gebhart/patrepeval huggingface dataset:
Mosaicing of Bladder Endoscopic Image Sequences: Distortion Calibration and Registration Algorithm (2008)

Cancers located on the internal wall of bladders can be detected in image sequences acquired with endoscopes. The clinical diagnosis and follow-up can be facilitated by building a unique panoramic image of the bladder with the images acquired from different viewpoints. This process, called image mosaicing, consists of two steps. In the first step, consecutive images are pairwise registered to find the local transformation matrices linking geometrically consecutive images. In the second step, all images are placed in a common and global coordinate system. In this contribution, a mutual information-based similarity measure and a stochastic gradient optimization method were implemented in the registration process. However, the images have to be preprocessed in order to register the data in a robust way. Thus, a simple correction method of the distortions affecting endoscopic images is presented. After the placement of all images in the global coordinate system, the parameters of the local transformation matrices are all adjusted to improve the visual aspect of the panoramic images. Phantoms are used to evaluate the global mosaicing accuracy and the limits of the registration algorithm. The mean distances between ground truth positions in the mosaiced image range typically in 1-3 pixels. Results given for in vivo patient data illustrate the ability of the algorithm to give coherent panoramic images in the case of bladders.
A regulatory system for use in gene transfer. (1994)

We recently have demonstrated that a C-terminal deletion mutant of the human progesterone receptor (hPRB891) fails to bind to progesterone but can bind RU 486 (Mifepristone) and other progesterone antagonists. Most significantly, this mutant receptor activates transcription of a reporter gene containing the progesterone response element in the presence of these antagonists. Taking advantage of this finding and the modular nature of functional domains of steroid receptors, we constructed a chimeric regulator (pGL-VP) by fusing the ligand-binding domain of human progesterone receptor hPRB891 to the yeast transcriptional activator GAL4 DNA-binding domain and the herpes simplex virus protein VP16 activation domain. We demonstrated that this chimeric regulator activates target genes containing the GAL4-binding sites in transient transfection assays in response to RU 486. In addition, this regulatory system has been validated by ex vivo transplantation of a stable cell line containing both the regulator and a reporter gene into rats. The dosage of RU 486 used is significantly lower than that required for antagonizing progesterone action. The gene-switch system reported here represents a regulatory system, which could be applicable for gene-transfer studies involving animals, as well as humans, in which the delivered gene(s) can be specifically turned on/off in response to an exogenous compound.
A multicenter comparison of quantification methods for antisense oligonucleotide-induced DMD exon 51 skipping in Duchenne muscular dystrophy cell cultures (2018)

Our results suggest that digital droplet PCR was the most precise and quantitative method. The quantification of exon 51 skipping by Agilent bioanalyzer after a single round of PCR was the second-best choice with a 2.3-fold overestimation of exon 51 skipping levels compared to digital droplet PCR.
Current trends in the treatment of hepatic encephalopathy (2009)

Hepatic encephalopathy (HE) is a common reversible neuropsychiatric syndrome associated with chronic and acute liver dysfunction and significant morbidity and mortality. Although a clear pathogenesis is yet to be determined, elevated ammonia in the serum and central nervous system are the mainstay for pathogenesis and treatment. Management includes early diagnosis and prompt treatment of precipitating factors (infection, gastrointestinal bleeding, electrolyte disturbances, hepatocellular carcinoma, dehydration, hypotension, and use of benzodiazepines, psychoactive drugs, and/or alcohol). Clinical trials have established the efficacy of lactulose and lactitol enemas in the treatment of acute hepatic encephalopathy. Extensive clinical experience has demonstrated the efficacy of oral lactulose and lactitol with the goal of two to three soft bowel movements a day for the treatment of chronic HE. However, lactulose and lactitol have significant gastrointestinal side effects. For patients unable to tolerate lactulose or lactitol or who still have persistent chronic HE with lactulose or lactitol, neomycin, metronidazole and rifaximin are second-line agents. More recent data supports the benefits of rifaximin used solely and as an additional agent with fewer side effects than neomycin or metronidazole. Newer therapies being investigated in humans with clinical promise include nitazoxanide, the molecular adsorbent recirculating system (MARS), L-ornithine phenylacetate, sodium benzoate, and/or sodium phenylacetate and Kremezin((R)) (AST-120).
MADS box genes control vernalization-induced flowering in cereals (2003)

