gebhart/patrepeval huggingface dataset:
The evidence on the effectiveness of management for malignant pleural effusion: a systematic review (2006)

The aim of this study was to review systematically the available evidence on pleurodesis for malignant effusion, focusing on the choice of the agents, route of delivery and other strategies to improve outcomes. Four electronic databases (MEDLINE, EMBASE, Web of Science and Cochrane Controlled Trials Register) were searched, reference lists checked and letters requesting details of unpublished trials and data sent to authors of previous trials. Studies of malignant pleural effusion in humans were selected with no language restrictions applied. Criteria for randomised clinical trial (RCT) eligibility were random allocation of patients and non-concurrent use of another experimental medication or device. Methodological quality evaluation of the trials was based on randomisation, blinding, allocation concealment and intention to treat analysis. A random effect model was used to combine the relative risk estimates of the treatment effects whenever pooling for an overall effect was considered appropriate. Forty-six RCTs with a total of 2053 patients with malignant pleural effusions were reviewed for effectiveness of pleurodesis. Talc tended to be associated with fewer recurrences when compared to bleomycin (RR, 0.64; 95% CI, 0.34-1.20) and, with more uncertainty, to tetracycline (RR, 0.50; 95% CI, 0.06-4.42). Tetracycline (or doxycycline) was not superior to bleomycin (RR, 0.92; 95% CI, 0.61-1.38). When compared with bedside talc slurry, thoracoscopic talc insufflation was associated with a reduction in recurrence (RR, 0.21; 95% CI, 0.05-0.93). Strategies such as rolling the patient after instillation of the sclerosing agent, protracted drainage of the effusion and use of larger chest tubes were not found to have any substantial advantages. Talc appears to be effective and should be the agent of choice for pleurodesis. Thoracoscopic talc insufflation is associated with fewer recurrences of effusions compared with bedside talc slurry, but this is based on two small studies. Where thoracoscopy is unavailable bedside talc pleurodesis has a high success rate and is the next best option.
FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma (2012)

Supplementary data are available at Bioinformatics online.
SSEA-4 identifies mesenchymal stem cells from bone marrow (2006)

Adult bone marrow (BM) contains hematopoietic stem cells (HSCs) as well as a nonhematopoietic, stromal cell population. Within this stromal population are mesenchymal stem cells (MSCs), which not only support hematopoiesis but also differentiate into multiple lineages, including fat, bone, and cartilage. Because of this multipotentiality, the MSC is an attractive candidate for clinical applications to repair or regenerate damaged tissues of mesenchymal origin. However, research progress has been hampered by the limited existing knowledge of the biology of these cells, particularly by the lack of a suitable marker for their prospective isolation. Here, we report that SSEA-4, an early embryonic glycolipid antigen commonly used as a marker for undifferentiated pluripotent human embryonic stem cells and cleavage to blastocyst stage embryos, also identifies the adult mesenchymal stem cell population.
Identification and formation of some selected sulfur-containing flavor compounds in various meat model systems (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification and formation of some selected sulfur-containing flavor compounds in various meat model systemsMatthias Guentert, Juergen Bruening, Roland Emberger, Manfred Koepsel, Walter Kuhn, Thomas Thielmann, and Peter WerkhoffCite this: J. Agric. Food Chem. 1990, 38, 11, 2027–2041Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://doi.org/10.1021/jf00101a007RIGHTS & PERMISSIONSArticle Views694Altmetric-Citations57LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
67-kD elastin-binding protein is a protective "companion" of extracellular insoluble elastin and intracellular tropoelastin. (1994)

The 67-kD elastin-binding protein (EBP) mediates cell adhesion to elastin and elastin fiber assembly, and it is similar, if not identical, to the 67-kD enzymatically inactive, alternatively spliced beta-galactosidase. The latter contains an elastin binding domain (S-GAL) homologous both to the aorta EBP and to NH2-terminal sequences of serine proteinases (Hinek, A., M. Rabinovitch, F. W. Keeley, and J. Callahan. 1993. J. Clin. Invest. 91:1198-1205). We now confirm the functional importance of this homology by showing that elastolytic activity of a representative serine elastase, porcine pancreatic elastase, was prevented by an antibody (anti-S-GAL) and by competing with purified EBP or S-GAL peptide. Immunohistochemistry of adult aorta indicates that the EBP exists as a permanent component of mature elastic fibers. This observation, together with the in vitro studies, suggests that the EBP could protect insoluble elastin from extracellular proteolysis and contribute to the extraordinary stability of this protein. Double immunolabeling of fetal lamb aorta with anti-S-GAL and antitropoelastin antibodies demonstrated, under light and electron microscopy, intracellular colocalization of the proteins in smooth muscle cells (SMC). Incubation of SMC with galactosugars to dissociate tropoelastin from EBP caused intracellular aggregation of tropoelastin. A tropoelastin/EBP complex was extracted from SMC lysates by coimmunoprecipitation and cross-linking, and its functional significance was addressed by showing that its dissociation by galactosugars caused degradation of tropoelastin by endogenous serine proteinase(s). This suggests that the EBP may also serve as a "companion" to intracellular tropoelastin, protecting this highly hydrophobic protein from self-aggregation and proteolytic degradation.
SEL1L expression decreases breast tumor cell aggressiveness in vivo and in vitro. (2002)

SEL1L, the human orthologue of the Caenorhabditis elegans sel-1 gene, is differentially expressed in breast primary tumors and in normal breast tissues. Analysis of a series of human primary breast carcinomas, using a monoclonal antibody raised against a SEL1L recombinant protein, revealed down-modulation or absence of SEL1L expression in about two-thirds of the tumors as compared with normal breast epithelial cells. Overall survival analysis of breast carcinoma patients indicated a statistically significant correlation between SEL1L down-modulation and poor prognosis. MCF-7, human breast carcinoma cells, were transfected with a construct containing the entire SEL1L cDNA driven by an inducible promoter and showed a dramatic reduction in anchorage-dependent growth and colony formation in soft agar. Growth of the transfected cells in Matrigel, an extracellular matrix rich with laminin, restored colony-formation ability. These results point to the role for SEL1L in breast tumor growth and aggressiveness, possibly involving cell-matrix interactions.
Dispersion characteristics of two-component two-dimensional mixtures (1993)

The effective dielectric constant and conductivity of a two-component two-dimensional composite material are functions of frequency. The dispersion characteristics are obtained in terms of the Bergman-Milton simple poles and are consistent with the Debye equation. Also, under certain conditions, enhancement of the effective dielectric constant may occur at low frequencies and enhancement of the effective conductivity may occur at high frequencies. The proposed method based on the Bergman-Milton simple-pole and Fourier-transform theory can be used to develop a three-dimensional mixing formula, which may be useful in predicting the dispersion properties of oil- or water-saturated rocks and other composite materials.
Production and characterization of pureClostridiumspore suspensions (2008)

Pure Clostridium spore suspensions are required for investigating species of medical and environmental importance. Defining the conditions for optimal spore production also provides insight into the underlying mechanisms of Clostridium sporulation.
Structural requirements for incorporation of J chain into human IgM and IgA (2000)

J chain is associated with pentameric IgM and dimeric IgA via disulfide bonds involving the penultimate cysteine residue in the secretory tailpiece of the mu or the alpha heavy chain. We have investigated the structural basis for incorporation of J chain by analyzing several IgM mutants, IgA mutants and IgG/IgM hybrid molecules. IgM mutants with the mu secretory tailpiece replaced by the alpha secretory tailpiece and/or Cys414 replaced by serine incorporated J chain, although in reduced amounts correlating with reduced pentamer/polymer formation. In addition to pentamers, tetramers of IgMC414S contained J chain, while no J chain was associated with smaller polymers or hexamers of IgM. An IgA/IgM hybrid tailpiece abolished J chain incorporation to pentameric IgM. Analysis of IgG molecules that have added a secretory tailpiece and/or have IgM domain replacements showed that J chain incorporation depends on regions of the C(mu)4 domain in addition to the tailpiece. Features of the C(mu)3 domain other than Cys414 also play a role in efficient formation of pentamers and J chain incorporation, while the C(mu)2 domain is not specifically required. By analysis of two IgA mutants that formed larger polymers than IgAwt, we found J chain equally incorporated into dimers, trimers, tetramers and pentamers. Thus, the results show that J chain incorporation into IgA does not depend on the polymeric structure, while J chain incorporation into IgM is restricted to certain polymeric conformations.
An IL-13 inhibitor blocks the development of hepatic fibrosis during a T-helper type 2–dominated inflammatory response (1999)

