gebhart/patrepeval huggingface dataset:
The Role and Function of Fcγ Receptors on Myeloid Cells (2016)

A key determinant for the survival of organisms is their capacity to recognize and respond efficiently to foreign antigens. This is largely accomplished by the orchestrated activity of the innate and adaptive branches of the immune system. Antibodies are specifically generated in response to foreign antigens, facilitating thereby the specific recognition of antigens of almost infinite diversity. Receptors specific for the Fc domain of antibodies, Fc receptors, are expressed on the surface of the various myeloid leukocyte populations and mediate the binding and recognition of antibodies by innate leukocytes. By directly linking the innate and the adaptive components of immunity, Fc receptors play a central role in host defense and the maintenance of tissue homeostasis through the induction of diverse proinflammatory, anti-inflammatory, and immunomodulatory processes that are initiated upon engagement by the Fc domain. In this chapter, we discuss the mechanisms that regulate Fc domain binding to the various types of Fc receptors and provide an overview of the astonishing diversity of effector functions that are mediated through Fc-FcR interactions on myeloid cells. Lastly, we discuss the impact of FcR-mediated interactions in the context of IgG-mediated inflammation, autoimmunity, susceptibility to infection, and responsiveness to antibody-based therapeutics.
Quantitative Gel Electrophoresis: Sources of Variation (2008)

Gel electrophoresis is known for its often unsatisfactory precision. Percental relative standard deviations (RSD%) in a range of 15-70% have been reported. Therefore, an improvement of precision in quantitative 2-DE is necessary. In the present, study we have analyzed the work flow of 2-DE in detail to assess the main error sources. Potential major sources of variability for this technique include the transfer between first and second dimension, the analyst's expertise, and the staining or rather detection of separated proteins. The remarkable and completely irregular changes of the background signal from gel to gel were identified as one of the governing error sources. These background changes can be strongly reduced by the direct detection of the separated proteins using native fluorescence. More than a 3-fold better signal-to-noise ratio was found compared to Ruthenium-(II)-tris-(bathophenanthroline disulfonat) (RuBPS) and Coomassie staining, although the sample was used in an 800-fold lower concentration. This improvement together with well-defined peaks resulted in a better quantitative spot reproducibility of approximately 12-16% RSD%. Possibly, the variabilities due to detection and evaluation were already reduced to minor error components. However, according to the law of error propagation, the major error sources dominate the total error. To really prove the good detection and evaluation, these other sources of variability such as sample preparation, strip rehydration, protein loading, transfer between dimensions, interactions between gel and proteins, gel scanning, and spot integration have to be reduced next.
Purification and sequencing of cytochrome b from potato reveals methionine cleavage of a mitochondriallly encoded protein (1993)

Several mitochondrial genes from a large number of different fungi, mammals and plants have been sequenced but little is known about the corresponding translation products. We have affinity purified cytochrome c reductase from potato mitochondria and isolated the mitochondrially encoded cytochrome b protein. Amino-terminal sequencing reveals that the polypeptide does not start with a methionine. Comparison of the amino acid sequence with the recently published sequence of the gene encoding the cytochrome b apoprotein suggests that the N-formylmethionine is removed. This result provides the first evidence for the presence of a deformylase and a methionine aminopeptidase in mitochondria.
Novel electrochemical sensors for neutral molecules (1997)

Two new ferrocene receptors bind to a series of neutral carboxylic acid guests via hydrogen bonding interactions; complexation induces a significant change in the electronic properties of the proximate ferrocene units, as evidenced by the recognition of these neutral guests by cyclic voltammetry.
Oocyte influences on early development: the regulatory proteins leptin and STAT3 are polarized in mouse and human oocytes and differentially distributed within the cells of the preimplantation stage embryo (1997)

