gebhart/patrepeval huggingface dataset:
Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification (2019)

Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate and reproducible. We use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencers and illustrate the impacts on interpretation of next-generation sequencing data and the economics of data generation.
Micro RNA -214,-150,-146a and-125b target<i>Huntingtin</i>gene (2011)

We observed earlier that expressions of several micro RNAs (miRNAs) are altered in a cell model of Huntington's disease (HD). As genes involved in different neurodegenerative diseases are targeted by miRNAs, we searched databases to find out whether Huntingtin gene (HTT), mutation to which causes HD, is a target of any miRNA. Among many miRNAs that are predicted to target HTT, we showed using various experimental approaches that miR-214, miR-150, miR-146a and miR-125b could target both human HTT and mouse Htt. Luciferase reporter vectors containing 3'-UTRs of mouse and human HTT showed reduction in relative luciferase activities on exogenous expression of cloned miRNAs. Loss of function studies with miRNA inhibitors led to the revival of luciferase activities of cloned 3'-UTR of HTT. Exogenous expression of these miRNAs reduced the expression of endogenous Htt in mouse cells. Expression of miRNAs with mutations at seed sequences neither reduced the reporter luciferase activities nor the endogenous expression of Htt. Taking together, we showed that miR-214, miR-150, miR-146a and miR-125b targeted HTT. Besides, the exogenous expression of wild type miRNAs reduced HTT aggregates formed by the recombinant exon1 of HTT gene that codes for 83Q tagged with 3'-UTR of Htt, as observed by filter retardation assay and confocal microscopy. In summary, regulation of HTT by miRNAs might provide a new mechanism for the modulation of HD.
Passive Immunization Through Avian Egg Antibodies (2004)

Abstract Oral administration of specific antibodies is an attractive approach to establish passive immunization against various pathogens in humans and animals. Egg yolk contains over 100 mg of IgY per egg and is considered to be a more hygienic and economical source of antibodies, than antibodies from mammalian sera. Recently, considerable research has focussed on the use of IgY as an alternative to mammalian antibodies for several applications, most notably for oral passive immunization against various bacteria and viruses. Oral administration of IgY has proven to be successful for the treatment of a variety of gastrointestinal (GI) pathogens such as bovine and human rotaviruses, bovine coronavirus, Yersinia ruckeri, enterotoxigenic Escherichia coli, Salmonella spp., Edwardsiella, Staphylococcus, and Pseudomonas. Recent advances in hybridoma technology, for the production of monoclonal IgY, also present many benefits for its universal application. IgY technology has significant future opportunities for the design of strategies for the prevention and treatment of infectious gastrointestinal diseases in humans and animals.
A Novel High Content Imaging-Based Screen Identifies the Anti-Helminthic Niclosamide as an Inhibitor of Lysosome Anterograde Trafficking and Prostate Cancer Cell Invasion (2016)

Lysosome trafficking plays a significant role in tumor invasion, a key event for the development of metastasis. Previous studies from our laboratory have demonstrated that the anterograde (outward) movement of lysosomes to the cell surface in response to certain tumor microenvironment stimulus, such as hepatocyte growth factor (HGF) or acidic extracellular pH (pHe), increases cathepsin B secretion and tumor cell invasion. Anterograde lysosome trafficking depends on sodium-proton exchanger activity and can be reversed by blocking these ion pumps with Troglitazone or EIPA. Since these drugs cannot be advanced into the clinic due to toxicity, we have designed a high-content assay to discover drugs that block peripheral lysosome trafficking with the goal of identifying novel drugs that inhibit tumor cell invasion. An automated high-content imaging system (Cellomics) was used to measure the position of lysosomes relative to the nucleus. Among a total of 2210 repurposed and natural product drugs screened, 18 "hits" were identified. One of the compounds identified as an anterograde lysosome trafficking inhibitor was niclosamide, a marketed human anti-helminthic drug. Further studies revealed that niclosamide blocked acidic pHe, HGF, and epidermal growth factor (EGF)-induced anterograde lysosome redistribution, protease secretion, motility, and invasion of DU145 castrate resistant prostate cancer cells at clinically relevant concentrations. In an effort to identify the mechanism by which niclosamide prevented anterograde lysosome movement, we found that this drug exhibited no significant effect on the level of ATP, microtubules or actin filaments, and had minimal effect on the PI3K and MAPK pathways. Niclosamide collapsed intralysosomal pH without disruption of the lysosome membrane, while bafilomycin, an agent that impairs lysosome acidification, was also found to induce JLA in our model. Taken together, these data suggest that niclosamide promotes juxtanuclear lysosome aggregation (JLA) via modulation of pathways involved in lysosome acidification. In conclusion, we have designed a validated reproducible high-content assay to screen for drugs that inhibit lysosome trafficking and reduce tumor invasion and we summarize the action of one of these drugs.
GRAPHICAL CONSTRUCTION OF THE GNOMONIC MAP PROJECTION (1949)

