gebhart/patrepeval huggingface dataset:
Synthesis of L-scyllo-inositol 1,2,4-trisphosphate, scyllo-inositol 1,2,4,5-tetrakisphosphate and phosphorothioate and DL-2-deoxy-2-fluoro-myo-inositol 1,4,5-trisphosphate: optical resolution of DL-1-O-allyl-3,6-di-O-benzyl-4,5-O-isopropylidene-scyllo-inositol (1996)

Routes for the synthesis of scyllo-inositol tris-and tetrakis-phosphates and 2-deoxy-2-fluoro-myo-inositol 1,4,5-trisphosphate from myo-inositol have been devised. For DL-scyllo-inositol 1,2,4-trisphosphate, DL-1-O-allyl 1–3,6-di-O-benzyl-4,5-O-isopropylidene-scyllo-inositol was prepared from the triflate of DL-1-O-allyl-3,6-di-O-benzyl-4–5-O-isopropylidene-myo-inositol by inversion at C-2. Removal of the isopropylidene group and phosphorylation gave the protected trisphosphate. Deblocking with sodium in liquid ammonia afforded racemic scyllo-inositol 1,2,4-trisphosphate. DL-1-O-Allyl-3,6-di-O-benzyl-4,5-O-isopropylidene-scyllo-inositol was resolved into its enantiomers by means of the crystalline 2-O-camphanate ester. The structure of one diastereoisomer, 1D-O-allyl-3,6-di-O-benzyl-2-O-[(–)-camphanate]-4,5–0-isopropylidene-scyllo-inositol was determined by single-crystal X-ray crystallography. 1D-(+)-1-O-Allyl-3,6-di-O-benzyl-4,5-O-isopropylidene-scyllo-inositol was used to prepare 1L(–)-scyllo-inositol 1,2,4-trisphosphate in a fashion analogous to the racemic modification. DL-1-O-Allyl-3,6-di-O-benzyl-scyllo-inositol was isomerised to the (Z)-prop-1-enyl derivative. The propenyl group was then removed to give the meso-1,4-di-O-benzyscyllo-inositol. Phosphitylation followed by oxidation or sulfoxidation gave the fully protected tetrakis-phosphate or -phosphorothioate, respectively. After deblocking and purification, scyllo-inositol 1,2,4,5-tetrakisphosphate and scyllo inositol 1,2,4,5-tetrakisphosphorothioate were obtained. DL-1-O-Allyl-3,6-di-O-benzyl-4,5-O-isopropylidene-scyllo-inositol was isomerised to the 1-O-[(Z)-prop-1-enyl] derivative which was converted into the 2-O-triflate. Displacement of the triflate using tetrabutylammonium fluoride proceeded with inversion of configuration to give DL-3,6-di-O-beflzyl-2-deoxy-2-fluoro-4,5-O-isopropylidene-1-O-([(Z)-prop-1-eny]-myo-inositol. Removal of propenyl and isopropylidene groups afforded DL-3,6-di-O-benzyl-2-deoxy-2-fluoro-myo-inositol, which was phosphitylated and the product oxidised to give the fully protected 2-fluoro trisphosphate. Deprotection furnished DL-2-deoxy-2-fluoro-myo-inositol 1,4,5-trisphosphate. These compounds will be useful probes for investigation of the polyphosphoinositide pathway of cellular signalling.
ADD1: a novel helix-loop-helix transcription factor associated with adipocyte determination and differentiation. (1993)

DNA-binding proteins containing the basic helix-loop-helix (bHLH) domain have been implicated in lineage determination and the regulation of specific gene expression in a number of cell types. By oligonucleotide screening of an adipocyte cDNA expression library, we have identified a novel member of the bHLH-leucine zipper transcription factor family designated ADD1. ADD1 mRNA is expressed predominantly in brown adipose tissue in vivo and is regulated during both determination and differentiation of cultured adipocyte cell lines. ADD1 can function as a sequence-specific transcriptional activator in that it stimulates expression of a chloramphenicol acetyltransferase vector containing multiple ADD1 binding sequences but is unable to activate the myosin light-chain enhancer, which contains multiple binding sites for another bHLH factor, MyoD. ADD1 can also activate transcription through a binding site present in the 5'-flanking region of the fatty acid synthetase gene which is expressed in a differentiation-dependent manner in adipose cells. These data suggest that ADD1 plays a role in the regulation of determination- and differentiation-specific gene expression in adipocytes.
A concurrent object-oriented switching program in Chill (1991)