Unique protein domains, concentration gradients, and asymmetric protein distributions or polarities are principle forces establishing the identity and fate of individual cells during early development in lower vertebrates and invertebrates. Here, we present evidence that these same forces exist during mammalian development in the form of two representative regulatory proteins, leptin and STAT3. Leptin, the 16 kDa cytokine product of the obese gene (ob) is involved in the activation of STAT3, a member of the signal transducer and activation of transcription family of proteins. We examined the temporal and spatial aspects of leptin and STAT3 immunofluorescence in mouse and human oocytes and preimplantation stage embryos. The findings demonstrate that both leptin and STAT3 are polarized in the oocyte and, as a consequence of their location and the position of the cleavage planes with respect to these protein domains: (i) differences in allocation of these proteins between blastomeres occur at the first cell division such that by the 8-cell stage; (ii) unique cellular domains consisting of leptin/STAT3 rich and leptin/STAT3 poor populations of cells are generated. By the morula stage, a cell-borne concentration gradient of these proteins extending along the surface of the embryo is observed. A potential role of these proteins in early development is indicated at the morula stage where the 'inner' cells consist of blastomeres that contain little, if any, leptin/STAT3 while 'outer' cells contain both leptin/STAT3 rich and poor cells. This pattern persists through the hatched blastocyst stage with little, if any, leptin/STAT3 detected in the inner cell mass and populations of leptin/STAT3 rich and poor cells forming the trophoblast. We have examined oocytes from mutant C57BL/6J ob/ob mice which are both obese and infertile (although fertility can be restored by the exogenous provision of leptin) and have found STAT3 and the mutant (truncated) leptin protein to be present and polarized, suggesting the possibility that the truncated leptin protein may still contain operational domains which are functional during oocyte development and early embryogenesis. Furthermore, analysis of leptin and STAT3 in intact ovarian follicles suggests that these proteins may be maternally derived and in particular, that a subpopulation of follicle cells may be partly responsible for the establishment of their polarized distribution in the oocyte. The results are discussed with respect to the proposition that leptin and STAT3 have critical roles in early mammalian development, and may be involved in the determination of the animal pole of the oocyte and in the establishment of the inner cell mass and trophoblast in the preimplantation stage embryo.
Activation of 2-5A-dependent RNase by analogs of 2-5A (5'-O-triphosphoryladenylyl(2'—-5')adenylyl(2'—-5')adenosine ) using 2',5'-tetraadenylate (core)-cellulose. (1986)

A variety of 2-5A (px(A2'p)nA; x = 2 or 3, n greater than or equal to 2) analogs were assayed for their abilities to activate murine 2-5A-dependent RNase (subsequently "the nuclease") using a recently developed method. This technique consists of immobilizing and partially purifying the nuclease using core-cellulose [A2'p)3A-cellulose) and then monitoring the breakdown of poly(U)-3'-[32P]Cp into acid-soluble fragments. Several 5'-adenosinecapped analogs of 2-5A (containing a tetra-, tri-, or diphosphate) were analyzed, and it was found that reducing the number of phosphoryl groups between the 5' to 5'-diadenosine linkages resulted in a progressive loss of activity. Because A5' pppp(A2'p)3A was a potent activator of the nuclease yet stable during the assay these results suggested that a free 5'-phosphoryl group may not be required for the activation of the nuclease. A number of 8-bromoadenosine-substituted analogs of 2-5A were also studied. Curiously, the brominations decreased the activities of the 5'-di- and triphosphorylated molecules while substantially increasing the activities of the 5'-monophosphorylated species. The results indicated that a tri- or diphosphate moiety on the 5'-end of 2-5A or the presence of ATP is not absolutely required for the nuclease to be active. Furthermore, the ATP analog, beta, gamma-methylene ATP, did not inhibit the activity of the nuclease. Finally, a 3',5'-phosphodiester linkage isomer of 2-5A and a 3'-deoxy (cordycepin) analog of 2-5A were tested, and both were found to be completely without activity.
Differential reactivity of the functional sulfhydryl groups of cysteine-32 and cysteine-35 present in the reduced form of thioredoxin from Escherichia coli. (1980)

Only one of the sulfhydryl groups from Cys-32 and Cys-35 in the active center of native Escherichia coli thioredoxin-(SH)2 was alkylated by excess iodoacetic acid at pH values below 8.0. Both groups reacted in the protein denatured with 4.5 M guanidine hydrochloride. The second order rate of alkylation of thioredoxin-(SH)2 with 1 eq of iodoacetic acid was pH-dependent and showed independent initial reactions of one thiolate ion with a pK value of 6.7 and a second with a pK value close to 9.0. The same pH dependence was observed for alkylation with iodoacetamide but the apparent rate constant, 107 M-1 S-1 at pH 7.2, was about 20-fold higher than the corresponding rate with iodoacetate. The sulfhydryl group with a pK value of 6.7 was shown to belong to Cys-32 by labeling thioredoxin with [14C]iodoacetic acid followed by complete alkylation with [3H]iodoacetate and amino acid sequence analysis of peptides from the active center. The abnormally low pK value of Cys-32 is suggested to arise by electrostatic influence from a positive charge on the amino group of Lys-36. A mechanism of action for thioredoxin-(SH)2 as a protein disulfide reductase has been formulated. This is based on an initial nucleophilic attack by the thiolate of Cys-32 with the formation of an unstable transient mixed disulfide involving Cys-32 and one of the sulfurs in the substrate. This is followed by a conformational change and a nucleophilic attack of Cys-35 to give the 14-membered disulfide ring in thioredoxin-S2 and the dithiol of the substrate.
Monocyclic Enediynes:  Relationships between Ring Sizes, Alkyne Carbon Distances, Cyclization Barriers, and Hydrogen Abstraction Reactions. Singlet−Triplet Separations of Methyl-Substituted p-Benzynes (1998)

The Bergman-type cyclizations of parent, 2,3-dimethyl, and monocyclic (ring sizes = 7−12) enediynes were studied in detail at the Becke−Lee−Yang−Parr (BLYP) density functional (DFT) level with 6-31G* as well as 6-311+G** basis sets for geometry optimizations and relative energy evaluations, respectively. Pure DFT methods work reasonably well for these reactions; the errors are somewhat larger (ca. 3−7 kcal mol-1) than for the much more time-consuming complete active space (CASPT2) and coupled-cluster [CCSD(T)] (both in error by ca. 2 kcal mol-1) methods with high-quality basis sets. The hybrid method B3LYP is unsuitable for this type of chemistry (errors of 14−20 kcal mol-1). The singlet−triplet energy separations (ΔEST) for p-benzynes are underestimated systematically by about 2 kcal mol-1 at BLYP; the ΔEST of 2-methyl-p-benzyne (−3.1 kcal mol-1) is close to that of p-benzyne (−3.8 kcal mol-1, i.e., singlet ground state) but the 2,3-dimethyl-p-benzyne ΔEST is only −0.6 kcal mol-1 due to singlet destabilization (methyl repulsion). 2,3-Dialkyl-p-benzynes thus have nearly degenerate singlet and triplet states. While we find that there is clearly no predictive relationship between the alkyne carbon distance (d) and the cyclization activation enthalpy (ΔH⧧) for monocyclic enediynes, Nicolaou's empirically determined “critical range” of 3.31−3.2 Å, where spontaneous cyclization should occur at room temperature, should be extended to 3.4−2.9 Å. However, ring strain effects may become more important than distance arguments. Dimethyl substitution increases the endothermicity of the Bergman reaction (by about 12 kcal mol-1). The cyclization of a nine-membered enediyne is only mildly endothermic; larger rings give larger endothermicities. The formation of final products via double hydrogen abstraction from 1,4-cyclohexadiene is highly exothermic. The exothermicity decreases with increasing ring size due to unfavorable H···H repulsion in the products.
Application of a Nitrospiropyran-FAD-Reconstituted Glucose Oxidase and Charged Electron Mediators as Optobioelectronic Assemblies for the Amperometric Transduction of Recorded Optical Signals:  Control of the “On”−“Off” Direction of the Photoswitch (1997)

Apo-glucose oxidase is reconstituted with the semisynthetic nitrospiropyran-FAD cofactor to yield a photoisomerizable glucose oxidase, 3a-GOx. The nitrospiropyran-FAD-reconstituted GOx, 3a-GOx, undergoes reversible photoisomerization to the protonated nitromerocyanine-FAD GOx, 3b-GOx. The photoisomerizable enzyme was assembled as a monolayer on a Au electrode. The bioelectrocatalyzed oxidation of glucose in the presence of ferrocenecarboxylic acid (4), ferrocene-1,1‘-dicarboxylic acid (5), or 1-[1-(dimethylamino)ethyl]ferrocene (6), acting as electron mediators, was examined in the different photoisomer states of the enzyme. With 4 and 5 acting as electron mediators, the enzyme in state 3b-GOx exhibited bioelectrocatalytic activities for the oxidation of glucose. The bioelectrocatalytic functions of the enzyme in state 3a-GOx were blocked in the presence of 4 or 5. With 6 acting as electron mediator, the enzyme in state 3a-GOx exhibits bioelectrocatalytic activities for the oxidation of glucose, whereas the bioelectrocatalytic functions of the 3b-GOx state are blocked. The directionality of the enzyme photoswitch is controlled by the affinities of the oxidized electron mediators to diffusionally penetrate the protein and reach appropriate electron transfer distances to oxidize the FADH2 redox center of the enzyme. In all of the systems, cyclic amperometric transduction of optical signals recorded by the photoisomerizable enzyme is accomplished. The enzyme photoisomer “on” or “off” switching direction is controlled by tuning the electrical interactions of the electron mediator and the photoisomerizable enzyme.
Tissue Doppler Imaging Is Superior to Strain Rate Imaging and Postsystolic Shortening on the Prediction of Reverse Remodeling in Both Ischemic and Nonischemic Heart Failure After Cardiac Resynchronization Therapy (2004)

Ts-SD is the most powerful predictor of LV reverse remodeling and was consistently useful for ischemic and nonischemic heart failure. However, PSS is useful only for nonischemic pathogenesis, whereas the role of SRI parameters was not supported by the present study.
Mechanochemical studies of enzymatic degradation of insoluble collagen fibers (1977)

A mechanochemical method was developed for studying the enzymatic degradation of insoluble collagen fibers. The method involves stretching the collagen fiber to a fixed extension in the presence of a solution of collagenase and measuring the rate of relaxation of the force induced in the fiber. In this work, bacterial collagenase was used for reasons of availability. We observed invariably an exponential decrease in force with respect to ttime. The slope of the linear plot of logarithm of the force versus time was taken as a measure of the rate of enzymatic degradation. This rate was found a) to vary linearly with collagenase concentration; b) to be maximal at pH 7-8; c) to vary with temperature according to the Arrhenius relationship in the range 10-56 degrees C; d) to be reduced to varying extent by addition of EDTA omicron-phenanthroline, 2,3-dimercaptopropanolol, and D,L-cysteine; e) to be minimal when the strain on the fiber was ca. 4%; f) to be increased dramatically by denaturation of the collagen fiber; and g) to be reduced by an increase in the crosslink density of the collagen fiber. Except for the effect of strain, which can not be conveniently studied by existing methods these results are consistent with those observed by other methods for the study of the enzymatic degradation of collagen. The mechanochemical method is, however, uniquely suited to monitor continuously the enzymatically induced decay in the stress-bearing ability of collagen fibers. It has also been found useful in the design of collagenous implants with specified resistance to enzymatic degradation in vivo.
The CD58 (LFA-3) binding site is a localized and highly charged surface area on the AGFCC'C" face of the human CD2 adhesion domain. (1993)

Using site-directed mutagenesis in conjunction with NMR structural data on the adhesion domain of human CD2, we have defined the binding region for CD58. Previous structural studies of rat and human CD2 indicate that this adhesion domain is immunoglobulin-like. Here we report that the CD58 binding site is a well-circumscribed, charged surface area covering approximately 770 A2 on the AGFCC'C" face of the CD2 beta barrel. This site contains beta-strand residues in the carboxyl-terminal half of the F strand (including Lys-82 and Tyr-86), the top of the C strand (Asp-32 and Lys-34), and the C' strand (Gln-46), which are all solvent exposed. In addition, several exposed residues on the FG loop (Gly-90, Lys-91, Asn-92, and Val-93), the CC' loop (Lys-41 and Lys-43), and the C'C" loop (Arg-48 and Lys-51) form this site. In contrast, neither residues on the more peripheral G and C" strands of the same CD2 surface nor residues on B, E, and D strands of the opposite face are involved in CD58 binding. This CD58 binding site is predicted to lie most distal to the T-lymphocyte surface membrane, with ready access to CD58 on the surface of the opposing antigen-presenting cell.
Detection of Postnatal Depression (1987)

The development of a 10-item self-report scale (EPDS) to screen for Postnatal Depression in the community is described. After extensive pilot interviews a validation study was carried out on 84 mothers using the Research Diagnostic Criteria for depressive illness obtained from Goldberg's Standardised Psychiatric Interview. The EPDS was found to have satisfactory sensitivity and specificity, and was also sensitive to change in the severity of depression over time. The scale can be completed in about 5 minutes and has a simple method of scoring. The use of the EPDS in the secondary prevention of Postnatal Depression is discussed.
A method for quantification of absolute amounts of nucleic acids by (RT)-PCR and a new mathematical model for data analysis (2000)

