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Datasets for Dependency Tree Reranking
No full textThis resource contains the datasets for dependency tree reranking in 3 languages: English, German and Czech.
The creation, analysis and experiment results of the datasets are described in the paper:
Do and Rehbein (2020). "Neural Reranking for Dependency Parsing: An Evaluation".</p
Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites [data]
No full textPlasmodium falciparum (Pf) is responsible for the most lethal form of malaria. VAR2CSA is an adhesin protein expressed by this parasite at the membrane of infected erythrocytes for attachment to the placenta, leading to pregnancy-associated malaria. VAR2CSA is a large 355 kDa multidomain protein composed of nine extracellular domains, a transmembrane helix, and an intracellular domain. VAR2CSA binds to Chondroitin Sulphate A (CSA) of the proteoglycan matrix of the placenta. Shear flow, as the one occurring in blood, has been shown to enhance the (VAR2CSA-mediated) adhesion of Pf-infected erythrocytes on the CSA-matrix. However, the underlying molecular mechanism governing this enhancement has remained elusive. Here, we address this question by using equilibrium, force-probe, and docking-based molecular dynamics simulations. We subjected the VAR2CSA protein-CSA sugar complex to a force mimicking the tensile force exerted on this system due to the shear of the flowing blood. We show that upon this force exertion, VAR2CSA undergoes a large opening conformational transition before the CSA sugar chain dissociates from its main binding site. This preferential order of events is caused by the orientation of the molecule during elongation, as well as the strong electrostatic attraction of the sugar to the main protein binding site. Upon opening, two additional cryptic CSA binding sites get exposed and a functional dodecameric CSA molecule can be stably accommodated at these force-exposed positions. Thus, our results suggest that mechanical forces increase the avidity of VAR2CSA by turning it from a monovalent to a multivalent state. We propose this to be the molecular cause of the observed shear-enhanced adherence. Mechanical control of the valency of VAR2CSA is an intriguing hypothesis that can be tested experimentally and which is of relevance for the understanding of the malaria infection and for the development of anti placental-malaria vaccines targeting VAR2CSA
Classification of Types of Changes in Gully Environments Using Time Series Forest Algorithm [data]
No full textThis code implements the TimeSeriesForest algorithm to classify different types of changes in gully environments.
i)gully topographical change, ii)no change outside gully, iii) no change inside gully, and iv) non-topographical change.
The algorithm is specifically designed for time series classification tasks, where the input data represents the characteristics of gullies over time.
The code follows a series of steps to prepare the data, train the classifier, calculate performance metrics, and generate predictions.
The data preparation phase involves importing training and testing data from CSV files. The training data is then divided into classes based on their labels,
and a subset of the top rows is selected for each class to create a balanced training dataset. Time series data and corresponding labels
are extracted from the training data, while only the time series data is extracted from the testing data.
Next, the code calculates various performance metrics to evaluate the trained classifier. It splits the training data into training and testing sets,
initializes the TimeSeriesForest classifier, and trains it using the training set. The accuracy of the classifier is calculated on the testing set,
and feature importances are determined. Predictions are generated for both the testing set and new data using the trained classifier.
The code then computes a confusion matrix to analyze the classification results, visualizing it using Seaborn and Matplotlib.
Performance metrics such as True Accuracy, Kappa, Producer's Accuracy, and User's Accuracy are calculated and printed to assess the classifier's
effectiveness in classifying gully changes.
Lastly, the code performs ensemble predictions by combining the testing data with the generated predictions.
The results, including predictions and associated probabilities, are saved to an output file.
Overall, this code provides a practical implementation of the TimeSeriesForest algorithm for classifying types of changes in gully environments,
demonstrating its potential for environmental monitoring and management
Codices Palatini latini - Quadriviums-Handschriften
No full textHere you can find the descriptions of the Latin Palatine manuscripts as published in the manuscripts catalog "Die Quadriviumshandschriften der Codices Palatini Latini in der Vatikanischen Bibliothek", edited by Ludwig Schuba, Wiesbaden 1992 (Kataloge der Universitätsbibliothek Heidelberg 2). The description for each manuscript was subsequently recorded as TEI-XML file by XML encoding in accordance with TEI-P5 using GND standard vocabulary.These TEI files follow an outdated TEI schema originally developed at the Herzog August Bibliothek Wolfenbüttel and contain some ad hoc solutions which were chosen pragmatically in Heidelberg and which do not always comply with the TEI Guidelines. A future migration of the dataset into a fully TEI-compliant format is considered as desirable
Optical and electronic properties of different thin-film polymorphs of PDIF-CN2 controlled by zone-casting conditions [data]
No full textUnderlying data for figures in the paper "Optical and electronic properties of different thin-film polymorphs of PDIF-CN2 controlled by zone-casting conditions
Second Generation of Cata-Annulated Azaacene Bisimides: Towards Electron Accepting Materials [research data]
No full textHerein we provide the reserach data for the puplication: "Second Generation of Cata-Annulated Azaacene Bisimides: Towards Electron Accepting Materials". Where we present the second generation of cata-annulated azaacene bisimides with increased electron affinities compared to their consaguine conventional azaacenes. These compounds were synthesized via Buchwald-Hartwig coupling followed by oxidation with MnO2. Crystal structure engineering through variation of the bisimide substituents furnished crystalline derivatives suitable for proof of concept organic field effect transistors. Moreover, we were able to characterize the charge carrying species, the radical anion
Implementation of deep learning in liver pathology optimizes diagnosis of benign lesions and adenocarcinoma metastasis [data]
No full textDifferentiation of neoplastic and non-neoplastic liver lesions using routine histological tissue sections can be challenging. Correct classification is paramount to forecast prognosis and to select the correct therapy. Deep learning algorithms have recently been suggested to support objective and consistent assessment of digital histopathological images.
