gebhart/patrepeval huggingface dataset:
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs (2004)

Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their experimental generation remains difficult. Consequently, interolog mapping--the transfer of interaction annotation from one organism to another using comparative genomics--is of significant value. Here we quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. Using interaction information from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Helicobacter pylori, we find that protein-protein interactions can be transferred when a pair of proteins has a joint sequence identity >80% or a joint E-value <10(-70). (These "joint" quantities are the geometric means of the identities or E-values for the two pairs of interacting proteins.) We generalize our interolog analysis to protein-DNA binding, finding such interactions are conserved at specific thresholds between 30% and 60% sequence identity depending on the protein family. Furthermore, we introduce the concept of a "regulog"--a conserved regulatory relationship between proteins across different species. We map interologs and regulogs from yeast to a number of genomes with limited experimental annotation (e.g., Arabidopsis thaliana) and make these available through an online database at http://interolog.gersteinlab.org. Specifically, we are able to transfer approximately 90,000 potential protein-protein interactions to the worm. We test a number of these in two-hybrid experiments and are able to verify 45 overlaps, which we show to be statistically significant.
Characterization and one- and two-electron redox chemistry of 1,5-dicarba-1,5-dideazaisoalloxazines (flavins) (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization and one- and two-electron redox chemistry of 1,5-dicarba-1,5-dideazaisoalloxazines (flavins)Rebecca L. Chan and Thomas C. BruiceCite this: J. Am. Chem. Soc. 1978, 100, 23, 7375–7382Publication Date (Print):November 1, 1978Publication History Published online1 May 2002Published inissue 1 November 1978https://doi.org/10.1021/ja00491a039RIGHTS & PERMISSIONSArticle Views129Altmetric-Citations5LEARN 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 InReddit PDF (884 KB) Get e-Alertsclose Get e-Alerts
Target Ranges of Oxygen Saturation in Extremely Preterm Infants (2010)

A lower target range of oxygenation (85 to 89%), as compared with a higher range (91 to 95%), did not significantly decrease the composite outcome of severe retinopathy or death, but it resulted in an increase in mortality and a substantial decrease in severe retinopathy among survivors. The increase in mortality is a major concern, since a lower target range of oxygen saturation is increasingly being advocated to prevent retinopathy of prematurity. (ClinicalTrials.gov number, NCT00233324.)
Identification of a RIP1 Kinase Inhibitor Clinical Candidate (GSK3145095) for the Treatment of Pancreatic Cancer (2019)

RIP1 regulates cell death and inflammation and is believed to play an important role in contributing to a variety of human pathologies, including immune-mediated inflammatory diseases and cancer. While small-molecule inhibitors of RIP1 kinase have been advanced to the clinic for inflammatory diseases and CNS indications, RIP1 inhibitors for oncology indications have yet to be described. Herein we report on the discovery and profile of GSK3145095 (compound <b>6</b>). Compound <b>6</b> potently binds to RIP1 with exquisite kinase specificity and has excellent activity in blocking RIP1 kinase-dependent cellular responses. Highlighting its potential as a novel cancer therapy, the inhibitor was also able to promote a tumor suppressive T cell phenotype in pancreatic adenocarcinoma organ cultures. Compound <b>6</b> is currently in phase 1 clinical studies for pancreatic adenocarcinoma and other selected solid tumors.
Lying obliquely--a clinical sign of cognitive impairment: cross sectional observational study (2009)

Clinicians might suspect cognitive impairment in mobile older inpatients with neurological disorders who spontaneously position themselves obliquely when asked to lie on a bed.
Induction of cytotoxic T lymphocytes in vivo with protein antigen entrapped in membranous vehicles (1992)

Intravenous administration of APC such as splenocytes loaded with a soluble protein Ag has been shown to prime for an Ag-specific CTL response. It is thought that the APC directly presents loaded Ag in a MHC-restricted manner. However, it is demonstrated in this study that allogeneic splenocytes, MHC-free RBC, and even synthetic lipid vesicles (liposomes) after loading with OVA can elicit an OVA-specific and MHC-restricted CTL response. Biodistribution studies of these Ag-associated vehicles showed that the liver, spleen, and lung were the major organs responsible to scavenge these carriers, suggesting that the monocyte-macrophage system was involved in the Ag presentation for CTL. Depletion of macrophages by a specific macrophage killer, Cl2MDP, containing liposomes, abolished the CTL induction by immunization with OVA Ag carried by these vehicles except the induction by syngeneic splenocytes. Thus, the syngeneic splenocytes present Ag directly to the T cells, but other membranous vehicles carry the Ag to the host APC including macrophages, which then present it to the T cells. These results indicate that formulation of an Ag in membranous/colloidal vehicles may be a way to prime for a CTL response.
Assembly Guidance in Augmented Reality Environments Using a Virtual Interactive Tool (2005)

