gebhart/patrepeval huggingface dataset:
Inferring sequences produced by pseudo-random number generators (1989)

In this paper, efficient algorithms are given for inferring sequences produced by certain pseudo-random number generators. The generators considered are all of the form X n = Σ k j-l α j φ j ( X o , X l , . . ., X n-l ) (mod m ). In each case, we assume that the functions φ j are known and polynomial time computable, but that the coefficients aj and the modulus m are unknown. Using this general method, specific examples of generators having this form, the linear congruential method, linear congruences with n terms in the recurrence, and quadratic congruences are shown to be cryptographically insecure.
Analysis of single mammalian cells on-chip (2007)

A goal of modern biology is to understand the molecular mechanisms underlying cellular function. The ability to manipulate and analyze single cells is crucial for this task. The advent of microengineering is providing biologists with unprecedented opportunities for cell handling and investigation on a cell-by-cell basis. For this reason, lab-on-a-chip (LOC) technologies are emerging as the next revolution in tools for biological discovery. In the current discussion, we seek to summarize the state of the art for conventional technologies in use by biologists for the analysis of single, mammalian cells, and then compare LOC devices engineered for these same single-cell studies. While a review of the technical progress is included, a major goal is to present the view point of the practicing biologist and the advances that might increase adoption by these individuals. The LOC field is expanding rapidly, and we have focused on areas of broad interest to the biology community where the technology is sufficiently far advanced to contemplate near-term application in biological experimentation. Focus areas to be covered include flow cytometry, electrophoretic analysis of cell contents, fluorescent-indicator-based analyses, cells as small volume reactors, control of the cellular microenvironment, and single-cell PCR.
Why Asparagine Needs Carbohydrates To Generate Acrylamide (2003)

Structural considerations dictate that asparagine alone may be converted thermally into acrylamide through decarboxylation and deamination reactions. However, the main product of the thermal decomposition of asparagine was maleimide, mainly due to the fast intramolecular cyclization reaction that prevents the formation of acrylamide. On the other hand, asparagine, in the presence of reducing sugars, was able to generate acrylamide in addition to maleimide. Model reactions were performed using FTIR analysis, and labeling studies were carried out using pyrolysis-GC/MS as an integrated reaction, separation, and identification system to investigate the role of reducing sugars. The data have indicated that a decarboxylated Amadori product of asparagine with reducing sugars is the key precursor of acrylamide. Furthermore, the decarboxylated Amadori product can be formed under mild conditions through the intramolecular cyclization of the initial Schiff base and formation of oxazolidin-5-one. The low-energy decarboxylation of this intermediate makes it possible to bypass the cyclization reaction, which is in competition with thermally induced decarboxylation, and hence promote the formation of acrylamide in carbohydrate/asparagine mixtures. Although the decarboxylated Amadori compound can be formed under mild conditions, it requires elevated temperatures to cleave the carbon-nitrogen covalent bond and produce acrylamide.
Responses of plasma concentrations of A type natriuretic peptide and B type natriuretic peptide to alacepril, an angiotensin-converting enzyme inhibitor, in patients with congestive heart failure. (1994)

The response of plasma BNP after alacepril administration occurred later and lasted longer than the plasma ANP response. This may indicate that the mechanisms of synthesis, secretion, or degradation of the two peptides are different.
Renal cell carcinoma: immunohistological investigation of expression of the integrin alpha v beta 3. (1999)

alpha v beta 3 Integrin has been shown in various tumor entities to promote binding to superficial structures of the basement membrane during metastasis. The goal of the present paper was a structural demonstration of this Integrin in renal cell carcinoma (RCC). After removal of paraffin from formalin-fixed tissue, the cells were labelled with the antibody (VNR 147, H. Biermann, Bad Nauheim) using the peroxidase-antiperoxidase method (DAKO Diagnostical GmbH, Hamburg). Evaluation was carried out microscopically and semiquantitatively from missing (-) through moderate (+) to strong (+2) staining. A total of n = 79 RCCs and n = 53 healthy areas were examined. Semiquantitative staining results: there was a grading-dependent increase (+2) of stainability and thus alpha v beta 3 expression. Two of 53 benign specimens showed strong staining, 11 of 53, only weak staining. Four of 18 G1 RCCs showed strong staining, 11 of 18 only weak staining. Results for G2-RCCs: 11 with strong staining, 21 of 40 with weak staining. G3-RCCs: 4 with strong staining, 2 of 7 with weak staining. Of the metastases, on the other hand, 2 of 14 showed strong staining, another 8 of 14 only weak staining. There were no deviations within the histologic (clear-cell, chromophil, or chromophobe) subpopulations. This grading-dependent expression permits the conclusion that the probability of binding to the human basement membrane mediated by alpha v beta 3 Integrin rises with increasing grading, but the already metastatic cell exhibited this Integrin less strongly, since a basement membrane adhesion is no longer necessary for this cell group.
The Ah receptor and the mechanism of dioxin toxicity (1991)

Research Article| June 01 1991 The Ah receptor and the mechanism of dioxin toxicity J P Landers; J P Landers *Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar N J Bunce N J Bunce †Department of Chemistry and Biochemistry, University of Guelph, Guelph, Ontario, Canada NIG 2W1 Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1991) 276 (2): 273–287. https://doi.org/10.1042/bj2760273 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation J P Landers, N J Bunce; The Ah receptor and the mechanism of dioxin toxicity. Biochem J 1 June 1991; 276 (2): 273–287. doi: https://doi.org/10.1042/bj2760273 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1991 The Biochemical Society, London1991 Article PDF first page preview Close Modal You do not currently have access to this content.
On-demand continuous-flow production of pharmaceuticals in a compact, reconfigurable system (2016)

Pharmaceutical manufacturing typically uses batch processing at multiple locations. Disadvantages of this approach include long production times and the potential for supply chain disruptions. As a preliminary demonstration of an alternative approach, we report here the continuous-flow synthesis and formulation of active pharmaceutical ingredients in a compact, reconfigurable manufacturing platform. Continuous end-to-end synthesis in the refrigerator-sized [1.0 meter (width) × 0.7 meter (length) × 1.8 meter (height)] system produces sufficient quantities per day to supply hundreds to thousands of oral or topical liquid doses of diphenhydramine hydrochloride, lidocaine hydrochloride, diazepam, and fluoxetine hydrochloride that meet U.S. Pharmacopeia standards. Underlying this flexible plug-and-play approach are substantial enabling advances in continuous-flow synthesis, complex multistep sequence telescoping, reaction engineering equipment, and real-time formulation.
Assembly of Mesoporous Molecular Sieves Containing Wormhole Motifs by a Nonionic Surfactant Pathway: Control of Pore Size by Synthesis Temperature (1997)

Nonionic polyethylene oxide surfactants are versatile structure-directing agents for the assembly of mesoporous molecular sieves, but their greatest benefit may lie in their ability to control the pore size of the mesostructure by the assembly temperature (see dependence of pore diameter R on temperature shown on the right). For mesostructured silicas with wormhole motifs, the average pore diameter can be altered by as much as 2.4 nm by varying the assembly temperature over a relatively narrow range below the cloud point temperature of the surfactant.
Direct Head-to-Head Evaluation of Recombinant Adeno-associated Viral Vectors Manufactured in Human versus Insect Cells (2017)

The major drawback of the Baculovirus/Sf9 system for recombinant adeno-associated viral (rAAV) manufacturing is that most of the Bac-derived rAAV vector serotypes, with few exceptions, demonstrate altered capsid compositions and lower biological potencies. Here, we describe a new insect cell-based production platform utilizing attenuated Kozak sequence and a leaky ribosome scanning to achieve a serotype-specific modulation of AAV capsid proteins stoichiometry. By way of example, rAAV5 and rAAV9 were produced and comprehensively characterized side by side with HEK293-derived vectors. A mass spectrometry analysis documented a 3-fold increase in both viral protein (VP)1 and VP2 capsid protein content compared with human cell-derived vectors. Furthermore, we conducted an extensive analysis of encapsidated single-stranded viral DNA using next-generation sequencing and show a 6-fold reduction in collaterally packaged contaminating DNA for rAAV5 produced in insect cells. Consequently, the re-designed rAAVs demonstrated significantly higher biological potencies, even in a comparison with HEK293-manufactured rAAVs mediating, in the case of rAAV5, 4-fold higher transduction of brain tissues in mice. Thus, the described system yields rAAV vectors of superior infectivity and higher genetic identity providing a scalable platform for good manufacturing practice (GMP)-grade vector production.
Hydrolysis and Erosion Studies of Autocatalyzed Poly(ortho esters) Containing Lactoyl−Lactyl Acid Dimers (1999)

Poly(ortho esters) based on 3,9-diethylidene-2,4,8,10-tetraoxaspiro[5.5]undecane, 1,10-decanediol, and 1,10-decanediol dilactate were prepared and their hydrolysis in phosphate buffer at 37 °C and pH 7.4 was determined as a function of time. Specifically, kinetics of polymer weight loss, polymer molecular weight changes, release of lactic acid and release of propionic acid were determined. A significant decrease in molecular weight occurred within about 20 days. Weight loss and evolution of hydrolysis product occurred after an induction period that decreased with increasing content of the lactoyl−lactyl segment in the polymer. After the induction period, a concomitant rate of weight loss and release of hydrolysis products was noted. The rate increased with increasing content of the lactoyl−lactide segment. After a certain time period, size-exclusion chromatography revealed the formation of a peak at an apparent molecular mass of about 550 Da. The compounds under the peak were analyzed by electrospray ionization/mass spectrometry (ESI/MS) and found to consist of a multiplicity of lower molecular weight polymer hydrolysis fragments. On the basis of expected hydrolysis products, it was possible to assign a structure to most molecular weight peaks in the ESI/MS spectrum. The data were found to be consistent with a hydrolysis that takes place predominantly in the surface layers of the solid polymer.
Growth of Large GaN Single Crystals on High-Quality GaN Seed by Carbon-Added Na Flux Method (2010)

Seeded growth on high-quality GaN seed was studied using a carbon-added Na flux method. A GaN single crystal (8.6 mm long, 5 mm high) was grown in 96 h without polycrystal formation on a crucible. Under a carbon-added condition, dependence of the growth rate of the seed and the growth habit on the flux composition was studied. We found that the growth rate was higher with Ga-poor flux, resulting in a high growth rate of 30 µm/h along the c-axis and 33 µm/h along the a-axis (66 µm/h for both sides). The growth habit changed from prismatic to pyramidal with increasing Ga composition.
Low Resistance Non-Alloy Ohmic Contact to p-Type GaN Using Mg-Doped InGaN Contact Layer (2001)

We investigated non-alloy Ohmic contact to p-type GaN using Mg-doped InGaN contact layer. The thickness and In mole fraction of the p-type InGaN were varied from 2 to 15 nm and from 0.14 to 0.23, respectively. Strained InGaN contact layers are effective in reducing the contact resistance. The lowest specific contact resistance of 1.1 × 10—6 Ω cm2 was obtained using a contact layer of 2 nm thick strained In0.19Ga0.81N. The mechanism for the lower contact resistance is ascribed to enhanced tunneling transport due to the large polarization-induced band bending at the surface as well as the high hole concentration in p-type InGaN.
Fibronectin aggregation in multiple sclerosis lesions impairs remyelination (2013)

