gebhart/patrepeval huggingface dataset:
Fluorescent Nanosensors for Intracellular Chemical Analysis:  Decyl Methacrylate Liquid Polymer Matrix and Ion-Exchange-Based Potassium PEBBLE Sensors with Real-Time Application to Viable Rat C6 Glioma Cells (2001)

Fluorescent spherical nanosensors, or PEBBLEs (probes encapsulated by biologically localized embedding), in the 500 nm-1 microm size range have been developed using decyl methacrylate as a matrix. A general scheme for the polymerization and introduction of sensing components creates a matrix that allows for the utilization of the highly selective ionophores used in poly(vinyl chloride) and decyl methacrylate ion-selective electrodes. We have applied these optically silent ionophores to fluorescence-based sensing by using ion-exchange and highly selective pH chromoionophores. This allows the tailoring of selective submicrometer sensors for use in intracellular measurements of important analytes for which selective enough fluorescent probes do not exist. The protocol for sensor development has been worked out for potassium sensing. It is based on the BME-44 ionophore (2-dodecyl-2-methyl-1,3-propanediylbis[N-[5'nitro(benzo-15-crown-5)-4'-yl]carbamate]). The general scheme should work for any available ionophore used in PVC or decyl methacrylate ion-selective electrodes, with minor adjustments to account for differences in ionophore charge and analyte binding constant. The reversible and highly selective sensors developed have a subsecond response time and an adjustable dynamic range. Applications to live C6 glioma cells demonstrate their utility; the intracellular potassium activity is followed in real time upon extracellular administration of kainic acid.
Natural-like Replication of an Unnatural Base Pair for the Expansion of the Genetic Alphabet and Biotechnology Applications (2013)

We synthesized a panel of unnatural base pairs whose pairing depends on hydrophobic and packing forces and identify dTPT3-dNaM, which is PCR amplified with a natural base pair-like efficiency and fidelity. In addition, the dTPT3 scaffold is uniquely tolerant of attaching a propargyl amine linker, resulting in the dTPT3(PA)-dNaM pair, which is amplified only slightly less well. The identification of dTPT3 represents significant progress toward developing an unnatural base pair for the in vivo expansion of an organism's genetic alphabet and for a variety of in vitro biotechnology applications where it is used to site-specifically label amplified DNA, and it also demonstrates for the first time that hydrophobic and packing forces are sufficient to mediate natural-like replication.
Generation and Study of the Reactivity of α-Ammonium Distonic Radical Cations in Solution (1996)

Peer reviewed: Yes
Intranasal administration of acetylcholinesterase inhibitors (2008)

This short review outlines the rationale, challenges, and opportunities for intranasal acetylcholinesterases, in particular galantamine. An in vitro screening model facilitated the development of a therapeutically viable formulation. In vivo testing confirmed achievement of therapeutically relevant drug levels that matched or exceeded those for oral dosing, with a dramatic reduction in undesired emetic responses. Intranasal drug delivery is an effective option for the treatment of Alzheimer's disease and other central nervous system disorders.
Role of the alpha 5 beta 1 integrin receptor in the proliferative response of quiescent human melanoma cells to fibronectin. (1992)

The possible mitogenic activity of fibronectin (FN) in human primary and metastatic melanoma lines and clones and the involvement of integrins in mediating this effect were evaluated. Quescent human melanoma cells cultured in serum-free medium proliferated in a dose- and time-dependent fashion to immobilized FN as indicated by [3H]thymidine incorporation, increment of cell number, and cell cycle analysis. This response to FN was observed with tumor clones isolated from a subcutaneous metastasis and with primary or metastatic melanomas from different patients, but only when tumor cells expressed the alpha 5 subunit of the FN receptor (i.e., VLA-5). Proliferation to FN by a primary tumor (Me4405) expressing all FN receptors and by a tumor clone (2/60) lacking only the alpha 4 subunit was inhibited by monoclonal antibodies to the alpha 5 and beta 1 but not by monoclonal antibodies to other subunits of FN receptors. Mapping of FN regions responsible for the proliferative signal was performed by stimulating melanoma cells with different FN proteolytic fragments and indicated that a significant mitogenic signal was provided by the M(r) 120,000 alpha-chymotrypsin fragment containing the Arg-Gly-Asp sequence. The proliferation of melanoma cells to FN and to FN fragments was also significantly inhibited by peptides containing the Arg-Gly-Asp sequence. These data indicate that FN can stimulate the proliferation of quiescent melanoma cells and that integrins as alpha 5 beta 1 are involved in the response of tumor cells to this extracellular matrix protein.
The metabolic pathway collection: an update (1997)

