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6,467 results for “process”
Dataset for Black Tea Fermentation Detection based on Image Processing and Machine Learning Techniques
<p>This is a dataset on black tea fermentation. The dataset contains black tea fermentation conditions and images. The fermentation conditions captured are: temperature, humidty and time. The images belong to black tea as they underwent the fermentation process. The dataset was collected in Sisibo tea factory, Kenya in July and August 2020.</p>
Commonalities and differences in predictive neural processing of discrete vs continuous action feedback
<p>Dataset relative to the following publication:</p> <p>Schmitter, C.V., Steinsträter, O., Kircher, T., van Kemenade, B.M., Straube, B. (2021). Commonalities and differences in predictive neural processing of discrete vs continuous action feedback. <em>NeuroImage.</em> DOI: <a href="https://doi.org/10.1016/j.neuroimage.2021.117745">10.1016/j.neuroimage.2021.117745</a></p> <p> </p> <p>Details can be found in the readme file.</p>
Replication Package for: Theodolite: Scalability Benchmarking of Distributed Stream Processing Engines in Microservice Architectures
<p>This repository contains a replication package and experimental results for our study <em>Theodolite: Scalability Benchmarking of Distributed Stream Processing Engines in Microservice Architectures</em>.</p> <p>The following description can also be found in the README.md file.</p> <p><strong>Repeating Benchmark Execution</strong></p> <p><em><strong>The following introduction describes how to repeat our scalability experiments. If you plan to conduct your own studies, we suggest to use the latest version of <a href="https://github.com/cau-se/theodolite">Theodolite</a> with significantly enhanced usability.</strong></em></p> <p>The Apache Kafka Streams scalability experiments of our study were executed with <a href="https://github.com/cau-se/theodolite/tree/v0.1.2">Theodolite v0.1.2</a>. To repeat our Kafka Streams experiments:</p> <ol> <li>Clone and install <a href="https://github.com/cau-se/theodolite/tree/v0.1.2">Theodolite v0.1.2</a> according to the official documentation located in <code>execution</code>.</li> <li>Copy the file <code>repeat-kstream.sh</code> into Theodolite's <code>execution</code> directory.</li> <li>Run the repetition file with <code>./repeat-kstream.sh</code> from within the <code>execution</code> directory.</li> </ol> <p>Our Apache Flink benchmark implementations are currently migrated to the latest version of Theodolite. <a href="https://github.com/cau-se/theodolite/tree/apache-flink">Theodolite's <code>apache-flink</code> Branch</a> provides the basis for our Flink scalability experiments. To repeat them:</p> <ol> <li>Clone <a href="https://github.com/cau-se/theodolite/tree/apache-flink">Theodolite's <code>apache-flink</code> Branch</a> and install Theodolite according to the official documentation located in <code>execution</code> (should be identical to the installation for Kafka Streams (see above)).</li> <li>Copy the files <code>repeat-flink-without-checkpointing.sh</code> and <code>repeat-flink-with-checkpointing.sh</code> into Theodolite's <code>execution</code> directory.</li> <li>Switch to the <code>execution</code> directory.</li> <li>Run the first repetition file with <code>./repeat-flink-with-checkpointing.sh</code>.</li> <li>Disable checkpointing by reconfiguring the Kubernetes resources <code>jobmanager-job.yaml</code> and <code>taskmanager-job-deployment.yaml</code> for each benchmark (<code>uc{1,2,3,4}-application</code>) by setting the environment variable <code>CHECKPOINTING</code> to <code>"false"</code>.</li> <li>Run the second repetition file with <code>./repeat-flink-without-checkpointing.sh</code>.</li> </ol> <p><em>Please note that the naming of our benchmarks recently changed. While our publication already uses the new naming, the corresponding Theodolite versions are is still using the old one. Specifically, this means that UC1 in the publication is UC1 in Theodolite, UC2 in the publication is UC3 in Theodolite, UC3 in the publication is UC4 in Theodolite, and UC4 in the publication is UC2 in Theodolite.</em></p> <p><strong>Raw Measurements</strong></p> <p>The results of above benchmark execution can be found in the <code>measurements</code> directory. These are CSV files, containing the measured lag trend over time for a certain subexperiment. Theodolite creates a bunch of additional files, which serve for debugging and preliminary interpretation. As these files are not required for replication, we do not included them in this package.</p> <p>The CSV files are named according to the schema <code>exp{id}_{uc}_{load}_{inst}_totallag.csv</code>, where <code>{id}</code> represents the experiment ID, assigned by Theodolite, <code>{uc}</code> the benchmark name, <code>{load}</code> the generated load, and <code>{inst}</code> the number of evaluated instances.</p> <p>The CSV table <code>experiments.csv</code> provides an overview about the configurations used in each experiment.