XCP-D: A Robust Pipeline for the post-processing of fMRI data.

Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.

Diffuse skeletal muscle extramedullary plasmacytomas: a rare case and review of the literature.

Extramedullary plasmacytomas are rare neoplasms arising from proliferations of monoclonal plasma cells. In primary form, these malignancies occur without other sites of plasma cell disease. Secondary extramedullary plasmacytomas occur in association with multiple myeloma and may be discovered during initial intramedullary disease or may occur during multiple myeloma relapse. In very rare instances, secondary extramedullary plasmacytomas have multifocal skeletal muscle involvement. We present a case of multifocal skeletal muscle plasmacytomas in a 58-year-old man with shoulder-reduced range of motion, pain, and a history of previously treated multiple myeloma. To our knowledge, the patient's unique relapse presentation of torso and shoulder soft tissue masses and the vast extent of skeletal muscle involvement are unique to cases in the current literature. This case also has MRI findings of a muscular plasmacytoma with internal hemorrhage which has not been previously reported. This case report will review imaging features and clinical presentations of intramuscular extramedullary plasmacytomas. Since imaging surveillance for multiple myeloma relapse is commonly performed, radiologists should be aware of these uncommon relapsing features including multifocal intramuscular masses which may contain internal hemorrhage.

Ultrasound Fatty Liver Indicator: A Simple Tool for Differentiating Steatosis From Nonalcoholic Steatohepatitis: Validity in the Average Obese Population.

OBJECTIVES: Steatosis, nonalcoholic steatohepatitis (NASH), and fibrosis/cirrhosis represent a spectrum of fatty liver disease. The ultrasound fatty liver indicator (US-FLI) evaluates ultrasound (US) features to identify stages of fatty liver disease. We hypothesized that US features could be independent predictors of NASH and that the US-FLI differentiates steatosis from NASH in the average obese population. METHODS: A retrospective analysis of 208 patients with normal (n = 14), steatotic (n = 89), and NASH (n = 105) livers was performed. Liver/biliary disease and a history of alcohol intake were excluded. Ultrasound metrics included liver-kidney contrast, posterior attenuation, vessel blurring, difficulty visualizing the gallbladder wall, difficulty visualizing the diaphragm, and areas of focal fatty sparing. A statistical comparison of the 3 groups as well as fibrosis stage I and II/III NASH groups was performed. Logistic regression identified independent predictors of NASH. RESULTS: Gallbladder wall visualization and vessel blurring were different between the steatosis and NASH groups (P ≤ .01). Gallbladder wall visualization was specific for NASH (89%), and vessel blurring was sensitive for NASH (93%). A US-FLI score of 4 or lower suggested the absence of NASH (negative predictive value, 88%; sensitivity, 91%). Logistic regression revealed vessel blurring as the only US predictor of NASH (P ≤ .01). However, the area under the curve (0.649) showed poor performance in differentiating steatosis from NASH when the US-FLI score was 5 or higher. CONCLUSIONS: Our data suggest that the US-FLI may differentiate steatosis from NASH in the average obese population. Vessel blurring and poor gallbladder wall visualization were the most important metrics. Identification of NASH was enhanced by including the US-FLI score with vessel blurring.

Incidental Renal Lesions on Lumbar Spine MRI: Who Needs Follow-Up?

OBJECTIVE: Incidentally discovered renal lesions on lumbar spine MRI are a common occurrence. Many follow-up recommendations are generated by radiologists encountering renal lesions to help characterize the finding as a benign cyst or a more complex, potentially malignant lesion. We hypothesized that analysis of T2-weighted imaging features of incidentally discovered renal lesions could reliably distinguish complex renal lesions from simple cysts. MATERIALS AND METHODS: Two independent readers retrospectively evaluated 149 renal lesions identified on lumbar spine MRI examinations. Presence or absence of a complex renal lesion was determined using T2-weighted imaging only. Using dedicated renal cross-sectional imaging examinations as the reference standard, statistical analysis was performed to determine the accuracy of lumbar spine MRI in predicting a complex and potentially neoplastic renal lesion. RESULTS: Of 149 renal lesions, 115 were simple cysts, and 34 were complex renal lesions (20 Bosniak II cysts, nine renal cell carcinomas, three Bosniak IIF cysts, and two angiomyolipomas). Lumbar spine MRI readers identified 72 lesions as simple cysts and 77 lesions as complex renal lesions. Reader sensitivity for detection of a complex renal lesion on lumbar spine MRI was 94% (95% CI, 80-99%); specificity, 63% (95% CI, 53-72%); positive predictive value, 43% (95% CI, 37-49%); and negative predictive value, 97% (95% CI, 90-99%). Readers correctly identified all neoplastic and potentially neoplastic lesions (≥ Bosniak IIF). Interreader agreement was excellent (κ = 0.84). CONCLUSION: Follow-up imaging may not be required in all cases of incidentally discovered renal lesions on lumbar spine MRI. Analysis of T2-weighted imaging alone appears to reliably rule out neoplastic and potentially neoplastic complex renal lesions.

Ekosonic Endovascular System (EKOS) in a trauma patient with intracranial bleed, recent major surgery, and massive pulmonary embolus: A case report.

Pulmonary embolism is a life-threatening condition treated with anticoagulation and systemic thrombolysis when appropriate. In patients with contraindications to thrombolysis, catheter-directed thrombolysis may be considered. Here, we present a patient with massive pulmonary embolus and 3 contraindications to systemic thrombolysis who was successfully treated with pharmacomechanical thrombolysis using the Ekosonic Endovascular System.

Intracranial neurenteric cyst mimicking an ependymoma: imaging features, pathologic correlation and review of literature.

We present a case of a 57-year-old female with four-months of diplopia and vertigo. MRI revealed a mixed cystic and solid partially enhancing lesion of the 4th ventricle, foramen of Luschka and cerebellopontine angle. Preoperative differential diagnosis favored ependymoma. Biopsy revealed a neurenteric cyst, a benign developmental lesion that rarely occurs intracranially. This case highlights several atypical manifestations of intracranial neurenteric cyst, with regions of histologically benign solid enhancement, multicompartmental extra-axial location mimicking an ependymoma, and rapid recurrence without evidence of underlying malignancy.

Toxic and teratogenic silica nanowires in developing vertebrate embryos.

Silica-based nanomaterials show promise for biomedical applications such as cell-selective drug delivery and bioimaging. They are easily functionalized, which allows for the conjugation or encapsulation of important biomolecules. Although recent in vitro studies suggested that silica-derived nanomaterials are nontoxic, in vivo studies of silica nanomaterial toxicity have not been performed. Using the embryonic zebrafish as a model system, we show that silica nanomaterials with aspect ratios greater than 1 are highly toxic (LD(50) = 110 pg/g embryo) and cause embryo deformities, whereas silica nanomaterials with an aspect ratio of 1 are neither toxic nor teratogenic at the same concentrations. Silica nanowires also interfere with neurulation and disrupt expression of sonic hedgehog, which encodes a key midline signaling factor. Our results demonstrate the need for further testing of nanomaterials before they can be used as platforms for drug delivery. FROM THE CLINICAL EDITOR: Silica-based nanomaterials show promise for biomedical applications such as cell-selective drug delivery and bioimaging. Using an embryonic zebrafish model system silica nanomaterials with aspect ratios greater than one were found to be highly toxic; whereas silica nanomaterials with an aspect ratio of one are neither toxic nor teratogenic. These results demonstrate the need for testing "nanomaterials" before they can be used as platforms for drug delivery.

TRPM1 is required for the depolarizing light response in retinal ON-bipolar cells.

The ON pathway of the visual system, which detects increases in light intensity, is established at the first retinal synapse between photoreceptors and ON-bipolar cells. Photoreceptors hyperpolarize in response to light and reduce the rate of glutamate release, which in turn causes the depolarization of ON-bipolar cells. This ON-bipolar cell response is mediated by the metabotropic glutamate receptor, mGluR6, which controls the activity of a depolarizing current. Despite intensive research over the past two decades, the molecular identity of the channel that generates this depolarizing current has remained elusive. Here, we present evidence indicating that TRPM1 is necessary for the depolarizing light response of ON-bipolar cells, and further that TRPM1 is a component of the channel that generates this light response. Gene expression profiling revealed that TRPM1 is highly enriched in ON-bipolar cells. In situ hybridization experiments confirmed that TRPM1 mRNA is found in cells of the retinal inner nuclear layer, and immunofluorescent confocal microscopy showed that TRPM1 is localized in the dendrites of ON-bipolar cells in both mouse and macaque retina. The electroretinogram (ERG) of TRPM1-deficient (TRPM1(-/-)) mice had a normal a-wave, but no b-wave, indicating a loss of bipolar cell response. Finally, whole-cell patch-clamp recording from ON-bipolar cells in mouse retinal slices demonstrated that genetic deletion of TRPM1 abolished chemically simulated light responses from rod bipolar cells and dramatically altered the responses of cone ON-bipolar cells. Identification of TRPM1 as a mGluR6-coupled cation channel reveals a key step in vision, expands the role of the TRP channel family in sensory perception, and presents insights into the evolution of vertebrate vision.

Retinal homeobox 1 is required for retinal neurogenesis and photoreceptor differentiation in embryonic zebrafish.

Retinal homeobox (Rx/Rax) genes are essential for the organogenesis of the vertebrate eye. These genes are dynamically expressed in a tissue-specific manner during eye development, suggesting pleiotropic roles. We use a temporally-selective gene knockdown approach to identify endogenous functions for the zebrafish rx genes, rx1 and rx2. Depletion of rx1 over the period of eye organogenesis resulted in severely reduced proliferation of retinal progenitors, the loss of expression of the transcription factor pax6, delayed retinal neurogenesis, and extensive retinal cell death. In contrast, depletion of rx2 over the same developmental time resulted in reduced expression of pax6 in the eye anlage, but only modest effects on retinal cell survival. Knockdown of rx1 specifically during photoreceptor development inhibited the expression of multiple photoreceptor-specific genes, while knockdown of rx2 over this time selectively inhibited the expression of a subset of these genes. Our findings support a function for rx2 in regulating pax6 within the optic primordia, a function for rx1 in maintaining the pluripotent, retinal progenitor cell state during retinal development, as well as selective functions for rx1 and rx2 in regulating photoreceptor differentiation.

The developmental sequence of gene expression within the rod photoreceptor lineage in embryonic zebrafish.

In postembryonic zebrafish, rod photoreceptors are continuously generated from progenitors in the inner nuclear layer, which are derived from radial Müller glia that express the transcription factor pax6. We used BrdU incorporation, in combination with in situ hybridization for cell-specific transcription factors, to establish the patterns of gene expression during rod lineage maturation in the embryonic zebrafish. Downregulation of pax6 expression was accompanied by sporadic upregulation of expression of the transcription factors NeuroD/nrd, rx1, crx, and Nr2e3/pnr. As cells of the rod lineage entered the outer nuclear layer, they became homogeneous, coordinately expressing NeuroD, rx1, crx, and Nr2e3. Postmitotic, maturing rods also expressed nrl, rod opsin, and rod transducin/gnat1. The presence of rx1 within the rod lineage and in maturing rods indicates that rx1 is not cone-specific, as previously reported, and suggests a high degree of molecular similarity between rod and cone progenitor populations in the zebrafish.