gebhart/patrepeval huggingface dataset:
Transcriptional regulation of alpha 2(I) collagen gene expression by fibroblast growth factor‐2 in MC3T3‐E1 osteoblast‐like cells (2001)

Fibroblast growth factor-2 (FGF-2) stimulates proliferation and inhibits differentiated function of osteoblasts by suppressing synthesis of type I collagen and other proteins. However, little is known regarding the molecular mechanisms regulating the suppressive effects of FGF-2 on type I collagen synthesis in osteoblasts. The zinc finger transcription factor Egr-1 and the basic helix-loop-helix (bHLH) family of proteins have been implicated in the regulation of genes crucial to mesodermal cell growth and differentiation. The aim of this study was to determine whether Egr-1 and TWIST might be potential transcriptional regulators of the inhibitory effects of FGF-2 on α2(I) collagen expression in MC3T3-E1 osteoblasts which undergo a developmental sequence in vitro. Upon treatment of undifferentiated MC3T3-E1 cells with 1 nM FGF-2, Egr-1 mRNA increased with the effect maximal after 30–60 min. TWIST mRNA also increased with the effect maximal at 2 h. We analyzed the transcriptional control of α2(I) collagen gene expression by FGF-2 by transient transfection of an α2(I) collagen-luciferase construct (pH5) into undifferentiated MC3T3-E1 cells. The activity of the pH5 luciferase promoter decreased in a dose-dependent manner following treatment with.01 and 1 nM FGF-2. We identified putative Egr-1 and TWIST recognition sequences in the proximal region of the promoter for the murine α2(I) collagen gene and a putative Egr-1 site in the 5′ region of the murine TWIST promoter. In gel mobility shift assays, potential Egr-1 response elements in the 5′ region of the murine TWIST and α2(I) collagen genes demonstrated specific Egr-1 binding activity with bFGF-treated nuclear extracts obtained from MC3T3-E1 cells. These results indicate that Egr-1 and TWIST are expressed in undifferentiated MC3T3-E1 osteoblast-like cells following treatment with FGF-2 and they may be potential transcriptional regulators of FGF-2s negative effects on α2(I) collagen gene expression. J. Cell. Biochem. 80:550–559, 2001. Published 2001 Wiley-Liss, Inc.
Differential Gene Expression of Primary Cultured Lymphatic and Blood Vascular Endothelial Cells (2007)

Blood vascular endothelial cells (BECs) and the developmentally related lymphatic endothelial cells (LECs) create complementary, yet distinct vascular networks. Each endothelial cell type interacts with flowing fluid and circulating cells, yet each vascular system has evolved specialized gene expression programs and thus both cell types display different phenotypes. BECs and LECs express distinct genes that are unique to their specific vascular microenvironment. Tumors also take advantage of the molecules that are expressed in these vascular systems to enhance their metastatic potential. We completed transcriptome analyses on primary cultured LECs and BECs, where each comparative set was isolated from the same individual. Differences were resolved in the expression of several major categories, such as cell adhesion molecules (CAMs), cytokines, and cytokine receptors. We have identified new molecules that are associated with BECs (e.g., claudin-9, CXCL11, neurexin-1, neurexin-2, and the neuronal growth factor regulator-1) and LECs (e.g., claudin-7, CD58, hyaluronan and proteoglycan link protein 1 (HAPLN1), and the poliovirus receptor-related 3 molecule) that may lead to novel therapeutic treatments for diseases of lymphatic or blood vessels, including metastasis of cancer to lymph nodes or distant organs.
Helicobacter pylori CagA: From Pathogenic Mechanisms to Its Use as an Anti-Cancer Vaccine (2013)

Helicobacter pylori colonizes the gastric mucosa of more than 50% of the human population, causing chronic inflammation, which however is largely asymptomatic. Nevertheless, H. pylori-infected subjects can develop chronic gastritis, peptic ulcer, gastric mucosa-associated lymphoid tissue lymphoma, and gastric cancer. Chronic exposure to the pathogen and its ability to induce epithelial to mesenchymal transition (EMT) through the injection of cytotoxin-associated gene A into gastric epithelial cells may be key triggers of carcinogenesis. By deregulating cell-cell and cell-matrix interactions as well as DNA methylation, histone modifications, expression of micro RNAs, and resistance to apoptosis, EMT can actively contribute to early stages of the cancer formation. Host response to the infection significantly contributes to disease development and the concomitance of particular genotypes of both pathogen and host may turn into the most severe outcomes. T regulatory cells (Treg) have been recently demonstrated to play an important role in H. pylori-related disease development and at the same time the Treg-induced tolerance has been proposed as a possible mechanism that leads to less severe disease. Efficacy of antibiotic therapies of H. pylori infection has significantly dropped. Unfortunately, no vaccine against H. pylori is currently licensed, and protective immunity mechanisms against H. pylori are only partially understood. In spite of promising results obtained in animal models of infection with a number of vaccine candidates, few clinical trials have been conducted so far and with no satisfactory outcomes. However, prophylactic vaccination may be the only means to efficiently prevent H. pylori-associated cancers.
Communicating the sum of sources over a network (2008)