</p> <p><strong>Reproducing Scalability Analysis</strong></p> <p><em><strong>The following introduction describes how to repeat our scalability analysis, either with our measurements or with your own. If you plan to conduct your own studies, we suggest to use the latest version of <a href="https://github.com/cau-se/theodolite">Theodolite</a> with significantly enhanced usability.</strong></em></p> <p>Analyzing the Theodolite's measurements is done using two Jupyter notebooks. In general, these notebooks should be runnable by any Jupyter server. Python 3.7 or 3.8 is required (e.g., in a virtual environment) as well as some Python libraries, which can be installed via: <code>pip install -r requirements.txt</code>. See the <a href="https://github.com/cau-se/theodolite/tree/master/analysis">Theodolite documentation</a> for additional installation guidance.</p> <p><strong>Obtaining a Scalability Graph as a CSV File</strong></p> <p>The <code>scalability-graph.ipynb</code> notebook combines the measurements (i.e., the <code>totallag.csv</code> files) of one experiment. It produces a CSV file, which provides a mapping of load intensities to minimum required resources for that load (i.e., the scalability graph). The CSV files are named according to the schema <code>exp{id}_min-suitable-instances.csv</code>, where <code>{id}</code> represents the experiment ID. Additional guidance is provided in the notebook.</p> <p><strong>Resulting Scalability Graph CSV Files</strong></p> <p>The <code>results</code> directory provides the scalability graphs for all our executed experiments.</p> <p><strong>Visualization of the Scalability Graph</strong></p> <p>The <code>scalability-graph-plotter.ipynb</code> notebook creates PDF plots of a scalability graph and allows to combine multiple scalability graphs in one plot. It can be adjusted to match the desired visualization.</p> <p><strong>Acknowledgments</strong></p> <p>This research is funded by the German Federal Ministry of Education and Research (BMBF) under grant no. 01IS17084 and is part of the <a href="https://www.industrial-devops.org">Titan project</a>.</p>
Data from: Holocene lake phosphorus species and primary producers reflect catchment processes in a small, temperate lake
<p>This palaeo data set consists of a Holocene record from a small, temperate lake (Lake Fuglsø, Denmark). It comprises radiocarbon (<sup>14</sup>C)-dating, pollen, X-ray fluorescence scanning, carbon and nitrogen (contents and stable isotopes), phosphorus (P) pools (from sequential P extraction and <sup>31</sup>P nuclear magnetic resonance spectroscopy), pigment, diatom, and plant macrofossil data. Our multi-proxy palaeolimnological study aimed to investigate how natural processes and anthropogenic land-use changes have affected sedimentary P forms and primary producers. We found three periods of human impact: (1) low disturbance from domestic grazing during the Early/Mid Neolithic (~3600 – ~2600 BC), (2) higher disturbance because of animal husbandry and some grain cultivation during the Late Bronze and Pre-Roman Iron Age (~800 BC – AD ~100) and (3) strong disturbance caused by domestic grazing, intensified crop cultivation and, in particular, by retting of fibre plants during the Middle Ages and Renaissance (AD ~1000 – ~1700). Cultural eutrophication during the latter phase caused unprecedented changes in the lake, including altered species composition, high production and strongly accelerated sediment accumulation rates. Generally, catchment deforestation was related to elevated proportions of metal (iron, aluminium, calcium)-bound P forms in the sediment, while high tree cover correlated with elevated proportions of P forms associated with organic material ("organic" P, humic-bound P, refractory organic P) and loosely bound P. During phases with forest in the catchment, silicon (Si) inputs to the lake were insufficient and diatom frustules were mostly absent in the sediments. In contrast, diatoms thrived in the lake when the landscape was open and erosional Si influx was high. This study is the first to show long-term (~eight millennia) and recurring Si limitation of diatoms, a finding that may explain the absence of diatoms in sediment records of other sites too. In summary, human land-use with preceding deforestation accelerated the transport of nutrients and elements from the terrestrial to the aquatic environment, leading to substantial and irreversible changes in Lake Fuglsø. Our study is a good example of the tight links between catchment processes and lake status, indicating that catchment dynamics should be considered in lake restoration projects, particularly for lowland lakes with high catchment:lake area ratios.</p>
Dataset for the paper "Ideology and identity in grammar: A diachronic-quantitative approach to language standardisation processes in Ancient Greek"
<p>This is the dataset for the paper "Ideology and identity in grammar: A diachronic-quantitative approach to language standardisation processes in Ancient Greek"</p>
Data from: Disentangling the steps of the infection process responsible for juvenile disease susceptibility
