3,593 research outputs found
A format for phylogenetic placements
We have developed a unified format for phylogenetic placements, that is,
mappings of environmental sequence data (e.g. short reads) into a phylogenetic
tree. We are motivated to do so by the growing number of tools for computing
and post-processing phylogenetic placements, and the lack of an established
standard for storing them. The format is lightweight, versatile, extensible,
and is based on the JSON format which can be parsed by most modern programming
languages. Our format is already implemented in several tools for computing and
post-processing parsimony- and likelihood-based phylogenetic placements, and
has worked well in practice. We believe that establishing a standard format for
analyzing read placements at this early stage will lead to a more efficient
development of powerful and portable post-analysis tools for the growing
applications of phylogenetic placement.Comment: Documents version 3 of the forma
PainDroid: An android-based virtual reality application for pain assessment
Earlier studies in the field of pain research suggest that little efficient intervention currently exists in response to the exponential increase in the prevalence of pain. In this paper, we present an Android application (PainDroid) with multimodal functionality that could be enhanced with Virtual Reality (VR) technology, which has been designed for the purpose of improving the assessment of this notoriously difficult medical concern. Pain- Droid has been evaluated for its usability and acceptability with a pilot group of potential users and clinicians, with initial results suggesting that it can be an effective and usable tool for improving the assessment of pain. Participant experiences indicated that the application was easy to use and the potential of the application was similarly appreciated by the clinicians involved in the evaluation. Our findings may be of considerable interest to healthcare providers, policy makers, and other parties that might be actively involved in the area of pain and VR research
Galaxy Spin Statistics and Spin-Density Correlation
We present a theoretical study of galaxy spin correlation statistics, with
detailed technical derivations. We also find an expression for the spin-density
cross-correlation, and apply that to the Tully galaxy catalog. The
observational results appear qualitatively consistent with the theoretical
predictions, yet the error bars are still large. However, we expect that
currently ongoing large surveys such as the Sloan Digital Sky survey (SDSS)
will enable us to make a precision measurement of these correlation statistics
in the near future. These intrinsic galaxy alignments are expected to dominate
over the weak lensing signal in SDSS, and we present the detailed algorithms
for the density reconstruction for this case.
These observables are tracers of the galaxy-gravity interaction, which may
provide us deeper insights into the galaxy formation and large scale matter
distribution as well.Comment: Accepted version, ApJ in press, remaining mistakes and typos
correctedd, LaTex file, 41 pages, 3 eps figure
Self-Dual Bending Theory for Vesicles
We present a self-dual bending theory that may enable a better understanding
of highly nonlinear global behavior observed in biological vesicles. Adopting
this topological approach for spherical vesicles of revolution allows us to
describe them as frustrated sine-Gordon kinks. Finally, to illustrate an
application of our results, we consider a spherical vesicle globally distorted
by two polar latex beads.Comment: 10 pages, 3 figures, LaTeX2e+IOPar
The cosmic web for density perturbations of various scales
We follow the evolution of galaxy systems in numerical simulation. Our goal
is to understand the role of density perturbations of various scales in the
formation and evolution of the cosmic web. We perform numerical simulations
with the full power spectrum of perturbations, and with spectrum cut at long
wavelengths. Additionally, we have one model, where we cut the intermediate
waves. We analyze the density field and study the void sizes and density field
clusters in different models. Our analysis shows that the fine structure
(groups and clusters of galaxies) is created by small-scale density
perturbations of scale \Mpc. Filaments of galaxies and clusters are
created by perturbations of intermediate scale from to \Mpc,
superclusters of galaxies by larger perturbations. We conclude that the scale
of the pattern of the cosmic web is determined by density perturbations of
scale up to \Mpc. Larger perturbations do not change the pattern of
the web, but modulate the richness of galaxy systems, and make voids emptier.
