gebhart/patrepeval huggingface dataset:
Effect of Rice Koji Fermentation on the Characteristics of Mackerel Muscle (2005)

To improve the quality and functionality of fish muscle, minced mackerel was fermented with Aspergillus oryzae BCRC 30118 and Aspergillus sojae BCRC 30103. The Enterbacteriaceae, Staphylococcus and Pseudomonas were completely inhibited during 7 days fermentation at 25℃ with 120rpm shaking on the medium preheated at 100℃ for 30min. During fermentation, the rice koji plate count increased from 10^4 to 10^5 CFU/mL. Change in total sugar was parallel to the increase of reducing sugar. Both amylase and protease activities increased during fermentation and the highest acid and neutral proteases activities were detected after 2-3 days fermentation. The amylase and protease activities were higher in those fermented with Aspergillus oryzae BCRC 30118 than those with Aspergillus sojae BCRC 30103. Comparing with the control samples, the free amino free acid increased significantly, especially glutamic acid, leucine and lysine. Changes in amino-nitrogen, free amino acid and SDS-PAGE indicated that severe hydrolysis of muscle protein occurred during fermentation. The DPPH scavenging capability, reducing power and chelating Cu(superscript 2+) capability of fermented mackerel mince significantly increased after 5 days fermentation (p＜0.05). These data suggested that the koji fermentation could substantially improve the digestibility, nutritional value and antioxidant ability of the fermented fish.
The Pre-Flood Floating Forest: A Study in Paleontological Pattern Recognition (2003)

The sessile status and high preservability of plants make them good taxa for studying fossil record order and discriminating among the various mechanisms creationists have advanced for explaining fossil order. Although the creation model does not make specific predictions about the order of fossil appearance for the plants, evolutionary theory does. The first appearance of higher plant taxa occur in an order strongly correlative with the order of evolutionary branching predicted from published cladograms. The higher plant taxa represent a strong stratomorphic series. The probability that this pattern could be arrived at randomly is so low as to suggest that an explanation is required in the young-age creation model. The synapomorphy sequence of plant cladograms is consistent with a character trend up the cladogram towards increased resistance to dessication (or increased terrestriality) and is highly correlative with the stratigraphic order of both first appearance and maximum diversity. It is proposed that the Flood destruction of pre-Flood floating forest biome would explain this data. In a fashion analogous to the plants of a quaking bog, it is suggested that the floating forest biome grew out over the ocean through an ecological succession of rhyzomous plants of steadily increasing size generating and thriving upon an increasingly thick mat of vegetation and soil. It is suggested that the plant succession from open water inward began with horneophytes, and continued with a sequence of rhyniophytes, zosterophyllites, and progymnosperms. This was followed in turn by a full forest biome including herbaceous lycopods and ferns on the forest floor, seed ferns in the understory, and arborescent sphenophytes and lycopods making up the canopy. It is also suggested that living in the floating forest was a succession of animals (the Paleozoic ‘land’ animals). This would have included the large Paleozoic insects as well as the Devonian aquatic tetrapods (like Ichthyostega) in pools on thinner portions of the forest floor and a wide variety of large amphibians (including the labyrinthodonts) on the thicker sections of the forest. Not only does the Flood destruction of the floating forest explain the first appearance and maximum abundance order of fossil plants and animals, it also explains the strong association of Paleozoic plants with marine sediments and how the pre-Flood world could support the plant biomass represented in the Carboniferous coals. It also incorporates the pre-Flood floating forest theory of Joachim Scheven, and the floating logmat theory of Steven A. Austin for the origin of coal. It is further suggested that the residual catastrophism of the post-Flood period prevented the restoration of the antediluvian floating forest biome and resulted in the extinction of most of the Paleozoic plants and ‘land’ animals.
Hourly Water Level Forecasting at Tributary Affected by Main River Condition (2017)

This study develops hourly water level forecasting models with lead-times of 1 to 3 h using an artificial neural network (ANN) for Anyangcheon stream, one of the major tributaries of the Han River, South Korea. To consider the backwater effect from this river, an enhanced tributary water level forecasting model is proposed by adding multiple water level data on the main river as input variables into the conventional ANN structure which often uses rainfall and upstream water level data. Four types of ANN models per each lead-time are built with increasing complexity of the input vector, and their performances are compared. The results indicate that the inclusion of multiple water level data on the main river to the network provides water level forecasts with greater accuracy at the Ogeumgyo gauging station of interest. The final best ANN models for water level forecasts with lead-times of 1 to 2 h show good performance with root mean square errors (RMSE) below 0.06 m and 0.12 m, respectively. However, the final best ANN model for forecasting 3 h ahead was unsatisfactory, showing underestimation at many rising parts of the hydrograph.
High density nanostructure transfer in soft molding using polyurethane acrylate molds and polyelectrolyte multilayers (2003)

