Bristle pattern formation in the thorax formation of Drosophila: a systems level approach

A fundamental question in developmental biology is how tissues are patterned to give rise to differentiated body structures with distinct morphologies. The Drosophila wing disc offers an accessible model to understand epithelial spatial patterning. It has been studied extensively using genetic and molecular approaches. Bristle patterns on the thorax, which arise from the medial part of the wing disc, are a classical model of pattern formation, dependent on a pre-pattern of trans-activators and –repressors. Despite of decades of molecular studies, we still only know a subset of the factors that determine the pre-pattern. We are applying a novel and interdisciplinary approach to predict regulatory interactions in this system. It is based on the description of expression patterns by simple logical relations (addition, subtraction, intersection and union) between simple shapes (graphical primitives). Similarities and relations between primitives have been shown to be predictive of regulatory relationships between the corresponding regulatory factors in other Systems, such as the Drosophila egg. Furthermore, they provide the basis for dynamical models of the bristle-patterning network, which enable us to make even more detailed predictions on gene regulation and expression dynamics. We have obtained a data-set of wing disc expression patterns which we are now processing to obtain average expression patterns for each gene. Through triangulation of the images we can transform the expression patterns into vectors which can easily be analysed by Standard clustering methods. These analyses will allow us to identify primitives and regulatory interactions. We expect to identify new regulatory interactions and to understand the basic Dynamics of the regulatory network responsible for thorax patterning. These results will provide us with a better understanding of the rules governing gene regulatory networks in general, and provide the basis for future studies of the evolution of the thorax-patterning network in particular.

Probabilistically analysable real-time systems (PROARTIS)

Critical real-time ebedded (CRTE) Systems require safe and tight worst-case execution time (WCET) estimations to provide required safety levels and keep costs low. However, CRTE Systems require increasing performance to satisfy performance needs of existing and new features. Such performance can be only achieved by means of more agressive hardware architectures, which are much harder to analyze from a WCET perspective. The main features considered include cache memòries and multi-core processors.Thus, althoug such features provide higher performance, corrent WCET analysis methods are unable to provide tight WCET estimations. In fact, WCET estimations become worse than for simple rand less powerful hardware. The main reason is the fact that hardware behavior is deterministic but unknown and, therefore, the worst-case behavior must be assumed most of the time, leading to large WCET estimations. The purpose of this project is developing new hardware designs together with WCET analysis tools able to provide tight and safe WCET estimations. In order to do so, those pieces of hardware whose behavior is not easily analyzable due to lack of accurate information during WCET analysis will be enhanced to produce a probabilistically analyzable behavior. Thus, even if the worst-case behavior cannot be removed, its probabilty can be bounded, and hence, a safe and tight WCET can be provided for a particular safety level in line with the safety levels of the remaining components of the system. During the first year the project we have developed molt of the evaluation infraestructure as well as the techniques hardware techniques to analyze cache memories. During the second year those techniques have been evaluated, and new purely-softwar techniques have been developed.

Performance of blood pressure-to-height ratio at a single screening visit for the identification of hypertension in children.

BACKGROUND: The diagnosis of hypertension in children is difficult because of the multiple sex-, age-, and height-specific thresholds to define elevated blood pressure (BP). Blood pressure-to-height ratio (BPHR) has been proposed to facilitate the identification of elevated BP in children. OBJECTIVE: We assessed the performance of BPHR at a single screening visit to identify children with hypertension that is sustained elevated BP. METHOD: In a school-based study conducted in Switzerland, BP was measured at up to three visits in 5207 children. Children had hypertension if BP was elevated at the three visits. Sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) for the identification of hypertension were assessed for different thresholds of BPHR. The ability of BPHR at a single screening visit to discriminate children with and without hypertension was evaluated with receiver operating characteristic (ROC) curve analyses. RESULTS: The prevalence of systolic/diastolic hypertension was 2.2%. Systolic BPHR had a better performance to identify hypertension compared with diastolic BPHR (area under the ROC curve: 0.95 vs. 0.84). The highest performance was obtained with a systolic BPHR threshold set at 0.80 mmHg/cm (sensitivity: 98%; specificity: 85%; PPV: 12%; and NPV: 100%) and a diastolic BPHR threshold set at 0.45 mmHg/cm (sensitivity: 79%; specificity: 70%; PPV: 5%; and NPV: 99%). The PPV was higher among tall or overweight children. CONCLUSION: BPHR at a single screening visit had a high performance to identify hypertension in children, although the low prevalence of hypertension led to a low PPV.

Identification of the Best Practices for Design, Construction, and Repair of Bridge Approches, 2005

Bridge approach settlement and the formation of the bump is a common problem in Iowa that draws upon considerable resources for maintenance and creates a negative perception in the minds of transportation users. This research study was undertaken to investigate bridge approach problems and develop new concepts for design, construction, and maintenance that will reduce this costly problem. As a result of the research described in this report, the following changes are suggested for implementation on a pilot test basis: • Use porous backfill behind the abutment and/or geocomposite drainage systems to improve drainage capacity and reduce erosion around the abutment. • On a pilot basis, connect the approach slab to the bridge abutment. Change the expansion joint at the bridge to a construction joint of 2 inch. Use a more effective joint sealing system at the CF joint. Change the abutment wall rebar from #5 to #7 for non-integral abutments. • For bridges with soft foundation or embankment soils, implement practices of better compaction, preloading, ground improvement, soil removal and replacement, or soil reinforcement that reduce time-dependent post construction settlements.

Predicting species distributions for conservation decisions.

Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on-ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision-making contexts when used within a structured and transparent decision-making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of 'translators' between modellers and decision makers. We encourage species distribution modellers to get involved in real decision-making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.

ExPASy: SIB bioinformatics resource portal.

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

Bloodstream and endovascular infections due to Abiotrophia defectiva and Granulicatella species.

BACKGROUND: Abiotrophia and Granulicatella species, previously referred to as nutritionally variant streptococci (NVS), are significant causative agents of endocarditis and bacteraemia. In this study, we reviewed the clinical manifestations of infections due to A. defectiva and Granulicatella species that occurred at our institution between 1998 and 2004. METHODS: The analysis included all strains of NVS that were isolated from blood cultures or vascular graft specimens. All strains were identified by 16S rRNA sequence analysis. Patients' medical charts were reviewed for each case of infection. RESULTS: Eleven strains of NVS were isolated during the 6-year period. Identification of the strains by 16S rRNA showed 2 genogroups: Abiotrophia defectiva (3) and Granulicatella adiacens (6) or "para-adiacens" (2). The three A. defectiva strains were isolated from immunocompetent patients with endovascular infections, whereas 7 of 8 Granulicatella spp. strains were isolated from immunosuppressed patients, mainly febrile neutropenic patients. We report the first case of "G. para-adiacens" bacteraemia in the setting of febrile neutropenia. CONCLUSION: We propose that Granulicatella spp. be considered as a possible agent of bacteraemia in neutropenic patients.

Long-Range Goals for Iowa's Criminal& Junvenile Justice Systems, 2005

The attached plan builds upon work done over the last decade. The first plan developed after the creation of the Division of Criminal and Juvenile Justice Planning in 1986 was issued in 1990 and annually updated through 1994. Since 1992, the CJJPAC has been required to coordinate their planning activities with those of the Iowa Juvenile Justice Advisory Council (JJAC). In 1995, these two councils developed a new plan consisting of a set of long-range justice system goals to assist policy makers and justice system practitioners as they plan and operate the justice system through the next twenty years. The statutory mandate for such long-range planning required the identification of goals specific enough to provide guidance, but broad enough to be of relevance over a long period of time. The long-range goals adopted by these councils in 1995 covered a wide variety of topics and offered a framework within which current practices could be defined and assessed. Collectively, these long-range goals were meant to provide a single source of direction to the complex assortment of practitioners and policymakers whose individual concerns and decisions collectively define the nature and effectiveness of Iowa’s justice system. The twenty-year goals established in 1995 were reviewed by the councils in 2000 to assess their current relevance. It was determined that, with a few revisions, the goals established in 1995 should be restated in 2000 with a renewed emphasis on their long-range status. This plan builds upon those issued in 1995 and 2000, continuing much of the emphasis of plans, with some new directions charted as appropriate.

