Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,878
datasets available to search
ShareScore release 0.9.0
Dataset results
3,878 results for “Molecular data”
FIG. 10. — Dorippinae H. Milne Edwards, 1837 n in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 10. — Dorippinae H. Milne Edwards, 1837 n. stat.: habitus: A, B, Dorippe quadridens (Fabricius, 1793): A, ♂ 36.3 × 38.1 mm, China Sea near Singapore, Hee Huat, ZRC 1984. 6308; B, ♀ 29.5 × 30 mm, NW Madagascar, Ambaro Bay, MNHN-IU-2018-5193 (= MNHN-B18279). C, D, Dorippe sinica Chen, 1980, China, Guangdong, Nanao Island, ZRC 1999.0470: C, ♂ 36.2 × 39.5 mm; D, ♀ 34.8 × 38.9 mm, specimen brushed.
FIG. 34. — A in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 34. — A, schematic cross-section of thoracic region at level of P3 to show in one diagram the two distinctive arrangements of female organs in Brachyura. On left, a typical podotreme, with coxal openings; on right, a typical eubrachyuran, with sternal openings or vulvae; B, schematic representation of the two types of brachyuran seminal receptacles, either of ventral type (left), or of dorsal type (right), and their connection to the oviduct (see Diesel 1991). Abbreviations: a, spermathecal aperture; cx, coxa; g, coxal female gonopore; od, oviduct; ov, ovary; sp, spermatheca; sr, seminal receptacle; st, thoracic sternum; v, vulva; vg, vagina. Modified from Hartnoll (1968: fig. 1), Guinot (1978: fig. 1; 1979a: fig. 38) and Vehof (2020: fig. 19).
FIG. 35 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 35. — Schematic illustrations of female reproductive systems in representatives of four dorippid subfamilies: A, B, Dorippinae n. stat.: A, Dorippe sinica Chen, 1980, as interpreted by Hayer et al. (2016a: fig. 2); B, Dorippe quadridens (Fabricius, 1793) and D. sinica, as interpreted by Vehof et al. (2017: fig. 2A); C, Medorippinae n. subfam.: Medorippe lanata (Linnaeus, 1767), as interpreted by Vehof et al. (2017: fig. 2B); D, Paradorippinae n. subfam.: Paradorippe granulata (De Haan, 1841), as interpreted by Vehof et al. (2018b: fig. 3). E, Heikeopsinae n. subfam.: Heikeopsis japonica (von Siebold, 1824), with the same pattern shared by Neodorippe callida (Fabricius, 1798) and Nobilum histrio (Nobili, 1903), as interpreted by Vehof (2020: fig. 4). Abbreviations: a, apodeme; amb, anteromedian bursa; bu, bursa; cu, cuticle; cv, cuticular valves; bu, bursa; ev, extension of vulva; ge, glandular epithelium; mu, musculature; oc, oocyte; od, oviduct; ov, ovary; plb, posterolateral bursa; sr, seminal receptacle; vg, vagina; v, vulva.
FIG. 40 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 40. — Fossil crabs: A, the poorly known true dorippid, Dorippe judicis Gripp, 1964 (pl. 17, fig. 7a), Lower Miocene of northern Germany, generic status to be reappraised: carapace and pleon partially dorsally exposed (photocopy from Gripp 1964: pl. 17, fig. 7a); B-F, Goniochele angulata Bell, 1858; B-D, F, Eocene London Clay, Ypresian, Isle of Sheppey, Kent; E, Ypresian, Forest, Brussels, Belgium: B, carapace with preserved lateral spines, except long epibranchial spine, broken, concealed with matrix (Griffiths' collection); C, carapace of paralectotype (lateral spines lost) with well-preserved protruding concave rim of posterior margin and narrow male pleon, with first three somites dorsally exposed (Wetherell's collection, NHM PL OR 59085); D, E, two views of male thoracic sternum, with triangular first sternites and press-buttons on suture 5/6 (D, Jeff Saward collection); E, original from Collins & Smith 1993: pl. 2, fig. 3, as Silvacarcinus laurae Collins & Smith, 1993; F, ventral view of a female, with narrow elongated sternites 1-4 and wider last sternites (Griffiths' collection, NHM 36652). Abbreviation: v, enormous vulvae. All, courtesy of Barry van Bakel.
