gebhart/patrepeval huggingface dataset:
Metal Film over Nanosphere (MFON) Electrodes for Surface-Enhanced Raman Spectroscopy (SERS):  Improvements in Surface Nanostructure Stability and Suppression of Irreversible Loss (2001)

The stability and reproducibility of most SERS-active electrode surfaces are far from ideal. We have focused on this problem by developing and characterizing a metal film over nanosphere (MFON) electrode which solves these shortcomings. Atomic force microscopy (AFM), cyclic voltammetry, and surface-enhanced Raman spectroscopy (SERS) of representative molecules were used to characterize and evaluate the electrochemical and SERS performance of MFON electrodes. Tremendous stability to extremely negative potential excursions is observed for MFON electrodes as compared to standard metal oxidation reduction cycle (MORC) roughened electrodes. Consequently, irreversible loss of SERS intensity at negative potentials is not observed on these MFON electrodes. We conclude that MFON electrodes present a significant advantage over MORC electrodes because SERS enhancement is not lost upon excursion to extremely negative potentials. This work demonstrates that the MFON substrate, while easily prepared and temporally stable, offers unprecedented stability and reproducibility for electrochemical SERS experiments. Furthermore, one can conclude that irreversible loss is not a distinguishing characteristic of electrochemical SERS and consequently cannot be used as evidence to support the chemical enhancement mechanism.
The study of the feasibility of segmental bone defect repair with tissue- engineered bone membrane: a qualitative observation (2008)

The objective of the study was to investigate the feasibility of intramembranous osteogenesis from tissue-engineered bone membrane in vivo. Bone marrow mesenchymal stem cells (MSCs) of rabbits were harvested, expanded and some of them were induced into osteoblasts. Porcine small intestinal submucosa (SIS) was converted by a series of physical and chemical procedures into a scaffold. MSCs and induced osteoblasts were seeded separately onto the scaffold, thus fabricating two kinds of tissue-engineered bone membrane. A total of 12 New Zealand rabbits were subjected to a surgical operation; a 15 mm bone segment, including the periosteum, was resected from the radius on both sides of each rabbit to create critical bone defects. The two kinds of tissue-engineered bone membrane and SIS (as control) were implanted randomly into the site of bone defect. The animals had radiographs and were killed after 4 weeks. The specimens were harvested and histological examination performed for evidence of osteogenesis. Bone tissue had formed in defects treated by the two kinds of tissue-engineered bone membrane at 4 weeks. This was supported by the X-ray and histological examination, which confirmed the segmental gap bridged by bone. There was no attempt to bridge in the bone defect treated by SIS. Tissue-engineered bone membrane, constructed by seeding allogeneic cells on an xenogeneic and bio-derived scaffold, can repair critical bone defects successfully.
Review: Oxidative Stress and Disease (2000)

This communication briefly reviews aspects of oxidative stress and disease, particularly maturity onset cataract. The review considers a number of issues such as why lens and cataract research is important, what is oxidative stress, its relationship to disease and how does a tissue defend itself against such stress. Three diseases (chronic lung disease, diabetes and Alzheimer's disease) in which oxidative stress has differing roles are briefly discussed. The impact of oxidative stress upon the development of maturity onset cataract is considered and approaches are delineated which will establish the importance of such stress.
SwissDock, a protein-small molecule docking web service based on EADock DSS (2011)

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.
[Dietary supplements from ground fish meat with DNA for treatment and prophylaxis]. (1998)

It has been developed a receipt of a new treatment-and-prophylactic products based on fish farce with treatment-and-prophylactic additive--DNA. It is recommended to be produced. As biological active additive keeps its initial pharmacological characteristics under technological processing this product is recommended for rendering general effect and increasing of physical and mental activity of organism.
Self-assembling resists for nanolithography (2006)

In this paper we present our approach for integrating block copolymers into the lithographic process so as to enable molecular-level control over the dimensions and shapes of nanoscale patterned resist features and simultaneously retain essential process attributes such as pattern perfection, registration, and the ability to create non-regular device-oriented structures. Combining self-assembling materials with advanced lithographic tools may allow current manufacturing techniques to be extended to the scale of 10 nm and below and meet the long-term requirements detailed in the International Technology Roadmap for Semiconductors (2004).
Quantum Treemaps and Bubblemaps for a Zoomable Image Browser (2001)

This paper describes two algorithms for laying out groups of objects in a 2D space-filling manner. Quantum Treemaps are a variation on existing treemap algorithms that are designed for laying out images or other objects of indivisible (quantum) size. They build on the Ordered Treemap algorithm, but guarantees that every generated rectangle will have a width and height that are an integral multiple of an input object size. Bubblemaps also fill space with groups of quantum-sized objects, but generate nonrectangular blobs, and utilize space more efficiently. Both algorithms have been applied to PhotoMesa, an application that supports browsing of large numbers of images. PhotoMesa uses a Zoomable User Interface with a simple interaction designed for novices and family use. Keywords Zoomable User Interfaces (ZUIs), Treemaps, Image Browsers, Animation, Graphics, Jazz.
A Randomized Placebo-Controlled Trial of Saccharomyces boulardii in Combination With Standard Antibiotics for Clostridium difficile Disease (1994)

OBJECTIVE--To determine the safety and efficacy of a new combination treatment for patients with Clostridium difficile-associated disease (CDD). The treatment combines the yeast Saccharomyces boulardii with an antibiotic (vancomycin hydrochloride or metronidazole). DESIGN--A double-blind, randomized, placebo-controlled, parallel-group intervention study in patients with active CDD. Patients received standard antibiotics and S boulardii or placebo for 4 weeks, and were followed up for an additional 4 weeks after therapy. Effectiveness was determined by comparing the recurrence of CDD in the two groups using multivariate analysis to control for other risk factors for CDD. SETTING--National referral study of ambulatory or hospitalized patients from three main study coordinating centers. PATIENTS--A total of 124 eligible consenting adult patients, including 64 who were enrolled with an initial episode of CDD, and 60 who had a history of at least one prior CDD episode. Patients who were immunosuppressed due to acquired immunodeficiency syndrome or cancer chemotherapy within 3 months were not eligible. INTERVENTION--Treatment with oral S boulardii (1 g/d for 4 weeks) or placebo in combination with a standard antibiotic. MAIN OUTCOME MEASURE--Recurrence of active CDD. RESULTS--A history of CDD episodes dramatically increased the likelihood of further recurrences. Multivariate analysis revealed that patients treated with S boulardii and standard antibiotics had a significantly lower relative risk (RR) of CDD recurrence (RR, 0.43; 95% confidence interval, 0.20 to 0.97) compared with placebo and standard antibiotics. The efficacy of S boulardii was significant (recurrence rate 34.6%, compared with 64.7% on placebo; P = .04) in patients with recurrent CDD, but not in patients with initial CDD (recurrence rate 19.3% compared with 24.2% on placebo; P = .86). There were no serious adverse reactions associated with S boulardii. CONCLUSIONS--The combination of standard antibiotics and S boulardii was shown to be an effective and safe therapy for these patients with recurrent CDD; no benefit of S boulardii was demonstrated for those with an initial episode of CDD.
A Single Ataxia Telangiectasia Gene with a Product Similar to PI-3 Kinase (1995)

A gene, ATM, that is mutated in the autosomal recessive disorder ataxia telangiectasia (AT) was identified by positional cloning on chromosome 11q22-23. AT is characterized by cerebellar degeneration, immunodeficiency, chromosomal instability, cancer predisposition, radiation sensitivity, and cell cycle abnormalities. The disease is genetically heterogeneous, with four complementation groups that have been suspected to represent different genes. ATM, which has a transcript of 12 kilobases, was found to be mutated in AT patients from all complementation groups, indicating that it is probably the sole gene responsible for this disorder. A partial ATM complementary DNA clone of 5.9 kilobases encoded a putative protein that is similar to several yeast and mammalian phosphatidylinositol-3' kinases that are involved in mitogenic signal transduction, meiotic recombination, and cell cycle control. The discovery of ATM should enhance understanding of AT and related syndromes and may allow the identification of AT heterozygotes, who are at increased risk of cancer.
YB-1 regulates stress granule formation and tumor progression by translationally activating G3BP1 (2015)

Under cell stress, global protein synthesis is inhibited to preserve energy. One mechanism is to sequester and silence mRNAs in ribonucleoprotein complexes known as stress granules (SGs), which contain translationally silent mRNAs, preinitiation factors, and RNA-binding proteins. Y-box binding protein 1 (YB-1) localizes to SGs, but its role in SG biology is unknown. We now report that YB-1 directly binds to and translationally activates the 5' untranslated region (UTR) of G3BP1 mRNAs, thereby controlling the availability of the G3BP1 SG nucleator for SG assembly. YB-1 inactivation in human sarcoma cells dramatically reduces G3BP1 and SG formation in vitro. YB-1 and G3BP1 expression are highly correlated in human sarcomas, and elevated G3BP1 expression correlates with poor survival. Finally, G3BP1 down-regulation in sarcoma xenografts prevents in vivo SG formation and tumor invasion, and completely blocks lung metastasis in mouse models. Together, these findings demonstrate a critical role for YB-1 in SG formation through translational activation of G3BP1, and highlight novel functions for SGs in tumor progression.
Human IgE against the major allergen Bet v 1 – defining an epitope with limited cross‐reactivity between different PR‐10 family proteins (2013)

