dataesr/scientific-paragraphs-categorization huggingface dataset:
It also ensures that the specimen is perfectly still after the rotation. The number N of radiographic images needed to perform a reconstruction can be estimated by measuring the maximum width W of the projected specimen on a radiograph (in pixels) using the formula N = π × W (for a 360° scan; Fig. 10 ). Note that to determine the maximum width the specimen should be rotated, as irregularly shaped specimens may have different widths at different angles. Acquiring less than N projection images will provide an incomplete dataset for the reconstruction algorithm. The reconstruction will be still possible, but its quality will be degraded. The total scanning time T (in seconds) can be computed with the following formula: T = N × (P + (E × A)). Other scanning settings include the selection of the rotation step, random movement and 180/360° scan.
Following the alignment of the projection images, the reconstruction software creates a histogram with the frequency the grayscale values representing the density distribution of the micro-CT dataset. The specific range of the histogram values can display different parts of the organisms (Fig. 11 ). Generally, the peaks in the histogram values represent different structures concerning the different densities. Dense structures such as bones and shells are represented by higher grayscale values compared to soft tissues. The user can choose to restrict the range of values, to suppress or include specific densities, in order to emphasize different structures in the reconstruction of the sample. The range of the grayscale values can also be taken into consideration in order to avoid noise and to isolate unwanted structures (e.
g. , sample holder). During the reconstruction procedure, the reconstruction can be restricted to a specific area of the specimen by creating a region of interest (ROI). For example, the reconstruction of the jaws of a polychaete can be achieved by the creation of a ROI which comprises only these target structures (Fig. 12 ). This method can minimise the time of the reconstruction procedure and the size of the reconstructed dataset. The reconstruction duration also depends on the computational resources and capacities, the size of the dataset and the algorithm used  (Sutton et al. 2014). European Journal of Taxonomy 522: 1-55 (  2019 ) can be achieved either manually, semi-automatically or automatically -a large number of algorithms exist for automatic segmentation. Segmentation can be used to include the removal of unwanted objects, to highlight certain structures with colour or to virtually dissect the sample  (Sutton et al.
Troubleshooting Micro-CT scanning is prone to artefacts which can degrade the quality of micro-CT images and the degree of image distortion can make the micro-CT datasets unusable  (Barrett & Keat 2004). Artefacts can be created by several processes during the acquisition of micro-CT images. The most common artefacts which are encountered on the micro-CT images are: a) beam hardening artefacts, b) ring artefacts, c) noise, d) partial volume, e) motion artefacts and f) metal artefacts. The avoidance or the correction of these artefacts is important to improve the resulting micro-CT image, but sometimes the effects may be irreversible, so that the scan will have to be repeated.
22 ). Scanning at high kVp is not possible for soft bodied samples like insects. Metal artefacts may be the result of several causes like noise, beam hardening, non-linear partial volume effect, and scatter  (de Man 2001). Visually, the metal artefact looks like an overexposed part on the micro-CT image slice with many streaks and star-like bright lines (Figs  20B, 22B ). In some cases reconstruction software contains a built-in Metal-Deletion-Technique  (Boas & Fleischmann 2012 ) that reduces or completely removes the metal artefact. Tests with this algorithm in the Xact reconstruction software (RX Solutions) proved successful for a leopard skull bearing metal screws, but failed for a scan with a pinned beetle.
Zoological samples The identification of zoological specimens is usually based on external, internal or on the combination of external and internal morphological characteristics. The 3D nature of the different structures is important for the classification of the organisms  (Boistel et al. 2011; Faulwetter et al. 2013a). The creation of 3D models at a resolution of a few microns, the accessibility of micro-CT scanners, the low cost and the use of these datasets for morphometric, functional, ecological and developmental analysis reveal the utility of this technology for zoological studies  (Faulwetter et al. 2013a; Fernández et al. 2014). According to  Boistel et al. (2011) , different scans -which are referred to as 'morphoscans' -should be included in a reliable 3D library with reference models (or gold standards) including intra-species variations and key references established by the community.
