An efficient probabilistic population-based descent for the median genome problem

We present a novel population-based local search algorithm for the median genome problem. The primary result of this article is that this probabilistic approach significantly improves the performance of ancestral genome reconstruction compared to existing methods, making it possible to tackle problems where the contemporary genomes may contain many hundreds of markers. Moreover, our method is not limited to triples of genomes, and thus solves the median genome problem in its generality. We show that in real application cases the computational results are highly robust, suggesting that we can interpret the computed median genomes as candidates carrying the semantics of ancestral architectures

Metabolic and Endocrine correlates of cognitive function in healthy young women

Obesity has been associated with cognitive decline in longitudinal studies of older individuals. We hypothesized that the cognitive sequelae of obesity may be detectable in the reproductive years. In addition, we explored the hypothesis that these associations may be mediated by the hormonal milieu. In this study of 49 young healthy lean and overweight women aged 20–45, we investigated the association between performance on a battery of cognitive tests, body composition parameters (BMI, total fat, abdominal (visceral, subcutaneous and total) adipose tissue, and muscle), and hormone levels (insulin, adiponectin, leptin, IGF-1, estrogen, testosterone, and vitamin D). We found a significant negative association between both visceral adiposity and muscle, and performance in the domain of verbal learning and memory, after controlling for age and education. Other body composition parameters showed similar trends (0.05<p<0.10). Additionally, the degree of insulin resistance was negatively associated with executive function domain. None of the associations between the other hormones examined (adipokines, IGF-1, gonadal hormones and vitamin D) and cognitive function were significant. These preliminary findings suggest a possible association between obesity and cognitive function in healthy young women of reproductive age. More research is warranted into the potential modulatory effect of insulin resistance on this association

Permeability and conductivity of platelet-reinforced membranes and composites

We present large scale simulations of the diffusion constant $D$ of a random composite consisting of aligned platelets with aspect ratio $a/b>>1$ in a matrix (with diffusion constant $D_0$) and find that $D/D_0 = 1/(1+ c_1 x + c_2 x^2)$, where $x= a v_f/b$ and $v_f$ is the platelet volume fraction. We demonstrate that for large aspect ratio platelets the pair term ($x^2$) dominates suggesting large property enhancements for these materials. However a small amount of face-to-face ordering of the platelets markedly degrades the efficiency of platelet reinforcement.Comment: RevTeX, 5 pages, 4 figures, submitted to PR

Heating, Ventilating, and Air-Conditioning: Recent Advances in Diagnostics and Controls to Improve Air-Handling System Performance

The performance of air-handling systems in buildings needs to be improved. Many of the deficiencies result from myths and lore and a lack of understanding about the non-linear physical principles embedded in the associated technologies. By incorporating these principles, a few important efforts related to diagnostics and controls have already begun to solve some of the problems. This paper illustrates three novel solutions: one rapidly assesses duct leakage, the second configures ad hoc duct-static-pressure reset strategies, and the third identifies useful intermittent ventilation strategies. By highlighting these efforts, this paper seeks to stimulate new research and technology developments that could further improve air-handling systems

‘O sibling, where art thou?’ – a review of avian sibling recognition with respect to the mammalian literature

Avian literature on sibling recognition is rare compared to that developed by mammalian researchers. We compare avian and mammalian research on sibling recognition to identify why avian work is rare, how approaches differ and what avian and mammalian researchers can learn from each other. Three factors: (1) biological differences between birds and mammals, (2) conceptual biases and (3) practical constraints, appear to influence our current understanding. Avian research focuses on colonial species because sibling recognition is considered adaptive where ‘mixing potential’ of dependent young is high; research on a wider range of species, breeding systems and ecological conditions is now needed. Studies of acoustic recognition cues dominate avian literature; other types of cues (e.g. visual, olfactory) deserve further attention. The effect of gender on avian sibling recognition has yet to be investigated; mammalian work shows that gender can have important influences. Most importantly, many researchers assume that birds recognise siblings through ‘direct familiarisation’ (commonly known as associative learning or familiarity); future experiments should also incorporate tests for ‘indirect familiarisation’ (commonly known as phenotype matching). If direct familiarisation proves crucial, avian research should investigate how periods of separation influence sibling discrimination. Mammalian researchers typically interpret sibling recognition in broad functional terms (nepotism, optimal outbreeding); some avian researchers more successfully identify specific and testable adaptive explanations, with greater relevance to natural contexts. We end by reporting exciting discoveries from recent studies of avian sibling recognition that inspire further interest in this topic

