gebhart/patrepeval huggingface dataset:
Epitope tagging of endogenous genes in diverse human cell lines (2008)

Epitope tagging is a powerful and commonly used approach for studying the physical properties of proteins and their functions and localization in eukaryotic cells. In the case of Saccharomyces cerevisiae, it has been possible to exploit the high efficiency of homologous recombination to tag proteins by modifying their endogenous genes, making it possible to tag virtually every endogenous gene and perform genome-wide proteomics experiments. However, due to the relative inefficiency of homologous recombination in cultured human cells, epitope-tagging approaches have been limited to ectopically expressed transgenes, with the attendant limitations of their nonphysiological transcriptional regulation and levels of expression. To overcome this limitation, a modification and extension of adeno-associated virus-mediated human somatic cell gene targeting technology is described that makes it possible to simply and easily create an endogenous epitope tag in the same way that it is possible to knock out a gene. Using this approach, we have created and validated human cell lines with epitope-tagged alleles of two cancer-related genes in a variety of untransformed and transformed human cell lines. This straightforward approach makes it possible to study the physical and biological properties of endogenous proteins in human cells without the need for specialized antibodies for individual proteins of interest.
Simulation of the Transient Behavior of Gels Based on an Analogy Between Diffusion and Heat Transfer (2012)

The transient behaviors of the swelling and deswelling of gels involve concurrent mechanical deformation and solvent diffusion and exhibit a fascinating phenomenon. In this paper, a simple numerical tool is developed by using an analogy between diffusion and heat transfer when large deformation presents for gels. Using this analogy, a finite element method is developed in the framework of a commercial finite element package ABAQUS via two material-specific user subroutines to describe the mechanical and mass diffusion behaviors of gels. The present method is not limited to any specific materials; therefore, this method can be extended to other materials that featured with coupled deformation and diffusion. This method is expected to be able to serve as a useful numerical tool to study related materials and problems due to its simplicity.
Nano–Bio Interactions of Extracellular Vesicles with Gold Nanoislands for Early Cancer Diagnosis (2018)

Extracellular vesicles or exosomes are membrane encapsulated biological nanometric particles secreted virtually by all types of cells throughout the animal kingdom. They carry a cargo of active molecules to proximal and distal cells of the body as mechanism of physiological communication, to maintain natural homeostasis as well as pathological responses. Exosomes carry a tremendous potential for liquid biopsy and therapeutic applications. Thus, there is a global demand for simple and robust exosome isolation methods amenable to point-of-care diagnosis and quality control of therapeutic exosome manufacturing. This can be achieved by molecular profiling of the exosomes for use with specific sets of molecular-markers for diagnosis and quality control. Liquid biopsy is undoubtedly the most promising diagnosis process to advance "personalized medicine." Currently, liquid biopsy is based on circulating cancer cells, cell free-DNA, or exosomes. Exosomes potentially provide promise for early-stage diagnostic possibility; in order to facilitate superior diagnosis and isolation of exosomes, a novel platform is developed to detect and capture them, based on localized surface plasmon resonance (LSPR) of gold nanoislands, through strong affinity between exosomes and peptide called Venceremin or Vn96. Physical modeling, based on the characteristics of the gold nanoislands and the bioentities involved in the sensing, is also developed to determine the detection capability of the platform, which is optimized experimentally at each stage. Preliminary results and modeling present a relationship between the plasmonic shift and the concentration of exosomes and, essentially, indicate possibilities for label-free early diagnosis.
Timing jitter reduction and single-frequency operation in an acousto-optic Q-switched Cr,Nd:YAG laser (2006)

A laser-diode-pumped watt-level single-frequency combined actively and passively Q-switched (CAPQ) laser with a wavelength of 1064 nm that simultaneously uses a codoped Cr(4+),Nd(3+):YAG crystal as the gain medium and mode selector is presented. The optimum repetition period of the CAPQ laser is approximately 1.5 times the natural repetition period of the passively Q-switched laser. The averaged timing jitter is approximately 400 ns in the CAPQ laser and the repetition rate of the CAPQ laser is experimentally shown to reach a time instability of 0.2% over 10(6) pulses. The output is a stable single frequency with a linewidth of 400 MHz at 20 W pump power.
<b>kml</b>and<b>kml3d</b>:<i>R</i>Packages to Cluster Longitudinal Data (2015)

Longitudinal studies are essential tools in medical research. In these studies, variables are not restricted to single measurements but can be seen as variable-trajectories, either single or joint. Thus, an important question concerns the identification of homogeneous patient trajectories. kml and kml3d are R packages providing an implementation of k-means designed to work specifically on trajectories (kml) or on joint trajectories (kml3d). They provide various tools to work on longitudinal data: imputation methods for trajectories (nine classic and one original), methods to define starting conditions in k-means (four classic and three original) and quality criteria to choose the best number of clusters (four classic and one original). In addition, they offer graphic facilities to “visualize” the trajectories, either in 2D (single trajectory) or 3D (joint-trajectories). The 3D graph representing the mean joint-trajectories of each cluster can be exported through LATEX in a 3D dynamic rotating PDF graph (Figures 1 and 9).
Cellular Studies of Mammary Tissue from Cows Hormonally Induced into Lactation: Lactose and Fatty Acid Synthesis (1976)

Temporal changes in ability of mammary gland to synthesize lactose and fatty acids were identified during the treatment of cows hormonally induced to lactate, and animal differences were compared to subsequent milk production. Hormonal treatment involved 17 beta-estradiol + progesterone on days 1 to 7 and dexamethasone on days 17 to 19. Mammary tissue obtained by biopsy on days 0, 8, 16, and 26 of treatment was examined for biosynthetic capacity by tissue slice incubations. In terms of peak daily milk yield, one cow was very successful (greater than 30 kg), two were intermediate (9 to 10 kg), and one cow was unsuccessful (less than 3 kg). Differences between cows in the capability to synthesize lactose and fatty acids were evident as early as day 8 and were further magnified by day 16. In particular, the tissue from the successful cow was undergoing lactogenesis by day 8 while this was not evident until the day 16 biopsy sample in the less successful cows. In contrast to the other cows, tissues from the unsuccessful animal regressed in its ability to synthesize lactose and fatty acids between day 16 and 26. Relative differences between animals in measurements of metabolic capacity were consistent with subsequent milk production.
Methanol synthesis gas from wood gasification (1983)

Findings indicated that RLA measurement in small-breed dogs with or without liver disease was useful and accurate for estimation of liver size, compared with CT measurement, and might be particularly useful for monitoring of changes in liver size.
A software planning tool for a business oriented optical access network-PREST (2002)

Currently optical fiber is largely used in the trunking network; its utilization has been increasing and it is expected to be introduced in access networks. In Brazil, some operating companies are considering the introduction of fiber in the local loop, to provide better services for their key customers. This article considers optical access network planning, describes possible topologies, proposes a network modelling approach and introduces a planning tool called PREST, which is aimed at helping the operating companies to accomplish the definition of a business oriented optical access network (BOAN).
Quantitative Fiber Mixture Analysis by Scanning Electron Microscopy (1986)

The possibilities and limitations of analyzing by scanning electron microscopy wool blended with two unmedullated specialty fibers, mohair and cashmere, were studied. The measurement of the height of the cuticle scale at the scale edge was used as an objective criterion for distinguishing between the wool and the specialty fibers. For both blend types and for the experimental procedure used, the mean absolute error of 1% was less than a third of the mean confidence distances and compared well with the accuracy of the chemical methods of analyzing fiber blends. The remaining errors were attributed to purely random variations, so that systematic errors of any kind can largely be excluded.
Return Dynamics and Trading Strategy in Alternative Trading Systems (2012)

This article examines intra-day price relationships between electronic and floor (pit) trading markets for the S&P 500 and Nasdaq 100 equity index futures. The two contracts trade in dual open outcry and electronic platforms during non-overlapping trading hours. The results indicate that closing transactions on the electronic market have a systematically negative influence on the opening prices established on the pit. In contrast, pit prices at the end of the regular trading have a positive, but less pronounced impact on the opening prices established in the electronic exchange. Based on this relationship, we document a profitable high-frequency trading strategy that can only be partly explained by macroeconomic news. <b>TOPICS:</b>Exchanges/markets/clearinghouses, portfolio construction, statistical methods
Dispersion of Nanoparticles in Lubricating Oil: A Critical Review (2019)

Nanolubricants have attracted great interest due to the promise of friction and wear reduction by introducing nanoparticles. To date, the foremost challenge for developing a new nanolubricant is particle suspension. To understand the mechanisms of nanoparticle dispersion and identify bottlenecks, we conducted a comprehensive review of published literature and carried out an analysis of dispersion based on available data from the past 20 years. This research has led to three findings. First, there are two primary methods in dispersion: formulation with dispersant and surface modification. Second, surfactant and alkoxysilanes are primary chemical groups used for surface modification. Third, functionalization using surfactant is found to be suitable for nanoparticles smaller than 50 nm. For larger particles (>50 nm), alkoxysilanes are the best. The existence of a critical size has not been previously known. To better understand these three findings, we conducted an analysis using a numerical calculation based on colloidal theory. It revealed that a minimal thickness of the grafted layer in surfactant-modified nanoparticles was responsible for suspending small nanoparticles. For larger nanoparticles (>50 nm), they were suitable for silanization of alkoxysilane due to increased grafting density. This research provides new understanding and guidelines to disperse nanoparticle in a lubricating oil.
High Spatial Resolution Observations of the 1998 and 1999 Leonid Meteors (2001)

Abstract We observed the Leonid meteor storm in 1998 and 1999. The light curves extracted from the 2-dimensional images of the bright Leonid meteors clearly show the sub-structures, which are consistent with the generally accepted dustball meteor model (Hawkes & Jones, 1975).
High efficiency FET power amplifier with very low drain bias for mobile communication (2002)

A high efficiency GaAs FET power amplifier with very low drain bias voltage 3 V was investigated at 1.6 GHz. The power amplifier was worked at F mode operation by using harmonic turning of output matching network and biasing near pinch off. The power efficiency of near 70 % with 25 dBm output was achieved. The low harmonic level shows the amplifier has the capability of the linear amplifier.
Cloning of the DNA-binding subunit of human nuclear factor kappa B: the level of its mRNA is strongly regulated by phorbol ester or tumor necrosis factor alpha. (1991)

The DNA binding subunit of nuclear factor kappa B (NF-kappa B), a B-cell protein that interacts with the immunoglobulin kappa light-chain gene enhancer, has been purified from nuclei of human HL-60 cells stimulated with tumor necrosis factor alpha (TNF alpha), and internal peptide sequences were obtained. Overlapping cDNA clones were isolated and sequenced. The encoded open reading frame of about 105 kDa contained at its N-terminal half all six tryptic peptide sequences, suggesting that the 51-kDa NF-kappa B protein is processed from a 105-kDa precursor. An in vitro synthesized protein containing most of the N-terminal half of the open reading frame bound specifically to an NF-kappa B binding site. This region also showed high homology to a domain shared by the Drosophila dorsal gene and the avian and mammalian rel (proto)oncogene products. The level of the 3.8-kilobase mRNA was strongly increased after stimulation with TNF alpha or phorbol ester. Thus, both factors not only activate NF-kappa B protein, as described previously, but also induce expression of the gene encoding the DNA-binding subunit of NF-kappa B.
Carbene chemistry. Part II. Migration in fluoroalkylcarbenes (1971)

Photolysis of 4-diazo-1,1,1,2,2,3,3-heptafluoropentane gives heptafluoropropyl(methyl)carbene, in which migration of hydrogen takes place to give 3,3,4,4,5,5,5-heptafluoropent-1-ene in high yield. Migration of fluorine or of the pentafluoroethyl group is not observed. The photolysis of 3-diazo-1,1,2,2-tetrafluoropropane gives the corresponding carbene in which migration of the difluoromethyl group is the major reaction; other minor products are believed to arise from a cyclopropane in an excited state, formed by insertion into the γ-CH bond.The exploration of routes to 2-diazo-1,1-difluoroethane and 2-diazo-1-fluoropropane, and the n.m.r. spectra of a number of compounds containing the CHF2·CF2· group are also reported.
Robustness issues and solutions in speech recognition based telephony services (2002)

HMM-based algorithms for speaker-dependent recognition as well as speaker-independent recognition form the basis of speech services developed at Nynex S&T and deployed widely by Nynex and other telephone service providers. Based on the analysis of the initially deployed VoiceDialing service, the robustness of these algorithms was recognized to be a dominant issue. We discuss the features of a high-performance, robust speaker-dependent recognition algorithm, and include some deployment issues that were successfully resolved.
DEER Distance Measurements on Proteins (2012)

Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.
Identification of T and B cell epitopes recognized by humans in the C-terminal 42-kDa domain of the <i>Plasmodium falciparum</i> merozoite surface protein (MSP)-1. (1995)

The 42-kDa, C-terminal region of the merozoite surface protein-1 (MSP-1) of Plasmodium falciparum is a putative malaria vaccine candidate Ag. Nine synthetic peptides corresponding to predicted T cell sites of MSP-1 in blocks 15 and 16 and eight overlapping peptides representing the conserved block 17 were used to identify naturally immunogenic epitopes. These peptides were tested for their ability to induce proliferation of PBMC from residents in western Kenya, where malaria transmission is holoendemic. Six peptides (PL145, PL146, PL147, PL148, PL149, and PL150) from blocks 15 and 16 induced a positive proliferative response in > 30% of the individuals tested, and three peptides (PL151, PL152, and PL153) induced a proliferative response in < 25% of the donors. Among these peptides, PL146 was from the highly conserved region, PL150 was from a polymorphic region, and all other peptides were from a dimorphic region of blocks 15 and 16. In block 17, only three peptides, PL99, PL100, and PL103, induced proliferation in 30 to 37% of the volunteers. The rest of the peptides induced a proliferative response in approximately 13 to 25% of the donors. The plasma from these donors widely reacted with different allelic forms of 19-kDa recombinant proteins representing block 17 and recognized at least two linear B epitopes, PL104 and PL97. In summary, this study revealed that a majority of immunodominant T and B epitopes are localized in the conserved or dimorphic regions that are nonpolymorphic in the 42-kDa protein of MSP-1. This study suggests that incorporation of T epitopes from the dimorphic blocks 15 and 16 in a vaccine construct may be useful to ensure Ag-specific memory responses.
Amylinʼs physiology and its role in diabetes (1997)

Amylin is a 37-amino-acid peptide hormone cosecreted with insulin from pancreatic β cells. In contrast to insulin, which controls plasma glucose concentrations primarily by increasing the rate of glucose disappearance, amylin appears to control plasma glucose via several mechanisms that reduce the rate of glucose appearance in plasma. By its effect on food intake, amylin limits nutrient inflow into the gut. By its effect on gastric emptying, it limits nutrient flux from gut to blood, and by its ability to suppress glucagon secretion, it is predicted to moderate the flux of glucose from liver to blood. Amylin is absolutely or relatively deficient in type I diabetes and in insulin-requiring type II diabetes. Amylin hormone replacement with an amylin agonist, such as the synthetic human amylin analogue, pramlintide, may, by mechanisms such as the preceding, assist in achieving metabolic control in individuals with type I and insulin-requiring type II diabetes.
First-principles calculations for charged states of hydrogen atoms in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">SiO</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1997)

Charged states of H atoms in defect-free ${\mathrm{SiO}}_{2}$ have been proposed from first-principles total-energy band-structure calculations within a framework of the local-density approximation. The polarities of the charged states are determined depending on the position of the Fermi level. A positively charged state forms an Si-(${\mathrm{OH}}^{+}$)-Si complex, while a negatively charged state forms an Si-${\mathrm{H}}^{\mathrm{\ensuremath{-}}}$ bond. Calculated vibrational frequencies of newly formed O-${\mathrm{H}}^{+}$ and Si-${\mathrm{H}}^{\mathrm{\ensuremath{-}}}$ bonds for each charge state are found to be lower than those for neutral O-H and Si-H bonds, so the H-originated charge traps are expected to be distinguishable by either Raman or infrared spectroscopies.
The Human Gene for the Regulatory Subunit RIα of Cyclic Adenosine 3′,5′-Monophosphate-Dependent Protein Kinase: Two Distinct Promoters Provide Differential Regulation of Alternately Spliced Messenger Ribonucleic Acids<sup>1</sup> (1997)

The present study reports the exon-intron organization of the human RI alpha gene of cAMP-dependent protein kinase and approximately kilobases (kb) of the 5'-flanking region obtained by isolation and sequencing of several phage clones from human genomic libraries. The RI alpha gene is composed of nine coding exons of varying lengths, separated by introns, giving the gene a total length of at least 21 kb. our recent cloning of a processed RI alpha pseudogene with a 5'-noncoding region different from the previously reported RI alpha complementary RNA indicated that the RI alpha gene may have multiple leader exons giving rise to alternately spliced messenger RNAs (mRNAs). Reverse transcription of human testis RNA followed by PCR identified two different RI alpha mRNA species (RI alpha 1a and RI alpha 1b) containing distinct sequences due to alternately splicing the gene. The previously known RI alpha 1b mRNA revealed low constitutive expression in a human B lymphoid cell line (Reh) and was stimulated only 4- to 6-fold by treatment with cAMP. In contrast, very low levels of the novel RI alpha 1a mRNA were present in untreated Reh cells, but were stimulated 40-to 50-fold by cAMP. The 5'-flanking sequence of the RI alpha gene was G/C rich and did not contain any TATA box. Several putative transcription initiation sites were identified in front of each leader exon (exons 1a and 1b) by the 5'-rapid amplification of complementary DNA ends technique. To determine whether the sequences 5' of both leader exons had promoter activities, the 5'-flanking sequences of exons 1a and 1b were inserted in front of a chloramphenicol acetyltransferase reporter gene, and their ability to direct transcription were examined. Transfection of these constructs into rat GH4C1 cells demonstrated that both constructs had promoter activities, as evidenced by high levels of chloramphenicol acetyltransferase activity.
Gendered Conversation in a Social Game-Streaming Platform (2016)

Online social media and games are increasingly replacing offline social activities. Social media is now an indispensable mode of communication; online gaming is not only a genuine social activity but also a popular spectator sport. With support for anonymity and larger audiences, online interaction shrinks social and geographical barriers. Despite such benefits, social disparities such as gender inequality persist in online social media. In particular, online gaming communities have been criticized for persistent gender disparities and objectification. As gaming evolves into a social platform, persistence of gender disparity is a pressing question. Yet, there are few large-scale, systematic studies of gender inequality and objectification in social gaming platforms. Here we analyze more than one billion chat messages from Twitch, a social game-streaming platform, to study how the gender of streamers is associated with the nature of conversation. Using a combination of computational text analysis methods, we show that gendered conversation and objectification is prevalent in chats. Female streamers receive significantly more objectifying comments while male streamers receive more game-related comments. This difference is more pronounced for popular streamers. There also exists a large number of users who post only on female or male streams. Employing a neural vector-space embedding (paragraph vector) method, we analyze gendered chat messages and create prediction models that (i) identify the gender of streamers based on messages posted in the channel and (ii) identify the gender a viewer prefers to watch based on their chat messages. Our findings suggest that disparities in social game-streaming platforms is a nuanced phenomenon that involves the gender of streamers as well as those who produce gendered and game-related conversation.