Accurate quantification of nucleic acids by competitive (RT)-PCR requires a valid internal standard, a reference for data normalization and an adequate mathematical model for data analysis. We report here an effective procedure for the generation of homologous RNA internal standards and a strategy for synthesizing and using a reference target RNA in quantification of absolute amounts of nucleic acids. Further, a new mathematical model describing the general kinetic features of competitive PCR was developed. The model extends the validity of quantitative competitive (RT)-PCR beyond the exponential phase. The new method eliminates the errors arising from different amplification efficiencies of the co-amplified sequences and from heteroduplex formation in the system. The high accuracy (relative error <2%) is comparable to the recently developed real time detection 5'-nuclease PCR. Also, corresponding computer software has been devised for practical data analysis.
The Adipose Tissue as a Source of Vasoactive Factors (2004)

Obesity is associated with increased incidence of cardiovascular mortality. However, the mechanisms that link increased fat mass with hypercholesterolemia, hypertension, endothelial dysfunction and coronary heart disease have not been fully elucidated. Unravelling the diverse neuroendocrine systems, which regulate energy balance and body fat has been a long-standing challenge in biology, with obesity as an increasingly important public health focus. Until recently, the adipocyte has been considered only a passive tissue for the storage of excess energy in the form of fat. However, there is now compelling evidence that adipocytes act as endocrine, secretory cells. It has been shown that several hormones, growth factors and cytokines are actually expressed in white adipose tissue. In a dynamic view of the adipocyte a wide range of signals emanates from white adipose tissue such as tumour necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and their respective soluble receptors. White adipose tissue also secretes important regulators of lipoprotein metabolism like lipoprotein lipase (LPL), apolipoprotein E (apoE) and cholesteryl ester transfer protein (CETP). The increasing number of products secreted by adipocytes also includes leptin, estrogen, angiotensinogen, plasminogen activator inhibitor-1 (PAI-1), tissue factor and transforming growth factor-beta (TGF-beta). Nitric oxide synthase (NOS) has been also reported to be expressed in white adipose tissue. Acylation stimulating protein (ASP), adipophilin, adipoQ, adipsin, monobutyrin, agouti protein and factors related to pro-inflammatory and immune processes have also been shown to be released by white adipocytes. Since blood vessels express receptors for most of the adipocyte-derived factors, adipose tissue seems to play a key role in cardiovascular physiology through the existence of a network of local and systemic signals. The current knowledge in this field will be reviewed in the broader perspective of cardiovascular physiology and pathophysiology.
Derivatives of 4(7)-methyl- and 5,6-dimethyl-benzimidazolyl-2-mercaptoacetic acids. (1977)

Esters, hydrazides and hydrazones of the in title mentioned acids were prepared and screened for tuberculostatic activity. The strongest activity (MIC at 15-6 mug/cm3) was shown by hydrazide 4 and its hydrazone 4a.
Tetrameric and Homodimeric Camelid IgGs Originate from the Same IgH Locus (2008)

In addition to producing conventional tetrameric IgGs, camelids have the particularity of producing a functional homodimeric IgG type lacking L (light) chains and only made up of two H (heavy) chains. This nonconventional IgG type is characterized by variable and constant regions referred to as V(H)H and C(H)H, respectively, and which differ from conventional V(H) and C(H) counterparts. Although the structural properties of homodimeric IgGs have been well investigated, the genetic bases involved in their generation are still largely unknown. In this study, we characterized the organization of genes coding for the H chains of tetrameric and homodimeric IgGs by constructing an alpaca (Lama pacos) genomic cosmid library. We showed that a single IgH locus in alpaca chromosome 4 contains all of the genetic elements required for the generation of the two types of Igs. The alpaca IgH locus is composed of a V region that contains both V(H)H and V(H) genes followed by a unique D(H)-J(H) cluster and C region genes, which include both C(H)H and C(H) genes. Although this general gene organization greatly resembles that of other typical mammalian V(n)-D(n)-J(n)-C(n) translocon IgH loci, the intermixed gene organization within the alpaca V and C regions reveals a new type of translocon IgH locus. Furthermore, analyses of cDNA coding for the membrane forms of IgG and IgM present in alpaca peripheral blood B cells are most consistent with the notion that the development of a B cell bearing homodimeric IgG passes through an IgM(+) stage, similar to the case for conventional IgG.