255 research outputs found
Hydration and nanomechanical changes in collagen fibrils bearing advanced glycation end-products
Full text linkAccumulation of advanced glycation end-products (AGEs) in biological tissues occurs as a consequence of normal ageing and pathology. Most biological tissues are composed of considerable amounts of collagen, with collagen fibrils being the most abundant form. Collagen fibrils are the smallest discernible structural elements of load-bearing tissues and as such, they are of high biomechanical importance. The low turnover of collagen cause AGEs to accumulate within the collagen fibrils with normal ageing as well as in pathologies. We hypothesized that collagen fibrils bearing AGEs have altered hydration and mechanical properties. To this end, we employed atomic force and Brillouin light scattering microscopy to measure the extent of hydration as well as the transverse elastic properties of collagen fibrils treated with ribose. We find that hydration is different in collagen fibrils bearing AGEs and this is directly related to their mechanical properties. Collagen fibrils treated with ribose showed increased hydration levels and decreased transverse stiffness compared to controlled samples. Our results show that BLS and AFM yield complementary evidence on the effect of hydration on the nanomechanical properties of collagen fibrils.</p
An Author Writing to Remember and Celebrate Black Children
No full textWith an undergraduate degree in sociology from Morgan State University (Baltimore, MD) and a master’s degree in Library Science from the Catholic University of America (Washington, DC), Sharon Bell Mathis is a librarian and a multiple award-winning children’s and young adult book author [...
Pretrained Transformers of "B-spline Curve Approximation With Transformer Neural Networks" article
No full textPretrained Transformers of B-spline Curve Approximation With Transformer Neural Networks article
This dataset contains model checkpoints along with configuration and log files of trained transformer neural networks. Those networks have been trained following the methodology described in the link article. The following github repository can be used to read, test and process the data found in this dataset : bspline-curve-approximation-transformer.
The Readme file can help you understand the nature of the data to help you in treating it yourself. A recent version of Pytorch is required to load some of the data (i.e. model checkpoints and parameters).
The training logs and inference results come as csv and txt files and can be read and processed by any software of your choice.
See Readme.md for a more detailed description of files and parameters. Feel free to contact the author regarding questions/problems with the data.</p
Global and local estimates of environmental flow requirements to sustain river ecosystems are poorly correlated
No full textData repository for ‘Global and local estimates of environmental flow requirements to sustain river ecosystems are poorly correlated ‘
prepared by Mathis L. Messager ([email protected])
1. Overview and background ----------------------------------------------------------
This documentation describes the input and output data associated with the analysis presented in: Messager, M. L., Dickens, W. S. C., Eriyagama, N., Tharme, R. E., Stassen, R. (2024). Limited comparability of global and local estimates of
environmental flow requirements to sustain river ecosystems. https://doi.org/10.1088/1748-9326/ad1cb5.
Environmental flows (e-flows) are a central element of sustainable water resource management to mitigate the detrimental impacts of hydrological alteration on freshwater ecosystems and their benefits to people. Many nations strive to protect e-flows through policy, and thousands of local-scale e-flows assessments have been conducted globally, leveraging data and knowledge to quantify how much water must be provided to river ecosystems, and when, to keep them healthy. However, e-flows assessments and implementation are geographically uneven and cover a small fraction of rivers worldwide. This hinders globally consistent target-setting, monitoring and evaluation for international agreements to curb water scarcity and biodiversity loss. Therefore, dozens of models have been developed over the past two decades to estimate the e-flows requirements of rivers seamlessly across basins and administrative boundaries at a global scale.There has been little effort, however, to benchmark these models against locally derived e-flows estimates, which may limit confidence in the relevance of global estimates. The aim of this study was to assess whether current global methods reflect e-flows estimates used on the ground, by comparing global and local estimates for 1194 sites across 25 countries. We found that while global approaches broadly approximate the bulk volume of water that should be precautionarily provided to sustain aquatic ecosystems at the scale of large basins or countries, they explain a remarkably negligible 0%–1% of the global variability in locally derived estimates of the percentage of river flow that must be protected at a given site. Even when comparing assessments for individual countries, thus controlling for differences in local assessment methods among jurisdictions, global e-flows estimates only marginally compared (R2 ⩽ 0.31) to local estimates. Such a disconnect between global and local assessments of e-flows requirements limits the credibility of global estimates and associated targets for water use. To accelerate the global implementation of e-flows requires further concerted effort to compile and draw from the thousands of existing local e-flows assessments worldwide for developing a new generation of global models and bridging the gap from local to global scales..
