gebhart/patrepeval huggingface dataset:
Functional expression of NOS 1 in vascular smooth muscle (2000)

Substances that increase intracellular calcium concentration ([Ca(2+)](i)), such as serotonin, are known to induce vascular smooth muscle (VSM) contraction. However, increases in [Ca(2+)](i) also activate Ca(2+)/calmodulin-dependent nitric oxide synthases (NOS), which leads to increases in cGMP and activation of cGMP-dependent protein kinase (PKG). One recently identified substrate protein of PKG is the small heat shock protein, HSP20. The purpose of this study was to determine if serotonin activates a Ca(2+)-dependent NOS in VSM. Strips of bovine carotid arterial smooth muscle denuded of endothelium were stimulated with serotonin in the presence and absence of the nonspecific NOS inhibitor N-monomethyl-L-arginine (L-NMMA). Activation of NOS was determined by increases in cGMP and in the phosphorylation of HSP20. Immunohistochemical and Western blotting techniques were performed to identify specific NOS isoforms in bovine carotid arterial smooth muscle preparations. Serotonin stimulation led to significant increases in cGMP and in the phosphorylation of HSP20, which were inhibited by pretreatment with L-NMMA. Antibodies against NOS 1 stained the media of bovine carotid and human renal arteries, whereas antibodies against NOS 3 stained only the endothelium. Additionally, the conversion of radiolabeled L-arginine to L-citrulline NOS activity demonstrated a consistent amount of activity present in the endothelium-denuded smooth muscle preparations that was reduced by 99% with an NOS 1 specific inhibitor. Finally, an NOS 1 specific inhibitor, 7-nitroindazole, augmented contractions induced by high extracellular KCl. This study demonstrates that NOS 1 is present in VSM and may effect physiological contractile responses.
The capacity of activated murine macrophages for augmented binding of neoplastic cells: analysis of induction by lymphokine containing MAF and kinetics of the reaction. (1982)

The capacity for augmented binding of tumor cells is an initial and necessary part of macrophage-mediated tumor cytotoxicity. To study the induction of binding capacity, we obtained FCS-elicited, inflammatory macrophages from C57BL/6J mice. Exposure of these macrophages to lymphokine(s) containing MAF induced augmented binding capacity in a dose-dependent fashion. Resident peritoneal macrophages did not respond to lymphokine, and endotoxin did not appreciably influence induction of binding. Maximum induction of binding required continuous interaction between macrophages and lymphokine for 6 to 10 hr. The conditions necessary for induction of binding closely paralleled those for induction of priming or cytolysis. Exposure of FCS-elicited macrophages from C3H/HeJ mice, although not of macrophages from A/J mice, induced augmented binding. The data suggest that the augmented capacity for binding tumor cells is induced by lymphokine(s) and that a major part of induction of priming for cytolysis by MAF is induction of such binding.
Evolution of Mammals and Their Gut Microbes (2008)

Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
Animal models of intestinal fibrosis: new tools for the understanding of pathogenesis and therapy of human disease (2012)

Fibrosis is a serious condition complicating chronic inflammatory processes affecting the intestinal tract. Advances in this field that rely on human studies have been slow and seriously restricted by practical and logistic reasons. As a consequence, well-characterized animal models of intestinal fibrosis have emerged as logical and essential systems to better define and understand the pathophysiology of fibrosis. In point of fact, animal models allow the execution of mechanistic studies as well as the implementation of clinical trials with novel, pathophysiology-based therapeutic approaches. This review provides an overview of the currently available animal models of intestinal fibrosis, taking into consideration the methods of induction, key characteristics of each model, and underlying mechanisms. Currently available models will be classified into seven categories: spontaneous, gene-targeted, chemical-, immune-, bacteria-, and radiation-induced as well as postoperative fibrosis. Each model will be discussed in regard to its potential to create research opportunities to gain insights into the mechanisms of intestinal fibrosis and stricture formation and assist in the development of effective and specific antifibrotic therapies.
Inhibition of Pneumococcal Adherence to Human Nasopharyngeal Epithelial Cells by Anti-PsaA Antibodies (2003)