A switching program structure that is expandable to allow inclusion of new service features and functions with minimum effort during run time, adaptable to handle enhanced services, allows new services to be added quickly, and is highly reliable, is proposed. It is based on the use of object-oriented programs, hierarchically structured programs, and building-block switching systems based on distributed processing. The discussion covers the logical switching system model, object-oriented switching program systems, concurrent object-oriented programming in Chill (CCITT high level languages), the software architecture, the building-block switching systems, and call processing. Early evaluation results are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Global Change and the Ecology of Cities (2008)

Urban areas are hot spots that drive environmental change at multiple scales. Material demands of production and human consumption alter land use and cover, biodiversity, and hydrosystems locally to regionally, and urban waste discharge affects local to global biogeochemical cycles and climate. For urbanites, however, global environmental changes are swamped by dramatic changes in the local environment. Urban ecology integrates natural and social sciences to study these radically altered local environments and their regional and global effects. Cities themselves present both the problems and solutions to sustainability challenges of an increasingly urbanized world.
Molecular cloning and characterization of the nontypeable Haemophilus influenzae 2019 rfaE gene required for lipopolysaccharide biosynthesis (1995)

The lipooligosaccharide (LOS) of nontypeable Haemophilus influenzae (NTHi) is an important factor in pathogenesis and virulence. In an attempt to elucidate the genes involved in LOS biosynthesis, we have cloned the rfaE gene from NTHi 2019 by complementing a Salmonella typhimurium rfaE mutant strain with an NTHi 2019 plasmid library. The rfaE mutant synthesizes lipopolysaccharide (LPS) lacking heptose, and the rfaE gene is postulated to be involved in ADP-heptose synthesis. Retransformation with the plasmid containing 4 kb of NTHi DNA isolated from a reconstituted mutant into rfaE mutants gave wild-type LPS phenotypes. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis confirmed the conversion of the rfaE mutant LPS to a wild-type LPS phenotype. Sequence analysis of a 2.4-kb BglII fragment revealed two open reading frames. One open reading frame encodes the RfaE protein with a molecular weight of 37.6 kDa, which was confirmed by in vitro transcription and translation, and the other encodes a polypeptide highly homologous to the Escherichia coli HtrB protein. These two genes are transcribed from the same promoter region into opposite directions. Primer extension analysis of the rfaE gene revealed a single transcription start site at 37 bp upstream of the predicted translation start site. The upstream promoter region contained a sequence (TA AAAT) homologous to the -10 region of the bacterial sigma 70-dependent promoters at an appropriate distance (7 bp), but not sequence resembling the consensus sequence of the -35 region was found. These studies demonstrate the ability to use complementation of defined LPS defects in members of the family Enterobacteriaceae to identify LOS synthesis genes in NTHi.
G–G Base‐Pairing in Nucleobase Adducts of the Anticancer Drug cis‐[PtCl2(NH3)(2‐picoline)] and Its trans Isomer (2005)

cis-[PtCl2(NH3)(2-picoline)] (AMD473) is a sterically-hindered anticancer complex with a profile of chemical and biological activity that differs significantly from that of cisplatin. Adducts of AMD473 with neutral 9-ethylguanine (9-EtGH) and anionic (N1-deprotonated) 9-ethylguanine (9-EtG) as perchlorate and nitrate salts, and also a nitrate salt of the trans isomer (AMD443), were prepared and their structures determined by X-ray crystallography: cis-[Pt(NH3)(2-pic)(9-EtGH)2](ClO4)2 (1).2H(2)OMe(2)CO, cis-[Pt(NH3)(2-pic)(9-EtGH)2](NO3)2 (2).2H2O, cis-[Pt(NH3)(2-pic)(9-EtGH)(9-EtG)]NO3 (3),3.5 H2O, trans-[Pt(NH3)(2-pic)(9-EtGH)(9-EtG)]NO3 (4).8H2O. In all cases, platinum coordination is through N7 of neutral (1, 2) and anionic (3, 4) guanine. In each complex, the guanine bases are arranged in the head-to-tail conformation. In complex 1, there is an infinite array of six-molecule cycles, based on both hydrogen bonding and pi-pi stacking of the 2-picoline and guanine rings. Platinum(II) coordinated at N7 acidifies the N1 proton of neutral 9-ethylguanine (pKa = 9.57) to give pKa1 = 8.40 and pKa2 = 8.75 for complex 2, and pKa1 = 7.77 and pKa2 = 9.00 for complex 4. In complexes 3 and 4, three intermolecular hydrogen bonds are formed between neutral and deprotonated guanine ligands involving O6, N1 and N2 sites. Unusually, both of the platinated guanine bases of complexes 3 and 4 participate in this triple G triple bond G hydrogen bonding. This is the first report of X-ray crystal structures of nucleobase adducts of the promising anticancer drug AMD473.
FaST Sliders: Integrating Marking Menus and the Adjustment of Continuous Values (2002)

