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Additional file 6. BLAST against B. glabrata: A reciprocal BLAST search against the recently published transcriptome of twelve pooled Biomphalaria glabrata tissues [3].

This dataset contains key characteristics about the data described in the Data Descriptor Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers. Contents: 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format

PubMed Central reuse of GEO datasets deposited in 2007This is the raw data behind the analysis. It contains one row for every mention of a 2007 GEO dataset in PubMed Central. Each row identifies the mentioned GEO dataset, the PubMed Central article that mentions the dataset's accession number, whether the authors of the dataset and the attributing article overlap, and whether this is considered an instance of third-party data reuse.PMC_reuse_of_2007_GEO_datasets.csvAggregate Table DataAggregate table data behind the figures and results in the README associated with the main dataset. Includes Baseline metrics used for extrapolating PubMed Central (PMC) results to PubMed, Number of mentions of a 2007 GEO dataset by authors who submitted the dataset, and Number of mentions of a dataset by authors who DID NOT submit the dataset across 2007-2010.tables.csv Funding agencies are reluctant to support data archiving, even though large research funders such as the National Science Foundation (NSF) and the National Institutes of Health acknowledge its importance for scientific progress. Our quantitative estimates of data reuse indicate that ongoing financial investment in data-archiving infrastructure provides a high scientific return.

Abstract Objective Globally, more than 200 million people live at risk of the neglected tropical disease schistosomiasis (or snail fever). Larval schistosomes require the presence of specific snail species that act as intermediate hosts, supporting their multiplication and transformation into forms that can infect humans. This project was designed to generate a transcriptome from the central nervous system (CNS) of Biomphalaria alexandrina, the major intermediate host for Schistosoma mansoni in Egypt. Results A transcriptome was generated from five pooled central nervous systems dissected from uninfected specimens of B. alexandrina. Raw Illumina RNA-seq data (~ 20.3 million paired end reads of 150 base pairs length each) generated a transcriptome consisting of 144,213 transcript elements with an N50 contig size of 716 base pairs. Orthologs of 15,246 transcripts and homologs for an additional 16,810 transcripts were identified in the UniProtKB/Swiss-Prot database. The B. alexandrina CNS transcriptome provides a resource for future research exploring parasite-host interactions in a simpler nervous system. Moreover, increased understanding of the neural signaling mechanisms involved in the response of B. alexandrina to infection by S. mansoni larvae could lead to novel and highly specific strategies for the control of snail populations.

Introduction The Surgical Planning Laboratory (SPL) and the National Center for Image Guided Therapy (NCIGT) are making this dataset available as a resource to aid in the development of algorithms and tools for deformable registration, segmentation and analysis of prostate magnetic resonance imaging (MRI) and ultrasound (US) images. Description This dataset contains anonymized images of the human prostate (N=3 patients) collected during two sessions for each patient: MRI examination of the prostate for the purposes of disease staging. US examination of the prostate for the purposes of volumetric examination in preparation to the brachytherapy implant. These are three-dimensional (multi-slice) scalar images. Image files are stored using NRRD file format (files with .nrrd extension), see details at http://teem.sourceforge.net/nrrd/format.html. Each image file includes a code for the case number (internal numbering at the research site) and the modality (US or MR). Image annotations were prepared by Dr. Fedorov (no professional training in radiology) and Dr. Tuncali (10+ in prostate imaging interpretation). Annotations include Manual contouring (segmentation) of the whole prostate gland, performed in 3D Slicer software. These segmentation images are coded in the same fashion as the image files, and saved in NRRD format, with "-label" suffix. Manually placed points (fiducials) corresponding to the location of urethra entry into the prostate at base (coded as UB), verumontanum (VM), urethra entry into the prostate at apex (UA), as well as centroids of cysts and calcifications. UB, UA and VM locations are annotated both in MR and US for all cases, while cysts and calcifications are annotated when applicable. Fiducial points are stored in comma-separated CSV-style format adopted by 3D Slicer software (.fcsv file extension). There is one row per point in these files, encoding the location of the point in RAS coordinate space relative to the image data, and the name of the point. Viewing the collection We tested visualization of images, segmentations and fiducials in 3D Slicer software, and thus recommend 3D Slicer as the platform for visualization. 3D Slicer is a free open source platform (see http://slicer.org), with the pre-compiled binaries available for all major operating systems. You can download 3D Slicer at http://download.slicer.org. Acknowledgments Preparation of this data collection was made possible thanks to the funding from the National Institutes of Health (NIH) through grants R01 CA111288 and P41 RR019703. If you use this dataset in a publication, please cite the following manuscript. You can also learn more about this dataset from the publication below. Fedorov, A., Khallaghi, S., Antonio Sánchez, C., Lasso, A., Fels, S., Tuncali, K., Sugar, E. N., Kapur, T., Zhang, C., Wells, W., Nguyen, P. L., Abolmaesumi, P. & Tempany, C. Open-source image registration for MRI–TRUS fusion-guided prostate interventions. Int J CARS 10, 925–934 (2015). https://pubmed.ncbi.nlm.nih.gov/25847666/ Contact Andrey Fedorov, fedorov@bwh.harvard.edu {"references": ["Fedorov, Andriy, Siavash Khallaghi, C Antonio S\u00e1nchez, Andras Lasso, Sidney Fels, Kemal Tuncali, Emily Neubauer Sugar, et al. 2015. \"Open-Source Image Registration for MRI\u2013TRUS Fusion-Guided Prostate Interventions.\" International Journal of Computer Assisted Radiology and Surgery, April. Springer Berlin Heidelberg, 1\u201310. doi:10.1007/s11548-015-1180-7.", "Fedorov, A., Beichel, R., Kalpathy-Cramer, J., Finet, J., Fillion -Robin, J. C., Pujol, S., ... & Kikinis, R. (2012). 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magnetic resonance imaging, 30(9), 1323-1341."]}

