gebhart/patrepeval huggingface dataset:
Runx2 Regulates Endochondral Ossification Through Control of Chondrocyte Proliferation and Differentiation (2014)

Synthesis of cartilage by chondrocytes is an obligatory step for endochondral ossification. Global deletion of the Runx2 gene results in complete failure of the ossification process, but the underlying cellular and molecular mechanisms are not fully known. Here, we elucidated Runx2 regulatory control distinctive to chondrocyte and cartilage tissue by generating Runx2 exon 8 floxed mice. Deletion of Runx2 gene in chondrocytes caused failure of endochondral ossification and lethality at birth. The limbs of Runx2(ΔE8/ΔE8) mice were devoid of mature chondrocytes, vasculature, and marrow. We demonstrate that the C-terminus of Runx2 drives its biological activity. Importantly, nuclear import and DNA binding functions of Runx2 are insufficient for chondrogenesis. Molecular studies revealed that despite normal levels of Sox9 and PTHrP, chondrocyte differentiation and cartilage growth are disrupted in Runx2(ΔE8/ΔE8) mice. Loss of Runx2 in chondrocytes also impaired osteoprotegerin-receptor activator of NF-κB ligand (OPG-RANKL) signaling and chondroclast development. Dwarfism observed in Runx2 mutants was associated with the near absence of proliferative zone in the growth plates. Finally, we show Runx2 directly regulates a unique set of cell cycle genes, Gpr132, Sfn, c-Myb, and Cyclin A1, to control proliferative capacity of chondrocyte. Thus, Runx2 is obligatory for both proliferation and differentiation of chondrocytes.
Quantifying Link Stability in Ad Hoc Wireless Networks Subject to Ornstein-Uhlenbeck Mobility (2019)

The performance of mobile ad hoc networks in general and that of the routing algorithm, in particular, can be heavily affected by the intrinsic dynamic nature of the underlying topology. In this paper, we build a new analytical/numerical framework that characterizes nodes' mobility and the evolution of links between them. This formulation is based on a stationary Markov chain representation of link connectivity. The existence of a link between two nodes depends on their distance, which is governed by the mobility model. In our analysis, nodes move randomly according to an Ornstein-Uhlenbeck process using one tuning parameter to obtain different levels of randomness in the mobility pattern. Finally, we propose an entropy-rate-based metric that quantifies link uncertainty and evaluates its stability. Numerical results show that the proposed approach can accurately reflect the random mobility in the network and fully captures the link dynamics. It may thus be considered a valuable performance metric for the evaluation of the link stability and connectivity in these networks.
Death vs. Data Science: Predicting End of Life (2018)

Death is an inevitable part of life and while it cannot be delayed indefinitely it is possible to predict with some certainty when the health of a person is going to deteriorate. In this paper, we predict risk of mortality for patients from two large hospital systems in the Pacific Northwest. Using medical claims and electronic medical records (EMR) data we greatly improve prediction for risk of mortality and explore machine learning models with explanations for end of life predictions. The insights that are derived from the predictions can then be used to improve the quality of patient care towards the end of life.
Betaomics: a combined proteome and transcriptome profiling approach to characterize seed germination and vigour in sugarbeet seeds. (2007)

Producing high-quality seed lots, in terms of germinability, is a major concern of seed companies. The availability of molecular and/or biochemical markers of seed vigour would allow seed producers to better characterize their germplasm and to better design invigoration seed treatments such as priming. The aim of this work is to use global expression profiling methods (i.e. transcriptomics and proteomics) to find such markers for sugarbeet (Beta vulgaris L.) seeds. This combined approach allows, for the first time, the comparison of proteomic and transcriptomic data for sugarbeet seed, and the characterization of the molecular and biochemical mechanisms underlying seed vigour and germination.
Water-soluble noncovalent adducts of the heterometallic copper subgroup complexes and human serum albumin with remarkable luminescent properties (2013)

