GCOD - GeneChip Oncology Database

<p>Abstract</p> <p>Background</p> <p>DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data.</p> <p>Description</p> <p>To address this issue we have collected published human cancer gene expression datasets generated on the Affymetrix GeneChip platform, and carefully annotated those studies with a focus on providing accurate sample annotation. To facilitate comparison between datasets, we implemented a consistent data normalization and transformation protocol and then applied stringent quality control procedures to flag low-quality assays.</p> <p>Conclusion</p> <p>The resulting resource, the GeneChip Oncology Database, is available through a publicly accessible website that provides several query options and analytical tools through an intuitive interface.</p

Development of the escape response in teleost fishes: do ontogenetic changes enable improved performance?

Teleost fishes typically first encounter the environment as free-swimming embryos or larvae. Larvae are morphologically distinct from adults, and major anatomical structures are unformed. Thus, larvae undergo a series of dramatic morphological changes until they reach adult morphology (but are reproductively immature) and are considered juveniles. Free-swimming embryos and larvae are able to perform a C-start, an effective escape response that is used evade predators. However, escape response performance improves during early development: as young fish grow, they swim faster (length-specific maximum velocity increases) and perform the escape more rapidly (time to complete the behavior decreases). These improvements cease when fish become juveniles, although absolute swimming velocity (m s(-1)) continues to increase. We use studies of escape behavior and ontogeny in California halibut (Paralichthys californicus), rainbow trout (Oncorhynchus mykiss), and razorback suckers (Xyrauchen texanus) to test the hypothesis that specific morphological changes improve escape performance. We suggest that formation of the caudal fin improves energy transfer to the water and therefore increases thrust production and swimming velocity. In addition, changes to the axial skeleton during the larval period produce increased axial stiffness, which in turn allows the production of a more rapid and effective escape response. Because escape performance improves as adult morphology develops, fish that enter the environment in an advanced stage of development (i.e., those with direct development) should have a greater ability to evade predators than do fish that enter the environment at an early stage of development (i.e., those with indirect development)

ThermoPixels:Toolkit for Personalizing Arousal-based Interfaces through Hybrid Crafting

Much research has shown the potential of affective interfaces to support people reflect on, and understand their bodily responses. Yet, people find it difficult to engage with, and understand their biodata which they have limited prior experience with. Building on affective interfaces and material-centered design, we developed ThermoPixels, a toolkit including thermochromic and heating materials, as well as galvanic skin response sensors for creating representations of physiological arousal. Within 10 workshops, 20 participants created personalized representations of physiological arousal and its real-time changes using the toolkit. We report on participants’ material exploration, their experience of creating shapes and the use of colors for emotional awareness and regulation. Reflecting on our findings, we discuss embodied exploration and creative expression, the value of technology in emotion regulation and its social context, and the importance of understanding material limitations for effective sense-making

Use of in vitro human keratinocyte models to study the effect of cooling on chemotherapy drug-induced cytotoxicity

A highly distressing side-effect of cancer chemotherapy is chemotherapy-induced alopecia (CIA). Scalp cooling remains the only treatment for CIA, yet there is no experimental evidence to support the cytoprotective capacity of cooling. We have established a series of in vitro models for the culture of human keratinocytes under conditions where they adopt a basal, highly-proliferative phenotype thus resembling the rapidly-dividing sub-population of native hair-matrix keratinocytes. Using a panel of chemotherapy drugs routinely used clinically (docetaxel, doxorubicin and the active metabolite of cyclophosphamide 4-OH-CP), we demonstrate that although these drugs are highly-cytotoxic, cooling can markedly reduce or completely inhibit drug cytotoxicity, in agreement with clinical observations. By contrast, we show that cytotoxicity caused by specific combinatorial drug treatments cannot be adequately attenuated by cooling, supporting data showing that such treatments do not always respond well to cooling clinically. Importantly, we provide evidence that the choice of temperature may be critical in determining the efficacy of cooling in rescuing cells from drug-mediated toxicity. Therefore, despite their reductive nature, these in vitro models have provided experimental evidence for the clinically-reported cytoprotective role of cooling and represent useful tools for future studies on the molecular mechanisms of cooling-mediated cytoprotection

