Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.

A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.

Conserved chamber-specific polyploidy maintains heart function in Drosophila.

Developmentally programmed polyploidy (whole-genome duplication) of cardiomyocytes is common across evolution. Functions of such polyploidy are essentially unknown. Here, in both Drosophila larvae and human organ donors, we reveal distinct polyploidy levels in cardiac organ chambers. In Drosophila, differential growth and cell cycle signal sensitivity leads the heart chamber to reach a higher ploidy/cell size relative to the aorta chamber. Cardiac ploidy-reduced animals exhibit reduced heart chamber size, stroke volume and cardiac output, and acceleration of circulating hemocytes. These Drosophila phenotypes mimic human cardiomyopathies. Our results identify productive and likely conserved roles for polyploidy in cardiac chambers and suggest that precise ploidy levels sculpt many developing tissues. These findings of productive cardiomyocyte polyploidy impact efforts to block developmental polyploidy to improve heart injury recovery.

Shot-noise limited optical hybrid based on fused fiber couplers.

We describe a fiber-based coherent receiver topology which utilizes intrinsic phase shifts from fiber couplers to enable instantaneous quadrature projection with shot-noise limited signal-to-noise ratio (SNR). Fused 3 × 3 fiber couplers generate three phase-shifted signals simultaneously that can be combined with quadrature projection methods to detect magnitude and phase unambiguously. We present a novel, to the best of our knowledge, differential detection topology which utilizes a combination of 3 × 3 and 2 × 2 couplers to enable quadrature projection with fully differential detection. We present a mathematical analysis of this 3 × 3 differential detection topology, extended methods for signal calibration, and SNR analysis. We characterize the SNR advantage of this approach and demonstrate a sample application illustrating simultaneous magnitude and phase imaging of a chrome-on-glass test chart.

IFI16 Partners with KAP1 to Maintain Epstein-Barr Virus Latency.

Herpesviruses establish latency to ensure permanent residence in their hosts. Upon entry into a cell, these viruses are rapidly silenced by the host, thereby limiting the destructive viral lytic phase while allowing the virus to hide from the immune system. Notably, although the establishment of latency by the oncogenic herpesvirus Epstein-Barr virus (EBV) requires the expression of viral latency genes, latency can be maintained with a negligible expression of viral genes. Indeed, in several herpesviruses, the host DNA sensor IFI16 facilitated latency via H3K9me3 heterochromatinization. This silencing mark is typically imposed by the constitutive heterochromatin machinery (HCM). The HCM, in an antiviral role, also silences the lytic phase of EBV and other herpes viruses. We investigated if IFI16 restricted EBV lytic activation by partnering with the HCM and found that IFI16 interacted with core components of the HCM, including the KRAB-associated protein 1 (KAP1) and the site-specific DNA binding KRAB-ZFP SZF1. This partnership silenced the EBV lytic switch protein ZEBRA, encoded by the BZLF1 gene, thereby favoring viral latency. Indeed, IFI16 contributed to H3K9 trimethylation at lytic genes of all kinetic classes. In defining topology, we found that IFI16 coenriched with KAP1 at the BZLF1 promoter, and while IFI16 and SZF1 were each adjacent to KAP1 in latent cells, IFI16 and SZF1 were not. Importantly, we also found that disruption of latency involved rapid downregulation of IFI16 transcription. These findings revealed a previously unknown partnership between IFI16 and the core HCM that supports EBV latency via antiviral heterochromatic silencing. IMPORTANCE The interferon-gamma inducible protein 16 (IFI16) is a nuclear DNA sensor that mediates antiviral responses by activating the inflammasome, triggering an interferon response, and silencing lytic genes of herpesviruses. The last, which helps maintain latency of the oncoherpesvirus Epstein-Barr virus (EBV), is accomplished via H3K9me3 heterochromatinization through unknown mechanisms. Here, we report that IFI16 physically partners with the core constitutive heterochromatin machinery to silence the key EBV lytic switch protein, thereby ensuring continued viral latency in B lymphocytes. We also find that disruption of latency involves rapid transcriptional downregulation of IFI16. These findings point to hitherto unknown physical and functional partnerships between a well-known antiviral mechanism and the core components of the constitutive heterochromatin machinery.

Multi-modal imaging using a cascaded microscope design.