In schistosomiasis, chronic parasite egg-induced granuloma formation can lead to tissue destruction and fibrosis, which causes much of the morbidity and mortality associated with this disease. Here we show the importance of IL-13 in the pathogenesis of schistosomiasis, and demonstrate, perhaps for the first time, the therapeutic efficacy of an IL-13 inhibitor, sIL-13Ralpha2-Fc, in the control of hepatic fibrosis. T-helper type 2 (Th2) cytokines dominate the immune response in mice infected with Schistosoma mansoni, yet the specific contributions of IL-13 and IL-4 to the development of fibrosis were not previously investigated. Our studies demonstrate that both cytokines play redundant roles in granuloma formation, which explains the ability of IL-4-deficient mice to form granulomas around eggs. More importantly, however, these studies demonstrate that IL-13 is the dominant Th2-type cytokine regulating fibrosis. IL-13 stimulated collagen production in fibroblasts, and procollagen I and procollagen III mRNA expression was decreased in sIL-13Ralpha2-Fc-treated mice. Moreover, the reduction in fibrosis observed in IL-4-deficient mice was much less pronounced than that in sIL-13Ralpha2-Fc-treated animals. Fibrosis is a major pathological manifestation of a number of allergic, autoimmune, and infectious diseases. Thus, our findings provide evidence that IL-13 inhibitors may be of general therapeutic benefit in preventing damaging tissue fibrosis resulting from Th2-dominated inflammatory responses.
Personalized protein corona on nanoparticles and its clinical implications (2017)

It is now well understood that once in contact with biological fluids, nanoscale objects lose their original identity and acquire a new biological character, referred to as a protein corona. The protein corona changes many of the physicochemical properties of nanoparticles, including size, surface charge, and aggregation state. These changes, in turn, affect the biological fate of nanoparticles, including their pharmacokinetics, biodistribution, and therapeutic efficacy. It is progressively being accepted that even slight variations in the composition of a protein source (e.g., plasma and serum) can substantially change the composition of the corona formed on the surface of the exact same nanoparticles. Recently it has been shown that the protein corona is strongly affected by the patient's specific disease. Therefore, the same nanomaterial incubated with plasma proteins of patients with different pathologies adsorb protein coronas with different compositions, giving rise to the concept of personalized protein corona. Herein, we review this concept along with recent advances on the topic, with a particular focus on clinical relevance.
A Repartitioning Agent to Improve Performance and Carcass Composition of Broilers (1984)

Clenbuterol [benzyl alcohol, 4-amino-alpha-(t-butylamino)methyl-3,5-dichloro] was tested in the finisher ration of broilers in three series of experiments for its effects on performance and carcass characteristics. In Experiment 1, administration of clenbuterol at feed levels of .25, .5, 1, 2, and 4 ppm from 28 to 49 days of age resulted in significant sex combined weight gain improvements at all levels except 4 ppm and significant feed efficiency improvements at all levels tested. Uneviscerated body composition analysis indicated that clenbuterol treatment significantly increased body protein and water content and decreased body fat in female birds. In males, body fat was significantly reduced by 1, 2, and 4 ppm clenbuterol. From these results the 1 ppm level was selected for further testing. In Experiments 2 and 3, clenbuterol fed from 28 to 49 days of age significantly improved sex combined weight gain and feed efficiency and both male and female 49-day weights. Carcass yield was significantly increased in males and females by 1.11 and 1.91 percentage points, respectively. Abdominal fat was significantly reduced by clenbuterol feeding only in females. Carcass analysis indicated that clenbuterol-fed birds had a significantly lower carcass fat content. In Experiments 4 to 7, clenbuterol was administered at 1 ppm in the finishing feed but was withdrawn 3 to 5 days prior to terminal performance and carcass evaluations. Clenbuterol significantly improved sex combined weight gain and feed efficiency, and 49-day weights for both sexes. Carcass yield was significantly increased in males and females by .54 and .98 percentage points, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Proteolytic Inactivation of MAP-Kinase-Kinase by Anthrax Lethal Factor (1998)

