The tropical Atlantic observing system

The tropical Atlantic is home to multiple coupled climate variations covering a wide range of timescales and impacting societally relevant phenomena such as continental rainfall, Atlantic hurricane activity, oceanic biological productivity, and atmospheric circulation in the equatorial Pacific. The tropical Atlantic also connects the southern and northern branches of the Atlantic meridional overturning circulation and receives freshwater input from some of the world’s largest rivers. To address these diverse, unique, and interconnected research challenges, a rich network of ocean observations has developed, building on the backbone of the Prediction and Research Moored Array in the Tropical Atlantic (PIRATA). This network has evolved naturally over time and out of necessity in order to address the most important outstanding scientific questions and to improve predictions of tropical Atlantic severe weather and global climate variability and change. The tropical Atlantic observing system is motivated by goals to understand and better predict phenomena such as tropical Atlantic interannual to decadal variability and climate change; multidecadal variability and its links to the meridional overturning circulation; air-sea fluxes of CO2 and their implications for the fate of anthropogenic CO2; the Amazon River plume and its interactions with biogeochemistry, vertical mixing, and hurricanes; the highly productive eastern boundary and equatorial upwelling systems; and oceanic oxygen minimum zones, their impacts on biogeochemical cycles and marine ecosystems, and their feedbacks to climate. Past success of the tropical Atlantic observing system is the result of an international commitment to sustained observations and scientific cooperation, a willingness to evolve with changing research and monitoring needs, and a desire to share data openly with the scientific community and operational centers. The observing system must continue to evolve in order to meet an expanding set of research priorities and operational challenges. This paper discusses the tropical Atlantic observing system, including emerging scientific questions that demand sustained ocean observations, the potential for further integration of the observing system, and the requirements for sustaining and enhancing the tropical Atlantic observing system

Atypical Neurophysiology Underlying Episodic and Semantic Memory in Adults with Autism Spectrum Disorder

Individuals with autism spectrum disorder (ASD) show atypicalities in episodic memory (Boucher et al. in Psychological Bulletin, 138 (3), 458-496, 2012). We asked participants to recall the colours of a set of studied line drawings (episodic judgement), or to recognize line drawings alone (semantic judgement). Cycowicz et al. (Journal of Experimental Child Psychology, 65, 171-237, 2001) found early (300 ms onset) posterior old-new event-related potential effects for semantic judgements in typically developing (TD) individuals, and occipitally focused negativity (800 ms onset) for episodic judgements. Our results replicated findings in TD individuals and demonstrate attenuated early old-new effects in ASD. Late posterior negativity was present in the ASD group, but was not specific to this time window. This non-specificity may contribute to the atypical episodic memory judgements characteristic of individuals with ASD

Multimodal neuroimaging in presurgical evaluation of childhood epilepsy

In pre-surgical evaluation of pediatric epilepsy, the combined use of multiple imaging modalities for precise localization of the epileptogenic focus is a worthwhile endeavor. Advanced neuroimaging by high field Magnetic resonance imaging (MRI), diffusion tensor images, and MR spectroscopy have the potential to identify subtle lesions. 18F-FDG positron emission tomography and single photon emission tomography provide visualization of metabolic alterations of the brain in the ictal and interictal states. These techniques may have localizing value for patients which exhibit normal MRI scans. Functional MRI is helpful for non-invasively identifying areas of eloquent cortex. These advances are improving our ability to noninvasively detect epileptogenic foci which have gone undetected in the past and whose accurate localization is crucial for a favorable outcome following surgical resection

A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns

<p>Abstract</p> <p>Background</p> <p>To understand the gene regulatory system that governs the self-renewal and pluripotency of embryonic stem cells (ESCs) is an important step for promoting regenerative medicine. In it, the role of several core transcription factors (TFs), such as Oct4, Sox2 and Nanog, has been intensively investigated, details of their involvement in the genome-wide gene regulation are still not well clarified.</p> <p>Methods</p> <p>We constructed a predictive model of genome-wide gene expression in mouse ESCs from publicly available ChIP-seq data of 12 core TFs. The tag sequences were remapped on the genome by various alignment tools. Then, the binding density of each TF is calculated from the genome-wide bona fide TF binding sites. The TF-binding data was combined with the data of several epigenetic states (DNA methylation, several histone modifications, and CpG island) of promoter regions. These data as well as the ordinary peak intensity data were used as predictors of a simple linear regression model that predicts absolute gene expression. We also developed a pipeline for analyzing the effects of predictors and their interactions.</p> <p>Results</p> <p>Through our analysis, we identified two classes of genes that are either well explained or inefficiently explained by our model. The latter class seems to be genes that are not directly regulated by the core TFs. The regulatory regions of these gene classes show apparently distinct patterns of DNA methylation, histone modifications, existence of CpG islands, and gene ontology terms, suggesting the relative importance of epigenetic effects. Furthermore, we identified statistically significant TF interactions correlated with the epigenetic modification patterns.</p> <p>Conclusions</p> <p>Here, we proposed an improved prediction method in explaining the ESC-specific gene expression. Our study implies that the majority of genes are more or less directly regulated by the core TFs. In addition, our result is consistent with the general idea of relative importance of epigenetic effects in ESCs.</p

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

Epigenetic reprogramming is a critical event in the generation of induced pluripotent stem cells (iPSCs). Here, we determined the DNA methylation profiles of 22 human iPSC lines derived from five different cell types (human endometrium, placental artery endothelium, amnion, fetal lung fibroblast, and menstrual blood cell) and five human embryonic stem cell (ESC) lines, and we followed the aberrant methylation sites in iPSCs for up to 42 weeks. The iPSCs exhibited distinct epigenetic differences from ESCs, which were caused by aberrant methylation at early passages. Multiple appearances and then disappearances of random aberrant methylation were detected throughout iPSC reprogramming. Continuous passaging of the iPSCs diminished the differences between iPSCs and ESCs, implying that iPSCs lose the characteristics inherited from the parent cells and adapt to very closely resemble ESCs over time. Human iPSCs were gradually reprogrammed through the “convergence” of aberrant hyper-methylation events that continuously appeared in a de novo manner. This iPS reprogramming consisted of stochastic de novo methylation and selection/fixation of methylation in an environment suitable for ESCs. Taken together, random methylation and convergence are driving forces for long-term reprogramming of iPSCs to ESCs

Dissociation between the Activity of the Right Middle Frontal Gyrus and the Middle Temporal Gyrus in Processing Semantic Priming

The aim of this event-related functional magnetic resonance imaging (fMRI) study was to test whether the right middle frontal gyrus (MFG) and middle temporal gyrus (MTG) would show differential sensitivity to the effect of prime-target association strength on repetition priming. In the experimental condition (RP), the target occurred after repetitive presentation of the prime within an oddball design. In the control condition (CTR), the target followed a single presentation of the prime with equal probability of the target as in RP. To manipulate semantic overlap between the prime and the target both conditions (RP and CTR) employed either the onomatopoeia “oink” as the prime and the referent “pig” as the target (OP) or vice-versa (PO) since semantic overlap was previously shown to be greater in OP. The results showed that the left MTG was sensitive to release of adaptation while both the right MTG and MFG were sensitive to sequence regularity extraction and its verification. However, dissociated activity between OP and PO was revealed in RP only in the right MFG. Specifically, target “pig” (OP) and the physically equivalent target in CTR elicited comparable deactivations whereas target “oink” (PO) elicited less inhibited response in RP than in CTR. This interaction in the right MFG was explained by integrating these effects into a competition model between perceptual and conceptual effects in priming processing

Known and unknown requirements in healthcare

We report experience in requirements elicitation of domain knowledge from experts in clinical and cognitive neurosciences. The elicitation target was a causal model for early signs of dementia indicated by changes in user behaviour and errors apparent in logs of computer activity. A Delphi-style process consisting of workshops with experts followed by a questionnaire was adopted. The paper describes how the elicitation process had to be adapted to deal with problems encountered in terminology and limited consensus among the experts. In spite of the difficulties encountered, a partial causal model of user behavioural pathologies and errors was elicited. This informed requirements for configuring data- and text-mining tools to search for the specific data patterns. Lessons learned for elicitation from experts are presented, and the implications for requirements are discussed as “unknown unknowns”, as well as configuration requirements for directing data-/text-mining tools towards refining awareness requirements in healthcare applications

Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: A systematic expression analysis

<p>Abstract</p> <p>Background</p> <p>The inter-alpha-trypsin inhibitors (ITI) are a family of plasma protease inhibitors, assembled from a light chain – bikunin, encoded by <it>AMBP </it>– and five homologous heavy chains (encoded by <it>ITIH1</it>, <it>ITIH2</it>, <it>ITIH3</it>, <it>ITIH4</it>, and <it>ITIH5</it>), contributing to extracellular matrix stability by covalent linkage to hyaluronan. So far, ITIH molecules have been shown to play a particularly important role in inflammation and carcinogenesis.</p> <p>Methods</p> <p>We systematically investigated differential gene expression of the <it>ITIH </it>gene family, as well as <it>AMBP </it>and the interacting partner <it>TNFAIP6 </it>in 13 different human tumor entities (of breast, endometrium, ovary, cervix, stomach, small intestine, colon, rectum, lung, thyroid, prostate, kidney, and pancreas) using cDNA dot blot analysis (Cancer Profiling Array, CPA), semiquantitative RT-PCR and immunohistochemistry.</p> <p>Results</p> <p>We found that <it>ITIH </it>genes are clearly downregulated in multiple human solid tumors, including breast, colon and lung cancer. Thus, <it>ITIH </it>genes may represent a family of putative tumor suppressor genes that should be analyzed in greater detail in the future. For an initial detailed analysis we chose <it>ITIH2 </it>expression in human breast cancer. Loss of <it>ITIH2 </it>expression in 70% of cases (n = 50, CPA) could be confirmed by real-time PCR in an additional set of breast cancers (n = 36). Next we studied ITIH2 expression on the protein level by analyzing a comprehensive tissue micro array including 185 invasive breast cancer specimens. We found a strong correlation (p < 0.001) between ITIH2 expression and estrogen receptor (ER) expression indicating that ER may be involved in the regulation of this ECM molecule.</p> <p>Conclusion</p> <p>Altogether, this is the first systematic analysis on the differential expression of <it>ITIH </it>genes in human cancer, showing frequent downregulation that may be associated with initiation and/or progression of these malignancies.</p

Critical literacy as a pedagogical goal in English language teaching

In this chapter, the authors provide an overview of the area of critical literacy as it pertains to second language pedagogy (curriculum and instruction). After considering the historical origins of critical literacy (from antiquity, and including in first language education), they consider how it began to penetrate the field of applied linguistics. They note the geographical and institutional spread of critical literacy practice as documented by published accounts. They then sketch the main features of L2 critical literacy practice. To do this, they acknowledge how practitioners have reported on their practices regarding classroom content and process. The authors also draw attention to the outcomes of these practices as well as challenges that practitioners have encountered in incorporating critical literacy into their second language classrooms