The role of pneumococcal (Pnc) surface adhesin A (PsaA) in the adherence of Streptococcus pneumoniae (pneumococcus) to host cells is not well defined. We examined the effect of anti-PsaA antibodies in an inhibition of adherence assay using Detroit 562 nasopharyngeal human epithelial cells. Rabbit polyclonal (Pab) anti-recombinant PsaA (rPsaA) sera, a purified mouse monoclonal antibody (MAb) (MAb 6F62G8E12), and 22 healthy adult sera with known anti-PsaA IgG levels (obtained by enzyme-linked immunosorbent assay) were evaluated for their abilities to inhibit Pnc adherence to confluent monolayers (measured as percent reduction in CFU counts compared to those of uninhibited controls). Pnc adherence was dependent on capsular phenotype (no or low adherence for opaque strains). With an inoculum of 10(4) to 10(5) bacteria/well, the mean +/- standard deviation count in controls was 163 +/- 32 CFU/well for transparent strains. Low adherence was observed for a PsaA-minus mutant even at higher inoculum doses. Mean percent inhibitions of adherence with Pab and MAb were 54 and 50%, respectively. Adult sera showed inhibition in a dose-response fashion with a range of 98 to 8%, depending on the serum anti-PsaA antibody concentration. Absorption of Pab with rPsaA restored Pnc adherence to control levels. Absorption of sera with a PsaA-minus mutant did not result in a significant decrease (P >0.05) of inhibition of adherence activity. Additionally, nearly 100% of Pnc adherence was inhibited by lipidated rPsaA at 2.5 micro g/ml. Our data support the argument that PsaA is an adhesin that mediates Pnc adherence to human nasopharyngeal cells. This functional assay may be useful in evaluating antibodies elicited in response to PsaA vaccination.
Transcriptome analysis of the Mg2+-responsive PhoP regulator inYersinia pestis (2005)

PhoP was previously shown to be important for Yersinia pestis survival in macrophage and under macrophage-induced stresses. In this work, a phoP disruptant of Y. pestis 201 was generated using the Red cloning procedure. The transcription profile of the wild-type Y. pestis was then compared with that of the phoP mutant under Mg2+-limiting conditions. It was revealed that PhoP/PhoQ governed a wide set of cellular pathways in Y. pestis, especially including the positive regulation of many metabolic processes, Mg2+ transport, peptidoglycan remodeling, lipopolysaccharide (LPS) modification and various stress-protective functions. The Mg2+ transport system regulated by PhoP may make Y. pestis to maintain the magnesium homeostasis under low Mg2+ environments. The PhoP-controlled stress-protective functions likely constitute the molecular basis for the observation that mutation of the phoP gene rendered the bacteria more sensitive to various macrophage-induced stresses. Modification of LPS mediated by PhoP is hypothesized to not only neutralize negative charges as normally done by Mg2+ ions, but also mediate the resistance of Y. pestis to antimicrobial peptides. The microarray results provide a population of candidate genes or pathways, and further biochemical experiments are needed to elucidate the PhoP-dependent mechanisms by which Y. pestis survives the antibacterial strategies employed by host macrophages.
SPC03-4: Exploiting Spatio-Temporal Correlations in MIMO Wireless Channel Prediction (2006)

We investigate prediction algorithms that exploit both temporal and spatial correlations in MIMO correlated narrowband fading wireless channels. We first derive the optimal two dimensional minimum mean square error (2D-MMSE) prediction filter that maximally exploits the available temporal and spatial correlations. We then propose a lower complexity 2-step prediction algorithm, which first exploits temporal correlations using a classical single-input single-output (SISO) MMSE time- domain prediction filter for each entry in the MIMO channel, followed by an MMSE spatial smoothing step to exploit the spatial correlations. Compared to the SISO and specular prediction approaches, this approach either achieves lower MSE with a slight increase in complexity, or comparable MSE with lower complexity, in a wide range of wireless channel conditions. The same advantage holds for the average mutual information.
Nanoscale Patterning of Flat Carbon Surfaces by Scanning Probe Lithography and Electrochemistry (2005)

We report the formation of carbon surfaces patterned at the nanoscale with organic functionalities. Thin (<10 nm) films are covalently grafted to the surface via the electrochemical reduction of aryl diazonium salts. Areas of the film are removed with an AFM tip, and a second modifier is electrochemically grafted to the exposed surface. The pattern can incorporate different chemical functionalities, or alternatively topographical patterns can be assembled, where the same functionality is present throughout the pattern.
Selective Synthesis of Primary Amines Directly from Alcohols and Ammonia (2008)

