarchical clustering and bioinformatic analysis indicated that the 514 cold-responsive transcripts could be assigned to one of seven distinct expression classes and identified multiple potential novel cis-acting cold-regulatory elements. Eighty-five cold-induced genes and eight cold-repressed genes were assigned to the CBF2 regulon. An additional nine cold-induced genes and 15 cold-repressed genes were assigned to a regulon controlled by ZAT12. Of the 25 core cold-induced genes that were most highly upregulated (induced over 15-fold), 19 genes (84%) were induced by CBF2 and another two genes (8%) were regulated by both CBF2 and ZAT12. Thus, the large majority (92%) of the most highly induced genes belong to the CBF and ZAT12 regulons. Constitutive expression of ZAT12 in Arabidopsis caused a small, but reproducible, increase in freezing tolerance, indicating a role for the ZAT12 regulon in cold acclimation. In addition, ZAT12 downregulated the expression of the CBF genes indicating a role for ZAT12 in a negative regulatory circuit that dampens expression of the CBF cold response pathway.
High Throughput Synthesis of Peptide α-Thioesters Through the Use of “Volatilizable” Support (2008)

ADVERTISEMENT RETURN TO ISSUEReportNEXTHigh Throughput Synthesis of Peptide α-Thioesters Through the Use of "Volatilizable" SupportYangmei Li†‡, Yongping Yu§†, Marc Giulianotti‡, and Richard A. Houghten*†‡View Author Information College of Pharmaceutical Science, Zhejiang University, Hangzhou, P. R. China 310058, Torrey Pines Institute for Molecular Studies, 3550 General Atomics Ct, San Diego, California 92121 and 5775 Old Dixie Highway, Fort Pierce, Florida 34946* Corresponding author. E-mail: [email protected]. Fax: (+1)858-455-3804.†Zhejiang University.‡Torrey Pines Institute for Molecular Studies.§E-mail: [email protected]. Fax: (+86)571-88208452.Cite this: J. Comb. Chem. 2008, 10, 5, 613–616Publication Date (Web):August 19, 2008Publication History Received3 May 2008Published online19 August 2008Published inissue 8 September 2008https://pubs.acs.org/doi/10.1021/cc800076bhttps://doi.org/10.1021/cc800076bbrief-reportACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views778Altmetric-Citations13LEARN 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 optionsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Monomers,Organic polymers,Peptides and proteins,Silica,Solid phase synthesis Get e-Alerts
Spatial Aliasing in Spherical Microphone Arrays (2007)

Performance of microphone arrays at the high-frequency range is typically limited by aliasing, which is a result of the spatial sampling process. This paper presents analysis of aliasing for spherical microphone arrays, which have been recently studied for a range of applications. The paper presents theoretical analysis of spatial aliasing for various sphere sampling configurations, showing how high-order spherical harmonic coefficients are aliased into the lower orders. Spatial antialiasing filters on the sphere are then introduced, and the performance of spatially constrained filters is compared to that of the ideal antialiasing filter. A simulation example shows how the effect of aliasing on the beam pattern can be reduced by the use of the antialiasing filters
Piecewise-consistent color mappings of images acquired under various conditions (2009)

Many applications in computer vision require comparisons between two images of the same scene. Comparison applications usually assume that corresponding regions in the two images have similar colors. However, this assumption is not always true. One way to deal with this problem is to apply a color mapping to one of the images. In this paper we address the challenge of computing color mappings between pairs of images acquired under different acquisition conditions, and possibly by different cameras. For images taken from different viewpoints, our proposed method overcomes the lack of pixel correspondence. For images taken under different illumination, we show that no single color mapping exists, and we address and solve a new problem of computing a minimal set of piecewise color mappings. When both viewpoint and illumination vary, our method can only handle planar regions of the scene. In this case, the scene planar regions are simultaneously co-segmented in the two images, and piecewise color mappings for these regions are calculated. We demonstrate applications of the proposed method for each of these cases.
Synthesis of ω-Phthalimidoalkylphosphonates (1994)

Diethyl phthalimidoalkylphosphonates were synthesized by the reaction of diethyl bromoalkylphosphonates with N-(tert-butyldimethylsilyl)phthalimide in the presence of tetrabutylammonium fluoride.
Antigen-Fixed Leukocytes Tolerize Th2 Responses in Mouse Models of Allergy (2011)

Allergic diseases, including asthma and food allergies, are an increasing health concern. Immunotherapy is an effective therapeutic approach for many allergic diseases but requires long dose escalation periods and has a high risk of adverse reactions, particularly in food allergy. New methods to safely induce Ag-specific tolerance could improve the clinical approach to allergic disease. We hypothesized that Ag-specific tolerance induced by the i.v. injection of Ags attached to the surface of syngeneic splenic leukocytes (Ag-coupled splenocytes [Ag-SPs]) with the chemical cross-linking agent ethylene-carbodiimide, which effectively modulate Th1/Th17 diseases, may also safely and efficiently induce tolerance in Th2-mediated mouse models of allergic asthma and food allergy. Mice were tolerized with Ag-SP before or after initiation of OVA/alum-induced allergic airway inflammation or peanut-induced food allergy. The effects on disease pathology and Th2-directed cytokine and Ab responses were studied. Ag-SP tolerance prevented disease development in both models and safely tolerized T cell responses in an Ag-specific manner in presensitized animals. Prophylactically, Ag-SP efficiently decreased local and systemic Th2 responses, eosinophilia, and Ag-specific IgE. Interestingly, Ag-SP induced Th2 tolerance was found to be partially dependent on the function of CD25(+) regulatory T cells in the food allergy model, but was regulatory T cell independent in the model of allergic airway inflammation. We demonstrate that Ag-SP tolerance can be rapidly, safely, and efficiently induced in murine models of allergic disease, highlighting a potential new Ag-specific tolerance immunotherapy for Th2-associated allergic diseases.
Uptake Characteristics of Oligonucleotides in the Isolated Rat Liver Perfusion System (1996)