<p>1. Juveniles of diverse host taxa, including vertebrates, invertebrates and plants, are more susceptible to parasitic infections than adults, a phenomenon still poorly understood.</p> <p>2. To shed light on the mechanisms underlying this host age effect, we investigated its expression during different steps of the infection process of a bacterial parasite of the planktonic crustacean <i>Daphnia</i>. To do so, we infected juvenile and adult <i>Daphnia magna</i> with the bacterium <i>Pasteuria ramosa</i> and monitored parasite development in experiments specific to different steps of the infection process.</p> <p>3. We did not find an effect of host age on parasite attachment, but found a strong increase in the penetration time of the parasite into hosts with increasing age. Host age at exposure also affected within-host parasite development, which was delayed in old adult <i>D. magna</i> in comparison to young adults and juveniles. Furthermore, parasite clearance was observed only in old adults, suggesting that old hosts have a better immune response than young adults and juveniles.</p> <p>4. Our results reveal a step-specific effect of host age on disease progression, giving support for different hypotheses explaining high juvenile disease susceptibility. While these mechanisms are likely to work independently from each other, earlier steps of the infection process influence later steps, and thus may respond more readily to selection than later steps.</p> <p>5. Our results also highlight that clearance can occur both during early parasite establishment and surprisingly at progressed infection phases, an undocumented phenomenon in invertebrates, where late infections are often considered chronic, lasting until host death.</p>
Data from: Fission–fusion processes weaken dominance networks of female Asian elephants in a productive habitat
Dominance hierarchies are expected to form in response to socioecological pressures and competitive regimes. We assess dominance relationships among free-ranging female Asian elephants (Elephas maximus) and compare them with those of African savannah elephants (Loxodonta africana), which are known to exhibit age-based dominance hierarchies. Both species are generalist herbivores, however, the Asian population occupies a more productive and climatically stable environment relative to that of the African savannah population. We expected this would lower competition relative to the African taxon, relaxing the need for hierarchy. We tested whether 1) observed dominance interactions among individuals were transitive, 2) outcomes were structured either by age or by social unit according to 4 independent ranking methods, and 3) hierarchy steepness among classes was significant using David's score. Elephas maximus displayed less than a third the number of dominance interactions as observed in L. africana, with statistically insignificant transitivity among individuals. There was weak but significant order as well as steepness among age-classes but no clear order among social units. Loxodonta africana showed significant transitivity among individuals, with significant order and steepness among age-classes and social units. Elephas maximus had a greater proportion of age-reversed dominance outcomes than L. africana. When dominance hierarchies are weak and nonlinear, signals of dominance may have other functions, such as maintaining social exclusivity. We propose that resource dynamics reinforce differences via influence on fission–fusion processes, which we term "ecological release." We discuss implications of these findings for conservation and management when animals are spatially constrained.
Data from: Pattern and process in hominin brain size evolution are scale-dependent
A large brain is a defining feature of modern humans, yet there is no consensus regarding the patterns, rates, and processes involved in hominin brain size evolution. We use a reliable proxy for brain size in fossils, endocranial volume (ECV), to better understand how brain size evolved at both clade- and lineage-level scales. For the hominin clade overall, the dominant signal is consistent with a gradual increase in brain size. This gradual trend appears to have been generated primarily by processes operating within hypothesized lineages – 64% or 88% depending on whether one uses a more or less speciose taxonomy, respectively. These processes were supplemented by the appearance in the fossil record of larger-brained Homo species and the subsequent disappearance of smaller-brained Australopithecus and Paranthropus taxa. When the estimated rate of within-lineage ECV increase is compared to an exponential model that operationalizes generation-scale evolutionary processes, it suggests that the observed data were the result of episodes of directional selection interspersed with periods of stasis and/or drift; all of this occurs on too fine a time scale to be resolved by the current human fossil record, thus producing apparent gradual trends within lineages. Our findings provide a quantitative basis for developing and testing scale-explicit hypotheses about the factors that led brain size to increase during hominin evolution.
