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Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019) in Variability of the gene cyt b in the Korean field mouse Apodemus peninsulae Thomas, 1906 - a reservoir host of AMRV in the Khasansky District of Primorsky Krai
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019)
ENTICE VM image analysis and optimised fragmentation frequently built images dataset
<p>As part of the evaluation of ENTICE VM image analysis and optimised fragmentation services we have implemented a simulation environment which analyses online software package repositories (e.g. ones offered by the maintainers of the Ubuntu and Debian Linux distributions) and deduces decomposition options as well as expected fragment sizes based on metadata acquired from these repositories. This dataset contains the collected recipes for several frequently built Ubuntu Linux based VMIs (e.g., LAMP, LAPP, LEMP, LLMP, LYME, MEAN/MERN, LTM, etc.) and the calculated fragments and their relations. The dataset is used to analyse and evaluate the behaviour of the fragmentation services. The dataset is in compressed LRZIP format.</p>
XRD-CT from paint fragment
<p>Reconstructed XRD-CT collected at beamline I18 Diamond Light Source on fragment of paint from Rembrandt's Homer.</p>
Data to accompany the paper "Improved fragment-based protein structure prediction by redesign of search heuristics"
<p>This repository contains the older and newer input fragment sets and other data used for the analyses in our paper. The filenames for each tarball contain the PDB identifier of each protein along with a chain ID if applicable, followed by 'old' or 'new' for old and new fragments, respectively. Each tarball contains: a .fasta file of the input sequence, a matching PDB structure file, the relevant PSIPRED secondary structure prediction file, and the 9mer and 3mer fragment files. <br> <br> An additional tarball, ScoreRMSDplots_3protocols.tgz, contains extended versions of Figure 3 which show score and RMSD distributions clearly. Additionally, the same data is shown for equivalent experiments using the older fragment set.</p>
Diffraction images of a crystal of the complex formed by fragments of the integrin beta4 and the bullous pemphigoid antigen 1 (BP230, BPAG1e). PDB entry 6GVL.
<p>Data were collected on a single crystal at the beamline i03 of the Diamond synchrotron facility (Didcot, UK) using radiation of 0.97625 Å wavelength and a PILATUS3 6M detector. The dataset consists of 2400 images (0.15 degree oscillation per image).</p>
Diffraction images of a crystal of the complex formed by fragments of the integrin beta4 and the bullous pemphigoid antigen 1 (BP230, BPAG1e). Integrin high affinity point mutant. PDB entry 6GVK.
<p>Data were collected on a single crystal at the beamline XALOC of the ALBA-CELLS synchrotron facility (Cerdanyola del Vallés, Barcelona, Spain) using radiation of 0.97915 Å wavelength and a PILATUS 6M detector. The complete dataset is build up of three sub-sets measured at three different positions of a single crystal. Each sub-set consists of 1800 images (0.2 degree oscillation per image).</p>
Data accompanying "Genomic data recover previously undetectable fragmentation effects in an endangered amphibian"
<p>Target sequences and SNP and genotype calls from the manuscript "Genomic data recover previously undetectable fragmentation effects in an endangered amphibian".</p>
An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies)
<p>Data files for construction of the haploid genetic map for Norway spruce (<em>Picea abies</em>). Available at <a href="https://doi.org/10.1101/292151">https://doi.org/10.1101/292151</a></p>
Bodhgayā, Bihār. Silver fragments.
<p>Bodhgayā, Bihār. Silver fragments, assemblage of. British Museum 1892,1103.36 (part b), presented by Alexander Cunningham.</p>
Cyprus. Carved marble fragment in Stamford, CT, USA.
<p>Cyprus. Carved marble fragment in the First Presbyterian Church, 1101 Bedford Street, Stamford, Connecticut. Width: 46.5 mm</p>
Bodhgayā, Bihār. Quartz, variety rock crystal, small fragments.
<p>Bodhgayā, Bihār. Quartz, variety rock crystal, small fragments. British Museum 1892,1103.54 presented by Alexander Cunningham.</p>
Dataset - Ionic Species in a Naphthalene Plasma: Understanding Fragmentation Patterns and Growth of PAHs
<p>All mass spectrometry scans presented in 10.1021/acs.jpca.9b00100</p>
Solvated protein fragments
<p>The solvated protein fragments dataset probes many-body intermolecular interactions between <br> "protein fragments" and water molecules, which are important for the description of many <br> biologically relevant condensed phase systems. It contains structures for all possible <br> "amons" [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms <br> (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural<br> amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur <br> in different charge states due to (de-)protonation (i.e. carboxylic acids that can be <br> negatively charged or amines that can be positively charged), all possible structures with <br> up to a total charge of +-2e are included. In total, the dataset provides reference energies, <br> forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP <br> level of theory [2-5] using the ORCA 4.0.1 code [6,7]. </p> <p>For more details, see https://arxiv.org/abs/1902.08408.</p> <p>[1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017).<br> [2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010).<br> [3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011).<br> [4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005).<br> [5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998).<br> [6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012).<br> [7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).</p>
Concordance of the Qumran Cave 4 'Unidentified fragments' on PAM 43691 (IAA # 96)
<p>Lists of agreement with the PAM 43691 (IAA # 96) Qumran Cave 4 unidentified fragments with fragments on earlier photographs in the series of Unidentified fragments (cf. DJD 33) </p>
Extended data for the paper "Reliable generation of native-like decoys limits predictive ability in fragment-based protein structure prediction"
<p>Extended data for the paper:<br> Reliable generation of native-like decoys limits predictive ability in fragment-based protein structure prediction</p> <p>Authors:<br> Shaun M Kandathil, Mario Garza-Fabre, Simon C Lovell and Julia Handl</p> <p>--------------------------------</p> <p>Contents of the zip file:</p> <p> </p> <p>Directory 'ECDFplots':<br> ----------------------<br> Data corresponding to Figure 3 for all targets, for the bilevel and ILS protocols. Data are available following stages 3 and 4 of the low-resolution protocol.</p> <p>Directory 'ScoreRMSDplots_3archivers':<br> --------------------------------------<br> Data corresponding to Figures 6 and 9 for all targets. Data corresponding to decoys obtained after low-resolution stages 3 and 4 can be found in subdirectories 'Stage3' and 'Stage4', respectively.<br> </p>
Text-fig. 4.—Right surangular fragment of the Jordan theropod (LACM 28471). Lined areas represent broken surfaces. in A new Theropod Dinosaur from the Upper Cretaceous of Central Montana
Text-fig. 4.—Right surangular fragment of the Jordan theropod (LACM 28471). Lined areas represent broken surfaces.
Figure 12 in Soldier flies (Diptera: Stratiomyidae) on semideciduous seasonal forest fragments, with a list of species for São Paulo State, Brazil, and two new records of species for the country
Figure 12 Map with the distribution of all 92 unique coordinates from the stratiomyid dataset throughout the Atlantic Forest remnants in the state of São Paulo, Brazil.
Figure 5 in Soldier flies (Diptera: Stratiomyidae) on semideciduous seasonal forest fragments, with a list of species for São Paulo State, Brazil, and two new records of species for the country
Figure 5 Stratiomyids from the Reserva Ecológica e Biológica Augusto Ruschi, Sertãozinho, São Paulo, Brazil. (a) Manotes sp. 1, male; (b) Manotes sp. 1, female; (c) Panacris lucida Gerstaecker, 1857, male; (d) Popanomyia sp. 1, female; (e) Psephiocera sp. 1, female; (f) Psephiocera sp. 2, male; (g) Strobilaspsis sp. 1, female; (h) Raphiocera sp. 1, male; (i) Acrochaeta ruschii Fachin & Amorim, 2015, female; (j) Merosargus brunneus Lindner, 1933, male; (k) M. cingulatus Schiner, 1868, male; (l) M. golbachi James, 1971 in James & McFadden, 1971, male. Scale bar, 1 mm.
Figure 4 in Soldier flies (Diptera: Stratiomyidae) on semideciduous seasonal forest fragments, with a list of species for São Paulo State, Brazil, and two new records of species for the country
Figure 4 Stratiomyids from the Reserva Ecológica e Biológica Augusto Ruschi, Sertãozinho, São Paulo, Brazil. (a) Diaphorostylus sp. 1, male; (b) Diaphorostylus sp. 1, female; (c) Euryneura sp. 1, male; (d) Euryneura sp. 1, female; (e) Hermetia albitarsis Fabricius, 1805, female; (f) H. brachygastropsis Fachin & Hauser, 2022, female; (g) H. illucens (Linnaeus, 1758), female; (h) H. currani Lindner, 1949, female; (i) Chorophthalmyia brevicornis Lindner, 1964, female; (j) Cyclotaspis sp. 1, female; (k) Eidalimus sp. 1, male; (l) Eidalimus sp. 1, female. Scale bar, 1 mm.
Figure 9 in Soldier flies (Diptera: Stratiomyidae) on semideciduous seasonal forest fragments, with a list of species for São Paulo State, Brazil, and two new records of species for the country
Figure 9 Climate and seasonal data of soldier flies collected using black roof Malaise traps at the Reserva Ecológica e Biológica de Sertãozinho, São Paulo, Brazil.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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