Novel water-soluble noncovalent adducts of the heterometallic copper subgroup complexes and human serum albumin (HSA) display strong phosphorescence, internalize into HeLa cells and can be used in time-resolved fluorescent imaging.
A Systematic Review of Prognosis and Therapy of Anal Malignant Melanoma: A Plea for More Precise Reporting of Location and Thickness (2012)

Anal malignant melanoma (AMM) is a rare tumor with poor prognosis. We performed a systematic review of reports on wide local excision (WLE) and abdominoperineal resection (APR) for treatment of AMM in an attempt to define a precise set of reporting measures for outcomes of treatment of AMM. A systematic review of the literature was performed. Demographic data, surgical treatment, pathology, and survival rates were recorded. We compared WLE versus APR in terms of the overall survival time, the disease-free survival, and overall survival at 60 months. Twenty-one reports met the inclusion criteria. Notably, of these, 10 did not specify thickness of the primary melanoma. Interestingly, groin lymph node status was described in 19 of 21 reports, whereas location was specified in only 12 papers and thickness (depth in mm) in only 11. The median survival times of patients undergoing WLE (n = 324) and those undergoing APR (n = 369) are comparable (20 and 21 months, respectively). The mean median survival at 60 months was 15 per cent for WLE and 14 per cent for APR. The mean disease-free survival at 60 months was found to be 10 per cent for WLE and 6 per cent for APR. Patient selection for such a rare neoplasm yields very similar outcomes for both conservative and radical treatments. There is a wide variation in the reporting of both clinical and treatment outcomes. More uniformity of reporting of pathologic features and node status is essential before rational assessment of results can be done.
Time-Resolved Resonance Raman Spectroscopy: Exploring Reactive Intermediates (2011)

The study of reaction mechanisms involves systematic investigations of the correlation between structure, reactivity, and time. The challenge is to be able to observe the chemical changes undergone by reactants as they change into products via one or several intermediates such as electronic excited states (singlet and triplet), radicals, radical ions, carbocations, carbanions, carbenes, nitrenes, nitrinium ions, etc. The vast array of intermediates and timescales means there is no single "do-it-all" technique. The simultaneous advances in contemporary time-resolved Raman spectroscopic techniques and computational methods have done much towards visualizing molecular fingerprint snapshots of the reactive intermediates in the microsecond to femtosecond time domain. Raman spectroscopy and its sensitive counterpart resonance Raman spectroscopy have been well proven as means for determining molecular structure, chemical bonding, reactivity, and dynamics of short-lived intermediates in solution phase and are advantageous in comparison to commonly used time-resolved absorption and emission spectroscopy. Today time-resolved Raman spectroscopy is a mature technique; its development owes much to the advent of pulsed tunable lasers, highly efficient spectrometers, and high speed, highly sensitive multichannel detectors able to collect a complete spectrum. This review article will provide a brief chronological development of the experimental setup and demonstrate how experimentalists have conquered numerous challenges to obtain background-free (removing fluorescence), intense, and highly spectrally resolved Raman spectra in the nanosecond to microsecond (ns-μs) and picosecond (ps) time domains and, perhaps surprisingly, laid the foundations for new techniques such as spatially offset Raman spectroscopy.
Modification Site Localization Scoring: Strategies and Performance (2012)

Using enrichment strategies many research groups are routinely producing large data sets of post-translationally modified peptides for proteomic analysis using tandem mass spectrometry. Although search engines are relatively effective at identifying these peptides with a defined measure of reliability, their localization of site/s of modification is often arbitrary and unreliable. The field continues to be in need of a widely accepted metric for false localization rate that accurately describes the certainty of site localization in published data sets and allows for consistent measurement of differences in performance of emerging scoring algorithms. In this article are discussed the main strategies currently used by software for modification site localization and ways of assessing the performance of these different tools. Methods for representing ambiguity are reviewed and a discussion of how the approaches transfer to different data types and modifications is presented.
A Diastereoselective Intermolecular Heck Reaction of 1,3-Dioxepins (2007)

