Separating Reflection and Transmission Images in the Wild

The reflections caused by common semi-reflectors, such as glass windows, can impact the performance of computer vision algorithms. State-of-the-art methods can remove reflections on synthetic data and in controlled scenarios. However, they are based on strong assumptions and do not generalize well to real-world images. Contrary to a common misconception, real-world images are challenging even when polarization information is used. We present a deep learning approach to separate the reflected and the transmitted components of the recorded irradiance, which explicitly uses the polarization properties of light. To train it, we introduce an accurate synthetic data generation pipeline, which simulates realistic reflections, including those generated by curved and non-ideal surfaces, non-static scenes, and high-dynamic-range scenes.Comment: accepted at ECCV 201

Estimating Depth from RGB and Sparse Sensing

We present a deep model that can accurately produce dense depth maps given an RGB image with known depth at a very sparse set of pixels. The model works simultaneously for both indoor/outdoor scenes and produces state-of-the-art dense depth maps at nearly real-time speeds on both the NYUv2 and KITTI datasets. We surpass the state-of-the-art for monocular depth estimation even with depth values for only 1 out of every ~10000 image pixels, and we outperform other sparse-to-dense depth methods at all sparsity levels. With depth values for 1/256 of the image pixels, we achieve a mean absolute error of less than 1% of actual depth on indoor scenes, comparable to the performance of consumer-grade depth sensor hardware. Our experiments demonstrate that it would indeed be possible to efficiently transform sparse depth measurements obtained using e.g. lower-power depth sensors or SLAM systems into high-quality dense depth maps.Comment: European Conference on Computer Vision (ECCV) 2018. Updated to camera-ready version with additional experiment

Retroviruses integrate into a shared, non-palindromic DNA motif.

Many DNA-binding factors, such as transcription factors, form oligomeric complexes with structural symmetry that bind to palindromic DNA sequences1. Palindromic consensus nucleotide sequences are also found at the genomic integration sites of retroviruses2-6 and other transposable elements7-9, and it has been suggested that this palindromic consensus arises as a consequence of the structural symmetry in the integrase complex2,3. However, we show here that the palindromic consensus sequence is not present in individual integration sites of human T-cell lymphotropic virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1), but arises in the population average as a consequence of the existence of a non-palindromic nucleotide motif that occurs in approximately equal proportions on the plus strand and the minus strand of the host genome. We develop a generally applicable algorithm to sort the individual integration site sequences into plus-strand and minus-strand subpopulations, and use this to identify the integration site nucleotide motifs of five retroviruses of different genera: HTLV-1, HIV-1, murine leukaemia virus (MLV), avian sarcoma leucosis virus (ASLV) and prototype foamy virus (PFV). The results reveal a non-palindromic motif that is shared between these retroviruses

Do health policy advisors know what the public wants? An empirical comparison of how health policy advisors assess public preferences regarding smoke-free air, and what the public actually prefers

Background: Health policy-making, a complex, multi-factorial process, requires balancing conflicting values. A salient issue is public support for policies; however, one reason for limited impact of public opinion may be misperceptions of policy makers regarding public opinion. For example, empirical research is scarce on perceptions of policy makers regarding public opinion on smoke-free public spaces. Methods: Public desire for smoke-free air was compared with health policy advisor (HPA) perception of these desires. Two representative studies were conducted: one with the public (N = 505), and the other with a representative sample of members of Israel’s health-targeting initiative, Healthy Israel 2020 (N = 34), in December 2010. Corresponding questions regarding desire for smoke-free areas were asked. Possible smoke-free areas included: 100% smoke-free bars and pubs; entrances to health facilities; railway platforms; cars with children; college campuses; outdoor areas (e.g., pools and beaches); and common areas of multi-dweller apartment buildings. A 1–7 Likert scale was used for each measure, and responses were averaged into a single primary outcome, DESIRE. Our primary endpoint was the comparison between public preferences and HPA assessment of those preferences. In a secondary analysis, we compared personal preferences of the public with personal preferences of the HPAs for smoke-free air. Results: HPAs underestimated public desire for smoke-free air (Public: Mean: 5.06, 95% CI:[4.94, 5.17]; HPA: Mean: 4.06, 95% CI:[3.61, 4.52]: p < .0001). Differences at the p = .05 level were found between HPA assessment and public preference for the following areas: 100% smoke-free bars and pubs; entrances to healthcare facilities; train platforms; cars carrying children; and common areas of multi-dweller apartment buildings. In our secondary comparison, HPAs more strongly preferred smoke-free areas than did the public (p < .0001). Conclusions: Health policy advisors underestimate public desire for smoke-free air. Better grasp of public opinion by policy makers may lead to stronger legislation. Monitoring policy-maker assessment of public opinion may shed light on incongruities between policy making and public opinion. Further, awareness of policy-maker misperceptions may encourage policy-makers to demand more accurate information before making policy

Infant motor development predicts the dynamics of movement during sleep

The characteristics of infant sleep change over the first year. Generally, infants wake and move less at night as they grow older. However, acquisition of new motor skills leads to temporary increases in night waking and movement at night. Indeed, sleep-dependent movement at night is important for sensorimotor development. Nevertheless, little is known about how movement during sleep changes as infants accrue locomotor experience. The current study investigated whether infant sleep and movement during sleep were predicted by infants\u27 walking experience. Seventy-eight infants wore an actigraph to measure physical activity during sleep. Parents reported when their infants first walked across a room \u3e10 feet without stopping or falling. Infants in the midst of walking skill acquisition had worse sleep than an age-group estimate. Infants with more walk experience had more temporally sporadic movement during sleep and a steeper hourly increase in physical activity over the course of the night. Ongoing motor skill consolidation changes the characteristics of movement during sleep and may alter sleep state-dependent memory consolidation. We propose a model whereby changes in gross motor activity during night sleep reflect movement-dependent consolidation

Genetically engineered minipigs model the major clinical features of human neurofibromatosis type 1.