Data from: The relevance of gene flow with wild relatives in understanding the domestication process
<p><span><span><span>The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the domestication process depends on having an adequate representation of wild relatives. Cultivated maize (<i>Zea mays</i> spp. <i>mays</i>) is one of the most important crops in the world, with a long and a relatively well documented history of domestication. The current consensus points towards a single domestication event from teosinte <i>Zea mays</i> spp. <i>parviglumis</i> from the Balsas Basin in Southwest central Mexico. However, the underlying diversity of teosintes from lowlands <i>Z. mays</i> spp<i>. parviglumis</i> and highlands <i>Zea mays</i> spp. <i>mexicana</i>) was not taken into account in early studies. We used 32,739 SNPs obtained from 29 teosinte populations and 43 maize landraces to explore the relationship between wild and cultivated members of <i>Zea.</i> We then inferred levels of gene flow among teosinte populations and maize, the degree of population structure of <i>Zea mays</i> subspecies, and potential domestication location of maize. We confirmed a strong geographic structure within <i>Z. mays </i>spp. <i>parviglumis</i> and documented multiple gene flow events with other members of the genus, including an event between <i>Z. mays</i> spp. <i>mexicana </i>and maize. Our results suggest that the likely ancestor of maize may have been domesticated not in the Balsas Basin as previously thought, but in Jalisco or in the Pacific coast, and that different populations of the teosinte subspecies have contributed to modern maize's gene pool. Our results points towards a long period of domestication marked by gene flow with wild relatives, making domestication a long and ongoing process. </span></span></span></p>
Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree
<p>Motivation: Sap flow sensors are crucial instruments to understand whole-tree water use. The lack of direct calibration of the available methods on large trees and the application of several data-processing procedures may jeopardize our understanding of water uptake dynamics by increasing the uncertainties around sensor-based estimates. We directly compared the heat ratio method (HRM) sap flow measurements to water uptake measured gravimetrically using the cut-tree method on a large mature aspen tree to quantify those uncertainties for ten consecutive days.</p> <p>Dataset: In this dataset, we provide sap flux density (ten-minutes intervals; g.cm-2.hr-1; corrected for wounding and sapwood thermal diffusivity) obtained from four HRM sap flow sensors installed at 2.5 m high on the focus tree (20 m tall, 60 years old trembling aspen in the boreal mixedwood region of Alberta) between July 18th and August 22nd 2017. We present the code and data (weather data from neighboring weather station) used to calculate whole-tree sap flux (L.hr-1) from each of the individual sensors using different methods of radial integration of sap flux density across the sapwood area estimated via different calculations, as well as different zero-flow corrections used. The cut-tree procedure was applied to the focus tree, and gravimetric measurements of water uptake (ten-minutes intervals) were made using a recording scale. We directly compared the different estimates of hourly, daily and cumulative sap flows obtained with gravimetric measurement of water uptake. We present the code providing the statistical analysis and results reported in the associated publication (Merlin, M., Solarik, K.A., Landhäusser, S.M. Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree. 2020. Agricultural and Forest Meteorology, http://dx.doi.org/10.1016/j.agrformet.2020.107926)</p>
Data from: How sea-level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes
Plate tectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea-level change interacted with variable near-shore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the Last Glacial Maximum, ~20 thousand years ago, to present from San Francisco, California, USA (~38 °N) to Reforma, Sinaloa, Mexico (~25 °N). We assessed range-wide genetic structure and diversity of three co-distributed tidal estuarine fishes (California Killifish, Shadow Goby, Longjaw Mudsucker) along ~4,600 km using mitochondrial control region and cytB sequence, and 16–20 microsatellite loci from a total of 524 individuals. Results show that glacial-associated sea-level change limited estuarine habitat to few, widely separated refugia at glacial lowstand, and present-day genetic clades were sourced from specific refugia. Habitat increased during postglacial sea-level rise and refugial populations admixed in newly formed habitats. Continental shelves with active tectonics and/or low sediment supply were steep and hosted fewer, smaller refugia with more genetically differentiated populations than on broader shelves. Approximate Bayesian computation favored the refuge-recolonization scenarios from habitat models over isolation by distance and seaway alternatives, indicating isolation at lowstand is a major diversification mechanism among estuarine (and perhaps other) coastal species. Because sea-level change is a global phenomenon, we suggest this top-down physical control of extirpation-isolation-recolonization may be an important driver of genetic diversification in coastal taxa inhabiting other topographically complex coasts globally during the Mid- to Late Pleistocene and deeper timescales.
