gebhart/patrepeval huggingface dataset:
Exact Reconstruction of Gene Regulatory Networks using Compressive Sensing (2014)

Background: We consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity. We assume that the network is sparse, meaning the connectivity among genes is much less than full connectivity. We develop a method for network reconstruction based on compressive sensing, which takes advantage of the network's sparseness. Results: For the case in which all genes are accessible for measurement, and there is no measurement noise, we show that our method can be used to exactly reconstruct the network. For the more general problem, in which hidden genes exist and all measurements are contaminated by noise, we show that our method leads to reliable reconstruction. In both cases, coherence of the model is used to assess the ability to reconstruct the network and to design new experiments. For each problem, a set of numerical examples is presented. Conclusions: The method provides a guarantee on how well the inferred graph structure represents the underlying system, reveals deficiencies in the data and model, and suggests experimental directions to remedy the deficiencies.
CALEB Binds via Its Acidic Stretch to the Fibrinogen-like Domain of Tenascin-C or Tenascin-R and Its Expression Is Dynamically Regulated after Optic Nerve Lesion (2001)

Recently, we described a novel chick neural transmembrane glycoprotein, which interacts with the extracellular matrix proteins tenascin-C and tenascin-R. This protein, termed CALEB, contains an epidermal growth factor-like domain and appears to be a novel member of the epidermal growth factor family of growth and differentiation factors. Here we analyze the interaction between CALEB and tenascin-C as well as tenascin-R in more detail, and we demonstrate that the central acidic peptide segment of CALEB is necessary to mediate this binding. The fibrinogen-like globe within tenascin-C or -R enables both proteins to bind to CALEB. We show that two isoforms of CALEB in chick and rodents exist that differed in their cytoplasmic segments. To begin to understand the in vivo function of CALEB and since in vitro antibody perturbation experiments indicated that CALEB might be important for neurite formation, we analyzed the expression pattern of the rat homolog of CALEB during development of retinal ganglion cells, after optic nerve lesion and during graft-assisted retinal ganglion cell axon regeneration by in situ hybridization. These investigations demonstrate that CALEB mRNA is dynamically regulated after optic nerve lesion and that this mRNA is expressed in most developing and in one-third of the few regenerating (GAP-43 expressing) retinal ganglion cells.
Apelin and APJ regulation in adipose tissue and skeletal muscle of type 2 diabetic mice and humans (2010)

Apelin, an adipocyte-secreted factor upregulated by insulin, is increased in adipose tissue (AT) and plasma with obesity. Apelin was recently identified as a new player in the control of glucose homeostasis. However, the regulation of apelin and APJ (apelin receptor) expression in skeletal muscle in relation to insulin resistance or type 2 diabetes is not known. Thus we studied apelin and APJ expression in AT and muscle in different mice models of obesity and in type 2 diabetic patients. In insulin-resistant high-fat (HF)-fed mice, apelin and APJ expression were increased in AT compared with control. This was not the case in AT of highly insulin-resistant db/db mice. In skeletal muscle, apelin expression was similar in control and HF-fed mice and decreased in db/db mice. APJ expression was decreased in both HF-fed and db/db mice. Control subjects and type 2 diabetic patients were subjected to a hyperinsulinemic-euglycemic clamp, and tissues biopsies were obtained before and at the end of the clamp. There was no significant difference in basal apelin and APJ expression in AT and muscle between control and diabetic patients. However, apelin plasma levels were significantly increased in diabetic patients. During the clamp, hyperinsulinemia increased apelin and APJ expression in AT of control but not in diabetic subjects. In muscle, only APJ mRNA levels were increased in control but also in diabetic patients. Taken together, these data show that apelin and APJ expression in mice and humans is regulated in a tissue-dependent manner and according to the severity of insulin resistance.
Levosimendan Potentiates the Inotropic Actions of Dopamine in Conscious Dogs (1996)