Even in cases where sectioning is allowed, the use of micro-CT can eliminate the time spent and the laboriousness traditionally faced during the serial sectioning of geological specimens. The digital character of a micro-CT dataset allows interactive manipulation of the data, better visualisation and animation and easier measurement of dimensions  (Carlson et al. 2003; Abel et al. 2011). Micro-CT is a useful tool for the visualization of fractures, pores or layers which are characterised by different densities  (Cnudde et al. 2006). According to  Stanley (1992) , among the types of rocks that can be examined using micro-CT are: -igneous rocks formed by cooling and hardening of molten material (magma), which are composed by interlocking grains, each consisting of a particular mineral). -rocks formed from sediments (mineral grains) that are deposited at the earth's surface by water, ice or air.
Data curation Given the importance of virtual specimens for future research -especially if datasets are designated as cybertypes for species descriptions (see e. g. ,  Akkari et al. 2015)  -data management (or curation) of micro-CT datasets should be performed with the same care as curating physical specimens. Currently, however, there are no universally accepted guidelines or standards concerning the curation, documentation and dissemination of micro-CT datasets. A recent overview and set of recommendations has been provided by  Davies et al. (2017). A few general suggestions are listed below, which should be taken into consideration by micro-CT laboratories wanting to develop or improve data management practices. Generally, data management / curation activities can be classified into three broad categories: a) documentation; b) data organization, storage and archival practices and c) data dissemination.
Documentation The documentation of the dataset through metadata is crucial. Metadata place the dataset into context, make it discoverable and retrievable, provide information on provenance, terms for re-use and document the steps performed to create the dataset. The required level of detail of the metadata is determined by a variety of factors, such as internal guidelines of the institution, every-day practices of the laboratory and demands of users, trying to strike a balance between the need for a full documentation of the dataset with a high level of detail, and the effort, time and costs required to create this documentation. Currently, no metadata standards or formats exist specifically for natural history specimens imaged through micro-CT. Several existing standards could be adapted to adequately describe these data, such as the DICOM (Digital Imaging and Communications in Medicine; http://dicom.
nema. org), ISA-TAB (Investigation-Study-Assay; http://isa-tools. org/; Sansone et al. 2012) or HDF5 (Hierarchical Data Format 5; https://www. hdfgroup. org/) format. DICOM is a file format and data exchange protocol extensively used in medical imaging and contains the metadata embedded together with the images. While the metadata can be adapted to individual needs, and thus could be tailored towards 3D natural history specimen data, DICOM is not straightforward to learn, dedicated software is required and DICOM is not produced directly by many scanner models. The ISA-TAB standard provides flexible options to describe protocols and parameters and to combine metadata terms. It has at least once been applied to document micro-CT data  (Stoev et al. 2013) , although in a simplified form. The Hierarchical Data Format (HDF5) is a generic format suitable for large datasets comprised of heterogeneous subsets, including user-defined embedded metadata.
The HDF5 format has been used for tomographic data (e. g. , De  Carlo et al. 2018; Mancini et al. 2018) , but its use requires some expertise and dedicated software is needed. However, many laboratories may decide to store metadata in a custom-made database or even in text files that are distributed along with the data. While a central database which includes documentation for all datasets allows for efficient search and retrieval of the datasets and enhances discoverability, care needs to be taken when data are re-distributed. In this case the metadata need to be extracted from the database and included together with the image files (e. g. , as a text file, or embedded in, e. g. , DICOM or HDF5 files). In the case of custom-made documentation systems, metadata should at least include: -unique identifier for the dataset.
Ideally, this should be a globally unique identifier, but in case the datasets are used only internally, they can be unique within the lab / institution KEKLIKOGLOU K. et al. , Micro-computed tomography for natural history specimens -description of specimen, including a link to an identifier for the specimen, e. g. , a catalogue number -purpose of dataset -person(s) involved (for each action, if this level of detail is required) -preparations of specimen (e. g. , staining) which influence the results -date/time of scanning and all scanning parameters (often recorded automatically by the machine) -description of / Link to the storage location of the dataset(s) -usage restrictions / licenses / copyright -information on provenance / changes / version of the dataset (or a "last modified" date) -links to or identifiers of derived publications or datasets.
Data organisation, storage and archival practice While careful metadata annotation can help to organise and retrieve the actual datasets, management of the actual files is equally important. Tomography data pose certain challenges due to their large volume, requiring adequate long-term storage, reliable backup systems and mechanisms to organise and retrieve files on storage media. Depending on the responsibilities of the laboratory, different data products may have to be managed: In some laboratories, only the raw data (projection images) are kept, and everything from the reconstructed cross sections to images, analyses and other derivative data falls under the responsibility of the customer/ scientist; other practices include keeping also the reconstructed set of images and/or derivative data.
-tape library storage is still a common backup option, but recovery of data can be time-consuming and difficult. -off-site storage (i. e. , in the cloud) should be considered as protection against local disasters, but the large datasets (often several terabyte of data) result in long transmission times over the internet. Whether online storage is a feasible option will therefore depend on the practices of the laboratory (e. g. , frequency and volume of data produced; type of data to be archived). Laboratories with limited storage capabilities may also consider using data compression methods (see, e. g. ,  Mancini et al. 2018  for an overview).
Data publication The publication of research data, either to underpin scientific publications or as a general good practice of data sharing, has gained increasing acceptance over the last years. Sharing tomography data, however, can be still a challenge due to the large data volume. Data can be shared either through an institutional file sharing server or be published through a public repository. Available repositories differ in their scope and features. The choice depends on the type and size of the data to be shared, on whether journal policies apply (e. g. , when data accompany a research article) and potentially on institutional practices. An overview of repositories is given in Table  10. European Journal of Taxonomy 522: 1-55 (2019) Both volumetric datasets (reconstructed images and/or projection images) as well as surface models can be shared and are of interest to the scientific, cultural/artistic and education/science communication community.
When sharing data, a suitable licence should be chosen that allow others to re-use and process the data. Creative Commons licenses (http://www. creativecommons. org), ideally CC-BY (attribution required) or even CC-Zero (release into the public domain) are the most suitable licenses for sharing scientific data  (Hagedorn et al. 2011). 5. 3. 2. Tools for outreach and interaction with 3D data Apart from making 3D datasets available for download, tools exists for remote on-the-fly interaction of users with the data. These tools are useful for giving users an overview of the data without having to download them first, and/or provide a suitable tool for outreach and education. Surface models can easily be rendered in a browser (e. g. , 3D Hop, http://vcg. isti. cnr. it/3dhop/) and allow the user to interact (rotate, zoom, change colours or lights) with them, and multiple technological solutions and ready-made portals exist (e.
g. , WebGL, Java, Flash). Rendering volumetric data online is still a challenge, and solutions are limited. Arivis Web View (https://www. arivis. com/de/imaging-science/arivis-webview) is a commercial solution and provides online 2D and 3D rendering even via limited bandwidth. 3D slicer (https://www. slicer. org/) is free software which likewise allows online rendering of volume data, with a variety of features to control opacity and colouring. In addition to browser-based tools, several applications for mobile phones exist as well (e. g. , the free CTVox app, https://www. bruker. com/products/microtomography/micro-ct-software/3dsuite. html; ImageVis3D, http://www. sci. utah. edu/cibc-software/imagevis3d. html; Volumize, http://www. volumize. be/; or DroidRender https://www. facebook. com/droidrender).
These applications do, however, not work on the full high-resolution dataset, but on a downscaled version, as neither memory nor graphics cards on mobile devices are as powerful as those on dedicated desktop computers. Another tool for interaction with 3D data, and especially suited for exhibitions, are touch-screen based volume rendering software packages which provide a simplified user interface, allowing children and non-technical users to explore 3D datasets. A commercial solution is the InsideExplorer (http://www. interspectral. com/inside-explorer/), which also provides support in setting up exhibitions. Similar features, but without technical support, are provided by the DrishtiPrayog software (http://nci. org. au/systems-services/scientific-visualisation/visualisation-services/drishti-prayog/).
Overview of repositories for 3D data. Not tailored towards large files, although they are accepted. Charges a publishing fee (currently $120 per dataset), unless waivers apply. All data are released under a CC-Zero waiver (public domain, copyright removed). Assigns DOIs to the data. http://www. datadryad. org Figshare generic data repository. Supports files up to 5 GB free (beyond that, institutional services can be purchased). License can be chosen by user. Assigns DOIs to the data. https://figshare. com GigaDB accepts almost only data accompanying articles in GigaScience. Data can, however, be described as a DataNote and then included in the repository. Focuses on large-size data, i. e. , volumetric data. Encourages publication of projection and reconstructed data. All data are released under a CC-Zero waiver (public domain, copyright removed).
Assigns DOIs to the data. LifewatchGreece micro-CT vlab accepts volumetric micro-CT datasets, provides extensive metadata and on-the-fly viewer of volumetric datasets. Several features, e. g. , raw data download, still under construction. Does not assign DOIs. https://microct. portal. lifewatchgreece. eu MorphDBase media database which also develops ontologies that describe morphological terminology. Not specifically targeted at 3D data but accepts media files in general. https://www. morphdbase. de Morphomuseum publishes data accompanying journal articles in MorphoMuseum, but not only. Focuses on surface models, but volume data can also be published if they accompany surface data. Focus on vertebrates, but does not explicitly exclude other taxa. Assigns DOIs. Only license available is CC-BY-NC.
Acknowledgements The creation of this handbook was funded by the  EU   FP7  programme  SYNTHESYS3  ( FP7 -312253 ) and further supported by the  LifeWatchGreece infrastucture  ( ESFRI -384676 ) and  BIOIMAGING-GR  ( ESFRI -5002755 ). The authors would like to thank all the SYNTHESYS participants for their contribution to this handbook and especially  Vincent S. Smith  ( Natural History Museum, UK ) and  Elspeth M. Haston  ( The Royal Botanic Garden Edinburgh, UK ) for their support, and  Alex Ball  and  Farah Ahmed  ( Natural History Museum, UK ) for their suggestions. The authors would also like to thank  Thaddaeus Buser  and one anonymous reviewer for providing comments and suggestions that improved the manuscript.
Questionnaire Four members (I. C. , B. F. , S. F. , F. S. ) of the study group of neonatal cardiology (SGNC) of the Italian society of neonatology (SIN) developed a 37-item questionnaire according to the CHERRIES method for internet e-surveys  [12]. The questionnaire was divided into 9 sections: epidemiological and organizational characteristics of the center; NICU link with pediatric cardiology service; echocardiographic equipment; imaging storage and reporting; infection control, cardiorespiratory and thermal stability; practice of structural echocardiography; practice of f-echo; parameters of f-echo used cot-side (data on f-echo and patent ductus arteriosus (PDA) were investigated in a different survey that will be published shortly); training needs. All questions were loaded to the Google Forms Website, a free tool for creating online survey forms (https://docs.
Web-based survey A cover letter containing a hyperlink to the survey was sent to the directors of Italian NICUs and to one attending neonatologist at each site with expertise in NPE, based on the database of the SIN and the SGNC. To ensure only one response for center a unique survey link was assigned to each institution. To prevent incomplete answers, the survey form could be submitted only when completed. The first email was sent in June 2017 and a reminder in September 2017. Those who did not replied were subsequently contacted by e-mail and/or phone call. No financial rewards were offered for participating in the survey. Completion of the questionnaire implied consent to participate in the survey. The identity of each participant was kept confidential throughout the data collection and analysis.