We propose a technique, called FaST Sliders, for selecting and adjusting continuous values using a fast, transient interaction much like pop-up menus. FaST Sliders combine marking menus and graphical sliders in a design that allows operation with quick ballistic movements for selection and coarse adjustment. Furthermore, additional controls can be displayed within the same interaction, for fine adjustments or other functions. We describe the design of FaST Sliders and a user study comparing FaST sliders to other transient techniques. The results of our user study indicate that FaST Sliders hold potential. We observed that users found FaST Slider easy to learn and made use of and preferred its affordances for ballistic movement and additional controls.
Introduction of Benzo[h]quinoline and 1,10-Phenanthroline Subunits by Friedländer Methodology (1996)

An improved preparation of 8-amino-7-quinolinecarbaldehyde has been developed. The methyl group of 7-methyl-8-nitroquinoline may be oxidized to an aldehyde by treatment first with dimethylformamide dimethyl acetal followed by sodium periodate. Reduction with iron provides the amino aldehyde. An analogous sequence affords 1-amino-2-naphthalenecarbaldehyde. Friedländer condensation of the quinoline derivative with a series of acetylaromatics provides the corresponding 2-aryl-1,10-phenanthrolines. Condensation of either amino aldehyde with 1,3-diacetylbenzene or 2,6-diacetylpyridine provides the expected Friedländer product. Similar chemistry is described for reactions of the amino aldehydes with 1,4-diacetylbenzene, 4,4‘-diacetylbiphenyl, 1,5-diacetylanthracene, 1,2,3,4,5,6,7,8-octahydroacridine-1,8-dione, and tetracyclo[6.3.0.0.4,1105,9]undecane-2,7-dione (TCU-2,7-dione).
Heparan sulfate proteoglycans of human lung fibroblasts. Structural heterogeneity of the core proteins of the hydrophobic cell-associated forms. (1987)

Heparan sulfate proteoglycans (HSPG) were solubilized from human lung fibroblast monolayers with detergent. Presumptive membrane-associated forms displaying hydrophobic properties were purified by gel filtration on Sepharose CL-4B, by ion-exchange chromatography on Mono Q and by incorporation in lipid vesicles. The HSPG preparations were 125I-iodinated and treated with heparitinase before sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Five radiolabeled proteins with apparent molecular weights of 125,000, 90,000, 64,000, 48,000, and 35,000 were visualized by autoradiography. A sixth protein, identified in nonreduced 125I-HSPG preparations, appeared as a non-HS chain-bearing Mr 35,000 peptide which was disulfide-linked to an HS chain-bearing peptide of similar size. This multiplicity of core proteins did not seem to result from proteolysis during the heparitinase treatment itself, since some of the core proteins migrated independently during gel filtration before heparitinase digestion. Moreover, heparitinase digestion of 125I-HSPG purified by affinity chromatography on an immobilized monoclonal antibody yielded only the Mr 64,000 protein. Alternative depolymerizations of the HS chains by heparinase or HNO2 also yielded multiple protein bands. These results imply that heterogeneity of the core protein moiety may be a genuine property of the hydrophobic HSPG of human lung fibroblasts. The occurrence of multiple integral membrane HSPG forms may be relevant for the multiple functions that have been ascribed to cell-surface HSPG.
Chernoff-Hoeffding bounds for applications with limited independence (1993)

Chernoff-Hoeffding bounds are fundamental tools used in bounding the tail probabilities of the sums of bounded and independent random variables. We present a simple technique which gives slightly better bounds than these and which, more importantly, requires only limited independence among the random variables, thereby importing a variety of standard results to the case of limited independence for free. Additional methods are also presented, and the aggregate results are very sharp and provide a better understanding of the proof techniques behind these bounds. They also yield improved bounds for various tail probability distributions and enable improved approximation algorithms for jobshop scheduling. The ``limited independence'''' result implies that weaker sources of randomness are sufficient for randomized algorithms whose analyses use the Chernoff-Hoeffding bounds; further, it leads to algorithms that require a reduced amount of randomness for any analysis which uses the Chernoff-Hoeffding bounds, e.g., the analysis of randomized algorithms for random sampling and oblivious packet routing.
Accuracies of the synthesized monochromatic CT numbers and effective atomic numbers obtained with a rapid kVp switching dual energy CT scanner (2011)