The application of augmented reality (AR) technology for assembly guidance is a novel approach in the traditional manufacturing domain. In this paper, we propose an AR approach for assembly guidance using a virtual interactive tool that is intuitive and easy to use. The virtual interactive tool, termed the Virtual Interaction Panel (VirIP), involves two tasks: the design of the VirIPs and the real-time tracking of an interaction pen using a Restricted Coulomb Energy (RCE) neural network. The VirIP includes virtual buttons, which have meaningful assembly information that can be activated by an interaction pen during the assembly process. A visual assembly tree structure (VATS) is used for information management and assembly instructions retrieval in this AR environment. VATS is a hierarchical tree structure that can be easily maintained via a visual interface. This paper describes a typical scenario for assembly guidance using VirIP and VATS. The main characteristic of the proposed AR system is the intuitive way in which an assembly operator can easily step through a pre-defined assembly plan/sequence without the need of any sensor schemes or markers attached on the assembly components.
Gap junction distribution in adult mammalian myocardium revealed by an anti-peptide antibody and laser scanning confocal microscopy (1991)

ABSTRACT A polyclonal antiserum, raised against a synthetic peptide matching part of the sequence of connexin43 (a rat cardiac gap-junctional protein), was used in combination with laser scanning confocal microscopy to investigate gap junction distribution in cardiac tissues from a range of mammalian species. Comparison of the localised punctate staining patterns obtained in ventricular tissue with the distribution of intercalated disks as viewed by conventional light microscopy and electron microscopy, and with the staining observed by standard light-microscope immunofluorescence using the same antiserum, demonstrated highly specific labelling of clearly resolved individual gap junctions. Laser scanning confocal microscopy of ventricular myocardium showed the immunostained gap junctions to be confined to well-defined intercalated disks bisecting the long axis of the muscle fibre, whereas in the atrial myocardium, gap junctions were commonly distributed widely over the lateral surfaces of the myocyte body. Rat atrial gap junctions were significantly larger (as measured by the longest axial lengths of fluorescent spots), and showed a narrower spread of sizes, than their counterparts in the ventricle. Ventricular myocardium from six mamalian species including man gave similar immunostaining patterns, indicating conservation both of the epitope(s) detected by the antiserum, and of the general organisation of the cell-to-cell pathways for electrical propagation, in the mammalian heart. Optical section series obtained by laser scanning confocal microscopy permitted the quantification and mapping of the three-dimensional distribution of gap junctions in ventricular intercalated disks with high clarity over substantial specimen depths. A consistent feature of gap junction organisation within disks of ventricular myocardium in all species studied was the presence of a conspicuous ring of large gap junctions around the periphery of the disk. Immunostained gap junctions lying within the interior zone delineated by the peripheral junctions generally occurred at lower numerical densities and were significantly smaller. In all species, less than 3 % of all immunolabelled gap junctions measured were &amp;gt;2 μm in maximal length, though a small proportion (0·06%? exceeded 4 μm. The numerical density of immunolabelled gap junctions in the disk was similar between species; however, within species there was a significant decrease in numerical density with increasing disk size. The new features of intercalated disk structure revealed in this study may have an important part to play in the intercellular communication and electrical propagation properties of the mammalian heart.
Functional and Edible Uses of Soy Protein Products (2008)

ABSTRACT: Consumers are becoming increasingly interested in healthful foods and are open to soy protein ingredients. Soybeans as food are very versatile and a rich source of essential nutrients. They are also an excellent source of good‐quality protein, comparable to other protein foods, and suitable for all ages. Adverse nutritional and other undesirable effects followed by the consumption of raw soybean meal have been attributed to the presence of endogenous inhibitors of digestive enzymes and lectins, as well as poor digestibility. To improve the nutritional quality of soy foods, inhibitors and lectins are generally inactivated by heat or eliminated by fractionation during food processing. Soybeans provide an alternative source of protein for people who are allergic to milk protein. Soy protein is highly digestible (92% to 100%) and contains all essential amino acids. Although relatively low in methionine, it is a good source of lysine. Soy‐protein products contain a high concentration of isoflavones, up to 1 g/kg. Increased acceptance of soy proteins is due to unmatched qualities like good functional properties in food applications, high nutritional quality, abundance, availability, and low cost. At present the various forms of soy proteins are primarily utilized for their functional effects rather than their nutritional properties. This article summarizes the integrated overview of the widely available, scattered information about the nutritional and functional uses of the soy proteins when applied in food systems and intends to present the most current knowledge with an interest to stimulate further research to optimize their beneficial effects.
Using Mixed Amine Solutions for Gas Sweetening (2014)