The Metabolic Pathway Collection from EMP is an extraction of data from the larger Enzymes and Metabolic Pathways database (EMP). This extraction has been made publicly available in the hope that others will find it useful for a variety of purposes. The original release in October 1995 contained 1814 distinct pathways. The current collection contains 2180. Metabolic reconstructions for the first completely sequenced organisms-Haemophilus influenzae,Mycoplasma genitalium,Saccharomyces cerevisiaeandMethanococcus janaschii-are all included in the current release. All of the pathways in the collections are available as ASCII files in the form generated by the main curator, Evgeni Selkov. In addition, we are offering a more structured encoding of a subset of the collection; our initial release of this subcollection includes all of the pathways inMycoplasma genitalium, and we ultimately intend to offer the entire collection in this form as well.
Advances in single-beacon one-way-travel-time acoustic navigation for underwater vehicles (2012)

This paper reports the formulation and evaluation of a centralized extended Kalman filter designed for a novel navigation system for underwater vehicles. The navigation system employs Doppler sonar, depth sensors, synchronous clocks, and acoustic modems to achieve simultaneous acoustic communication and navigation. The use of a single moving reference beacon eliminates the requirement for the underwater vehicle to remain in a bounded navigable area; the use of underwater modems and synchronous clocks enables range measurements based on one-way time-of-flight information from acoustic data-packet broadcasts. The acoustic data packets are broadcast from a single, moving reference beacon and can be received simultaneously by multiple vehicles within acoustic range. We report results from a simulated deep-water survey and real field data collected from an autonomous underwater vehicle survey in 4000 m of water on the southern Mid-Atlantic Ridge with an independent long-baseline navigation system for ground truth.
Leukotriene B4 Is a Physiologically Relevant Endogenous Peroxisome Proliferator-activated Receptor-α Agonist (2010)

Peroxisome proliferator-activated receptors (PPARs) are nuclear transcription factors that play central roles in metabolism and inflammation. Although a variety of compounds have been shown to activate PPARs, identification of physiologically relevant ligands has proven difficult. In silico studies of lipid derivatives reported here identify specific 5-lipoxygenase products as candidate physiologically relevant PPAR-alpha activators. Subsequent studies show both in vitro and in a murine model of inflammation that 5-lipoxygenase stimulation induces PPAR-alpha signaling and that this results specifically from production of the inflammatory mediator and chemoattractant leukotriene B(4) (LTB(4)). Activation of PPAR-alpha is a direct effect of intracellularly generated LTB(4) binding to the nuclear receptor and not of secreted LTB(4) acting via its cell-surface receptors. Activation of PPAR-alpha reduces secretion of LTB(4) by stimulating degradation of this fatty acid derivative. We also show that the LTB(4) precursors leukotriene A(4) (LTA(4)) and 5-hydroperoxyeicosatetrenoic acid (5-HPETE) activate PPAR-alpha but have no significant endogenous effect independent of conversion to LTB(4). We conclude that LTB(4) is a physiologically relevant PPAR-alpha activator in cells of the immune system. This, together with previous findings, demonstrates that different types of lipids serve as endogenous PPAR-alpha ligands, with the relevant ligand varying between functionally different cell types. Our results also support the suggestion that regulation of inflammation may involve balancing proinflammatory effects of LTB(4), exerted through cell-surface receptors, and anti-inflammatory effects exerted through PPAR-alpha activation.
Synthesis and structure‐property relationship of new donor–acceptor‐type conjugated monomers and polymers on the basis of thiophene and benzothiadiazole (2001)