The data repository includes data required to perform this analysis as well as the data outputs from this analysis. Input data from local e-flow assessments included herein were either provided by collaborators or extracted from published governmental and academic reports by the authors. Input hydrographic data not available for download elsewhere were provided by Dr. Bernhard Lehner and hydrological simulations from PCR-GLOBWB 2.0 at a spatial resolution of 5 arc-min (not provided herein) were provided by Dr. ir. Edwin H. Sutanudjaja.
All scripts necessary to reproduce this analysis are freely available for all purposes (and can be copied, modified and distributed) at: https://github.com/messamat/globalEF_testPy (for data-preformatting and global e-flow calculations) and https://github.com/messamat/globalEF_testR (for comparing global and local MAF and e-flow estimates). The structure of the analysis relies as much as possible on good enough practices in scientific computing, which users are encouraged to read.
2. Repository content ----------------------------------------------------------
The data repository has the following structure, which must be conserved to run the analysis workflow:
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data/
Formatted_data_Chandima_20211018: pre-formatted local e-flow assessment sites.
Formatted_data_Chandima_20211102: pre-formatted local e-flow assessment sites.
GEFIS_test_data/:
Master Data Table_20230424.xlsx: final database of local e-flow assessments.
HydroATLAS/: hydrographic data required for downscaling and mapping global MAF and e-flow estimates
HydroATLAS_metadata_MLMv11.xlsx: metadata of RiverATLAS attributes used in producing distribution histogram in Supplementary Material.
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results/
france_preprocessing.gdb: outputs from spatial formatting of local e-flow assessment data for the Rhone River basin in France. The main output file is /Rhone_EFpoints_cleanjoin.
mexico_preprocessing.gdb: outputs from spatial formatting of local e-flow assessment data for Mexico. The main output file is /Mexico_EFpoints_cleanjoin.
processing_outputs.gdb: outputs from overall spatial formatting of local e-flow assessment data. The fully formatted point data of the sites is: EFpoints_20230424_clean_riverjoin. Associated with global e-flow estimates: EFpoints_20230424_clean_globalEF.
victoria_preprocessing.gdb: outputs from spatial formatting of local e-flow assessment data for the state of Victoria, Australia. The main output file is /Victoria_EFpoints_cleanjoin.
EFpoints_20230424_clean_globalEF.csv: all global e-flow estimates extracted for local e-flow assessment sites.
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isimp2_qtot_accumulated15s.gdb.zip: all global MAF and e-flow estimates in raster format. In the analytical workflow, these data are in the results/ folder but here they have been placed outside to conform with the maximum file size limit of this dataverse.
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README_Technical_documentation_globalEFcomparison_Messageretal2023.pdf : documentation for this repository
3. Data format and projection ----------------------------------------------------------
The spatial datasets are distributed in ESRI® file geodatabase format. Please contact the author should you want the data in another format. These datasets are available in compressed zip file format. To use the data files, the zip files must first be decompressed.
All data layers are provided in geographic (latitude/longitude) projection, referenced to datum WGS84. In ESRI® software this projection is defined by the geographic coordinate system GCS_WGS_1984 and datum D_WGS_1984 (EPSG: 4326).
4. License and citations ----------------------------------------------------------
4.1 License agreement
This documentation and datasets are licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC-BY-4.0 License). For all regulations regarding license grants, copyright, redistribution restrictions, required attributions, disclaimer of warranty, indemnification, liability, waiver of damages, and a precise definition of licensed materials, please refer to the License Agreement (https://creativecommons.org/licenses/by/4.0/legalcode). For a human-readable summary of the license, please see https://creativecommons.org/licenses/by/4.0/.