NAVIGATION is a quarterly journal published by the Institute of Navigation. The journal publishes original, peer-reviewed articles on all aspects of positioning, navigation, and timing. The journal also publishes selected technical notes and survey articles, as well as papers of exceptional quality drawn from the Institute’s conference proceedings.
Ranking of Regional Blogs by Suitability for Sonification (2006)

Media content presented to a vehicle driver is mainly auditory, since visual content is distracting and viewing it increases the risk of an accident. Music and radio are thus commonly listened to while driving. However, these types of content rarely reflect regional characteristics and are therefore not well suited for tourists who want to get information about the region they are visiting. We have developed the Blog Car Radio system that presents blog entries in auditory style using sonification (speech synthesis). Blog entries are obtained from blog search engines, selected by distances from the vehicle’s current location, and ranked based on their suitability for sonification and relevance to the userspecified category. By using Blog Car Radio, a driver can obtain local information with only a small amount of distraction. In this paper, we particularly discussed the method to rank text contents which is suitable for sonification.
Modelling and filtering of MPEG-7-compliant meta-data for digital video (2004)

The recent MPEG-7 standard specifies a semi-structured meta-data format for open interoperability of multimedia. However, the standard refrains from specifying how the meta-data is to be used or how meta-data inappropriate to user requirements may be filtered out. Consequently, we propose COSMOS-7, which produces structured MPEG-7-compliant meta-data for digital video and enables content-based hybrid filtering of that meta-data.
Estimation of Irradiation History of a Spent Fuel by Gamma-Ray Spectroscopy (1976)

A method has been developed to estimate the irradiation history and burnup of a spent fuel by gamma-ray spectroscopy. The gamma-ray spectrum, measured by using a Ge(Li) detector, is analyzed by the standard spectrum method to obtain the activity of the fission product. The irradiation history is fitted by the least-squares method to reproduce the activity of each fission-product nuclide. For this purpose, the irradiation history is divided into several time intervals and the contribution of each interval to the production of each fission product is calculated analytically by repeatedly using the Bateman equation. The method was successfully applied to the Materials Testing Reactor-type fuel element irradiated in the core of Japan Research Reactor-4 for about four years.
Low Threshold Lasing in Cholesteric Liquid Crystals (2001)

Abstract Cholesteric liquid crystals, due to their periodic structure and large birefringence, are 1-d photonic band-gap materials. Circularly polarized light of the same handedness as the cholesteric structure cannot propagate in the reflection band. We have studied the effects of this band-gap structure on the fluorescence spectrum of dyes dissolved in the cholesteric liquid crystal, as well as on the fluorescence spectrum of the liquid crystal itself. We have found that emission is enhanced at the band edges, and, above a certain pump threshold, lasing occurs both in dye-doped and in pure liquid crystals. Extremely low lasing thresholds and high efficiencies were observed in dye-doped systems. The results suggest an active energy transfer mechanism between the LC host and the fluorescent dye molecules.
The Effect of Cumulative Photosynthetically Active Radiation on the Growth and Flowering of the Seedling Geranium, Pelargonium × hortorum Bailey1 (1980)

Abstract Growth and flowering of Pelargonium × hortorum Bailey cvs. Sprinter Scarlet, Sprinter White, and Ringo were associated with cumulative photosynthetically active radiation (PAR); 41-65% of the variability in days to flower was attributed to cumulative PAR. Vegetative and total plant height decreased as cumulative PAR increased. The number of lateral breaks increased as irradiance increased while fresh weight showed no consistent pattern.
Getting Kathleen Home Again (1948)