Initial tests indicate that the Z(eff) values computed with DECT on this scanner are reasonably accurate; however, the synthesized monochromatic CT numbers can be very inaccurate, especially for dense tissue mimicking materials at low energies. Furthermore, the synthesized monochromatic CT numbers of materials still depend on the amount of the surrounding tissues especially at low keV, demonstrating that the numbers are not truly monochromatic. Further research is needed to develop DE methods that produce more accurate synthesized monochromatic CT numbers.
Imaging of the Dynamics of Glucose Uptake in the Cytosol of COS-7 Cells by Fluorescent Nanosensors (2003)

Glucose homeostasis is a function of glucose supply, transport across the plasma membrane, and metabolism. To monitor glucose dynamics in individual cells, a glucose nanosensor was developed by flanking the Escherichia coli periplasmic glucose/galactose-binding protein with two different green fluorescent protein variants. Upon binding of substrate the FLIPglu-170n sensor showed a concentration-dependent decrease in fluorescence resonance energy transfer between the attached chromophores with a binding affinity for glucose of 170 nm. Fluorescence resonance energy transfer measurements with different sugars indicated a broad selectivity for monosaccharides. An affinity mutant with a Kd of approximately 600 microM was generated, which showed higher substrate specificity, and thus allowed specific monitoring of reversible glucose dynamics in COS-7 cells in the physiological range. At external glucose concentrations between 0.5 and 10 mM, reflecting typical blood levels, free cytosolic glucose concentrations remained at approximately 50% of external levels. The removal of glucose lead to reduced glucose levels in the cell, demonstrating reversibility and visualizing homeostasis. Glucose levels dropped even in the presence of the transport inhibitor cytochalasin B, indicating rapid metabolism. Consistently, the addition of 2-deoxyglucose, which is not recognized by the sensor, affects glucose uptake and metabolism rates. Within the physiological range, glucose utilization, i.e. hexokinase activity, was not limiting. Furthermore, the results show that in COS-7 cells, cytosolic glucose concentrations can vary over at least two orders of magnitude. The glucose nanosensor provides a novel tool with numerous scientific, medical, and environmental applications.
Comparison between time‐correlated single photon counting and fluorescence correlation spectroscopy in single molecule identification (1998)

Currently, two methods of detection and identification of single molecules are widely used: fluorescence correlation spectroscopy (FCS) and time-correlated single photon counting (TCSPC). We present a thorough theoretical analysis of the error rates for identifying single molecules according to their diffusion coefficients (using FCS), and to their fluorescence lifetimes (using TCSPC). In most cases, the error rate using TCSPC is much lower. TCSPC is thus proven to be more versatile for analyzing single molecule events. The study is significant for a broad range of ultra-sensitive fluorescence detection applications.
Reorganization of polymerized actin: a possible trigger for induction of procollagenase in fibroblasts cultured in and on collagen gels. (1986)

Changes in cell shape are postulated to modulate gene expression during differentiation of a number of cell types, including rabbit synovial fibroblasts, which are inducible for expression of the zymogen form of the metalloendopeptidase, collagenase. In the work presented here, fibroblasts cultured on and within hydrated collagen gels were allowed to contract by release of the gels from the sides of the culture dish. Within 24 h of cell release, synthesis and secretion of procollagenase was initiated in the absence of any chemical manipulation. Fibroblasts grown in and on collagen also responded to 12-O-tetradecanoylphorbol-13-acetate and cytochalasin B with morphologic change and induced procollagenase. However, colchicine, which altered morphology to varying degrees in cells on plastic, on collagen, and within collagen gels, did not induce procollagenase expression. In all cases, the enzyme was induced only after reorganization of polymerized actin, rather than after a change in cellular morphology per se. As a first approach to identifying other aspects of the stimulated phenotype that could affect collagen turnover, the expression of collagen and endogenous metalloproteinase inhibitors in relation to procollagenase secretion was investigated. Collagen secretion by fibroblasts decreased when procollagenase secretion was induced by the pharmacologic agents, but not when cells were stimulated by contraction on or within collagen gels. The expression of two endogenous inhibitors was not coordinately regulated with induction of procollagenase. Therefore, the extracellular matrix and the cellular actin cytoskeleton may transduce signals that modulate the tissue remodeling phenotype of fibroblasts.
Flow cytometric analysis of altered mononuclear cell transmembrane potential induced by cyclosporin (1993)