By comparing expression levels of MADS box transcription factor genes between near-isogenic winter and spring lines of bread wheat, Triticum aestivum, we have identified WAP1 as the probable candidate for the Vrn-1 gene, the major locus controlling the vernalization flowering response in wheat. WAP1 is strongly expressed in spring wheats and moderately expressed in semispring wheats, but is not expressed in winter wheat plants that have not been exposed to vernalization treatment. Vernalization promotes flowering in winter wheats and strongly induces expression of WAP1. WAP1 is located on chromosome 5 in wheat and, by synteny with other cereal genomes, is likely to be collocated with Vrn-1. These results in hexaploid bread wheat cultivars extend the conclusion made by Yan et al. [Yan, L., Loukoianov, A., Tranquilli, G., Helguera, M., Fahima, T. & Dubcovsky, J. (2003) Proc. Natl. Acad. Sci. USA 100, 6263-6268] in the diploid wheat progenitor Triticum monococcum that WAP1 (TmAP1) corresponds to the Vrn-1 gene. The barley homologue of WAP1, BM5, shows a similar pattern of expression to WAP1 and TmAP1. BM5 is not expressed in winter barleys that have not been vernalized, but as with WAP1, expression of BM5 is strongly induced by vernalization treatment. In spring barleys, the level of BM5 expression is determined by interactions between the Vrn-H1 locus and a second locus for spring habit, Vrn-H2. There is now evidence that AP1-like genes determine the time of flowering in a range of cereal and grass species.
Photoreceptor loss in age-related macular degeneration. (1996)

Photoreceptors are lost in NE-AMD as well as in the more severe exudative form, consistent with functional and clinical studies. The authors propose that rods die in older eyes without evidence of overt retinal pigment epithelial disease. In persons susceptible to AMD, the retinal pigment epithelium becomes dysfunctional. Secondarily, rod loss continues and cones begin to degenerate. Eventually, only degenerate cones remain; ultimately, all photoreceptors may disappear.
Successful tips of DNA extraction and PCR of plants for beginners (2018)

DNA extraction and PCR are among the most fundamental, essential, and inevitable experiments in plant genetics and biotechnology. Despite their long history, these protocols are still improved by researchers to perform more efficient and more successful experiments. In this review, we will try to introduce the key to successful DNA extraction and PCR experiments, especially for beginners of genetic analyses, to avoid making easy mistakes which often result in great waste of time and reagent. These keys are related to how to correctly measure DNA amount/purity, how to extract DNA from 'difficult' plant species, and how to successfully amplify target DNA sequence from huge plant genomic DNA.
Silicide formation and silicide-mediated crystallization of nickel-implanted amorphous silicon thin films (1993)

The nucleation and growth of isolated nickel disilicide precipitates in Ni-implanted amorphous Si thin films and the subsequent low-temperature silicide-mediated crystallization of Si was studied using in situ transmission electron microscopy. Analysis of the spatial distribution of the NiSi2 precipitates strongly suggested the occurrence of site saturation during nucleation. NiSi2 precipitates were observed in situ to migrate through the amorphous Si thin films leaving a trail of crystalline Si at temperatures as low as ∼484 °C. Initially, a thin region of epitaxial Si formed on {111} faces of the octahedral NiSi2 precipitates with a coherent interface which was shown by high-resolution electron microscopy to be Type A. Migration of the NiSi2 precipitates led to the growth of needles of Si which were parallel to 〈111〉 directions. The growth rate of the crystalline Si was limited by diffusion through the NiSi2 precipitates, and an effective diffusivity was determined at 507 and 660 °C. A mechanism for the enhanced growth rate of crystalline Si is proposed.
Satyal, Prabodh, William N. Setzer (2014)