FIG. 8 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 8. — Particular structures of some dorippids: A, B, rim and strip along posterior margin of carapace: A, Dorippoides facchino (Herbst, 1785), ovigerous ♀ 20.3 × 26.2 mm, South China Sea, ZRC 1984.5347; B, Paradorippe granulata (De Haan, 1841), ♂ 23.6 × 27.3 mm, NE Taiwan, ZRC 2001.0014; C, retention of female pleon by process of sternite 8 overhanging pleonal somite 2: Dorippe quadridens (Fabricius, 1793), ♀ 38.1 × 33.7 mm, South China Sea, Hee Huat, ZRC 1984.6307; D, retention of telson engaged between edges of sternite 5: Dorippoides facchino (Herbst, 1785), ovigerous ♀ 20.3 × 26.2 mm, same data as A. Abbreviations: cx3-cx5, coxae of P3-P5; p, process of sternite 8; p2, p3, pereiopod 2, 3; r, rim; s, strip; sp, spur-like process on P3 ischium; 1, pleonal somite 1; 7, 8, dorsally exposed thoracic sternites 7, 8.
FIG. 6. — A-C in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 6. — A-C, nomenclature of various carapace regions and location of cervical groove in Eubrachyura, exemplified by: A, Mithrax spinosissimus (Lamarck, 1818); B, by Zosimus aeneus (Linnaeus, 1758), according to H. Milne Edwards (1851: pl. 8, figs 6, 9, respectively); C, by a species of 'Cancer group' with numbered regions, according to Dana (1851: 95-98, fig. 1); D: homology of gastric regions defined by H. Milne Edwards (1851) and those numbered by Dana (1851) (after Guinot 1979a: fig. 7D). Abbreviations: cd, cardiac region; epg, epigastric lobe; f.g., gastric pit; in, intestinal region; mag, metagastric region; mog, mesogastric region; ptg, protogastric lobe; s.c., cervical groove; s.b.c., branchiocardiac groove; s.g.h., hepatic groove; urg, urogastric region.
FIG. 7. — A, B in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 7. — A, B, exposure of latero-external ends of pleurites 5-7 in Medorippe lanata (Linnaeus, 1767), skeleton prepared by S. Secretan, MNHN: A, carapace (partially removed) covering all pleurites except exposed latero-external portions of pleurites 5-7; B, close-up view of lateroposterior region of carapace to show calcified exposed external portion of pleurites 5-7, with setting gutter for carapace; red line indicates location of carapace margin. Modified from Guinot et al. (2013: fig. 46A, B). C, thoracic sternum/pterygostome junction, oxystomatous condition, Milne Edwards openings in Medorippe lanata (Linnaeus, 1767), ♀ 17.8 × 23.0 mm, Mediterranean Sea (MNHN, skeleton prepared by S. Secretan). Modified from Guinot et al. 2013: fig. 42C. D, articulation of pleonal somites, dorsal view of female Medorippe lanata (Linnaeus, 1767). Modified from Guinot et al. (2013: fig. 51G). Abbreviations: a1-a3, first to third pleonal somites; c, carapace margin; ce, ventral extension of carapace posterior margin; cm, mxp3 coxa; cp5, cp6, calcified portion of pleurites 5, 6 covered by carapace; cx2-cx5, coxae of P2-P5; c6, c7, coxo-pleural condyles of P3, P4; e, sternal extension; e6, extension of pleurite 6 covered by carapace; ep5-ep7, exposed pleurites 5-7; g, setting gutter of carapace; M, Milne Edwards openings as pterygostomial slits; m, articulating membrane; p, sternal boutonniere of suture 3/4; pn, penis; pt, pterygostome; p.b., press-button; r, rim; s, strip; t, telson; v, vulva on a prominence and with operculum; 3-6, thoracic sternites 3-6; 8, exposed portion of thoracic sternite 8; 3/4, 4/5, thoracic sternal sutures 3/4, 4/5.
FIG. 5 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 5. — Terminology of main grooves on dorsal carapace of Dorippidae: A, diagrammatic figure of Holthuis & Manning (1990: fig. 1, based on a Dorippe species) without any mention of 'precervical groove'. B-D, terminology used in the present paper and only partially used by Holthuis & Manning (1990). B, Dorippe tenuipes Chen, 1980: after Holthuis & Manning (1990: fig. 18a); C, Heikeopsis japonica (von Siebold, 1824): after Holthuis & Manning (1990: fig. 30a, as Heikea japonica); D, Neodorippe callida (Fabricius, 1795): after Holthuis & Manning (1990: fig. 39). The strip, which runs posteriorly along the rim, was only figured in C. Abbreviations: b.c., branchiocardiac groove; c.g., cervical groove; l.b., branchial lobe; p.g., precervical groove; r, rim; s, strip.