Immunosuppression by the fungal metabolite cyclosporin A (CsA) is characterized by functional inhibition, rather than destruction of cells. Because activation of immune cells involves intracellular signalling events associated with modulations of cell transmembrane potential (TMP), we tested the ability of cyclosporin A (CsA) to modulate immune mononuclear cell TMP in vitro using a TMP sensitive cationic dye, dihexyloxacarbocyanine (DIOC6(3)). All analyses were performed by flow cytometry. CsA increased TMP in monocytes and lymphocytes isolated from the blood of healthy human volunteers. CsA-induced hyperpolarization was time and concentration dependent in monocytes while the lymphocyte hyperpolarization, although time dependent, was evident over the entire range of CsA concentrations tested. CsA-induced hyperpolarization of lymphocytes was dependent on potassium ion (K+) efflux as indicated by the absence of hyperpolarization in 154 mM KCl or with pretreatment with 100 microM quinine (an inhibitor of K+ channels). Monocyte hyperpolarization by CsA was not inhibited in either system. Dihydrocyclosporin C (DH-CsC), an immunosuppressive analog of CsA, also hyperpolarized mononuclear cells. The anionic TMP sensitive dye bis oxonal (diBA-C4) indicated that CsA treatment depolarized mononuclear cell plasma membranes. The mitochondrial poison carbonyl cyanide p-trifluoromethoxy-phenyl-hydrazine (FCCP) eliminated CsA induced hyperpolarization and also indicated that CsA caused plasma membrane depolarization. We conclude that brief in vitro exposure to cyclosporin alters the transmembrane electrical potential of human lymphocytes and monocytes.
Commitment of B Lymphocytes to a Plasma Cell Fate Is Associated with Blimp-1 Expression In Vivo (2000)

B lymphocyte-induced maturation protein-1 (Blimp-1) is a transcriptional repressor that is sufficient to trigger terminal differentiation in the B cell lymphoma BCL-1. In this study, we have determined the expression pattern of Blimp-1 in vivo in primary and secondary lymphoid organs of humans and immunized mice. Blimp-1 is expressed in plasma cells derived from either a T-independent or T-dependent response in plasma cells that have undergone isotype switching and those resulting from secondary immunization. Blimp-1 is also present in long-lived plasma cells residing in the bone marrow. However, Blimp-1 was not detected in memory B cells. This expression pattern provides further evidence of a critical role for Blimp-1 in plasma cell development, supporting earlier studies in cultured lines. Significantly, Blimp-1 was also found in a fraction (4-15%) of germinal center B cells in murine spleen and human tonsils. Blimp-1 expression in the germinal center is associated with an interesting subset of cells with a phenotype intermediate between germinal center B cells and plasma cells. In the mouse, Blimp-1(+) germinal center B cells peak at day 12 postimmunization and disappear soon thereafter. They are not apoptotic, some are proliferating, they express germinal center markers peanut agglutinin or CD10 but not Bcl-6, and most express CD138 (syndecan-1), IRF4, and cytoplasmic Ig. Together, these data support a model in which B cell fate decisions occur within the germinal center and Blimp-1 expression is critical for commitment to a plasma cell, rather than a memory cell, fate.
The Immune Epitope Database (IEDB): 2018 update (2018)

The Immune Epitope Database (IEDB, iedb.org) captures experimental data confined in figures, text and tables of the scientific literature, making it freely available and easily searchable to the public. The scope of the IEDB extends across immune epitope data related to all species studied and includes antibody, T cell, and MHC binding contexts associated with infectious, allergic, autoimmune, and transplant related diseases. Having been publicly accessible for >10 years, the recent focus of the IEDB has been improved query and reporting functionality to meet the needs of our users to access and summarize data that continues to grow in quantity and complexity. Here we present an update on our current efforts and future goals.
Regulatory mechanisms, prophylaxis and treatment of vascular leakage following severe trauma and shock (2017)

Vascular leakage, or increased vascular permeability, is a common but important pathological process for various critical diseases, including severe trauma, shock, sepsis, and multiple organ dysfunction syndrome (MODS), and has become one of the most important causes of death for intensive care units (ICU) patients. Currently, although there has been some progress in knowledge of the pathogenesis of these vascular disorders, the detailed mechanisms remain unclear, and effective prophylaxis and treatment are still lacking. In this study, we aimed to provide a review of the literature regarding the regulatory mechanisms and prophylaxis as well as the treatment of vascular leakage in critical diseases such as severe trauma and shock, which could be beneficial for the overall clinical treatment of vascular leakage disorders.