Cannabis sativa was collected from a wildgrowing population in Biratnagar, Nepal. The essential oil was obtained by hydrodistillation and analyzed by gas chromatography – mass spectrometry. A total of 107 constituents were identified in the oil accounting for 94.2% of the composition. This Nepalese chemotype is characterized by a predominance of sesquiterpenoids (68.1%) dominated by (E)-caryophyllene (20.4%), α-humulene (7.0%), and α-bisabolol (5.8%), but a paucity of monoterpene hydrocarbons (0.9%). In particular, neither myrcene nor terpinolene were detected. The oil in the Nepalese Cannabis plants did contain small amounts of cannabidiol (1.6%), cannabichromene (0.2%) and Δ9-tetrahydrocannabinol (0.4%). The essential oil from Nepalese Cannabis sativa was screened for antimicrobial, cytotoxic, larvicidal, and insecticidal activity, and it appears as though C. sativa is relatively non-toxic.
Mutational analysis of arsonate binding by a CRIA+ antibody. VH and VL junctional diversity are essential for binding activity. (1991)

To assess the impact of various heavy and light chain mutations on p-azophenylarsonate binding, murine antibodies have been produced in insect cells (SF9) utilizing a baculovirus expression system. When expressed in this system, an antibody composed of a canonical CRIA+ heavy and light chain can bind antigen and express idiotype indistinguishably from analogous hybridoma-derived antibodies. Antibodies comprised of either light chains mutant at the V-J junction or heavy chains mutant at the V-D junction were found to be incapable of binding arsonate. In addition, substitutions in the first and second complementarity determining regions of the heavy chain were shown to play a role in arsonate binding, most likely related to affinity maturation targeted at the carrier protein. These results confirm the obligatory role that junctional diversity plays in the generation of arsonate-specific antibodies, as well as extend our understanding of the role of other variable region amino acids in arsonate binding.
Restoring accommodation: surgical technique and preliminary evaluation in rabbits (1999)

Purpose. To evaluate an innovative surgical technique for phaco-ersatz, a cataract surgery designed to restore accommodation. Techniques for very small capsulorhexis as well as the refilling procedure were developed. This study evaluates the feasibility and reproducibility of the surgical technique. Methods. The right eye of 8 NZW rabbits (&asymp; 2 Kg) were operated following the ARVO Statements for the Use of Animals in Ophthalmic and Vision Research. The surgery is begun by making a small peripheral capsulorhexis of about 1 mm using. The lens content is then removed. The lens is then refilled with a novel in situ polymerizable gel and the corneal incision is closed using one 10/0 Nylon interrupted stitch. Results. The capsulorhexis technique was succesfully performed and reproducible in all animals. The average size of the capsulorhexis opening was 1. 2 mm (&plusmn;0.14). Lens material removal and refilling of the capsular bag with an in situ polymerizable material was also performed in each trial study. Conclusion. This surgical technique seemed feasible and reproducible.
Synthesis, purification, and characterization of an Arg152 .fwdarw. Glu site-directed mutant of recombinant human blood clotting factor VII (1990)

Coagulation factor VII circulates in blood as a single-chain zymogen of a serine protease and is converted to its activated two-chain form, factor VIIa, by cleavage of an internal peptide bond located at Arg152-Ile153. Previous studies using serine protease active-site inhibitors suggest that zymogen factor VII may possess sufficient proteolytic activity to initiate the extrinsic pathway of blood coagulation. In order to assess the putative intrinsic proteolytic activity of single-chain factor VII, we have constructed a site-specific mutant of recombinant human factor VII in which arginine-152 has been replaced with a glutamic acid residue. Mutant factor VII was purified in a single step from culture supernatants of baby hamster kidney cells transfected with a plasmid containing the sequence for Arg152----Glu factor VII using a calcium-dependent, murine anti-factor VII monoclonal antibody column. Purified mutant factor VII was indistinguishable from plasma-derived or recombinant wild-type factor VII by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and migrated as a single band with an apparent molecular weight of 50,000. The average specific activity of several mutant factor VII preparations was 0.00025 unit/micrograms, or 0.01% of that observed for recombinant wild-type factor VII preparations. The clotting activity of mutant factor VII was, however, completely inhibited following incubation with dansyl-Glu-Gly-Arg chloromethyl ketone, suggesting that the apparent clotting activity of mutant factor VII was due to a contaminating serine protease.(ABSTRACT TRUNCATED AT 250 WORDS)
Improving reservoir management with complex well architectures (1997)