The stop of the increase of the scale of the pattern of the cosmic web with
increasing scale of density perturbations can probably be explained as the
freezing of the web at redshift .Comment: 12 pages, 7 figures, accepted for publication in Astronomy and
Astrophysic
The Gtpase Rho Controls a P53-Dependent Survival Checkpoint during Thymopoiesis
During the early stages of thymopoiesis, cell survival is controlled by cytokines that regulate the expression of antiapoptotic proteins such as Bcl-2. At the pre-T cell stage, a critical checkpoint for β chain selection is monitored by the tumor suppressor p53: pre-T cells can survive and differentiate when p53 is removed genetically or when its proapoptotic function is inactivated physiologically as a consequence of signaling through the pre-T cell receptor complex. Previous work has shown that the guanine nucleotide binding protein Rho controls cell survival in T cell progenitors. Here we define the survival pathways controlled by Rho in pre-T cells and show that this GTPase is a pivotal regulator of the p53-mediated checkpoint operating at the time of β selection: loss of Rho function results in apoptosis in pre-T cells, but this cell death is prevented by loss of p53. The prevention of cell death by loss of p53 restored numbers of early T cell progenitors but did not fully restore thymic cellularity. Further analysis revealed that loss of Rho function caused survival defects in CD4/8 double-positive thymocytes that is independent of p53 but can be prevented by ectopic expression of Bcl-2. These studies highlight that the GTPase Rho is a crucial component of survival signaling pathways in at least two different thymocyte subpopulations: Rho controls the p53 survival checkpoint in pre-T cells and is also crucial for a p53 independent survival signaling pathway in CD4/8 double positives
Search for the lepton-family-number nonconserving decay \mu -> e + \gamma
The MEGA experiment, which searched for the muon- and electron-number
violating decay \mu -> e + \gamma, is described. The spectrometer system, the
calibrations, the data taking procedures, the data analysis, and the
sensitivity of the experiment are discussed. The most stringent upper limit on
the branching ratio of \mu -> e + \gamma) < 1.2 x 10^{-11} was obtained
Offspring Hormones Reflect the Maternal Prenatal Social Environment: Potential for Foetal Programming?
Females of many species adaptively program their offspring to predictable environmental conditions, a process that is often mediated by hormones. Laboratory studies have shown, for instance, that social density affects levels of maternal cortisol and testosterone, leading to fitness-relevant changes in offspring physiology and behaviour. However, the effects of social density remain poorly understood in natural populations due to the difficulty of disentangling confounding influences such as climatic variation and food availability. Colonially breeding marine mammals offer a unique opportunity to study maternal effects in response to variable colony densities under similar ecological conditions. We therefore quantified maternal and offspring hormone levels in 84 Antarctic fur seals (Arctocephalus gazella) from two closely neighbouring colonies of contrasting density. Hair samples were used as they integrate hormone levels over several weeks or months and therefore represent in utero conditions during foetal development. We found significantly higher levels of cortisol and testosterone (both P < 0.001) in mothers from the high density colony, reflecting a more stressful and competitive environment. In addition, offspring testosterone showed a significant positive correlation with maternal cortisol (P < 0.05). Although further work is needed to elucidate the potential consequences for offspring fitness, these findings raise the intriguing possibility that adaptive foetal programming might occur in fur seals in response to the maternal social environment. They also lend support to the idea that hormonally mediated maternal effects may depend more strongly on the maternal regulation of androgen rather than cortisol levels
c-MYC expression sensitizes medulloblastoma cells to radio- and chemotherapy and has no impact on response in medulloblastoma patients
BACKGROUND: To study whether and how c-MYC expression determines response to radio- and chemotherapy in childhood medulloblastoma (MB).
METHODS: We used DAOY and UW228 human MB cells engineered to stably express different levels of c-MYC, and tested whether c-MYC expression has an effect on radio- and chemosensitivity using the colorimetric 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) assay, clonogenic survival, apoptosis assays, cell cycle analysis, and western blot assessment. In an effort to validate our results, we analyzed c-MYC mRNA expression in formalin-fixed paraffin-embedded tumor samples from well-documented patients with postoperative residual tumor and compared c-MYC mRNA expression with response to radio- and chemotherapy as examined by neuroradiological imaging.
RESULTS: In DAOY - and to a lesser extent in UW228 - cells expressing high levels of c-MYC, the cytotoxicity of cisplatin, and etoposide was significantly higher when compared with DAOY/UW228 cells expressing low levels of c-MYC. Irradiation- and chemotherapy-induced apoptotic cell death was enhanced in DAOY cells expressing high levels of c-MYC. The response of 62 of 66 residual tumors was evaluable and response to postoperative radio- (14 responders (CR, PR) vs. 5 non-responders (SD, PD)) or chemotherapy (23 CR/PR vs. 20 SD/PD) was assessed. c-MYC mRNA expression was similar in primary MB samples of responders and non-responders (Mann-Whitney U test, p = 0.50, ratio 0.49, 95% CI 0.008-30.0 and p = 0.67, ratio 1.8, 95% CI 0.14-23.5, respectively).
CONCLUSIONS: c-MYC sensitizes MB cells to some anti-cancer treatments in vitro. As we failed to show evidence for such an effect on postoperative residual tumors when analyzed by imaging, additional investigations in xenografts and larger MB cohorts may help to define the exact function of c-MYC in modulating response to treatment
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