gebhart/patrepeval huggingface dataset:
Synthesis of a new substrate analog of firefly luciferin. Active-site probe (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of a new substrate analog of firefly luciferin. Active-site probeLemuel J. Bowie, Vaclav Horak, and Marlene DeLucaCite this: Biochemistry 1973, 12, 10, 1845–1852Publication Date (Print):May 1, 1973Publication History Published online1 May 2002Published inissue 1 May 1973https://pubs.acs.org/doi/10.1021/bi00734a001https://doi.org/10.1021/bi00734a001research-articleACS PublicationsRequest reuse permissionsArticle Views177Altmetric-Citations9LEARN 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
Fast maximum intensity projection algorithm using shear warp factorization and reduced resampling (2002)

Maximal intensity projection (MIP) is routinely used to view MRA and other volumetric angiographic data. The straightforward implementation of MIP is ray casting that traces a volumetric data set in a computationally expensive manner. This article reports a fast MIP algorithm using shear warp factorization and reduced resampling that drastically reduced the redundancy in the computations for projection, thereby speeding up MIP by more than 10 times.
Comparison of multiple comparison methods for identifying differential gene expression in simulated and real papillary thyroid cancer microarray data (2009)

The difficulty of detecting differential gene expression in microarray data has existed for many years. Several correction procedures try to avoid the family-wise error rate in multiple comparison process, including the Bonferroni and Sidak single-step p-value adjustments, Holm's step-down correction method, and Benjamini and Hochberg's false discovery rate (FDR) correction procedure. Each multiple comparison technique has its advantages and weaknesses. We studied each multiple comparison method through numerical studies (simulations) and applied the methods to the real exploratory DNA microarray data, which detect of molecular signatures in papillary thyroid cancer (PTC) patients. According to our results of simulation studies, Benjamini and Hochberg step-up FDR controlling procedure is the best process among these multiple comparison methods and we discovered 1277 potential biomarkers among 54675 probe sets after applying the Benjamini and Hochberg's method to PTC microarray data.
Electrocatalytic hydrogenation of lignin models at Raney nickel and palladium-based electrodes (2000)

The electrocatalytic hydrogenation (ECH) of β-O-4 lignin model compounds has been carried out at constant current at Raney nickel and palladium-based cathodes in aqueous sodium hydroxide solution at temperatures ranging from 25 to 75°C. It was found that the hydrogenolysis of phenolic β-arylethyl-aryl ethers with one β-O-4 linkage takes place at both types of electrodes to give a mixture of phenolic compounds. The ECH of 1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)-1-ethanol (model 1) at Raney nickel gives guaiacol (9), acetovanillone (11b), alpha-methylvanillyl alcohol (12b), and products derived from their further hydrogenation. The β-O-4 bond is more difficult to cleave upon replacing one hydrogen of the methylene group of 1 by a hydroxymethyl group (see 2). However, model 4 with two β-O-4 linkages obtained by the introduction of an α-methylvanillyl group at the phenolic position of 1 is hydrogenolysed at the same rate as 1 at Raney nickel. Only the C-O aryl bond attached to the hydroxyethylphenol moiety is cleaved. At palladium, the hydrogenolysis of 1 requires only half of the theoretical amount of electricity due to the generation of chemisorbed hydrogen by dehydrogenation of 1 followed by hydrogenolysis of the resulting ketone. A general reaction scheme is proposed for the ECH of model 1.Key words: Lignins, lignin models, electrocatalytic hydrogenation, Raney nickel electrodes, palladium electrodes.
Structure-based analysis of the ultraspiracle protein and docking studies of putative ligands (2002)