Remyelination following central nervous system demyelination is essential to prevent axon degeneration. However, remyelination ultimately fails in demyelinating diseases such as multiple sclerosis. This failure of remyelination is likely mediated by many factors, including changes in the extracellular signalling environment. Here, we examined the expression of the extracellular matrix molecule fibronectin on demyelinating injury and how this affects remyelination by oligodendrocytes progenitors. In toxin-induced lesions undergoing efficient remyelination, fibronectin expression was transiently increased within demyelinated areas and declined as remyelination proceeded. Fibronectin levels increased both by leakage from the blood circulation and by production from central nervous system resident cells. In chronically demyelinated multiple sclerosis lesions, fibronectin expression persisted in the form of aggregates, which may render fibronectin resistant to degradation. Aggregation of fibronectin was similarly observed at the relapse phase of chronic experimental autoimmune encephalitis, but not on toxin-induced demyelination, suggesting that fibronectin aggregation is mediated by inflammation-induced demyelination. Indeed, the inflammatory mediator lipopolysaccharide induced fibronectin aggregation by astrocytes. Most intriguingly, injection of astrocyte-derived fibronectin aggregates in toxin-induced demyelinated lesions inhibited oligodendrocyte differentiation and remyelination, and fibronectin aggregates are barely expressed in remyelinated multiple sclerosis lesions. Therefore, these findings suggest that fibronectin aggregates within multiple sclerosis lesions contribute to remyelination failure. Hence, the inhibitory signals induced by fibronectin aggregates or factors that affect fibronectin aggregation could be potential therapeutic targets for promoting remyelination.
Generation of wideband frequency combs by continuous-wave seeding of multistage mixers with synthesized dispersion (2012)

We numerically and experimentally demonstrate efficient generation of an equalized optical comb with 150-nm bandwidth. The comb was generated by low-power, continuous-wave seeds, eliminating the need for pulsed laser sources. The new architecture relies on efficient creation of higher-order mixing tones in phase-matched nonlinear fiber stages separated by a linear compressor. Wideband generation was enabled by precise dispersion engineering of multiple-stage parametric mixers.
Rapid, High‐Yield Recovery of a Recombinant Digoxin Binding Single Chain Fv from Escherichia coli (1995)

We have isolated milligram quantities of active single chain antibody from the insoluble fraction of Escherichia coli cultures. The system relies on high-level expression from a T7 RNA polymerase-directed gene construct, 8 M urea to dissolve the desired protein out of the insoluble fraction, presumably inclusion bodies, isolation and concentration of the desired protein by nickel chelate [IDA-Ni(II)] immobilized metal-ion affinity chromatography (IMAC), and removal of urea from column fractions by dialysis directly into storage buffer. Routinely, about 50% of the protein loaded onto an IMAC column is recovered as single chain Fv at a concentration of approximately 0.7 mg/mL. As little as 3 days are required to obtain 10 mg of final product when starting with an overnight inoculum.
Effects of Aminoguanidine on Lipid and Protein Oxidation in Diabetic Rat Kidneys (2001)

Nonenzymatic glycation of tissue and plasma proteins may stimulate the production of oxidant and carbonyl stress in diabetes. The aim of this study was to evaluate the effects of aminoguanidine (AG) on lipid peroxidation, protein oxidation and nitric oxide (NO) release in diabetic rat kidneys. After induction of diabetes with streptozotocin, female Wistar rats were divided into 2 groups. Group DAG (n=9) rats were given AG hydrogen carbonate (1 g/L) in drinking water and group D (n=8) was diabetic control rats given only tap water. Group H (n=8) was followed as healthy controls. At the end of an 8 week period, NO release, lipid and protein oxidation were determined in kidney tissues. NO release was significantly lower in diabetic rats compared with healthy controls (p<0.05). Lipid peroxidation was significantly high in group D (3.9 +/- 0.3 nmol MDA/g tissue) compared with the group DAG (2.6 0.1 nmol MDA/g tissue, p<0.01) and group H (2.4 +/- 0.2 nmol MDA/g tissue). Protein oxidation was significantly higher in diabetics than healthy controls (563.8 +/- 23.9, 655.8 +/- 7.2, 431.5 +/- 8.8 mmol carbonyl / g tissue for group DAG, D and H, respectively, p< 0.05). A positive correlation between albuminuria and thiobarbituric acid reactive substance (TBARS) levels (r= 0.54,p<0.005) and carbonyl content (r=0.70, p<0.0005) in kidney homogenate were observed. Although AG treatment had no effect on NO release, it significantly decreased lipid peroxidation in diabetic rat cortices. Consequently increased lipid peroxidation -as well as- protein oxidation could be involved in the pathogenesis of diabetic albuminuria.
Fundamentals of Polymer Gel Dosimeters (2006)