Anthrax lethal toxin, produced by the bacterium Bacillus anthracis, is the major cause of death in animals infected with anthrax. One component of this toxin, lethal factor (LF), is suspected to be a metalloprotease, but no physiological substrates have been identified. Here it is shown that LF is a protease that cleaves the amino terminus of mitogen-activated protein kinase kinases 1 and 2 (MAPKK1 and MAPKK2) and that this cleavage inactivates MAPKK1 and inhibits the MAPK signal transduction pathway. The identification of a cleavage site for LF may facilitate the development of LF inhibitors.
Structural Basis for the Inhibition of RNase H Activity of HIV-1 Reverse Transcriptase by RNase H Active Site-Directed Inhibitors (2010)

HIV/AIDS continues to be a menace to public health. Several drugs currently on the market have successfully improved the ability to manage the viral burden in infected patients. However, new drugs are needed to combat the rapid emergence of mutated forms of the virus that are resistant to existing therapies. Currently, approved drugs target three of the four major enzyme activities encoded by the virus that are critical to the HIV life cycle. Although a number of inhibitors of HIV RNase H activity have been reported, few inhibit by directly engaging the RNase H active site. Here, we describe structures of naphthyridinone-containing inhibitors bound to the RNase H active site. This class of compounds binds to the active site via two metal ions that are coordinated by catalytic site residues, D443, E478, D498, and D549. The directionality of the naphthyridinone pharmacophore is restricted by the ordering of D549 and H539 in the RNase H domain. In addition, one of the naphthyridinone-based compounds was found to bind at a second site close to the polymerase active site and non-nucleoside/nucleotide inhibitor sites in a metal-independent manner. Further characterization, using fluorescence-based thermal denaturation and a crystal structure of the isolated RNase H domain reveals that this compound can also bind the RNase H site and retains the metal-dependent binding mode of this class of molecules. These structures provide a means for structurally guided design of novel RNase H inhibitors.
Augmented digitally reconstructed radiographs of aortic dissection CTA images (2012)

To deal with aortic dissections, physicians require preoperative 3D Computed Tomography Angiography - or CTA - images, then intraoperative 2D fluoroscopic X-ray angiographic images. In one hand, only the injected contrast agent/X-rays combination allows physicians to detect aorta's contour, but it remains very difficult to obtain the adequate acquisition parameters. In another hand, the Digitally Reconstructed Radiograph method allows us to obtain a simulated rendering of a CTA with a fluoroscopic shading, but due to aorta's tissue, the aorta is not visible. In a recent study, we have proposed an interactive segmentation of aortic dissection CTA images which produces a tubular envelope wrapping aorta's wall. In this study, by computing and simply overlapping both Digitally Reconstructed Radiographs of the initial CTA image and of its corresponding tubular envelope image, we easily obtain a 2D view - called Augmented Digitally Reconstructed Radiograph - that makes aorta visible. Thus, such a preoperative work gives physicians a synthesis view the most similar possible to the one acquired during intervention, but with additional features (aorta's contour, aortic dissection features ...). This work will be used to automatically propose the best acquisition parameters, for aortic prostheses implantation.
Antibodies to various bacterial cell wall peptidoglycans in human and rabbit sera (1987)

Sera from patients with verified systemic staphylococcal infection contained antibodies reactive with peptidoglycan (PG) from Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes, Micrococcus lysodeikticus, Bacillus subtilis, and Escherichia coli. The presence of anti-PG cross-reactive antibodies was verified in patient sera by inhibition studies with the various bacterial PGs. Antibodies to nonstaphylococcal PGs were also elevated in sera from rabbits immunized with S. aureus PG. Antibodies to S. aureus PG were removed with the synthetic peptide analogs of S. aureus PG, the L-Lys-D-Ala-D-Ala, L-Lys-D-Ala, and (Gly)5 determinants, as well as with an S. aureus PG peptide fragment containing the determinants D-Ala-D-Ala and L-Lys-D-Ala. Isolated antibodies to the PG peptides, both synthetic and native, were reactive with S. aureus and S. epidermidis PGs. The antibodies to the D-Ala-D-Ala and the L-Lys-D-Ala determinants were also reactive with S. pyogenes PG, but not with PGs from M. lysodeikticus, B. subtilis, and E. coli.
Digital Signal Processing: Principles, Algorithms, and Applications (1992)

A significant revision of a best-selling text for the introductory digital signal processing course. This book presents the fundamentals of discrete-time signals, systems, and modern digital processing and applications for students in electrical engineering, computer engineering, and computer science.The book is suitable for either a one-semester or a two-semester undergraduate level course in discrete systems and digital signal processing. It is also intended for use in a one-semester first-year graduate-level course in digital signal processing.
Specific flavonoids induced nod gene expression and pre‐activated nod genes of Rhizobium leguminosarum increased pea (Pisum sativum L.) and lentil (Lens culinaris L.) nodulation in controlled growth chamber environments (2001)

The gram-negative soil bacteria Rhizobium spp. infect and establish a nitrogen-fixing symbiosis with legume crops which involves the mutual exchange of diffusable signal molecules. In this study, Rhizobium leguminosarum containing a nod-lacZ gene fusion was used to screen the most effective plant-to-bacteria signal molecules for pea and lentil and the induction conditions. Out of a number of signal compounds including apigenin, daidzein, genistein, hesperetin, kaempferol, luteolin, naringenin, and rutin, hesperetin and naringenin were found to be the most effective plant-to-bacteria signal molecules. The induction of nod genes was temperature-dependent, where nod gene induction was decreased with dropping incubation temperature. The combination of hesperetin at 7 microM and naringenin at 3 microM resulted in better induction of nod gene activities compared to either hesperetin or naringenin alone. Nodulation and plant dry matter accumulation of pea and lentil plants receiving preinduced R. leguminosarum were higher than those of plants receiving uninduced R. leguminosarum cells in controlled environment growth chamber conditions. Preinduced Rhizobium with hesperetin at a concentration of 10 microM increased nodule number on average by 60.5% and dry matter accumulation by 14% in field pea at 17 degrees C, while it was 32% and 9% at 24 degrees C, respectively. Similarly, averaged over two rhizobial strains, a 59% and 6% increase in nodule number and biomass production at 17 degrees C, and a 39% and 27% at 24 degrees C, were obtained from lentil inoculated with hesperetin-induced R. leguminosarum, respectively.
Miconazole chewing gum as a drug delivery system test of release promoting additives (1991)

The release of the antifungal drug miconazole from chewing gum formulations was evaluated in vitro and in vivo. It was proven that the addition of the anionic surfactant Panodan® 165 and polyethyleneglycol 6000 increased the release of miconazole. The anionic surfactant made the chewing gum tacky. The addition of polyethyleneglycol 6000 reduced the tacky properties of the chewing gum. 4 healthy volunteers obtained therapeutically active concentrations of miconazole in saliva when they chewed gum. The salivary concentrations of miconazole were estimated, both by a reverse phase HPLC method and a plate microbioassay.
Encoding universal computation in the ground states of Ising lattices (2012)

We characterize the set of ground states that can be synthesized by classical two-body Ising Hamiltonians. We then construct simple Ising planar blocks that simulate efficiently a universal set of logic gates and connections, and hence any Boolean function. We therefore provide a new method of encoding universal computation in the ground states of Ising lattices and a simpler alternative demonstration of the known fact that finding the ground state of a finite Ising spin glass model is NP complete. We relate this with our previous result about emergent properties in infinite lattices.