Neurofibromatosis Type 1 (NF1) is a genetic disease caused by mutations in Neurofibromin 1 (NF1). NF1 patients present with a variety of clinical manifestations and are predisposed to cancer development. Many NF1 animal models have been developed, yet none display the spectrum of disease seen in patients and the translational impact of these models has been limited. We describe a minipig model that exhibits clinical hallmarks of NF1, including café au lait macules, neurofibromas, and optic pathway glioma. Spontaneous loss of heterozygosity is observed in this model, a phenomenon also described in NF1 patients. Oral administration of a mitogen-activated protein kinase/extracellular signal-regulated kinase inhibitor suppresses Ras signaling. To our knowledge, this model provides an unprecedented opportunity to study the complex biology and natural history of NF1 and could prove indispensable for development of imaging methods, biomarkers, and evaluation of safety and efficacy of NF1-targeted therapies

Genetic markers of Restless Legs Syndrome in Parkinson disease

INTRODUCTION: Several studies proposed that Restless Legs Syndrome (RLS) and Parkinson disease (PD) may be clinically and/or etiologically related. To examine this hypothesis, we aimed to determine whether the known RLS genetic markers may be associated with PD risk, as well as with PD subtype. METHODS: Two case-control cohorts from Tel-Aviv and New-York, including 1133 PD patients and 867 controls were genotyped for four RLS-related SNPs in the genes MEIS1, BTBD9, PTPRD and MAP2K5/SKOR1. The association between genotype, PD risk and phenotype was tested using multivariate regression models. RESULTS: None of the tested SNPs was significantly associated with PD risk, neither in any individual cohort nor in the combined analysis after correction for multiple comparisons. The MAP2K5/SKOR1 marker rs12593813 was associated with higher frequency of tremor in the Tel-Aviv cohort (61.0% vs. 46.5%, p = 0.001, dominant model). However, the risk allele for tremor in this gene has been associated with reduced RLS risk. Moreover, this association did not replicate in Tremor-dominant PD patients from New-York. CONCLUSION: RLS genetic risk markers are not associated with increased PD risk or subtype in the current study. Together with previous genetic, neuropathological and epidemiologic studies, our results further strengthen the notion that RLS and PD are likely to be distinct entities

GBA mutations are associated with Rapid eye movement sleep behavior disorder

Rapid eye movement sleep behavior disorder and GBA mutations are both associated with Parkinson’s disease. The GBA gene was sequenced in idiopathic rapid eye movement sleep behavior disorder patients (n = 265), and compared to controls (n = 2240). Rapid eye movement sleep behavior disorder questionnaire was performed in an independent Parkinson’s disease cohort (n = 120). GBA mutations carriers had an OR of 6.24 (10.2% in patients vs. 1.8% in controls, P < 0.0001) for rapid eye movement sleep behavior disorder, and among Parkinson’s disease patients, the OR for mutation carriers to have probable rapid eye movement sleep behavior disorder was 3.13 (P = 0.039). These results demonstrate that rapid eye movement sleep behavior disorder is associated with GBA mutations, and that combining genetic and prodromal data may assist in identifying individuals susceptible to Parkinson’s disease

Intrinsic Disorder in BAP1 and Its Association with Uveal Melanoma.

BACKGROUND: Specific subvariants of uveal melanoma (UM) are associated with increased rates of metastasis compared to other subvariants. BRCA1 (BReast CAncer gene 1)-associated protein-1 (BAP1) is encoded by a gene that has been linked to aggressive behavior in UM. METHODS: We evaluated BAP1 for the presence of intrinsically disordered protein regions (IDPRs) and its protein-protein interactions (PPI). We evaluated specific sequence-based features of the BAP1 protein using a set of bioinformatic databases, predictors, and algorithms. RESULTS: We show that BAP1\u27s structure contains extensive IDPRs as it is highly enriched in proline residues (the most disordered amino acid; p-value \u3c 0.05), the average percent of predicted disordered residues (PPDR) was 57.34%, and contains 9 disorder-based binding sites (ie. molecular recognition features (MoRFs)). BAP1\u27s intrinsic disorder allows it to engage in a complex PPI network with at least 49 partners (p-value \u3c 1.0 × 10-16). CONCLUSION: These findings show that BAP1 contains IDPRs and an intricate PPI network. Mutations in UM that are associated with the BAP1 gene may alter the function of the IDPRs embedded into its structure. These findings develop the understanding of UM and may provide a target for potential novel therapies to treat this aggressive neoplasm

Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set and motif we optimized the sequence similarity score threshold, independently for every location window (measured with respect to the TSS), taking into account the location dependent nucleotide heterogeneity along the promoters of the target genes. We performed a high throughput analysis, searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology classes and for 412 known DNA motifs. When combined with binding site and location conservation between human and mouse, the method identifies with high probability functional binding sites that regulate groups of biologically related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were put to several experimental tests. By allowing a "flexible" threshold and combining our functional class and location specific search method with conservation between human and mouse, we are able to identify reliably functional TF binding sites. This is an essential step towards constructing regulatory networks and elucidating the design principles that govern transcriptional regulation of expression. The promoter region proximal to the TSS appears to be of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure