gebhart/patrepeval huggingface dataset:
Lateral force microscopy using acoustic friction force microscopy (1999)

Conventional friction force microscopy (FFM) is widely used for tribological studies of engineering surfaces. It is, however, difficult to separate friction forces resulting from interactions dependent upon interfacial material properties from surface topography-induced lateral forces. We have developed and employed a technique to operate acoustic friction force microscopy (AFFM) by oscillating the sample laterally at megahertz frequencies. The in-plane vibrations perpendicular to the longitudinal axis of the cantilever are generated because of lateral forces between the probe tip and the sample. Torsional cantilever vibrations were detected at frequencies of up to 2 MHz. A mean cantilever lift-off was observed that can be explained by elastohydrodynamic lubrication. The high-frequency torsional vibration amplitude provides information about the lateral forces that can be used to calculate the friction and viscosity of thin surface films. The AFFM images of metal-particle magnetic tapes were produced, revealing a resolution apparently better than FFM images. Unlike FFM images, AFFM images are independent of the scanning direction, indicating that AFFM images are less sensitive to topography-induced lateral forces. Also, AFFM, allows friction measurements at relative velocities of the order of 1 mm s −1 which is much larger than that obtained in conventional FFM (several μm s−1). Copyright © 1999 John Wiley & Sons, Ltd.
Growth and luminescence spectroscopy of a CuCl quantum well structure (1988)

A structure of the type CaF2/CuCl/CaF2, in which the confined layer is 150 Å thick, has been grown on a Si(111) surface by molecular beam epitaxy in ultrahigh vacuum. The optical properties of the CuCl film have been characterized by low-temperature photoluminescence as a function of excitation density. Striking differences in the excitonic emissions are observed between the quantum well structure and a bulk single crystal of CuCl, and are discussed in terms of film purity and thickness.
The role of SOS boxes in enteric bacteriocin regulation (2008)

Bacteriocins are a large and functionally diverse family of toxins found in all major lineages of Bacteria. Colicins, those bacteriocins produced by Escherichia coli, serve as a model system for investigations of bacteriocin structure-function relationships, genetic organization, and their ecological role and evolutionary history. Colicin expression is often dependent on host regulatory pathways (such as the SOS system), is usually confined to times of stress, and results in death of the producing cells. This study investigates the role of the SOS system in mediating this unique form of toxin expression. A comparison of all the sequenced enteric bacteriocin promoters reveals that over 75 % are regulated by dual, overlapping SOS boxes, which serve to bind two LexA repressor proteins. Furthermore, a highly conserved poly-A motif is present in both of the binding sites examined, indicating enhanced affinity of the LexA protein for the binding site. The use of gene expression analysis and deletion mutations further demonstrates that these unique LexA cooperative binding regions result in a fine tuning of bacteriocin production, limiting it to times of stress. These results suggest that the evolution of dual SOS boxes elegantly accomplishes the task of increasing the amount of toxin produced by a cell while decreasing the rate of uninduced production, effectively reducing the cost of colicin production. This hypothesis may explain why such a promoter motif is present at such high frequencies in natural populations of bacteriocin-producing enteric bacteria.
The Kinetics and Mechanism of the Reaction of Diphenyldiazomethane and Benzoic Acid in Ethanol1 (1951)

The reactions of substituted diazomethanes with carboxylic acids have been studied mainly in nonhydroxylic solvents. In one of the earliest papers published on this subject, Staudinger and Gaule reported that a variety of diazomethane derivatives reacted with substituted acetic acids in cumene at rates which depended on the strengths of the acids. Similar observations were later made by Norris and Strain with di-p-tolyldiazomethane and substituted benzoic acids in benzene, toluene and ethyl acetate solutions. The reaction of diazoacetic ester in aprotic solvents with various carboxylic acids has also been investigated and found to be roughly second-order in acid in contrast to the reaction of di-p-tolyldiazomethane with benzoic acid in toluene, which has been reported to be accurately first-order in acids. In non-hydroxylic solvents, the principal (if not the exclusive) reaction products are the carboxylic esters. Thus, diphenyldiazomethane reacts with benzoic acid in ether to give a 92% yield of benzhydryl benzoate' and recently Hardegger, El Heweihi and Robinet found that a large variety of carboxylic acids react similarly in non-hydroxylic solvents to form the corresponding benzhydryl esters in high yields.
Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs (2014)