Scheduling and Airport Taxiway Path Planning Under Uncertainty

Congestion and uncertainty on the airport surface are major constraints to the available capacity of the air transport system. This project is to study the problem of planning and scheduling airport surface movement at large airports. Specifically, we focus on the departure time scheduling and taxiway path planning of multiple aircraft under uncertainty. We also developed a simulation tool that is capable of simulating aircraft movement along the taxiway and possible uncertainty during the movement

Comparison of embedded and added motor imagery training in patients after stroke: Results of a randomised controlled pilot trial

Copyright @ 2012 Schuster et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Motor imagery (MI) when combined with physiotherapy can offer functional benefits after stroke. Two MI integration strategies exist: added and embedded MI. Both approaches were compared when learning a complex motor task (MT): ‘Going down, laying on the floor, and getting up again’. Methods: Outpatients after first stroke participated in a single-blinded, randomised controlled trial with MI embedded into physiotherapy (EG1), MI added to physiotherapy (EG2), and a control group (CG). All groups participated in six physiotherapy sessions. Primary study outcome was time (sec) to perform the motor task at pre and post-intervention. Secondary outcomes: level of help needed, stages of MT-completion, independence, balance, fear of falling (FOF), MI ability. Data were collected four times: twice during one week baseline phase (BL, T0), following the two week intervention (T1), after a two week follow-up (FU). Analysis of variance was performed. Results: Thirty nine outpatients were included (12 females, age: 63.4 ± 10 years; time since stroke: 3.5 ± 2 years; 29 with an ischemic event). All were able to complete the motor task using the standardised 7-step procedure and reduced FOF at T0, T1, and FU. Times to perform the MT at baseline were 44.2 ± 22s, 64.6 ± 50s, and 118.3 ± 93s for EG1 (N = 13), EG2 (N = 12), and CG (N = 14). All groups showed significant improvement in time to complete the MT (p < 0.001) and degree of help needed to perform the task: minimal assistance to supervision (CG) and independent performance (EG1+2). No between group differences were found. Only EG1 demonstrated changes in MI ability over time with the visual indicator increasing from T0 to T1 and decreasing from T1 to FU. The kinaesthetic indicator increased from T1 to FU. Patients indicated to value the MI training and continued using MI for other difficult-to-perform tasks. Conclusions: Embedded or added MI training combined with physiotherapy seem to be feasible and benefi-cial to learn the MT with emphasis on getting up independently. Based on their baseline level CG had the highest potential to improve outcomes. A patient study with 35 patients per group could give a conclusive answer of a superior MI integration strategy.The research project was partially funded by the Gottfried und Julia Bangerter-Rhyner Foundation

Safety evaluation of a β-amylase food enzyme obtained from wheat (Triticum spp.)

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Phosphorous application improves drought tolerance of phoebe zhennan

Phoebe zhennan (Gold Phoebe) is a threatened tree species in China and a valuable and important source of wood and bioactive compounds used in medicine. Apart from anthropogenic disturbances, several biotic constraints currently restrict its growth and development. However, little attention has been given to building adaptive strategies for its conservation by examining its morphological and physio-biochemical responses to drought stress, and the role of fertilizers on these responses. A randomized experimental design was used to investigate the effects of two levels of irrigation (well-watered and drought-stressed) and phosphorous (P) fertilization treatment (with and without P) to assess the morphological and physio-biochemical responses of P. zhennan seedlings to drought stress. In addition, we evaluated whether P application could mitigate the negative impacts of drought on plant growth and metabolism. Drought stress had a significant negative effect on the growth and metabolic processes of P. zhennan. Despite this, reduced leaf area, limited stomatal conductance, reduced transpiration rate, increased water use efficiency, enhanced antioxidant enzymes activities, and osmolytes accumulation suggested that the species has good adaptive strategies for tolerating drought stress. Application of P had a significant positive effect on root biomass, signifying its improved water extracting capacity from the soil. Moreover, P fertilization significantly increased leaf relative water content, net photosynthetic rate, and maximal quantum efficiency of PSII under drought stress conditions. This may be attributable to several factors, such as enhanced root biomass, decreased malondialdehyde content, and the up-regulation of chloroplast pigments, osmolytes, and nitrogenous compounds. However, P application had only a slight or negligible effect on the growth and metabolism of well-watered plants. In conclusion, P. zhennan has a strong capability for drought resistance, while P application facilitates and improves drought tolerance mostly through physio-biochemical adjustments, regardless of water availability. It is imperative to explore the underlying metabolic mechanisms and effects of different levels of P fertilization on P. zhennan under drought conditions in order to design appropriate conservation and management strategies for this species, which is at risk of extinction.Fil: Tariq, Akash. Chinese Academy of Sciences; República de ChinaFil: Pan, Kaiwen. Chinese Academy of Sciences; República de ChinaFil: Olatunji, Olusanya A.. Chinese Academy of Sciences; República de ChinaFil: Graciano, Corina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Li, Zilong. Chinese Academy of Sciences; República de ChinaFil: Sun, Feng. Chinese Academy of Sciences; República de ChinaFil: Sun, Xiaoming. Chinese Academy of Sciences; República de ChinaFil: Song, Dagang. Chinese Academy of Sciences; República de ChinaFil: Chen, Wenkai. Chinese Academy of Sciences; República de ChinaFil: Zhang, Aiping. Chinese Academy of Sciences; República de ChinaFil: Wu, Xiaogang. Chinese Academy of Sciences; República de ChinaFil: Zhang, Lin. Chinese Academy of Sciences; República de ChinaFil: Mingrui, Deng. Chinese Academy of Sciences; República de ChinaFil: Xiong, Qinli. Chinese Academy of Sciences; República de ChinaFil: Liu, Chenggang. Chinese Academy of Sciences; República de Chin

Phylogenetic and molecular characterization of coxsackievirus A24 variant isolates from a 2010 acute hemorrhagic conjunctivitis outbreak in Guangdong, China

<p>Abstract</p> <p>Background</p> <p>Acute hemorrhagic conjunctivitis is a common disease in China. As a notifiable disease, cases are registered by ophthalmologists on the AHC surveillance system. An AHC outbreak caused by CA24v was observed in Guangdong Province in 2007 by the National Disease Supervision Information Management System. Three years later, a larger outbreak occurred in Guangdong during the August-October period (2010). To characterize the outbreak and compare the genetic diversity of CA24v, which was determined to be the cause of the outbreak, the epidemiology and the molecular characterization of CA24v were analyzed in this study.</p> <p>Results</p> <p>A total of 69,635 cases were reported in the outbreak. 73.5% of index cases originated from students, children in kindergarten and factory workers, with the ≦ 9 age group at the highest risk. The male to female ratio was 1.84:1 among 0-19 years. 56 conjunctival swabs were collected to identify the causative agent from five cities with the AHC outbreak. 30 virus strains were isolated, and two of the genomes had the highest identity values (95.8%) with CA24v genomes. Four CA24v genotypes were identified by phylogenetic analysis for the VP1 and 3C regions. CA24v which caused the outbreak belonged to genotype IV. Furthermore, full nucleotide sequences for four representative isolates in 2010 and 2007 were determined and compared. 20 aa mutations, two nt insertions and one nt deletion were observed in the open reading frame, with 5'- and 3'- UTR respectively between them.</p> <p>Conclusions</p> <p>CA24v was determined to be the pathogen causing the outbreak and belongs to genotype IV. VP1 is more informative than 3C^Profor describing molecular epidemiology and we hypothesize that accumulative mutations may have promoted the outbreak.</p

Safety evaluation of the food enzyme β-amylase obtained from barley (Hordeum vulgare)

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