Like in other European countries, there is no legal impediment to doctors to use ultrasound imaging, this probably was, among others, an essential factor that allowed widespread utilization of functional echocardiography in Italy  [3, 15]. F-echo was mainly performed by neonatologists rather than cardiologists and the clinical indications were: PDA, PPHN, perinatal asphyxia, hypotension/shock, cardiac tamponade, assessment of line position. These data were similar to the ones from other European countries, Australia, and New Zealand  [3, 15]. Almost all units had an exclusive ultrasound machine and the echocardiographic equipment fulfilled the requirements of the ESPR/ESN Consensus Statement (i. e. high frequency probe, B-mode, M-mode, pulse wave doppler, continuous wave doppler). Instead, ECG tracing during echocardiography, digital image archiving system and standardized reporting, that were considered by the ESPR/ ESN recommendations essential components in every scan, were still not widespread.
Courses offered both nationally and internationally had nonhomogeneous programs, greatly lacking in practical training. The development of an accredited training pathway in NPE was perceived essential by the majority of respondents. Our data highlight many issues related to acquirement of competency, health care organization and training, similarly to those observed in other countries  [8, 16, 17]. In response to these needs the SGNC, in agreement with the SIN, is currently designing and implementing a formalized and accredited training program in NPE. A close collaboration is retained with the Italian society of pediatric cardiology (SICPED), that supported and endorsed this project. Aims are to offer adequate training to meet the standards required by the ESPR/ESN recommendations, to ensure safety and to uniform practice of NPE.
phagosomal compartment, and nutrient shifts during intracellular trafficking  (5). Molecular components of the cell envelope play a key role in the ability of Brucella spp. to survive these stresses and to replicate in the intracellular niche  (6, 7). As part of a systematic experimental survey of conserved Alphaproteobacterial protein domains of unknown function (DUFs), we recently described envelope integrity protein A (EipA). This periplasmic protein confers resistance to cell envelope stressors and determines Brucella abortus virulence in a mouse model of infection  (8). In this study, we report a functional and structural analysis of envelope integrity protein B (EipB), a member of the uncharacterized gene family DUF1849. DUF1849 (Pfam PF08904  [9] ) is widespread among the Rhizobiales, Rhodospirillales, and Rhodobacterales (Fig.
2B ). We conclude that eipB is not In vivo mouse infection assay: female BALB/c mice were injected intraperitoneally with the wild-type, ΔeipB, or ΔeipB complementation strain. Spleen weights (upper graph) and bacterial burdens (lower graph) were measured at 1, 4, and 8 weeks postinfection. Naïve, uninfected, naive mice. Data are means Ϯ the standard errors of the mean (n ϭ 5 mice per strain per time point). One-way analysis of variance (ANOVA), followed by Dunnett's posttest (to wild type), supports the conclusion that spleens infected with the eipB deletion strain were significantly smaller at 4 (****, P Ͻ 0. 0001) and 8 (****, P Ͻ 0. 0001) weeks and had fewer CFU than spleens infected with the wild type at 4 (****, P Ͻ 0. 0001) and 8 (***, P Ͻ 0. 0007) weeks. (C to F) Antibody quantification in mouse sera harvested at 8 weeks postinfection from naive control mice or from mice infected with the wild-type, ΔeipB, or complementation strain.
The amounts of total IgG (C), Brucella-specific IgG (D), IgG1 (E), and IgG2a (F) at 8 weeks were determined by ELISA. Each data point (naive, n ϭ 3; WT, n ϭ 2, ΔeipB; complementation, n ϭ 4) indicates the mean Ϯ the standard error of the mean. required for initial spleen colonization but is necessary for full virulence and persistence in the spleen over an 8-week time course. To assess the pathology of mice infected with wild-type and ΔeipB strains, we harvested spleens at 8 weeks postinfection and fixed, mounted, and subjected the samples to hematoxylin and eosin (H&E) staining (see Fig. S1  in the supplemental material). Compared to naive (uninfected) mice (Fig. S1A ), we observed higher extramedullary hematopoiesis, histiocytic proliferation, granulomas, and the presence of Brucella immunoreactivities in spleens of mice infected with wild-type B.