• The problems of protein fold recognition and remote homology detection have recently attracted a great deal of interest as they represent challenging multi-feature multi-class problems for which modern pattern recognition methods achieve only modest levels of performance. (videolectures.net)
  • Furthermore, we examine the performance of our methodology on the SCOP 1.53 benchmark data-set that simulates remote homology detection and examine the combination of various state-of-the-art string kernels that have recently been proposed. (videolectures.net)
  • Cara Therapeutics, Inc. (Nasdaq: CARA), a commercial-stage biopharmaceutical company leading a new treatment paradigm to improve the lives of patients suffering from pruritus, today announced financial results and operational highlights for the second quarter ended June 30, 2023. (biospace.com)
  • ET to report second quarter 2023 financial results and provide a corporate update. (biospace.com)
  • The learned representation space has a multi-scale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. (biorxiv.org)
  • The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family. (plos.org)
  • The structural models of the IF proteins were generated by homology modelling. (uni-duesseldorf.de)
  • Moreover, mTORC1 also phosphorylates eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1), which will result in the separation of 4EBP1 from eukaryotic translation initiation factor 4E (eIF4E) for the translation of viral proteins in shrimp. (genscript.com)
  • PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)
  • The results show that nonnative proteins are more structured and less solvent exposed than commonly believed. (lu.se)
  • Its main tool is persistent homology, which is based on other homology theory, usually simplicial homology. (helsinki.fi)
  • Simplicial homology applies to finite data in real space, and thus it is mainly used in applications. (helsinki.fi)
  • We propose the Shapley homology framework, which provides a quantitative metric for the influence of a sample of the homology of a simplicial complex. (mit.edu)
  • These days, molecular evolution studies, which use DNA sequence analysis as data, are popular. (wikipedia.org)
  • Results: The best performance which we report on the SCOP PDB-40D benchmark data-set is a 70% accuracy by combining all the available feature groups from global protein characteristics but also including sequence-alignment features. (videolectures.net)
  • IL-10 shares over 80% sequence homology with the Epstein-Barr virus protein BCRFI. (biolegend.com)
  • In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. (biorxiv.org)
  • In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
  • Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)
  • Many aspects of data integration presented at the Alliance require a common set of orthology relationships among genes for the organisms represented, including human. (yeastgenome.org)
  • Homology candidate relations are integrated into a global network and groups of homologous genes are extracted by applying a community detection algorithm. (biomedcentral.com)
  • Homologous genes can be distinguished into paralogous, when homology occurs within the same genome, or orthologous, when homology occurs between different genomes. (biomedcentral.com)
  • Advantages of Zebrafish: The zebrafish has a sequenced genome and 80% homology of genes associated with human disease. (cdc.gov)
  • As a result, the linkage between the autoimmune experimental arthritis phenotype and the genomic region, that is, the quantitative trait locus, can cover several hundred genes. (medscape.com)
  • The purpose of this work was to facilitate the search for candidate genes in such regions by introducing a web tool called Candidate Gene Capture (CGC) that takes advantage of free text data on gene function. (medscape.com)
  • To facilitate this kind of data mining, we have created a tool, the Candidate Gene Capture (CGC) application, that makes keyword-based searches on textual information for genes situated within selected human chromosomal intervals that are homologous to a given rat QTL. (medscape.com)
  • Sequencing at that time directly resulted from the need to understand an experimentally determined phenotype or biochemical activity. (plos.org)
  • The CGC tool was developed by combining genomic regions in the rat, associated with the autoimmune experimental arthritis phenotype, with rat/human gene homology data, and with descriptions of phenotypic gene effects and selected keywords. (medscape.com)
  • Homology calls are sourced from the Alliance of Genome Resources . (yeastgenome.org)
  • Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. (biomedcentral.com)