Abstract We have synthesized three new donor–acceptor‐type monomers to achieve soluble and processable low‐band gap polymers, 4,7‐bis(4‐octyl‐2‐thienyl)‐2,1,3‐benzothiadiazole (B4TB), 4,7‐bis(3‐octyl‐2‐thienyl)‐2,1,3‐benzothiadiazole (B3TB), and 4‐(3‐octyl‐2‐thienyl)‐7‐(4‐octyl‐2‐thienyl)‐2,1,3‐benzothiadiazole (B34TB), by the Suzuki coupling reaction. Using B4TB and B3TB, two soluble high molecular weight regioregular head‐to‐head and tail‐to‐tail polymers poly[4,7‐bis(4‐octyl‐2‐thienyl)‐2,1,3‐ benzothiadiazole] (PB4TB) and poly[4,7‐bis(3‐octyl‐2‐thienyl)‐2,1,3‐benzothiadiazole] (PB3TB) were prepared via iron(III) chloride‐mediated oxidative polymerization. The structures of the polymers were confirmed by 1 H and 13 C NMR, and the molecular weights were determined by size exclusion chromatography. The optical properties (absorbance and fluorescence) of the monomers and polymers were studied and compared with unsubstituted analogues. The monomers and polymers bearing octyl substituents on the thiophene rings pointing away from the benzothiadiazole units (B4TB and PB4TB) possess a more planar structure, and their optical spectra appear redshifted as compared with those having the octyl chain nearer to the benzothiadiazole (B3TB and PB3TB). The optical band gaps of PB3BT ( E g = 2.01 eV) and PB4BT ( E g = 1.96 eV), however, are at much higher energy levels than that of the unsubstituted electrochemically polymerized PBTB material ( E g = 1.1–1.2 eV) as a result of steric effects of the octyl chains. The electrochemical properties of the monomers and polymers were examined using cyclic voltammetry and reflect the effect of alkyl substitution. B4TB and PB4TB were oxidized at a lower potential than B3TB and PB3TB, whereas their reduction potentials were less negative. The electrochemical band gap calculated from the onset of the reduction and oxidation process agreed with the optical band gap calculated from the absorption edges. © 2001 John Wiley &amp; Sons, Inc. J Polym Sci Part A: Polym Chem 40: 251–261, 2002
Cytokine concentration in serum of lupus erythematosus patients: the effect on acute phase response. (1997)

In order to get a better insight into cytokine network regulation in systemic lupus erythematosus (SLE), we analyzed levels of interleukin-10 (IL-10), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-alpha), and interferon-gamma (IFN-gamma) in the sera from 36 SLE patients. Moreover, C-reactive protein (CRP), alpha-1-acid-glycoprotein (AGP), and alpha-1-antichymotripsin (ACT) serum levels were evaluated. Serum levels of IL-10 and IL-6 were significantly increased when compared with healthy controls. TNF-alpha and IFN-gamma did not differ from normal values. We established the relationship between IL-10 and IL-6 as well as between IL-10 and TNF-alpha. None of the analyzed cytokines correlated with the acute phase protein levels. Based on the obtained data, we conclude that IL-10 may play the superior regulating role in SLE. A lack of correlation between the cytokines and acute phase proteins suggests their independence from cytokine regulation.
Interaction of the Cytosolic Domains of sorLA/LR11 with the Amyloid Precursor Protein (APP) and β-Secretase β-Site APP-Cleaving Enzyme (2006)

sorLA is a recently identified neuronal receptor for amyloid precursor protein (APP) that is known to interact with APP and affect its intracellular transport and processing. Decreased levels of sorLA in the brain of Alzheimer's disease (AD) patients and elevated levels of amyloid-beta peptide (Abeta) in sorLA-deficient mice point to the importance of the receptor in this neurodegenerative disorder. We analyzed APP cleavage in an APP-shedding assay and found that both sorLA and, surprisingly, a sorLA tail construct inhibited APP cleavage in a beta-site APP-cleaving enzyme (BACE)-dependent manner. In line with this finding, sorLA and the sorLA tail significantly reduced secreted Abeta levels when BACE was overexpressed, suggesting that sorLA influences beta-cleavage. To understand the effect of sorLA on APP cleavage by BACE, we analyzed whether sorLA interacts with APP and/or BACE. Because both full-length sorLA and sorLA C-terminal tail constructs were functionally relevant for APP processing, we analyzed sorLA-APP for a potential cytoplasmatic interaction domain. sorLA and C99 coimmunoprecipitated, pointing toward the existence of a new cytoplasmatic interaction site between sorLA and APP. Moreover, sorLA and BACE also coimmunoprecipitate. Thus, sorLA interacts both with BACE and APP and might therefore directly affect BACE-APP complex formation. To test whether sorLA impacts BACE-APP interactions, we used a fluorescence resonance energy transfer assay to evaluate BACE-APP interactions in cells. We discovered that sorLA significantly reduced BACE-APP interactions in Golgi. We postulate that sorLA acts as a trafficking receptor that prevents BACE-APP interactions and hence BACE cleavage of APP.
Software implementations of the Q-Coder (1988)

The Q-Coder is an important new development in arithmetic coding. It combines a simple but efficient arithmetic approximation for the multiply operation, a new formalism which yields optimally efficient hardware and software implementations, and a new technique for estimating symbol probabilities which matches the performance of any method known. This paper describes implementations of the Q-Coder following both the hardware and software paths. Detailed flowcharts are given.
Decomposition and cycloaddition reactions of some bis(azodicarbonyl) compounds (1975)

During oxidation of 1,5-dibenzoylcarbonohydrazide and 1,6-dibenzoyloxalohydrazide with N-bromosuccinimide and pyridine evidence was obtained for the formation of the corresponding bisazo-compounds (4a and b). Both oxidations yielded the oxadiazolone (6), which was the main product in the former. The oxalohydrazide reaction also gave minor products, perhaps attributable to the intermediacy of benzoyldi-imide. Oxidation of 1,7-dibenzoylmalonohydrazide led to intractable mixtures.Oxidation of 1,8-dibenzoylsuccino- and 1,10-dibenzoyladipo-hydrazides and of the bisethoxycarbonyl and dipivaloyl derivatives of terephthalohydrazide gave the fairly stable bisazo-compounds (5a–d) which could be trapped as the meso- and racemic mixture of bisadducts with cyclopentadiene (7a–d). The stereochemical possibilities for the concerted rearrangement of such adducts to bis-1,3,4-oxadiazines are fully discussed. In the adducts (7a and b) only participation of the outer (benzoyl) group and in the ester adduct (7c) only participation of the inner (tetraphthaloyl) group was observed, a diastereomeric pair of structures being produced in each case. The dipivaloyl adduct (7d) showed all three possible modes of isomerisation, utilising both inner and outer acyl groups; one of the pair of diastereoisomers formed was isolated pure in each case.
Non‐invasive ventilation improves peripheral oxygen saturation and reduces fatigability of quadriceps in patients with COPD (2009)

BV improved SpO(2) and reduced the fatigability of the quadriceps muscle in patients with severe COPD. These results support the need for further evaluation of BV as adjunct during high-intensity strength exercise training in these patients.
The human A33 antigen is a transmembrane glycoprotein and a novel member of the immunoglobulin superfamily (1997)

The mAb A33 detects a membrane antigen that is expressed in normal human colonic and small bowel epithelium and > 95% of human colon cancers. It is absent from most other human tissues and tumor types. The murine A33 mAb has been shown to target colon cancer in clinical trials, and the therapeutic potential of a humanized antibody is currently being evaluated. Using detergent extracts of the human colon carcinoma cell lines LIM1215 and SW1222, in which the antigen is highly expressed, the molecule was purified, yielding a 43-kDa protein. The N-terminal sequence was determined and further internal peptide sequence obtained following enzymatic cleavage. Degenerate primers were used in PCRs to produce a probe to screen a LIM1215 cDNA library, yielding clones that enabled us to deduce the complete amino acid sequence of the A33 antigen and express the protein. The available data bases have been searched and reveal no overall sequence similarities with known proteins. Based on a hydrophilicity plot, the A33 protein has three distinct structural domains: an extracellular region of 213 amino acids (which, by sequence alignment of conserved residues, contains two putative immunoglobulin-like domains), a single hydrophobic transmembrane domain, and a highly polar intracellular tail containing four consecutive cysteine residues. These data indicate that the A33 antigen is a novel cell surface receptor or cell adhesion molecule in the immunoglobulin superfamily.
Efficient transformation ofAgrobacteriumspp. by eletroporation (1989)

Journal Article Efficient transformation of Agrobacterium spp. by eletroporation Get access Diethard Mattanovich, Diethard Mattanovich Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Florian Rüker, Florian Rüker Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Artur da Cämara Machado, Artur da Cämara Machado Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Margit Laimer, Margit Laimer Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Ferdinand Regner, Ferdinand Regner Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Herta Steinkeliner, Herta Steinkeliner Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Gottfried Himmler, Gottfried Himmler Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Herman Katinger Herman Katinger Institute for Applied Microbiology, University of AgriculturePeter Jordanstraβe 82, A-1190 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 16, 25 August 1989, Page 6747, https://doi.org/10.1093/nar/17.16.6747 Published: 25 August 1989 Article history Received: 19 July 1989 Published: 25 August 1989
Physical and functional interaction between mortalin and Mps1 kinase (2007)

Mortalin is a member of Hsp70 chaperoning protein family involved in various cellular functions. Through the search of the kinases that mortalin physically interact with, we identified Mps1 as such a kinase. Mps1 kinase has been implicated in the regulation of centrosome duplication and mitotic checkpoint response. Mortalin binds to Mps1, and is phosphorylated by Mps1 on Thr62 and Ser65. The phosphorylated mortalin then super-activates Mps1 in a feedback manner. Mortalin has been previously shown to localize to centrosomes, and to be involved in the regulation of centrosome duplication. We found that centrosomal localization of mortalin depends on the presence of Mps1. Moreover, Mps1-associated acceleration of centrosome duplication depends on the presence of mortalin and super-activation by the Thr62/Ser65 phosphorylated mortalin.
Human colorectal carcinomas express high levels of high mobility group HMGI(Y) proteins. (1996)

A correlation has previously been demonstrated between the presence of the three HMGI proteins (HMGI, HMGY, and HMGI-C) and the expression of a highly malignant phenotype in epithelial and fibroblastic rat thyroid cells; this being subsequently extended to experimental thyroid, lung, prostate, mammary, and skin carcinomas. Recently, we have demonstrated that expression of HMGI and HMGY proteins, coded for by the HMGI(Y) gene, is associated with the malignant phenotype of human thyroid neoplasias. Here, we show that HMGI(Y) gene expression is present both at the RNA and protein level in human colorectal carcinoma cell lines and tissues examined in this study. Conversely, no HMGI(Y) proteins were detected in normal intestinal mucosa. Therefore, these results suggest an involvement of HMGI and HMGY proteins overexpression in colorectal tumorigenesis.
[Interaction between mixed-lineage leukemia and Menin proteins]. (2009)

The study was aimed to investigate the subcellular localization of mixed-lineage leukemia (MLL) and Menin proteins, and to explore the interaction between these two proteins. The recombinant eukaryotic cell expression vectors of pcDNA3.1-myc-MLL and pCMV-flag-Menin were constructed respectively, and transfected into the HEK293T cells. Immunofluorescence technique was used to observe the subcellular localization of the two proteins. Co-immunoprecipitation and Western blot methods were applied to evaluate the expression and interaction of the two proteins. The results showed that MLL and Menin proteins could be co-localized in cell nuclei, and the study of binding in vivo revealed that MLL protein could be detected in the immunoprecipitation complex of anti-FLAG, while Menin proteins could also be found in the immunoprecipitation complex of anti-MYC. It is concluded that MLL and Menin proteins co-localized in cell nuclei have same location and the interaction exists between MLL and Menin proteins.