FIG. 1. — A in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 1. — A typical dorippid crab, Heikeopsis japonica (von Siebold, 1824), the iconic 'samurai crab' known in Japan as 'heike-gani', whose carapace looks like a human face: A, the species represented by De Haan (1839: pl. 31, fig. 1, as Dorippe japonica) in Fauna Japonica: top, a female; below, chelae of a male; B, lectotype selected by Yamaguchi & Baba (1993: 300, fig. 90-A.a-2, as Heikea japonica) from type series material labelled "Types, Japan, 1823, Leg. P. H. von Siebold", RMNH CRUS D 822 (see Fransen et al. 1997: 83); C, ♂ 25.0 × 27.3 mm, ♀ 23.5 × 26.7 mm, Japan, Chaffanjon, 174-96, E.-L. Bouvier det. 1899 Dorippe japonica, dry condition, MNHN-IU-2000-4091 (= MNHN-B4091).
FIG. 4 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 4. — Dorippid thoracic sternum exemplified here by Medorippe lanata (Linnaeus, 1767), Mediterranean Sea, dehydrated specimens for skeletal preparation by Sylvie Secretan (MNHN): A, ♂; B, ♀. Abbreviations: b.p., press-button located in curved sternal suture 5/6; cx4, P4 coxa: e, episternite; G1, G2, first and second gonopods; j, sternum/pterygostome junction; m, membrane; m.o., Milne Edwards opening as pterygostomial slit; p, perforation at the end of sternal suture 3/4; r, sternal ridge; s.p., sternal prominence; v, vulva; 1-8, thoracic sternites 1-8; 2/3-7/8, sternal sutures 2/3-7/8. Photographs by Barry van Bakel.
FIG. 2 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 2. — Colour print by Utagawa Kuniyoshi in 1851: The ghost of Taira Tomomori along with the anchor he drowned with, and heikegani with faces of fallen soldiers; A, Heikeopsis japonica (von Siebold, 1824), the 'heike-gani' or 'samurai crab', during the naval battle at Dan-no-ura (1185) in Japan's Inland Sea; B, closeup view of the crabs, easily recognisable by their carapaces bearing like a human face, their last two legs, reduced and carried dorsally, and the dorsally visible pleon (See also Fig. 39).
Research data supporting: "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling"
<p>This repository contains the set of data shown in the paper "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling" published on PNAS (DOI: 10.1073/pnas.2300565120).</p>
Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"
<p># 2023-06-28<br> # Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"<br> # Summary<br> This ZIP-file contains the supplementary files of our SMARCC2 study "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals". <br> Suppl. File S2 contains comprehensive clinical data<br> Suppl. File S3 contains comprehensive genetic data<br> Suppl. File S4 contains files of the SMARCC2 N-terminal homology model</p> <p># Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S2 and Suppl.File S3, and ZIP Suppl.File S4)</p> <p># Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 003A879AA75CF8B5C4E3E05F76C4EB4C SMARCC2-Supplementary\Files\FileS2_cases_clinical-table.xlsx<br> MD5 73B4F9E83419A8404345101CAA4D2205 SMARCC2-Supplementary\Files\FileS3_variants-and-domains.xlsx<br> MD5 B0A12F36B4801EB6C4D21BA02B4270BB SMARCC2-Supplementary\Files\FileS4_SMARCC2 N-terminal homology model.zip</p>
Fig. 1 in Novel distribution records and molecular data for species of Macrogyrodactylus Malmberg, 1957 (Monogenea: Gyrodactylidae) from Clarias gariepinus (Burchell) (Siluriformes: Clariidae) in southern Africa
Fig. 1. Map illustrating the sampling localities of Clarias gariepinus (Burchell) during the present study. A – Zambia; B – South Africa.