Aging is a progressive process that results in the accumulation of intra- and extracellular alterations that in turn contribute to a reduction in health. Age-related changes in DNA methylation have been reported before and may be responsible for aging-induced changes in gene expression, although a causal relationship has yet to be shown. Using genome-wide assays, we analyzed age-induced changes in DNA methylation and their effect on gene expression with and without transient induction with the synthetic transcription modulating agent WY14,643. To demonstrate feasibility of the approach, we isolated peripheral blood mononucleated cells (PBMCs) from five young and five old healthy male volunteers and cultured them with or without WY14,643. Infinium 450K BeadChip and Affymetrix Human Gene 1.1 ST expression array analysis revealed significant differential methylation of at least 5 % (ΔYO > 5 %) at 10,625 CpG sites between young and old subjects, but only a subset of the associated genes were also differentially expressed. Age-related differential methylation of previously reported epigenetic biomarkers of aging including ELOVL2, FHL2, PENK, and KLF14 was confirmed in our study, but these genes did not display an age-related change in gene expression in PBMCs. Bioinformatic analysis revealed that differentially methylated genes that lack an age-related expression change predominantly represent genes involved in carcinogenesis and developmental processes, and expression of most of these genes were silenced in PBMCs. No changes in DNA methylation were found in genes displaying transiently induced changes in gene expression. In conclusion, aging-induced differential methylation often targets developmental genes and occurs mostly without change in gene expression.
Unusual xanthomas in a young patient with heterozygous familial hypercholesterolemia and type III hyperlipoproteinemia (1996)

We report on a 20-year-old man with the combination of two independent familial lipoprotein disorders: heterozygous familial hypercholesterolemia (FH) and type III hyperlipoproteinemia (HLP). Familial hypercholesterolemia was diagnosed by elevated total and low density lipoprotein cholesterol levels and family history. By denaturing gradient gel electrophoresis, DNA sequencing and restriction fragment length polymorphism analysis, a G --> A splice donor mutation in intron 3 of the proband's low density lipoprotein receptor gene was identified as the underlying molecular defect. This mutation was described previously as a receptor-negative founder mutation in Norway (FH-Elverum) and subsequently in 6 unrelated heterozygous English patients, creating a severe phenotype of familial hypercholesterolemia. Type III HLP was confirmed by homozygosity for apolipoprotein (apo) E2 and an elevated ratio of very low density lipoprotein cholesterol to serum triglycerides (0.40; normal ratio about 0.20). The patient has unusual flat xanthomas in the interdigital webs of the hands which are normally not found in either disease. These dermatological findings might therefore be indicative of the rare combination of both disorders of lipoprotein metabolism in one individual.
Extracellular domain-IgG fusion proteins for three human natriuretic peptide receptors. Hormone pharmacology and application to solid phase screening of synthetic peptide antisera. (1991)

The natriuretic peptide receptors (NPRs) are a family of three cell surface glycoproteins, each with a single transmembrane domain. Two of these receptors, designated NPR-A and NPR-B, are membrane guanylyl cyclases that synthesize cGMP in response to hormone stimulation. The third receptor, NPR-C, has been reported to function in the metabolic clearance of ligand and in guanylyl cyclase-independent signal transduction. We engineered three chimeric proteins consisting of the natriuretic peptide receptor extracellular domains fused to the Fc portion of human IgG-gamma 1. These molecules provide material for detailed studies of the human receptor's extracellular domain structure and interaction with the three human natriuretic peptides, atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and type-C natriuretic peptide (CNP). The homodimeric fusion proteins, designated A-IgG, B-IgG, and C-IgG, were secreted from Chinese hamster ovary cells and purified by protein-A affinity chromatography. We present here the primary characterization of these fusion proteins as represented by the intrinsic hormone affinities measured by saturation binding and competition assays. The dissociation constant of 125I-ANP for A-IgG was 1.6 pM and for C-IgG, 1.2 pM. The dissociation constant of 125I-Y0-CNP (CNP with addition of tyrosine at the amino terminus) for B-IgG was 23 pM. The rank order of potency in competitive binding for A-IgG was ANP greater than BNP much greater than CNP, whereas for B-IgG the ranking was CNP much greater than ANP greater than BNP. For C-IgG, we observed ANP greater than CNP greater than or equal to BNP. These data demonstrate that the receptor-IgG fusion proteins discriminate among the natriuretic peptides in the same manner as the native receptors and provide a basis for future structural studies with these molecules. The purified fusion proteins have a variety of potential applications, one of which we illustrate by a solid phase screening assay in which rabbit sera from a series of synthetic-peptide immunizations were titered for receptor reactivity and selectivity.
Effects of quinidine and related compounds on cytotoxicity and cellular accumulation of vincristine and adriamycin in drug-resistant tumor cells. (1984)