The objective of this study was to examine the hepatic disposition characteristics of 20-mer model phosphodiester oligonucleotide (PO) and its partially phosphorothioated (PS3) and fully phosphorothioated (PS) derivatives in the single-pass isolated rat liver perfusion system. [32P]-labeled oligonucleotides were momentarily introduced into this system through the portal vein as a bolus input mode, and the venous outflow patterns were evaluated using statistical moment analysis. The apparent volumes of distribution of these oligonucleotides were greater than those of reference substances for vascular space (erythrocytes) and extracellular space (human serum albumin), indicating a significant interaction between oligonucleotides and the liver. Significant hepatic uptake of oligonucleotides was also observed. About 20%, 36%, and 52% of the injected dose (3 micrograms/rat) was taken up by the liver during a single passage after bolus injection of PO, PS3, and PS, respectively. In the case of PS injection, slow efflux from the liver was observed in the latter phase of perfusion. This suggests that the hepatic uptake process of these oligonucleotides greatly depended on their types. The results of collagenase perfusion experiments suggest that PS3 oligonucleotides were taken up by both liver parenchymal and nonparenchymal cells. The amount of total recovery in the liver decreased substantially by coadministration of polyinosinic acid, dextran sulfate, polycytidic acid and 4-acetamido-4'-isothiocyano-stilbene-2,2'-disulfonic acid. This suggests that PS3 was taken up by the liver as an anionic molecule in a nonspecific manner.
Allorestricted T cells with specificity for the FMNL1-derived peptide PP2 have potent antitumor activity against hematologic and other malignancies (2007)

Cell-based immunotherapy in settings of allogeneic stem cell transplantation or donor leukocyte infusion has curative potential, especially in hematologic malignancies. However, this approach is severely restricted due to graft-versus-host disease (GvHD). This limitation may be overcome if target antigens are molecularly defined and effector cells are specifically selected. We chose formin-related protein in leukocytes 1 (FMNL1) as a target antigen after intensive investigation of its expression profile at the mRNA and protein levels. Here, we confirm restricted expression in peripheral blood mononuclear cells (PBMCs) from healthy donors but also observe overexpression in different leukemias and aberrant expression in transformed cell lines derived from solid tumors. We isolated allorestricted T-cell clones expressing a single defined TCR recognizing a particular HLA-A2-presented peptide derived from FMNL1. This T-cell clone showed potent antitumor activity against lymphoma and renal cell carcinoma cell lines, Epstein-Barr virus (EBV)-transformed B cells, and primary tumor samples derived from patients with chronic lymphocytic leukemia (CLL), whereas nontransformed cells with the exception of activated B cells were only marginally recognized. Allorestricted TCRs with specificity for naturally presented FMNL1-derived epitopes may represent promising reagents for the development of adoptive therapies in lymphoma and other malignant diseases.
Minimal Important Difference (MID) of the Dermatology Life Quality Index (DLQI): Results from patients with chronic idiopathic urticaria (2005)

An MID for the DLQI in the range of 2.24 to 3.10 is recommended in interpreting results for patients with CIU.
Conservation in hedgehog signaling: induction of a chicken patched homolog by Sonic hedgehog in the developing limb (1996)

Hedgehog genes have been implicated in inductive signaling during development in a variety of organisms. A key element of the hedgehog signaling system is encoded by the gene patched. In Drosophila hedgehog regulates gene expression by antagonizing the action of patched. In addition, patched is itself a transcriptional target of hedgehog signaling. We have isolated a chicken patched homolog and find it to be strongly expressed adjacent to all tissues where members of the hedgehog family are expressed. As in Drosophila, ectopic expression of Sonic hedgehog leads to ectopic induction of chicken Patched. Based on this regulatory conservation, vertebrate Patched is likely to be directly downstream of Sonic hedgehog signaling. An important role of Sonic hedgehog is the regulation of anterior/posterior pattern in the developing limb bud. Since Patched is directly downstream of the hedgehog signal, the extent of high level Patched expression provides a measure of the distance that Sonic hedgehog diffuses and directly acts. On this basis, we find that Sonic hedgehog directly acts as a signal over only the posterior third of the limb bud. During limb patterning, secondary signals are secreted in both the mesoderm (e.g. Bone Morphogenetic Protein-2) and apical ectodermal ridge (e.g. Fibroblast Growth Factor-4) in response to Sonic hedgehog. Thus knowing which is the direct target tissue is essential for unraveling the molecular patterning of the limb. The expression of Patched provides a strong indication that the mesoderm and not the ectoderm is the direct target of Sonic hedgehog signaling in the limb bud. Finally we demonstrate that induction of Patched requires Sonic hedgehog but, unlike Bone Morphogenetic Protein-2 and Hox genes, does not require Fibroblast Growth Factor as a co-inducer. It is therefore a more direct target of Sonic hedgehog than previously reported patterning genes.