Chromatin segmentation

A method of segmenting chromatin particles in a nucleus of a cell by locating regional minima in an image, computing a zone of influence (ZOI) around each regional minimum, and segmenting a single chromatin blob within each ZOI using a region growing procedure. The method can be used as the basis of a method of qualitatively characterizing the distribution of nuclear chromatin by computing features for individual chromatin particles. Chromatin features can be synthesized from the features of individual particles and particle features can be synthesized into nucleus features and slide features. The method is useful for detecting malignancy associated changes and changes during neoplasia. The method may also be used more generally to assess chromatin patterns in living cells during the cell life cycle. This makes it possible to measure alternations in the evolving patterns that result from pathological or environmental influences

A Systematic Approach from a Comparison of Three Glucocorticoids

Solid lipid nanoparticles (SLNs) can enhance drug penetration into the skin, yet the mechanism of the improved transport is not known in full. To unravel the influence of the drug-particle interaction on penetration enhancement, 3 glucocorticoids (GCs), prednisolone (PD), the diester prednicarbate (PC) and the monoester betamethasone 17-valerate (BMV), varying in structure and lipophilicity, were loaded onto SLNs. Theoretical permeability coefficients (cm/s) of the agents rank BMV (–6.38) ≧ PC (–6.57) > PD (–7.30). GC-particle interaction, drug release and skin penetration were investigated including a conventional oil-in-water cream for reference. Both with SLN and cream, PD release was clearly superior to PC release which exceeded BMV release. With the cream, the rank order did not change when studying skin penetration, and skin penetration is thus predominantly influenced by drug release. Yet, the penetration profile for the GCs loaded onto SLNs completely changed, and differences between the steroids were almost lost. Thus, SLNs influence skin penetration by an intrinsic mechanism linked to a specific interaction of the drug-carrier complex and the skin surface, which becomes possible by the lipid nature and nanosize of the carrier and appears not to be derived by testing drug release. Interestingly, PC and PD uptake from SLN even resulted in epidermal targeting. Thus, SLNs are not only able to improve skin penetration of topically applied drugs, but may also be of particular interest when specifically aiming to influence epidermal dysfunction

Engineering with logic: Rigorous test-oracle specification and validation for TCP/IP and the Sockets API

Conventional computer engineering relies on test-and-debug development processes, with the behavior of common interfaces described (at best) with prose specification documents. But prose specifications cannot be used in test-and-debug development in any automated way, and prose is a poor medium for expressing complex (and loose) specifications. The TCP/IP protocols and Sockets API are a good example of this: they play a vital role in modern communication and computation, and interoperability between implementations is essential. But what exactly they are is surprisingly obscure: their original development focused on “rough consensus and running code,” augmented by prose RFC specifications that do not precisely define what it means for an implementation to be correct. Ultimately, the actual standard is the de facto one of the common implementations, including, for example, the 15 000 to 20 000 lines of the BSD implementation—optimized and multithreaded C code, time dependent, with asynchronous event handlers, intertwined with the operating system, and security critical. This article reports on work done in the Netsem project to develop lightweight mathematically rigorous techniques that can be applied to such systems: to specify their behavior precisely (but loosely enough to permit the required implementation variation) and to test whether these specifications and the implementations correspond with specifications that are executable as test oracles . We developed post hoc specifications of TCP, UDP, and the Sockets API, both of the service that they provide to applications (in terms of TCP bidirectional stream connections) and of the internal operation of the protocol (in terms of TCP segments and UDP datagrams), together with a testable abstraction function relating the two. These specifications are rigorous, detailed, readable, with broad coverage, and rather accurate. Working within a general-purpose proof assistant (HOL4), we developed language idioms (within higher-order logic) in which to write the specifications: operational semantics with nondeterminism, time, system calls, monadic relational programming, and so forth. We followed an experimental semantics approach, validating the specifications against several thousand traces captured from three implementations (FreeBSD, Linux, and WinXP). Many differences between these were identified, as were a number of bugs. Validation was done using a special-purpose symbolic model checker programmed above HOL4. Having demonstrated that our logic-based engineering techniques suffice for handling real-world protocols, we argue that similar techniques could be applied to future critical software infrastructure at design time, leading to cleaner designs and (via specification-based testing) more robust and predictable implementations. In cases where specification looseness can be controlled, this should be possible with lightweight techniques, without the need for a general-purpose proof assistant, at relatively little cost.EPSRC Programme Grant EP/K008528/1 REMS: Rigorous Engineering for Mainstream Systems EPSRC Leadership Fellowship EP/H005633 (Sewell) Royal Society University Research Fellowship (Sewell) St Catharine's College Heller Research Fellowship (Wansbrough), EPSRC grant GR/N24872 Wide-area programming: Language, Semantics and Infrastructure Design EPSRC grant EP/C510712 NETSEM: Rigorous Semantics for Real Systems EC FET-GC project IST-2001-33234 PEPITO Peer-to-Peer Computing: Implementation and Theory CMI UROP internship support (Smith) EC Thematic Network IST-2001-38957 APPSEM 2 NICTA was funded by the Australian Government's Backing Australia's Ability initiative, in part through the Australian Research Council