Quinidine, which has antiarrhythmic activity, greatly enhanced the cytotoxicity of vincristine (VCR) in tumor cells and especially in VCR-resistant sublines of P388 leukemia (P388/VCR) and human myelogenous leukemia. A nontoxic concentration of quinidine increased VCR cytotoxicity in these resistant tumor cells about 50 to 80 times, and the drug in combination with VCR could completely reverse VCR resistance of these cell lines. Quinidine also enhanced the cytotoxicity of Adriamycin, especially in the Adriamycin-resistant subline of P388 leukemia; this enhancement (8-fold) was less than that of VCR toxicity in the VCR-resistant tumor line. When administered daily for 10 days with VCR, quinidine at doses of 50 to 125 mg/kg significantly enhanced the chemotherapeutic effect of VCR in P388/VCR-bearing mice. Some other antiarrhythmic agents also showed similar effects in vitro, but these effects were considerably lower than that of quinidine. Quinidine increased the cellular levels of VCR and daunomycin in VCR-resistant sublines of mouse and human tumors and the ADM-resistant mouse tumor line in vitro, respectively. Quinidine also enhanced the cellular accumulation of VCR in P388/VCR cells in vivo. Thus, the therapeutic effect observed in P388/VCR-bearing mice might be due to the enhanced accumulation of VCR in P388/VCR cells by quinidine. The increase of cellular accumulation of VCR was partly explained by inhibition of efflux of VCR and daunomycin from the resistant tumor cells. The mechanism of this phenomenon is discussed in relation to previous findings on calcium channel blockers.
Selective adhesion of platelets on a polyion complex composed of phospholipid polymers containing sulfonate groups and quarternary ammonium groups (1994)

We investigated the effects of electrical charges on cell-polymer interactions of poly[2-methacryloyloxyethyl phosphorylcholine(MPC)-co-n-butyl methacrylate (BMA)] (PMB) having excellent blood compatibility, by copolymerizing anionic or cationic methacrylates with MPC and BMA. A polyion complex (PIC) composed of anionic and cationic MPC copolymers was also prepared. When the cell adhesion on these polymer surfaces from rabbit whole blood was evaluated, we observed a considerable reduction in cell adhesion on the MPC copolymers compared with that on poly(BMA), even when the MPC copolymer was electrically charged. On the other hand, many platelets selectively adhered to the PIC surface from whole blood, but the adherent platelets maintained a discoid shape. The amount of adenosine triphosphate (ATP) in platelets adherent on the PMB or the PIC from a platelet-rich plasma (PRP) was more than 75% of that in the original PRP, which indicated that the activity of these platelets remained high. However, in the platelets adherent to poly(BMA), only a small amount of ATP remained. Protein adsorption on the polymer surface from human plasma was investigated using a gold-colloid-labeled immunoassay against albumin gamma-globulin, and fibrinogen. Many of these proteins adsorbed on poly(BMA), whereas a small amount of protein was observed on the MPC copolymers that had an electrical charge. Albumin adsorption and suppression of gamma-globulin and fibrinogen adsorption were found on the PIC. Therefore, the introduction of electrical charges in the PMB did not have an adverse effect on cell adhesion and protein adsorption.(ABSTRACT TRUNCATED AT 250 WORDS)
Differential spectral interferometry: an imaging technique for biomedical applications (2003)

Differential spectral interferometry (DSI), a novel method of biomedical imaging that combines the high dynamic range of optical coherence tomography (OCT) with inherently parallel low-bandwidth image acquisition of spectral interferometry (SI), is described. DSI efficiently removes the deleterious dc background inherent in SI measurements while maintaining the parallel nature of SI. We demonstrate DSI on both synthetic and biological samples. Because DSI preserves the low-bandwidth, parallel nature of SI, it is competitive with OCT for biomedical applications in terms of image quality and acquisition rate.
Evaluation of 3-Dimensional Superimposition Techniques on Various Skeletal Structures of the Head Using Surface Models (2015)

Superimposition of 3D datasets using surface models created from voxel data can provide accurate, precise, and reproducible results, offering also high efficiency and increased post-processing capabilities. In the present study population, the BZ superimposition was comparable to AC, with the added advantage of being applicable to scans with a smaller field of view.
Transport of p-nitrophenyl-alpha-maltoside by the maltose transport system of Escherichia coli and its subsequent hydrolysis by a cytoplasmic alpha-maltosidase (1986)

In wild-type Escherichia coli the activity of the maltose transport system is dependent on a periplasmic maltose-binding protein. It has been possible, however, to isolate mutants in which transport activity is mediated by the membrane components of the system and is no longer dependent on the periplasmic binding protein. In this manuscript we show that in these binding protein-independent strains, p-nitrophenyl-alpha-maltoside is a potent inhibitor of maltose transport. In contrast, p-nitrophenyl-alpha-maltoside is only a weak inhibitor of maltose transport in wild-type bacteria. In addition, we show that p-nitrophenyl-alpha-maltoside is transported by the binding protein-independent strains but not by wild-type bacteria. We were able to detect transport of this compound because there is a cytoplasmic enzyme that cleaves p-nitrophenyl-alpha-maltoside. This enzyme has not previously been described. We show that although the synthesis of this enzyme is subject to the same regulation as the components of the maltose regulon, and is MalT dependent, it is not coded for by a known mal gene. We refer to this enzyme as alpha-maltosidase. These results strengthen our proposal that the membrane components of the maltose transport system comprise a recognition site for maltose and related substrates.
Cortical Stimulation and Epileptic Seizure: A Study of the Potential Risk in Primates (1999)

It thus seems that motor cortex stimulation does not induce epileptic complications when the classic clinical criteria of stimulation are respected. Nevertheless, it would be wise to subject candidates for implantation to intermittent light stimulation before and after a period of stimulation to ascertain the innocuousness of the cortical stimulation.
Targeting Double Stranded DNA with Peptide Nucleic Acid (PNA) (2001)

PNA (peptide nucleic acid) is a DNA mimic with a pseudopeptide (polyamide) backbone which can be used to target double stranded DNA with high sequence specificity. PNA therefore has great potential in the development of biomolecular tools for manipulation of DNA as well as for the development of DNA targeted gene therapeutic drugs. The status of this field is discussed in terms of PNA binding modes and mechanism as well as applications.
Lifelong Aspirin Supplementation as a Means to Extending Life Span (2004)

Arising from an initiative by the National Institute of Aging (NIA) requesting novel proposals challenged with increasing lifespan and longevity, our laboratory has generated a hypothesis to test the efficacy of lifelong, low-dosage aspirin administration as a means to achieving this goal. The intervention testing program (currently underway) proposing aspirin as an anti-aging agent evolved from the multitude of properties encompassed in aspirin and the potential of these attributes to prevent the cellular and functional declines, particularly from inflammatory and oxidative sources, evidenced to contribute to aging. Aspirin is a widely administered, cheap, anti-inflammatory, and antioxidant compound that has a variety of positive effects on the immune system and cardiovascular health. Notably, aspirin may affect oxidant production, cytokine responses, and block glycooxidation reactions, thus posing it as a triple threat against the symptoms of aging. Whether aging is molded by interplay between oxidative stress and inflammatory mediators has received little attention; however, we and other laboratories have explored this notion and have observed an elevated inflammatory status with age. Stemming from these observations and in view of the limited success of antioxidant therapies in improving lifespan in long-lived species, in this article we propose a protocol to examine life-long use of a very low dose anti-inflammatory compound such as aspirin to engage the inflammatory and endogenous oxidative insults accompanying aging and, in so doing, attempt to increase maximum and mean life span.
[Growth factors as neuroprotective treatment in Parkinson disease?]. (2006)