We consider a network (that is capable of network coding) with a set of sources and terminals, where each terminal is interested in recovering the sum of the sources. Considering directed acyclic graphs with unit capacity edges and independent, unit-entropy sources, we show the rate region when (a) there are two sources and $n$ terminals, and (b) $n$ sources and two terminals. In these cases as long as there exists at least one path from each source to each terminal we demonstrate that there exists a valid assignment of coding vectors to the edges such that the terminals can recover the sum of the sources.
ISOELECTRIC FOCUSING OF BOVINE MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES (1989)

The products of the major histocompatibility complex (MHC) loci regulate an individual's immune response to pathogens. Cattle provide an important model to study the relationship between disease susceptibility and MHC haplotype since large half-sibling families are common. The definitive demonstration, however, of a firm relationship between MHC phenotype and disease susceptibility in cattle will require a precise definition of the bovine MHC allelic products. Available reagents for serological characterization of the bovine MHC gene products have not been adequate for these purposes. We have shown that existing mouse monoclonal antibodies and rabbit anti-human antisera precipitate bovine class I molecules, that these structures separate well by one-dimensional isoelectric focusing (1-D IEF), and that immunoprecipitation followed by 1-D IEF allows the detection of bovine class I MHC allelic products. Through this technique, we have identified previously undetected class I products. This approach will facilitate a detailed characterization of the bovine MHC class I gene products.
Automated Event Detection and Denoising Method for Passive Seismic Data Using Residual Deep Convolutional Neural Networks (2021)

There has been a recent rise in the uses and applications of passive seismic data, such as tomographic imaging, volcanic monitoring, and hydrocarbon exploration. Consequently, the sharp increase in passive seismic applications requires real-time event detection capabilities with high accuracy. Proper analysis of such events depends largely on the signal-to-noise ratio improvement through noise suppression techniques. Recent advances in the fields of signal processing and deep learning coupled with the available computational resources provide a great opportunity to address this challenge. In this work, a workflow is proposed where a residual deep neural network is customized and employed to detect passive seismic events. The automated detection is followed by a denoising step to extract the signal of interest from background noise using an IIR Wiener filter. The proposed method does not require any prior knowledge of the signal/noise, and therefore, it can work with various types of signals/noises. Another benefit of the proposed detection method is that the deep neural network is trained only on synthetic seismic data without the need to use real data in the training process. Nevertheless, it exhibits high accuracy in detecting and denoising events from real passive seismic data sets. In particular, field seismic data is recorded in northern Saudi Arabia and used to test the complete detection and denoising method. The detection method proved its capability of detecting events automatically in large data sets and in real time (due to off-line training).
Heating by collisional slowing of fast ions in non-circular tokamaks (1980)

Plasma heating by energetic, charged fusion-products is a crucial issue for obtaining fusion reactors conditions. The evolution of alpha particle density, momentum, kinetic energy and heat flux is important in the study of start-up and ignition scenarios as well as in steady-state operation. Since fast ions have large banana-width guiding-center orbits in tokamaks, the usual locally-defined particle distribution function loses its usefulness. Accordingly, the fast ion collisional slowing-down problem has been formulated to describe these orbits in an axisymmetric, non-circular tokamak.
Distinct GluN1 and GluN2 Structural Determinants for Subunit-Selective Positive Allosteric Modulation of N-Methyl-d-aspartate Receptors (2020)

<i>N</i>-Methyl-d-aspartate receptors (NMDARs) are ionotropic ligand-gated glutamate receptors that mediate fast excitatory synaptic transmission in the central nervous system (CNS). Several neurological disorders may involve NMDAR hypofunction, which has driven therapeutic interest in positive allosteric modulators (PAMs) of NMDAR function. Here we describe modest changes to the tetrahydroisoquinoline scaffold of GluN2C/GluN2D-selective PAMs that expands activity to include GluN2A- and GluN2B-containing recombinant and synaptic NMDARs. These new analogues are distinct from GluN2C/GluN2D-selective compounds like (+)-(3-chlorophenyl)(6,7-dimethoxy-1-((4-methoxyphenoxy)methyl)-3,4-dihydroisoquinolin-2(1<i>H</i>)-yl)methanone (CIQ) by virtue of their subunit selectivity, molecular determinants of action, and allosteric regulation of agonist potency. The (<i>S</i>)-enantiomers of two analogues (EU1180-55, EU1180-154) showed activity at NMDARs containing all subunits (GluN2A, GluN2B, GluN2C, GluN2D), whereas the (<i>R</i>)-enantiomers were primarily active at GluN2C- and GluN2D-containing NMDARs. Determination of the actions of enantiomers on triheteromeric receptors confirms their unique pharmacology, with greater activity of (<i>S</i>) enantiomers at GluN2A/GluN2D and GluN2B/GluN2D subunit combinations than (<i>R</i>) enantiomers. Evaluation of the (<i>S</i>)-EU1180-55 and EU1180-154 response of chimeric kainate/NMDA receptors revealed structural determinants of action within the pore-forming region and associated linkers. Scanning mutagenesis identified structural determinants within the GluN1 pre-M1 and M1 regions that alter the activity of (<i>S</i>)-EU1180-55 but not (<i>R</i>)-EU1180-55. By contrast, mutations in pre-M1 and M1 regions of GluN2D perturb the actions of only the (<i>R</i>)-EU1180-55 but not the (<i>S</i>) enantiomer. Molecular modeling supports the idea that the (<i>S</i>) and (<i>R</i>) enantiomers interact distinctly with GluN1 and GluN2 pre-M1 regions, suggesting that two distinct sites exist for these NMDAR PAMs, each of which has different functional effects.
A Small Molecule Promotes Mitochondrial Fusion in Mammalian Cells (2012)

Mitochondriendynamik: Durch ein bildgebendes Verfahren konnte eine niedermolekulare Verbindung, M1, identifiziert werden, die spezifisch die Fusion fragmentierter Mitochondrien fördert und Zellen vor dem durch Mitochondrienfragmentierung ausgelösten Zelltod schützt. Mechanistische Untersuchungen zeigen, dass M1 das Gleichgewicht der Mitochondriendynamik in Richtung der Fusion verschiebt (siehe Bild). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Tapered Dual-Core Fiber for Efficient and Robust Coupling to InP Photonic Integrated Circuits (2009)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text C. R. Doerr, L. Zhang, L. Buhl, V. I. Kopp, D. Neugroschl, and G. Weiner, "Tapered Dual-Core Fiber for Efficient and Robust Coupling to InP Photonic Integrated Circuits," in Optical Fiber Communication Conference and National Fiber Optic Engineers Conference, OSA Technical Digest (CD) (Optica Publishing Group, 2009), paper OThN5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Pilot and Data Power Allocation in Poisson Interference Field With Protected Zone for Physical-Layer Security (2020)

Physical-layer security has become widely recognized as a promising technique to enhance wireless security by exploiting the characteristics including fading, noise, and interference. This letter explores an opportunity to enhance physical-layer security by balancing the power expense between pilot and payload signals without any prior knowledge related to eavesdroppers. In lieu of presuming perfect channel acquisition, we consider a practical wiretap channel with the receivers enabled by pilot-aided channel estimation (CE). The problem is tackled by accounting for the network interference from cochannel interferers in unknown locations by which the secrecy level is significantly affected. Specifically, the secrecy transmission rate (STR) reflecting the CE errors is derived for the worst-case within the use of a protected zone. We investigate the feasible region of pilot and data power allocation under reliability and secrecy constraints, and the optimal power allocation for pilot and data to maximize the STR is proposed, whose performance is verified via simulations.
Hexamethylenebisacetamide-induced erythroleukemia cell differentiation involves modulation of events required for cell cycle progression through G1. (1993)

