Altered reward system reactivity for personalized circumscribed interests in autism

Abstract Background Neurobiological research in autism spectrum disorders (ASD) has paid little attention on brain mechanisms that cause and maintain restricted and repetitive behaviors and interests (RRBIs). Evidence indicates an imbalance in the brain’s reward system responsiveness to social and non-social stimuli may contribute to both social deficits and RRBIs. Thus, this study’s central aim was to compare brain responsiveness to individual RRBI (i.e., circumscribed interests), with social rewards (i.e., social approval), in youth with ASD relative to typically developing controls (TDCs). Methods We conducted a 3T functional magnetic resonance imaging (fMRI) study to investigate the blood-oxygenation-level-dependent effect of personalized circumscribed interest rewards versus social rewards in 39 youth with ASD relative to 22 TDC. To probe the reward system, we employed short video clips as reinforcement in an instrumental incentive delay task. This optimization increased the task’s ecological validity compared to still pictures that are often used in this line of research. Results Compared to TDCs, youth with ASD had stronger reward system responses for CIs mostly within the non-social realm (e.g., video games) than social rewards (e.g., approval). Additionally, this imbalance within the caudate nucleus’ responsiveness was related to greater social impairment. Conclusions The current data support the idea of reward system dysfunction that may contribute to enhanced motivation for RRBIs in ASD, accompanied by diminished motivation for social engagement. If a dysregulated reward system indeed supports the emergence and maintenance of social and non-social symptoms of ASD, then strategically targeting the reward system in future treatment endeavors may allow for more efficacious treatment practices that help improve outcomes for individuals with ASD and their families

The Distance to SN 1999em from the Expanding Photosphere Method

We present optical and IR spectroscopy of the first two months of evolution of the Type II SN 1999em. We combine these data with high-quality optical/IR photometry beginning only three days after shock breakout, in order to study the performance of the ``Expanding Photosphere Method'' (EPM) in the determination of distances. With this purpose we develop a technique to measure accurate photospheric velocities by cross-correlating observed and model spectra. The application of this technique to SN 1999em shows that we can reach an average uncertainty of 11% in velocity from an individual spectrum. Our analysis shows that EPM is quite robust to the effects of dust. In particular, the distances derived from the VI filters change by only 7% when the adopted visual extinction in the host galaxy is varied by 0.45 mag. The superb time sampling of the BVIZJHK light-curves of SN 1999em permits us to study the internal consistency of EPM and test the dilution factors computed from atmosphere models for Type II plateau supernovae. We find that, in the first week since explosion, the EPM distances are up to 50% lower than the average, possibly due the presence of circumstellar material. Over the following 65 days, on the other hand, our tests lend strong credence to the atmosphere models, and confirm previous claims that EPM can produce consistent distances without having to craft specific models to each supernova. This is particularly true for the VI filters which yield distances with an internal consistency of 4%. From the whole set of BVIZJHK photometry, we obtain an average distance of 7.5+/-0.5 Mpc, where the quoted uncertainty (7%) is a conservative estimate of the internal precision of the method obtained from the analysis of the first 70 days of the supernova evolution.Comment: 68 pages, 15 tables, 22 figures, to appear in Ap

Does codon bias have an evolutionary origin?

<p>Abstract</p> <p>Background</p> <p>There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.</p> <p>Results</p> <p>Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 ± 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.</p> <p>Conclusion</p> <p>The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.</p

Climate Change and invasibility of the Antarctic benthos

Benthic communities living in shallow-shelf habitats in Antarctica (&lt;100-m depth) are archaic in their structure and function. Modern predators, including fast-moving, durophagous (skeleton-crushing) bony fish, sharks, and crabs, are rare or absent; slow-moving invertebrates are the top predators; and epifaunal suspension feeders dominate many soft substratum communities. Cooling temperatures beginning in the late Eocene excluded durophagous predators, ultimately resulting in the endemic living fauna and its unique food-web structure. Although the Southern Ocean is oceanographically isolated, the barriers to biological invasion are primarily physiological rather than geographic. Cold temperatures impose limits to performance that exclude modern predators. Global warming is now removing those physiological barriers, and crabs are reinvading Antarctica. As sea temperatures continue to rise, the invasion of durophagous predators will modernize the shelf benthos and erode the indigenous character of marine life in Antarctica

phyloXML: XML for evolutionary biology and comparative genomics

<p>Abstract</p> <p>Background</p> <p>Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types.</p> <p>Results</p> <p>We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data.</p> <p>Conclusion</p> <p>PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at <url>http://www.phyloxml.org</url>.</p

Enhancing value chain innovation through collective action: Lessons from the Andes, Africa, and Asia

The development community has shown increasing interest in the potential of innovation systems and value chain development approaches for reducing poverty and stimulating greater gender equity in rural areas. Nevertheless, there is a shortage of systematic knowledge on how such approaches have been implemented in different contexts, the main challenges in their application, and how they can be scaled to enable large numbers of poor people to benefit from participation in value chains. This chapter provides an overview of value chain development and focuses on the International Potato Center’s experiences with the Participatory Market Chain Approach (PMCA), a flexible approach that brings together smallholder farmers, traders, processors, researchers, and other service providers in a collective process to explore potential business opportunities and develop innovations to exploit them. The PMCA is an exemplary case of South–South knowledge exchange: it was first developed and implemented in the Andes, but has since been introduced, adapted, and applied to different market chains in Africa and Asia, where it has contributed to improved rural livelihoods. The experiences of adjusting and implementing the approach in these different contexts and the outcomes of those interventions, and complementary approaches, are examined in this chapter. Lessons learned from these experiences are shared with a goal of informing the promotion, improvement, and scaling of value chain approaches in the future

Optical and Infrared Photometry of the Nearby Type Ia Supernovae 1999ee, 2000bh, 2000ca, and 2001ba

We present near infrared photometry of the Type Ia supernova 1999ee; also, optical and infrared photometry of the Type Ia SNe 2000bh, 2000ca, and 2001ba. For SNe 1999ee and 2000bh we present the first-ever SN photometry at 1.035 microns (the Y-band). We present K-corrections which transform the infrared photometry in the observer's frame to the supernova rest frame. Using our infrared K-corrections and stretch factors derived from optical photometry, we construct JHK templates which can be used to determine the apparent magnitudes at maximum if one has some data in the window -12 to +10 d with respect to T(B_max). Following up previous work on the uniformity of V minus IR loci of Type Ia supernovae of mid-range decline rates, we present unreddened loci for slow decliners. We also discuss evidence for a continuous change of color at a given epoch as a function of decline rate.Comment: 53 pages, 14 figures, to be published in the March 2004 issue of the Astronomical Journa

Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies

This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, using multiple technologies, perform experiments to understand the mechanism of virulence. It is hard to integrate these data sources in a flexible manner that allows new experimental data to be added and compared when required