Registration evaluation of dynamic breast MR images

The interpretation of dynamic contrast-enhanced breast MR images is predicated on the assumption of minimal voxel movement during the time course of the image acquisition. Misalignment of the dynamic image sequence as a result of movement during image acquisition can lead to potentially misleading diagnostic conclusions. In this paper a new methodology is presented for assessing the degree of in-plane (intra-slice) movement in a dynamic image sequence. The method is demonstrated on data from six subjects. The conclusion is that the method makes it possible to quantitatively qualify the accuracy of computed enhancement curves and more importantly to identify unacceptably poor registration

High-Resolution Optical Functional Mapping of the Human Somatosensory Cortex

Non-invasive optical imaging of brain function has been promoted in a number of fields in which functional magnetic resonance imaging (fMRI) is limited due to constraints induced by the scanning environment. Beyond physiological and psychological research, bedside monitoring and neurorehabilitation may be relevant clinical applications that are yet little explored. A major obstacle to advocate the tool in clinical research is insufficient spatial resolution. Based on a multi-distance high-density optical imaging setup, we here demonstrate a dramatic increase in sensitivity of the method. We show that optical imaging allows for the differentiation between activations of single finger representations in the primary somatosensory cortex (SI). Methodologically our findings confirm results in a pioneering study by Zeff et al. (2007) and extend them to the homuncular organization of SI. After performing a motor task, eight subjects underwent vibrotactile stimulation of the little finger and the thumb. We used a high-density diffuse-optical sensing array in conjunction with optical tomographic reconstruction. Optical imaging disclosed three discrete activation foci one for motor and two discrete foci for vibrotactile stimulation of the first and fifth finger, respectively. The results were co-registered to the individual anatomical brain anatomy (MRI) which confirmed the localization in the expected cortical gyri in four subjects. This advance in spatial resolution opens new perspectives to apply optical imaging in the research on plasticity notably in patients undergoing neurorehabilitation

Development and validation of the predicted heat strain model

Abstract Eight laboratories participated in a concerted research project on the assessment of hot working conditions. The objectives were, among others, to co-ordinate the work of the main European research teams in the field of thermal factors and to improve the methods available to assess the risks of heat disorders at the workplace, and in particular the "Required Sweat Rate" model as presented in International Standard ISO 7933 Standard (1989). The scientific bases of this standard were thoroughly reviewed and a revised model, called "Predicted Heat Strain" (PHS), was developed. This model was then used to predict the minute by minute sweat rates and rectal temperatures during 909 laboratory and field experiments collected from the partners. The Pearson correlation coefficients between observed and predicted values were equal to 0.76 and 0.66 for laboratory experiments and 0.74 and 0.59 for field experiments, respectively, for the sweat rates and the rectal temperatures. The change in sweat rate with time was predicted more accurately by the PHS model than by the required sweat rate model. This suggests that the PHS model would provide an improved basis upon which to determine allowable exposure times from the predicted heat strain in terms of dehydration and increased core temperature

Avelumab in patients with previously treated metastatic Merkel cell carcinoma (JAVELIN Merkel 200): updated overall survival data after >5 years of follow-up

Background: Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer that has a poor prognosis in patients with advanced disease. Avelumab [anti-programmed death-ligand 1 (PD-L1)] became the first approved treatment for patients with metastatic MCC (mMCC), based on efficacy and safety data observed in the JAVELIN Merkel 200 trial. We report long-term overall survival (OS) data after >5 years of follow-up from the cohort of patients with mMCC whose disease had progressed after one or more prior lines of chemotherapy. Patients and methods: In Part A of the single-arm, open-label, phase II JAVELIN Merkel 200 trial, patients with mMCC that had progressed following one or more prior lines of chemotherapy received avelumab 10 mg/kg by intravenous infusion every 2 weeks until confirmed disease progression, unacceptable toxicity, or withdrawal. In this analysis, long-term OS was analyzed. Results: In total, 88 patients were treated with avelumab. At data cut-off (25 September 2020), median follow-up was 65.1 months (range 60.8-74.1 months). One patient (1.1%) remained on treatment, and an additional patient (1.1%) had reinitiated avelumab after previously discontinuing treatment. Median OS was 12.6 months [95% confidence interval (CI) 7.5-17.1 months], with a 5-year OS rate of 26% (95% CI 17% to 36%). In patients with PD-L1+ versus PD-L1- tumors, median OS was 12.9 months (95% CI 8.7-29.6 months) versus 7.3 months (95% CI 3.4-14.0 months), and the 5-year OS rate was 28% (95% CI 17% to 40%) versus 19% (95% CI 5% to 40%), respectively (HR 0.67; 95% CI 0.36-1.25). Conclusion: Avelumab monotherapy resulted in meaningful long-term OS in patients with mMCC whose disease had progressed following chemotherapy. These results further support the role of avelumab as a standard of care for patients with mMCC