Hexamethylenebisacetamide (HMBA), a potent inducer of differentiation of transformed cells such as murine erythroleukemia cells, causes a prolongation of the G1 phase of the cell cycle during which commitment to terminal differentiation is first detected. Removal of HMBA prior to the G1 phase aborts commitment. To further define the relationship between the G1 phase and commitment to differentiation, we used two inhibitors of cell cycle progression: aphidicolin, which blocks cells at the G1/S interphase, and deferoxamine, which blocks cells at an earlier stage during G1. HMBA-induced prolongation of G1 is associated with the accumulation of underphosphorylated retinoblastoma protein, decrease in cyclin A protein levels, and commitment to differentiation. G1 arrest of murine erythroleukemia cells induced by aphidicolin or deferoxamine is not associated with accumulation of under-phosphorylated retinoblastoma protein, suppression of cyclin A protein, or commitment of cells to terminal differentiation. Neither of the cell cycle inhibitors alters the effect of HMBA in inducing the G1-associated changes or commitment to differentiation. Taken together, the present findings indicate that the site of action of HMBA which leads to commitment is in a stage of the G1 phase prior to the point of cell cycle block caused by deferoxamine or aphidicolin. HMBA appears to cause cell differentiation with suppression of cell cycle progression by an action that affects events required for cell progression through G1, including accumulation of underphosphorylated retinoblastoma protein and changes in regulation of cyclin levels.
Ein durch Doxycyclin reguliertes allosterisches Ribozym (2001)

In der Zuschrift von V. Thuillier und M. Famulok et al. (Angew. Chem. 2000, 112, 4538–4542) muss die Abbildung 3 korrigiert werden: Die Autoren haben festgestellt, dass Klon D16-05 einen zusätzlichen C-Rest in Position 42 zwischen G41 und U43 enthält (5′-Ende des hellorange dargestellten Sequenzbereichs). Diese Mutation verändert die computergenerierte Sekundärstruktur der Punktmutante D16-05 zu der in Abbildung 3 b gezeigten Faltung. In den Spuren 7, 8, 10 und 11 in Abbildung 3 a wurde D16-05 mit RNA-Ködern inkubiert, bei denen C42 fehlte, da diese von einer Templat-DNA transkribiert worden waren, die durch PCR unter Verwendung eines C42-defizienten 5′-Primers hergestellt wurde. Die Autoren haben daher die in Abbildung 3 skizzierte Analyse mit korrekten Primern wiederholt. Es zeigte sich, dass die Konstrukte 10 und 11 in Abbildung 3 a die Spaltaktivität effizient wiederherstellen können. Die frühere Schlussfolgerung, dass Helix I (rot) eine wichtige strukturelle Rolle bei der Doxycyclinbindung spielt, ist daher nach wie vor richtig, aber es zeigt sich nun, dass der Effekt von Helix I unabhängig von ihrer Sequenz ist. Alle weiteren Schlussfolgerungen dieser Zuschrift bleiben hiervon unberührt.3 Bestimmung der Minimalsequenz von Klon D16-05. a) Relative Aktivität kabs(norm) der Spaltreaktion unter verschiedenen Bedingungen (immer in Gegenwart von 1 μM tRNA als unspezifischem Kompetitor). 1: Spaltaktivität von D16-05 (1 nM), 2: zusätzlich 200 nM 1, 3: wie 2. Lauf, zusätzlich 2 μM unselektierte Bibliothek als unspezifischer Kompetitor; 4–8: wie 2. Lauf, zusätzlich 2 μM spaltungsinaktive Punktmutante M16-05 (4), Konstrukt T16-05.4 (5), Konstrukt T16-05.9 (6), Konstrukt T16-05.13 (7), Konstrukt T16-05.1 (8); 9–11: wie 2. Lauf, zusätzlich 2 μM Konstrukt T16-05.9 mit den gezeigten Variationen in der Helix I. b) Computer-generierte Sekundärstruktur der Punktmutante D16-05. Die Markierungssymbole flankieren die getesteten Sequenzen der verkürzten Versionen. Um die T7-Transkription zu ermöglichen, wurden zwei Guanosinreste in die 5′-Positionen der verkürzten Konstrukte eingefügt, die hier nicht gezeigt sind. Orange: die ursprüngliche randomisierte Region; rot: konstante Regionen aus dem Hammerhead-Ribozym (Helix I); grün: katalytisch aktives Zentrum. Der schwarz unterlegte Guanosinrest zeigt die Punktmutation C–G. Die Zahlen in Klammern beziehen sich auf die Numerierung in (a).
Precise Analysis of the Autofluorescence Characteristics of Rat Colon Under UVA and Violet Light Excitation (2013)

The mucosal layer is the important source of the autofluorescence observed under excitation with UVA/violet light in multilayered colonic structures. Illumination of 365-nm wavelength light is a suitable means of analyzing the autofluorescence of mucosal epithelia.
Electronic structures and electrochemistry of boronated cyanometalates (2019)

We have synthesized and structurally characterized a series of organoboron-modified cyanometalates. The redn. potentials of these modified metal complexes span an exceptionally wide range, owing to variations in the electronic properties of the appended organoboron derivs. Selected highly sol. redox pairs exhibit electrochem. reversibility over a 2.1 V range in non-aq. solvents, making them excellent candidates for non-aq. redox flow batteries. Our model flow battery systems exhibit near unity Coulombic efficiencies and high energy efficiencies.
Automated Sleep Apnea Detection in Raw Respiratory Signals Using Long Short-Term Memory Neural Networks (2018)

Sleep apnea is one of the most common sleep disorders and the consequences of undiagnosed sleep apnea can be very severe, ranging from increased blood pressure to heart failure. However, many people are often unaware of their condition. The gold standard for diagnosing sleep apnea is an overnight polysomnography in a dedicated sleep laboratory. Yet, these tests are expensive and beds are limited as trained staff needs to analyze the entire recording. An automated detection method would allow a faster diagnosis and more patients to be analyzed. Most algorithms for automated sleep apnea detection use a set of human-engineered features, potentially missing important sleep apnea markers. In this paper, we present an algorithm based on state-of-the-art deep learning models for automatically extracting features and detecting sleep apnea events in respiratory signals. The algorithm is evaluated on the Sleep-Heart-Health-Study-1 dataset and provides per-epoch sensitivity and specificity scores comparable to the state of the art. Furthermore, when these predictions are mapped to the apnea-hypopnea index, a considerable improvement in per-patient scoring is achieved over conventional methods. This paper presents a powerful aid for trained staff to quickly diagnose sleep apnea.
The LOT: a link between block transform coding and multirate filter banks (2003)

The lapped orthogonal transform (LOT) is a novel transform for block signal processing with overlapping basis functions. The LOT can also be viewed as an efficient quadrature-mirror-filter bank in which the analysis and synthesis filters have identical FIR (finite-impulse-response) responses. The author shows that the LOT filter bank leads to perfect signal reconstruction with a relative low level of spectral images. The main advantages of the LOT filter bank are its short filter lengths (twice the number of bands) and its fast algorithm, based on the fast discrete cosine transform.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MTF Measurements of Wide Field of View Cameras (2016)

In this paper we present an algorithm for estimating camera system modulation transfer functions (MTF) from highly distorted images. This algorithm estimates multiple oversampled line spread functions using different order polynomials and binning. The ensemble of oversampled line spread functions (LSF) are used to estimate the final system MTF. Moreover, the LSF derived from the highest order polynomial without overfitting is used to estimate the system MTF. We show the performance of this algorithm on synthetically generated images and on image captures from a commercially available camera. We compare this algorithm to the ISO 12233 standard.
Cuffed Tracheal Tubes???Physical and Behavioral Characteristics (1982)

This study compares physical and behavioral characteristics of currently used cuffed tracheal tubes. Variability in physical and behavioral characteristics between size 8 tracheal tubes and cuffs exists: radius of tube curvature varies from 12.1 to 15.8 cm, bevel angle 39 to 56 degrees, bevel direction 73 to 107 degrees, distance from proximal end of bevel to cuff 15.4 to 24.4 mm, internal tube diameter 7.5 to 8.8 mm, wall thickness 1.14 to 2.37 mm, force to collapse 1020 to 3103 g, angle to kink 52 to 96 degrees, and indentation hardness 65.4 to 83.1. Cuff lengths vary from 29.7 to 45.3 mm, thickness 0.03 to 0.54 mm, diameter 14.5 to 32 mm, and cuff resting volume 0.15 to 19.9 ml. We recommend use of a soft, thermolabile, kink- and collapse-resistant tracheal tube fitted with a soft, thin-walled, tough, compliant, moderately long cuff, with a moderately large resting volume and diameter larger than tracheal diameter. Argyle, National Catheter, Ohio, Portex, Rusch "safety," and Shiley tracheal tubes resist collapse and kinking. Argyle, Lanz, National Catheter "hi-lo," National Catheter "intermediate hi-lo," Ohio, and Portex "profile" cuffs are thin and have diameters larger than the average male tracheal diameter.