We here display the usefulness of allergen-specific human monoclonal IgE as a tool in studies of the crucial molecular interaction taking place at the initiation of an allergic response. Such studies may aid us in development of better diagnostic tools and guide us in the development of new therapeutic compounds.
Central Apnea Index Decreases after Prolonged Treatment with Acetazolamide (1995)

Only a limited number of studies dealing with the epidemiology and therapy of central sleep apnea syndrome (CA) are available. The treatment strategies are poorly defined and not well evaluated. The aim of our present study was to treat selected CA patients with low dose acetazolamide (ACET) for a longer time period than has been done before. Previous studies were performed with high dose ACET provoking severe metabolic acidosis, not for more than 1 wk or only in obstructive apnea patients. Referred patients with suspicion of sleep-related breathing disorders (SRBD) were included in the study if, after a first selection night, their central apnea index (CAI) was > 5 or their apnea-hypopnea index (AHI) > 10 and their obstructive apnea index (OAI) < 5. Of 327 screened patients, 14 (4.3%) fulfilled these criteria. Patients were then treated with ACET (250 mg, 1 h before sleep): Polysomnography was repeated once after one single dose (N2) and twice after 1-mo chronic treatment without (N3) and with (N4) additional ACET administration. After each study night, arterial blood gases and chemical drive were measured. CAI (25.5 +/- 6.8 at N1) already decreased during N2 (13.8 +/- 5.2) and further during N3 (6.6 +/- 2.9) and N4 (6.8 +/- 2.8) p < 0.01). OAI remained unchanged. Total sleep time (TST) and sleep efficiency index (SEI) did not change significantly. The number of arousals decreased from 62 +/- 11 at N1 to 40 +/- 5 at N3 (p = 0.019).(ABSTRACT TRUNCATED AT 250 WORDS)
Stimulation of DNA and Collagen Synthesis by Autologous Growth Factor in Cultured Fetal Rat Calvaria (1980)

Conditioned medium derived from organ or cell cultures prepared from 19- to 21-day fetal rat calvaria stimulated the incorporation of [3H]proline collagen and of [3H]thymidine into DNA in organ cultures of the same tissue. Addition of cortisol enhanced the effect on collagen but not on DNA synthesis. These effects appeared to be due to a nondialyzable and heat-stable growth factor.
Immunocytochemical Localization of Carcinoembryonic Antigen (CEA), Alpha-Fetoprotein (AFP), and Human Chorionic Gonadotropin (HCG) in Cervical Neoplasia (1983)

Sixty-one cases of invasive cervical carcinoma and 40 cases of dysplasia and carcinoma in situ were studied by peroxidase-antiperoxidase method (PAP) for the presence of carcinoembryonic antigen (CEA). Forty-two cases (13 carcinomas in situ and 29 invasive carcinomas) also were tested for alpha-fetoprotein (AFP) and human chorionic gonadotropin hCG. CEA was not detected in normal cervical epithelium but was present in 90% of the neoplastic lesions. Not mere presence, but a pattern of CEA tissue distribution emerged as the main differential point between noninvasive and invasive lesions. Twenty-nine of 51 invasive squamous carcinomas (57%) contained CEA-positive cells at the stromal edge of epithelium, while this feature was not found in dysplasia and carcinoma in situ. Adenocarcinomas and adenosquamous carcinomas all were positive for CEA, while clear-cell carcinomas were negative. AFP was present only in a case of poorly differentiated adenosquamous ("glassy cell") carcinoma. hCG has not been revealed in any of the tumors.
Experimental Determination of the Extinction Coefficient of CdTe, CdSe and CdS Nanocrystals. (2004)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionExperimental Determination of the Extinction Coefficient of CdTe, CdSe and CdS Nanocrystals.W. William Yu, Lianhua Qu, Wenzhuo Guo, and Xiaogang PengCite this: Chem. Mater. 2004, 16, 3, 560Publication Date (Web):January 13, 2004Publication History Published online13 January 2004Published inissue 1 February 2004https://pubs.acs.org/doi/10.1021/cm033007zhttps://doi.org/10.1021/cm033007zcorrectionACS PublicationsCopyright © 2004 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views10928Altmetric-Citations129LEARN 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 InRedditEmail PDF (16 KB) Get e-Alertsclose Get e-Alerts
ConCISe: a compiler-driven CPLD-based instruction set accelerator (2003)

We propose a smart compilation chain in which the compiler is no longer limited by a pre-defined instruction set, but can generate application-specific custom instructions and synthesise them in Field-Programmable Logic. We also present a RISC micro-architecture enhanced by a CPLD-based Reconfigurable Functional Unit (RFU) which supports our compiler approach. The main difference between our smart compiler and similar methods is the ability to encode multiple custom instructions in a single RFU configuration, cross-minimising the logic among them. The objective is to reduce (or eliminate) the reconfiguration overhead and optimise the utilisation of resources. The CPLD core that implements the RFU is based on the Philips XPLA2 architecture. We discuss the advantages of using the XPLA2 instead of conventional FPGAs. Application examples are also presented, which show that our RFU-extended CPU can achieve speed-ups of more than 40% for encryption algorithms, when compared to the standard CPU core alone.
Deblender: a semi−/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples (2018)

Our results corroborate that Deblender can be a valuable tool to improve understanding of gene expression datasets with implications for prediction and clinical utilization. Deblender is implemented in MATLAB and is available from ( https://github.com/kondim1983/Deblender/ ).
Accumulation of a nod gene inducer, the flavonoid naringenin, in the cytoplasmic membrane of Rhizobium leguminosarum biovar viciae is caused by the pH-dependent hydrophobicity of naringenin (1989)

Most Sym plasmid-localized nodulation genes of Rhizobium leguminosarum bv. viciae are only expressed upon activation of the NodD protein by plant flavonoids, e.g., naringenin (S. A. J. Zaat, C. A. Wijffelman, H. P. Spaink, A. A. N. van Brussel, and B. J. J. Lugtenberg, J. Bacteriol, 169:198-204, 1987). As part of a study on the mechanism of NodD protein activation, the mechanism of uptake and the intracellular fate of [3H]naringenin were studied. Naringenin was accumulated by Rhizobium cells without apparent metabolic conversion to an 80-fold-higher concentration in a process which did not require any of the other Sym plasmid-localized nod genes. Naringenin accumulation was nonsaturable, highly reversible, and not inhibited by the presence of other flavonoids or the metabolic inhibitors potassium cyanide, sodium azide, 2,4-dinitrophenol, and carbonyl cyanide m-chlorophenylhydrazone. These data indicate an accumulation mechanism without high affinity sites which does not use cellular energy. In vitro, naringenin has high affinity for the cytoplasmic membrane. This binding was pH dependent, very high at pH 5.7 and not present anymore at pH 9.7. A similar pH dependency was found for the affinity of naringenin for the olive oil fraction of a biphasic olive oil-water system. pH-dependent changes in the UV spectrum indicate ionization of naringenin at high pH to a negatively charged form. Since it has recently been shown that the nodD gene product is located in the cytoplasmic membrane (H. R. M. Schlaman, H. P. Spaink, R. J. H. Okker, and B. J. J. Lugtenberg, J. Bacteriol., in press), our data are consistent with a model in which the un-ionized form of naringenin accumulates in the cytoplasmic membrane and activates, in a metabolically unaltered form, the NodD protein.
p53 Binds Telomeric Single Strand Overhangs and t-Loop Junctions in Vitro (2002)

The interaction of p53 with a human model telomere in vitro was examined by electron microscopy. p53 demonstrated a sequence-independent affinity for telomeric DNA in vitro, localizing to the 3' single strand overhang and the t-loop junction both in the presence and absence of associated TRF2. Binding was not observed above background along the duplex telomeric repeats. However, the efficiency of TRF2-catalyzed t-loop formation on the model DNA was increased 2-fold in the presence of p53 although a variety of single strand or Holliday junction-binding proteins did not facilitate t-loop formation. These results suggest that p53 has an active role in telomere maintenance and structure through association with the t-loop junction.
Dynamic Spreading of Nanofluids on Solids. Part I: Experimental (2012)

Nanofluids have enhanced thermophysical properties compared to fluids without nanoparticles. Recent experiments have clearly shown that the presence of nanoparticles enhances the spreading of nanofluids. We report here the results of our experiments on the spreading of nanofluids comprising 5, 10, and 20 vol % silica suspensions of 19 nm particles displacing a sessile drop placed on a glass surface. The contact line position is observed from both the top and side views simultaneously using an advanced optical technique. It is found that the nanofluid spreads, forming a thin nanofluid film between the oil drop and the solid surface, which is seen as a bright inner contact line distinct from the conventional three-phase outer contact line. For the first time, the rate of the nanofluidic film spreading is experimentally observed as a function of the nanoparticle concentration and the oil drop volume. The speed of the inner contact line is seen to increase with an increase in the nanoparticle concentration and decrease with a decrease in the drop volume, that is, with an increase in the capillary pressure. Interestingly, the formation of the inner contact line is not seen in fluids without nanoparticles.
The X Files--One Step Closer to Closure (2001)

There may be drugs and a useful vaccine available to combat the hepatitis B virus, but one aspect of this pathogen remains a puzzle: the function of its HBx protein. As Ganem reveals in his Perspective, new findings (Bouchard et al.) show that this versatile viral protein is an activator of calcium-dependent Ras signaling, an observation that may explain many of its biological effects.