We examined the hemodynamic and left ventricular (LV) functional actions of dopamine with and without levosimendan in dogs chronically instrumented for measurement of aortic and LV pressure, +dP/dtmax, subendocardial segment length, and cardiac output (CO). On different experimental days, dogs were randomly assigned to receive dopamine (2.5, 5.0, and 10.0 micrograms kg-1 min-1) in the absence and presence of levosimendan (0.125, 0.25, and 0.5 microgram kg-1 min-1) or levosimendan alone. Dopamine increased heart rate (HR), CO, stroke volume (SV), and pressure-work index (PWI) and decreased systemic vascular resistance (SVR). Dopamine also increased LV systolic and end-diastolic pressures (LVSP and LVEDP) and mean arterial pressure (MAP). Dopamine caused dose-related positive inotropic [increases in preload recruitable stroke work (Mw) and + dP/ dtmax] and lusitropic effects [decreases in the time constant of isovolumic relaxation (tau) and increases in maximum segment-lengthening velocity (dL/dtmax)]. Dopamine also increased the regional chamber thickness constant (Kp) concomitant with increases in LVEDP. In the presence of levosimendan, dopamine-induced increases in HR, PWI, CO, and SV and decreases in SVR were enhanced. Increases in MAP, LVSP, and LVEDP observed with dopamine alone were attenuated by the addition of levosimendan. Dopamine-induced increases in Mw and +dP/dtmax were enhanced by levosimendan. Reductions in tau and increases in dL/dtmax produced by dopamine were similar with and without levosimendan. However, levosimendan abolished increases in Kp caused by dopamine alone. Levosimendan alone caused dose-related improvements in indices of LV systolic and diastolic function. The results indicate that levosimendan potentiates the positive inotropic effects of dopamine in conscious, unsedated dogs, while attenuating the deleterious action of dopamine on chamber compliance.
Control of coleader formations in the plane (2009)

This paper addresses the n-agent formation shape maintenance problem in the plane. We consider a class of directed information architectures associated with so called minimally persistent coleader formations. The formation shape is specified by certain interagent distances. Only one agent is responsible for maintaining each distance. We propose a control law where each agent executes its control using only the relative position measurements of agents it must maintain its distance to. The resulting nonlinear closed-loop system has a manifold of equilibria; thus the linearized system is nonhyperbolic. We apply center manifold theory to show local exponential stability of the desired formation shape that circumvents the non-compactness of the equilibrium manifold. Choosing stabilizing gains is possible if a certain submatrix of the rigidity matrix has all leading principal minors nonzero, and we show that this condition holds for all minimally persistent coleader formations with generic agent positions.
Role of the N-Terminal Seven Residues of Surfactant Protein B (SP-B) (2013)

Breathing is enabled by lung surfactant, a mixture of proteins and lipids that forms a surface-active layer and reduces surface tension at the air-water interface in lungs. Surfactant protein B (SP-B) is an essential component of lung surfactant. In this study we probe the mechanism underlying the important functional contributions made by the N-terminal 7 residues of SP-B, a region sometimes called the "insertion sequence". These studies employed a construct of SP-B, SP-B (1-25,63-78), also called Super Mini-B, which is a 41-residue peptide with internal disulfide bonds comprising the N-terminal 7-residue insertion sequence and the N- and C-terminal helices of SP-B. Circular dichroism, solution NMR, and solid state (2)H NMR were used to study the structure of SP-B (1-25,63-78) and its interactions with phospholipid bilayers. Comparison of results for SP-B (8-25,63-78) and SP-B (1-25,63-78) demonstrates that the presence of the 7-residue insertion sequence induces substantial disorder near the centre of the lipid bilayer, but without a major disruption of the overall mechanical orientation of the bilayers. This observation suggests the insertion sequence is unlikely to penetrate deeply into the bilayer. The 7-residue insertion sequence substantially increases the solution NMR linewidths, most likely due to an increase in global dynamics.
Nonvolatile low-voltage memory transistor based on SiO2 tunneling and HfO2 blocking layers with charge storage in Au nanocrystals (2011)

We demonstrate a low voltage nonvolatile memory field effect transistor comprising thermal SiO2 tunneling and HfO2 blocking layers as the gate dielectric stack and Au nanocrystals as charge storage nodes. The structure exhibits a memory window of ∼2 V at an applied sweeping voltage of ±3 V which increases to 12.6 at ±12 V. Retention tests show an extrapolated loss of 16% after ten years in the hysteresis width of the threshold voltage. Dynamic program/erase operation reveal an approximately pulse width independent memory for pulse durations of 1 μs to 10 ms; longer pulses increase the memory window while for pulses shorter than 1 μs, the memory windows vanishes. The effective oxide thickness is below 10 nm with very low gate and drain leakage currents.
The predictive value of bcl-2, bax, bcl-xL, bag-1, fas, and fasL for chemotherapy response in advanced breast cancer. (2002)

None of the investigated apoptosis-related factors of primary tumor could predict the later response to either D or MF treatment. However, fasL and bcl-2 were strong prognostic factors. Patients who had tumors with high fasL and low bcl-2 expression had the shortest OS.
A Comparative Study of Clinical Outcomes and Second-Look Arthroscopic Findings between Remnant-Preserving Tibialis Tendon Allograft and Hamstring Tendon Autograft in Anterior Cruciate Ligament Reconstruction: Matched-Pair Design (2017)

When an autograft is not feasible in anterior cruciate ligament reconstruction, the remnant-preserving technique can produce comparable results in terms of restoration of function, stability of the knee, and degree of synovium coverage at second-look arthroscopy compared to remnant-sacrificing hamstring autograft.
Diastereoselective Synthesis of Optically Active C2-Substituted Spiro(4.5)decanes: Two Key Intermediates for Spirovetivane Sesquiterpenes. (1997)

We investigated the stereoselective construction of the C2 stereogenic center of the spiro[4.5]decane skeleton present in the spirovetivanes, spirolaurane, and spiroaxanes, and succeeded in synthesizing 2α- and 2β-substituted 6-spiro[4.5]decanones with diastereoselectivity by employing n-Bu3-SnH-mediated spiroannulation of the alkylmercury chloride, and Pd(II)-mediated spiroannulation followed by catalytic hydrogenation of the resulting unsaturated ester, respectively.
Long-term survival and functional capacity in cardiac surgery patients after prolonged intensive care (2000)

Many survivors of prolonged intensive care die soon after hospital discharge and many longer term survivors have a poor functional state. Therefore, hospital discharge is an incomplete measure of outcome for these patients, and longer follow-up is more appropriate. The relatively small number of patients who require prolonged intensive care consumes a disproportionate amount of the total ICU and total hospital direct cost.
LEGAN: Disentangled Manipulation of Directional Lighting and Facial Expressions by Leveraging Human Perceptual Judgements (2020)

Building facial analysis systems that generalize to extreme variations in lighting and facial expressions is a challenging problem that can potentially be alleviated using natural-looking synthetic data. Towards that, we propose LEGAN, a novel synthesis framework that leverages perceptual quality judgments for jointly manipulating lighting and expressions in face images, without requiring paired training data. LEGAN disentangles the lighting and expression subspaces and performs transformations in the feature space before upscaling to the desired output image. The fidelity of the synthetic image is further refined by integrating a perceptual quality estimation model, trained with face images rendered using multiple synthesis methods and their crowd-sourced naturalness ratings, into the LEGAN framework as an auxiliary discriminator. Using objective metrics like FID and LPIPS, LEGAN is shown to generate higher quality face images when compared with popular GAN models like StarGAN and StarGAN-v2 for lighting and expression synthesis. We also conduct a perceptual study using images synthesized by LEGAN and other GAN models and show the correlation between our quality estimation and visual fidelity. Finally, we demonstrate the effectiveness of LEGAN as training data augmenter for expression recognition and face verification tasks.
ChemInform Abstract: One‐Pot Synthesis of Furo‐ or Thienoquinolines Through Sequential Imination and Intramolecular Palladium‐Catalyzed Direct Arylation. (2013)

Abstract The two‐step one‐pot reaction proceeds via in situ generated N‐(2‐haloaryl)‐thiophene‐ or ‐furan imines to afford the corresponding thieno‐ [cf.
Extensibility in Automotive Security (2017)

A modern automotive design contains over a hundred microprocessors, several cyber-physical modules, connectivity to a variety of networks, and several hundred megabytes of software. The future is anticipated to see an even sharper rise in complexity of this electronics, with the imminence of driverless vehicles, the potential of connected automobiles within a few years, and work towards seamless integration of automobiles with smart cities and infrastructure systems. Security is a fundamental challenge in the design of automotive systems. Unfortunately, security considerations in automotive systems are complicated by two factors: (1) need for real-time mitigation against in-field threats; and (2) in-field configurability and extensibility of security features. This paper examines the trade-offs between security countermeasures, real-time requirements, and in-field configurability needs for modern automotive systems. We discuss the current state of the practice in automotive security architecture, as well as gaps and challenges that need to be addressed for a viable security solution in future.
An Integrated Approach for Assessment of Levees in the Lower Rio Grande Valley (2003)

