gebhart/patrepeval huggingface dataset:
The soluble human IL-6 receptor. Mutational characterization of the proteolytic cleavage site. (1994)

Like many proteins with a single transmembrane domain the IL-6R exists in a membrane-associated and soluble form. The soluble IL-6R is generated by limited proteolysis of the membranous receptor. This process, also called shedding, is drastically enhanced by PMA, an activator of protein kinase C. The soluble receptor protein was purified to homogeneity from supernatants of COS-7 cells transfected with a cDNA coding for the transmembrane IL-6R. The COOH-terminus of the shed receptor protein was analyzed by carboxypeptidase treatment and subsequent amino acid analysis. The established cleavage site Gln357/Asp358 was extensively altered by point mutations and small deletions to define the structural requirements for cleavage. Although point mutations around the cleavage site reduced shedding of the IL-6R up to fivefold, deletions of 5 or 10 amino acids almost completely abolished shedding. Deletion of the cytoplasmic domain of the receptor had no influence on shedding of the protein. It turned out that a potential N-glycosylation site close to the proteolytic cleavage site of the IL-6R is used. However this N-glycosylation does not affect the efficiency of the shedding process. Furthermore, we demonstrate for the first time that the human IL-6R is constitutively phosphorylated and that this phosphorylation can be stimulated by PMA but is not correlated with shedding of the receptor protein. The knowledge of the mechanism by which the soluble IL-6R is generated will help to identify the processing enzyme involved and to analyze its regulation.
Synthesis and radical polymerization of spiro orthocarbonates bearing exomethylene groups (1994)

Abstract Synthesis and radical polymerization of spiro orthocarbonates (SOCs) bearing exomethylene groups at the α to the ether oxygen ( 1a–1e ) were studied. SOCs 1a–1e were prepared by the successive reactions of dichlorodiphenoxymethane with two different diols followed by dehydrochlorination. Radical polymerization of the SOCs was carried out in the presence of an appropriate initiator (3 mol % versus monomer) at 130 and 180°C. The obtained polymer insoluble in n ‐hexane contained both vinyl polymerization unit 13 and double ring‐opening polymerization unit 14 (ketone‐carbonates). The degree of ring‐opening followed the order: 1a &lt;1b &lt; 1d, 1e . n ‐Hexane‐insoluble polymer was not obtained in the polymerization of 1c . Both steric hindrance of methyl group and ring size affected the degree of ring‐opening. The introduction of methyl group into SOC increased the degree of ring‐opening ( 1a &lt;1b ), whereas the degree of ring‐opening of either 1d , consisting of six‐ and seven‐membered rings, and 1e , consisting of two seven‐membered rings, was higher than those of 1a and 1b , consisting of five and seven‐membered rings. From the molecular orbital calculation (PM3, UHF method), it was concluded that if the first single ring‐opening occurs, then the successive second ring‐opening takes place more smoothly. The first ring‐opening requires more energy than the vinyl polymerization does. © 1994 John Wiley &amp; Sons, Inc.
Adsorption of Harmful Organic Vapors by Flexible Hydrophobic Bis-pyrazolate Based MOFs (2010)

Highly porous homoleptic Ni(bpb) and Zn(bpb) materials have been obtained by reaction of nickel(II) and zinc(II) salts with the deprotonated form of the 1,4-(4-bispyrazolyl)benzene ligand (H2bpb). Ab-initio structure solution methods and thermodiffractometry have allowed the determination of their crystal structures, framework flexibility, and thermal stability. The different stereochemical requirements of the Ni(II) and Zn(II) ions induce, in Ni(bpb) and Zn(bpb), rhombic and square channels, respectively, accounting for 57 and 65% of the total cell volume. The two materials feature high adsorption capacities toward small gaseous molecules (N2 and Ar at 77 K, CO2 and CH4 at 273 K), peaking at 22 mmol g−1 of N2 in the case of the zinc(II) derivative, which is reflected by a very large surface area (above 2000 m2 g−1). The flexibility, size, and hydrophobic nature of their channels are adequate also for the incorporation of organic vapors. In this regard, the adsorption of benzene and cyclohexane has been studied under static conditions at 303 K, while that of thiophene has been investigated in dynamic conditions, by measurement, at 298 K, of the breakthrough curves of a flow of CH4/CO2 containing 30 ppm of thiophene. Ni(bpb) and Zn(bpb) are outperforming adsorbents, uptaking up to 0.34 g of thiophene per gram of material. The presence of humidity (60%), which is a major drawback for practical applications of MOFs, does not significantly affect the performance of Ni(bpb) in the removal of thiophene, at variance with Zn(bpb) and HKUST-1, Cu3(btc)2 (btc = benzene-1,3,5-tricarboxylate), which become ineffective in the presence of moisture. Additional XRPD studies have been performed on benzene-loaded Ni(bpb) samples in order to shed some light on the affinity of this material for aromatic guests.
The ribulose monophosphate pathway operon encoding formaldehyde fixation in a thermotolerant methylotroph, Bacillus brevis S1 (2002)