Fig. 2 in Novel distribution records and molecular data for species of Macrogyrodactylus Malmberg, 1957 (Monogenea: Gyrodactylidae) from Clarias gariepinus (Burchell) (Siluriformes: Clariidae) in southern Africa
Fig. 2. Micrographs showing the morphological features of Macrogyrodactylus clarii Gussev, 1961 (A–C), M. congolensis (Prudhoe, 1957) (D–F), and M. karibae Douëllou et Chishawa, 1995 (G, H). A, D, G – hamuli complex; B, E, H – sickle of marginal hook; C, F, I – cirrus with spines.
Molecular dynamics simulation data 3: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes: Production run gromacs trajectories for the Cx43 gap junction channel (500 mV)</p>
Molecular dynamics simulation data 2: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 hemichannel</p>
Data from: Effects of fungicides on aquatic fungi and bacteria: a comparison of morphological and molecular approaches from a microcosm experiment
<p>Data files and R code for the manuscript: Effects of fungicides on aquatic fungi and bacteria: a comparison of morphological and molecular approaches from a microcosm experiment. Published in Environmental Sciences Europe.</p>
Extending a generic and fast coarse-grained molecular dynamics model to examine the mechanical behavior of grafted polymer nanocomposites: data set
<p>Abstract:<br> from [1]</p> <blockquote> <p>Polymer nanocomposites are an important class of materials for engineering applications due to their high versatility and good mechanical properties combined with low density. By directly attaching the polymer chains to the nanofillers, the so-called grafting, a better load transfer between matrix and filler is achieved, and, in addition, a better dispersion of the fillers is obtained. Both result in enhanced mechanical properties. Since experimental investigations on the nanoscale are extremely challenging, complementary numerical studies are needed to unravel the mechanical behavior of polymer nanocomposites. To this end, molecular dynamics is ideally suited since it captures the microstructure, but is also numerically expensive. Therefore, this contribution presents a fast coarse-grained molecular dynamics model for the investigation of the mechanical behavior of grafted polymer nanocomposites. For this purpose, we extend an existing model by grafting bonds, which allows us to compare the effect of untreated and grafted fillers directly. In particular, we investigate the influence of filler content, grafting degree, and filler size on the stiffness and strength of the polymer (grafted) nanocomposites. We conclude that the grafting bonds have little effect on the stiffness, while the strength is significantly improved compared to the untreated fillers, which is in agreement with the literature. The presented molecular dynamics model for polymer grafted nanocomposites provides the basis for further investigations, particularly of the crucial matrix-filler interphase. In addition, this contribution translates molecular dynamics insights into mechanical properties, which bridges the gap to the engineering scale and thus represents a step towards exploiting the full potential of polymer (grafted) nanocomposites.</p> </blockquote> <p> </p> <p><strong>Contact:</strong></p> <p>Maximilian Ries<br> Institute of Applied Mechanics<br> Friedrich-Alexander-Universität Erlangen-Nürnberg<br> Egerlandstr. 5<br> 91058 Erlangen</p> <p><strong>Software:</strong></p> <p>All MD simulations were performed with LAMMPS [2,3], version: 29 Oct 2020 / 20201029</p> <p>Compiled with<br> Compiler: GNU C++ 4.8.5 20150623 (Red Hat 4.8.5-39) with OpenMP not enabled<br> C++ standard: C++11</p> <p>Active compile time flags:<br> -DLAMMPS_GZIP<br> -DLAMMPS_SMALLBIG</p> <p>Installed packages:<br> CLASS2, KSPACE, MANYBODY, MC, MOLECULE, MPIIO, OPT, VORONOI, USER-INTEL, USER-MISC, USER-MOLFILE, USER-NETCD</p> <p>Polymer and polymer composite samples generated with self-avoiding random-walk algorithm [4]</p> <p>Post-processing Matlab R2019b</p> <p><strong>License:</strong></p> <p>Creative Commons Attribution 4.0 International</p> <p><strong>Context:</strong></p> <p>Data set supplementing journal paper:</p> <p>[1] M. Ries, S. Reber, P. Steinmann, & S. Pfaller, “Extending a generic and fast coarse-grained molecular dynamics model to examine the mechanical behavior of grafted polymer nanocomposites,” <em>Forces in Mechanics</em>, vol. 12, p. 100 207, <strong>2023</strong>.