  • A challenge on this field is that of designing fast and adaptive similarity measures in order to find a suitable pan-genome structure of homology relations. (biomedcentral.com)
  • Individual BLASTN query jobs each involved a data set of 40,000 chimpanzee whole genome shotgun sequences (WGSS) obtained from the National Center for Biotechnology (NCBI) and queried against four different human genome assemblies (GRCH37, GRCH36, Alternate SNP Assembly, and the Celera Assembly). (icr.org)
  • The chimp sequences were subsequently implicated by personal correspondence with NCBI staff and supporting data from this study to be pre-screened for some level of homology to the human genome. (icr.org)
  • Information about RA and related genome data is available in several different forms, from raw data to descriptive text. (medscape.com)
  • Thus, human considerations bring an added value to genome data, which makes textual description an important source for investigating gene function. (medscape.com)
  • He has contributed significantly to the state-of-the-art by frequently presenting novel ideas, methods and results and have pioneered several important proof-of-concepts relevant for the project, including the conceptualization of DNA, RNA and protein variation to Variation Ontology (Vihinen, Genome Res . (lu.se)
  • Homology Medicines, Inc. (Nasdaq: FIXX), a genetic medicines company, announced today six presentations supporting its gene editing, gene therapy and GTx-mAb programs at the American Society of Gene & Cell Therapy (ASGCT) 26th Annual Meeting. (biospace.com)
  • Homology Medicines, Inc. (Nasdaq: FIXX), a genetic medicines company, announced today the presentation of preclinical data that supports the targeted, prophylactic immunosuppression regimen in the ongoing pheEDIT gene editing clinical trial in adults with phenylketonuria (PKU) and juMPStart gene therapy trial in adults with Hunter syndrome (MPS II). (advfn.com)
  • The topological data analysis studies the shape of a space at multiple scales. (helsinki.fi)
  • Given a henselian pair (R,I) of commutative rings, we show that the relative K-theory and relative topological cyclic homology with finite coefficients are identified via the cyclotomic trace K→TC. (ku.dk)
  • We deduce that the cyclotomic trace is an equivalence in large degrees between p-adic K-theory and topological cyclic homology for a large class of p-adic rings. (ku.dk)
  • Our proposed framework consists of two main parts: homology analysis, where we compute the Betti number of the target topological space, and Shapley value calculation, where we decompose the topological features of a complex built from data points to individual points. (mit.edu)
  • Being a spherical 3-manifold, it is the only homology 3-sphere (besides the 3-sphere itself) with a finite fundamental group. (wikipedia.org)
  • Empirical studies show that when the zero-dimensional Shapley homology is used on neighboring graphs, samples with higher influence scores have a greater impact on the accuracy of neural networks that determine graph connectivity and on several regular grammars whose higher entropy values imply greater difficulty in being learned. (mit.edu)
  • Empirical data support seafloor spreading and catastrop. (icr.org)
  • Nevertheless, while Q44R led to recovery of viruses that maintained the mutation, Q44D resulted in selection of infective viruses with substitution D44E with acidic charge but with structural features similar to those of the parental virus, suggesting that Q44 is involved in functions other than 3A dimerization. (asm.org)
  • The results imply that, in addition to PAL, other lignin-specific enzymes and/or tissue structural changes may have more significant roles in tissue toughening of broccoli branchlets. (scialert.net)
  • and probable cases of primary structural homology. (fapesp.br)
  • A rational homology sphere is defined similarly but using homology with rational coefficients. (wikipedia.org)
  • As one ingredient of the proofs of the above results we generalize computations of the homotopical invariants of contact structures to contact surgeries with more general surgery coefficients which might be of independent interest. (hu-berlin.de)
  • For a certain D. melanogaster gene, show the results from the BDGP in situ project. (flymine.org)
  • Homology also shared additional details of the optimized, in vivo gene therapy candidate HMI-204 for metachromatic leukodystrophy (MLD) during the 19th Annual WORLDSymposium™ Meeting. (advfn.com)
  • We are pleased to share our work outlining the impact immunosuppression regimens had on outcomes following AAVHSC dosing in NHPs, as it contributes to a key area of research in the gene therapy and gene editing field," stated Albert Seymour, Ph.D., President and Chief Executive Officer of Homology Medicines. (advfn.com)
