gebhart/patrepeval huggingface dataset:
Bacteriological studies of developing supragingival dental plaque (1977)

The predominant flora of plaque developing on an area of about 1 sq cm. on the middle third of the buccal surface of the upper first molar of one individual was studied. Samples were taken at 5 and 15 min, 1, 2, 4 and 8 hr, and 1, 2, 4, 8 and 16 days; the tooth surface was cleaned prior to each period. Plaque samples were handled and cultured under anaerobic conditions utilizing various growth media. AH isolates from blood agar plates in Brewer jars with 30 to 100 colonies were characterized. Streptococcus sanguis , the single‐most predominant organism, and Actinomyces viscosus were consistently found. Streptococcus mitis, Staphylococcus epidermidis, Actinomyces israelii, Peptostreptococcus sp. and Veillonella alcalescens were found at more than one time period. High proportions of “suspected pairs” (mixtures of 2 or more intimately‐associated organisms), were regularly detected. Bacterial population changes with time were observed. Many isolates, particularly those present in plaques up to 8 hr, agglutinated in the presence of saliva. Less than half of the isolates, including Gram‐positive saccharolytic rods, staphylococci and some S. sanguis strains, formed plaque in vitro on wires in the presence of sucrose or glucose. The data suggest that the nature of the early microflora observed is determined by bacterial attachment which may be influenced by, amongst others, salivary constituents. Subsequent cell multiplication leads to a large bacterial increase in which proportional changes may occur as a result of differences in bacterial growth.
Radical species in the catalytic pathways of enzymes from anaerobes (1998)

Radicals are reactive intermediates of growing importance in enzymatic catalysis. There are reactions in which neutral radicals participate and those where radical anions are involved. The former class is illustrated by lysine 2,3-aminomutase and also by enzymes dependent on coenzyme B IP , that catalyse carbon skeleton rearrangements (e.g. glutamate mutase). A substrate-based radical for both lysine 2,3-aminomutase and glutamate mutase has been characterised by EPR spectroscopy. Representatives of the second class are 2-hydroxyglutaryl-CoA dehydratase, benzoyl-CoA reductase, DNA photolyase and chorismate synthase, all of which may generate the radical anion by one-electron reduction. 4-Hydroxybutyryl-CoA dehydratase, pyruvate formate lyase, and the coenzyme B IP -dependent eliminases (ribonucleotide reductase, ethanolamine ammonia lyase and diol dehydratase) could be examples of radical anion formation by one-electron oxidation. The electronrich ketyl-like radical anions cause the elimination of an adjacent group. The advantages of using radicals as intermediates in enzymatic transformations are their high reactivity and special properties. However, this reactivity includes rapid bimolecular combination with dioxygen and radicals are therefore primarily utilised as intermediates by anaerobic organisms. z
DNA fragmentation and NAD depletion. Their relation to the turnover of endogenous mono(ADP-ribosyl) and poly(ADP-ribosyl) proteins. (1982)

Treatment of Ehrlich ascites tumor cells with the trifunctional alkylating agent 2,3-5-tris(ethyleneimino)benzoquinone-1,4 (triaziquonum) led to rapid fragmentation of DNA and depletion of NAD while poly(ADP-ribose) synthetase activity showed a retarded increase. Poly(ADP-ribosyl) residues in treated cells increased 4- to 30-fold, but transiently, and in a dose-dependent manner, exhibiting the same initial kinetics as the loss of NAD and the appearance of DNA strand breaks when determined by the nucleoid method. Although the amounts of "activated ADP-ribosyl" groups present in the substrate NAD (80 nmol/10(8) cells) exceeded by far basal and triaziquonum-induced poly(ADP-ribosyl) groups (up to 250 pmol/10(8) cells), accelerated formation of the polymer, nevertheless, may explain at least partially the loss of NAD seen under these conditions. Addition of benzamide, a potent inhibitor of poly(ADP-ribose) synthetase, to triaziquonum-treated cells effected an immediate drop of poly(ADP-ribose) to basal values. The data indicate a biphasic decay, the half-life of greater than 85% of the polymeric ADP-ribosyl groups exhibiting a t1/2 less than 1 min under these conditions, while the residual fraction died away with t1/2 approximately 6 min. Treatment with the DNA fragmenting agent also led to a 9-fold increase of nuclear mono(ADP-ribosyl) groups, while cytoplasmic mono(ADP-ribosyl) protein conjugates were not significantly affected. The apparent half-life of nuclear mono (ADP-ribosyl) protein conjugates (8-10 min) at peak elevation was definitely longer than that of poly(ADP-ribosyl) residues. This result is consistent with the interpretation that accumulation of mono(ADP-ribosyl) groups is due to a retarded removal of the primary ADP-ribosyl group from the acceptor protein by a separate mono(ADP-ribosyl) protein glycohydrolase, being the rate-limiting step in the overall turnover of poly(ADP-ribosyl) residues.
Differential Modification of p27 Kip1 Controls Its Cyclin D-cdk4 Inhibitory Activity (2007)