Identification of the Best Practices for Design, Construction, and Repair of Bridge Approaches, January 2005

Bridge approach settlement and the formation of the bump is a common problem in Iowa that draws upon considerable resources for maintenance and creates a negative perception in the minds of transportation users. This research study was undertaken to investigate bridge approach problems and develop new concepts for design, construction, and maintenance that will reduce this costly problem. As a result of the research described in this report, the following changes are suggested for implementation on a pilot test basis: • Use porous backfill behind the abutment and/or geocomposite drainage systems to improve drainage capacity and reduce erosion around the abutment. • On a pilot basis, connect the approach slab to the bridge abutment. Change the expansion joint at the bridge to a construction joint of 2 inch. Use a more effective joint sealing system at the CF joint. Change the abutment wall rebar from #5 to #7 for non-integral abutments. • For bridges with soft foundation or embankment soils, implement practices of better compaction, preloading, ground improvement, soil removal and replacement, or soil reinforcement that reduce time-dependent post construction settlements.

Testing for local adaptation in brown trout using reciprocal transplants.

ABSTRACT: BACKGROUND: Local adaptation can drive the divergence of populations but identification of the traits under selection remains a major challenge in evolutionary biology. Reciprocal transplant experiments are ideal tests of local adaptation, yet rarely used for higher vertebrates because of the mobility and potential invasiveness of non-native organisms. Here, we reciprocally transplanted 2500 brown trout (Salmo trutta) embryos from five populations to investigate local adaptation in early life history traits. Embryos were bred in a full-factorial design and raised in natural riverbeds until emergence. Customized egg capsules were used to simulate the natural redd environment and allowed tracking the fate of every individual until retrieval. We predicted that 1) within sites, native populations would outperform non-natives, and 2) across sites, populations would show higher performance at 'home' compared to 'away' sites. RESULTS: There was no evidence for local adaptation but we found large differences in survival and hatching rates between sites, indicative of considerable variation in habitat quality. Survival was generally high across all populations (55% +/- 3%), but ranged from 4% to 89% between sites. Average hatching rate was 25% +/- 3% across populations ranging from 0% to 62% between sites. CONCLUSION: This study provides rare empirical data on variation in early life history traits in a population network of a salmonid, and large-scale breeding and transplantation experiments like ours provide powerful tests for local adaptation. Despite the recently reported genetic and morphological differences between the populations in our study area, local adaptation at the embryo level is small, non-existent, or confined to ecological conditions that our experiment could not capture.

Identification of a new murine tumor necrosis factor receptor locus that contains two novel murine receptors for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL).

Tumor necrosis factor (TNF) ligand and receptor superfamily members play critical roles in diverse developmental and pathological settings. In search for novel TNF superfamily members, we identified a murine chromosomal locus that contains three new TNF receptor-related genes. Sequence alignments suggest that the ligand binding regions of these murine TNF receptor homologues, mTNFRH1, -2 and -3, are most homologous to those of the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptors. By using a number of in vitro ligand-receptor binding assays, we demonstrate that mTNFRH1 and -2, but not mTNFRH3, bind murine TRAIL, suggesting that they are indeed TRAIL receptors. This notion is further supported by our demonstration that both mTNFRH1:Fc and mTNFRH2:Fc fusion proteins inhibited mTRAIL-induced apoptosis of Jurkat cells. Unlike the only other known murine TRAIL receptor mTRAILR2, however, neither mTNFRH2 nor mTNFRH3 has a cytoplasmic region containing the well characterized death domain motif. Coupled with our observation that overexpression of mTNFRH1 and -2 in 293T cells neither induces apoptosis nor triggers NFkappaB activation, we propose that the mTnfrh1 and mTnfrh2 genes encode the first described murine decoy receptors for TRAIL, and we renamed them mDcTrailr1 and -r2, respectively. Interestingly, the overall sequence structures of mDcTRAILR1 and -R2 are quite distinct from those of the known human decoy TRAIL receptors, suggesting that the presence of TRAIL decoy receptors represents a more recent evolutionary event.

Predictors of political orientation among US-born Mexican Americans: cultural identification, acculturation attitudes and socioeconomic status

With each passing election, U.S. political campaigns have renewed their efforts in courting the “Latino vote,” yet the Latino population is not a culturally homogenous voting bloc. This study examined how cultural identifications and acculturation attitudes in U.S. born Mexican Americans interacted with socioeconomic status (SES) to predict political orientation. Individuals who held stronger Mexican identity and supported biculturalism as an acculturation strategy had a more liberal orientation, while belonging to a higher SES group and holding stronger assimilation attitudes predicted a less liberal orientation. Mexican cultural identification interacted with SES such that those who held a weaker Mexican identity, but came from a higher social class were less liberal and more moderate in their political orientation. Weak Mexican identification and higher SES also predicted weaker endorsement of bicultural acculturation attitudes, which in turn, mediated the differences in political orientation. The acceptance of one’s ethnic identity and endorsement of bicultural attitudes predicted a more liberal political orientation. In light of these findings, political candidates should be cautious in how they pander to Latino constituents—referencing the groups’ ethnic culture or customs may distance constituents who are not strongly identified with their ethnic culture.

Echo-time independent signal modulations for strongly coupled systems in triple echo localization schemes: an extension of S-PRESS editing.

The double spin-echo point resolved spectroscopy sequence (PRESS) is a widely used method and standard in clinical MR spectroscopy. Existence of important J-modulations at constant echo times, depending on the temporal delays between the rf-pulses, have been demonstrated recently for strongly coupled spin systems and were exploited for difference editing, removing singlets from the spectrum (strong-coupling PRESS, S-PRESS). A drawback of this method for in vivo applications is that large signal modulations needed for difference editing occur only at relatively long echo times. In this work we demonstrate that, by simply adding a third refocusing pulse (3S-PRESS), difference editing becomes possible at substantially shorter echo times while, as applied to citrate, more favorable lineshapes can be obtained. For the example of an AB system an analytical description of the MR signal, obtained with this triple refocusing sequence (3S-PRESS), is provided.

IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction.

Approximately 3% of the world population is chronically infected with the hepatitis C virus (HCV), with potential development of cirrhosis and hepatocellular carcinoma. Despite the availability of new antiviral agents, treatment remains suboptimal. Genome-wide association studies (GWAS) identified rs12979860, a polymorphism nearby IL28B, as an important predictor of HCV clearance. We report the identification of a novel TT/-G polymorphism in the CpG region upstream of IL28B, which is a better predictor of HCV clearance than rs12979860. By using peripheral blood mononuclear cells (PBMCs) from individuals carrying different allelic combinations of the TT/-G and rs12979860 polymorphisms, we show that induction of IL28B and IFN-γ-inducible protein 10 (IP-10) mRNA relies on TT/-G, but not rs12979860, making TT/-G the only functional variant identified so far. This novel step in understanding the genetic regulation of IL28B may have important implications for clinical practice, as the use of TT/G genotyping instead of rs12979860 would improve patient management.

Relatedness influences signal reliability in evolving robots.

Communication is an indispensable component of animal societies, yet many open questions remain regarding the factors affecting the evolution and reliability of signalling systems. A potentially important factor is the level of genetic relatedness between signallers and receivers. To quantitatively explore the role of relatedness in the evolution of reliable signals, we conducted artificial evolution over 500 generations in a system of foraging robots that can emit and perceive light signals. By devising a quantitative measure of signal reliability, and comparing independently evolving populations differing in within-group relatedness, we show a strong positive correlation between relatedness and reliability. Unrelated robots produced unreliable signals, whereas highly related robots produced signals that reliably indicated the location of the food source and thereby increased performance. Comparisons across populations also revealed that the frequency for signal production-which is often used as a proxy of signal reliability in empirical studies on animal communication-is a poor predictor of signal reliability and, accordingly, is not consistently correlated with group performance. This has important implications for our understanding of signal evolution and the empirical tools that are used to investigate communication.