  • Dr. Seymour continued, "Also at WORLD, we presented the details of our optimized gene therapy development candidate for MLD, which showed the ability to cross the blood-brain-barrier following a single I.V. administration in the murine disease model and resulted in levels of enzyme activity predicted to lead to efficacy in vivo. (advfn.com)
  • Why an HR targeting vector is a recommended Even though gene knock-outs can result from DSBs caused by Cas9 alone, SBI recommends the use of HR targeting vectors (also called HR donor vectors) for more efficient and precise mutation. (reportergene.com)
  • In addition, HR donors can include up to 6-8 kb of open reading frame for gene knock-ins or tagging, and, when small mutations are included in either 5' or 3' homology arms, can make specific, targeted gene edits. (reportergene.com)
  • The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)
  • X-linked hypophosphatemic rickets and autosomal recessive hypophosphatemic rickets are the result of mutations in PHEX (a phosphate-regulating gene with homologies to endopeptidases on the X chromosome) and dentin matrix protein 1 ( DMP1 ), respectively. (medscape.com)
  • If p, q, and r are pairwise relatively prime positive integers then the link of the singularity xp + yq + zr = 0 (in other words, the intersection of a small 5-sphere around 0 with this complex surface) is a Brieskorn manifold that is a homology 3-sphere, called a Brieskorn 3-sphere Σ(p, q, r). (wikipedia.org)
  • Moreover, we completely classify the contact structures with contact surgery number one on S¹xS², the Poincaré homology sphere, and the Brieskorn sphere Σ(2,3,7). (hu-berlin.de)
  • Random Amplified Polymorphic DNA (RAPD)-PCR was used for a phylogenetic study to check the homology of pairs of isolates. (biomedcentral.com)
  • While the homology of the isolates was low among different patients during hospitalization, identical (9%) and similar (21%) RAPD-PCR patterns were detected between pairs of isolates from each patient. (biomedcentral.com)
  • Positive identification was established for 63 isolates based upon draft genomic data. (awri.com.au)
  • The Poincaré homology sphere (also known as Poincaré dodecahedral space) is a particular example of a homology sphere, first constructed by Henri Poincaré. (wikipedia.org)
  • Since the fundamental group of the 3-sphere is trivial, this shows that there exist 3-manifolds with the same homology groups as the 3-sphere that are not homeomorphic to it. (wikipedia.org)
  • Alternatively, the Poincaré homology sphere can be constructed as the quotient space SO(3)/I where I is the icosahedral group (i.e., the rotational symmetry group of the regular icosahedron and dodecahedron, isomorphic to the alternating group A5). (wikipedia.org)
  • More intuitively, this means that the Poincaré homology sphere is the space of all geometrically distinguishable positions of an icosahedron (with fixed center and diameter) in Euclidean 3-space. (wikipedia.org)
  • The Poincaré homology sphere results from +1 surgery on the right-handed trefoil knot. (wikipedia.org)
  • Surgery on a knot in the 3-sphere S3 with framing +1 or −1 gives a homology sphere. (wikipedia.org)
  • More generally, surgery on a link gives a homology sphere whenever the matrix given by intersection numbers (off the diagonal) and framings (on the diagonal) has determinant +1 or −1. (wikipedia.org)
  • The connected sum of two oriented homology 3-spheres is a homology 3-sphere. (wikipedia.org)
  • A homology 3-sphere that cannot be written as a connected sum of two homology 3-spheres is called irreducible or prime, and every homology 3-sphere can be written as a connected sum of prime homology 3-spheres in an essentially unique way. (wikipedia.org)
  • There is always a way to choose the b′s, and the homology sphere does not depend (up to isomorphism) on the choice of b′s. (wikipedia.org)
  • Mutations in MYH9 result in the May-Hegglin anomaly, and Fechtner and Sebastian syndromes. (nih.gov)
  • Thus, our results suggest that mutations in MYH9 result in three megakaryocyte/platelet/leukocyte syndromes and are important in the pathogenesis of sensorineural deafness, cataracts and nephritis. (nih.gov)
  • When confronted with the task of finding homology to large numbers of sequences, database searching tools such as Blast and Fasta generate prohibitively large amounts of information. (aaai.org)
  • See Seifert-Weber space for a similar construction, using more "twist", that results in a hyperbolic 3-manifold. (wikipedia.org)
  • Recent research has demonstrated that this assumption can be problematic as it simplifies the manifold of structured data. (mit.edu)
  • By interpreting the influence as a probability measure, we further define an entropy that reflects the complexity of the data manifold. (mit.edu)
  • As of 2016, the publication of data analysis from the Planck spacecraft suggests that there is no observable non-trivial topology to the universe. (wikipedia.org)
  • Homology analysis indicates at least 37 different species of yeast across the dataset, with some species present in more than one sample. (awri.com.au)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
  • Achieving high analysis sensitivity and few false-negative fetal RHD results will make RhD typing of the newborn redundant. (bvsalud.org)
  • CONCLUSION: Few false-negative results support the good analysis quality of fetal RHD genotyping. (bvsalud.org)
  • Throughout his career, his aim has been to combine experimental, theoretical and data analysis methods to obtain holistic understanding of biological and medical problems. (lu.se)
  • We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. (nature.com)
  • The results will be compared between the species and their different types of ligules, being subsequently confronted with the available data in the literature and discussed inside Poaceae. (fapesp.br)
  • Increased insulin resistance (IR) and immune tolerance in pregnant women result in metabolic and immunological alterations, which may aggravate the development of gestational diabetes mellitus (GDM). (hindawi.com)
  • In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. (biorxiv.org)
  • This set of rules proved to be robust for most cases and gives high fidelity separation between real homologies and spurious matches. (aaai.org)
  • Again, let me try to put the idea of quantities of data into some kind of terms that intuitively give you an idea. (scienceblogs.com)
  • We're routinely carrying around quantities of data that we simply don't have the ability to intuitively understand. (scienceblogs.com)
  • This suggests a possible extension of our results to L-space knots. (hu-berlin.de)
  • The remethylation pathway comprises 2 intersecting biochemical pathways and results in the transfer of a methyl group (CH3) to homocysteine from methylcobalamin, which receives its methyl group from S-adenosylmethionine (SAM), from 5-methyltetrahydrofolate (an active form of folic acid), or from betaine (trimethylglycine). (medscape.com)
  • More concretely, we show that the first Khovanov homology is supported in a single quantum grading determined by the Seifert genus of the link, where the group is free abelian and of rank determined by the Seifert graph of any of its positive link diagrams. (hu-berlin.de)
  • We also show that several infinite families of Heegaard Floer L-space knots have vanishing first Khovanov homology. (hu-berlin.de)
  • Additional in vitro and in vivo data show that PilT and PilU act as independent homo-hexamers that may form a complex to facilitate pilus retraction. (biorxiv.org)
  • NovaDock explores protein flexibility when docking, resulting in more accurate protein-protein interaction predictions. (dnastar.com)
  • In this case the situation for starting the investigation of the protein protein interactions was especially difficult, because there was no experimental data which limited the protein interface of both interaction partners in more detail. (uni-duesseldorf.de)
  • The resulting first hypothesis for the interaction region on the KBD B was based on a „computational chemistry " aided approach. (uni-duesseldorf.de)
  • Calmodulin then promotes the activation of protein kinase B (AKT) by interaction with the pleckstrin homology (PH) domain of AKT. (genscript.com)
  • Persistent homology is motivated by the question of which scale is the most essential to study data shape. (helsinki.fi)
  • Alcon, the global leader in eye care dedicated to helping people see brilliantly, revealed final data from its Vivity® Registry Study, which monitored real-world patient experiences for up to 12 months post cataract surgery with implantation of either AcrySof® IQ Vivity® or AcrySof® IQ Vivity® Toric presbyopia-correcting intraocular lens. (biospace.com)
  • Results from this study unequivocally indicate that the human and chimpanzee genomes are at least 10-12% less identical than is commonly claimed. (icr.org)
  • Research to practice potential : results of this study will emphasize importance of cleaning turnout gear, and proper handling of AFFF waste. (cdc.gov)
  • That's scale - the amount of data I can afford to carry with me has changed dramatically, and as a result, my expectations about what's normal have changed. (scienceblogs.com)
  • These likenesses were defined as being the result of common ancestry. (creation.com)
  • We will found that these provide sufficient tools to consider homology classes birth and deaths, but they are not particularly easy to use in practice. (helsinki.fi)
