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190 results for “Homo”
Research compendium for 'Refitting the Context: A Reconsideration of Cultural Change among Early Homo sapiens at Fumane Cave through Blade Break Connections, Spatial Taphonomy, and Lithic Technology'
<div> <h3>Compendium DOI:</h3> <p><a href="../doi/10.5281/zenodo.10965413">https://zenodo.org/doi/10.5281/zenodo.10965413</a> </p> </div> <p>The content available at the above provided URL will reproduce the results as documented in the publication. Instead, the files hosted at <a href="https://github.com/ArmandoFalcucci/Refitting-The-Context">https://github.com/ArmandoFalcucci/Refitting-The-Context</a> represent the developmental versions and might have undergone modifications since the paper's publication.</p> <div> <h3>Maintainer of this repository:</h3> </div> <p>Armando Falcucci (<a href="mailto:armando.falcucci@uni-tuebingen.de">armando.falcucci@uni-tuebingen.de</a>)</p> <div> <h3>Published paper:</h3> </div> <p>Armando Falcucci, Domenico Giusti, Filippo Zangrossi, Matteo De Lorenzi, Letizia Ceregatti, Marco Peresani. Refitting the Context: Revisiting the Aurignacian sequence at Fumane Cave through blade fragment connections, spatial taphonomy, and lithic technology. <em>Journal of Paleolithic Archaeology</em> (2024). DOI: <a href="https://doi.org/10.1007/s41982-024-00203-0" rel="nofollow">10.1007/s41982-024-00203-0</a></p> <div> <h3>Abstract:</h3> </div> <p>High-resolution stratigraphic frameworks are crucial for unraveling the biocultural processes behind the dispersals of Homo sapiens across Europe. Detailed technological studies of lithic assemblages retrieved from multi-stratified sequences allow archaeologists to precisely model the chrono-cultural dynamics of the early Upper Paleolithic. However, it is of paramount importance to verify the integrity of these assemblages before building explanatory models of cultural change. In this study, multiple lines of evidence suggest that the stratigraphic sequence of Fumane Cave in northeastern Italy experienced minor post-depositional reworking, establishing it as a pivotal site for exploring the earliest stages of the Aurignacian. By conducting a systematic search for break connections between blade fragments and applying spatial analysis techniques, we identified three well-preserved areas of the excavation containing assemblages suitable for renewed archaeological investigations. Subsequent technological analyses, incorporating attribute analysis, reduction intensity, and multivariate statistics, have allowed us to discern the spatial organization of the site during the formation of the Protoaurignacian palimpsest A2–A1. Moreover, diachronic comparisons between three successive stratigraphic units prompted us to reject the hypothesis of techno-cultural continuity of the Protoaurignacian in northeastern Italy after the onset of the Heinrich Event 4. Based on the variability of the lithic and osseous artifacts, the most recent assemblage analyzed, D3b alpha, is now ascribed to the Early Aurignacian, aligning the evidence from Fumane with the current understanding of the development of the Aurignacian across Europe. Overall, this study demonstrates the high effectiveness of the break connection method when combined with detailed spatial analysis and lithic technology, providing a methodological tool particularly amenable to be applied to sites excavated in the past with varying degrees of recording accuracy.</p> <div> <h3>Keywords:</h3> </div> <p>Protoaurignacian; Early Aurignacian; Lithics; Refittings; Assemblage integrity; Spatial analysis; Italy</p> <div> <h3>Overview of contents and how to reproduce:</h3> </div> <p>Within this repository, various folders house data (<code>data</code>), code (<code>script</code>), and output files (<code>output</code>) pertinent to the paper. The data folder encompasses the blank and core datasets from the Aurignacian of Fumane Cave and the dataset of the blade fragment connection study. To replicate the results, download the entire repository and employ <code>Refitting-The-Context.Rproj</code> and open the folder <code>script</code>. For ensuring reproducibility, the <code>renv</code> package (v. 1.0.3) was utilized, following the procedures detailed in its vignette. All analyses and visualizations in the paper were conducted using R 4.3.1 on Microsoft Windows 10.0.19045 (64-bit). As the necessary packages are available in the <code>renv</code> folder, they are not explicitly listed here.</p> <div> <h3>Licenses:</h3> </div> <p>Code: <strong>MIT</strong> <a href="http://opensource.org/licenses/MIT" rel="nofollow">http://opensource.org/licenses/MIT</a>, copyright holder: Armando Falcucci (2024).</p> <p>Data and intellectual work: <strong>Creative Commons Attribution 4.0 International License</strong> (<a href="http://creativecommons.org/licenses/by/4.0/" rel="nofollow">http://creativecommons.org/licenses/by/4.0/</a>), copyright holder: the authors (2024).</p>
Host removal database: Homo sapiens, Sars-Cov-2, PhiX174
<p>💾 <strong>cleanup-db</strong></p> <p>Kraken2 database, built upon a viral sequence masked human reference from:</p> <ul> <li>Handley, Scott A. (2020). <strong>Virus+ Sequence Masked Human Reference Genome (hg19)</strong> (1.0) [Data set]. Zenodo. [<a href="https://zenodo.org/record/4116107">10.5281/zenodo.4116107</a>]</li> </ul> <p>but separating chromosomes as artificial taxa to allow for QC, and includes Sars-Cov-2 and PhiX 174</p> <p>💾 <strong>gutcheck-db</strong></p> <p>A very small DB containg some common gut bacteria and Human and Murine mitochondrial genome:</p> <ul> <li><em>Akkermansia muciniphila</em></li> <li><em>Bacteroides fragilis</em></li> <li><em>Bifidobacterium longum</em></li> <li><em>Blautia obeum strain</em></li> <li><em>Escherichia coli</em></li> <li><em>Enterococcus faecium</em></li> <li><em>Prevotella copri</em></li> </ul> <p> </p> <p>See: <a href="https://github.com/telatin/cleanup">https://github.com/telatin/cleanup</a></p>
The immature Homo naledi ilium from the Lesedi Chamber, Rising Star Cave, South Africa
<p>To use any of these data, please cite: Cofran Z, VanSickle C, Valenzuela R, García-Martínez D, Walker CS, Hawks J, Zipfel B, Williams SA, & Berger LR. 2022. The immature <em>Homo naledi</em> ilium from the Lesedi Chamber, Rising Star Cave, South Africa. American Journal of Biological Anthropology 179:3–17. (https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.24522)</p> <p>Lesedi Ilium Landmark Dataset_R1.csv = A comma separated values (.csv) format file containing 148 3D landmarks describing shape of the right ilium, for 23 immature humans, <em>Australopithecus</em> fossils MLD 7 and MLD 25, and two reconstructions of the <em>Homo naledi</em> fossil U.W. 102a-138. The first naledi reconstruction utilizes a reference template based on MLD 7 and MLD 25, and the second reconstruction is based on the average of the human ilia. The .csv file contains columns for individual ID, landmark name, and the x-, y-, and z-coordinates of the landmark, and each row is a unique landmark coordinate.</p> <p>Lesedi_Ilium_Height_Data.csv = A comma separated values (.csv) format file containing developmental stage and iliac height (in mm) for 43 humans, U.W. 102a-138, and three <em>Australopithecus</em> fossils (MLD 7, MLD 25, and the left and right sides of Sts 14).</p> <p>A 3D mesh of the U.W. 102a-138 ilium is available on Morphosource: https://www.morphosource.org/concern/media/000383216?locale=en</p>
Orthologs for Homo Sapiens and Drosophila Melanogaster from the Roundup Orthology Database Version 4
<p>This dataset contains orthologs for Homo sapiens and Drosophila melanogaster, computed with the Reciprocal Smallest Distance algorithm using a divergence threshold of 0.8 and an e-value threshold of 1e-5. The orthologs were downloaded from version 4 of the Roundup database, which is no longer available.</p>
ePSproc: ABCO, HOMO ioinzation (A1), orb 31
<p>ABCO, HOMO ioinzation (A1), orb 31 - photoionization calculations with ePolyScat (ePS) + ePSproc.<br> <br> *Web version*: <a href="https://phockett.github.io/ePSdata/ABCO/ABCO_1-50eV_orb31_A1.html">https://phockett.github.io/ePSdata/ABCO/ABCO_1-50eV_orb31_A1.html</a><br> <br> For more details of the calculations, see readme.txt, or:</p> <ul> <li><a href="https://phockett.github.io/ePSdata/about.html">About ePSdata</a></li> <li><a href="http://epsproc.readthedocs.io/en/latest/about.html">About ePSproc</a></li> <li><a href="http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html">About ePS</a></li> </ul>
ePSproc: DABCO, HOMO-1 ionization (orb 30, A2PP), 1 - 50eV
DABCO, HOMO-1 ionization (orb 30, A2PP), 1 - 50eV - photoionization calculations with ePolyScat (ePS) + ePSproc.<br><br>*Web version*: <a href="https://phockett.github.io/ePSdata/DABCO/DABCO_1-50.0eV_orb30_A2PP.html">https://phockett.github.io/ePSdata/DABCO/DABCO_1-50.0eV_orb30_A2PP.html</a><br><br>For more details of the calculations, see readme.txt, or: <ul><li><a href="https://phockett.github.io/ePSdata/about.html">About ePSdata</a></li><li><a href="http://epsproc.readthedocs.io/en/latest/about.html">About ePSproc</a></li><li><a href="http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html">About ePS</a></li></ul>
ePSproc: Ethylene (C2H4), orb 7 (HOMO-1) ionization (B3g), wavefn run, 1.0:2.5:100.0
Ethylene (C2H4), orb 7 (HOMO-1) ionization (B3g), wavefn run, 1.0:2.5:100.0 - photoionization calculations with ePolyScat (ePS) + ePSproc.<br><br>*Web version*: <a href="https://phockett.github.io/ePSdata/C2H4_1.0-100.0eV/C2H4_1.0-100.0eV_orb7_B3g.html">https://phockett.github.io/ePSdata/C2H4_1.0-100.0eV/C2H4_1.0-100.0eV_orb7_B3g.html</a><br><br>For more details of the calculations, see readme.txt, or: <ul><li><a href="https://phockett.github.io/ePSdata/about.html">About ePSdata</a></li><li><a href="http://epsproc.readthedocs.io/en/latest/about.html">About ePSproc</a></li><li><a href="http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html">About ePS</a></li></ul>
ePSproc: Naphthalene HOMO Orb 34 (Au) ionization, 1.0 - 30.1 eV
Naphthalene HOMO Orb 34 (Au) ionization, 1.0 - 30.1 eV - photoionization calculations with ePolyScat (ePS) + ePSproc.<br><br>*Web version*: <a href="https://phockett.github.io/ePSdata/naphthalene/naphthalene_wf_1.0-30.1eV_orb34.html">https://phockett.github.io/ePSdata/naphthalene/naphthalene_wf_1.0-30.1eV_orb34.html</a><br><br>For more details of the calculations, see readme.txt, or: <ul><li><a href="https://phockett.github.io/ePSdata/about.html">About ePSdata</a></li><li><a href="http://epsproc.readthedocs.io/en/latest/about.html">About ePSproc</a></li><li><a href="http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html">About ePS</a></li></ul>
ePSproc: Naphthalene HOMO Orb 34 (Au) ionization, 1-10eV
Naphthalene HOMO Orb 34 (Au) ionization, 1-10eV - photoionization calculations with ePolyScat (ePS) + ePSproc.<br><br>*Web version*: <a href="https://phockett.github.io/ePSdata/naphthalene/naphthalene_wf_1.0-10.1eV_orb34.html">https://phockett.github.io/ePSdata/naphthalene/naphthalene_wf_1.0-10.1eV_orb34.html</a><br><br>For more details of the calculations, see readme.txt, or: <ul><li><a href="https://phockett.github.io/ePSdata/about.html">About ePSdata</a></li><li><a href="http://epsproc.readthedocs.io/en/latest/about.html">About ePSproc</a></li><li><a href="http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html">About ePS</a></li></ul>
SUBATOMIC analysis of Homo sapiens integrated multi-edge networks
<p>We applied SUBATOMIC (https://github.com/CBIGR/SUBATOMIC/) to analyze a composite <em>H. sapiens</em> network containing transcription factor-target gene, miRNA-target gene, protein-protein, homologous and co-functional interactions from three different databases. We derived and annotated 5586 modules with diverse topological, regulatory and functional properties.</p>
US Hetero–Homo conversion test
<p># US Hetero–Homo conversion test</p> <p> </p> <p>## Paper information</p> <p>(under review)</p> <p>Deep Learning for Hetero–Homo Conversion in Channel-Domain for Phase Aberration Correction in Ultrasound Imaging</p> <p>Tatsuki Koike, Naoki Tomii, Yoshiki Watanabe, Takashi Azumaa, Shu Takagi</p> <p> </p> <p>## Required</p> <p>+ Matlab 2018b</p> <p> + Matlab Signal Processing Toolbox version 8.1</p> <p> + Matlab Image Processing Toolbox version >= 9.3</p> <p>+ Docker version 20.10.14</p> <p> </p> <p>## How to test</p> <p> </p> <p>### RF Data Cropping</p> <p>[Shell]</p> <p>> cd code/rfdata_cropping</p> <p>> matlab ./RFDataCropping</p> <p> </p> <p>### RF Data Conversion Using Deep Neural Network</p> <p>[Shell]</p> <p>> cd code/prediction</p> <p>> ./build.sh</p> <p>> ./run.sh</p> <p> </p> <p>### B-Mode Image Reconstruction</p> <p>[Shell]</p> <p>> cd code/analysis</p> <p>> matlab ./BModeReconstruction\(true\)</p> <p>\# boolean flag is true if image reconstruction is performed using rf data processed by DNN</p> <p> </p> <p>## Contents</p> <p> </p> <p>+ code</p> <p> + analysis : Matlab scripts for B-mode image reconstruction</p> <p> + item : Matlab matrices</p> <p> + prediction : python scripts for Hetero–Homo conversion test</p> <p> + rfdata_cropping : Matlab scripts for rf data cropping</p> <p>+ data</p> <p> + test</p> <p> + hetero : cropped rf data for Hetero–Homo conversion</p> <p>+ result</p> <p> + dnn_result : trained model</p> <p> + images : B-mode images of test data</p> <p> + sim_result : K-wave simlation results</p> <p> </p>
Fig. 13a-m in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 13a-m Tyrrhenocythere ex. gr. bailovi (Livental) in Mandelstam et al., 1962; a LV, external view, ♂; b RV, external view, ♂; c LV, external view, ♀; d RV, external view, ♀; e LV, internal view, ♀; f RV, internal view, ♂; g Carapace, dorsal view, ♀; h LV, external view, ♂; i LV, external view, A1 juvenile; j LV, external view, A2 juvenile; k RV, external view, A2 juvenile; l LV, external view, A3 juvenile; m RV, external view, A3 juvenile (all specimens from sample DE06, DE08 and DE11, Faber Quarry, Kocabaş, Denizli).