After 20 years of research and pilot applications, horizontal wells are now widely used as standard procedure. Further, new developments in drilling technology are starting to strongly modify concepts of well architecture. The new techniques of lateral arms, cluster wells or extended reach drilling can improve reservoir management, giving economical access to new reserves and optimizing marginal or mature fields. This article shows how complex well architectures can improve oil production through judicious placement by taking into account reservoir heterogeneity as well as the drive mechanisms involved. Production can be optimized by monitoring different sections within a well architecture, thus extending well life. Potential applications for Middle East reservoir conditions are reviewed. The appealing potential use of complex well architecture for characterization purposes at an early development stage is also introduced. Identification of the types of well architectures which could optimize pertinent data to be used by geostatistical models is presented. Methods of data acquisition within such complex well architectures are shown and new avenues in this field of research are investigated. Finally, from the above, a new characterization methodology based on hard data acquisition and geostatistical methods is proposed.
Penetration of ocular tissues and fluids by moxalactam in rabbits with staphylococcal endophthalmitis (1981)

Moxalactam was administered subconjunctivally in 100-mg doses to rabbits with infected eyes (Staphylococcus aureus endophthalmitis). High concentrations of drug were detected in the sclera, cornea, and choroid; much lower levels were found in the retina, whereas peak concentrations in the vitreous were about 6 microgram/ml. Repeated intramuscular injections of 50 mg/kg every 4 h produced peak serum levels of about 100 microgram/ml. A gradient between the choroid and the retina was again evident, and peak vitreous levels were about 6 microgram/ml after six injections. These data are consistent with the concept of a blood-retina barrier analogous to the blood-brain barrier. Moxalactam appears to penetrate the eye somewhat better than do other beta-lactams; however, the peak levels produced in the vitreous humor in this animal model were below the level required to inhibit most strains of Pseudomonas aeruginosa.
EZH2 Expression Is Associated With High Proliferation Rate and Aggressive Tumor Subgroups in Cutaneous Melanoma and Cancers of the Endometrium, Prostate, and Breast (2005)

Strong EZH2 expression was associated with increased tumor cell proliferation in all four cancer types. Associations were also found between EZH2 and important clinicopathologic variables. EZH2 expression showed significant prognostic impact in melanoma, prostate, and endometrial carcinoma in univariate survival analyses, and revealed independent prognostic importance in carcinoma of the endometrium and prostate. CONCLUSION Our findings point at EZH2 as a novel and independent prognostic marker in endometrial cancer, and validate previous findings on prostate and breast cancer. Further, EZH2 expression was associated with features of aggressive cutaneous melanoma. The fact that EZH2 might identify increased tumor cell proliferation and aggressive subgroups in several cancers may be of practical interest because the polycomb group proteins have been suggested as candidates for targeted therapy. EZH2 expression should, therefore, be further examined as a possible predictive factor.
Inhibition of c-Met as a Therapeutic Strategy for Esophageal Adenocarcinoma (2006)