Data from: Response to persistent er stress in plants: a multiphasic process that transitions cells from prosurvival activities to cell death
The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family of peroxidase genes. RIDD resulted from the activation of ZmIRE1 for promiscuous ribonuclease activity that attacks the mRNAs of secreted proteins. This was followed by an upsurge in expression of the canonical UPR genes indirectly driven by ZmIRE1 due to its splicing of Zmbzip60 to make an active transcription factor that directly upregulates many of the UPR genes. At the peak of UPR gene expression, a global wave of alternative RNA processing led to the production of many aberrant UPR gene transcripts, likely tempering the ER stress response. During later stages of ER stress, ZmIRE1's activity declined as did the expression of survival modulating genes, Bax inhibitor1 and Bcl-2-associated athanogene7, amidst a rising tide of cell death. Thus, in response to persistent ER stress, maize seedlings embark on a course of gene expression and cellular events progressing from adaptive responses to cell death.
Dynamic inferential NOx emission prediction model with delay estimation for SCR de-NOx process in coal-fired power plants
<p><span><span>The selective catalytic reduction (SCR) de</span><span>-</span><span>NO<sub>x</sub> </span><span>process in coal-fired power plants not only displays nonlinearity, large inertia, and time variation but also a lag in NO<sub>x</sub> analysis; </span><span>hence,</span><span> it is difficult to obtain an accurate model </span><span>that </span><span>can be used to control NH<sub>3</sub> injection </span><span>during changes in the </span><span>operating state. </span><span>In this work,</span><span> a novel dynamic inferential model with delay estimation was proposed for NO<sub>x</sub> emission prediction. First, k-nearest neighbour mutual information (knnMI) was used to estimate the time-delay of the descriptor variables, followed by reconstruction of the phase space of the model data. Second, multi-scale wavelet kernel partial least square (mwKPLS) was</span><span> used</span><span> to improve the prediction ability, </span><span>and this was followed by verification using </span><span>benchmark dataset experiments. Finally, the delay-time difference (DTD) method and feedback correction strategy </span><span>were </span><span>proposed to deal with the time variation of the SCR de</span><span>-</span><span>NO<sub>x</sub> process.</span> <span>Through the analysis of the </span><span>experimental field data </span><span>in the</span> <span>steady state, </span><span>the variable</span><span> state and </span><span>the </span>NO<sub>x</sub> analyser blowback process<span>, the results proved that</span><span> this dynamic model has </span><span>high prediction accuracy</span><span> during</span><span> state changes and can </span><span>realize</span><span> advance prediction of the NO<sub>x</sub> emission. </span></span></p>
Interindividual differences influence multisensory processing during spatial navigation
<p>The dataset contains the raw data from two experiments. We investigate the ability of spatial navigation using auditory, visual or audiovisual landmarks in the environment.</p>
Data from: Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5′-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.
Knowledge Freedom in computational science: a two stage peer-review process with KF Eligibility Access Review
<p>What is explained below is the <em>peer review process</em> applied by <em>Notes on Transdisciplinar</em><em>y Modelling for Environment </em>(NTMe). Authors and readers are encouraged to understand not only the process, but also the rationale behind the process, which is closely connected with the peculiar challenges faced by the scientific problems (computational-science modelling under uncertainty, in broad and heterogeneous contexts) in the scope of the journal. </p> <p> </p> <p><span class="math-tex">\(\mathsf{\Large\text{The rationale behind the peer-review process}}\)</span></p> <p><strong>Computational research problems for more than one discipline. </strong>Research specific to a particular disciplinary domain is typically authored, and then studied, by experts in that domain. Several conventions, assumptions, fundamental protocols and methodology practices, are shared by domain experts as a common ground. Given that proficiency in these aspects is a precondition for domain experts, this kind of knowledge is often implicit, and not well communicated within domain-specific literature. "Typical" data preprocessing, model settings, quality-assessment assumptions (and their "default" simplifications and shortcuts), in this literature are often minimally reported or omitted, because the domain-specific community of researchers and practitioners knows them so well that they may resemble a sort of acquired conditioned response. However, when in a wider research more than one disciplinary domain is connected among each other, then implicit unexpressed knowledge may lead to ambiguity, misuse of results, and avoidable errors - sometimes challengly difficult to detect. The more and more diverse the domains, the higher this risk might be.</p> <p><strong>Useful cross-domain building blocks. </strong>"Transdisciplinary" research may risk being misinterpreted as just the final summary list of results grabbed by autonomous disciplinary silos run in parallel. However, a poor ability to communicate computational methods and data - and their limitations - between multiple disciplinary domains would jeopardise the collective (cross-domain) ability to distill truly integrated computational science. Computational science for transdisciplinary problems requires a pragmatic, engineered, but reasonably simple and modular approach to break and connect disciplinary silos - when appropriate for the problems investigated. Publishing <em>useful</em> cross-domain building blocks of this approach is the aim of the peer-review process in NTMe.</p> <p><strong>Connecting disciplines, space and time scales under uncertainty: the need for a shared semantics. </strong>Wide-scale transdisciplinary modelling (WSTM) relies on methods proper to computational science for connecting multiple scientific disciplines, and shedding light on broad, complex problems. Several of the most pressing problems we face as a human society are only partially known in their chain of consequences, and hopelessly difficult to address by a single discipline and a narrow perspective. Some of these problems capture the specific interest by particularly exposed regions, but their mechanism is more general, with essential knowledge often lying in other spatial areas - or even other time periods - hence calling for a wider perspective. Multiple spatial and temporal scales, with dissimilar data resolution, are frequent in WSTM problems, since they are often dictated by the complexity of reality and the available data. A wide-scale extent typically implies uneven quality and availability of data, and many sources of uncertainty - which increases when assumptions, methods and semantics by different disciplines or research institutions do not easily merge. A truly transdisciplinary communication of this essential semantics requires the <em>freedom </em>to communicate scientific knowledge, accurately and transparently, between disciplinary and corporate barriers.</p> <p><strong>Real knowledge sharing in computational science. </strong>As a consequence, wide-scale transdisciplinary modelling demands a focus on reproducible research and real scientific knowledge freedom. Data and software freedom are essential aspects of knowledge freedom in computational science. Therefore, ideally published articles should also provide the readers with the data and source code of the described mathematical modelling. To maximise transparency, replicability, reproducibility and reusability, published data should be made available as open data while source code should be made available as free software. Communicating semantics even to non-experts in a given domain requires that mathematical assumptions, otherwise obvious within a specific discipline, are duly annotated in a portable and concise way. Accordingly, brief but semantically clear documentation of data, methods and software is a key precondition. Here, a two-stage peer review process is described in which scientific knowledge freedom is considered with a dedicated Eligibility Access Review. This new peer review process is applied by <em>Notes on Transdisciplinary Modelling for Environment</em> with a focus on WSTM for environment.</p> <p> </p> <p><span class="math-tex">\(\mathsf{\Large\text{The peer-review process}}\)</span></p> <p><strong>A two-stage peer review process to avoid single-use disposable computational science. </strong>The two-stage peer review process requires discussion papers to be published so as to receive feedback from the scientific community before their possible finalisation. Initial manuscript submission is subject to the soundness review outlined above, also ensuring eligibility criteria to be fulfilled so as to support scientific knowledge freedom. Although this concept is multifaceted, some few dimensions might be emphasised which broadly apply in computational science and engineering (CSE). Among the many possible eligibility criteria in CSE, it should be highlighted at least the need for: </p> <ul> <li>free software to have been published so as for it to be persistently available;</li> <li>appropriate licensing and source code review to have been done (portable modularisation, with semantics of mathematical data-transformation methods clearly annotated);</li> <li>free data to have been published so as for it to be persistently available (with semantics of quantities clearly annotated);</li> <li>a minimal share of free-access core references to be selected in order for scientists and research organisations not to be discriminated on the basis of their funding availability, when they try to access the core literature cited in the manuscript.</li> </ul> <p>Before acceptance for discussion, a manuscript (and its potential data, parameters and software) may be revised, without exposing to the public immature versions, until it becomes able to fulfil the eligibility criteria. These iterations between author(s) and editors/reviewers remain confidential, and a potential manuscript rejection does not preclude resubmission. Acceptance of the manuscript to the discussion stage is followed by the permanent publication of the accepted version. This does not preclude, and actually encourages, further revised versions to be resubmitted. Any new revision is subject to eligibility access review, which takes into account the submission history of the manuscript and the already accepted public older versions.