Here we present an alternative, new, unconventional lithographic technique developed to create dense and multilevel nanostructure pattern transfer using a highly accurate polyurethane acrylate (PU, MINS101m, Minuta Tech.) mold and a polyelectrolyte multilayer as the adhesion promotion layer. Specifically, we demonstrate the pattern transfer of periodic 80 nm lines with 400 nm height and complex and multilevel nanostructures to a polymer layer on various substrates, such as Si or SiO2 wafers, glass and flexible polymer films. This new, unconventional lithographic technique presented here would open the door to a variety of applications in the fields of electronic, optical and biological devices.
Autoantibody Profiling in Multiple Sclerosis Using Arrays of Human Protein Fragments (2013)

Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing ∼38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.
Synthesis of Silver and Gold Nanoparticles by a Novel Electrochemical Method (2004)

Spherical silver and gold nanoparticles with narrow size distributions were conveniently synthesized in aqueous solution by a novel electrochemical method. The technological keys to the electrochemical synthesis of monodispersed metallic nanoparticles lie in the choice of an ideal stabilizer for the metallic nanoclusters and the use of a rotating platinum cathode. Poly(N-vinylpyrrolidone) (PVP) was chosen as the stabilizer for the silver and gold clusters. PVP not only protects metallic particles from agglomeration, but also promotes metal nucleation, which tends to produce small metal particles. Using a rotating platinum cathode effectively solves the technological difficulty of rapidly transferring the (electrochemically synthesized) metallic nanoparticles from the cathode vicinity to the bulk solution, avoiding the occurrence of flocculates in the vicinity of the cathode, and ensuring the monodispersity of the particles. The particle size and particle size distribution of the silver and gold nanoparticles were improved by adding sodium dodecyl benzene sulfonate (SDBS) to the electrolyte. The electrochemically synthesized nanoparticles were characterized by TEM and UV/Vis spectroscopy.
Maculas Affected by Age-Related Macular Degeneration Contain Increased Chelatable Iron in the Retinal Pigment Epithelium and Bruch's Membrane (2003)

Oxidative stress has been implicated in the pathogenesis of AMD by the Age-Related Eye Disease Study. Increased concentrations of iron, which generate highly reactive hydroxyl radicals via the Fenton reaction, may induce oxidative stress in the macula and lead to AMD. As the increased iron concentrations in AMD-affected eyes consist in part of a chelatable iron pool, treatment of patients who have AMD with iron chelators might be considered a potential therapy. While there are, as yet, no clinical data indicating that the treatment of patients who have AMD with iron chelators is beneficial, data presented herein indicate that further investigation of iron concentrations in postmortem tissues and the mechanisms of iron transport in the retina is warranted.
Electrochemical fabrication of cadmium chalcogenide microdiode arrays (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochemical fabrication of cadmium chalcogenide microdiode arraysJonathan D. Klein, Robert D. Herrick, II, Dean Palmer, Michael J. Sailor, Charles J. Brumlik, and Charles R. MartinCite this: Chem. Mater. 1993, 5, 7, 902–904Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/cm00031a002https://doi.org/10.1021/cm00031a002research-articleACS PublicationsRequest reuse permissionsArticle Views959Altmetric-Citations216LEARN 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-Alertsclose Get e-Alerts
Allele-specific expression in the germline of patients with familial pancreatic cancer: An unbiased approach to cancer gene discovery (2008)

Physiologic allele-specific expression (ASE) in germline tissues occurs during random X-chromosome inactivation and in genomic imprinting, wherein the two alleles of a gene in a heterozygous individual are not expressed equally. Recent studies have confirmed the existence of ASE in apparently non-imprinted autosomal genes; however, the extent of ASE in the human genome is unknown. We explored ASE in lymphoblastoid cell lines of 145 individuals using an oligonucleotide array based assay. ASE of autosomal genes was found to be a very common phenomenon in approximately 20% of heterozygotes at 78% of SNPs at 84% of the genes examined. Comparison of 100 affected individuals from familial pancreatic cancer kindreds and 45 controls revealed three types of changes in the germline: (a) loss of ASE, (b) gain of ASE, and, (c) rare instances of "extreme" (near monoallelic) ASE. The latter changes identified heterozygous deleterious mutations in a subset of these genes. Consequently, an ASE assay efficiently identifies candidate disease genes with altered germline expression properties as compared to controls, and provides insights into mechanisms that confer an inherited disease risk for pancreatic cancer.
ESTROGEN RECEPTORS IN BREAST CANCER ASSOCIATION WITH EPIDEMIOLOGIC RISK FACTORS (1986)

Journal Article ESTROGEN RECEPTORS IN BREAST CANCER ASSOCIATION WITH EPIDEMIOLOGIC RISK FACTORS Get access RACHEL BALLARD-BARBASH, RACHEL BALLARD-BARBASH 1Department of Preventive Medicine, Mayo ClinicRochester, MN2Department of Medical Statistics and Epidemiology, Mayo ClinicRochester, MN 55905 Reprint requests to Dr. Rachel Ballard-Barbash at this address Search for other works by this author on: Oxford Academic PubMed Google Scholar MARIE R. GRIFFIN, MARIE R. GRIFFIN 2Department of Medical Statistics and Epidemiology, Mayo ClinicRochester, MN 55905 Search for other works by this author on: Oxford Academic PubMed Google Scholar LLOYD D. FISHER, LLOYD D. FISHER 2Department of Medical Statistics and Epidemiology, Mayo ClinicRochester, MN 55905 Search for other works by this author on: Oxford Academic PubMed Google Scholar MICHAEL A. COVALCIUC, MICHAEL A. COVALCIUC 1Department of Preventive Medicine, Mayo ClinicRochester, MN Search for other works by this author on: Oxford Academic PubMed Google Scholar NAI-SAIANG JIANG NAI-SAIANG JIANG 3Department of Clinical Chemistry, Mayo ClinicRochester, MN Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 124, Issue 1, July 1986, Pages 77–84, https://doi.org/10.1093/oxfordjournals.aje.a114372 Published: 01 July 1986 Article history Received: 25 November 1985 Published: 01 July 1986
Vasoactive factors in sickle cell disease: In vitro evidence for endothelin‐1‐mediated vasoconstriction (2004)

While systemic plasma endothelin-1 (ET-1) levels are increased during acute crisis in sickle cell disease, the relative levels of potent vasoactive factors that contribute to the regulation of vascular function, such as ET-1, NO, and cell-free hemoglobin, during the course of periodic vaso-occlusive episodes remain unclear. Moreover, whether and to what extent sickling-induced release of ET-1 alters vascular tone is not completely understood. To investigate the sequential changes in circulating vasoactive factors, we measured plasma ET-1, NO metabolites (NOx), and cell-free hemoglobin (Hb) before (steady-state), during (crisis), and after a vaso-occlusive (post-crisis) episode. Steady-state ET-1 levels (fmol/mL) increased from 2.3 +/- 0.4 to 11.0 +/- 1.4 and 4.2 +/- 1.0 during crisis and post-crisis periods, respectively. There was no significant difference in plasma NOx levels. Cell-free Hb levels were significantly higher in sickle cell patients in all phases as compared to the control group, and especially during crisis cell-free Hb levels were elevated by 4-fold (209,000 +/- 31,000 vs. 46,000 +/- 5,300 ng/mL in steady-state). Conditioned medium from human pulmonary artery endothelial cells exposed to sickled erythrocytes prepared by deoxygenation induced contraction of aortic rings, and this effect was blocked by an ET(A) receptor antagonist. These findings indicate that ET-1 is the predominant contractile factor released by cultured endothelial cells upon exposure to deoxygenated sickled SS erythrocytes and ET-1-NO-NO scavenger balance is altered in favor of vasoconstriction during an acute episode in SCD.
Use of PRINS for preconception screening of polar bodies for common aneuploidies (2000)

It has been shown that preconceptional screening for oocyte aneuploidies could help increase the pregnancy rate after in vitro fertilization (IVF), particularly in cases of advanced maternal age. The FISH (fluorescent in situ hybridization) technique is usually used to examine the first polar body (I-PB) for oocyte screening and so avoid fertilizing and transferring embryos from aneuploid oocytes. We have tested the feasibility of using another technique, the primed in situ (PRINS) reaction for this purpose. PRINS is a rapid, inexpensive method of labelling chromosomes. Chromosomes were labelled by in situ annealing with chromosome-specific oligonucleotide primers, followed by primer extension with labelled nucleotides using Taq DNA polymerase. A total of 183 PRINS reactions were performed with primers for chromosomes 13, 16, 18, 21 or X on 63 I-PBs removed from oocytes that failed to become fertilized during IVF. Each I-PB underwent three successive double-labelling reactions and intense signals were obtained in less than 40 min. Our data suggest that PRINS may be a useful alternative or a complement to FISH for detecting the main aneuploidies in all oocytes obtained after follicular puncture.
Experiments on visual cells by nature and man: in search of treatment for photoreceptor degeneration. Friedenwald lecture. (1989)

In this lecture I attempt to provide an overview of pathogenetic factors of photoreceptor degeneration as well as the alterations of the visual cells and their cellular environment in photoreceptor degeneration. A therapeutic approach to photoreceptor degeneration was developed based on the experimental model of photic retinopathy
Logging framework for cloud computing forensic environments (2014)

