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opencc-by-4.0Nov 2019View details →

All Computer Science Papers @ arXiv.org -- A High-Quality Gold Standard for Citation-based Tasks

We propose a newly-created gold standard data set for citation-based tasks. This gold standard is based on all computer science papers in arXiv.org. Abstract. Analyzing and recommending citations with their specific citation contexts have recently received much attention due to the growing number of available publications. Although data sets such as CiteSeerX have been created for evaluating approaches for such tasks, those data sets exhibit striking defects. This is understandable if one considers that both information extraction and entity linking as well as entity resolution need to be performed. In this paper, we propose a new evaluation data set for citation-dependent tasks based on arXiv.org publications. Our data set is characterized by the fact that it exhibits almost zero noise in the extracted content and that all citations are linked to their correct publications. Besides the pure content, available on a sentence-basis, cited publications are annotated directly in the text via global identifiers. As far as possible, referenced publications are further linked to DBLP. Our data set consists of over 15M sentences and is freely available for research purposes. It can be used for training and testing citation-based tasks, such as recommending citations, determining the functions or importance of citations, and summarizing documents based on their citations.   More information can be found in our publication "<a href="http://www.lrec-conf.org/proceedings/lrec2018/pdf/283.pdf">A High-Quality Gold Standard for Citation-based Tasks</a>" (LREC'18). You can cite the data set as follows: <pre><code>@inproceedings{DBLP:conf/lrec/0001TJ18, author = {Michael F{\"{a}}rber and Alexander Thiemann and Adam Jatowt}, title = "{A High-Quality Gold Standard for Citation-based Tasks}", booktitle = "{Proceedings of the Eleventh International Conference on Language Resources and Evaluation}", series = "{LREC'18}", location = "{Miyazaki, Japan}", year = {2018}, url = {http://www.lrec-conf.org/proceedings/lrec2018/summaries/283.html} } </code></pre>

openapache2.0Aug 2024View details →

High-throughput Computational Screening of Hydrocarbon Molecules for Long-wavelength Infrared Imaging

This repository contains datasets associated with the paper titled "High-throughput Computational Screening of Hydrocarbon Molecules for Long-wavelength Infrared Imaging," accepted at ACS Materials Letters Journal. Contents: <ol> <li> Optimized XYZ Coordinates: The hydrocarbon molecules' XYZ coordinates, obtained using the B3LYP functional and the 6-31g(d,p) basis set in Gaussian 16 software, used to simulate the IR spectra (including transition energies and absorption intensities) of the molecules. </li> <li> Broadened Molar Absorptivity IR Spectra: The dataset's IR spectra, broadened using a Lorentzian band shape with a gamma (half-width at half-height) value of 5 cm⁻¹. Molecules with imaginary frequencies have been excluded. </li> <li> Related SMILES Strings: Contains SMILES strings for these hydrocarbons. </li> <li> NUMBERS_SMILES.csv: Provides the associated SMILES string for each numerated XYZ coordinate. </li> </ol> For any inquiries, please contact Dr. Maliheh Shaban Tameh at malihe.shaban<a rel="noreferrer">@gmail.com</a>

opencc-by-4.0Aug 2024View details →

Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA

Data deposition for "Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA" published in Nucleic Acids Research. Data includes custom paramaterized nucleobase residues for use in AMBER molecular dyanmics simulations. Initial structures and setup code along with starting structures for generation of simulations in AMBER (pmemd.cuda). A in-house "MD-Generator" script to create nessessary files with our select simulation settings. Lastly, also included are CPPTRAJ analysis commands and scripts with visualizion scripts for use in Pymol 2.5 and above.

opencc-by-4.0Dec 2013View details →

Figure 1 in Strategies for false positive reduction and multimodal lesion characterization in computer-aided diagnosis of breast cancer

Figure 1. - Representative ultrasound images at four-month post copulation (8 Sep. 2010) before resorption, five-month post copulation (20 Oct. 2010) during resorption, and six-month post copulation (3 Nov. 2010) after resorption. A: Uterine horn; B: Fetus; C: Ovary; D: Follicle.

opencc-by-4.0Dec 2019View details →

Fig. 1 in Hydrodynamic performance of psammosteids: new insights from computational fluid dynamics simulations

Fig. 1. Box-shaped flow domain, mesh and coordinate system used for computational fluid dynamics (A ); A , enlargement view on the mesh.

opencc-by-4.0Dec 2019View details →

Fig. 2 in Hydrodynamic performance of psammosteids: new insights from computational fluid dynamics simulations

Fig. 2. Distribution of pressure on the fish bodies at flow velocity 1.5 ms-1, in anterior (A) and lateral (A) views.

opencc-by-4.0Dec 2019View details →

Fig. 4. Vorticity patterns using Q-criterion for 0 in Hydrodynamic performance of psammosteids: new insights from computational fluid dynamics simulations

Fig. 4. Vorticity patterns using Q-criterion for 0 angles of attack and flow velocity 1.5 ms-1 in Errivaspis (A), Guerichosteus (B), and Tartuosteus (C). Models displayed in left lateral (A 1 –C 1) and top (A 2 –C 2) views. Iso-vorticity surface is colored by the magnitude of velocity.