The recent literature on polymer gel dosimetry contains application papers and basic experimental studies involving polymethacrylic-acid-based and polyacrylamide-based gel dosimeters. The basic studies assess the relative merits of these two most commonly used dosimeters, and explore the effects of tetrakis hydroxymethyl phosphonium chloride (THPC) antioxidant on dosimeter performance. Polymer gel dosimeters that contain THPC or other oxygen scavengers are called normoxic dosimeters, because they can be prepared under normal atmospheric conditions, rather than in a glove box that excludes oxygen. In this review, an effort is made to explain some of the underlying chemical phenomena that affect dosimeter performance using THPC, and that lead to differences in behaviour between dosimeters made using the two types of monomer systems. Progress on the development of new more effective and less toxic dosimeters is also reported.
Characterization of Two New Experimental Collections in Computer and Information Science Containing Textual and Bibliographic Concepts (1983)

Two new collections are described which are particularly useful for investigating the interaction between textual and bibliographic data in the automatic indexing and retrieval of documents. An extension to the vector space model has been proposed whereby various types of concepts are included in the representation of such documents. Experiments using an enhanced version of the SMART system have shown such an extended model to perform better than simpler schemes. The CACM and ISI collections developed for this research should be of value for future related studies. The ISI collection has author, title/abstract, and co-citation data for the 1460 most highly cited articles and manuscripts in information science in the 1969-1977 period. The CACM collection contains 7 types of concepts for the 3204 articles published in the Communication of the ACM up through 1979. These collections have 76 and 52 queries, respectively, along with relevance judgments.
Activation of EVI1 gene expression in human acute myelogenous leukemias by translocations spanning 300-400 kilobases on chromosome band 3q26. (1992)

Retroviral activation of Evi-1 gene expression is one of the most common transforming events in murine myeloid leukemias. To evaluate the role of the EVI1 gene in human acute myelogenous leukemia (AML), leukemic blasts or cell lines from 116 patients were examined. In eight patients the EVI1 gene was expressed and all but one had cytogenetically detectable translocations of chromosome 3q26 where the EVI1 gene has been localized. To identify breakpoints, a restriction map that spans 1700 kilobases (kb) of the EVI1 locus was developed by pulsed-field gel electrophoresis. In one case, t(3;3)(q21;q26), a rearrangement was localized to 170-330 kb 5' of the gene. In a second case, t(3;3)(q21;q26), there was a rearrangement 13 kb 5' of the gene. This rearrangement was cloned and shown to be due to the fusion of sequences from 3q21-22 with the EVI1 locus. In the third case, ins(3)-(q21q25q27), there was a rearrangement that mapped 150 kb downstream from the 5' end of the gene.
Some Polyamides, Polyesters, and Polyurethanes Containing AZO Groups (1992)

Abstract The paper discusses the synthesis of the N,N,′-azobis(formamidopropionic) acid (AFP), along with some characteristics determined from NMR spectrum, differential thermal analysis, and DSC. The behavior of AFP acid—as well as of its analogue, N,N′-azobis(formamidoacetic) acid (AFA)—has been studied in the reaction with aromatic diamine and with bis(glycol)terephthalate, leading to azopolymers of the azopolyamide, or azopolyester, type. On employing N,N′-bis(β-hydroxyethyl) azobis-formamide (HEAF) as the azo bifunctional compound in the reaction with diphenylmethane diisocyanate, a polyurethane possessing azo groups was obtained. The structure of the azopolymers has been spectroscopically confirmed.
Sequence Variation and Haplotype Structure Surrounding the Flowering Time Locus FRI in Arabidopsis thaliana (2002)

Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima's D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.
METABOLISM OF ISOLATED FAT CELLS. I. EFFECTS OF HORMONES ON GLUCOSE METABOLISM AND LIPOLYSIS. (1964)

This article marks the beginning of Rodbell's interest in cell receptors. In it, he related his discovery that fat cells could be isolated from other cells by treating them with preparations of collagenase, and also found that insulin could stimulate glucose uptake. This had far-reaching implications for the treatment of various diseases, as it was the first demonstration that insulin acted on individual cells.