</p> <p><strong>Not a static publication. </strong>The discussion stage of the peer review process allows short comments to be submitted by referees and the scientific community, while authors are encouraged to interact with pending comments by providing their responses. During this stage, the paper accepted for discussion is already citable. Depending on the specific goals of each research problem, the discussion may remain open for a short time interval, or instead for a noticeably longer period of time (even indefinitely, if appropriate: for example, whenever authors do consider publishing cumulative milestone versions as important). There is not an a-priori limit to the duration of this first stage, and to the number of intermediate public revisions (which are optional), for a paper accepted for discussion. The second stage of peer review concludes the discussion stage with the submission of a revised manuscript, with final review and corrections. Fulfilment of the eligibility criteria is required over all the publication stages.<br> The published materials might be updated from time to time (at the authors' discretion), and - after peer-reviewing the changes - published so that the evolution is clear and available to others. Although preferred and encouraged in the discussion stage, updates are possible even after the final stage. Revisions offering a noticeably different content, compared with the previous versions, might sometime be recommended by editors/reviewers as deserving the status of a new publication - not to confuse the readers. This implies the full two-stage review process has to be applied to the new publication (as an independent publication), while the previous accepted publication is considered as the final permanent version. Recalling an analogy with the typical evolution of free-software, a software package is frequently subject to future improvements and corresponding new versions. If a new version is too different from the original package, it may become a new independent package. </p> <p><strong>Scientific opinions, perspectives, and overviews.</strong> Manuscripts focusing on computational science methods, data, parameters, and software are expected to contribute practical components of scientific knowledge which can be adapted, modified, or generally integrated within the future body of knowledge - potentially in unexpected ways. Therefore, the aforementioned two-stage review is, overall, meant to ease the future invention of derivative works. On the other hand, manuscripts offering expert opinions on these topics do not contribute "practical" components to be directly modified. Instead, they contribute organised ideas to support the evolution of scientific knowledge. Therefore, the peer review process for this typology of manuscripts focuses on:</p> <ul> <li>the broad understandability and potential interest of the expert opinions, and</li> <li>the factual correctness of the objective elements included in the opinion (with adequate bibliographic, tabular, visual support where appropriate). </li> </ul> <p><strong>Preregistration, protocols and methods. </strong>NTMe accepts a third typology of manuscripts, focusing on anticipated results (hence not yet computed) which are expected following a modelling procedure to transform input data and parameters into the desired output. As data and software are only anticipated in this typology of manuscripts, the peer-review process focuses on:</p> <ul> <li>the broad understandability and potential interest of the proposed protocol or methodology,</li> <li>the correctness and clarity of the mathematical formulation of the proposed computational-modelling steps (data-transformation modules),</li> <li>the discussion of anticipated results, pitfalls, sources of uncertainty and their proper management, bifurcations of the methodology depending on the potential variants that a user may desire to apply (depending on available data and their quality, and on the desired specialisation of the proposed general method), and</li> <li>the adequacy of bibliographic, tabular, visual supports where appropriate. </li> </ul> <p><strong>Abstract, and plain language summary. </strong>Each article includes a technical abstract. Although the topics of published content might deal with domain-specific aspects of computational/environmental science, their focused analysis is expected to support wider research in a transdisciplinary context. Therefore, the abstract is expected to be accessible beyond the domain-specific research community. Each article, either in the discussion or in the final stage, in addition to a technical abstract needs a <em>plain language summary</em> so that non-experts and readers with a basic scientific and technical literacy can understand the main contributions of the article. The aim of the plain language summary is to support educational dissemination. The summary is not a simpler abstract, and typically offers a longer, more comprehensive description. It is realised with an editorial support to authors, so as to respect a general structure (unless otherwise agreed):</p> <ul> <li>first, the general context of the work is presented (the general topics in which the work is situated);</li> <li>second, the general open questions are introduced to which the work aims to contribute;</li> <li>third, the specific way is described in which the work contributes to progress on the general open questions;</li> <li>fourth, the implications, new opportunities or suggested lines of research, and potential limitations and unaswered questions are summarised.