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  • 1
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    The Carboniferous Timescale (2020)
    London : The Geological Society
    Details
    Keywords: Carboniferous; Pangaea; ice age; biochronology; biostratigraphy; magnetostratigraphy; radioisotopic age
    Description / Table of Contents: 10 December 2020 --- Proposed chronostratigraphic units for the Carboniferous and Early Permian of the southwestern Gondwana margin / Carlos R. González and Pamela Díaz Saravia / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-48 --- 7 December 2020 --- A geomagnetic polarity timescale for the Carboniferous / Mark W. Hounslow / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-102 --- 1 December 2020 --- Carboniferous Smaller Foraminifera: Convergences and Divergences / Daniel Vachard and François Le Coze / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-42 --- 30 November 2020 --- Carboniferous Crinoids / William I. Ausich, Thomas W. Kammer and Georgy V. Mirantsev / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-71 --- 27 November 2020 --- Carboniferous macrofloral biostratigraphy – an overview / Stanislav Opluštil, Christopher J. Cleal, Jun Wang and Mingli Wan / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-97 --- 26 November 2020 --- The biostratigraphy of Carboniferous chondrichthyans / Michał Ginter / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-91 --- 25 November 2020 --- Carboniferous isotope stratigraphy / Jitao Chen, Bo Chen and Isabel P. Montañez / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-72 --- 24 November 2020 --- Carboniferous conodont biostratigraphy / James E. Barrick, Alexander S. Alekseev, Silvia Blanco-Ferrera, Natalia V. Goreva, Keyi Hu, Lance L. Lambert, Tamara I. Nemyrovska, Yuping Qi, Scott M. Ritter and Javier Sanz-López / Geological Society, London, Special Publications, 512, https://doi.org/10.1144/SP512-2020-38
    Pages: Illustrationen, Diagramme, Karten
    Edition: online first
    URL: https://sp.lyellcollection.org/online-first/512
    Language: English
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  • 2
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    Towards translating research to clinical practice: Novel Strategies for Discovery and Validation of Biomarkers for Brain Injury (2021)
    Frontiers Media SA
    Details
    Publication Date: 2023-12-21
    Description: Traumatic brain injury (TBI) is a major cause of death and disability and one of the greatest unmet needs in medicine and public health. TBI not only has devastating effects on patients and their relatives but results in huge direct and indirect costs to society. Although guidelines for the management of patients have been developed and more than 200 clinical trials have been conducted, they have resulted in few improvements in clinical outcomes and no effective therapies approved for TBI. It is now apparent that the heterogeneity of clinical TBI is underlain by molecular phenotypes more complex and interactive than initially conceived and current approaches to the characterization, management and outcome prediction of TBI are antiquated, unidimensional and inadequate to capture the interindividual pathophysiological heterogeneity. Recent advances in proteomics and biomarker development provide unparalleled opportunities for unraveling substantial injury-specific and patient-specific variability and refining disease characterization. The identification of novel, sensitive, objective tools, referred to as biomarkers, can revolutionize pathophysiological insights, enable targeted therapies and personalized approaches to clinical management. In this Research Topic, we present novel approaches that provide an infrastructure for discovery and validation of new biomarkers of acute brain injury. These techniques include refined mass spectrometry technology and high throughput immunoblot techniques. Output from these approaches can identify potential candidate biomarkers employing systems biology and data mining methods. In this Research Topic, we present novel approaches that provide an infrastructure for discovery and validation of new biomarkers of acute brain injury. These techniques include refined mass spectrometry technology and high throughput immunoblot techniques. Output from these approaches can identify potential candidate biomarkers employing systems biology and data mining methods. Finally, suggestions are provided for the way forward, with an emphasis on need for a multidimensional approach that integrate a panel of pathobiologically diverse biomarkers with clinical variables and imaging-based assessments to improve diagnosis and classification of TBI and to develop best clinical practice guidelines.
    Keywords: R5-920 ; RC346-429 ; Traumatic Brain Injury ; Brain Injury ; discovery ; clinical practice ; biomarker ; bic Book Industry Communication::M Medicine
    Language: English
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  • 3
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    FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-27
    Description: : Recent advances in high-throughput sequencing technologies have enabled us to sequence large number of cancer samples to reveal novel insights into oncogenetic mechanisms. However, the presence of intratumoral heterogeneity, normal cell contamination and insufficient sequencing depth, together pose a challenge for detecting somatic mutations. Here we propose a fast and an accurate somatic single-nucleotide variations (SNVs) detection program, FaSD-somatic. The performance of FaSD-somatic is extensively assessed on various types of cancer against several state-of-the-art somatic SNV detection programs. Benchmarked by somatic SNVs from either existing databases or de novo higher-depth sequencing data, FaSD-somatic has the best overall performance. Furthermore, FaSD-somatic is efficient, it finishes somatic SNV calling within 14 h on 50X whole genome sequencing data in paired samples. Availability and implementation: The program, datasets and supplementary files are available at http://jjwanglab.org/FaSD-somatic/ . Contact: wangdatou2009@gmail.com . Supplementary information: Supplementary data are available at Bioinformatics online
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Research Articles: Microclimate regulating functions of urban forests in Changchun City (north-east China) and their associations with different factors (2018)
    Italian Society of Silviculture and Forest Ecology
    Details
    Publication Date: 2018-12-17
    Description: Wang W, Wang H, Xiao L, He X, Zhou W, Wang Q, Wei C MICROCLIMATE REGULATING FUNCTIONS OF URBAN FORESTS IN CHANGCHUN CITY (NORTH-EAST CHINA) AND THEIR ASSOCIATIONS WITH DIFFERENT FACTORS Abstract : Microclimate regulating functions of urban trees and their associations with environmental factors and tree-growth characteristics are important for management and ecological evaluations. In this study, a total of 637 trees distributed in the Changchun urban region (ca. 400 km2, northeastern China) were sampled in four different types of urban forests (AF: affiliated forests; RF: roadside forests; LF: landscape and relaxation forests; EF: ecological welfare forests). Tree growth-related parameters and environmental factors (inside and outside the forest) were simultaneously measured, and location-dependent differences in shading, cooling and humidifying effects were assessed, along with their associations with the measured variables. We found that urban forests in Changchun reduced the incident sunlight by 74-86% and increased air relative humidity by 3-7%, on average. Air, soil, and upper-canopy temperatures were decreased approximately by 3 °C,
    Electronic ISSN: 1971-7458
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Italian Society of Silviculture and Forest Ecology
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  • 5
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    GED: a manually curated comprehensive resource for epigenetic modification of gametogenesis (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-10
    Description: Reproductive infertility affects seventh of couples, which is most attributed to the obstacle of gametogenesis. Characterizing the epigenetic modification factors involved in gametogenesis is fundamental to understand the molecular mechanisms and to develop treatments for human infertility. Although the genetic factors have been implicated in gametogenesis, no dedicated bioinformatics resource for gametogenesis is available. To elucidate the relationship of epigenetic modification and mammalian gametogenesis, we developed a new database, gametogenesis epigenetic modification database (GED), a manually curated database, which aims at providing a comprehensive resource of epigenetic modification of gametogenesis. The database integrates three kinds information of epigenetic modifications during gametogenesis (DNA methylation, histone modification and RNA regulation), and the gametogenesis has been detailed as 16 stages in seven mammal species ( Homo sapiens , Mus musculus , Rattus norvegicus , Sus scrofa , Bos taurus , Capra hircus and Ovis aries ). Besides, we have predicted the linear pathways of epigenetic modification which were composed of 211 genes/proteins and microRNAs that were involved in gametogenesis. GED is a user-friendly Web site, through which users can obtain the comprehensive epigenetic factor information and molecular pathways by visiting our database freely. GED is free available at http://gametsepi.nwsuaflmz.com .