PreviousNext No AccessSymposium on the Application of Geophysics to Engineering and Environmental Problems 2003An Integrated Approach for Assessment of Levees in the Lower Rio Grande ValleyAuthors: Joseph B. DunbarJames E. StefanovMichael J. BishopLinda Peyman‐DoveJosé L. LlopisWilliam L. MurphyRobert F. BallardJoseph B. DunbarERDC, Vicksburg, MS, James E. StefanovU.S. IBWC, El Paso, TX, Michael J. BishopERDC, Vicksburg, MS, Linda Peyman‐DoveERDC, Vicksburg, MS, José L. LlopisERDC, Vicksburg, MS, William L. MurphyERDC, Vicksburg, MS, and Robert F. BallardERDC contractor, Vicksburg, MShttps://doi.org/10.4133/1.2923176 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Abstract Introductory paragraph for this paper is available only in the PDF and GZipped PS filesPermalink: https://doi.org/10.4133/1.2923176FiguresReferencesRelatedDetailsCited ByAdvanced Airborne Geophysics for Engineering Solutions20 June 2012 Symposium on the Application of Geophysics to Engineering and Environmental Problems 2003ISSN (online):1554-8015Copyright: 2003 Pages: 1491 publication data© 2003 Copyright © 2003 The Environmental and Engineering Geophysical SocietyPublisher:Environmental & Engineering Geophysical Society HistoryPublished: 30 Sep 2008 CITATION INFORMATION Joseph B. Dunbar, James E. Stefanov, Michael J. Bishop, Linda Peyman‐Dove, José L. Llopis, William L. Murphy, and Robert F. Ballard, (2003), "An Integrated Approach for Assessment of Levees in the Lower Rio Grande Valley," Symposium on the Application of Geophysics to Engineering and Environmental Problems Proceedings : 350-362. https://doi.org/10.4133/1.2923176 Plain-Language Summary PDF DownloadLoading ...
First‐in‐man study to investigate safety, pharmacokinetics and exploratory pharmacodynamics of HTL0018318, a novel M1‐receptor partial agonist for the treatment of dementias (2020)

HTL0018318 showed well-characterized pharmacokinetics and following single doses were generally well tolerated in the dose range studied. These provide encouraging data in support of the development for HTL0018318 for Alzheimer's disease and other dementias.
Molecular mapping with functional antibodies localizes critical sites on the human IL receptor common gamma (gamma c) chain. (1998)

The IL receptor common gamma (gamma c) chain is required for the formation of high affinity cytokine receptor complexes for IL-2, IL-4, IL-7, IL-9, and IL-15, and for signals regulating cell survival, growth, and differentiation. Our current understanding of how gamma c chain associates with multiple ligands and receptor subunits is drawn largely from its structural homology to the human growth hormone (hGH) receptor and known structure of the hGH/hGH receptor complex. These receptors share distinct features in their extracellular portions and are believed to function by a mechanism of ligand-induced association of receptor subunits. Here, we report the first directed mutational analysis of the human gamma c chain by alanine scanning conducted across seven regions likely to contain residues required for intermolecular contact. Functionally distinct, neutralizing anti-gamma c mAbs were employed to define critical residues. One particular mAb, CP.B8, unique in its ability to inhibit IL-2-, IL-4-, IL-7-, and IL-15-induced proliferation and high affinity cytokine binding of normal T cells as an intact mAb and as a Fab fragment, localized critical residues to four noncontinuous stretches, namely residues in loops AB and EF of domain 1, in the interdomain segment, and in loop FG of domain 2. Notably, these residues form a contiguous patch on the gamma c chain surface in a three-dimensional structural model. These results provide functional evidence for the location of contact points on gamma c chain required for its association with multiple ligands.
Dependence of the 0.5 × (2e2/h) conductance plateau on the aspect ratio of InAs quantum point contacts with in-plane side gates (2017)