The hps and phi genes encoding 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase, the key enzymes of the ribulose monophosphate (RuMP) pathway for formaldehyde fixation, were cloned from the chromosomal DNA of a thermotolerant methylotroph, Bacillus brevis S1. Enzyme induction and Northern blot analyses revealed that both the hps and phi genes are induced by methanol or ethanol, and that their expression is controlled polycistronically at the transcription stage. Sequence analysis also suggested that the hps and phi genes constitute an RuMP operon. The gene organization of the RuMP operon and its surrounding region are unique among bacteria possessing the RuMP pathway genes.
Second-Generation Computer-Assisted Inhibitor Design Method (1989)

We present a second generation computer-assisted method to provide novel candidates for drug design. The method utilizes a rapid and automatic method of locating sterically reasonable orientations of small molecules in a receptor site of known three-dimensional structure combined with a scoring scheme that ranks the orientations by how well they fit the site (DesJarlais, et al., J. Med. Chem., 1988, 31 722). This docking procedure is the first step in a two step process to provide candidates for novel enzyme inhibitors. A large database of small molecule structures is searched for those molecules with shapes complementary to the receptor structure. This ensures good van der Waals interactions between the receptor and the top scoring molecules, but it is unlikely that any of these molecules will have the appropriate electrostatic and hydrogen bonding properties to interact favorably with the receptor. To the docking procedure, we have added a second step that examines the electrostatic and hydrogen bonding properties of the receptor site. These properties are displayed with computer graphics models and are used to suggest chemical modifications to the correctly shaped skeleton structures in order to provide chemical complementarity as well as shape complementarity to the receptor site. At the present time, evaluation of the chemical properties is performed by the chemist. It is our long-term goal to use what is learned from this interactive design to automate the process of modifying the molecular frameworks found in the shape search.
Invited Review: Gravitational biology of the neuromotor systems: a perspective to the next era (2000)

Earth's gravity has had a significant impact on the designs of the neuromotor systems that have evolved. Early indications are that gravity also plays a key role in the ontogenesis of some of these design features. The purpose of the present review is not to assess and interpret a body of knowledge in the usual sense of a review but to look ahead, given some of the general concepts that have evolved and observations made to date, which can guide our future approach to gravitational biology. We are now approaching an era in gravitational biology during which well-controlled experiments can be conducted for sustained periods in a microgravity environment. Thus it is now possible to study in greater detail the role of gravity in phylogenesis and ontogenesis. Experiments can range from those conducted on the simplest levels of organization of the components that comprise the neuromotor system to those conducted on the whole organism. Generally, the impact of Earth's gravitational environment on living systems becomes more complex as the level of integration of the biological phenomenon of interest increases. Studies of the effects of gravitational vectors on neuromotor systems have and should continue to provide unique insight into these mechanisms that control and maintain neural control systems designed to function in Earth's gravitational environment. A number of examples are given of how a gravitational biology perspective can lead to a clearer understanding of neuromotor disorders. Furthermore, the technologies developed for spaceflight studies have contributed and should continue to contribute to studies of motor dysfunctions, such as spinal cord injury and stroke. Disorders associated with energy support and delivery systems and how these functions are altered by sedentary life styles at 1 G and by space travel in a microgravity environment are also discussed.
Synthesis of the 4-oxygenated retinoid metabolites. (1987)