Thomas Paine Westendorf wrote I'll Take You Home Again, Kathleen, in 1875, and John Church & Co. published it in 1876. It became popular quite rapidly, considering that there were no radios or phonographs to plug it, and it kept that popularity amazingly well. Henry Ford thought highly of it that he is reported to have gone to some pains to get an autographed copy for the Ford Museum, and Thomas Edison once wrote a letter to Westendorf, commending the song and, according to Westendorf's brother-in-law, Mancha Bruggemeyer, enclosing a check for $250.00 that he might feel free to use it on his phonographs. It was broadcast during Edison's funeral services. Judge Bruggemeyer also states that John Church & Co. sent Westendorf $50.00 a month for many years, so that he wrote or did not write, just as he pleased. Generally, he pleased, particularly during the 1870's and 1880's. F. O. Jones' A Handbook of American Music and Musicians (Canaseraga, N.Y., 1886; Buffalo, 1887) credits him thus early in his career with having written about 300 vocal and nearly as many instrumental pieces. Probably not all of them were published, but approximately 280 have been examined in the course of preparing this paper. Even more astounding is the fact that many publishers were willing to issue his songs when, as it turned out, Kathleen was the only song which had sufficient viability to justify renewing the copyright at the end of the first twenty-eight year period of protection. True, some of his other songs had a brief period of popularity, but only the hope of drawing another Kathleen could have kept the publishers turning out from ten to forty-five pieces a year over a period of fifteen years. It is potent testimony to the esteem in which they held Kathleen. John Church & Co. kept the song protected and in print, bringing out a new arrangement for boy's voices as late as 1928. The first renewal was sent to the Copyright Office in 1904. At that time, it was possible to get additional protection for only fourteen years, but in 1909 the Copyright Law was revised, making the renewal period twenty-eight years and providing that compositions whose fourteen year period was still running might re-renew for another fourteen years when the first renewal period was up. The composer therefore sent in a second renewal in 1918, immediately assigning his rights back to John Church & Co., and the full fifty-six years of protection did not run out until July 18, 1932. The Theodore Presser Co. had bought out Church in 1930, and enjoyed exclusive rights to the song for a short period before it finally fell into the public domain. Just what the public gained by this fall is doubtful. If anyone had a copy of the original version published by Church or Presser, they could,
ATM: the broadband telecommunications solution (1993)

Since ATM was identified by the CCITT in 1988 as the target transfer mode for broadband communications, there has been considerable research activity on the topic world-wide. Within Europe, the RACE programme of the European Community has brought together experts from a wide variety of organisations to work on several projects. This book results from the work of one of those projects. Aimed at those interested in ATM generally, or those needing to understand the issues in designing or implementing broadband networks, the book draws on the results of the research project to present a description of ATM from a network point of view. Starting with the principles of ATM, it goes on to cover topics such as network performance, network structure, evolution and interworking. It also discusses more general issues including numbering, charging and the need for intelligence in the network. It concludes by explaining the current position on traffic engineering for broadband ATM networks.
Iatrogenic Cushing's syndrome related to the interaction between oral budesonide with fluvoxamine: a case report (2015)

Practitioners should take into consideration the possibility of iatrogenic Cushing's syndrome caused by the association of oral budesonide with a P450 cytochrome inhibitor.
Restoration of Audio Documents by Means of Extended Kalman Filter (2009)

We present some results on audio restoration obtained with an algorithm that solves the problems of broadband noise filtering, signal parameters tracking, and impulsive noise removal by using the Extended Kalman Filter (EKF) theory. We show that, to achieve maximum performance, it is essential to optimize the EKF implementation. To this purpose, having to cope with the nonstationarity of the audio signal, we use two properly combined EKF filters (forward and backward), and introduce a bootstrapping procedure for model tracking. The careful combination of the proposed techniques and an accurate choice of some critical parameters, allows to improve the performance of the EKF algorithm. The presented procedure is validated by listening tests.
HIV-1 Tat Addresses Dendritic Cells to Induce a Predominant Th1-Type Adaptive Immune Response That Appears Prevalent in the Asymptomatic Stage of Infection (2009)

Tat is an early regulatory protein that plays a major role in human HIV-1 replication and AIDS pathogenesis, and therefore, it represents a key target for the host immune response. In natural infection, however, Abs against Tat are produced only by a small fraction (approximately 20%) of asymptomatic individuals and are rarely seen in progressors, suggesting that Tat may possess properties diverting the adaptive immunity from generating humoral responses. Here we show that a Th1-type T cell response against Tat is predominant over a Th2-type B cell response in natural HIV-1 infection. This is likely due to the capability of Tat to selectively target and very efficiently enter CD1a-expressing monocyte-derived dendritic cells (MDDC), which represent a primary target for the recognition and response to virus Ag. Upon cellular uptake, Tat induces MDDC maturation and Th1-associated cytokines and beta-chemokines production and polarizes the immune response in vitro to the Th1 pattern through the transcriptional activation of TNF-alpha gene expression. This requires the full conservation of Tat transactivation activity since neither MDDC maturation nor TNF-alpha production are found with either an oxidized Tat, which does not enter MDDC, or with a Tat protein mutated in the cysteine-rich region (cys22 Tat), which enters MDDC as the wild-type Tat but is transactivation silent. Consistently with these data, inoculation of monkeys with the native wild-type Tat induced a predominant Th1 response, whereas cys22 Tat generated mostly Th2 responses, therefore providing evidence that Tat induces a predominant Th1 polarized adaptive immune response in the host.
Purification and characterization of a novel broad‐specificity (α1 → 2, α1 → 3 and α1 → 6) mannosidase from rat liver (1991)

We have identified a mannosidase in rat liver that releases alpha 1----2, alpha 1----3 and alpha 1----6 linked manose residues from oligosaccharide substrates, MannGlcNAc where n = 4-9. The end product of the reaction is Man alpha 1----3[Man alpha 1----6]Man beta 1----4GlcNAc. The mannosidase has been purified to homogeneity from a rat liver microsomal fraction, after solubilization into the aqueous phase of Triton X-114, by anion-exchange, hydrophobic and hydroxyapatite chromatography followed by chromatofocusing. The purified enzyme is a dimer of a 110-kDa subunit, has a pH optimum between 6.1 and 6.5 and a Km of 65 microM and 110 microM for the Man5GlcNAc-oligosaccharide or Man9GlcNAc-oligosaccharide substrates, respectively. Enzyme activity is inhibited by EDTA, by Zn2+ and Cu2+, and to lesser extent by Fe2+ and is stabilized by Co2+. The pattern of release of mannose residues from a Man6GlcNAc substrate shows an ordered hydrolysis of the alpha 1----2 linked residue followed by hydrolysis of alpha 1----3 and alpha 1----6 linked residues. The purified enzyme shows no activity against p-nitrophenyl-alpha-mannoside nor the hybrid GlcNAc Man5GlcNAc oligosaccharide. The enzyme activity is inhibited by swainsonine and 1-deoxymannojirimycin at concentrations 50-500-fold higher than required for complete inhibition of Golgi-mannosidase II and mannosidase I, respectively. The data indicate strongly that the enzyme has novel activity and is distinct from previously described mannosidases.
Surface structure of epitaxial Pd2Si thin films (1982)

The surface structure of Pd2Si thin films epitaxially grown on clean Si (111) 7×7 surfaces has been studied by low-energy electron diffracton (LEED) and Auger electron spectroscopy (AES). Heat treatment in the range of 200–600 °C causes surface segregation of elementary Si over a Pd2Si (0001) surface and produces a reconstructed 3×3 superstructure of Pd2Si. A nonreconstructed Pd2Si-1×1 surface is produced after removing the segregated Si layer by Ar ion beams and its ordering is found to be not damaged by ion sputtering. A possible cause for the thermally induced Si segregation is also examined experimentally and discussed.
Nanometre-scale deposition of colloidal Au particles using electrophoresis in a nanopipette probe (2007)

We describe a novel technique of local electrophoretic deposition of colloidal particles using a scanning probe microscope with a nanopipette probe filled with a colloidal solution. The colloidal solution including nanometre-scale particles was put into the nanopipette probe. A thin metal wire was inserted into the nanopipette probe as an electrode for the electrophoretic deposition. With the probe edge nearly in contact with the conductive surface and with an electric potential applied between the electrode and the surface, the colloidal particles migrated toward the edge of the probe, causing them to be deposited on the surface. It was possible for nanometre-scale Au colloidal particles in an aqueous solution to be deposited on Si surfaces. The size of the Au dots could be modified by adjusting the deposition time and voltage. Dot array and line patterns were successfully plotted on the surface. This technique of local deposition should provide the possibility for fabricating nanostructures such as nanomachines and nanoelectronics.
Denaturation and renaturation of Penicillium chrysogenum mycophage double-stranded ribonucleic acid in tetraalkylammonium salt solutions (1981)

The base composition dependence of double-stranded ribonucleic acid (RNA) melting was studied by observing the structure and widths of melting transitions for Penicillium chrysogenum mycophage RNA as well as differences in melting temperatures of two RNAs of different base composition. Double-stranded RNA melting is independent of base compositions in 3.5 M Et4NCl and 4.6 M Me4NCl, where the melting temperatures are 25 and 92 degrees C, respectively. Double-stranded RNA renaturation rate constants are reported in Et4NCl solutions. The nucleation rate constant is about 10 times lower than that for double-stranded deoxyribonucleic acid. Analyses of renaturation kinetics results lead to the conclusion that each of the three similar but separable RNA segments of Penicillium chrysogenum mycophage is unique.
Modeling discrete choice behavior based on explicit information integration and its application to the route choice problem (1998)

Two-stage framework for modeling discrete choice behavior in the presence of new information is presented. It is based on explicit information integration at the first stage, and a decision process based on the integrated information at the second stage. The first stage is conducted using an integration scheme which is source- and content-dependent, and the second stage is implemented using an approximate-reasoning-based choice model. The existence of an explicit information integration stage provides the advantage of improving the calibration procedure of the choice model by facilitating a two-phase calibration process in which both rules and membership functions are calibrated. A simple case study demonstrates the applicability of the approach for modeling human route choice decisions in transportation networks when updated online traffic information is available to drivers. The case study also provides interesting insights on the trade-offs between the number of rules and the importance of generating good membership functions. The suggested decision model is roughly compared to traditional random utility model, and provides favourable results.