Air stable and waterproof: Selective and efficient synthesis of primary amines directly from alcohols and ammonia is achieved under mild conditions (see scheme). The reaction is homogenously catalyzed by a novel air-stable ruthenium pincer complex and can proceed in toluene or even in the absence of solvent or “on water”.
Highly Regio- and Enantioselective Reduction of 3,5-Dioxocarboxylates (2000)

Only the keto group in position C-5 is reduced in the enzymatic reduction of 3,5-dioxocarboxylates by the alcohol dehydrogenase of Lactobacillus brevis (LBADH; see scheme). The strategy of nature for manipulating β-keto metabolites inspired the development of a chemoenzymatic approach to virtually enantiopure 3,5-dihydroxycarboxylate building blocks. The crucial enzymatic step can be performed on an attractively large scale.
Quantitative Analysis of Irbesartan in Commercial Dosage Forms by Kinetic Spectrophotometry (2006)

The objective of this work is to develop a new kinetic spectrophotometric method for the determination of irbesartan in pharmaceutical formulations. The method is based on the reaction of carboxylic acid group of the oxidized irbesartan with a mixture of potassium iodate (KIO(3)) and iodide (KI) to form yellow colored triiodide ions in aqueous medium at 30+/-1 degrees C. The reaction is followed spectrophotometrically by measuring the rate of change of absorbance at 352 nm. The initial-rate and fixed-time (DeltaA) methods are adopted for constructing the calibration curves, which were found to be linear over the concentration ranges of 10.0-60.0 and 7.5-60.0 microg ml(-1) respectively. The regression analysis of calibration data yielded the linear equations: rate=-2.138 x 10(-6)+1.058 x 10(-4)C and DeltaA=-3.75 x 10(-3)+3.25 x 10(-3)C for initial rate and fixed time (DeltaA) methods, respectively. The limit of detection for initial rate and fixed time methods are 0.21 and 2.40 mug ml(-1), respectively. The various activation parameters such as E(a), DeltaH++, DeltaS++ and DeltaG++ are also calculated for the reaction and found to be 70.95+/-0.43 kJ mol(-1), 68.48+/-0.21 kJ mol(-1), 16.54+/-0.24 J K(-1) mol(-1) and -4.94+/-0.07 kJ mol(-1), respectively. The proposed methods are optimized and validated as per the guidelines of International Conference on Harmonisation (U.S.A.). The point and interval hypothesis tests have been performed which indicate that there is no significant difference between the proposed methods and the reference method. The methods have been successfully applied to the determination of irbesartan in commercial dosage forms.
Determination of Serum Physiological Concentration of Methylmalonic Acid by Gas Chromatography-Mass Spectrometry with Selected Ion Monitoring (1998)

We developed a sensitive assay for the rapid determination of serum methylmalonic acid concentration using capillary gas chromatography-mass spectrometry (GC/MS) with selected ion monitoring and a simple solid-phase extraction. The assay was linear up to 10,000 nmol/L and had a detection limit < 50 nmol/L, average recovery of 98% and between-day coefficient of variation at concentrations of 570 and 2206 nmol/L of 7.7% and 5.4%, respectively (n = 25). Comparison with another validated GC/MS method using sera with a wide range of methylmalonic acid concentrations (94-2020 nmol/L) revealed a slope and intercept of 0.97 and 17 nmol/L, respectively (n = 38). Methylmalonic acid concentrations determined by this assay in a group of apparently healthy individuals ranged from 64-331 nmol/L (n = 81). We conclude that the method is ideally suited for the determination of methylmalonic acid at physiological concentrations in both clinical and research laboratories.
The Author Responds (1992)

1Head Nurse and Charge Nurse Orthopedic, Vascular, and Urology Surgical Unit Carl T. Hayden VA Medical Center Phoenix, AZ
Four different monoclonal antibodies against type C1 toxin of Clostridium botulinum (1982)