</li> </ul> <p><strong>Constructive peer review.</strong> The ultimate aim of the peer review process is to support authors, and future readers, in sharing useful, durable, and understandable notes of transdisciplinary knowledge. Given the very nature of the topics in NTMe, the need for a cogent peer review on a multiplicity of expertise fields is essential. Rarely a single reviewer is able to cover all the aspects of transdiciplinary computational science. Even so, different opinions by different reviewers may emerge on specific points. Therefore, a <em>constructive </em>approach is promoted during each step of the peer review process, so that authors are guided to understand the peer review, and a compendium of recommandations may be presented in a consistent way.</p> <p> </p> <p><sup>© 2012-2020 Daniele de Rigo. This work is licensed under a </sup><a href="http://creativecommons.org/licenses/by-nd/4.0/legalcode"><sup>Creative Commons Attribution No Derivatives 4.0 International</sup></a><sup> license. Please, cite as<br> de Rigo, D., 2012. </sup><strong><sup>Knowledge Freedom in computational science: a two stage peer-review process with KF eligibility access review</sup></strong><sup>. </sup><em><sup>Zenodo, </sup></em><sup>CERN. </sup><a href="https://doi.org/10.5281/zenodo.7578"><sup>https://doi.org/10.5281/zenodo.7578</sup></a><sup> </sup></p> <p> </p>
Learning stochastic process-based models of dynamical systems from knowledge and data - Libraries, incomplete models and data
<p>The archive contains all libraries of domain knowledge, the incomplete models and the data used in the experiments described in the manuscript titled "Learning stochastic process-based models of dynamical systems from knowledge and data" pubilshed in BMC Systems Biology</p>
SARWIND LG-Mod (v4.01) output data with reference to the Sentinel-1A (2014/12/07, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ the additional SKYRON reference wind)
<p>A zipped folder containing SARWIND LG-Mod (v4.01) output data obtained by processing the Sentinel-1A (2014/12/07, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ the additional SKYRON reference wind).</p> <p>Pre-processed data derived from the Sentinel-1 SAR image have been obtained by using the Sentinel Application Platform (SNAP), ver. 3.0.3, distributed by the European Space Agency (ESA). The reference wind components have been provided by the Numerical Weather Model (NWM) SKYRON.</p> <p>These Earth Observation (EO) data have been used as inputs to the SARWIND LGMod algorithm, ver. 4.01, developed by Rana Fabio Michele (2014-2016) for the sea surface wind field retrieval.</p> <p>The available Sentinel-1, Extra Wide Swath Mode, Ground Range, Multi-look, Detected, Medium Resolution, Vertical polarisation on transmit, Vertical polarisation on receive, Descending orbit, C-band SAR image, has been acquired on the 7th Dec 2014, 05:51:54.</p>
Sentinel-1A (2014/12/07, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ additional SKYRON reference wind) for SARWIND LG-Mod (v4.01)
<p>A zipped folder containing pre-processed data from a Sentinel-1 SAR image by using the Sentinel Application Platform (SNAP), ver. 3.0.3, distributed by the European Space Agency (ESA). The reference wind components provided by the Numerical Weather Model (NWM) SKYRON is also added in the folder.</p> <p>These Earth Observation (EO) data can be used as inputs to the SARWIND LGMod algorithm, ver. 4.01, developed by Rana Fabio Michele (2014-2016), with the aim at retrieving the sea surface wind field by exploiting the single co-polarized Sentinel-1 image available.</p> <p>In particular, the latter is the Sentinel-1, Extra Wide Swath Mode, Ground Range, Multi-look, Detected, Medium Resolution, Vertical polarisation on transmit, Vertical polarisation on receive, Descending orbit, C-band SAR image, acquired on the 7th Dec 2014, 05:51:54</p>
Sentinel-1A (2014/12/31, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ additional SKYRON reference wind) for SARWIND LG-Mod (v4.01)
<p>A zipped folder containing pre-processed data from a Sentinel-1 SAR image by using the Sentinel Application Platform (SNAP), ver. 3.0.3, distributed by the European Space Agency (ESA). The reference wind components provided by the Numerical Weather Model (NWM) SKYRON is also added in the folder.</p> <p>These Earth Observation (EO) data can be used as inputs to the SARWIND LGMod algorithm, ver. 4.01, developed by Rana Fabio Michele (2014-2016), with the aim at retrieving the sea surface wind field by exploiting the single co-polarized Sentinel-1 image available.</p> <p>In particular, the latter is the Sentinel-1, Extra Wide Swath Mode, Ground Range, Multi-look, Detected, Medium Resolution, Vertical polarisation on transmit, Vertical polarisation on receive, Descending orbit, C-band SAR image, acquired on the 31st Dec 2014, 05:51:53.</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.