The hepatocyte growth factor (HGF) receptor c-Met is a tyrosine kinase receptor with established oncogenic properties. We have previously shown that c-Met is usually overexpressed in esophageal adenocarcinoma (EA), yet the implications of c-Met inhibition in EA remain unknown. Three c-Met-overexpressing EA cell lines (Seg-1, Bic-1, and Flo-1) were used to examine the effects of a c-Met-specific small molecule inhibitor (PHA665752) on cell viability, apoptosis, motility, invasion, and downstream signaling pathways. PHA665752 demonstrated dose-dependent inhibition of constitutive and/or HGF-induced phosphorylation of c-Met, which correlated with reduced cell viability and inhibition of extracellular regulated kinase 1/2 phosphorylation in all three EA cell lines. In contrast, PHA665752 induced apoptosis and reduced motility and invasion in only one EA cell line, Flo-1. Interestingly, Flo-1 was the only cell line in which phosphatidylinositol 3-kinase (PI3K)/Akt was induced following HGF stimulation. The PI3K inhibitor LY294002 produced effects equivalent to those of PHA665752 in these cells. We conclude that inhibition of c-Met may be a useful therapeutic strategy for EA. Factors other than receptor overexpression, such as c-Met-dependent PI3K/Akt signaling, may be predictive of an individual tumor's response to c-Met inhibition.
Probing Protein–Carbohydrate Interactions with Microarrays of Synthetic Oligosaccharides (2004)

On the spot: Carbohydrate microarrays, in concert with surface plasmon resonance, are valuable tools in the rapid identification of carbohydrate–protein interactions, like those between high-mannose oligosaccharides and cyanovirin-N (see picture). By utilizing chemical methods amenable to current high-throughput screening technologies, high-density carbohydrate microarrays can be prepared and screened by using conventional and widely accessible DNA microarray screening instrumentation.
Surface Plasmon Resonance Imaging Using a High Numerical Aperture Microscope Objective (2007)

We designed, constructed, and tested a surface plasmon resonance (SPR) microscope using a high numerical aperture objective from a commercially available inverted optical microscope. Such a configuration, combined with various methods to shorten the surface plasmon propagation length, achieves diffraction-limited spatial resolution in the transverse direction and near-diffraction-limited resolution in the longitudinal direction. A virtue of the objective-type SPR imaging is that we achieve distortion-free angle-resolved SPR imaging, allowing the angle-dependent reflectivity of the sample to be examined on a pixel-by-pixel basis, thus offering high-resolution information about surface properties.
Chiral Lewis acid catalysis. Enantioselective addition of azide to meso epoxides (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChiral Lewis acid catalysis. Enantioselective addition of azide to meso epoxidesWilliam A. NugentCite this: J. Am. Chem. Soc. 1992, 114, 7, 2768–2769Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://pubs.acs.org/doi/10.1021/ja00033a090https://doi.org/10.1021/ja00033a090research-articleACS PublicationsRequest reuse permissionsArticle Views1414Altmetric-Citations188LEARN 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 Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Mechanisms of Action of the 5-HT1B/1D Receptor Agonists (2002)

Recent studies of the pathophysiology of migraine provide evidence that the headache phase is associated with multiple physiologic actions. These actions include the release of vasoactive neuropeptides by the trigeminovascular system, vasodilation of intracranial extracerebral vessels, and increased nociceptive neurotransmission within the central trigeminocervical complex. The 5-HT(1B/1D) receptor agonists, collectively known as triptans, are a major advance in the treatment of migraine. The beneficial effects of the triptans in patients with migraine are related to their multiple mechanisms of action at sites implicated in the pathophysiology of migraine. These mechanisms are mediated by 5-HT(1B/1D) receptors and include vasoconstriction of painfully dilated cerebral blood vessels, inhibition of the release of vasoactive neuropeptides by trigeminal nerves, and inhibition of nociceptive neurotransmission. The high affinity of the triptans for 5-HT(1B/1D) receptors and their favorable pharmacologic properties contribute to the beneficial effects of these drugs, including rapid onset of action, effective relief of headache and associated symptoms, and low incidence of adverse effects.
Dremel (2010)

Dremel is a scalable, interactive ad-hoc query system for analysis of read-only nested data. By combining multi-level execution trees and columnar data layout, it is capable of running aggregation queries over trillion-row tables in seconds. The system scales to thousands of CPUs and petabytes of data, and has thousands of users at Google. In this paper, we describe the architecture and implementation of Dremel, and explain how it complements MapReduce-based computing. We present a novel columnar storage representation for nested records and discuss experiments on few-thousand node instances of the system.