Tiling array data analysis: a multiscale approach using wavelets

<p>Abstract</p> <p>Background</p> <p>Tiling array data is hard to interpret due to noise. The wavelet transformation is a widely used technique in signal processing for elucidating the true signal from noisy data. Consequently, we attempted to denoise representative tiling array datasets for ChIP-chip experiments using wavelets. In doing this, we used specific wavelet basis functions, <it>Coiflets</it>, since their triangular shape closely resembles the expected profiles of true ChIP-chip peaks.</p> <p>Results</p> <p>In our wavelet-transformed data, we observed that noise tends to be confined to small scales while the useful signal-of-interest spans multiple large scales. We were also able to show that wavelet coefficients due to non-specific cross-hybridization follow a log-normal distribution, and we used this fact in developing a thresholding procedure. In particular, wavelets allow one to set an unambiguous, absolute threshold, which has been hard to define in ChIP-chip experiments. One can set this threshold by requiring a similar confidence level at different length-scales of the transformed signal. We applied our algorithm to a number of representative ChIP-chip data sets, including those of Pol II and histone modifications, which have a diverse distribution of length-scales of biochemical activity, including some broad peaks.</p> <p>Conclusions</p> <p>Finally, we benchmarked our method in comparison to other approaches for scoring ChIP-chip data using spike-ins on the ENCODE Nimblegen tiling array. This comparison demonstrated excellent performance, with wavelets getting the best overall score.</p

What the ‘Moonwalk’ Illusion Reveals about the Perception of Relative Depth from Motion

When one visual object moves behind another, the object farther from the viewer is progressively occluded and/or disoccluded by the nearer object. For nearly half a century, this dynamic occlusion cue has beenthought to be sufficient by itself for determining the relative depth of the two objects. This view is consistent with the self-evident geometric fact that the surface undergoing dynamic occlusion is always farther from the viewer than the occluding surface. Here we use a contextual manipulation ofa previously known motion illusion, which we refer to as the‘Moonwalk’ illusion, to demonstrate that the visual system cannot determine relative depth from dynamic occlusion alone. Indeed, in the Moonwalk illusion, human observers perceive a relative depth contrary to the dynamic occlusion cue. However, the perception of the expected relative depth is restored by contextual manipulations unrelated to dynamic occlusion. On the other hand, we show that an Ideal Observer can determine using dynamic occlusion alone in the same Moonwalk stimuli, indicating that the dynamic occlusion cue is, in principle, sufficient for determining relative depth. Our results indicate that in order to correctly perceive relative depth from dynamic occlusion, the human brain, unlike the Ideal Observer, needs additionalsegmentation information that delineate the occluder from the occluded object. Thus, neural mechanisms of object segmentation must, in addition to motion mechanisms that extract information about relative depth, play a crucial role in the perception of relative depth from motion

Extended weekly dose-dense paclitaxel/carboplatin is feasible and active in heavily pre-treated platinum-resistant recurrent ovarian cancer

There is increasing evidence of the efficacy of dose-dense therapy in the management of platinum-resistant/refractory ovarian cancer. We report our experience of extended weekly carboplatin and paclitaxel in this population group. Twenty patients with platinum-resistant/refractory ovarian cancer received carboplatin AUC 3 and paclitaxel 70 mg m−2 on day 1, 8, 15 q 4 weekly for six planned cycles. Toxicity was assessed using Common Toxicity Criteria. Response was evaluated using radiological and CA125 criteria. Median age was 61 years (range 40–74 years). Median number of prior therapies is three (range 1–8). Response rate was 60% by radiological criteria (RECIST) and 76% by CA125 assessment. Grade 3 toxicities consisted of neutropenia (29% of patients) and anaemia (5%). One patient experienced grade 4 neutropenia. No grade 3/4 thombocytopaenia was reported. Fatigue, nausea and peripheral neuropathy were the most frequent non-hematological side effects. Median progression-free survival was 7.9 months and overall survival was 13.3 months. The dynamics of response to dose-dense therapy were as rapid as with front-line therapy within the same patient. This dose-dense regimen can be extended to at least 18 weekly cycles over 6 months and is well tolerated with high response rates in heavily pre-treated, platinum-resistant ovarian cancer. It forms a highly active and tolerable cytotoxic scaffold to which molecular-targeted therapies can be added in platinum-resistant ovarian cancer

Levetiracetam Reverses Synaptic Deficits Produced by Overexpression of SV2A

Levetiracetam is an FDA-approved drug used to treat epilepsy and other disorders of the nervous system. Although it is known that levetiracetam binds the synaptic vesicle protein SV2A, how drug binding affects synaptic functioning remains unknown. Here we report that levetiracetam reverses the effects of excess SV2A in autaptic hippocampal neurons. Expression of an SV2A-EGFP fusion protein produced a ∼1.5-fold increase in synaptic levels of SV2, and resulted in reduced synaptic release probability. The overexpression phenotype parallels that seen in neurons from SV2 knockout mice, which experience severe seizures. Overexpression of SV2A also increased synaptic levels of the calcium-sensor protein synaptotagmin, an SV2-binding protein whose stability and trafficking are regulated by SV2. Treatment with levetiracetam rescued normal neurotransmission and restored normal levels of SV2 and synaptotagmin at the synapse. These results indicate that changes in SV2 expression in either direction impact neurotransmission, and suggest that levetiracetam may modulate SV2 protein interactions