We present a multi-modal fiber array snapshot technique (M-FAST) based on an array of 96 compact cameras placed behind a primary objective lens and a fiber bundle array. Our technique is capable of large-area, high-resolution, multi-channel video acquisition. The proposed design provides two key improvements to prior cascaded imaging system approaches: a novel optical arrangement that accommodates the use of planar camera arrays, and a new ability to acquire multi-modal image data acquisition. M-FAST is a multi-modal, scalable imaging system that can acquire snapshot dual-channel fluorescence images as well as differential phase contrast measurements over a large 6.59 mm × 9.74 mm field-of-view at 2.2-µm center full-pitch resolution.

Increasing a microscope's effective field of view via overlapped imaging and machine learning.

This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth product (SBP) of conventional microscopes. Here, we show both in simulation and experiment that overlapped imaging and co-designed analysis software can achieve accurate detection of diagnostically-relevant features for several applications, including counting of white blood cells and the malaria parasite, leading to multi-fold increase in detection and processing throughput with minimal reduction in accuracy.

Stellar Shocks from Dark Matter Asteroid Impacts.

Macroscopic dark matter is almost unconstrained over a wide "asteroidlike" mass range, where it could scatter on baryonic matter with geometric cross section. We show that when such an object travels through a star, it produces shock waves that reach the stellar surface, leading to a distinctive transient optical, UV, and x-ray emission. This signature can be searched for on a variety of stellar types and locations. In a dense globular cluster, such events occur far more often than flare backgrounds, and an existing UV telescope could probe orders of magnitude in dark matter mass in one week of dedicated observation.

Distal Medium Vessel Occlusions Can Be Accurately and Rapidly Detected Using Tmax Maps.

Background and Purpose: Distal medium vessel occlusions (DMVOs) are increasingly considered for endovascular thrombectomy but are difficult to detect on computed tomography angiography (CTA). We aimed to determine whether time-to-maximum of tissue residue function (Tmax) maps, derived from CT perfusion, can be used as a triage screening tool to accurately and rapidly identify patients with DMVOs. Methods: Consecutive code stroke patients who underwent multimodal CT were screened retrospectively. Two experienced readers evaluated all patients' Tmax maps in consensus for presence of delay in an arterial territory (territorial Tmax delay). The diagnostic accuracy of this surrogate for identifying DMVOs was determined using receiver-operating characteristic analysis. CTA, interpreted by 2 experienced neuroradiologists with access to all imaging data, served as the reference standard. Diagnostic performance of 4 other readers with different levels of experience for identifying DMVOs on Tmax versus CTA was also assessed. These readers independently assessed patients' Tmax maps and CTAs in 2 separate timed sessions, and areas under the receiver-operating characteristic curves were compared using the DeLong algorithm. The Wilcoxon signed-rank test was used to comparatively assess diagnostic speed. Results: Three hundred seventy-three code stroke patients (median age, 70 years; 56% male, 70 with a DMVO) were included. Territorial Tmax delay had a sensitivity of 100% (CI95, 94.9%­100%) and specificity of 87.8% (CI95, 83.6%­91.3%) for presence of a DMVO, yielding an area under the receiver-operating characteristic curves of 0.939 (CI95, 0.920­0.957). All 4 readers achieved sensitivity >95% and specificity >84% for detecting DMVOs using Tmax maps, with diagnostic accuracy (area under the receiver-operating characteristic curves) and speed that were significantly (P<0.001) higher than on CTA. Conclusions: Territorial Tmax delay had perfect sensitivity and high specificity for a DMVO. Tmax maps were accurately and rapidly interpreted by even inexperienced readers, and causes of false positives are easy to recognize and dismiss. These findings encourage the use of Tmax to identify patients with DMVOs.

Diffraction tomography with a deep image prior.

We present a tomographic imaging technique, termed Deep Prior Diffraction Tomography (DP-DT), to reconstruct the 3D refractive index (RI) of thick biological samples at high resolution from a sequence of low-resolution images collected under angularly varying illumination. DP-DT processes the multi-angle data using a phase retrieval algorithm that is extended by a deep image prior (DIP), which reparameterizes the 3D sample reconstruction with an untrained, deep generative 3D convolutional neural network (CNN). We show that DP-DT effectively addresses the missing cone problem, which otherwise degrades the resolution and quality of standard 3D reconstruction algorithms. As DP-DT does not require pre-captured data or pre-training, it is not biased towards any particular dataset. Hence, it is a general technique that can be applied to a wide variety of 3D samples, including scenarios in which large datasets for supervised training would be infeasible or expensive. We applied DP-DT to obtain 3D RI maps of bead phantoms and complex biological specimens, both in simulation and experiment, and show that DP-DT produces higher-quality results than standard regularization techniques. We further demonstrate the generality of DP-DT, using two different scattering models, the first Born and multi-slice models. Our results point to the potential benefits of DP-DT for other 3D imaging modalities, including X-ray computed tomography, magnetic resonance imaging, and electron microscopy.

