Cycloidal CT with CNN-based sinogram completion and in-scan generation of training data

In x-ray computed tomography (CT), the achievable image resolution is typically limited by several pre-fixed characteristics of the x-ray source and detector. Structuring the x-ray beam using a mask with alternating opaque and transmitting septa can overcome this limit. However, the use of a mask imposes an undersampling problem: to obtain complete datasets, significant lateral sample stepping is needed in addition to the sample rotation, resulting in high x-ray doses and long acquisition times. Cycloidal CT, an alternative scanning scheme by which the sample is rotated and translated simultaneously, can provide high aperture-driven resolution without sample stepping, resulting in a lower radiation dose and faster scans. However, cycloidal sinograms are incomplete and must be restored before tomographic images can be computed. In this work, we demonstrate that high-quality images can be reconstructed by applying the recently proposed Mixed Scale Dense (MS-D) convolutional neural network (CNN) to this task. We also propose a novel training approach by which training data are acquired as part of each scan, thus removing the need for large sets of pre-existing reference data, the acquisition of which is often not practicable or possible. We present results for both simulated datasets and real-world data, showing that the combination of cycloidal CT and machine learning-based data recovery can lead to accurate high-resolution images at a limited dose

Sparse Matrix-Based HPC Tomography

Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster frame rates, larger fields of view or higher resolution, so high performance solutions are currently widely used for analysis. Tomographic instruments can vary significantly from one to another, including the hardware employed for reconstruction: from single CPU workstations to large scale hybrid CPU/GPU supercomputers. Flexibility on the software interfaces and reconstruction engines are also highly valued to allow for easy development and prototyping. This paper presents a novel software framework for tomographic analysis that tackles all aforementioned requirements. The proposed solution capitalizes on the increased performance of sparse matrix-vector multiplication and exploits multi-CPU and GPU reconstruction over MPI. The solution is implemented in Python and relies on CuPy for fast GPU operators and CUDA kernel integration, and on SciPy for CPU sparse matrix computation. As opposed to previous tomography solutions that are tailor-made for specific use cases or hardware, the proposed software is designed to provide flexible, portable and high-performance operators that can be used for continuous integration at different production environments, but also for prototyping new experimental settings or for algorithmic development. The experimental results demonstrate how our implementation can even outperform state-of-the-art software packages used at advanced X-ray sources worldwide

MEF2 impairment underlies skeletal muscle atrophy in polyglutamine disease

Polyglutamine (polyQ) tract expansion leads to proteotoxic misfolding and drives a family of nine diseases. We study spinal and bulbar muscular atrophy (SBMA), a progressive degenerative disorder of the neuromuscular system caused by the polyQ androgen receptor (AR). Using a knock-in mouse model of SBMA, AR113Q mice, we show that E3 ubiquitin ligases which are a hallmark of the canonical muscle atrophy machinery are not induced in AR113Q muscle. Similarly, we find no evidence to suggest dysfunction of signaling pathways that trigger muscle hypertrophy or impairment of the muscle stem cell niche. Instead, we find that skeletal muscle atrophy is characterized by diminished function of the transcriptional regulator Myocyte Enhancer Factor 2 (MEF2), a regulator of myofiber homeostasis. Decreased expression of MEF2 target genes is age- and glutamine tract length-dependent, occurs due to polyQ AR proteotoxicity, and is associated with sequestration of MEF2 into intranuclear inclusions in muscle. Skeletal muscle from R6/2 mice, a model of Huntington disease which develops progressive atrophy, also sequesters MEF2 into inclusions and displays age-dependent loss of MEF2 target genes. Similarly, SBMA patient muscle shows loss of MEF2 target gene expression, and restoring MEF2 activity in AR113Q muscle rescues fiber size and MEF2-regulated gene expression. This work establishes MEF2 impairment as a novel mechanism of skeletal muscle atrophy downstream of toxic polyglutamine proteins and as a therapeutic target for muscle atrophy in these disorders

Predicting consumer biomass, size-structure, production, catch potential, responses to fishing and associated uncertainties in the world's marine ecosystems