In thisstudy, annotation of 7 different classes, namely non-neoplastic bile ducts, benign biliary lesions and liver metastases from colorectal and pancreatic adenocarcinoma, was performed, resulting in a total of 204.159 image patches. The patient cohort was split into three datasets and an EfficientNetV2 and ResNetRS deep learning algorithm to classify the respective categories was trained, optimized, and ultimately tested. Model performance was evaluated on validation and test data using confusion matrices.
In summary, a hereinafter proposed automated classification to identify benign and malignant liver lesions by deep learning methods was described, which performed with high diagnostic accuracy. Furthermore, a huge curated liver dataset was provided
Multi Profile Curvature Analysis (MPCA) algorithm for gully detection using TanDEM X Digital elevation model.
No full textCharacterization of micro-terrain features has been explored to detect convex and concave features in the terrain. The analysis of first and second derivatives of
a function fitted to the terrain is a frequently used resource to describe terrain characteristics and to undertake GIS-based analysis for use in erosion models.
Infinitesimal calculus is applied in this approach for the detection of gullies, based on their morphology and profile curvature, under the assumption that a gully represents
a Relative Minimum (RM) with convex form. The algorithm is based on the analysis of the different profiles presented in a square kernel (with odd number of pixels),
which is iterated over the full image (Digital Elevation Model). Four axes are drawn on this kernel (one vertical, one horizontal and two oblique) representing a row vector, a column vector and the two diagonal vectors of the kernel, respectively. Once these vectors are identified, a second-degree function is adjusted to each.
According to the resultant functions, the first and second derivatives are calculated. A condition is stated to define a favorable case of gully candidate for each profile if four or three functions (profiles) present an RM (first derivative equal to zero and second derivative positive). Then a gully is assumed to exist within the kernel. For fewer than three local minima in a kernel, it is assumed that there is no gully in this window.
The results are generated in .txt format, where the coordinates of the centroids of the original pixels from the TanDEM-X DEM are provided, along with the number of RMs
found for the corresponding Kernel, of which they are the center
Optical properties of doped and undoped 9-armchair graphene nanoribbons [data]
No full textGraphene nanoribbons are one-dimensional stripes of graphene with width- and edge-structure-dependent electronic properties. They can be synthesized bottom-up to obtain precise ribbon geometries. Here we investigate the optical properties of solution-synthesized 9-armchair graphene nanoribbons (9-aGNRs) that are stabilized as dispersions in organic solvents and further fractioned by liquid cascade centrifugation (LCC). Absorption and photoluminescence spectroscopy reveal two near-infrared absorption and emission peaks whose ratios depend on the LCC fraction. Similarly, the Raman D/G-mode ratios vary with fraction and indicate a higher defect density for fractions obtained at higher centrifugal forces. Low-temperature single-nanoribbon photoluminescence spectra suggest the presence of two different nanoribbon species. Based on density functional theory (DFT) and time-dependent DFT calculations, pristine 9-aGNRs are assigned to the lowest energy transitions and 9-aGNRs with edge-defects, introduced by an incomplete graphitization, are assigned to more blue-shifted transition peaks. Hole doping of 9-aGNRs dispersion with the electron acceptor F4TCNQ leads to concentration dependent bleaching of the main absorption bands and redshifted, charge-induced absorption features but no new emission features, thus, indicating the formation of polarons instead of trions (charged excitons) in charged 9-aGNRs
Synthesis of a Benzotrisazulene via Trioxobenzotrisazulene [data]
No full textA benzotrisazulene was synthesized on the basis of a truxene precursor by a series of Suzuki–Miyaura reactions via the intermediate trisoxo compound. The latter occurs in two forms (syn and anti), and the syn forms porous crystals