Key Physiological Parameters Dictate Triggering of Activity-Dependent Bulk Endocytosis in Hippocampal Synapses

To maintain neurotransmission in central neurons, several mechanisms are employed to retrieve synaptically exocytosed membrane. The two major modes of synaptic vesicle (SV) retrieval are clathrin-mediated endocytosis and activity-dependent bulk endocytosis (ADBE). ADBE is the dominant SV retrieval mode during intense stimulation, however the precise physiological conditions that trigger this mode are not resolved. To determine these parameters we manipulated rat hippocampal neurons using a wide spectrum of stimuli by varying both the pattern and duration of stimulation. Using live-cell fluorescence imaging and electron microscopy approaches, we established that stimulation frequency, rather than the stimulation load, was critical in the triggering of ADBE. Thus two hundred action potentials, when delivered at high frequency, were sufficient to induce near maximal bulk formation. Furthermore we observed a strong correlation between SV pool size and ability to perform ADBE. We also identified that inhibitory nerve terminals were more likely to utilize ADBE and had a larger SV recycling pool. Thus ADBE in hippocampal synaptic terminals is tightly coupled to stimulation frequency and is more likely to occur in terminals with large SV pools. These results implicate ADBE as a key modulator of both hippocampal neurotransmission and plasticity

VAMP4 directs synaptic vesicles to a pool that selectively maintains asynchronous neurotransmission

Synaptic vesicles in the brain harbor several soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) proteins. With the exception of synaptobrevin2, or VAMP2 (syb2), which is directly involved in vesicle fusion, the role of these SNAREs in neurotransmission is unclear. Here we show that in mice syb2 drives rapid Ca2+-dependent synchronous neurotransmission, whereas the structurally homologous SNARE protein VAMP4 selectively maintains bulk Ca2+-dependent asynchronous release. At inhibitory nerve terminals, up- or downregulation of VAMP4 causes a correlated change in asynchronous release. Biochemically, VAMP4 forms a stable complex with SNAREs syntaxin-1 and SNAP-25 that does not interact with complexins or synaptotagmin-1, proteins essential for synchronous neurotransmission. Optical imaging of individual synapses indicates that trafficking of VAMP4 and syb2 show minimal overlap. Taken together, these findings suggest that VAMP4 and syb2 diverge functionally, traffic independently and support distinct forms of neurotransmission. These results provide molecular insight into how synapses diversify their release properties by taking advantage of distinct synaptic vesicle–associated SNAREs

Genome-scale screen for DNA methylation-based detection markers for ovarian cancer.

The identification of sensitive biomarkers for the detection of ovarian cancer is of high clinical relevance for early detection and/or monitoring of disease recurrence. We developed a systematic multi-step biomarker discovery and verification strategy to identify candidate DNA methylation markers for the blood-based detection of ovarian cancer

Outcome reporting across randomized trials and observational studies evaluating treatments for twin–twin transfusion syndrome: systematic review

Objective Twin–twin transfusion syndrome (TTTS) is associated with significant mortality and morbidity. Potential treatments for the condition require robust evaluation. The aim of this study was to evaluate outcome reporting across observational studies and randomized controlled trials assessing treatments for TTTS. Methods Cochrane Central Register of Controlled Trials, EMBASE and MEDLINE were searched from inception to August 2016. Observational studies and randomized controlled trials reporting outcome following treatment for TTTS in monochorionic–diamniotic twin pregnancy and monochorionic–triamniotic or dichorionic–triamniotic triplet pregnancy were included. Outcome reporting was systematically extracted and categorized. Results Six randomized trials and 94 observational studies were included, reporting data from 20 071 maternal participants and 3199 children. Six different treatments were evaluated. Included studies reported 62 different outcomes, including six fetal, seven offspring mortality, 25 neonatal, six early childhood and 18 maternal/operative outcomes. Outcomes were reported inconsistently across trials. For example, when considering offspring mortality, 31 (31%) studies reported live birth, 31 (31%) reported intrauterine death, 49 (49%) reported neonatal mortality and 17 (17%) reported perinatal mortality. Four (4%) studies reported respiratory distress syndrome. Only 19 (19%) studies were designed for long‐term follow‐up and 11 (11%) of these reported cerebral palsy. Conclusions Studies evaluating treatments for TTTS have often neglected to report clinically important outcomes, especially neonatal morbidity outcomes, and most are not designed for long‐term follow‐up. The development of a core outcome set could help standardize outcome collection and reporting in TTTS studies. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd