366 research outputs found
Sparse annotation strategies for segmentation of short axis cardiac MRI
Short axis cardiac MRI segmentation is a well-researched topic, with
excellent results achieved by state-of-the-art models in a supervised setting.
However, annotating MRI volumes is time-consuming and expensive. Many different
approaches (e.g. transfer learning, data augmentation, few-shot learning, etc.)
have emerged in an effort to use fewer annotated data and still achieve similar
performance as a fully supervised model. Nevertheless, to the best of our
knowledge, none of these works focus on which slices of MRI volumes are most
important to annotate for yielding the best segmentation results. In this
paper, we investigate the effects of training with sparse volumes, i.e.
reducing the number of cases annotated, and sparse annotations, i.e. reducing
the number of slices annotated per case. We evaluate the segmentation
performance using the state-of-the-art nnU-Net model on two public datasets to
identify which slices are the most important to annotate. We have shown that
training on a significantly reduced dataset (48 annotated volumes) can give a
Dice score greater than 0.85 and results comparable to using the full dataset
(160 and 240 volumes for each dataset respectively). In general, training on
more slice annotations provides more valuable information compared to training
on more volumes. Further, annotating slices from the middle of volumes yields
the most beneficial results in terms of segmentation performance, and the
apical region the worst. When evaluating the trade-off between annotating
volumes against slices, annotating as many slices as possible instead of
annotating more volumes is a better strategy
Research and Analysis of Fisheries in Illinois
Reports on progress and results for the following project objectives: sport fish population and sport fishing metrics; enhanced field sampling of sport fish populations; determination of factors affecting fishing quality; coordination with ongoing fisheries research projects; support for and enhance of web interface; fishes of Champaign County; recovery of urban stream sport fisheries.Illinois Department of Natural Resources, Division of Fisheries, Federal Aid Project F-69-R Segment 28unpublishednot peer reviewedOpe
Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant
The Lantern Vol. 75, No. 2, Spring 2008
• In a French Courtyard at the Philadelphia Museum of Art • Picky Mangoes • And for My Un-Birthday I Drank Poets\u27 Tea and Got to See • Tree-Baby • Wrestling With Plants • I Smile • Walking Home • The Wall Between • Phalangese, or the Art of Speaking to Fingers • Early Spring • Karma Kids • A Bazaar Triptych • The Joys of Ritual Circumcision • [Of] Archetype[s] or I Don\u27t Like Your Poetry • Truth and Beauty Bombed • Chevalier Anachronistic • Kinds of Birds • Sparknotes Entry for The Changing Tide by Eric Relvas • Thirst • The Devil\u27s Dictionary • Portrait of an Artist Who Loves Icarus • Dinner at the Old House • The Meaning of a Dust-Busterhttps://digitalcommons.ursinus.edu/lantern/1172/thumbnail.jp
A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale
In this era of complete genomes, our knowledge of neuroanatomical circuitry
remains surprisingly sparse. Such knowledge is however critical both for basic
and clinical research into brain function. Here we advocate for a concerted
effort to fill this gap, through systematic, experimental mapping of neural
circuits at a mesoscopic scale of resolution suitable for comprehensive,
brain-wide coverage, using injections of tracers or viral vectors. We detail
the scientific and medical rationale and briefly review existing knowledge and
experimental techniques. We define a set of desiderata, including brain-wide
coverage; validated and extensible experimental techniques suitable for
standardization and automation; centralized, open access data repository;
compatibility with existing resources, and tractability with current
informatics technology. We discuss a hypothetical but tractable plan for mouse,
additional efforts for the macaque, and technique development for human. We
estimate that the mouse connectivity project could be completed within five
years with a comparatively modest budget.Comment: 41 page
SN Zwicky: uncovering a population of gravitational lens galaxies with magnified "standard candles"
We report the discovery of a very rare phenomenon, a multiply-imaged
gravitationally lensed Type Ia supernova (SNe Ia), "SN Zwicky", a.k.a. SN
2022qmx, magnified nearly twenty-five times by a foreground galaxy. The system
was identified as intrinsically bright thanks to the "standard candle" nature
of SNe Ia. Observations with high-spatial resolution instruments resolved a
system with four nearly simultaneous images, with an Einstein radius of only