4.2 Citations and acknowledgements.
Citations and acknowledgements of this dataset should be made as follows:
Messager, M. L., Dickens, W. S. C., Eriyagama, N., Tharme, R. E., Stassen, R. (2024). Limited comparability of global and local estimates of
environmental flow requirements to sustain river ecosystems. Environmental Research Letters. https://doi.org/10.1088/1748-9326/ad1cb5.
We kindly ask users to cite this study in any published material produced using it. If possible, online links to this repository (DOI) should also be provided
Data for Contrasting action and posture coding with hierarchical deep neural network models of proprioception
No full text#############
Contrasting action and posture coding with hierarchical deep neural network models of proprioception, eLife 2023
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Authors: Kai J Sandbrink, Pranav Mamidanna, Claudio Michaelis, Matthias Bethge, Mackenzie W Mathis and Alexander Mathis
Affiliation: Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland, The Rowland Institute at Harvard, Harvard University, United States; Tübingen AI Center, Eberhard Karls Universität Tübingen & Institute for Theoretical Physics, Germany
Date of upload: December, 2024
Earlier the data was available via dropbox (see github).
Link to the eLife article:
https://elifesciences.org/articles/81499
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Here we provide the data and code for this project:
We share the proprioceptive character recognition dataset (contained in 'pcr_data.zip') it has approximately ~29GB when uncompressed.
We share the weights of all the trained networks (contained in 'network-weights.zip'): about ~3.5GB
The compressed code is also available here ('DeepDrawCode.zip').
The activations are shared in a separate Zenodo project (due to the size). Check out the repository below to find the link.
The up to date code is at: https://github.com/amathislab/DeepDraw
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The datasets, weights, activations and predictions are released with Creative Commons Attribution 4.0 license.
If you find this useful, please cite:
@article{sandbrink2023contrasting, title={Contrasting action and posture coding with hierarchical deep neural network models of proprioception}, author={Sandbrink, Kai J and Mamidanna, Pranav and Michaelis, Claudio and Bethge, Matthias and Mathis, Mackenzie Weygandt and Mathis, Alexander}, journal={Elife}, volume={12}, pages={e81499}, year={2023}, publisher={eLife Sciences Publications Limited}}UPAMATHISUPMWMATHI
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Efficiency Instead of Justice? ::Searching for the Philosophical Foundations of the Economic Analysis of Law /
No full textEconomic analysis of law is an interesting and challenging attempt to employ the concepts and reasoning methods of modern economic theory so as to gain a deeper understanding of legal problems. According to Richard A. Posner it is the role of the law to encourage market competition and, where the market fails because transaction costs are too high, to simulate the result of competitive markets. This would maximize economic efficiency and social wealth. In this work, the lawyer and economist Klaus Mathis critically appraises Posner's normative justification of the efficiency paradigm from the perspective of the philosophy of law. Posner acknowledges the influences of Adam Smith and Jeremy Bentham, whom he views as the founders of normative economics. He subscribes to Smith's faith in the market as an ideal allocation model, and to Bentham's ethical consequentialism. Finally, aligning himself with John Rawls's contract theory, he seeks to legitimize his concept of wealth maximization with a consensus theory approach. In his interdisciplinary study, the author points out the possibilities as well as the limits of economic analysis of law. It provides a method of analysing the law which, while very helpful, is also rather specific. The efficiency arguments therefore need to be incorporated into a process for resolving value conflicts. In a democracy this must take place within the political decision-making process. In this clearly written work, Klaus Mathis succeeds in making even non-economists more aware of the economic aspects of the law. "Mathis gives a succinct and lucid presentation of the economic theory of law, and of the problems associated with its application as a normative theory in law. At the same time, he rightly draws attention to the advantages associated with this approach, and provides a helpful and thoroughly ambitious introduction to its fundamental principles." Prof. Dr. Jan-R. Sieckmann, Archives for Philosophy of Law and Social Philosophy (ARSP), Vol. 91/2 (2006)
Sepedonea giovana Marinoni & Mathis, 2006, sp. nov.