Monoclonal antibodies against type C1 toxin produced by Clostridium botulinum type C strain Stockholm (C-ST) were prepared by fusion of BALB/c myeloma cells P3X63-Ag8, with spleen cells from the mice immunized by C-ST toxoid. About 5% of single-cell colonies in wells were found to produce antibodies against the toxin as determined by an enzyme-linked immunosorbent assay (ELISA). Four different hybridoma cell lines, no. 9, 12, 14, and 17, were established, cloned by limiting dilution, and intraperitoneally injected into mice to obtain the ascites fluids containing high-titered antibodies. The reactions of these antibodies to type C1 and D toxins of strains C-ST, D-1873, and D-South African (D-SA) were observed by both neutralization and ELISA tests. Three monoclonal antibodies, no. 9, 14, and 17, reacted with C-ST toxin, but only no. 17 highly neutralized the toxin. These antibodies did not react with type D toxins. On the contrary, no. 12 reacted with toxins of both C-ST and D-SA (but not of D-1873) and commonly neutralized these two toxins. This indicates that there is a common antigenic part between C-ST and D-SA toxin molecules which participates in the toxin-neutralizing reaction. The neutralization profiles of C-ST toxin by no. 12 and 17 antibodies were different in a time-to-death test of mice. The mechanisms of neutralization by no. 12 and 17 may be different.
A randomised trial evaluating anakinra in early active rheumatoid arthritis. (2016)

Anakinra (combined with methotrexate) is not effective in early, active RA. It provided no clinical benefits beyond methotrexate monotherapy.
Effect of doxycycline on the generation of reactive oxygen species: a possible mechanism of action of acne therapy with doxycycline. (1992)

On the basis of a recent report that minocycline is effective in the treatment of acne inflammation by acting directly as an antioxidant on infiltrating neutrophils, we investigated whether doxycycline might also be capable of reducing the generation of reactive oxygen species, using human neutrophils and a cell-free, xanthine-xanthine oxidase system. The species investigated are superoxide radical anion (O2-), hydrogen peroxide (H2O2) and hydroxyl radical (OH.). Doxycycline significantly reduced the levels of O2-, H2O2 and OH. generated by both systems. Our results seem to suggest that the clinical effectiveness of doxycycline in the treatment of acne inflammation is due partly to its antioxidant effect on neutrophils.
Under the lash: Demodex mites in human diseases (2009)

Demodex mites, class Arachnida and subclass Acarina, are elongated mites with clear cephalothorax and abdomens, the former with four pairs of legs. There are more than 100 species of Demodex mite, many of which are obligatory commensals of the pilosebaceous unit of mammals including cats, dogs, sheep, cattle, pigs, goats, deer, bats, hamsters, rats and mice. Among them, Demodex canis, which is found ubiquitously in dogs, is the most documented and investigated. In excessive numbers D. canis causes the inflammatory disease termed demodicosis (demodectic mange, follicular mange or red mange), which is more common in purebred dogs and has a hereditary predisposition in breeding kennels1. Two distinct Demodex species have been confirmed as the most common ectoparasite in man. The larger Demodex folliculorum, about 0.3-0.4 mm long, is primarily found as a cluster in the hair follicle (Figure 1a), while the smaller Demodex brevis, about 0.2-0.3 mm long with a spindle shape and stubby legs, resides solitarily in the sebaceous gland (Figure 1b). These two species are also ubiquitously found in all human races without gender preference. The pathogenic role of Demodex mites in veterinary medicine is not as greatly disputed as in human diseases. In this article, we review the key literature and our joint research experience regarding the pathogenic potential of these two mites in causing inflammatory diseases of human skin and eye. We hope that the evidence summarized herein will invite readers to take a different look at the life of Demodex mites in several common human diseases.
Human chondrogenic paraxial mesoderm, directed specification and prospective isolation from pluripotent stem cells (2012)