The observation of a 0.5 × (2e2/h) conductance plateau in asymmetrically biased quantum point contacts (QPCs) with in-plane side gates (SGs) has been attributed to the onset of spin-polarized current through these structures. For InAs QPCs with the same width but a longer channel length, there is roughly a fourfold increase in the range of common sweep voltage applied to the SGs over which the 0.5 × (2e2/h) plateau is observed when the QPC aspect ratio (ratio of length over the width of the narrow portion of the structure) is increased by a factor 3. Non-equilibrium Green's function simulations indicate that the increase in the size of the 0.5 × (2e2/h) plateau is due to an increased importance, over a larger range of common sweep voltage, of the effects of electron-electron interactions in QPC devices with a larger aspect ratio. The use of asymmetrically biased QPCs with in-plane SGs and large aspect ratio could therefore pave the way to build robust spin injectors and detectors for the successful implementation of spin field effect transistors.
N-Heterocyclic Carbenes, Part 33.[1] Combining Stable NHC and Chelating Pyridinyl-Alcoholato Ligands: A Ruthenium Catalyst for Applications at Elevated Temperatures (2002)

Ruthenium alkylidene complexes bearing one NHC ligand and one chelating pyridinyl alcoholate ligand 6 are generated by exchange of a phosphine ligand. Two synthetic approaches are presented: reacting the NHC phosphine complex 5 with the chelating ligand or reacting the pyridinyl-alcoholatophosphine complex 3 with a free NHC ligand. To evaluate the properties of 6 as metathesis catalysts, ROMP experiments with the strained olefin norbornene and the less strained cyclooctene were performed at different temperatures.
Autologous Cultured Melanocytes in Vitiligo Treatment Comparison of Two Techniques to Prepare the Recipient Site: Erbium-Doped Yttrium Aluminum Garnet Laser Versus Dermabrasion (2012)

In neonatal intensive care units, extravasation is one of the most common injuries occurring in infants as a complication of infusion therapy. These very preterm infants have immature skin which is easily damaged. They often require a longer duration of intravenous therapy, and obtaining intravenous access can be difficult. An invasive treatment should be avoided, whenever possible, particularly for very immature infants. In our Special Operative Unit for ulcers and difficult-to-heal wounds, University of Rome, we successfully treated a premature neonate, who experienced extravasation of hypertonic fluid, using dermal substitutes and products of regenerative medicine.
Magnetic Resonance Studies of the Bacteriorhodopsin Pump Cycle (2002)

Active transport requires the alternation of substrate uptake and release with a switch in the access of the substrate binding site to the two sides of the membrane. Both the transfer and switch aspects of the photocycle have been subjects of magnetic resonance studies in bacteriorhodopsin. The results for ion transfer indicate that the Schiff base of the chromophore is hydrogen bonded before, during, and after its deprotonation. This suggests that the initial complex counterion of the Schiff base decomposes in such a way that the Schiff base carries its immediate hydrogen-bonding partner with it as it rotates during the first half of the photocycle. If so, bacteriorhodopsin acts as an inward-directed hydroxide pump rather than as an outward-directed proton pump. The studies of the access switch explore both protein-based and chromophore-based mechanisms. Combined with evidence from functional studies of mutants and other forms of spectroscopy, the results suggest that maintaining access to the extracellular side of the protein after photoisomerization involves twisting of the chromophore and that the decisive switch in access to the cytoplasmic side results from relaxation of the chromophore when the constraints on the Schiff base are released by decomposition of the complex counterion.
Comprehensive Volumetric Microscopy with Fourier-Domain OCT (2006)

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 B. E. Bouma, "Comprehensive Volumetric Microscopy with Fourier-Domain OCT," in Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference and Photonic Applications Systems Technologies, Technical Digest (CD) (Optica Publishing Group, 2006), paper PWC3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Supplementary Materials and Methods from Asporin Restricts Mesenchymal Stromal Cell Differentiation, Alters the Tumor Microenvironment, and Drives Metastatic Progression (2023)

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Radiotherapy quality assurance of the IAEA-HypoX trial of the accelerated radiotherapy in the treatment of head and neck squamous cell carcinoma with or without the hypoxic radiosensitizer nimorazole (2015)

Radiotherapy quality assurance of the IAEA-HypoX trial of the accelerated radiotherapy in the treatment of head and neck squamous cell carcinoma with or without the hypoxic radiosensitizer nimorazole