  • Data were reviewed from all patients with suspected or confirmed EVD hospitalised in these two ETCs during the outbreak (14 February 2021 - 19 June 2021). (bvsalud.org)
  • These data also are helpful in guiding outbreak investigations and identifying targets for development of diagnostic assays and antivirals. (cdc.gov)
  • This targeted, prophylactic approach is part of our ongoing pheEDIT and juMPStart trials, from which we expect to share initial clinical data mid-year and in the second half of the year, respectively. (advfn.com)
  • Our data revealed a novel pathway for WSSV proliferation in shrimp and indicated that mTORC1 may represent a potential clinical target for WSSV control in shrimp aquaculture. (genscript.com)
  • Clinical results and laboratory examination findings vary with each disorder. (medscape.com)
  • This thesis aims to introduce the theories behind persistent homology and its application, image completion algorithm. (helsinki.fi)
  • We discuss that algorithm has potential since it does need any training or other input parameters than data. (helsinki.fi)
  • Utilizing the SwarmDock algorithm, NovaDock explores protein flexibility when docking, resulting in more accurate predictions. (dnastar.com)
  • Results were believed to be consistent with the evolutionary evidence from anatomy. (creation.com)
  • This is because good embryologists came to one dead end after another trying to fit their data into an evolutionary pattern. (creation.com)
  • The data also included HMI-204's optimized tissue expression profile and improvements in productivity packaging. (advfn.com)
  • Activated AKT phosphorylates mTOR and results in the activation of the mTORC1 signaling pathway to promote its downstream effectors, ribosomal protein S6 kinase (S6Ks), for viral protein translation. (genscript.com)
  • These conditions may result in failure of osteoid calcification (rickets) in children because of a disruption in the pathway of either vitamin D or phosphate metabolism. (medscape.com)
  • v3 (Aug 2020): Paper thoroughly revised, with improved results and updated methodology. (biorxiv.org)
  • Data for 2017-2020 are reported. (bvsalud.org)
  • In this paper, we provide a brief review of COMBREX, focusing on its overall design, its computational resources, and the experimental results from the first phase of the project. (plos.org)
  • One important difference between raw data and data based on human evaluation is that human evaluation often yields an interpretation that gives meaning to the data. (medscape.com)
  • These results are more clearly in line with the large anatomical and behavioral differences observed between human and chimp. (icr.org)
  • However, through vigilant daily monitoring of national surveillance data by surveillance officers at the national level, including fellows of the Field Epidemiology Training Program at the National Institute of Infectious Diseases, and their close communication with local public health staff, five cases were found to have been present at a large international airport on the same day as a possible index case was found. (who.int)
  • We determine the structure of the Khovanov homology groups in homological grading 1 of positive links. (hu-berlin.de)
  • Although the precise pathogenic mechanism of GDM has not been fully elucidated, it may occur as a result of abnormal glucose regulation and increased IR, inducing the disorders of glucose metabolism. (hindawi.com)
  • the amount of information that we use on a daily basis has increased dramatically, and the amount of dramatic, fundamental change that has resulted is both amazing, and amazingly unnoticed by most people. (scienceblogs.com)
  • In addition, we also discuss characterizing slopes and provide results in the opposite direction, i.e. describe cases in which the Stein trace, or the contactomorphism type of an r-surgery, uniquely determines the Legendrian isotopy type. (hu-berlin.de)
  • Furthermore, we provide a preliminary discussion of the connection of the Shapley homology to the Vapnik-Chervonenkis dimension. (mit.edu)
  • Discussion: Although Federal OSHA SIR data do not include SIRs from state-plan jurisdictions, the data provide a timely national trend of SIR. (cdc.gov)
  • Further improvement in the timeliness of feedback through the development of a NESS website to allow access to historic data and to the information on circulating serotypes can provide additional incentives to public health laboratories to participate in NESS. (cdc.gov)
  • Demonstration that Perl can be used as a programming tool in applications beyond retrieving/manipulating text data. (lu.se)
  • Web accessible data needs to increase in granularity and cross linkage. (w3.org)