, corresponding to a lens mass of solar masses
within a physical size below kiloparsecs. A smooth lens model fails to
reproduce the image flux ratios, suggesting significant additional
magnification from compact objects. Given the small image splitting and a
relatively faint deflecting galaxy, the lensing system would not have been
found through the angular separation technique generally used in large imaging
surveys
LabKey Server: An open source platform for scientific data integration, analysis and collaboration
<p>Abstract</p> <p>Background</p> <p>Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely.</p> <p>Results</p> <p>To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment.</p> <p>Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers.</p> <p>Conclusions</p> <p>Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at <url>http://www.labkey.org</url>. Documentation and source code are available under the Apache License 2.0.</p
Smaller total and subregional cerebellar volumes in posttraumatic stress disorder:a mega-analysis by the ENIGMA-PGC PTSD workgroup
Although the cerebellum contributes to higher-order cognitive and emotional functions relevant to posttraumatic stress disorder (PTSD), prior research on cerebellar volume in PTSD is scant, particularly when considering subregions that differentially map on to motor, cognitive, and affective functions. In a sample of 4215 adults (PTSD n = 1642; Control n = 2573) across 40 sites from the ENIGMA-PGC PTSD working group, we employed a new state-of-the-art deep-learning based approach for automatic cerebellar parcellation to obtain volumetric estimates for the total cerebellum and 28 subregions. Linear mixed effects models controlling for age, gender, intracranial volume, and site were used to compare cerebellum volumes in PTSD compared to healthy controls (88% trauma-exposed). PTSD was associated with significant grey and white matter reductions of the cerebellum. Compared to controls, people with PTSD demonstrated smaller total cerebellum volume, as well as reduced volume in subregions primarily within the posterior lobe (lobule VIIB, crus II), vermis (VI, VIII), flocculonodular lobe (lobule X), and corpus medullare (all p -FDR < 0.05). Effects of PTSD on volume were consistent, and generally more robust, when examining symptom severity rather than diagnostic status. These findings implicate regionally specific cerebellar volumetric differences in the pathophysiology of PTSD. The cerebellum appears to play an important role in higher-order cognitive and emotional processes, far beyond its historical association with vestibulomotor function. Further examination of the cerebellum in trauma-related psychopathology will help to clarify how cerebellar structure and function may disrupt cognitive and affective processes at the center of translational models for PTSD.</p
Smaller total and subregional cerebellar volumes in posttraumatic stress disorder:a mega-analysis by the ENIGMA-PGC PTSD workgroup
Although the cerebellum contributes to higher-order cognitive and emotional functions relevant to posttraumatic stress disorder (PTSD), prior research on cerebellar volume in PTSD is scant, particularly when considering subregions that differentially map on to motor, cognitive, and affective functions. In a sample of 4215 adults (PTSD n = 1642; Control n = 2573) across 40 sites from the ENIGMA-PGC PTSD working group, we employed a new state-of-the-art deep-learning based approach for automatic cerebellar parcellation to obtain volumetric estimates for the total cerebellum and 28 subregions. Linear mixed effects models controlling for age, gender, intracranial volume, and site were used to compare cerebellum volumes in PTSD compared to healthy controls (88% trauma-exposed). PTSD was associated with significant grey and white matter reductions of the cerebellum. Compared to controls, people with PTSD demonstrated smaller total cerebellum volume, as well as reduced volume in subregions primarily within the posterior lobe (lobule VIIB, crus II), vermis (VI, VIII), flocculonodular lobe (lobule X), and corpus medullare (all p -FDR < 0.05). Effects of PTSD on volume were consistent, and generally more robust, when examining symptom severity rather than diagnostic status. These findings implicate regionally specific cerebellar volumetric differences in the pathophysiology of PTSD. The cerebellum appears to play an important role in higher-order cognitive and emotional processes, far beyond its historical association with vestibulomotor function. Further examination of the cerebellum in trauma-related psychopathology will help to clarify how cerebellar structure and function may disrupt cognitive and affective processes at the center of translational models for PTSD.</p
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