No full text<i>Sepedonea giovana</i>, sp. nov. (Figs. 1 –11; 27; 41) <p> <i>Sepedonea guianica</i> of authors, not Steyskal [misidentification]. Knutson et al. 1976: 11 [Neotropical catalog; partim]. Knutson & Valley 1978: 198 [review; partim]. Freidberg <i>et al</i>. 1991: 16 [revision; partim].</p> <p> <i>Sepedonea vau.</i> Mello and Bredt 1978: 1459 [nomen nudum; phenology].</p> <p> <b>Diagnosis.</b> This species is distinguished from congeners (described in Freidberg <i>et al.</i>, 1991) especially <i>S. guianica,</i> by the following combination of characters: Mesonotum grayish black; setulae near posterior thoracic spiracle moderately numerous, weak but well developed. Wing (Fig. 5) infuscate, clouded. Midfemur bearing 3–5 spine­like setae posteroventrally; hindfemur with more or less discrete, usually dark, preapical lateral mark.</p> <p> <b>Description.</b> Adult. <i>Head:</i> Ocellar seta absent; postocellar seta absent. Fronto­orbital spot absent; orbito­antennal spot absent; face with a large brown spot at ventral corner.</p> <p> <i>Thorax:</i> Mesonotum grayish black; postpronotum brownish; setulae near posterior spiracle moderately strong and dense; setation near posterior spiracle weakly developed; setae on katatergal callus absent. Wing: Length 5.0–6.0 mm; brownish, usually clouded anteroapically and over crossveins r­m and dm­cu. Legs: Forefemur bearing at least 1 well­developed seta; midfemur usually bearing 3–6 spine­like setae posteroventrally, not extended beyond half distance to base, lacking setae along anterior surface; hindcoxa bearing short setulae posteriorly, mostly restricted to medial portion; hindfemur claviform, usually with dark, preapical marks, height/width ratio 4.5–5.0; hindtibia with a spinelike projection but lacking a distinctive seta at ventroapical margin.</p> <p> <i>Abdomen:</i> Male terminalia (Figs. 6–10): Posterior margin of 4th sternite deeply emarginate, with 2 lateral processes (Fig. 7); anterior plate of 5th sternite not reduced, with wide, indented flange at posteromedial margin folded ventrally (Fig. 6), posterior portion with a pair of moderately­sized processes; distiphallus (Fig. 8) sinuous, with posteroventral angle covered by large flat, setulose epiphallus; anterior surstylus small, indistinct; posterior surstyli completely fused to form a medial structure, this structure without a medial lobe; posterior surstylus with lateral lobe moderately strongly curved anteriorly (Fig. 9); epiphallus large; distiphallus absent. Female synsternite (Figs. 11; 27): Posterior margin in ventral view with ventral surface more or less straight, and with posterior ridge distinctly projected, rounded (Fig. 11); spermathecal duct at junction with spermatheca divided in 2 portions, portion closest to spermatheca wide (Fig. 27).</p> <p> <b>FIGURES 6–11.</b> <i>Sepedonea giovana</i> <b>sp. n.</b> 6. male 5th sternite; 7. male 4th sternite; 8. distiphallus lateral view; 9. posterior surstyli, posterior view; 10. posterior surstyli, lateral view; 11. female synsternite, ventral view.</p> <p> <b>Type specimens.</b> The holotype male is labeled “ BRAZIL: Minas Gerais: 17 km N of Belo Horizonte [43°56’W. 19°45’S] C. O. Berg 18–23 July 1964 / HOLOTYPE ɗ <i>Sepedonea giovana</i> Marinoni & Mathis [red].” The holotype is directly pinned, is in excellent condition, and is deposited in the USNM. Twenty­five male paratypes bear the same locality label as the holotype (DZUP, USNM). Other paratypes are as follows: BRAZIL. <i>Minas Gerais:</i> Belo Horizonte (43°56’W. 19°55’S), 18–23 Jul 1964, C. O. Berg (3ɗ, 3Ψ; USNM). <i>Paraná</i>: Curitiba (61 km S), Rio Varzea (49°15’W. 25°58’S), 16 May 1967, J. Abercrombie, C. O. Berg (5ɗ, 2Ψ; USNM); Morretes (6 km SE; 48°46.7’W. 25°30.3’S), 4–17 May 1967, J. Abercrombie, C. O. Berg (1Ψ; USNM); Praia do Leste (48°28’W. 25°41.5’S), 4 May 1967, J. Abercrombie, C. O. Berg (10ɗ, 11Ψ; DZUP, USNM); Rio Iguassu at Araucaria (51°12’W. 30°48’S), 1 May 1967, J. Abercrombie, C. O. Berg (1ɗ; USNM). <i>Rio Grande do Sul:</i> Porto Alegre (87 km S; 51°12’W. 30°48’S), 10 May 1967, J. Abercrombie, C. O. Berg (1Ψ; USNM). <i>Santa Catarina:</i> Lajes (5 km W; 50°21.7’W. 27°48’S), 6 May 1967, J. Abercrombie, C. O. Berg (1ɗ; USNM); Lajes (30 km S; 50°19’W. 28°04.2’S), 12 May 1967, J. Abercrombie, C. O. Berg (1Ψ; USNM). <i>São Paulo</i>: São José do Rio Preto (48°23’W. 20°48.1’S), 27 Jul 1966, N. Papavero (1ɗ; USNM).</p> <p> <b>Type locality.</b> Brazil. Minas Gerais: Belo Horizonte (17 km N; 43°56’W. 19°45’S).</p> <p> <b>Other specimens examined.</b> ARGENTINA. <i>Tucumán:</i> Monteros (65°30’W. 27°12’S), 7 Feb 1967, C. O. Berg, J. Abercrombie (1ɗ; USNM).</p> <p> BRAZIL. <i>Minas Gerais</i>: Jockey Club, 23 Aug–15 Sep 1966, C. O. Berg (12ɗ, 3Ψ; USNM).</p> <p> <b>Locality records from Mello & Bredt (1978).</b> BRAZIL. <i>Distrito Federal:</i> Núcleo Bandeirantes (47°58’W. 15°52’S), 11 Nov 1974, D. A. Mello, A. Bredt; Riberão Extrema, DF 21, 6 Feb 1974, D. A. Mello, A. Bredt. <i>Minas Gerais:</i> Hipódromo Serra Verde, Santa Luzia (43°20.6’W. 21°47.3’S), 24 Aug 1974, D. A. Mello, A. Bredt. <i>Goiás:</i> Rio Preto, Formosa (47°20’W. 15°32’S), 19 Jun 1974, Jan–May, Jul–Oct, Dec 1975, 1976, D. A. Mello, A. Bredt.</p> <p> <b>Distribution (Fig. 41).</b> Neotropical: Argentina (Tucumán) and Brazil (Goiás, Distrito Federal, Espirito Santo, Minas Gerais, Paraíba, Paraná, São Paulo).</p> <p> <b>Etymology.</b> The species epithet, <i>giovana,</i> is a noun in apposition and is named after the delightful daughter of the first author and her husband, Sionei Ricardo Bonatto, whose support is also appreciated.</p> <p> <b>Remarks.</b> Externally, the species of <i>Sepedonea</i> are difficult to distinguish and reference to structures of the male terminalia is usually needed to determine species accurately.</p> <p> The distribution map includes a few localities that we extracted from Mello & Bredt (1978), as noted above. We did not include localities they listed that may apply to another species, such as <i>S. guianica,</i> as we did not have access to these specimens to verify determinations of species.</p>Published as part of <i>Marinoni, Luciane & Mathis, Wayne N., 2006, A cladistic analysis of the Neotropical genus Sepedonea Steyskal (Diptera: Sciomyzidae), pp. 37-52 in Zootaxa 1236</i> on pages 40-43, DOI: <a href="http://zenodo.org/record/172789">10.5281/zenodo.172789</a>
: The print that no longer existed
No full textThe author, Rémi Mathis, curator at the École des Chartes library, recounts how he acquired an engraved copper plate by a young woman from the Ancien Régime, Marie-Adélaïde Quatremère. No proof of this engraving existed, so he had a copy made during a course he organised on engraving and gave the proof to the Ecole des Chartes library. The library now has a unique document that bears witness to the artistic practices of women in the Ancien Régime, their education and their family life.L'auteur, Rémi Mathis, conservateur à la bibliothèque de l'Ecole des chartes, raconte comment il a acquis une matrice gravée par une jeune femme de l'Ancien Régime, Marie-Adélaïde Quatremère. Aucune épreuve de cette gravure n'existait : il a donc fait tirer un exemplaire lors d'un stage qu'il organise sur la gravure et en a donné l'épreuve à la bibliothèque de l'Ecole des chartes. Cette dernière possède donc un document unique, témoin des pratiques artistiques des femmes de l'Ancien Régime, de leur éducation et de leur vie familiale
Entwicklung einer Zugprüfmaschine für einzelne Kollagenfibrillen und andere nanoskalige Fasern