Fig. 9 in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 9. Evolution of bioerosion intensity and boring depth throughout the Phanerozoic. The line graph (scale at left hand side) illustrates the percentage of reefs with evidence of macroborings, based on the PaleoReefs database (after Kiessling 2002). The shaded columns (scale on right hand side) shows the number of classes with endolithic representatives (light grey) and those reaching penetration depths in excess of 50 mm (dark grey) (after Vermeij 1993). Note the significant increase of boring intensity and penetration depth during the "Mesozoic Marine Revolution".

Fig. 7. 3D in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 7. 3D reconstruction of traces visualised for observation with anaglyph glasses (red/blue). A. Borings filled by micritic material within Densastroma pexisum. Arrow indicating holotype. B. Holotype of Osprioneides kampto Beuck and Wisshak, igen. et isp. nov. showing a maximal diameter of 17 mm. C. Micritic matrix of boring infills with interfering micritic compounds augmented in the host skeleton. D. Holotype of O. kampto Beuck and Wisshak, igen. et isp. nov. indicated by arrow. Scale bars 10 mm.

Fig. 6. 3D in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 6. 3D reconstruction of Osprioneides kampto Beuck and Wisshak, igen. et isp. nov. (CT scan analysis). Cubes indicating the spatial orientation of sample based on medical terms. A. Semi−transparent visualisation of the of stromatoporoid's surface and the micritic matrix of its boring infill. Grey−dashed lines indicate virtual sections that have been visualised parallel but are not pictured. B. O. kampto Beuck and Wisshak, igen. et isp. nov. mainly located in the upper part of host substrate. C. O. kampto Beuck and Wisshak, igen. et isp. nov. gently curved and presumably secondarily settled by Trypanites weisei. D. Tapered and rounded terminus of O. kampto Beuck and Wisshak, igen. et isp. nov. E. O. kampto Beuck and Wisshak, igen. et isp. nov. interwoven with Trypanites isp. F. Three traces of O. kampto Beuck and Wisshak, igen. et isp. nov. meet. G. Holotype of O. kampto Beuck and Wisshak, igen. et isp. nov. showing a strongly oval cross−section and a slightly bent course (arrow). Scale bars 10 mm.

Fig. 3 in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 3. Large stromatoporoid Densastroma pexisum from the Upper Visby Formation at "Halls Huk 3" of Gotland, Sweden, with multiple macroborings (dashed rectangles indicate close−ups illustrated in Fig. 4). A. Transverse fracture surface showing dense host skeleton with concentric growth laminae, and large Osprioneides kampto Beuck and Wisshak, igen. et isp. nov. macroborings filled with a fine micrite matrix. B. Densely pitted, partly eroded surface of the stromatoporoid with numerous unroofed O. kampto Beuck and Wisshak, igen. et isp. nov. macroborings, occasionally truncating each other.

Fig. 5 in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 5. Spatial distribution of traces (CT scan analysis). Cubes indicating the spatial orientation of sample based on medical terms; grey−dashed lines indicate further virtual sections that have been visualised parallel but are not pictured. A. 3D reconstruction of Densastroma pexisum with semi−transparent adjustment of it's skeleton, exposing trace fillings. White lines indicate the section planes of C–F. Cutting sites of C/D and E/F show meeting points of individual Osprioneides kampto Beuck and Wisshak, igen. et isp. nov. B. Virtual section partially exposing a 120 mm long trace of O. kampto Beuck and Wisshak, igen. et isp. nov. C. White line indicating section plane of B. C–F. O. kampto Beuck and Wisshak, igen. et isp. nov. traces feigning ramification (see arrows).

Fig. 2. A in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 2. A. Stable carbon isotope stratigraphy across the Silurian Lower/Upper Visby Formation boundary (metres according to the Ireviken type section; after Munnecke et al. 2003). B. Conodont stratigraphy after Jeppsson (1997). C. Formations on Gotland. D. Series. δ13C data from micritic material indicarb cate a stratigraphic position within the upper part of the Lower Kockelella ranuliformis Conodont Zone.