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 6
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    3D steerable, acoustically powered microswimmers for single-particle manipulation (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉The ability to precisely maneuver micro/nano objects in fluids in a contactless, biocompatible manner can enable innovative technologies and may have far-reaching impact in fields such as biology, chemical engineering, and nanotechnology. Here, we report a design for acoustically powered bubble-based microswimmers that are capable of autonomous motion in three dimensions and selectively transporting individual synthetic colloids and mammalian cells in a crowded group without labeling, surface modification, or effect on nearby objects. In contrast to previously reported microswimmers, their motion does not require operation at acoustic pressure nodes, enabling propulsion at low power and far from an ultrasonic transducer. In a megahertz acoustic field, the microswimmers are subject to two predominant forces: the secondary Bjerknes force and a locally generated acoustic streaming propulsive force. The combination of these two forces enables the microswimmers to independently swim on three dimensional boundaries or in free space under magnetical steering.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Allele-specific copy-number discovery from whole-genome and whole-exome sequencing (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-18
    Description: Copy-number variants (CNVs) are a major form of genetic variation and a risk factor for various human diseases, so it is crucial to accurately detect and characterize them. It is conceivable that allele-specific reads from high-throughput sequencing data could be leveraged to both enhance CNV detection and produce allele-specific copy number (ASCN) calls. Although statistical methods have been developed to detect CNVs using whole-genome sequence (WGS) and/or whole-exome sequence (WES) data, information from allele-specific read counts has not yet been adequately exploited. In this paper, we develop an integrated method, called AS-GENSENG, which incorporates allele-specific read counts in CNV detection and estimates ASCN using either WGS or WES data. To evaluate the performance of AS-GENSENG, we conducted extensive simulations, generated empirical data using existing WGS and WES data sets and validated predicted CNVs using an independent methodology. We conclude that AS-GENSENG not only predicts accurate ASCN calls but also improves the accuracy of total copy number calls, owing to its unique ability to exploit information from both total and allele-specific read counts while accounting for various experimental biases in sequence data. Our novel, user-friendly and computationally efficient method and a complete analytic protocol is freely available at https://sourceforge.net/projects/asgenseng/ .
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Experimental and theoretical determination of σ bands on (“2 sqrt[3] ×2 sqrt[3] ”) silicene grown on Ag(111) (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-11-26
    Description: Author(s): W. Wang, W. Olovsson, and R. I. G. Uhrberg Silicene, the two-dimensional (2D) allotrope of silicon, has very recently attracted a lot of attention. It has a structure that is similar to graphene and it is theoretically predicted to show the same kind of electronic properties which have put graphene into the focus of large research and develo… [Phys. Rev. B 92, 205427] Published Mon Nov 23, 2015
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Novel ncRNA, NfiS, optimizes nitrogen fixation [Microbiology] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-07-28
    Description: Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-08
    Description: The rpoS mRNA, which encodes the master regulator S of general stress response, requires Hfq-facilitated base pairing with DsrA small RNA for efficient translation at low temperatures. It has recently been proposed that one mechanism underlying Hfq action is to bridge a transient ternary complex by simultaneously binding to rpoS and DsrA. However, no structural evidence of Hfq simultaneously bound to different RNAs has been reported. We detected simultaneous binding of Hfq to rpoS and DsrA fragments. Crystal structures of AU6A•Hfq•A7 and Hfq•A7 complexes were resolved using 1.8- and 1.9-Å resolution, respectively. Ternary complex has been further verified in solution by NMR. In vivo , activation of rpoS translation requires intact Hfq, which is capable of bridging rpoS and DsrA simultaneously into ternary complex. This ternary complex possibly corresponds to a meta-stable transition state in Hfq-facilitated small RNA–mRNA annealing process.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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