Fourier ptychography: current applications and future promises.

Traditional imaging systems exhibit a well-known trade-off between the resolution and the field of view of their captured images. Typical cameras and microscopes can either "zoom in" and image at high-resolution, or they can "zoom out" to see a larger area at lower resolution, but can rarely achieve both effects simultaneously. In this review, we present details about a relatively new procedure termed Fourier ptychography (FP), which addresses the above trade-off to produce gigapixel-scale images without requiring any moving parts. To accomplish this, FP captures multiple low-resolution, large field-of-view images and computationally combines them in the Fourier domain into a high-resolution, large field-of-view result. Here, we present details about the various implementations of FP and highlight its demonstrated advantages to date, such as aberration recovery, phase imaging, and 3D tomographic reconstruction, to name a few. After providing some basics about FP, we list important details for successful experimental implementation, discuss its relationship with other computational imaging techniques, and point to the latest advances in the field while highlighting persisting challenges.

Spectroscopic optical coherence refraction tomography.

In optical coherence tomography (OCT), the axial resolution is often superior to the lateral resolution, which is sacrificed for long imaging depths. To address this anisotropy, we previously developed optical coherence refraction tomography (OCRT), which uses images from multiple angles to computationally reconstruct an image with isotropic resolution, given by the OCT axial resolution. On the other hand, spectroscopic OCT (SOCT), an extension of OCT, trades axial resolution for spectral resolution and hence often has superior lateral resolution. Here, we present spectroscopic OCRT (SOCRT), which uses SOCT images from multiple angles to reconstruct a spectroscopic image with isotropic spatial resolution limited by the OCT lateral resolution. We experimentally show that SOCRT can estimate bead size based on Mie theory at simultaneously high spectral and isotropic spatial resolution. We also applied SOCRT to a biological sample, achieving axial resolution enhancement limited by the lateral resolution.

Sex differences in aneurysmal subarachnoid haemorrhage (aSAH): aneurysm characteristics, neurological complications, and outcome.

BACKGROUND: Women are over-represented in aSAH cohorts, but whether their outcomes differ to men remains unclear. We examined if sex differences in neurological complications and aneurysm characteristics contributed to aSAH outcomes. METHODS: In a retrospective cohort (2010-2016) of all aSAH cases across two hospital networks in Australia, information on severity, aneurysm characteristics and neurological complications (rebleed before/after treatment, postoperative stroke < 48 h, neurological infections, hydrocephalus, seizures, delayed cerebral ischemia [DCI], cerebral infarction) were extracted. We estimated sex differences in (1) complications and aneurysm characteristics using chi square/t-tests and (2) outcome at discharge (home, rehabilitation or death) using multinomial regression with and without propensity score matching on prestroke confounders. RESULTS: Among 577 cases (69% women, 84% treated) aneurysm size was greater in men than women and DCI more common in women than men. In unadjusted log multinomial regression, women had marginally greater discharge to rehabilitation (RRR 1.15 95% CI 0.90-1.48) and similar likelihood of in-hospital death (RRR 1.02 95% CI 0.76-1.36) versus discharge home. Prestroke confounders (age, hypertension, smoking status) explained greater risk of death in women (rehabilitation RRR 1.13 95% CI 0.87-1.48; death RRR 0.75 95% CI 0.51-1.10). Neurological complications (DCI and hydrocephalus) were covariates explaining some of the greater risk for poor outcomes in women (rehabilitation RRR 0.87 95% CI 0.69-1.11; death RRR 0.80 95% CI 0.52-1.23). Results were consistent in propensity score matched models. CONCLUSION: The marginally poorer outcome in women at discharge was partially attributable to prestroke confounders and complications. Improvements in managing complications could improve outcomes.

Optical Coherence Tomography-Guided Robotic Ophthalmic Microsurgery via Reinforcement Learning from Demonstration.

Ophthalmic microsurgery is technically difficult because the scale of required surgical tool manipulations challenge the limits of the surgeon's visual acuity, sensory perception, and physical dexterity. Intraoperative optical coherence tomography (OCT) imaging with micrometer-scale resolution is increasingly being used to monitor and provide enhanced real-time visualization of ophthalmic surgical maneuvers, but surgeons still face physical limitations when manipulating instruments inside the eye. Autonomously controlled robots are one avenue for overcoming these physical limitations. We demonstrate the feasibility of using learning from demonstration and reinforcement learning with an industrial robot to perform OCT-guided corneal needle insertions in an ex vivo model of deep anterior lamellar keratoplasty (DALK) surgery. Our reinforcement learning agent trained on ex vivo human corneas, then outperformed surgical fellows in reaching a target needle insertion depth in mock corneal surgery trials. This work shows the combination of learning from demonstration and reinforcement learning is a viable option for performing OCT guided robotic ophthalmic surgery.

The 100 most cited articles in the endovascular treatment of thoracic and abdominal aortic aneurysms.

OBJECTIVE: Since the introduction of endovascular technology to treat thoracic and abdominal aortic aneurysms, there has been a global research effort focused on assessing the effectiveness of treatment. A bibliometric analysis is used to identify the scientific impact of an article, impactful authors, institutions, and collaborative groups. Our objective was to identify and to analyze the 100 most cited articles in the field of endovascular treatment of thoracic and abdominal aortic aneurysms. METHODS: We performed a retrospective bibliometric analysis in April 2018. Articles were searched on the Science Citation Index Expanded database using Web of Science to identify the most cited articles in endovascular therapy for thoracic and aortic aneurysms since 1945. Use of selected key terms ("AAA," "aortic aneurysm," "thoracic aneurysm," "abdominal aneurysm," "endovascular," "endoluminal," "stent," "graft," "repair," "EVAR," and "TEVAR") yielded a total of 23,354 articles. The top 100 articles were identified and analyzed to extract relevant information including year of publication, citation count, journal, authorship country of origin, and article type. RESULTS: The earliest articles were published in 1991, with the majority being published in the 2000s (n = 59). The number of citations for the top 100 articles ranged from 151 to 1142, with a median citation count of 212. All articles were cited an average of 22.4 times per year. Almost half (n = 46) of the top 100 articles were published in the Journal of Vascular Surgery. Thirty-nine authors contributed four or more articles, with two being credited on 10 papers to make the list. The majority (n = 62) of the articles arose from the United States, while the United Kingdom contributed 11 articles. There were 7 guidelines and 12 randomized controlled trials, and the majority constituted level III or level IV evidence. CONCLUSIONS: This study provides a comprehensive and informative analysis of the most cited and impactful research undertaken in the field of endovascular treatment of abdominal and thoracic aortic aneurysms. By quantitatively assessing the 100 most cited articles in the field, we recognize the contributions of key authors, institutions, and collaborative groups and develop an understanding of the strengths of past research and the requirements for future global efforts.

Quantifying uncertainty in the phylogenetics of Australian numeral systems.

Researchers have long been interested in the evolution of culture and the ways in which change in cultural systems can be reconstructed and tracked. Within the realm of language, these questions are increasingly investigated with Bayesian phylogenetic methods. However, such work in cultural phylogenetics could be improved by more explicit quantification of reconstruction and transition probabilities. We apply such methods to numerals in the languages of Australia. As a large phylogeny with almost universal 'low-limit' systems, Australian languages are ideal for investigating numeral change over time. We reconstruct the most likely extent of the system at the root and use that information to explore the ways numerals evolve. We show that these systems do not increment serially, but most commonly vary their upper limits between 3 and 5. While there is evidence for rapid system elaboration beyond the lower limits, languages lose numerals as well as gain them. We investigate the ways larger numerals build on smaller bases, and show that there is a general tendency to both gain and replace 4 by combining 2 + 2 (rather than inventing a new unanalysable word 'four'). We develop a series of methods for quantifying and visualizing the results.

Influence of TNF-α and biomechanical stress on matrix metalloproteinases and lysyl oxidases expressions in human knee synovial fibroblasts.

PURPOSE: It was reported that not only ACL but also the synovium may be the major regulator of matrix metalloproteinases (MMPs) in synovial fluids after ACL injury. In order to further confirm whether synovium is capable of regulating the microenvironment in the process of ACL injury, the complicated microenvironment of joint cavity after ACL injury was mimicked and the combined effects of mechanical injury and inflammatory factor [tumour necrosis factor-α (TNF-α)] on expressions of lysyl oxidases (LOXs) and MMPs in synovial fibroblasts derived from normal human synovium were studied. METHODS: Human normal knee joint synovial fibroblasts were stimulated for 1-6 h with mechanical stretch and inflammatory factor (TNF-α). Total RNA was harvested, reverse transcribed and assessed by real-time polymerase chain reaction for the expression of LOXs and MMP-1, 2, 3 messenger RNAs. MMP-2 activity was assayed from the collected culture media samples using zymography. RESULTS: Compared to control group, our results showed that 6% physiological stretch increased MMP-2 and LOXs (except LOXL-3), decreased MMP-1 and MMP-3; injurious stretch (12%) decreased LOXs (except LOXL-2)and increased MMP-1, 2 and 3; the combination of injurious stretch and TNF-α decreased LOXs and increased MMP-1, 2 and 3 in synovial fibroblasts in a synergistical manner. CONCLUSION: This study demonstrated that combination of mechanical injury and inflammatory factors up-regulated the expressions of MMPs and down-regulated the expressions of LOXs in synovial fibroblasts, eventually alter the balance of tissue healing. Thus, synovium may be involved in regulating the microenvironment of joint cavity. Based on the mechanism, early interventions to inhibit the production of MMPs or promote the production of LOXs in the synovial fibroblasts should be performed to facilitate the healing of tissue.

Persistent bleeding following biopsy of an epidermoid cyst within the parotid gland.

Epidermoid cysts are benign lesions most commonly found in the skin but which can arise in many other locations including, very rarely the salivary glands. This rarity often leaves them off standard differential lists and can create a diagnostic dilemma. A patient with an incidentally detected parotid mass on MRI underwent core biopsy, which was unfortunately complicated by formation of a pseudoaneurysm and persistent arterial bleeding requiring coil embolisation. The histology showed only keratinous material and, in retrospect, the signal characteristics of the mass were entirely typical of an epidermoid cyst. Recognition of this common, benign entity in a very rare location can obviate the need for invasive tests and potential complications and direct management to more appropriate imaging follow-up.

Primary small intestine angiosarcoma mimicking Crohn's disease.

A man in his 40s presented to an emergency department after experiencing worsening abdominal pain for 2 days. Contrast-enhanced CT of the abdomen and pelvis revealed circumferential mural thickening and luminal narrowing of the distal ileum and upstream dilatation of the small intestine, indicating small intestine obstruction. This prompted emergency laparotomy, where two lesions in the distal ileum were identified as the source of his bowel obstruction and resected. Immunohistochemistry of the resected segment revealed a primary small intestine angiosarcoma acting positively for vascular markers ERG and CD31. A subsequent positron emission tomography (PET) scan revealed positive mediastinal metastatic lymphadenopathy without organ metastases.Following his surgery, the patient recovered well and was promptly referred to an oncology unit at a specialised health centre for further treatment. Primary small intestine angiosarcoma is a rare entity in which patients present with non-specific symptoms requiring prompt tissue diagnosis to facilitate multidisciplinary management.

A novel sorting method for the enrichment of early human spermatocytes from clinical biopsies.

OBJECTIVE: To determine if early spermatocytes can be enriched from a human testis biopsy using fluorescence-activated cell sorting (FACS). DESIGN: Potential surface markers for early spermatocytes were identified using bioinformatics analysis of single-cell RNA-sequenced human testis tissue. Testicular sperm extraction samples from three participants with normal spermatogenesis were digested into single-cell suspensions and cryopreserved. Two to four million cells were obtained from each and sorted by FACS as separate biologic replicates using antibodies for the identified surface markers. A portion from each biopsy remained unsorted to serve as controls. The sorted cells were then characterized for enrichment of early spermatocytes. SETTING: A laboratory study. PATIENTS: Three men with a diagnosis of obstructive azoospermia (age range, 30-40 years). INTERVENTION: None. MAIN OUTCOME MEASURES: Sorted cells were characterized for RNA expression of markers encompassing the stages of spermatogenesis. Sorting markers were validated by their reactivity on human testis formalin-fixed paraffin-embedded tissue. RESULTS: Serine protease 50 (TSP50) and SWI5-dependent homologous recombination repair protein 1 were identified as potential surface proteins specific for early spermatocytes. After FACS sorting, the TSP50-sorted populations accounted for 1.6%-8.9% of total populations and exhibited the greatest average-fold increases in RNA expression for the premeiotic marker stimulated by retinoic acid (STRA8), by 23-fold. Immunohistochemistry showed the staining pattern for TSP50 to be strong in premeiotic undifferentiated embryonic cell transcription factor 1-/doublesex and Mab-3 related transcription factor 1-/STRA8+ spermatogonia as well as SYCP3+/protamine 2- spermatocytes. CONCLUSION: This work shows that TSP50 can be used to enrich early STRA8-expressing spermatocytes from human testicular biopsies, providing a means for targeted single-cell RNA sequencing analysis and in vitro functional interrogation of germ cells during the onset of meiosis. This could enable investigation into details of the regulatory pathways underlying this critical stage of spermatogenesis, previously difficult to enrich from whole tissue samples.