Abstract Background Animal responses to thermal stimuli involve intricate contributions of genetics, neurobiology and physiology, with temperature variation providing a pervasive environmental factor for natural selection. Thermal behavior thus exemplifies a dynamic trait that requires non-trivial phenotypic summaries to appropriately capture the trait in response to a changing environment. To characterize the deterministic and plastic components of thermal responses, we developed a novel micro-droplet assay of nematode behavior that permits information-dense summaries of dynamic behavioral phenotypes as reaction norms in response to increasing temperature (thermal tolerance curves, TTC). Results We found that C. elegans TTCs shift predictably with rearing conditions and developmental stage, with significant differences between distinct wildtype genetic backgrounds. Moreover, after screening TTCs for 58 C. elegans genetic mutant strains, we determined that genes affecting thermosensation, including cmk-1 and tax-4, potentially play important roles in the behavioral control of locomotion at high temperature, implicating neural decision-making in TTC shape rather than just generalized physiological limits. However, expression of the transient receptor potential ion channel TRPA-1 in the nervous system is not sufficient to rescue rearing-dependent plasticity in TTCs conferred by normal expression of this gene, indicating instead a role for intestinal signaling involving TRPA-1 in the adaptive plasticity of thermal performance. Conclusions These results implicate nervous system and non-nervous system contributions to behavior, in addition to basic cellular physiology, as key mediators of evolutionary responses to selection from temperature variation in nature.

Khoomei is a unique singing style originating from the Central Asian republic of Tuva. Singers produce two pitches simultaneously: a booming low-frequency rumble alongside a hovering high-pitched whistle-like tone. The biomechanics of this biphonation are not well-understood. Here, we use sound analysis, dynamic magnetic resonance imaging, and vocal tract modeling to demonstrate how biphonation is achieved by modulating vocal tract morphology. Tuvan singers show remarkable control in shaping their vocal tract to narrowly focus the harmonics (or overtones) emanating from their vocal cords. The biphonic sound is a combination of the fundamental pitch and a focused filter state, which is at the higher pitch (1-2 kHz) and formed by merging two formants, thereby greatly enhancing sound-production in a very narrow frequency range. Most importantly, we demonstrate that this biphonation is a phenomenon arising from linear filtering rather than a nonlinear source. Data is placed in four zipped files (compression done via Mac OS 10.12.4). The four files each contain a particular subset of the data: 1. Model.zip - Modeling software (Tube Talker) and several illustrative simulations 2. CroppedMRI_CB.zip - Both statis and dynamic MRI images (as .dcm files). Note that the DICOM files have been cropped (so to only show the relevant anatomical features) and metadata have been stripped. 3. SoundboothRecordings.zip - All soundbooth recordings, saved as .wav files (SR 96 kHz) 4. STL.zip - Reonstruction of the 3-D airspace, saved as a .stl file 5. MRIaudio.zip - Audio files collected during the MRI runs 6. MRImoviesC.zip - Movies of the dynamic data (with audio). Data is a combination of acoustical recordings, MRI data, and vocal tract modeling. Movie of the dynamic MRI data are also included. All details are included in the manuscript "Overtone focusing in biphonic Tuvan throat singing".

Additional file 3. Homologous Transcripts: Transcripts with significant one-way BLAST hits against the UniProtKB/Swiss-Prot database.