Fig. 4 in A giant boring in a Silurian stromatoporoid analysed by computer tomography

Fig. 4. Close−ups of the bored Densastroma pexisum stromatoporoid (positions indicated by dashed lines in Fig. 3). A. Undulating course of a deeply penetrating Osprioneides kampto Beuck and Wisshak, igen. et isp. nov. in longitudinal section. B. Two unroofed O. kampto Beuck and Wisshak, igen. et isp. nov. specimen, one of which showing the growth increments of the host stromatoporoid on the boring walls where the micritic infill is eroded. Boring direction was from the eroded aperture at the right towards the left hand side. C. The densely pitted outer surface of the stromatoporoid showing circular apertures of Trypanites and Palaeosabella of various size. D. The nearby fracture surface, exposing longitudinal to oblique sections of small Trypanites and Palaeosabella borings. Scale bars 10 mm.

Fig. 4 in Characterisation of Crassicauda fuelleborni nematode infection in Indo-Pacific finless porpoises (Neophocaena phocaenoides) using postmortem computed tomography

Fig. 4. PMCT and necropsy images of lesions caused by the nematode Crassicauda fuelleborni or Crassicauda sp. in the male reproductive organs of Indo-Pacific finless porpoises Neophocaena phocaenoides stranded in Hong Kong waters. (A) Case 11, subadult male, heterogeneous lesion (arrowhead) with both isoattenuated and hyperattenuated content associated with the prostate (asterisk), nematode found was later identified as C. fuelleborni. (B) Case 13, adult male, homogenous hyperattenuated probable Crassicauda-related lesion in the tissues surrounding the penis (asterisk). (C) Case 6, juvenile male, isoattenuated lesion with some hypoattenuated and hyperattenuated foci associated with the right testis (arrowhead). (D) Case 6, juvenile male, the corresponding abscessed lesion at the right epididymis with nematodes later identified as Crassicauda sp.

Fig. 2 in Characterisation of Crassicauda fuelleborni nematode infection in Indo-Pacific finless porpoises (Neophocaena phocaenoides) using postmortem computed tomography

Fig. 2. PMCT and necropsy images of lesions caused by the nematode Crassicauda sp. in an Indo-Pacific finless porpoise Neophocaena phocaenoides stranded in Hong Kong waters. (A) Case 1, subadult female, homogeneous isoattenuated lesion (arrowhead) in the ventral abdominal muscle (upper) and the corresponding nodule containing coiled and fragmented nematodes later identified as Crassicauda sp. (lower). (B) Case 1, subadult female, heterogeneous lesion (arrowhead) with isoattenuated content and hypoattenuated foci interpreted as small gas collections in the ventral abdominal muscle (upper) and the intact and coiled nematodes collected from the corresponding nodule and later identified as Crassicauda sp. (lower).

Fig. 3 in Characterisation of Crassicauda fuelleborni nematode infection in Indo-Pacific finless porpoises (Neophocaena phocaenoides) using postmortem computed tomography

Fig. 3. PMCT and necropsy images of probable Crassicauda-related lesions in Indo-Pacific finless porpoises Neophocaena phocaenoides stranded in Hong Kong waters. (A) Case 8, adult female, heterogeneous lesion (arrowhead) with a hyperattenuated rim and isoattenuated content in the ventral abdominal muscle (upper) and the corresponding nodule containing decomposed worms among caseous debris (lower). (B) Case 8, adult female, heterogeneous lesion (arrowhead) with both hyperattenuated and isoattenuated content in the ventral abdominal muscle (upper) and the corresponding nodule containing creamy pink caseous debris (lower). (C) Case 1, subadult female, homogeneous hyperattenuated lesion (arrowhead) in the ventral abdominal muscle (upper) and the corresponding nodule containing dried and pale yellow caseous debris (lower). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Characterisation of Crassicauda fuelleborni nematode infection in Indo-Pacific finless porpoises (Neophocaena phocaenoides) using postmortem computed tomography

Fig. 1. PMCT images showing the anatomy of the mammary glands and adjacent structures, as well as an example of Crassicauda-related mammary gland pathology in Indo-Pacific finless porpoises Neophocaena phocaenoides. (A) Recently pregnant adult female, axial cross-section of the mammary glands (MG) and adjacent structures (H: m. hypaxialis lumborum, AC: abdominal cavity, RA: m. rectus abdominis, MA: mm. abdominales, SM: superficial muscles between the mammary glands and blubber). (B) Recently pregnant adult female, longitudinal cross-section of the mammary glands, with branch-like ducts converging into the central lactiferous ducts (CLD). (C) Sexually mature adult female with severe parasitic infection of the mammary glands and adjacent muscles, notably with multiple hyperattenuated lesions in the muscles dorsal to the mammary glands with one invading and compressing the mammary gland tissues on the right side.

opencc-by-4.0Dec 2016View details →

FIGURE 2 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 2. Reconstructed tomographic images of the specimen (1) and its internal structure in median section (2). The lower and upper jaws are enlarged in (3) and (4), respectively.