A communication profiler to optimize embedded resource usage

While the number of cores in both embedded MultiProcessor Systems-on-Chip and general purpose processors keeps rising, on-chip communication becomes more and more important. In order to write efficient programs for these architectures, it is therefore necessary to have a good idea of the communication behavior of an application. We present a communication profiler that extracts this behavior from compiled sequential C/C++ programs, and constructs a dynamic dataflow graph at the level of major functional blocks. In contrast to existing methods of measuring inter-program communication, our tool automatically generates the program's dataflow graph and is less demanding for the developer. It can also be used to view differences between program phases (such as different video frames), which allows both input- and phase-specific optimizations to be made. We also look at how this information can subsequently be used to guide the effort of parallelizing the application, to co-design the software, memory hierarchy and communication hardware, and to provide new sources of communication-related runtime optimizations

Idiopathic pleuroparenchymatous fibroelastosis: A case report and brief review of the literature

AbstractWe describe a patient with idiopathic pleuroparenchymal fibroelastosis (IPPFE). This rare clinicopathological syndrome is characterized by typical apical alterations op chest imaging, such as pleural thickening and subpleural fibrosis. Thickened visceral pleura and subpleural fibrosis consisting of dense collagen and elastin, are the main histopathological features. Etiology is unknown but a link between recurrent infections (in particular aspergillosis) and autoimmune diseases is suspected. At this time there is no standardized treatment regimen and the prognosis is variable

CNV-WebStore: Online CNV Analysis, Storage and Interpretation

<p>Abstract</p> <p>Background</p> <p>Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system.</p> <p>Results</p> <p>We present CNV-WebStore, an online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analsyis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results.</p> <p>Conclusion</p> <p>CNV-WebStore is able to present copy number data in an intuitive way to both lab technicians and clinicians, making it a useful tool in daily clinical practice.</p

Broncho-alveolar lavage fluid recovery correlates with airway neutrophilia in lung transplant patients

SummaryBroncho-alveolar lavage (BAL) is important to assess airway inflammation. There is debate about the volume instilled, but the variation of BAL fluid recovery (BFR) has received little attention. We investigated the association between BFR and rejection/infection status after lung transplantation (LTx).We combined clinical findings, FEV1, transbronchial biopsies and BAL analysis (BFR, interleukin-8 (IL8), cell counts, microbiology) of 115 samples/LTx patients. The patients were divided into 4 groups: stable (subdivided in colonized and non-colonized), acute rejection (AR), Bronchiolitis Obliterans Syndrome (BOS) and infection.BFR was significantly lower in AR, BOS and infection, and correlated with the severity of AR and BOS. A 10ml decrease of BFR was associated with a FEV1 decrease of 4.4% and a %neutrophils and IL8 increase of 9.6% and 9.7pg/ml, respectively. Colonized stable patients had no significant differences in airway inflammation, FEV1 and BFR compared to the non-colonized stable patients.We conclude that a low BFR is an indicator of lung rejection or infection. BFR variation is related to airway obstruction and neutrophilic inflammation, which can cause an increased compliance of the airway wall, making it more collapsible. Airway colonization in stable patients had no effect on airway inflammatory parameters, BFR and FEV1

Identifying unmet needs in SSc-ILD by semi-qualitative in-depth interviews

Objectives Interstitial lung disease is frequent in SSc (SSc-ILD) and associates with significantly reduced quality of life. Here we aimed to analyse patient pathways, and experiences of patients and healthcare providers (HCPs) in order to identify unmet needs in the management of SSc-ILD patients. Methods Semi-structured qualitative interviews conducted in eight European countries looked at HCP (n = 95) and patient perspectives (n = 47) using two sets of 70 research questions. Pre-diagnostic, diagnostic and post-diagnostic phases of the patient pathway were systematically explored. Results (i) In the pre-diagnostic phase several gaps were identified by HCPs and patients in all participating countries: limited disease knowledge among primary care physicians and specialists, lack of accurate patient information, and delayed and/or inappropriate referral. (ii) The diagnostic phase is in most countries coordinated by rheumatologists, who are also the main point of care. Depending on the local health system, organization of multidisciplinary collaboration varies. HCPs issued lack of national guidelines, while patients stated difficulties obtaining disease-related information. (iii) In the post-diagnostic phase, HCPs and patients indicated lack of curative treatment, specialized nurses, and paramedical and psychological support. Patients and caregivers additionally expressed the need for clear information on SSc-ILD. Conclusion Lack of disease specific knowledge, gaps in national healthcare systems and insufficient information and support for patients and caregivers were identified as unmet needs to ensure timely diagnosis, provide better patient management and to improve quality of life in SSc-ILD patients.Peer reviewe

Airway Measurement by Refinement of Synthetic Images Improves Mortality Prediction in Idiopathic Pulmonary Fibrosis

Several chronic lung diseases, like idiopathic pulmonary fibrosis (IPF) are characterised by abnormal dilatation of the airways. Quantification of airway features on computed tomography (CT) can help characterise disease progression. Physics based airway measurement algorithms have been developed, but have met with limited success in part due to the sheer diversity of airway morphology seen in clinical practice. Supervised learning methods are also not feasible due to the high cost of obtaining precise airway annotations. We propose synthesising airways by style transfer using perceptual losses to train our model, Airway Transfer Network (ATN). We compare our ATN model with a state-of-the-art GAN-based network (simGAN) using a) qualitative assessment; b) assessment of the ability of ATN and simGAN based CT airway metrics to predict mortality in a population of 113 patients with IPF. ATN was shown to be quicker and easier to train than simGAN. ATN-based airway measurements were also found to be consistently stronger predictors of mortality than simGAN-derived airway metrics on IPF CTs. Airway synthesis by a transformation network that refines synthetic data using perceptual losses is a realistic alternative to GAN-based methods for clinical CT analyses of idiopathic pulmonary fibrosis. Our source code can be found at https://github.com/ashkanpakzad/ATN that is compatible with the existing open-source airway analysis framework, AirQuant

Pathology of Idiopathic Pulmonary Fibrosis Assessed by a Combination of Microcomputed Tomography, Histology, and Immunohistochemistry

Idiopathic pulmonary fibrosis (IPF) is a fibrotic disease showing the histology of usual interstitial pneumonia (UIP). While the pathologist's visual inspection is central in histological assessments, three-dimensional microCT assessment may complement pathologist's scoring. This study examined associations between the histopathological features of UIP/IPF in explanted lungs and quantitative microCT measurements including alveolar surface density, total lung volume taken up by tissue (tissue%), and terminal bronchiolar number. Sixty frozen samples from 10 air-inflated explanted lungs with severe IPF and 36 samples from 6 donor control lungs were scanned with microCT and processed for histology. An experienced pathologist scored 3 major UIP criteria (patchy fibrosis, honeycomb, and fibroblastic foci), 5 additional pathological changes such as emphysema, and immunohistochemical staining for CD68, CD4, CD8, and CD79a positive cells, graded on a 0-3+ scale. The alveolar surface density and terminal bronchiolar number decreased and the tissue% increased in IPF compared to controls. In lungs with IPF, lower alveolar surface density and higher tissue% were correlated with greater scores of patchy fibrosis, fibroblastic foci, honeycomb, CD79a-positive cells, and lymphoid follicles. A decreased number of terminal bronchioles was correlated with honeycomb score, but not with the other scores. The three-dimensional microCT measurements reflect the pathological UIP/IPF criteria and further suggest that the reduction in the terminal bronchioles may be associated with honeycomb cyst formation