Fig. 16a-p in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 16a-p Loxoconchissa (Loxocaspia) aff. reticulata Faranda, Gliozzi and Ligios; a LV, external view, ♀; b RV, external view, ♀; c RV, internal view, ♀; d RV, internal view, ♀; e Carapace, dorsal view, ♀; f Carapace, ventral view, ♀; g, i LV, external view, ♂; h, j RV, external view, ♂; k Carapace, dorsal view, ♂; l Carapace, ventral view, ♂; m LV, internal view, ♂; n RV, dorsal-internal view, ♂; o LV, external view, A1 juvenile; p LV, external view, A2 juvenile (a-f, o, p from sample DE06, g-n from sample DE9, Faber Quarry, Kocabaş, Denizli).
Fig. 12a-l in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 12a-l Tyrrhenocythere pontica (Livental); a LV, external view, ♂; b RV, external view, ♂; c LV, external view, ♀; d RV, external view, ♀; e LV, internal view, ♀; f RV, internal view, ♀; g Carapace, dorsal view, ♂; h Carapace, ventral view, ♀; i LV, external view, A1 juvenile; j RV, external view, A1 juvenile; k LV, external view, A2 juvenile; l RV, external view, A2 juvenile (all specimens from sample DE06, DE08 and DE11, Faber Quarry, Kocabaş, Denizli).
Fig. 9a-m in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 9a-m Prionocypris zenkeri (Chyzer & Toth); a, c LV, external view; b, d RV, external view; e LV, internal view; f RV, internal view; g LV, external view, A1 juvenile; h RV, external view, A1 juvenile; i LV, external view, A2 juvenile; j RV, external view, A2 juvenile; k RV, external view, A3 juvenile; l LV, external view, A4 juvenile; m RV, external view, A4 juvenile (all specimens from sample DE11, Faber Quarry, Kocabaş, Denizli).
Fig. 1a in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 1a Location of the Denizli Basin; b. Geological map of the Denizli Basin with indication of travertine units exposed (based on Sun, 1990).
Fig. 8a-i in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 8a-i Lineocypris sp.; a, c LV, external view; b, d, g RV, external view; e LV, internal view; f RV, internal view; h RV, external view, A1 juvenile; i RV, external view, A2 juvenile (all specimens from sample DE06, Faber Quarry, Kocabaş, Denizli).
Fig. 11a-d in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 11a-d Cyprideis torosa (Jones), un- nodded specimens; a LV, external view, ♀; b RV, external view, ♀; c LV, external view, ♂; d RV, external view, ♂; e-l Cyprideis sp.; e, g LV, external view, ♀; f RV, external view, ♀; h RV, external view, ♂; i LV, internal view, ♀; j RV, internal view, ♂; k Carapace, ventral view, ♀; l Carapace, dorsal view, ♀ (all specimens from sample DE06, Faber Quarry, Kocabaş, Denizli).
Fig. 7a-f in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 7a-f Cypria sp.; a, c LV, external view; b. RV, external view; d, e Carapace, lateral view from RV; f RV, internal view; g-k Darwinula stevensoni (Brady & Robertson); g LV, external view; h RV, external view; i, j LV, internal view; k Carapace, ventral view (a-f, sample DE09; g-k, sample DE07; Faber Quarry, Kocabaş, Denizli).
Fig. 15a-j in AN EARLY PLEISTOCENE ANOMALOHALINE WATER OSTRACOD FAUNA FROM LAKE DEPOSITS OF THE HOMO ERECTUS-BEARING KOCABAŞ LOCALITY (SW TURKEY)
Fig. 15a-j Amnicythere pediformis (Schornicov); a LV, external view, ♂; b RV, external view, ♂; c LV, external view,?♀; d RV, external view,?♀; e LV, internal view, ♀; f RV, internal view, ♂; g Carapace, dorsal view, ♀; h Carapace, ventral view, ♂; i LV, external view, A1 juvenile; j LV, external view, A2 juvenile; k-o Amnicythere multituberculata (Livental); k LV, external view, ♀; l RV, external view, ♀; m LV, external view, ♂; n RV, internal view, ♂; o Carapace, dorsal view, ♀ (all specimens from sample DE08, Faber Quarry, Kocabaş, Denizli).
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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.