Interplay of structural and electronic phase separation in single crystalline La(2)CuO(4.05) studied by neutron and Raman scattering

We report a neutron and Raman scattering study of a single-crystal of La(2)CuO(4.05) prepared by high temperature electrochemical oxidation. Elastic neutron scattering measurements show the presence of two phases, corresponding to the two edges of the first miscibility gap, all the way up to 300 K. An additional oxygen redistribution, driven by electronic energies, is identified at 250 K in Raman scattering (RS) experiments by the simultaneous onset of two-phonon and two-magnon scattering, which are fingerprints of the insulating phase. Elastic neutron scattering measurements show directly an antiferromagnetic ordering below a N\'eel temperature of T_N =210K. The opening of the superconducting gap manifests itself as a redistribution of electronic Raman scattering below the superconducting transition temperature, T_c = 24K. A pronounced temperature-dependent suppression of the intensity of the (100) magnetic Bragg peak has been detected below T_c. We ascribe this phenomenon to a change of relative volume fraction of superconducting and antiferromagnetic phases with decreasing temperature caused by a form of a superconducting proximity effect.Comment: 9 pages, including 9 eps figures, submitted to PR

Feline mammary carcinoma stem cells are tumorigenic, radioresistant, chemoresistant and defective in activation of the ATM/p53 DNA damage pathway

AbstractCancer stem cells were identified in a feline mammary carcinoma cell line by demonstrating expression of CD133 and utilising the tumour sphere assay. A population of cells was identified that had an invasive, mesenchymal phenotype, expressed markers of pluripotency and enhanced tumour formation in the NOD-SCID mouse and chick embryo models. This population of feline mammary carcinoma stem cells was resistant to chemotherapy and radiation, possibly due to aberrant activation of the ATM/p53 DNA damage pathway. Epithelial–mesenchymal transition was a feature of the invasive phenotype. These data demonstrate that cancer stem cells are a feature of mammary cancer in cats

Balancing end-to-end budgets of the Georges Bank ecosystem

Author Posting. © Elsevier, 2007. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Progress In Oceanography 74 (2007): 423-448, doi:10.1016/j.pocean.2007.05.003.Oceanographic regimes on the continental shelf display a great range in the time scales of physical exchange, biochemical processes and trophic transfers. The close surface-to-seabed physical coupling at intermediate scales of weeks to months means that the open ocean simplification to a purely pelagic food web is inadequate. Top-down trophic depictions, starting from the fish populations, are insufficient to constrain a system involving extensive nutrient recycling at lower trophic levels and subject to physical forcing as well as fishing. These pelagic-benthic interactions are found on all continental shelves but are particularly important on the relatively shallow Georges Bank in the northwest Atlantic. We have generated budgets for the lower food web for three physical regimes (well mixed, transitional and stratified) and for three seasons (spring, summer and fall/winter). The calculations show that vertical mixing and lateral exchange between the three regimes are important for zooplankton production as well as for nutrient input. Benthic suspension feeders are an additional critical pathway for transfers to higher trophic levels. Estimates of production by mesozooplankton, benthic suspension feeders and deposit feeders, derived primarily from data collected during the GLOBEC years of 1995-1999, provide input to an upper food web. Diets of commercial fish populations are used to calculate food requirements in three fish categories, planktivores, benthivores and piscivores, for four decades, 1963-2002, between which there were major changes in the fish communities. Comparisons of inputs from the lower web with fish energetic requirements for plankton and benthos indicate that we obtained reasonable agreement for the last three decades, 1973 to 2002. However, for the first decade, the fish food requirements were significantly less than the inputs. This decade, 1963-1972, corresponds to a period characterized by a strong Labrador Current and lower nitrate levels at the shelf edge, demonstrating how strong bottom-up physical forcing may determine overall fish yields.The research was done under the aegis of the U.S.-GLOBEC Northwest Atlantic Georges Bank Study, a program sponsored jointly by the U.S. National Science Foundation and the U.S. National Oceanic and Atmospheric Administration. We acknowledge NOAA-CICOR award NA17RJ1233 (J.H. Steele), NSF awards OCE0217399 (D.J. Gifford), OCE0217122 (J.J. Bisagni) and OCE0217257 (M.E. Sieracki). W.T. Stockhausen was supported by the NOAA Sponsored Coastal Ocean Research Program

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types