The improved motor function following growth factor treatment in this rat model might be due to a delayed retrograde degeneration of the nigrostriatal nerve fibers. Growth factor infusion also clearly stimulated endogenous stem cells and caused their migration towards the striatum. Our observations indicate that the infusion of growth factors into the brain have a symptomatic and neuroprotective effect in this model.
Evidence for Decreased Transport of PNMT Protein in Advanced Alzheimer's Disease (1990)

Phenylethanolamine N-methyltransferase (PNMT) is the rate-limiting enzyme in the synthesis of epinephrine and a specific marker for adrenergic neurons. PNMT protein is decreased in axon terminals in brains from patients with Alzheimer's disease due to retrograde degeneration of epinephrine neurons. To determine the subcellular mechanism underlying retrograde degeneration, the distribution of PNMT between axon terminal and cell body was calculated in early and advanced Alzheimer cases compared with age-matched controls. In early Alzheimer's disease there is a decrease in PNMT in axon terminals and in total PNMT in epinephrine cell bodies and terminals compared with control values. There is no difference in the ratio of PNMT in cell body/axon terminal compared with controls. In contrast, in advanced Alzheimer's disease, PNMT activity increases by 124% in epinephrine neuronal cell bodies compared with controls. Immunochemical titration shows that this increased enzyme activity is due to an increase in PNMT protein. The cell body/axon terminal ratio of PNMT is increased 2.5-fold in advanced Alzheimer's disease compared with controls. These findings are consistent with the hypothesis that in early Alzheimer's disease there is a decreased synthesis or increased degradation of PNMT. However, in advanced Alzheimer's disease we propose that the accumulation of this enzyme in the perikarya results from a diminished transport of PNMT to axon terminals. We further postulate that epinephrine, the product of PNMT, and its further metabolites are endogenous neurotoxins. Therefore, the accumulation of PNMT in epinephrine cell bodies may contribute to the degeneration of these neurons in Alzheimer's disease.
Therapeutic Modulation and Reestablishment of the Intestinal Microbiota With Fecal Microbiota Transplantation Resolves Sepsis and Diarrhea in a Patient (2014)

Li, Qiurong MD, PhD; Wang, Chenyang MA; Tang, Chun BA; He, Qin MA; Zhao, Xiaofan BA; Li, Ning MD; Li, Jieshou MD Author Information
Comparative field study: impact of laboratory assay variability on the assessment of recombinant factor IX Fc fusion protein (rFIXFc) activity (2014)

Due to variability in the one-stage clotting assay, the performance of new factor IX (FIX) products should be assessed in this assay. The objective of this field study was to evaluate the accuracy of measuring recombinant FIX Fc fusion protein (rFIXFc) activity in clinical haemostasis laboratories using the one-stage clotting assay. Human haemophilic donor plasma was spiked with rFIXFc or BeneFIX® at 0.80, 0.20, or 0.05 IU/ml based on label potency. Laboratories tested blinded samples using their routine one-stage assay and in-house FIX plasma standard. The mean spike recoveries for BeneFIX (n=30 laboratories) were 121 %, 144 %, and 168 % of expected at nominal 0.80, 0.20, and 0.05 IU/ml concentrations, respectively. Corresponding rFIXFc spike recoveries were 88 %, 107 %, and 132 % of expected, respectively. All BeneFIX concentrations were consistently overestimated by most laboratories. rFIXFc activity was reagent-dependent; ellagic acid and silica gave higher values than kaolin, which underestimated rFIXFc. BeneFIX demonstrated significantly reduced chromogenic assay activity relative to one-stage assay results and nominal activity, while rFIXFc activity was close to nominal activity at three concentrations with better dilution linearity than the typical one-stage assay. In conclusion, laboratory- and reagent-specific assay variabilities were revealed, with progressively higher variability at lower FIX concentrations. Non-parallelism against the FIX plasma standard was observed in all one-stage assays with rFIXFc and BeneFIX, leading to significant overestimation of FIX activity at lower levels and generally high inter-laboratory variability. Compared to the accuracy currently achieved in clinical laboratories when measuring other rFIX products, most laboratories measured rFIXFc activity with acceptable accuracy and reliability using routine one-stage assay methods and commercially available plasma standards.