The ultraspiracle protein (USP) is the insect ortholog of the mammalian retinoid X receptor (RXR). Fundamental questions concern the functional role of USP as the heterodimerization partner of insect nuclear receptors such as the ecdysone receptor. The crystallographic structures of the ligand binding domain of USPs of Heliothis virescens and Drosophila melanogaster solved recently show that helix 12 is locked in an antagonist conformation raising the question whether USPs could adopt an agonist conformation as observed in RXRα. In order to investigate this hypothesis, a homology model for USP is proposed that allows a structural analysis of the agonist conformation of helix 12 based on the sequence comparison with RXR. For USP, one of the main issues concerns its function and in particular whether its activity is ligand independent or not. The x-ray structures strongly suggest that USP can bind ligands. Putative ligands have therefore been docked in the USP homology model. Juvenile hormones and juvenile hormone analogs were chosen as target ligands for the docking study. The interaction between the ligand and the receptor are examined in terms of the pocket shape as well as in terms of the chemical nature of the residues lining the ligand binding cavity.
Octanol-Water Partition Coefficients of Simple Organic Compounds (1989)

Octanol-water partition coefficients (log P) for 611 simple organic compounds representing all principal classes have been retrieved from the literature. Available experimental details of measurement are documented from original articles. Pertinent thermodynamic relations are presented, with a discussion of direct and indirect methods of measurement. Reported log P data for each compound have been evaluated according to stated criteria, and recommended values (with uncertainty) are given.
Nucleotide sequence of thefadRgene, a multifunctional regulator of fatty acid metabolism inEscherichia coli (1988)

The Escherichia coli fadR gene is a multifunctional regulator of fatty acid and acetate metabolism. In the present work the nucleotide sequence of the 1.3 kb DNA fragment which encodes FadR has been determined. The coding sequence of the fadR gene is 714 nucleotides long and is preceded by a typical E. coli ribosome binding site and is followed by a sequence predicted to be sufficient for factor-independent chain termination. Primer extension experiments demonstrated that the transcription of the fadR gene initiates with an adenine nucleotide 33 nucleotides upstream from the predicted start of translation. The derived fadR peptide has a calculated molecular weight of 26,972. This is in reasonable agreement with the apparent molecular weight of 29,000 previously estimated on the basis of maxi-cell analysis of plasmid encoded proteins. There is a segment of twenty amino acids within the predicted peptide which resembles the DNA recognition and binding site of many transcriptional regulatory proteins.
SynergyFinder: a web application for analyzing drug combination dose–response matrix data (2017)

jing.tang@helsinki.fi.
Monoclonal antibodies distinguish phosphorylated and nonphosphorylated forms of neurofilaments in situ. (1983)

The immunocytochemical staining patterns of 37 neuron-specific monoclonal antibodies previously described fell into four groups: (i) anti-synapse-associated, (ii) anti-neurofibrillar, (iii) anti-perikaryonal-neurofibrillar, and (iv) a single antibody reactive with a widely distributed epitope that covered the patterns of groups ii and iii. Antibodies of groups ii, iii, and iv were shown to be specific to neurofilament triplet subunits, even though there was little overlap in staining patterns between groups ii and iii. We examined nine of these antibodies as to their ability to distinguish functional states of neurofilaments dependent upon phosphorylation. Upon digestion with phosphatase, electroblot staining of neurofilament components was abolished with the five antibodies from group ii, enhanced with the three antibodies from group iii, and unaffected with antibody iv. Immunocytochemical staining of Bouin-fixed paraffin sections of rat brain was unaffected by phosphatase pretreatment. With antibodies of group ii, digestion with trypsin also left staining unaffected, but when followed by digestion with phosphatase, staining was diminished with three out of five antibodies. In contrast, digestion with trypsin abolished all staining with each antibody from group iii. If followed by digestion with phosphatase, staining reappeared, but the group iii pattern was replaced by a group ii pattern. Staining of this pattern was again abolished upon a second treatment with trypsin. The antibody from group iv lost most of its groups ii and iii staining patterns when sections were digested with trypsin. The group ii pattern reappeared and, indeed, was enhanced upon a subsequent phosphatase treatment and was reduced again upon a second trypsin treatment. Staining by four out of five antibodies from group ii was inhibited by inorganic phosphate. The data indicate that certain nerve cell bodies, their dendrites, and at least proximal axons possess nonphosphorylated neurofilaments and that long fibers, including terminal axons, possess phosphorylated neurofilaments. We propose that phosphorylation may be a factor in stabilizing compacted forms of neurofilaments and that heterogeneity of the compacted structures may play a role in a possible multiplicity of function within individual nerve cells.
Performance of a high-intensity 508-gene circulating-tumor DNA (ctDNA) assay in patients with metastatic breast, lung, and prostate cancer. (2017)

LBA11516 The full, final text of this abstract will be available at abstracts.asco.org at 7:30 AM (EDT) on Saturday, June 3, 2017, and in the Annual Meeting Proceedings online supplement to the June 20, 2017, issue of the Journal of Clinical Oncology. Onsite at the Meeting, this abstract will be printed in the Saturday edition of ASCO Daily News.
Exposure of human ovarian carcinoma to cisplatin transiently sensitizes the tumor cells for liposome-mediated gene transfer. (1994)

Human ovarian carcinoma cells (line 2008) grown as subcutaneous solid tumor in the severe combined immunodeficient mouse can be transfected by directly injecting a plasmid DNA-liposome complex into the tumor (in situ lipofection). The level of reporter gene expression in the tumor cells was significantly elevated if the animal received a single i.p. injection of cisplatin 1 week before the lipofection. Sensitization of the tumor for lipofection peaked 1 week after cisplatin injection and declined thereafter. Cells exposed to low concentration of cisplatin in vitro for four to five doubling times also showed elevated sensitivity for lipofection in vitro. Cisplatin was the only anticancer drug tested that exhibited this activity. These results suggest a sequential combinational gene therapy protocol with cisplatin for the ovarian carcinoma.
Leydig-Cell Tumors Caused by an Activating Mutation of the Gene Encoding the Luteinizing Hormone Receptor (1999)

The receptor for luteinizing hormone and chorionic gonadotropin plays a major part in normal and abnormal reproductive function.1–4 In males, activation of the receptor regulates the development and function of Leydig cells.5 Testosterone secreted by Leydig cells promotes male sexual differentiation, pubertal androgenization, and fertility. The human luteinizing hormone receptor is a G protein–coupled receptor with a transmembrane domain composed of seven segments. Activation of the receptor by luteinizing hormone leads to activation of Gs, the G protein that is coupled to adenylyl cyclase, and to an increase in cyclic AMP (cAMP). High concentrations of luteinizing hormone . . .
MEROPS: the protease database (2002)

The MEROPS database (http://www.merops.ac.uk) has been redesigned to accommodate increased amounts of information still in pages of moderate size that load rapidly. The information on each PepCard, FamCard or ClanCard has been divided between several sub-pages that can be reached by use of navigation buttons in a frame at the top of the screen. Several important additions have also been made to the database. Amongst these are CGI searches that allow the user to find a peptidase by name, its MEROPS identifier or its human or mouse chromosome location. The user may also list all published tertiary structures for a peptidase clan or family, and search for peptidase specificity data by entering either a peptidase name, substrate or bond cleaved. The PepCards, FamCards and ClanCards now have literature pages listing about 10 000 key papers in total, mostly with links to MEDLINE. Many PepCards now include a protein sequence alignment and data table for matching human, mouse or rat expressed sequence tags. FamCards and ClanCards contain Structure pages showing diagrammatic representations of known secondary structures of member peptidases or family type examples, respectively. Many novel peptidases have been added to the database after being discovered in complete genomes, libraries of expressed sequence tags or data from high-throughput genomic sequencing, and we describe the methods by which these were found.
CD137 Enhancement of HPV Positive Head and Neck Squamous Cell Carcinoma Tumor Clearance (2014)

Standard-of-care cisplatin and radiation therapy (CRT) provides significant tumor control of human papillomavirus (HPV)-mediated head and neck squamous cell carcinomas (HNSCCs); this effectiveness depends on CRT-mediated activation of the patient's own immune system. However, despite good survival, patients suffer significant morbidity necessitating on-going studies to define novel therapies that alleviate this burden. Given the role of the immune system in tumor clearance, immune modulation may further potentiate the CRT-activated response while potentially decreasing morbidity. CD137, an inducible cell surface receptor found on activated T cells, is involved in differentiation and survival signaling in T cells upon binding of its natural partner (CD137L). A number of studies have shown the effectiveness of targeting this immune-stimulatory pathway in regards to tumor clearance. Here we test its role in HPV+ HNSCC tumor clearance using a previously characterized mouse model. We show that amplification of this stimulatory pathway synergizes with CRT for enhanced tumor clearance. Interestingly, tumor clearance is further potentiated by local tumor cell expression of CD137L.
Trans-cellular Propagation of Tau Aggregation by Fibrillar Species (2012)

Aggregation of the microtubule associated protein Tau is associated with several neurodegenerative disorders, including Alzheimer disease and frontotemporal dementia. In Alzheimer disease, Tau pathology spreads progressively throughout the brain, possibly along existing neural networks. However, it is still unclear how the propagation of Tau misfolding occurs. Intriguingly, in animal models, vaccine-based therapies have reduced Tau and synuclein pathology by uncertain mechanisms, given that these proteins are intracellular. We have previously speculated that trans-cellular propagation of misfolding could be mediated by a process similar to prion pathogenesis, in which fibrillar Tau aggregates spread pathology from cell to cell. However, there has been little evidence to demonstrate true trans-cellular propagation of Tau misfolding, in which Tau aggregates from one cell directly contact Tau protein in the recipient cell to trigger further aggregation. Here we have observed that intracellular Tau fibrils are directly released into the medium and then taken up by co-cultured cells. Internalized Tau aggregates induce fibrillization of intracellular Tau in these naive recipient cells via direct protein-protein contact that we demonstrate using FRET. Tau aggregation can be amplified across several generations of cells. An anti-Tau monoclonal antibody blocks Tau aggregate propagation by trapping fibrils in the extracellular space and preventing their uptake. Thus, propagation of Tau protein misfolding among cells can be mediated by release and subsequent uptake of fibrils that directly contact native protein in recipient cells. These results support the model of aggregate propagation by templated conformational change and suggest a mechanism for vaccine-based therapies in neurodegenerative diseases.
IL-13R(alpha)2, a decoy receptor for IL-13 acts as an inhibitor of IL-4-dependent signal transduction in glioblastoma cells. (2002)

Interleukin (IL)-4 and IL-13 share the type II IL-4 receptor for cell signaling. We show that despite expressing the necessary signaling components, glioblastoma cells failed to respond to either IL-4 or IL-13. This was in part because of the expression of a high-affinity IL-13-binding transmembrane protein IL-13R(alpha)2 that inhibited IL-13-mediated Stat6 activation by acting as a decoy receptor. In contrast, normal human astrocytes that did not express the IL-13R(alpha)2 gene efficiently induced Stat6 activation in response to both IL-4 and IL-13. Transient expression of the IL-13R(alpha)2 transgene in nonexpressing heterologous cells inhibited not only IL-13- but also IL-4-mediated signal transduction and Stat6-responsive gene expression. The inhibition was likely mediated through the physical interaction between the short intracellular domain of the IL-13R(alpha)2 protein and the cytoplasmic domain of the IL-4R(alpha) chain that harbors the Stat6 docking sites. Thus, IL-13R(alpha)2 acts as an inhibitor of IL-4-dependent signal transduction pathways via a novel mechanism that is independent of ligand binding.
Electrical Field and Temperature Model of Nonthermal Irreversible Electroporation in Heterogeneous Tissues (2009)

Nonthermal irreversible electroporation (NTIRE) is a new minimally invasive surgical technique that is part of the emerging field of molecular surgery, which holds the potential to treat diseases with unprecedented accuracy. NTIRE utilizes electrical pulses delivered to a targeted area, producing irreversible damage to the cell membrane. Because NTIRE does not cause thermal damage, the integrity of all other molecules, collagen, and elastin in the targeted area is preserved. Previous theoretical studies have only examined NTIRE in homogeneous tissues; however, biological structures are complex collections of diverse tissues. In order to develop electroporation as a precise treatment in clinical applications, realistic models are necessary. Therefore, the purpose of this study was to refine electroporation as a treatment by examining the effect of NTIRE in heterogeneous tissues of the prostate and breast. This study uses a two-dimensional finite element solution of the Laplace and bioheat equations to examine the effects of heterogeneities on electric field and temperature distribution. Three different heterogeneous structures were taken into account: nerves, blood vessels, and ducts. The results of this study demonstrate that heterogeneities significantly impact both the temperature and electrical field distribution in surrounding tissues, indicating that heterogeneities should not be neglected. The results were promising. While the surrounding tissue experienced a high electrical field, the axon of the nerve, the interior of the blood vessel, and the ducts experienced no electrical field. This indicates that blood vessels, nerves, and lactiferous ducts adjacent to a tumor treated with electroporation will survive, while the cancerous lesion is ablated. This study clearly demonstrates the importance of considering heterogeneity in NTIRE applications.
Evidence of large high frequency complete phononic band gaps in silicon phononic crystal plates (2008)

We show the evidence of the existence of large complete phononic band gaps (CPBGs) in two-dimensional phononic crystals (PCs) formed by embedding cylindrical air holes in a solid plate (slab). The PC structure is made by etching a hexagonal array of air holes through a freestanding plate of silicon. A fabrication process compatible with metal-oxide-semiconductor technology is used on silicon-on-insulator substrate to realize the PC devices. Measuring the transmission of elastic waves through eight layers of the hexagonal lattice PC in the ΓK direction, more than 30dB attenuation is observed at a high frequency; i.e., 134MHz, with a band gap to midgap ratio of 23%. We show that this frequency region matches very well with the expected CPBG found through theoretical calculations.
Role of colony stimulating factor‐1 (CSF‐1) and other lympho‐hematopoietic growth factors in mouse pre‐implantation development (1991)

Abstract Mouse pre‐implantation development appears to be under the control of paracrine and autocrine growth factors. The epithelium of the oviduct and the uterus together, with the population of macrophages and lymphocytes present in the reproductive tract from the onset of pregnancy, are thought to be the major sources of paracrine growth factors targeted to the developing embryos. Some of the growth factors are synthesized by both uterine epithelial cells and activated lympho‐hematopoietic cells, suggesting a partial overlap of the regulatory signals used by the reproductive and lympho‐hematopoietic systems. Such growth factors may be the long sought‐after mediators of the synchrony between the pre‐implantation embryo and the sex‐steroid hormone‐induced changes in the uterus.
Electromagnetic tracking for abdominal interventions in computer aided surgery (2006)

Electromagnetic tracking has great potential for assisting physicians in precision placement of instruments during minimally invasive interventions in the abdomen, since electromagnetic tracking is not limited by the line-of-sight restrictions of optical tracking. A new generation of electromagnetic tracking has recently become available, with sensors small enough to be included in the tips of instruments. To fully exploit the potential of this technology, our research group has been developing a computer aided, image-guided system that uses electromagnetic tracking for visualization of the internal anatomy during abdominal interventions. As registration is a critical component in developing an accurate image-guided system, we present three registration techniques: 1) enhanced paired-point registration (time-stamp match registration and dynamic registration); 2) orientation-based registration; and 3) needle shape-based registration. Respiration compensation is another important issue, particularly in the abdomen, where respiratory motion can make precise targeting difficult. To address this problem, we propose reference tracking and affine transformation methods. Finally, we present our prototype navigation system, which integrates the registration, segmentation, path-planning and navigation functions to provide real-time image guidance in the clinical environment. The methods presented here have been tested with a respiratory phantom specially designed by our group and in swine animal studies under approved protocols. Based on these tests, we conclude that our system can provide quick and accurate localization of tracked instruments in abdominal interventions, and that it offers a user-friendly display for the physician.