A highly diastereoselective intermolecular Heck reaction of 1,3-dioxepins is reported. Substitution at both the 2- and 4-positions of the dioxepin directs the Pd coordination and subsequent olefin insertion to provide the trans-disubstituted adduct in good yield and high diastereoselectivity. Chemoselective Heck reaction occurs at the dioxepin alkene in the presence of other olefinic functional groups. A labeling study has been conducted which suggests that the reaction is under kinetic control.
Redundancy optimization for clock-free nanowire crossbar architecture (2007)

In this paper a method is being proposed to find the optimal dimension of Programmable Gate Macro Block (PGMB) in clock-free nanowire crossbar architecture. A PGMB is a nanowire crossbar matrix with discrete number of rows and columns on which the NCL (Null Convention Logic) gates can be programmed. This method uses inherent redundancy to route through defective crosspoints. A 6 X 10 defect-free crossbar can be used to program any of the 27 threshold gates. Due to imperfections and variations in nanoscale manufacturing process, high defect densities are anticipated. Thus, such defects should be located when tested and the logic has to be rerouted around them to maintain proper functionality. This paper discusses this problem and tried to find an optimal solution through simulations. In the final submission, more effective logic mapping techniques will be proposed and validated.
Room‐Temperature Ultrafast Synthesis of NiCo‐Layered Double Hydroxide as an Excellent Electrocatalyst for Water Oxidation (2019)

Abstract Designing and synthesis of efficient, highly active with longer stability and earth abundant catalysts for the oxygen evolution reaction (OER) is urgent need for the electrochemical production of fuels. In this aspect, herein, facile room‐temperature electrodeposited NiCo layered double hydroxide (NiCo‐LDH) is reported as a highly active and stable electrocatalyst for OER in aqueous solution. In alkaline media, as obtained NiCo LDH shows superior electrocatalytic activity towards water oxidation with overpotential of 270 mV at 10 mA/cm 2 with low Tafel slope of 61 mV/dec. The 3D NiCo‐LDH network exhibits excellent structural stability for 36 hours in alkaline media. After testing for stability test, the NiCo‐LDH catalyst maintains its hierarchical 3D network with insignificant degradation in the catalytic activity.
An Algorithmic Approach to Managing Parotid Duct Injury Following Buccal Fat Pad Removal (2022)

Abstract The principles of achieving an aesthetically pleasing and harmonious facial appearance are influenced by our evolving understanding of the three-dimensional topography of the face coupled with novel approaches to midface volumization and contouring. In parallel with the evolving landscape of facial aesthetic surgery, an increasing number of publications have emerged focusing on the role of intraoral buccal fat pad removal (BFPR) for the purposes of aesthetic midface contouring. The authors sought to emphasize an underreported and potentially preventable and untoward complication involving iatrogenic parotid duct injury following BFPR. The purpose of this publication is 3-fold: (1) to review the relevant anatomy and literature on intraoral BFPR, (2) to present a case example of this complication, and (3) to discuss treatment options as part of a proposed management algorithm. The authors detail the surgical indications for performing BFPR and review the relevant anatomic considerations. Complication prevention strategies are outlined, and details regarding avoidance of parotid duct injury are reviewed. The diagnostic criteria and clinical presentation of parotid duct injuries following BFPR are comprehensively outlined. The authors present a clinically actionable algorithm for managing a suspected or diagnosed parotid duct injury following BFPR. A clinical case example is discussed to highlight this complication, the diagnostic criteria, and the systematic and algorithmic approach to management. Intraoral BFPR is an incredibly valuable and powerful procedure that can improve facial contour in patients with buccal lipodystrophy or buccal fat pad pseudoherniation. The authors propose a proper diagnostic approach and treatment algorithm to manage this untoward complication. Level of Evidence: 5
Design and Performance of the X-ray polarimeter X-Calibur (2014)

X-ray polarimetry promises to give qualitatively new information about high-energy astrophysical sources, such as binary black hole systems, micro-quasars, active galactic nuclei, neutron stars, and gamma-ray bursts. We designed, built and tested a X-ray polarimeter, X-Calibur, to be used in the focal plane of the balloon-borne InFOCuS grazing incidence X-ray telescope. X-Calibur combines a low-Z scatterer with a CZT detector assembly to measure the polarization of 20-80keV X-rays making use of the fact that polarized photons scatter preferentially perpendicular to the electric field orientation. X-Calibur achieves a high detection efficiency of ~80%. The X-Calibur detector assembly is completed, tested, and fully calibrated. The response to a polarized X-ray beam was measured successfully at the Cornell High Energy Synchrotron Source. This paper describes the design, calibration and performance of the X-Calibur polarimeter. In principle, a similar space-borne scattering polarimeter could operate over the broader 2-100keV energy band.
Hey network, can you understand me? (2017)

In this paper, we introduce Natural Language Processing to network management by leveraging the capabilities of Natural Language Processing tools, such as speech recognition and text parsing, to extract useful information to build network tasks. We propose an intermediate network-agnostic layer that acts as the medium between natural language input (spoken or written) and different network implementations. We have leveraged the programmability that Software Defined Networks (SDN) offers to build a prototype tool that takes natural language text as an input and uses it to build abstract tasks. Such tasks are then passed to a network controller to be performed in real time. To our knowledge, this is the first work that provides such interface between network users (in the form of natural language) and different network systems.
Melanopsin Mediates Retrograde Visual Signaling in the Retina (2012)

The canonical flow of visual signals proceeds from outer to inner retina (photoreceptors → bipolar cells → ganglion cells). However, melanopsin-expressing ganglion cells are photosensitive and functional sustained light signaling to retinal dopaminergic interneurons persists in the absence of rods and cones. Here we show that the sustained-type light response of retinal dopamine neurons requires melanopsin and that the response is mediated by AMPA-type glutamate receptors, defining a retrograde retinal visual signaling pathway that fully reverses the usual flow of light signals in retinal circuits.
Plasma Polymerization Coating of DT-Filled Glass Shells for Laser Fusion Targets (1979)

As a part of our national program to fulfill our growing energy needs, considerable effort is being made to achieve controlled fusion by using laser beams to heat and compress deuterium/tritium-containing (DT) targets. One of the requirements for the development of laser fusion as a viable energy source is the ability to produce spherical targets for the laser-driven implosion. One practical target design consists of a multilayer composite shell. A thin inner glass shell contains the pressurized DT gas. An outer plastic coating absorbs the laser energy and ablatively compresses the glass shell and the DT fuel. The outer plastic coating material must satisfy a number of special requirements. It must have a density near that of the glass shell and be of low atomic number. It should be smooth and uniform in thickness to prevent Rayleigh-Taylor instabilities from disrupting the spherical symmetry of the fuel during compression. Many technologies
Segmented photorefractive waveguides in LiNbO 3 :Fe (1998)

We propose what is, to our knowledge, a novel technique for fabricating a segmented waveguide by optical irradiation in a photorefractive LiNbO3:Fe crystal. The waveguide consists of many localized high-refractive-index regions that are fabricated by illumination of a focused laser beam. We fabricate straight, curved, and Y-branch waveguides. In the straight waveguides the transmitted power of a guided beam as a function of the period of segmentation and the dark decay time are measured. The tolerance for fabrication errors is also investigated both experimentally and numerically. The fabricated waveguide can be optically modified. We demonstrate that a curved structure can be transformed into a Y-branch structure.
Evaluation of skin spectral features for biometrie (2017)

In the recent years, multispectral imaging has been successfully used in various biometric authentication applications. However, in most cases, the frames of multispectral images are consolidated simply by using data fusion techniques rather than contributing directly to the recognition process. This paper evaluates the viability of face skin spectrum for biometric authentication by comparing inter- and intra-user spectral distance. The experiment of this work is conducted using the hyperspectral face database of the Stanford Center for Image Systems Engineering (SCIEN). Obtained results demonstrate that, even if not sufficient by itself, human skin spectra contain useful information to the person authentications, and it potentially allows to improve the accuracy and ergonomics performances of biometric systems.
Inhibition of hypoxia-inducible factor via upregulation of von Hippel-Lindau protein induces “angiogenic switch off” in a hepatoma mouse model (2015)

"Angiogenic switch off" is one of the ideal therapeutic concepts in the treatment of cancer. However, the specific molecules which can induce "angiogenic switch off" in tumor have not been identified yet. In this study, we focused on von Hippel-Lindau protein (pVHL) in hepatocellular carcinoma (HCC) and investigated the effects of sulfoquinovosyl-acylpropanediol (SQAP), a novel synthetic sulfoglycolipid, for HCC. We examined mutation ratio of VHL gene in HCC using 30 HCC samples and we treated the HCC-implanted mice with SQAP. Thirty clinical samples showed no VHL genetic mutation in HCC. SQAP significantly inhibited tumor growth by inhibiting angiogenesis in a hepatoma mouse model. SQAP induced tumor "angiogenic switch off" by decreasing hypoxia-inducible factor (HIF)-1, 2α protein via pVHL upregulation. pVHL upregulation decreased HIFα protein levels through different multiple mechanisms: (i) increasing pVHL-dependent HIFα protein degradation; (ii) decreasing HIFα synthesis with decrease of NF-κB expression; and (iii) decrease of tumor hypoxia by vascular normalization. We confirmed these antitumor effects of SQAP by the loss-of-function experiments. We found that SQAP directly bound to and inhibited transglutaminase 2. This study provides evidence that upregulation of tumor pVHL is a promising target, which can induce "angiogenic switch off" in HCC.
ChemInform Abstract: 14‐O‐Benzoyl‐8‐ethoxybikhaconine and 14‐O‐Benzoyl‐8‐methoxybikhaconine. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Structure and genetic basis of <i>Yersinia similis</i> serotype O:9 O-specific polysaccharide (2013)

The O-polysaccharide (OPS, O-Ag) cap of LPS is a major virulence factor of Yersinia species and also serves as a receptor for the binding of lytic bacteriophage φR1-37. Currently, the OPS-based serotyping scheme for the Yersinia pseudotuberculosis complex includes 21 known O-serotypes that follow three distinct lineages: Y. pseudotuberculosis sensu stricto, Y. similis and the Korean group of strains. Elucidation of the Y. pseudotuberculosis complex OPS structures and characterization of the OPS genetics (altogether 18 O-serotypes studied thus far) allows a better understanding of the relationships among the various O serotypes and will facilitate the analysis of the evolutionary processes giving rise to new serotypes. Here we present the characterization of the OPS structure and gene cluster of Y. similis O:9. Bacteriophage φR1-37, which uses the Y. similis O:9 OPS as a receptor, also infects a number of Y. enterocolitica serotypes, including O:3, O:5,27, O:9 and O:50. The Y. similis O:9 OPS structure resembled none of the receptor structures of the Y. enterocolitica strains, suggesting that φR1-37 can recognize several surface receptors, thus promoting broad host specificity.
Methyl esters (biodiesel) from <i>Melanolepis multiglandulosa</i> (alim) seed oil and their properties (2017)

Sufficient supply of feedstock oils is a major issue facing biodiesel production. In this work, methyl esters, also known as biodiesel, of the seed oil of Melanolepis multiglandulosa, a member of the Euphorbiaceae family, were prepared using standard conditions, with sodium methoxide as catalyst, and characterized regarding their fuel properties in relation to biodiesel standards. Melanolepis multiglandulosa methyl esters generally meet the requirements of biodiesel standards, with cold flow (cloud point of 5°C) likely being the major technical issue to resolve.
Dinoflagellida (Phylum Sarcomastigophora). (1995)

Irrespective of the initiating stimuli, neurodegenerative disorders including multiple sclerosis (MS), Alzheimer's disease, Parkinson's disease and stroke share many characteristics of inflammation and autoimmunity. This review summarizes and correlates the information relating to the role of cytokines and chemokines in initiating and propagating the inflammatory/immune response in these pathologies. For example, in MS there is a continuous realignment in the inflammatory and immune response. However, due to the redundancy in the cytokine/chemokine response, it is extremely unlikely that any one therapy will be successful in treating neurodegenerative diseases. This review attempts to highlight specific targets for therapeutic intervention.