Whether p27 is a cyclin D-cdk4/6 inhibitor or not is controversial, and how it might switch between these two modes is unknown. Arguing for a two-state mechanism, we show that p27 bound to cyclin D-cdk4 can be both inhibitory and noninhibitory, due to its differential-growth-state-dependent tyrosine phosphorylation. We found that p27 from proliferating cells was noninhibitory but that p27 from arrested cells was inhibitory, and the transition from a bound noninhibitor to a bound inhibitor was not due to an increase in p27 concentration. Rather, two tyrosine residues (Y88 and Y89) in p27's cdk interaction domain were phosphorylated preferentially in proliferating cells, which converted p27 to a noninhibitor. Concordantly, mutation of these sites rendered p27 resistant to phosphorylation and locked it into the bound-inhibitor mode in vivo and in vitro. Y88 was directly phosphorylated in vitro by the tyrosine kinase Abl, which converted p27 to a cdk4-bound noninhibitor. These data show that the growth-state-dependent tyrosine phosphorylation of p27 modulates its inhibitory activity in vivo.
Biochemical investigations on a patient with a defect in cytosolic acetoacetyl‐CoA thiolase, associated with mental retardation (1984)

A severely mentally retarded boy with two normal siblings was persistently found to excrete elevated amounts of 3-hydroxybutyrate and acetoacetate. Enzyme analysis in cultured fibroblasts revealed a probable deficiency in cytosolic acetoacetyl-CoA thiolase which was about half the control activity with normal mitochondrial thiolase activities. Treatment with reduced dietary fat was initiated and a rapid reduction of the ketosis to biochemical normality was demonstrated. Shortly after initiating dietary treatment he presented with severe gastrointestinal problems and the histological features of colitis cystica superficialis. This appeared to respond to intravenous hydrocortisone therapy with an apparent complete recovery.
Molecular Heterogeneity in Acute Renal Allograft Rejection Identified by DNA Microarray Profiling (2003)

Systematic analysis of gene-expression patterns provides a window on the biology and pathogenesis of renal allograft rejection. Biopsy samples from patients with acute rejection that are indistinguishable on conventional histologic analysis reveal extensive differences in gene expression, which are associated with differences in immunologic and cellular features and clinical course. The presence of dense clusters of B cells in a biopsy sample was strongly associated with severe graft rejection, suggesting a pivotal role of infiltrating B cells in acute rejection.
Amino acid sequence of the encephalitogenic basic protein from human myelin (1971)

Myelin from the central nervous system contains an unusual basic protein, which can induce experimental autoimmune encephalomyelitis. The basic protein from human brain was digested with trypsin and other enzymes and the sequence of the 170 amino acids was determined. The localization of the encephalitogenic determinants was described. Possible roles for the protein in the structure and function of myelin are discussed.
Induction of the estrogen-regulated "24K" protein by heat shock. (1989)

We have previously demonstrated an estrogen-regulated protein, termed 24K, in human breast cancer cell lines and human tumor biopsies. The presence of the protein correlates well with the presence of steroid hormone receptors. We have cloned a partial complementary DNA to 24K and show that the nucleotide and deduced amino acid sequence contains a striking homology to the low molecular weight heat shock proteins of Drosophila and the mammalian alpha-crystallins. Our complementary DNA is identical to that reported for the 3' region of human heat shock protein 27/28 with the mRNAs for the gene significantly induced by both heat shock and estradiol treatment in MCF-7 breast cancer cells. A variant polymorphism of the gene was detected in two estrogen-unresponsive cell lines, but not in other human breast cancer cell lines or human placenta; the polymorphism did not affect heat shock induction of the gene. The heat shock protein 27/28 model system in MCF-7 cells will afford a valuable tool to analyze the molecular events underlying the hormonal regulation of gene expression; heat shock may offer an approach to manipulate the hormonal regulation of the heat shock protein 27/28 gene.
Novel Indolyl Aryl Sulfones Active against HIV-1 Carrying NNRTI Resistance Mutations:  Synthesis and SAR Studies (2003)