In the past few years, mixed amine solvents for the removal of acid gases have received increased attention. In most cases, the mixtures contain MDEA as the base amine with the addition of one or two more reactive amines such as MEA or DEA. These amine mixtures have been called a variety of names including formulated amines and MDEA based amines.
The Anti-inflammatory Effects of Selenium Are Mediated through 15-Deoxy-Δ12,14-prostaglandin J2 in Macrophages (2007)

Selenium is an essential micronutrient that suppresses the redox-sensitive transcription factor NF-kappaB-dependent pro-inflammatory gene expression. To understand the molecular mechanisms underlying the anti-inflammatory property of selenium, we examined the activity of a key kinase of the NF-kappaB cascade, IkappaB-kinase beta (IKKbeta) subunit, as a function of cellular selenium status in murine primary bone marrow-derived macrophages and RAW264.7 macrophage-like cell line. In vitro kinase assays revealed that selenium supplementation decreased the activity of IKKbeta in lipopolysaccharide (LPS)-treated macrophages. Stimulation by LPS of selenium-supplemented macrophages resulted in a time-dependent increase in 15-deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2) formation, an endogenous inhibitor of IKKbeta activity. Further analysis revealed that inhibition of IKKbeta activity in selenium-supplemented cells correlated with the Michael addition product of 15d-PGJ2 with Cys-179 of IKKbeta, while the formation of such an adduct was significantly decreased in the selenium-deficient macrophages. In addition, anti-inflammatory activities of selenium were also mediated by the 15d-PGJ2-dependent activation of the peroxisome proliferator-activated nuclear receptor-gamma in macrophages. Experiments using specific cyclooxygenase (COX) inhibitors and genetic knockdown approaches indicated that COX-1, and not the COX-2 pathway, was responsible for the increased synthesis of 15d-PGJ2 in selenium-supplemented macrophages. Taken together, our results suggest that selenium supplementation increases the production of 15d-PGJ2 as an adaptive response to protect cells against oxidative stress-induced pro-inflammatory gene expression. More specifically, modification of protein thiols by 15d-PGJ2 represents a previously undescribed code for redox regulation of gene expression by selenium.
Corpus Variation and Parser Performance (2001)

Most work in statistical parsing has focused on a single corpus: the Wall Street Journal portion of the Penn Treebank. While this has allowed for quantitative comparison of parsing techniques, it has left open the question of how other types of text might a#ect parser performance, and how portable parsing models are across corpora. We examine these questions by comparing results for the Brown and WSJ corpora, and also consider which parts of the parser&amp;apos;s probability model are particularly tuned to the corpus on which it was trained. This leads us to a technique for pruning parameters to reduce the size of the parsing model. 1
Optimization of a Series of Bivalent Triazolopyridazine Based Bromodomain and Extraterminal Inhibitors: The Discovery of (3<i>R</i>)-4-[2-[4-[1-(3-Methoxy-[1,2,4]triazolo[4,3-<i>b</i>]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one (AZD5153) (2016)

Here we report the discovery and optimization of a series of bivalent bromodomain and extraterminal inhibitors. Starting with the observation of BRD4 activity of compounds from a previous program, the compounds were optimized for BRD4 potency and physical properties. The optimized compound from this campaign exhibited excellent pharmacokinetic profile and exhibited high potency in vitro and in vivo effecting c-Myc downregulation and tumor growth inhibition in xenograft studies. This compound was selected as the development candidate, AZD5153. The series showed enhanced potency as a result of bivalent binding and a clear correlation between BRD4 activity and cellular potency.
Diagnostic Criteria for Parkinson Disease (1999)

The clinical diagnosis of Parkinson disease (PD) is based on the identification of some combination of the cardinal motor signs of bradykinesia, rigidity, tremor, and postural instability, but few attempts have been made to develop explicit diagnostic criteria. We propose a clinical diagnostic classification based on a comprehensive review of the literature regarding the sensitivity and specificity of the characteristic clinical features of PD. Three levels of diagnostic confidence are differentiated: Definite, Probable, and Possible. The diagnoses of Possible and Probable PD are based on clinical criteria alone. Neuropathologic confirmation is required for the diagnosis of Definite PD in patients with the clinical diagnosis of Possible or Probable PD. Criteria for histopathologic confirmation of PD are also presented.
Biomaterials by freeze casting (2010)

The functional requirements for synthetic tissue substitutes appear deceptively simple: they should provide a porous matrix with interconnecting porosity and surface properties that promote rapid tissue ingrowth; at the same time, they should possess sufficient stiffness, strength and toughness to prevent crushing under physiological loads until full integration and healing are reached. Despite extensive efforts and first encouraging results, current biomaterials for tissue regeneration tend to suffer common limitations: insufficient tissue-material interaction and an inherent lack of strength and toughness associated with porosity. The challenge persists to synthesize materials that mimic both structure and mechanical performance of the natural tissue and permit strong tissue-implant interfaces to be formed. In the case of bone substitute materials, for example, the goal is to engineer high-performance composites with effective properties that, similar to natural mineralized tissue, exceed by orders of magnitude the properties of its constituents. It is still difficult with current technology to emulate in synthetic biomaterials multi-level hierarchical composite structures that are thought to be the origin of the observed mechanical property amplification in biological materials. Freeze casting permits to manufacture such complex, hybrid materials through excellent control of structural and mechanical properties. As a processing technique for the manufacture of biomaterials, freeze casting therefore has great promise.
Indoor Geolocation Distance Error Modeling using UWB Channel Measurements (2006)

In this paper we introduce a model for the distance error measured from the estimated time of arrival (TOA) of the direct path (DP) in a typical multipath indoor environment. We use the results of our ultra-wideband (UWB) measurement database in a sample office environment. To begin modeling, first we separate the causes of the error into multipath and undetected direct path (UDP), and then we model them separately considering the variation of bandwidth of the system. We show that the behavior of the distance error consists of two parts; one that is from multipath, and the other one from UDP. Both errors can be modeled as Gaussian, so the final distance error is a mixture of two Gaussian distributions. We also related the statistics of the distributions to the bandwidth of the system.
Magnetic shielding of the channel walls in a Hall plasma accelerator (2011)

In a qualification life test of a Hall thruster it was found that the erosion of the acceleration channel practically stopped after ∼5600 h. Numerical simulations using a two-dimensional axisymmetric plasma solver with a magnetic field-aligned mesh reveal that when the channel receded from its early-in-life to its steady-state configuration the following changes occurred near the wall: (1) reduction of the electric field parallel to the wall that prohibited ions from acquiring significant impact kinetic energy before entering the sheath, (2) reduction of the potential fall in the sheath that further diminished the total energy ions gained before striking the material, and (3) reduction of the ion number density that decreased the flux of ions to the wall. All these changes, found to have been induced by the magnetic field, constituted collectively an effective shielding of the walls from any significant ion bombardment. Thus, we term this process in Hall thrusters “magnetic shielding.”
Endovascular packing of carotid bifurcation aneurysm with polyester fiber-coated platinum coils in a rabbit model. (1993)

Endovascular packing of human bifurcation aneurysms with current commercially available polyester fiber-coated platinum coils may not result in complete obliteration of the aneurysm with reendothelialization occurring across the aneurysm neck.
Production of hydroxy fatty acids in the seeds of <i>Arabidopsis thaliana</i> (2000)

Seed-specific expression in Arabidopsis thaliana of oleate hydroxylase enzymes from castor bean and Lesquerella fendleri resulted in the accumulation of hydroxy fatty acids in the seed oil. By using various Arabidopsis mutant lines it was shown that the endoplasmic reticulum (ER) n-3 desaturase (FAD3) and the FAE1 condensing enzyme are involved in the synthesis of polyunsaturated and very-long-chain hydroxy fatty acids, respectively. In Arabidopsis plants with an active ER Delta12-oleate desaturase the presence of hydroxy fatty acids corresponded to an increase in the levels of 18:1 and a decrease in 18:2 levels. Expression in yeast indicates that the castor hydroxylase also has a low level of desaturase activity.
Oxygen Permeation Properties of Co-Free Perovskite-Type Oxide Membranes Based on BaFe[sub 1−y]Zr[sub y]O[sub 3−δ] (2009)

Partially Zr-substituted membranes were developed as a Co-free oxygen permeable membrane. In order to stabilize the cubic perovskite structure, Fe sites in were partially substituted with . In the substitution range of , the cubic perovskite structure was stabilized even at room temperature. Among the membranes prepared, a material showed the highest oxygen permeation flux of (standard temperature pressure) at under an air/He gradient. The oxygen permeation flux was higher than that of partially Ce-substituted membranes reported previously. From the results obtained by chemical and scanning electron microscope analyses, it appears that the oxygen permeability for membranes was well correlated with the amount of oxygen defects in the lattice as well as the grain size. In addition, the oxygen permeation flux of the membrane was significantly increased after decreasing the thickness of the membrane from . For thin membranes , the thickness dependence of the oxygen permeability deviated from the Wagner equation, suggesting that the oxygen permeation of is controlled by not only bulk diffusion of oxide ions but also their surface reactions.
Yield-oriented computer-aided defect diagnosis (1995)

Any good yield-oriented defect strategy must have two main components-(a) the ability to perform rapid defect diagnosis for yield learning, and (b) the ability to efficiently extract defect parameters from the manufacturing line. In this work, an inductive fault analysis (IFA)-based defect methodology is investigated to see if it meets the above requirements. Using an SRAM test vehicle as an example, the research analyzes whether computer-generated mappings between defect types and tester fail data can provide sufficient resolution for both, defect diagnosis and defect parameter characterization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>