Existing estimates of fish and consumer biomass in the world’s oceans are disparate. This creates uncertainty about the roles of fish and other consumers in biogeochemical cycles and ecosystem processes, the extent of human and environmental impacts and fishery potential. We develop and use a size-based macroecological model to assess the effects of parameter uncertainty on predicted consumer biomass, production and distribution. Resulting uncertainty is large (e.g. median global biomass 4.9 billion tonnes for consumers weighing 1 g to 1000 kg; 50% uncertainty intervals of 2 to 10.4 billion tonnes; 90% uncertainty intervals of 0.3 to 26.1 billion tonnes) and driven primarily by uncertainty in trophic transfer efficiency and its relationship with predator-prey body mass ratios. Even the upper uncertainty intervals for global predictions of consumer biomass demonstrate the remarkable scarcity of marine consumers, with less than one part in 30 million by volume of the global oceans comprising tissue of macroscopic animals. Thus the apparently high densities of marine life seen in surface and coastal waters and frequently visited abundance hotspots will likely give many in society a false impression of the abundance of marine animals. Unexploited baseline biomass predictions from the simple macroecological model were used to calibrate a more complex size- and trait-based model to estimate fisheries yield and impacts. Yields are highly dependent on baseline biomass and fisheries selectivity. Predicted global sustainable fisheries yield increases ≈4 fold when smaller individuals (< 20 cm from species of maximum mass < 1kg) are targeted in all oceans, but the predicted yields would rarely be accessible in practice and this fishing strategy leads to the collapse of larger species if fishing mortality rates on different size classes cannot be decoupled. Our analyses show that models with minimal parameter demands that are based on a few established ecological principles can support equitable analysis and comparison of diverse ecosystems. The analyses provide insights into the effects of parameter uncertainty on global biomass and production estimates, which have yet to be achieved with complex models, and will therefore help to highlight priorities for future research and data collection. However, the focus on simple model structures and global processes means that non-phytoplankton primary production and several groups, structures and processes of ecological and conservation interest are not represented. Consequently, our simple models become increasingly less useful than more complex alternatives when addressing questions about food web structure and function, biodiversity, resilience and human impacts at smaller scales and for areas closer to coasts

FADS2 Function Loss at the Cancer Hotspot 11q13 Locus Diverts Lipid Signaling Precursor Synthesis to Unusual Eicosanoid Fatty Acids

Background: Genes coding for the fatty acid desaturases (FADS1, 2, 3) localized at the cancer genomic hotspot 11q13 locus are required for the biosynthesis of 20 carbon polyunsaturated fatty acids (PUFA) that are direct eicosanoid precursors. In several cancer cell lines, FADS2 encoded D6 and D8 desaturation is not functional. Methodology/Principal Findings: Analyzing MCF7 cell fatty acids with detailed structural mass spectrometry, we show that in the absence of FADS2 activity, the FADS1 product D5-desaturase operates to produce 5,11,14–20:3 and 5,11,14,17–20:4. These PUFA are missing the 8–9 double bond of the eicosanoid signaling precursors arachidonic acid (5,8,11,14–20:4) and eicosapentaenoic acid (5,8,11,14,17–20:5). Heterologous expression of FADS2 restores D6 and D8-desaturase activity and normal eicosanoid precursor synthesis. Conclusions/Significance: The loss of FADS2-encoded activities in cancer cells shuts down normal PUFA biosynthesis, deleting the endogenous supply of eicosanoid and downstream docosanoid precursors, and replacing them with unusual butylene-interrupted fatty acids. If recapitulated in vivo, the normal eicosanoid and docosanoid cell signaling milieu would be depleted and altered due to reduction and substitution of normal substrates with unusual substrates, with unpredictable consequences for cellular communication

Selection of a phylogenetically informative region of the norovirus genome for outbreak linkage

The recognition of a common source norovirus outbreak is supported by finding identical norovirus sequences in patients. Norovirus sequencing has been established in many (national) public health laboratories and academic centers, but often partial and different genome sequences are used. Therefore, agreement on a target sequence of sufficient diversity to resolve links between outbreaks is crucial. Although harmonization of laboratory methods is one of the keystone activities of networks that have the aim to identify common source norovirus outbreaks, this has proven difficult to accomplish, particularly in the international context. Here, we aimed at providing a method enabling identification of the genomic region informative of a common source norovirus outbreak by bio-informatic tools. The data set of 502 unique full length capsid gene sequences available from the public domain, combined with epidemiological data including linkage information was used to build over 3,000 maximum likelihood (ML) trees for different sequence lengths and regions. All ML trees were evaluated for robustness and specificity of clustering of known linked norovirus outbreaks against the background diversity of strains. Great differences were seen in the robustness of commonly used PCR targets for cluster detection. The capsid gene region spanning nucleotides 900–1,400 was identified as the region optimally substituting for the full length capsid region. Reliability of this approach depends on the quality of the background data set, and we recommend periodic reassessment of this growing data set. The approach may be applicable to multiple sequence-based data sets of other pathogens

Enhanced ERbeta immunoexpression and apoptosis in the germ cells of cimetidine-treated rats

<p>Abstract</p> <p>Background</p> <p>Cimetidine, refereed as antiandrogenic drug, causes hormonal changes in male patients such as increased testosterone and FSH levels. In the rat testis, structural alterations in the seminiferous tubules have been related to germ cell loss and Sertoli cell death by apoptosis. Regarding the important role of Sertoli cells in the conversion of testosterone into estrogen, via aromatase, the immunoexpression of estrogen receptors-beta (ERbeta) was evaluated in the germ cells of untreated and treated rats with cimetidine. A relationship between ERbeta immunoreactivity and apoptosis was also investigated in the germ cells of damaged tubules.</p> <p>Methods</p> <p>Immunohistochemistry for detection of ERbeta and TUNEL method were performed in testicular sections of adult male rats treated with 50 mg/Kg of cimetidine (CmG) or saline solution (CG) for 52 days.</p> <p>Results</p> <p>In CG, a cytoplasmic immunoexpression for ERbeta was observed in spermatogonia, primary spermatocytes and spermatids. An evident ERbeta immunoreactivity was always observed in the flagellum and residual bodies of late spermatids. In CmG, the cytoplasm or cytoplasm and nuclei of germ cells of the damaged tubules by cimetidine showed enhanced ERbeta immunostaining. TUNEL-labeling was usually observed in the same germ cell types exhibiting enhanced ERbeta immunoreactivity.</p> <p>Conclusion</p> <p>The presence of ERbeta immunolabeling in the flagellum and residual bodies of spermatids reinforces the role of estrogen in spermiogenesis. The overexpression of ERbeta in the germ cells of CmG could be related to a possible interference of cimetidine on tubular androgenization and/or on the intratubular aromatase due to Sertoli cell damage. The parallelism between ERbeta overexpression and apoptosis indicates a participation of ERbeta on germ cell death.</p

Psychological quality of life and its association with academic employability skills among newly-registered students from three European faculties

In accord with new European university reforms initiated by the Bologna Process, our objectives were to assess psychological quality of life (QoL) and to analyse its associations with academic employability skills (AES) among students from the Faculty of Language, Literature, Humanities, Arts and Education, Walferdange Luxembourg (F1, mostly vocational/applied courses); the Faculty of Social and Human Sciences, Liege, Belgium (F2, mainly general courses); and the Faculty of Social Work, Iasi, Romania (F3, mainly vocational/professional courses). Method: Students who redoubled or who had studied at other universities were excluded. 355 newly-registered first-year students (145 from F1, 125 from F2, and 85 from F3) were invited to complete an online questionnaire (in French, German, English or Romanian) covering socioeconomic data, the AES scale and the QoL-psychological, QoL-social relationships and QoL-environment subscales as measured with the World Health Organisation Quality of Life short-form (WHOQoL-BREF) questionnaire. Analyses included multiple regressions with interactions. Results: QoL-psychological, QoL-social relationships and QoL-environment’ scores were highest in F1 (Luxembourg), and the QoL-psychological score in F2 (Belgium) was the lower. AES score was higher in F1 than in F3 (Romania). A positive link was found between QoL-psychological and AES for F1 (correlation coefficient 0.29, p < 0.01) and F3 (correlation coefficient 0.30, p < 0.05), but the association was negative for F2 (correlation coefficient -0.25, p < 0.01). QoL-psychological correlated positively with QoL-social relationships (regression coefficient 0.31, p < 0.001) and QoL-environment (regression coefficient 0.35, p < 0.001). Conclusions: Psychological quality of life is associated with acquisition of skills that increase employability from the faculties offering vocational/applied/professional courses in Luxembourg and Romania, but not their academically orientated Belgian counterparts. In the context of developing a European Higher Educational Area, these measurements are major indicators that can be used as a guide to promoting programs geared towards counseling, improvement of the social environment, and services to assist with university work and facilitate achievement of future professional projects. Keywords: students WHOQoL-BREF, QoL-psychological, employability, academic skills, QoL-environmental, QoLsocial relationship

Über eine Klasse polynomialer Scharen selbstadjungierter Operatoren im Hilbertraum

HEK293A cells expressing either mouse MOG (mMOG) or rat MOG (rMOG) C terminally tagged with EGFP. (DOCX 2792 kb