The potent anti-HIV-1 activities of L-737,126 (2) and PAS sulfones prompted us to design and test against HIV-1 in acutely infected MT-4 cells a number of novel 1- and 3-benzenesulfonylindoles. Indoles belonging to the 1-benzenesulfonyl series were found poorly or totally inactive. On the contrary, some of the 3-benzenesulfonyl derivatives turned out to be as potent as 2, being endowed with potencies in the low nanomolar concentration range. In particular, (2-methylphenyl)sulfonyl (72) and (3-methylphenyl)sulfonyl (73) derivatives showed EC(50) values of 1 nM. Introduction of two methyl groups at positions 3 and 5 of the phenyl ring of 2 furnished derivatives (80 and 83) which showed very potent and selective anti-HIV-1 activity not only against the wt strain, but also against mutants carrying NNRTI-resistant mutations at positions 103 and 181 of the reverse transcriptase gene.
The Vfl1 Protein in Chlamydomonas Localizes in a Rotationally Asymmetric Pattern at the Distal Ends of the Basal Bodies (2001)

In the unicellular alga Chlamydomonas, two anterior flagella are positioned with 180 degrees rotational symmetry, such that the flagella beat with the effective strokes in opposite directions (Hoops, H.J., and G.B. Witman. 1983. J. Cell Biol. 97:902-908). The vfl1 mutation results in variable numbers and positioning of flagella and basal bodies (Adams, G.M.W., R.L. Wright, and J.W. Jarvik. 1985. J. Cell Biol. 100:955-964). Using a tagged allele, we cloned the VFL1 gene that encodes a protein of 128 kD with five leucine-rich repeat sequences near the NH(2) terminus and a large alpha-helical-coiled coil domain at the COOH terminus. An epitope-tagged gene construct rescued the mutant phenotype and expressed a tagged protein (Vfl1p) that copurified with basal body flagellar apparatuses. Immunofluorescence experiments showed that Vfl1p localized with basal bodies and probasal bodies. Immunogold labeling localized Vfl1p inside the lumen of the basal body at the distal end. Distribution of gold particles was rotationally asymmetric, with most particles located near the doublet microtubules that face the opposite basal body. The mutant phenotype, together with the localization results, suggest that Vfl1p plays a role in establishing the correct rotational orientation of basal bodies. Vfl1p is the first reported molecular marker of the rotational asymmetry inherent to basal bodies.
Role of mantle flow at the North Fiji Basin: Insights from anomalous topography (2006)

The North Fiji Basin is a complex back‐arc system situated between the opposite‐verging Tonga and New Hebrides subduction zones. On the basis of two independent calculations, we find that the back‐arc region is anomalously high with topography residuals reaching up to 2000 m above what should be isostatically supported. Our study aims to test whether a hot buoyant upwelling is required beneath the North Fiji Basin to support the observed high elevation. The mantle thermal structure beneath the North Fiji Basin is inferred from the global tomographic model S20RTS, where seismic velocity anomalies are converted to density/temperature anomalies. This thermal structure is input into a three‐dimensional mantle convection code, CitcomS, and the flow‐induced surface topography is calculated and compared with the observed anomalous topography. In a series of experiments, we eliminate various portions of the mantle structure to consider what type of mantle flow can support the anomalous topography. The experiments suggest that the observed topography in the North Fiji Basin is consistent with the support of hot buoyant upper mantle upwelling, and specifically rising material in the depth range from 70 to 120 km is the most critical component. A relatively thin/weak lithosphere is required to produce the high‐amplitude and short‐wavelength topography residuals, and the presence of discrete breaks in the plate produces further localization of flow‐induced topography.
Generation of PSA-reactive effector cells after vaccination with a PSA-based vaccine in patients with prostate cancer (2000)

Vaccination with PSA formulated into liposomes induced T-cell responses in 8/10 patients with prostate carcinoma. The frequency of PSA-reactive precursor T cells was relatively low in the blood of these patients, and IVS, leading to amplification of the precursor cells prior to ELISPOT, was necessary for quantification of the PSA-responding T cells. Cellular responses to PSA were predominantly mediated by CD4(+) T lymphocytes.
An electrically trainable artificial neural network (ETANN) with 10240 'floating gate' synapses (1989)

The use of floating-gate nonvolatile memory technology for analog storage of connection strengths, or weights, has previously been proposed and demonstrated. The authors report the analog storage and multiply characteristics of a new floating-gate synapse and further discuss the architecture of a neural network which uses this synapse cell. In the architecture described 8192 synapses are used to interconnect 64 neurons fully and to connect the 64 neurons to each of 64 inputs. Each synapse in the network multiplies a signed analog voltage by a stored weight and generates a differential current proportional to the product. Differential currents are summed on a pair of bit lines and transferred through a sigmoid function, appearing at the neuron output as an analog voltage. Input and output levels are compatible for ease in cascade-connecting these devices into multilayer networks. The width and height of weight-change pulses are calculated. The synapse cell size is 2009 mu m/sup 2/ using 1- mu m CMOS EEPROM technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Before You Analyze a Human Specimen, Think Quality, Variability, and Bias (2010)

Personalized medicine requires capabilities to detect and measure health-associated biomarkers with increasingly specific and sensitive methods, putting analytical chemists at the front lines of translational research. Analytical scientists must be upstream in the experimental design process because the analysis of a biospecimen (tissue, blood, etc.) presents technical and experimental design complexities. (To listen to a podcast about this feature, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).
A Comparison of Continuous Intravenous Epoprostenol (Prostacyclin) with Conventional Therapy for Primary Pulmonary Hypertension (1996)

As compared with conventional therapy, the continuous intravenous infusion of epoprostenol produced symptomatic and hemodynamic improvement, as well as improved survival in patients with severe primary pulmonary hypertension.
Cavity quantum electrodynamics (2006)

This paper reviews the work on cavity quantum electrodynamics of free atoms. In recent years, cavity experiments have also been conducted on a variety of solid-state systems resulting in many interesting applications, of which microlasers, photon bandgap structures and quantum dot structures in cavities are outstanding examples. Although these phenomena and systems are very interesting, discussion is limited here to free atoms and mostly single atoms because these systems exhibit clean quantum phenomena and are not disturbed by a variety of other effects. At the centre of our review is the work on the one-atom maser, but we also give a survey of the entire field, using free atoms in order to show the large variety of problems dealt with. The cavity interaction can be separated into two main regimes: the weak coupling in cavity or cavity-like structures with low quality factors Q and the strong coupling when high-Q cavities are involved. The weak coupling leads to modification of spontaneous transitions and level shifts, whereas the strong coupling enables one to observe a periodic exchange of photons between atoms and the radiation field. In this case, atoms and photons are entangled, this being the basis for a variety of phenomena observed, some of them leading to interesting applications in quantum information processing. The cavity experiments with free atoms reached a new domain with the advent of experiments in the visible spectral region. A review on recent achievements in this area is also given.
Development and maturation of cerebral cortex (1988)

The previous volumes in this series have dealt with the mature cerebral cortex. In those volumes many of the structurally and physiologically distinct areas of the cerebral cortex, their connections, the various types of neurons and neuroglial cells they contain, and the functions of those cells have been considered. In the present volume the contributions focus on the development of the neocortex and hippocampus. Chapters in this volume describe how the neurons migrate in the cortex to attain their ultimate positions, and emphasize the role played by the preexisting pallium or primordial plexiform layer of the cerebral vesicle in the development of the cerebral cortex. The primordial plexiform layer becomes split by the invasion of neurons that will form the cortical plate, and mutants in which the neuronal migration is abnormal provide valuable information about the role of the radial glial cells in this migration. It is also made clear that although the mechanics of development in the hippocampus are similar to those in the neocortex, the development of the hippocampus involves some unique features. For example, neuronal proliferation in the dentate gyrus continues well into postnatal life.
Purification and Properties of Electron-transferring Flavoprotein from Peptostreptococcus elsdenii (1974)

An electron-transferring flavoprotein (ETF) which couples the oxidation of NADH to the reduction of butyryl coenzyme A dehydrogenase has been purified in large quantities from the anaerobic bacterium Peptostreptococcus elsdenii. The purified protein appears to be homogeneous on the basis of polyacrylamide disc gel electrophoresis, thin layer isoelectric focusing, sedimentation velocity, and the Sephadex G-100 elution profile. Preliminary evidence suggests that ETF is also found in a complex with another flavoprotein. ETF has a molecular weight of 72,000 to 75,000 by Sephadex G-100 chromatography and is a dimer of two nonidentical subunits of approximate molecular weights of 33,000 and 41,000 determined by sodium dodecyl sulfate disc gel electrophoresis. Based on amino acid analyses, there are 2 moles of FAD per mole of protein of molecular weight 75,600. Possibly each subunit is associated with 1 FAD. The protein-bound FAD is 2.4 times more fluorescent than free FAD. Both tyrosine and tryptophan contribute to the protein fluorescence of ETF. Although the major prosthetic group of ETF is FAD, the isolated protein contains variable amounts of 6-hydroxy-7,8-dimethyl-10-(ribityl-5′-ADP)-isoalloxazine and 7-methyl-8-hydroxy-10-(ribityl-5′-ADP)-isoalloxazine. The isolated protein binds 30% more FAD to give enhanced activity and marked changes in the absorption spectrum. The spectrum of the oxidized isolated ETF is also drastically changed when the protein is maintained for long periods in its reduced form before subsequent reoxidation. In both cases, the major change is a large increase in the absorption around 400 nm. Apo-ETF has been prepared by treatment of the native protein with guanidine HCl. Catalytic activity is restored to the apoprotein by addition of FAD but not FMN. The reconstituted ETF also has increased absorption around 400 nm and decreased absorption at 450 nm compared to the isolated ETF. Unlike many other flavoprotein dehydrogenases which stabilize the neutral, blue flavin semiquinone and do not react with sulfite, ETF stabilizes the red, anionic semiquinone and also reacts with sulfite. Anaerobic titration of ETF with NADH or sodium dithionite resulted in a 2-electron reduction per protein-bound FAD, indicating that there are no colorless oxidation-reduction active groups present.
Pancreatic β-Cell Function and Immune Responses to Insulin After Administration of Intranasal Insulin to Humans At Risk for Type 1 Diabetes (2004)

Results from this pilot study suggest that intranasal insulin does not accelerate loss of beta-cell function in individuals at risk for type 1 diabetes and induces immune changes consistent with mucosal tolerance to insulin. These findings justify a formal trial to determine if intranasal insulin is immunotherapeutic and retards progression to clinical diabetes.
Mannheimia ( Pasteurella ) haemolytica Leukotoxin Binding Domain Lies within Amino Acids 1 to 291 of Bovine CD18 (2005)

Previously, we identified bovine CD18 as the receptor for leukotoxin secreted by Mannheimia (Pasteurella) haemolytica. In this study, we constructed bovine-murine CD18 chimeras to locate the leukotoxin binding domain on CD18. Leukotoxin specifically lysed transfectants expressing bovine CD18 fragment encompassing amino acids 1 to 291, indicating that leukotoxin binding domain lies within amino acids 1 to 291 of bovine CD18.
FGF23 induces left ventricular hypertrophy (2011)

Chronic kidney disease (CKD) is a public health epidemic that increases risk of death due to cardiovascular disease. Left ventricular hypertrophy (LVH) is an important mechanism of cardiovascular disease in individuals with CKD. Elevated levels of FGF23 have been linked to greater risks of LVH and mortality in patients with CKD, but whether these risks represent causal effects of FGF23 is unknown. Here, we report that elevated FGF23 levels are independently associated with LVH in a large, racially diverse CKD cohort. FGF23 caused pathological hypertrophy of isolated rat cardiomyocytes via FGF receptor-dependent activation of the calcineurin-NFAT signaling pathway, but this effect was independent of klotho, the coreceptor for FGF23 in the kidney and parathyroid glands. Intramyocardial or intravenous injection of FGF23 in wild-type mice resulted in LVH, and klotho-deficient mice demonstrated elevated FGF23 levels and LVH. In an established animal model of CKD, treatment with an FGF-receptor blocker attenuated LVH, although no change in blood pressure was observed. These results unveil a klotho-independent, causal role for FGF23 in the pathogenesis of LVH and suggest that chronically elevated FGF23 levels contribute directly to high rates of LVH and mortality in individuals with CKD.
Lineage-Specific Hematopoietic Growth Factors (2006)

This review surveys the mechanisms and clinical applications of three hematopoietic growth factors: erythropoietin, granulocyte colony-stimulating factor, and thrombopoietin.