CRONOS: the cross-reference navigation server.
Ontology highlight
ABSTRACT: Unlabelled
Cross-mapping of gene and protein identifiers between different databases is a tedious and time-consuming task. To overcome this, we developed CRONOS, a cross-reference server that contains entries from five mammalian organisms presented by major gene and protein information resources. Sequence similarity analysis of the mapped entries shows that the cross-references are highly accurate. In total, up to 18 different identifier types can be used for identification of cross-references. The quality of the mapping could be improved substantially by exclusion of ambiguous gene and protein names which were manually validated. Organism-specific lists of ambiguous terms, which are valuable for a variety of bioinformatics applications like text mining are available for download.Availability
CRONOS is freely available to non-commercial users at http://mips.gsf.de/genre/proj/cronos/index.html, web services are available at http://mips.gsf.de/CronosWSService/CronosWS?wsdl.
SUBMITTER: Waegele B
PROVIDER: S-EPMC2638938 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:UNLABELLED: Femoral intramedullary canal referencing is used by most knee arthroplasty systems. Fat embolism, activation of coagulation, and bleeding may occur from the reamed canal. The purpose of our study was to evaluate a new extramedullary device that relies on templated data. We randomized 100 consecutive patients undergoing primary total knee arthroplasty through a limited parapatellar approach to use of either standard intramedullary femoral instruments (IM group) or a new extramedullary device (EM group). The extramedullary instrument was calibrated using templated data obtained from a preoperative full-limb weightbearing anteroposterior view of the knee. In both groups, an intraoperative double check was performed using an extramedullary rod referring to the anterosuperior iliac spine. Femoral component coronal alignment was within 0 degrees +/- 2 degrees of the mechanical axis in 84% of the IM group and 86% of the EM group. Sagittal alignment of the femoral component was 0 degrees +/- 2 degrees in 78% of the IM group and 90% of the EM group. We observed no difference in the average operative time between the two groups. The two groups showed similar postoperative blood loss. Extramedullary reference with careful preoperative templating can be safely used during TKA. LEVEL OF EVIDENCE: Level II, therapeutic study. See the Guidelines for Authors for a complete description of levels of evidence.
| S-EPMC2565017 | biostudies-other
Project description:PurposeIn this study, we sought to develop a self-navigation strategy for improving the reconstruction of diffusion weighted 3D multishot echo planar imaging (EPI). We propose a method for extracting the phase correction information from the acquisition itself, eliminating the need for a 2D navigator, further accelerating the acquisition.MethodsIn-vivo acquisitions at 3T with 0.9 mm and 1.5 mm isotropic resolutions were used to evaluate the performance of the self-navigation strategy. Sensitivity to motion was tested using a large difference in pitch position of the head. Using a multishell diffusion weighted acquisition, tractography results were obtained at (0.9 mm)3 to validate the quality with conventional acquisition.ResultsThe use of 3D multislab EPI with self-navigation enables 3D diffusion-weighted spin echo EPI acquisitions that have the same efficiency as 2D single-shot acquisition. For matched acquisition time the image signal-to-noise ratio (SNR) between 3D and 2D acquisition is shown to be comparable for whole-brain coverage with (1.5 mm)3 resolution and for (0.9 mm)3 resolution the 3D acquisition has higher SNR than what can be obtained with 2D acquisitions using current state-of-art multiband techniques. The self-navigation technique was shown to be stable under inter-volume motion. In tractography analysis, the higher resolution afforded by our technique enabled clear delineation of the tapetum and posterior corona radiata.ConclusionThe proposed self-navigation approach utilized a self-consistent phase in 3D diffusion weighted acquisitions. Its efficiency and stability were demonstrated for a plurality of common acquisitions. The proposed self-navigation approach allows for faster acquisition of 3D multishot EPI desirable for large field of view and/or higher resolution.
| S-EPMC7329618 | biostudies-literature
Project description:Multi-CSAR is a web server that can efficiently and more accurately order and orient the contigs in the assembly of a target genome into larger scaffolds based on multiple reference genomes. Given a target genome and multiple reference genomes, Multi-CSAR first identifies sequence markers shared between the target genome and each reference genome, then utilizes these sequence markers to compute a scaffold for the target genome based on each single reference genome, and finally combines all the single reference-derived scaffolds into a multiple reference-derived scaffold. To run Multi-CSAR, the users need to upload a target genome to be scaffolded and one or more reference genomes in multi-FASTA format. The users can also choose to use the 'weighting scheme of reference genomes' for Multi-CSAR to automatically calculate different weights for the reference genomes and choose either 'NUCmer on nucleotides' or 'PROmer on translated amino acids' for Multi-CSAR to identify sequence markers. In the output page, Multi-CSAR displays its multiple reference-derived scaffold in two graphical representations (i.e. Circos plot and dotplot) for the users to visually validate the correctness of scaffolded contigs and in a tabular representation to further validate the scaffold in detail. Multi-CSAR is available online at http://genome.cs.nthu.edu.tw/Multi-CSAR/.
| S-EPMC9252826 | biostudies-literature
Project description:BackgroundReference frames ground spatial communication by mapping ambiguous language (for example, navigation: "to the left") to properties of the speaker (using a Relative reference frame: "to my left") or the world (Absolute reference frame: "to the north"). People's preferences for reference frame vary depending on factors like their culture, the specific task in which they are engaged, and differences among individuals. Although most people are proficient with both reference frames, it is unknown whether preference for reference frames is stable within people or varies based on the specific spatial domain. These alternatives are difficult to adjudicate because navigation is one of few spatial domains that can be naturally solved using multiple reference frames. That is, while spatial navigation directions can be specified using Absolute or Relative reference frames ("go north" vs "go left"), other spatial domains predominantly use Relative reference frames. Here, we used two domains to test the stability of reference frame preference: one based on navigating a four-way intersection; and the other based on the sport of ultimate frisbee. We recruited 58 ultimate frisbee players to complete an online experiment. We measured reaction time and accuracy while participants solved spatial problems in each domain using verbal prompts containing either Relative or Absolute reference frames. Details of the task in both domains were kept as similar as possible while remaining ecologically plausible so that reference frame preference could emerge.ResultsWe pre-registered a prediction that participants would be faster using their preferred reference frame type and that this advantage would correlate across domains; we did not find such a correlation. Instead, the data reveal that people use distinct reference frames in each domain.ConclusionThis experiment reveals that spatial reference frame types are not stable and may be differentially suited to specific domains. This finding has broad implications for communicating spatial information by offering an important consideration for how spatial reference frames are used in communication: task constraints may affect reference frame choice as much as individual factors or culture.
| S-EPMC7644680 | biostudies-literature
Project description:MotivationMetagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.ResultsHere, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.
| S-EPMC3519457 | biostudies-literature
Project description:The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well.
| S-EPMC3776805 | biostudies-literature
Project description:BackgroundAfrica has a large burden of spine pathology but has limited and insufficient infrastructure to manage these spine disorders. Therefore, we conducted this e-survey to assess the prevalence and identify the determinants of the availability of spine surgery navigation techniques in Africa.Materials and methodsA two-part questionnaire was disseminated amongst African neurological and orthopedic surgery consultants and trainees from January 24 to February 23, 2021. The Chi-Square, Fisher Exact, and Kruskal-Wallis tests were used to evaluate bivariable relationships, and a p-value <0.05 was considered statistically significant.ResultsWe had 113 respondents from all regions of Africa. Most (86.7 %) participants who practiced or trained in public centers and centers had an annual median spine case surgery volume of 200 (IQR = 190) interventions. Fluoroscopy was the most prevalent spine surgery navigation technique (96.5 %), followed by freehand (55.8 %), stereotactic without intraoperative CT scan (31.9 %), robotic with intraoperative CT scan (29.2 %), stereotactic with intraoperative CT scan (8.8 %), and robotic without intraoperative CT scan (6.2 %). Cost of equipment (94.7 %), lack of trained staff to service (63.7 %), or run the equipment (60.2 %) were the most common barriers to the availability of spine instrumentation navigation. In addition, there were significant regional differences in access to trained staff to run and service the equipment (P = 0.001).ConclusionThere is a need to increase access to more advanced navigation techniques, and we identified the determinants of availability.
| S-EPMC8346523 | biostudies-literature
Project description:Behavioral studies for humans, monkeys, and rats have shown that, while traversing an environment, these mammals tend to use different frames of reference and frequently switch between them. These frames represent allocentric, egocentric, or route-centric views of the environment. However, combinations of either of them are often deployed. Neurophysiological studies on rats have indicated that the hippocampus, the retrosplenial cortex, and the posterior parietal cortex contribute to the formation of these frames and mediate the transformation between those. In this paper, we construct a computational model of the posterior parietal cortex and the retrosplenial cortex for spatial navigation. We demonstrate how the transformation of reference frames could be realized in the brain and suggest how different brain areas might use these reference frames to form navigational strategies and predict under what conditions an animal might use a specific type of reference frame. Our simulated navigation experiments demonstrate that the model's results closely resemble behavioral findings in humans and rats. These results suggest that navigation strategies may depend on the animal's reliance in a particular reference frame and shows how low confidence in a reference frame can lead to fluid adaptation and deployment of alternative navigation strategies. Because of its flexibility, our biologically inspired navigation system may be applied to autonomous robots.
| S-EPMC5293834 | biostudies-other
Project description:The establishment of a (set of) stably expressed reference gene(s) is required to normalize transcription data. Polyploidy is very common in the plant kingdom, but it is not necessarily the case that a reference gene which works well at the diploid level will also work well at the polyploid level. Here, ten candidate reference genes are compared in the context of gene transcription in the genus Chrysanthemum. The robustness of some, but not all, of these was shown to be high across ploidy levels. MTP (metalloprotease) and ACTIN (actin) were the most stable in diploid and tetraploid C. nankingense, while PSAA (photosynthesis-related plastid gene representing photosystem I) and EF-1? (elongation factor-1?) were the most stable in tetraploid and hexaploid C. zawadskii. EF-1? and PGK (phosphoglycerate kinase) was the best combination for the complete set of four taxa. These results suggest that when making cross-species comparison of transcript abundance involving different ploidy levels, care needs to be taken in the selection of reference gene(s).
| S-EPMC4308696 | biostudies-literature
Project description:Normalization of quantitative gene expression data with a suitable reference gene is essential for accurate and reliable results. However, the availability and choice of most suitable reference gene(s) showing uniform expression across all the experimental conditions remain a drawback. We have developed a web server, PlantRGS (http://www.nipgr.res.in/PlantRGS), for the identification of most suitable candidate reference gene(s) at the whole-genome level using microarray data for quantitative gene expression studies in plants. Microarray data from more than 11 000 tissue samples for nine plant species have been included in the PlantRGS for meta-analysis. The web server provides a user-friendly graphical user interface-based analysis tool for the identification of most suitable reference genes in the selected plant species under user-defined experimental conditions. Various parameter options and output formats will help users to investigate desired number of most suitable reference genes with wide range of expression levels. Validation of results revealed that novel reference genes identified by the PlantRGS outperforms the traditionally used reference genes in terms of expression stability. We anticipate that the PlantRGS will provide a platform for the identification of most suitable reference gene(s) under given experimental conditions and facilitate quantitative gene expression studies in plants.
| S-EPMC3223078 | biostudies-literature