Full text linkCollagens constitute approximately 30 % of the total protein mass in the human body and serve as the primary structural proteins. They provide tensile strength and toughness to tissues such as tendons, ligaments, vessels, and bones. Collagens are also abundant in the extracellular matrix (ECM) of almost all tissue types, providing sites for cell attachment and playing a crucial role in cellular processes. The unique mechanical properties of these collagen rich tissues are achieved through their complex nano- and microstructure, in which they form collagen fibrils. Collagen fibrils are nanoscale fibers, formed by fibril-forming collagen molecules in a self-assembly process. They are the smallest discernable structural unit of collagenous tissue that can be visualized with high-power microscopes. Collagen fibrils have diameters ranging from tens to hundreds of nanometers and lengths of up to several millimeters. It is debated, whether altered mechanical properties of collagen fibrils contribute to ageing and disease progression (or vice versa). In this context, there is increasing evidence that understanding changes in the viscoelasticity of collagenous tissues is paramount to gaining a better knowledge of disease progression and altered cell behavior. However, current methods for conducting tensile tests on collagen fibrils are very time-consuming and/or lack the capability to precisely determine their viscoelastic properties.The first objective of this thesis was to provide a novel method to overcome current technical limitations and achieve higher sample throughput. This was accomplished by developing the NanoTens, a nano tensile testing instrument that uses a 3D-printed gripper attached to a fiber-optic force probe. Reversible sample attachment to the force probe was achieved through magnetic manipulation. This increases sample throughput at least 25-fold. The NanoTens was utilized to explore the mechanical behavior of collagen fibrils from a mouse model of osteogenesis imperfecta, or brittle bone disease, manifested by a genetic defect that affects the synthesis of collagen molecules. As a result, the synthesized collagen molecules have an impaired structure. The study, surprisingly, revealed that collagen fibrils from the osteogenesis imperfecta mouse model have superior mechanical properties compared to collagen fibrils from wild-type mice, despite the defective collagen molecules. Fibrils from the tail tendons of the osteogenesis mouse model exhibited the characteristics of densely cross-linked collagen fibrils, which hints at elevated cross-linking in the osteogenesis imperfecta mouse model.The second objective was to enhance NanoTens with the capability to perform force-controlled tensile tests. This was done to quantify viscoelastic material properties. Following successful implementation, force-controlled tensile tests were utilized in two studies. The first study compared the viscoelastic properties of collagen fibrils to those of individual electrospun nanofibers. These nanofibers are used in tissue grafts that mimic the mechanical properties of native tendons. It was discovered that collagen fibrils exhibit lower energy dissipation while demonstrating similar elastic properties. In the second study, collagen fibrils were artificially cross-linked using methylglyoxal (MGO), a fast-reacting sugar. Subsequently, creep experiments were performed at relatively low fibril strains (below 10 %) to determine the effect of advanced glycation endproducts (AGEs), i.e. cross-links (and adducts), on viscoelasticity in the physiological strain range. It appears that AGE cross-links reduce molecular sliding even at physiological strains, as determined by reduced creep and residual strain in the MGO cross-linked fibrils. Interestingly, the same fibrils do not display significant differences in transient viscoelasticity
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