Directed specification and prospective isolation of chondrogenic paraxial mesoderm progeny from human pluripotent stem (PS) cells have not yet been achieved. Here we report the successful generation of KDR(-)PDGFRα(+) progeny expressing paraxial mesoderm genes and the mesendoderm reporter MIXL1-GFP in a chemically defined medium containing the canonical WNT signaling activator, BMP-inhibitor, and the Nodal/Activin/TGFβ signaling controller. Isolated (GFP(+))KDR(-)PDGFRα(+) mesoderm cells were sensitive to sequential addition of the three chondrogenic factors PDGF, TGFβ and BMP. Under these conditions, the cells showed robust chondrogenic activity in micromass culture, and generated a hyaline-like translucent cartilage particle in serum-free medium. In contrast, both STRO1(+) mesenchymal stem/stromal cells from adult human marrow and mesenchymal cells spontaneously arising from hPS cells showed a relatively weaker chondrogenic response in vitro, and formed more of the fibrotic cartilage particles. Thus, hPS cell-derived KDR(-)PDGFRα(+ )paraxial mesoderm-like cells have potential in engineered cartilage formation and cartilage repair.
Developing a trust-wide centralised approach to the use of VAC (2002)

Use of topical negative pressure, also known as VAC, gradually increased throughout a trust following its success in a burns and plastic surgery unit. A trust-wide centralised approach set out to standardise its use and to reduce costs.
Stability and convergence of distributed algorithms for the OPF problem (2013)

Many modern power networks are partitioned in nature, with disjoint components of the overall network controlled by competing operators. The problem of solving the Optimal Power Flow (OPF) problem in a distributed manner is therefore of significant interest. For networks in which the high-level structure has tree topology, we analyze a dual decomposition approach to solving a recent convex relaxation of the OPF problem for the overall network in a distributed manner. Incorporating higher-order dynamics in terms of local auxiliary variables, we prove a result of guaranteed convergence to the solution set for sufficiently small values of the step size.
LSD1 controls metastasis of androgen-independent prostate cancer cells through PXN and LPAR6 (2014)

Lysine-specific demethylase 1 (LSD1) was shown to control gene expression and cell proliferation of androgen-dependent prostate cancer (PCa) cells, whereas the role of LSD1 in androgen-independent metastatic prostate cancer remains elusive. Here, we show that depletion of LSD1 leads to increased migration and invasion of androgen-independent PCa cells. Transcriptome and cistrome analyses reveal that LSD1 regulates expression of lysophosphatidic acid receptor 6 (LPAR6) and cytoskeletal genes including the focal adhesion adaptor protein paxillin (PXN). Enhanced LPAR6 signalling upon LSD1 depletion promotes migration with concomitant phosphorylation of PXN. In mice LPAR6 overexpression enhances, whereas knockdown of LPAR6 abolishes metastasis of androgen-independent PCa cells. Taken together, we uncover a novel mechanism of how LSD1 controls metastasis and identify LPAR6 as a promising therapeutic target to treat metastatic prostate cancer.
Directed evolution of gene-shuffled IFN-α molecules with activity profiles tailored for treatment of chronic viral diseases (2007)

Type I IFNs are unusually pleiotropic cytokines that bind to a single heterodimeric receptor and have potent antiviral, antiproliferative, and immune modulatory activities. The diverse effects of the type I IFNs are of differential therapeutic importance; in cancer therapy, an enhanced antiproliferative effect may be beneficial, whereas in the therapy of viral infections (such as hepatitis B and hepatitis C), the antiproliferative effects lead to dose limiting bone marrow suppression. Studies have shown that various members of the natural IFN-alpha family and engineered variants, such as IFN-con1, vary in the ratios between various IFN-mediated cellular activities. We used DNA shuffling to explore and confirm the hypothesis that one could simultaneously increase the antiviral and Th1-inducing activity and decrease the antiproliferative activity. We report IFN-alpha hybrids wherein the ratio of antiviral:antiproliferative and Th1-inducing: antiproliferative potencies are markedly increased with respsect to IFN-con1 (75- and 80-fold, respectively). A four-residue motif that overlaps with the IFNAR1 binding site and is derived by cross breeding with a pseudogene contributes significantly to this phenotype. These IFN-alphas have an activity profile that may result in an improved therapeutic index and, consequently, better clinical efficacy for the treatment of chronic viral diseases such as hepatitis B virus, human papilloma virus, HIV, or chronic hepatitis C.
Variable DNA Methylation Is Associated with Chronic Obstructive Pulmonary Disease and Lung Function (2011)

Genetic and epigenetic pathways may both contribute to COPD. Many of the top associations between COPD and DNA methylation occur in biologically plausible pathways. This large-scale analysis suggests that DNA methylation may be a biomarker of COPD and may highlight new pathways of COPD pathogenesis.