</p> <p><strong>Content:</strong></p> <p>structure of data set:</p> <ul> <li>04_Equilibration<br> folders containing the sample equilibration used in the presented parameter study <ul> <li>01_filler_content<br> variation of filler content</li> <li>02_grafting_density<br> variation of grafting density</li> <li>03_grafting_potential<br> variation of grafting potential</li> <li>04_filler_size<br> variation of filler size</li> <li>05_reference<br> reference samples without grafting</li> </ul> </li> <li>05_UT<br> folders containing the uniaxial tension simulations used in the presented parameter study <ul> <li>01_filler_content<br> variation of filler content</li> <li>02_grafting_density<br> variation of grafting density</li> <li>03_grafting_potential<br> variation of grafting potential</li> <li>04_filler_size<br> variation of filler size</li> <li>05_reference<br> reference samples without grafting</li> </ul> </li> </ul> <p>Each simulation directory contains:</p> <ul> <li> <p>lammps input file (*.in) of the specific simulation</p> </li> <li> <p>data file (*.data) containing the initial sample configuration</p> </li> <li> <p>input.prm: input parameters of the specific simulation (read by the input file)</p> </li> <li> <p>meta.info: meta data of the specific simulation run</p> </li> <li> <p>LAMMPS_out:<br> simulation results (lammps thermo_out) in tabulated form, an overview of columns is given below</p> <ul> <li> <p>thermo_out.Dat: raw output </p> </li> <li> <p>thermo_out_SG.Dat: smoothed output (Savitzky-Golay filter)</p> </li> <li> <p>thermo_out_STD.Dat: standard deviation of raw output</p> </li> </ul> </li> </ul> <p>Output quantities (columns of *.Dat files):<br> Please note that the normalized Lennard-Jones unit set is used, so all quantities are normalized to fundamental mass, length, energy, time and the Boltzmann constant. Thus all entries are unitless [1].</p> <ul> <li> <p>Step: time step </p> </li> <li> <p>Time: time </p> </li> <li> <p>TotEng: total energy </p> </li> <li> <p>PotEng: potential energy</p> </li> <li> <p>KinEng: kinetic energy </p> </li> <li> <p>E_pair: pair energy </p> </li> <li> <p>E_bond: bond energy </p> </li> <li> <p>E_angle: angle energy </p> </li> <li> <p>E_dihed: dihedral energy </p> </li> <li> <p>Temp: temperature</p> </li> <li> <p>Press: hydrostatic pressure</p> </li> <li> <p>Pxx: xx component of pressure tensor </p> </li> <li> <p>Pyy: yy component of pressure tensor </p> </li> <li> <p>Pzz: zz component of pressure tensor </p> </li> <li> <p>Pxy: xy component of pressure tensor</p> </li> <li> <p>Pxz: xz component of pressure tensor</p> </li> <li> <p>Pyz: yz component of pressure tensor</p> </li> <li> <p>Volume: volume of simulation box </p> </li> <li> <p>Lx: box length in x direction </p> </li> <li> <p>Ly: box length in y direction </p> </li> <li> <p>Lz: box length in z direction </p> </li> <li> <p>Density: density </p> </li> <li> <p>c_RG: radius of gyration scalar </p> </li> <li> <p>c_RG[1]: squared radius of gyration tensor (xx component) </p> </li> <li> <p>c_RG[2]: squared radius of gyration tensor (yy component) </p> </li> <li> <p>c_RG[3]: squared radius of gyration tensor (zz component) </p> </li> <li> <p>c_RG[4]: squared radius of gyration tensor (xy component) </p> </li> <li> <p>c_RG[5]: squared radius of gyration tensor (xz component) </p> </li> <li> <p>c_RG[6]: squared radius of gyration tensor (yz component) </p> </li> <li> <p>c_bondave[1]: bond energy averaged over all atoms </p> </li> <li> <p>c_bondave[2]: bond distance averaged over all atoms </p> </li> <li> <p>c_bondave[3]: squared bond distance averaged over all atoms </p> </li> <li> <p>c_angleave[1]: angle energy averaged over all atoms </p> </li> <li> <p>c_angleave[2]: angle averaged over all atoms degree</p> </li> <li> <p>c_angleave[3]: cosine of angle </p> </li> <li> <p>c_angleave[4]: squared cosine of angle </p> </li> <li> <p>c_MSD[1]: mean squared displacement x-direction </p> </li> <li> <p>c_MSD[2]: mean squared displacement y-direction </p> </li> <li> <p>c_MSD[3]: mean squared displacement z-direction </p> </li> <li> <p>c_MSD[4]: total mean squared displacement </p> </li> <li> <p>c_COM[1]: x coordinate of center of mass </p> </li> <li> <p>c_COM[2]: y coordinate of center of mass </p> </li> <li> <p>c_COM[3]: z coordinate of center of mass </p> </li> <li> <p>v_strain_xx: xx component of engineering strain tensor </p> </li> <li> <p>v_strain_yy: yy component of engineering strain tensor </p> </li> <li> <p>v_strain_zz: zz component of engineering strain tensor </p> </li> <li> <p>v_vMisesequivstress: von Mises equivalent stress </p> </li> <li> <p>v_Cauchy_xx: xx component of stress tensor </p> </li> <li> <p>v_Cauchy_yy: yy component of stress tensor</p> </li> <li> <p>v_Cauchy_zz: zz component of stress tensor</p> </li> <li> <p>v_Cauchy_xy: xy component of stress tensor </p> </li> <li> <p>v_Cauchy_xz: xz component of stress tensor </p> </li> <li> <p>v_Cauchy_yz: yz component of stress tensor </p> </li> <li> <p>v_strain_xy: xy component of engineering strain tensor </p> </li> <li> <p>v_strain_xz: xz component of engineering strain tensor </p> </li> <li> <p>v_strain_yz: yz component of engineering strain tensor </p> </li> </ul> <p><strong>References</strong>:</p> <p>[1] M. Ries et al., “Extending a generic and fast coarse-grained molecular dynamics model to examine the mechanical behavior of grafted polymer nanocomposites,” <em>Forces in Mechanics</em>, vol. 12, p. 100 207, <strong>2023</strong>.</p> <p>[2] S. Plimpton, “Fast parallel algorithms for short-range molecular dynamics,” <em>Journal of computational physics</em>, <strong>1995</strong>, 117, 1-19.</p> <p>[3] A. P. Thompson et al., “LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales,” <em>Computer Physics Communications</em>, vol. 271, p. 108171, <strong>2022</strong>.</p> <p>[4] M. Ries, V. Dötschel, J. Seibert, S. Pfaller. “A self-avoiding random walk algorithm (SARW) for generic thermoplastic polymers and nanocomposites”, <em>Zenodo</em>, 2022. <a href="https://doi.org/10.5281/zenodo.6245699">https://doi.org/10.5281/zenodo.6245699</a></p>
A human genome editing-based MLL-AF4 acute lymphoblastic leukemia model recapitulates key cellular and molecular leukemogenic features. (Processed data)
<p>The prognosis of infant B-cell acute lymphoblastic leukemia (iB-ALL) remains dismal, especially in patients harboring the MLL-AF4 (KTM2A-AFF1) rearrangement, which arises prenatally in early hematopoietic stem/progenitor cells (HSPCs) and accounts for 80% of iB-ALL and 10% of non-infant cases. MLL-AF4+ B-ALL shows a bimodal localization of the MLL gene breakpoint within the MLL break cluster region, and two subgroups of patients based on the gene expression pattern of the HOXA/MEIS cluster have been identified. The pathogenic mechanisms in MLL- AF4+ B-ALL are challenging to study functionally due to the absence of faithful human cellular models recapitulating the disease phenotype and latency. Here, we assess the molecular contribution and leukemogenic capacity of MLL breakpoints occurring in either intron 10 (MLL i10 , centromeric) or intron 12 (MLL i12 , telomeric) in ontogenically-different human HSPCs sourced prenatally (fetal liver) and neonatally (cord blood). CRISPR-Cas9-induced MLL-AF4 (MA) targeting either MLL i10 (M i10 A) or MLL i12 (M i12 A) causes MA-driven in vitro myeloid immortalization in both fetal liver- and cord blood-CD34+ HSPCs. The centromeric location of the MLL breakpoint, but not the cellular ontogeny, determined the expression of HOXA/MEIS1 genes in MLL-edited cells. Centromeric MLL breakpoints endowed enhanced myeloid clonogenic replating to MLL- edited CD34+ HSPCs. The cellular ontogeny and the location of the MLL breakpoint also influenced the capacity of MLL-edited CD34+ HSPCs to initiate pro-B-ALL in vivo, which faithfully recapitulated the molecular, transcriptomic and methylome profiles of patients with primary MA+ iB-ALL. Our data provide key insights into the cellular and molecular leukemogenic determinants of MA+ iB-ALL. This dataset contains processed RNAseq and DNA methylation data from the abovementioned study.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.