Cloud computing has emerged as a paradigm that attracts more and more researchers. In this context, the need for knowing where, how and under what conditions data is either processed or stored in datacenters, becomes a prime interest due to the continuously developing field of cloud computing forensics. In this paper we describe in a detailed manner an essential part of our cloud forensic framework that can be built on top of both new and existing datacenters - the logging part. We discuss the problems that must be dealt with in such architectures and we detail our proposed solutions to them. We explain how our architecture and findings can help forensics investigators that conduct investigations in a cloud environment.
Molecular identification of the lobster muscle protein tropomyosin as a seafood allergen. (1998)

Crustaceans are a major cause of seafood allergy. Recent studies have identified tropomyosin as the major allergen in shrimp. However, such data are lacking in other crustaceans. In the present study lobster allergens were identified and characterized by molecular cloning, sequencing, and expression. An IgE-reactive complementary DNA clone of 2 kilobase pairs (kb) was identified by screening an expression library of the spiny lobster Panulirus stimpsoni using sera from subjects with crustacean allergy. Expression and sequencing of this clone showed that it has an opening reading frame of 274 amino acids, coding for a 34-kDa protein designated as Pan s I. In addition, we expressed the fast muscle tropomyosin from the American lobster Homarus americanus and found that this protein, coined Hom a I, was also recognized by IgE from patients with crustacean allergies. The deduced amino acid sequences of Pan s I and Hom a I, which are the first identified lobster allergens, show significant homology to shrimp tropomyosin. Sera from subjects with crustacean allergies, when preabsorbed with recombinant proteins Pan s I or Hom a I, lost their IgE reactivity to muscle extract of P. stimpsoni and H. americanus. Preincubation of crustacean allergy sera with the recombinant shrimp tropomyosin Met e I also removed their IgE reactivity to lobster muscle extracts. The results suggest that patients with allergic reactions to crustaceans have common and possibly cross-reactive IgE-reactive epitopes in lobster and shrimp.
Transcriptional Activation by Tetracyclines in Mammalian Cells (1995)

A transcriptional transactivator was developed that fuses the VP16 activation domain with a mutant Tet repressor from Escherichia coli. This transactivator requires certain tetracycline (Tc) derivatives for specific DNA binding. Thus, addition of doxycycline to HeLa cells that constitutively synthesized the transactivator and that contained an appropriate, stably integrated reporter unit rapidly induced gene expression more than a thousandfold. The specificity of the Tet repressor-operator-effector interaction and the pharmacological characteristics of Tc's make this regulatory system well suited for the control of gene activities in vivo, such as in transgenic animals and possibly in gene therapy.
The gene encoding the cellulase (Avicelase) Cell from Streptomyces reticuli and analysis of protein domains (1992)

Streptomyces reticuli produces an unusual cellulase (Avicelase), with an apparent molecular weight of 82 kDa, which is solely sufficient to degrade crystalline cellulose. During cultivation the processing of the Avicelase to a truncated enzyme (42 kDa) and an inactive protein (40 kDa) correlated with the occurrence of an extracellular protease. After its purification this 36 kDa protease cleaved the S. reticuli Avicelase in vitro in the same manner. Using antibodies raised against the Avicelase and its truncated form (42 kDa) and gene libraries of S. reticuli DNA in the Escherichia coli phage vectors lambda gt11 and Charon 35, the Avicelase gene (cel1) was identified. Further subcloning and DNA-sequencing revealed a G+C rich (72%) reading frame of 2238 bp encoding a protein of 746 amino acids. The transcriptional start site was mapped about 180 bp upstream from the GTG start codon. A signal sequence of 29 amino acids was identified by aligning the deduced amino acids with the characterized N-terminus of the 82 kDa Avicelase. Comparison of the N-terminal amino acids from the purified proteins with the amino acid sequence derived from the Avicelase gene revealed that the truncated enzyme (42 kDa) corresponds to the C-terminal region whereas the inactive proteolytically derived protein (40 kDa) represents the N-terminal part of the 82 kDa Avicelase. Comparisons with amino acid sequences deduced from known cellulase genes indicated the presence of three putative protein domains: (i) an N-terminal part showing significant similarity with a repeat region of endoglucanase C from Cellulomonas fimi, recently shown to be a cellulose-binding domain; (ii) an adjoining region sharing homology with the N-terminal domains with unknown function of endoglucanase A from Pseudomonas fluorescens, endoglucanase D from Clostridium thermocellum and a cellodextrinase from Butyrivibrio fibrisolvens, and (iii) a C-terminal catalytic domain belonging to cellulase family E.