gebhart/patrepeval huggingface dataset:
PIG-A and PIG-H, Which Participate in Glycosylphosphatidylinositol Anchor Biosynthesis, Form a Protein Complex in the Endoplasmic Reticulum (1996)

Many eukaryotic cell surface proteins are bound to the membrane via a glycosylphosphatidylinositol (GPI) anchor. Assembly of the GPI anchor precursor is a sequential addition of components to phosphatidylinositol (PI) in the endoplasmic reticulum (ER). The first step is the transfer of N-acetylglucosamine (GlcNAc) to PI from UDP-GlcNAc to generate GlcNAc-PI. This simple step, however, is regulated by at least three genes because in both mammals and yeasts, there are three mutants of different complementation classes. To clarify this complexity, we analyzed the products of two cloned human genes, PIG-A and PIG-H. Here we demonstrate 1) that PIG-A is an ER transmembrane protein with a large cytoplasmic domain that has homology to a bacterial GlcNAc transferase and a small lumenal domain; 2) that PIG-H is a cytoplasmically oriented, ER-associated protein; and 3) that they form a protein complex. We also show that part of the small lumenal domain of PIG-A plays an essential functional role in targeting itself to the rough ER. Taken together with the cytoplasmic orientation of GlcNAc-PI, these results indicated that PIG-A and PIG-H are subunits of the GPI GlcNAc transferase that transfers GlcNAc to PI on the cytoplasmic side of the ER.
Thermoelastic FEM-BEM model for Solidly Mounted Resonator (2008)

A Solidly Mounted Resonator (SMR) is an ultra-thin piezoelectric layer deposited between two electrodes which operates in longitudinal thickness mode. Minimization of dissipative losses is a major goal in SMR designs. For an accurate simulation of a SMR vibrating in vacuum, thermoelastic damping phenomenon related to the irreversible heat dissipation induced by the coupling between heat transfer and strain rate during the resonator vibration and acoustic radiation into the substrate have to be taken into account. The finite element method (FEM) is suitable for structural simulation, especially for thermoelastic damped structures vibrating in vacuum. When the vibrating structure is deposited on an unbounded elastic medium, the boundary element method (BEM) is suitable because it prescribes exact radiating conditions. Numerical FEM-BEM results are presented for an aluminum nitride resonator with molybdenum electrodes operating at 2.10 GHz and decoupled from the substrate by a tungsten-silicon dioxide or a silicon nitride-silicon oxycarbide Bragg reflector. Thermoelastic effect is shown to affect mainly SMR quality factor and temperature coefficient of frequency.
Reinforcement learning from simultaneous human and MDP reward (2012)

As computational agents are increasingly used beyond research labs, their success will depend on their ability to learn new skills and adapt to their dynamic, complex environments. If human users---without programming skills---can transfer their task knowledge to agents, learning can accelerate dramatically, reducing costly trials. The tamer framework guides the design of agents whose behavior can be shaped through signals of approval and disapproval, a natural form of human feedback. More recently, tamer+rl was introduced to enable human feedback to augment a traditional reinforcement learning (RL) agent that learns from a Markov decision process's (MDP) reward signal. We address limitations of prior work on tamer and tamer+rl, contributing in two critical directions. First, the four successful techniques for combining human reward with RL from prior tamer+rl work are tested on a second task, and these techniques' sensitivities to parameter changes are analyzed. Together, these examinations yield more general and prescriptive conclusions to guide others who wish to incorporate human knowledge into an RL algorithm. Second, tamer+rl has thus far been limited to a sequential setting, in which training occurs before learning from MDP reward. In this paper, we introduce a novel algorithm that shares the same spirit as tamer+rl but learns simultaneously from both reward sources, enabling the human feedback to come at any time during the reinforcement learning process. We call this algorithm simultaneous tamer+rl. To enable simultaneous learning, we introduce a new technique that appropriately determines the magnitude of the human model's influence on the RL algorithm throughout time and state-action space.
Tactile Detection Thresholds for a Single Asperity on an Otherwise Smooth Surface (1983)

An investigation was made of the capacities of humans to detect, by actively touching with the fingertip, the presence of a single, small asperity on a very smooth background. The asperity consisted of either a raised dot having a diameter of 602, 231, or 40 micron, or an edge, each etched into a silicon wafer using the methods of contact photolithography. The height of each dot or edge was varied and the subject was asked to make a forced choice on each test trial as to which of two wafers, one of which was blank, contained the asperity. The mean detection threshold, or minimal height of asperity corresponding to a d' of 1.35, was lowest for edges (0.85 +/- 0.22 micron, SD) and increased with decreases in the diameter of dot from 1.09 +/- 0.19 micron for a diameter of 602 micron to 2.94 +/- 1.19 micron and 5.97 +/- 2.02 micron for diameters of 231 micron and 40 micron, respectively. The type of skin displacement required for the detection of these small asperities was believed to be a local lateral deformation of the papillary ridges.
Rectal Nitric Oxide Gas and Stool Cytokine Levels during the Course of Infectious Gastroenteritis (2004)

Nitric oxide (NO) is known to be an important inflammatory mediator with a potential role in gastrointestinal diseases. We prospectively studied the luminal NO levels in 51 patients with infectious gastroenteritis, 35 patients with nonenteric bacterial infections, and 11 healthy control subjects. The levels of proinflammatory cytokines were simultaneously measured in the stools of patients with gastroenteritis. Rectal gas was sampled with balloon catheters made of silicone and was analyzed for NO levels by chemiluminescence. The median rectal NO level was 2,450 ppb in the acute phase of gastroenteritis and gradually decreased to 225 ppb after 3 to 8 weeks, whereas the median NO values were 150 ppb in patients with nonenteric bacterial infections and 100 ppb in healthy control subjects. Patients with Salmonella, Shigella, and Campylobacter infections generally had more severe symptoms and a higher median NO level (17,250 ppb) than patients with Clostridium difficile-associated diarrhea (median NO value, 275 ppb). Interleukin-1 beta levels were elevated in 82% of the patients at disease onset and decreased during the convalescent phase. In contrast, gamma interferon was detected in only 16% of the patients and was predominantly collected in stool samples collected during the subacute and convalescent stages. Our data point to the possibility of using this easy, minimally invasive method for luminal NO measurement as a diagnostic tool, among others, to evaluate the degree of intestinal inflammation in patients with infectious gastroenteritis.
Sub-MHz ultrahigh-resolution optical spectrometry based on Brillouin dynamic gratings (2014)

We propose and demonstrate an ultrahigh-resolution optical spectrometry based on Brillouin dynamic gratings (BDGs). Taking advantage of creating a long grating in an optical fiber, an ultra-narrow bandwidth optical filter is realized by operating a BDG in a long single-mode fiber (SMF), and the optical spectrometry is performed by sweeping the center wavelength of the BDG-based filter through a swept-tuned laser. The BDG-based optical spectrometry features ultrahigh resolution, large wavelength coverage, and a simple direction-detection scheme. In the experiment, a 4 fm (0.5 MHz) spectral resolution is achieved by operating a BDG in a 400 m SMF, and the wavelength coverage can be readily extended to C+L bands with a commercial tunable laser.
Immunologic regulation in pregnancy (1979)

Abstract Theories to explain the failure of rejection of the fetus by the mother during pregnancy include immunologic privilege of the uterus as a graft site, lack of transplantation antigen expression on the trophoblast, weakening of maternal cellular immunity during pregnancy, and separation of maternal and fetal circulations. Evidence for and against each of these theories is discussed. Local concentration of a variety of hormones, including human chorionic gonadotropin (HCG), sex steroids, alpha‐fetoprotein, and immunoglobulins, could provide a blocking mechanism to prevent maternal cellular immune attack. Possibly, progesterone, antibodies, and immune complexes are important in protecting the placenta and ultimately the fetus from rejection. Elucidation of regulatory mechanisms in pregnancy may be applicable to other problems in immunology.
Hematopoietic and Lymphopoietic Responses in Human Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF ) Receptor Transgenic Mice Injected With Human GM-CSF (1997)

Using a clonal assay of bone marrow (BM) cells from transgenic mice (Tg-mice) expressing the human granulocyte-macrophage colony-stimulating factor receptor (hGM-CSFR), we found in earlier studies that hGM-CSF alone supported the development not only of granulocyte-macrophage colonies, but also of erythrocytes, megakaryocytes, mast cells, blast cells, and mixed hematopoietic colonies. In this report, we evaluated the in vivo effects of hGM-CSF on hematopoietic and lymphopoietic responses in the hGM-CSFR Tg-mice. Administration of this factor to Tg-mice resulted in dose-dependent increases in numbers of reticulocytes and white blood cells (WBCs) in the peripheral blood. Morphological analysis of WBCs showed that the numbers of all types of the cell, including neutrophils, eosinophils, monocytes, and lymphocytes increased; the most remarkable being in lymphocytes that contained a number of large granular lymphocytes (LGLs) in addition to mature T and B cells. However, total cellularity of the BM of the Tg-mice decreased in a dose-dependent manner when hGM-CSF was injected. In sharp contrast to the BM, spleens of the Tg-mice were grossly enlarged. Although all types of blood cells and hematopoietic progenitors increased in the spleen, erythroid cells and their progenitors showed the most significant increase. Increased numbers of megakaryocytes and LGLs were also observed in spleen and liver of the treated Tg-mice. Flow cytometric analysis showed that LGLs expanded in Tg-mice expressed Mac-1+CD3−NK1.1+. The thymus of Tg-mice treated with hGM-CSF exhibited a dose-dependent shrinkage and a remarkable decrease in CD4+CD8+ cells. Thus, hGM-CSF stimulated not only myelopoiesis but also erythropoiesis and megakaryopoiesis of hGM-CSFR Tg-mice in vivo, in accordance with our reported in vitro findings. In addition, hGM-CSF affected the development of lymphoid cells, including natural killer cells of these Tg-mice.
SYNTHESIS OF 11-KETO STEROIDS (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSYNTHESIS OF 11-KETO STEROIDSE. Schoenewaldt, L. Turnbull, E. M. Chamberlin, D. Reinhold, A. E. Erickson, W. V. Ruyle, J. M. Chemerda, and M. TishlerCite this: J. Am. Chem. Soc. 1952, 74, 10, 2696Publication Date (Print):May 1, 1952Publication History Published online1 May 2002Published inissue 1 May 1952https://pubs.acs.org/doi/10.1021/ja01130a524https://doi.org/10.1021/ja01130a524research-articleACS PublicationsRequest reuse permissionsArticle Views78Altmetric-Citations17LEARN 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
Network analysis of microRNAs, transcription factors, target genes and host genes in nasopharyngeal carcinoma (2016)

Numerous studies on the morbidity of nasopharyngeal carcinoma (NPC) have identified several genes, microRNAs (miRNAs or miRs) and transcription factors (TFs) that influence the pathogenesis of NPC. However, summarizing all the regulatory networks involved in NPC is challenging. In the present study, the genes, miRNAs and TFs involved in NPC were considered as the nodes of the so-called regulatory network, and the associations between them were investigated. To clearly represent these associations, three regulatory networks were built seperately, namely, the differentially expressed network, the associated network and the global network. The differentially expressed network is the most important one of these three networks, since its nodes are differentially expressed genes whose mutations may lead to the development of NPC. Therefore, by modifying the aberrant expression of those genes that are differentially expressed in this network, their dysregulation may be corrected and the tumorigenesis of NPC may thus be prevented. Analysis of the aforementioned three networks highlighted the importance of certain pathways, such as self-adaptation pathways, in the development of NPC. For example, cyclin D1 (CCND1) was observed to regulate <i>Homo sapiens</i>-miR-20a, which in turn targeted CCND1. The present study conducted a systematic analysis of the pathogenesis of NPC through the three aforementioned regulatory networks, and provided a theoretical model for biologists. Future studies are required to evaluate the influence of the highlighted pathways in NPC.
Periodate Oxidation of Methylcellulose: Characterization and Properties of Oxidized Derivatives (2010)

In this paper, the behavior of oxidized methylcelluloses is compared with that of the initial methylcellulose, an amphiphilic cellulose derivative. Methylcelluloses are important for many applications in the cosmetic and food industries. The mechanism of thermo-gelation of methylcellulose is briefly explained as well as the method of oxidation of polysaccharides. Then, our experiments involve the preparation of oxidized methylcelluloses: three degrees of oxidation are prepared and the new polymers are characterized by NMR, IR, SEC and rheology. Oxidation with periodate theoretically allows introduction of two aldehydic groups on C2–C3 glycol positions of anhydroglucose units. This reaction not only enhances the flexibility of the cellulosic backbone, but also causes a decrease in the molecular weight. In particular, the rheological behavior of methylcellulose and oxidized methylcellulose as a function of temperature is examined. The oxidized methylcelluloses prepared, being rich in aldehyde functions, become interesting intermediaries to prepare new cellulose derivatives. In this paper, three examples of reductive amination based on the reaction of modified methylcelluloses and −NH2 groups of different molecules are described: β-alanine produces a polyelectrolyte; chitosan and hyaluronan-ADH (derivative obtained with adipic dihydrazide allowing introduction of −NH2 functions on HA backbone) are crosslinked and give new biocompatible hydrogels.
Deep Learning-Based Detection of Pipes in Industrial Environments (2020)

Robust perception is generally produced through complex multimodal perception pipelines, but these kinds of methods are unsuitable for autonomous UAV deployment, given the restriction found on the platforms. This chapter describes developments and experimental results produced to develop new deep learning (DL) solutions for industrial perception problems. An earlier solution combining camera, LiDAR, GPS, and IMU sensors to produce high rate, accurate, robust detection, and positioning of pipes in industrial environments is to be replaced by a single camera computationally lightweight convolutional neural network (CNN) perception technique. In order to develop DL solutions, large image datasets with ground truth labels are required, so the previous multimodal technique is modified to be used to capture and label datasets. The labeling method developed automatically computes the labels when possible for the images captured with the UAV platform. To validate the automated dataset generator, a dataset is produced and used to train a lightweight AlexNet-based full convolutional network (FCN). To produce a comparison point, a weakened version of the multimodal approach—without using prior data—is evaluated with the same DL-based metrics.
New technique for dispersion compensation in compact femtosecond lasers (2003)

Summary form only given. Femtosecond laser sources usually require negative group delay dispersion (GDD) to compensate for the positive dispersion of the gain material and possibly other cavity elements. Various techniques to generate negative GDD from wavelength-dependent refraction at Brewster interfaces have been demonstrated. The resulting negative GDD is usually the product of a purely material-dependent factor and the distance L between the Brewster interface and the X-point, which we define as the point where the axes of the resonator modes with different frequencies intersect. Therefore, large values of negative GDD normally require large distances L, which may be a problem, e.g. when a short cavity length is required. We demonstrate that, for a given value of L, both the angular dispersion and the negative group delay dispersion generated by a Brewster interface can be strongly enhanced by the influence of a focusing action, which may arise from a curved surface or a thermal lens in the gain medium. We verified our theoretical prediction in a diode-pumped high-power Nd:glass laser.
Subcellular Nanorheology Reveals Lysosomal Viscosity as a Reporter for Lysosomal Storage Diseases (2018)

We describe a new method to measure viscosity within subcellular organelles of a living cell using nanorheology. We demonstrate proof of concept by measuring viscosity in lysosomes in multiple cell types and disease models. The lysosome is an organelle responsible for the breakdown of complex biomolecules. When different lysosomal proteins are defective, they are unable to break down specific biological substrates, which get stored within the lysosome, causing about 70 fatal diseases called lysosomal storage disorders (LSDs). Although the buildup of storage material is critical to the pathology of these diseases, methods to monitor cargo accumulation in the lysosome are lacking for most LSDs. Using passive particle tracking nanorheology and fluorescence recovery after photobleaching, we report that viscosity in the lysosome increases significantly during cargo accumulation in several LSD models. In a mammalian cell culture model of Niemann Pick C, lysosomal viscosity directly correlates with the levels of accumulated cholesterol. We also observed increased viscosity in diverse LSD models in Caenorhabditis elegans, revealing that lysosomal viscosity is a powerful reporter with which to monitor substrate accumulation in LSDs for new diagnostics or to assay therapeutic efficacy.
CS Freiburg: coordinating robots for successful soccer playing (2002)

Robotic soccer is a challenging research domain because many different research areas have to be addressed in order to create a successful team of robot players. The paper presents the CS Freiburg team, the winner in the middle-size league at RoboCup 1998, 2000, and 2001. The paper focuses on multiagent coordination for both perception and action. The contributions of the paper are new methods for tracking ball and players observed by multiple robots, team coordination methods for strategic team formation and dynamic role assignment; a rich set of basic skills allowing robots to respond to a large range of situations in an appropriate way, and an action-selection method based on behavior networks, as well as a method to learn the skills and their selection. As demonstrated by evaluations of the different methods and by the success of the team, these methods permit the creation of a multirobot group which is able to play soccer successfully. In addition, the developed methods promise to advance the state of the art in the multirobot field.
Effect of Wavelength Drift on Single- and Multi-Instrument Calibration Using Genetic Regression (1998)

The ability of genetic regression (GR) to correct for wavelength drift in instrument responses was investigated in single- and multiinstrument calibrations. Sample spectra of ternary mixtures were collected on two near-infrared (NIR) spectrometers, one a dispersive instrument and one a Fourier transform instrument, with different resolutions. In the first and second cases, calibration models were generated with the use of spectra collected on a single instrument. For the third case, hybrid calibration models (HCMs) were built in order to combine spectra from two instruments into one calibration model. In order to simulate a wavelength shift, some of the spectra were shifted along the wavelength axis from 0 nm to 6 nm. The performance of GR was poor when calibration models produced from unshifted spectra were used to predict shifted spectra. However, the inclusion of shifted spectra in the calibration model corrected the prediction of shifted and unshifted spectra at levels similar to those of models built and evaluated by using only unshifted spectra.
REGULATORY MUTATIONS OF INOSITOL BIOSYNTHESIS IN YEAST: ISOLATION OF INOSITOL-EXCRETING MUTANTS (1982)

The enzyme inositol-1-phosphate synthase (I-1-P synthase), product of the INO1 locus, catalyzes the synthesis of inositol-1-phosphate from the substrate glucose-6-phosphate. The activity of this enzyme is dramatically repressed in the presence of inositol. By selecting for mutants which overproduce and excrete inositol, we have identified mutants constitutive for inositol-1-phosphate synthase as well as a mutation in phospholipid biosynthesis. Genetic analysis of the mutants indicates that at least three loci (designated OPI1, OPI2 and OPI4) direct inositol-mediated repression of I-1-P synthase. Mutants of these loci synthesize I-1-P synthase constitutively. Three loci are unlinked to each other and to INO1, the structural gene for the enzyme. A mutant of a fourth locus, OPI3, does not synthesize I-1-P synthase constitutively, despite its inositol excretion phenotype. This mutant is preliminarily identified as having a defect in phospholipid synthesis.
Geodesy by very long base line interferometry (1975)

Important advances were made between 1971 and 1974 in the development of very long base line interferometry (VLBI) techniques for precision geodesy, including repeated determinations of the length of a transcontinental base line within 5 parts in 10 8 , accurate measurements of polar motion and the variation of universal time, and the establishment of a catalog of extragalactic radio sources with positional uncertainties smaller than 0.1 arc sec. An introduction to VLBI and an account of its early development have been given by Cohen [1973]. Counselman [1973] has reviewed applications of VLBI to geodesy and astrometry prior to 1973, and recently, Moran [1975 a ] has described the geodetic and astrometric results which have been obtained by VLBI through June 1974. Moran's review is particularly timely because he discusses important unpublished data, preliminary results, and work now in progress or being planned by the major VLBI groups in the United States.