The efficient synthesis of 4-hydroxylated metabolites of various retinoids is described. Allylic bromination of beta-ionone, retinal, and methyl retinoate followed by treatment with aqueous AcOH and saponification afforded the 4-hydroxy analogues in 64-79% yields. With the conjugated polyenes, retinal and methyl retinoate, about 25% of the products were found to be the 13-cis isomers. Purification of isomer mixtures by HPLC permitted stereochemical assignments after 1H NMR analysis.
Stability of Omeprazole Solutions at Various ph Values as Determined by High-Performance Liquid Chromatography (1995)

A stability-indicating HPLC assay method for the quantitation of omeprazole has been developed. The developed method was used to study the effect of pH on the stability of omeprazole and to quantify the drug in capsules. The excipients present in the capsules did not interfere with the assay procedure. The pH-rate profile curve indicated that the maximum stability was at pH 11. Below pH 7.8, the decomposition was very fast. The decomposition constants have a direct relationship with the H+ concentrations of the solutions.
A Facile Approach to Architecturally Defined Nanoparticles via Intramolecular Chain Collapse (2002)

A novel approach is presented for the controlled intramolecular collapse of linear polymer chains to give well-defined single-molecule nanoparticles whose structure is directly related to the original linear polymer. By employing a combination of living free radical polymerization and benzocyclobutene (BCB) chemistry, nanoparticles can be routinely prepared in multigram quantities with the size being accurately controlled by either the initial degree of polymerization of the linear chain or the level of incorporation of the BCB coupling groups. The latter also allows the cross-link density of the final nanoparticles to be manipulated. In analogy with dendritic macromolecules, a significant reduction of up to 75% in the hydrodynamic volume is observed on going from the starting random coil linear chains to the corresponding nanoparticles. The facile nature of the living free radical process also permits wide variation in monomer selection and functional group incorporation and allows novel macromolecular architectures to be prepared. Furthermore, the use of block copolymers functionalized with benzocyclobutene groups in only one of the blocks gives, after intramolecular collapse, a hybrid architecture in which a single linear polymer chain is attached to the globular nanoparticle.
DNA Looping by Saccharomyces cerevisiae High Mobility Group Proteins NHP6A/B (1995)

The formation of higher order protein.DNA structures often requires bending of DNA strands between specific sites, a process that can be facilitated by the action of nonspecific DNA-binding proteins which serve as assembly factors. A model for this activity is the formation of the invertasome, an intermediate structure created in the Hin-mediated site-specific DNA inversion reaction, which is stimulated by the prokaryotic nucleoid-associated protein HU. Previously, we have shown that the mammalian HMG1/2 proteins substitute for HU in this system and display efficient DNA wrapping activity in vitro. In the present work, we isolate the primary sources of assembly factor activity in Saccharomyces cerevisiae, as measured by the ability to stimulate invertasome formation, and show that these are the previously identified NHP6A/B proteins. NHP6A/B have comparable or greater activity in DNA binding, bending, and supercoiling with respect to HU and HMG1 and appear to form more stable protein.DNA complexes. In addition, expression of NHP6A in mutant Escherichia coli cells lacking HU and Fis restores normal morphological appearance to these cells, specifically in nucleoid condensation and segregation. From these data we predict diverse architectural roles for NHP6A/B in manipulating chromosome structure and promoting the assembly of multicomponent protein.DNA complexes.
Adult T cell leukemia: a potential target for ricin A chain immunotoxins (1985)

Adult T cell leukemia (ATL) is an almost uniformly fatal malignancy of mature T cells associated with human T cell leukemia/lymphoma virus type 1 (HTLV-1) infection. Cells from this leukemia are characterized by the expression of large numbers of receptors for interleukin 2 (IL-2). In an attempt to prepare an immunotoxin with selective cytotoxicity for ATL cells, we conjugated anti-Tac, a monoclonal anti-IL-2 receptor antibody, to purified ricin A chains. Although unmodified anti-Tac had no effect on the protein synthesis of these cells, anti-Tac-ricin A chain conjugates produced half-maximal inhibition of protein synthesis in HTLV-1-infected leukemic T cell lines at concentrations of 2 to 6 X 10(-10) mol/L (ID50). An essentially identical ID50 was obtained with leukemic peripheral blood T lymphocytes isolated from two patients with ATL. In contrast, half-maximal inhibition of protein synthesis in HTLV-uninfected, IL-2 receptor-negative T and B cell lines required 200- to 1,000-fold higher concentrations of anti-Tac-ricin A chain conjugates. Both unconjugated anti-Tac and immunoaffinity-purified IL-2 completely inhibited the toxic effects of anti-Tac-ricin A, confirming the specificity of the conjugate-IL-2 receptor interaction. Clonogenic assays demonstrated that anti-Tac-ricin A chain was able to eliminate greater than 99.9% of an HTLV-1-infected T cell population at concentrations only marginally affecting IL-2 receptor-negative cells. The data presented demonstrate that anti-Tac-ricin A is selectively cytotoxic for HTLV-1-infected leukemic T cells in vitro and raises the future possibility of specific therapeutic intervention with immunotoxins in this disease.
Three‐arm star ring opening metathesis polymers via alkyne‐azide click reaction (2009)

Abstract The click chemistry strategy is successfully applied for the preparation of three‐arm star (A 3 ) ring opening metathesis polymers. A well‐defined monoazide end‐functionalized poly( N ‐ethyl oxanorbornene) and a poly( N ‐butyl oxanorbornene) obtained via ring opening metathesis polymerization using first generation Grubbs' catalyst are simply clicked with the trisalkyne core affording the synthesis of target star polymers. The obtained star polymers are characterized via nuclear magnetic resonance spectroscopy and gel permeation chromatography (GPC). The deconvolution analyses of GPC traces reveal that the click reaction efficiency for the star formation strongly depends on the chemical nature and the molecular weight of ROM polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2344–2351, 2009
Anti-mouse FcγRIV antibody 9E9 also blocks FcγRIII in vivo (2015)

To the editor:

Monoclonal antibodies (mAbs), such as the anti-CD20 mAb rituximab, have transformed the treatment of malignant disease and are now a first-line treatment of many hematologic conditions. Although in many cases their precise mechanism of action is not fully elucidated, where target
Mutation in the Jak Kinase JH2 Domain Hyperactivates Drosophila and Mammalian Jak-Stat Pathways (1997)

The Jak (Janus) family of nonreceptor tyrosine kinases plays a critical role in cytokine signal transduction pathways. In Drosophila melanogaster, the dominant hop(Tum-l) mutation in the Hop Jak kinase causes leukemia-like and other developmental defects. Previous studies have suggested that the Hop(Tum-l) protein might be a hyperactive kinase. Here, we report on the new dominant mutation hop(T42), which causes abnormalities that are similar to but more extreme than those caused by hop(Tum-l). We determined that Hop(T42) contains a glutamic acid-to-lysine substitution at amino acid residue 695 (E695K). This residue occurs in the JH2 (kinase-like) domain and is conserved among all Jak family members. We determined that Hop(Tum-1) and Hop(T42) both hyperphosphorylated and hyperactivated D-Stat when overexpressed in Drosophila cells. Moreover, we found that the hop(T42) phenotype was partially rescued by a reduction of wild-type D-stat activity. Finally, generation of the corresponding E695K mutation in murine Jak2 resulted in increased autophosphorylation and increased activation of Stat5 in COS cells. These results demonstrate that the mutant Hop proteins do indeed have increased tyrosine kinase activity, that the mutations hyperactivate the Hop-D-Stat pathway, and that Drosophila is a relevant system for the functional dissection of mammalian Jak-Stat pathways. Finally, we propose a model for the role of the Hop-D-Stat pathway in Drosophila hematopoiesis.
Transport of coenzyme M (2-mercaptoethanesulfonic acid) in Methanobacterium ruminantium (1979)

A system for transport of coenzyme M, 2-mercaptoethanesulfonic acid (HS--CoM), in Methanobacterium ruminatium strain M1 required energy, showed saturation kinetics, and concentrated the coenzyme against a gradient. The process was sensitive to temperature and was maximally active at pH 7.1. Cells took up HS--CoM at a linear rate, with a Vmax of 312 pmol/min per mg (dry weight) and an apparent Km of 73 nM. An intracellular pool of up to 5 mM accumulated which was not exchangeable with the medium. Uptake required both hydrogen and carbon dioxide; it was inhibited by O2. Bromoethanesulfonic acid (BrCH2CH2SO3-), a potent inhibitor of methanogenesis in cell-free extracts, inhibited both uptake and methane production. Results of inhibitor studies with derivatives and analogs of the coenzyme showed that the specificity of the carrier is restricted to a limited range of thioether, thioester, and thiocarbonate derivatives. 2-(Methylthio)ethanesulfonic acid (CH3--S--CoM) showed an apparent Ki for HS--CoM uptake of 15 nM, being taken up itself with a Vmax of 320 pmol/min per mg (dry weight) and an apparent Km of 50 nM. An analysis of intracellular pools after HS--CoM uptake indicated that the predominant forms are a heterodisulfide of unknown composition and CH3--S--CoM.
Development of Clinical Methods of Iron Deprivation for Suppression of Neoplastic and Infectious Diseases (1999)

Hosts attempt to withhold growth-essential iron from neoplastic and microbial cells. This review focuses on the development of medical and pharmaceutical methods designed to enhance the iron-withholding defense system.
Induction of human monocyte to macrophage maturation in vitro by 1,25- dihydroxyvitamin D3 (1990)

Cells of the mononuclear phagocyte system arise from circulating blood monocytes (MO) that undergo further maturation on leaving the vasculature and migration into the various tissues and body cavities. This terminal differentiation step is also observed in vitro when blood MO are cultured in the presence of serum. Yet, the inducing signals present in serum are not defined. We have established primary cultures from elutriation-purified blood MO and found that the active metabolite of vitamin D3 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) could induce maturation of MO to macrophages (MAC) in the absence of any serum proteins. Cells were cultured for 7 days with AB-group serum or 1,25(OH)2D3, respectively, and MO maturation analyzed by morphology, functional activity, and the expression of lineage-restricted maturation-associated antigens (MAX.1, MAX.3). At an optimal concentration of 10(-8) mol/L, 1,25(OH)2D3 promoted the development of fully differentiated MAC whose phenotype and functional competence in terms of cytokine release (tumor necrosis factor alpha, interleukin-6, fibronectin, and lysozyme) was comparable with MAC grown in serum. In conclusion, our data may add to the immunoregulatory potential of 1,25(OH)2D3, which may play an essential role in the ontogeny of the mononuclear phagocyte system.
Confirmation of a BRAF mutation‐associated gene expression signature in melanoma (2007)

Mutations in the BRAF oncogene occur in the majority of melanomas, leading to the activation of the mitogen-activated protein kinase pathway and the transcription of downstream effectors. As BRAF and its effectors could be good melanoma therapy targets, defining the repertoire of genes that are differentially regulated because of BRAF mutational activation is an important objective. Towards this goal, we and others have attempted to determine whether a BRAF mutation-associated gene expression profile exists. Results have been mixed, with some groups reporting a BRAF-signature and another group not. Here we resolve this issue and confirm that while gene-by-gene correlations fail to reveal a specific gene(s) whose expression correlates with BRAF status, a BRAF signature can be distinguished by analysis of global expression patterns. Specifically, we have here applied support vector machine (SVM) analysis to Affymetrix microarray data from a panel of 63 melanoma cell lines. SVMs found a BRAF signature in training samples and predicted BRAF mutation status with high accuracy (AUC=0.840) in the remaining samples. We verified this is a generalized BRAF signature by repeating the analysis in three published microarray datasets, and again found that SVMs predicted BRAF mutation well (Philadelphia: AUC=0.788; Zurich: AUC=0.688; Mannheim: AUC=0.686). An ensemble of 300 SVMs trained on our data also predicted BRAF mutation status in two of the three published datasets (Philadelphia AUC=0.778; Zurich AUC=0.719; Mannheim AUC=0.564). Taken together, these data support the existence of a BRAF mutation-specific expression signature.