1,051 research outputs found
Unifying Parsimonious Tree Reconciliation
Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach to address this research problem is to describe each individual
evolution as a phylogenetic tree and construct a tree reconciliation which is
parsimonious with respect to a given event model. Unfortunately, most of the
previous approaches are designed only either for host-parasite systems, for
gene tree/species tree reconciliation, or biogeography. Hence, a method is
desirable, which addresses the general problem of mapping phylogenetic trees
and covering all varieties of coevolving systems, including e.g., predator-prey
and symbiotic relationships. To overcome this gap, we introduce a generalized
cophylogenetic event model considering the combinatorial complete set of local
coevolutionary events. We give a dynamic programming based heuristic for
solving the maximum parsimony reconciliation problem in time O(n^2), for two
phylogenies each with at most n leaves. Furthermore, we present an exact
branch-and-bound algorithm which uses the results from the dynamic programming
heuristic for discarding partial reconciliations. The approach has been
implemented as a Java application which is freely available from
http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Distributed Management of Massive Data: an Efficient Fine-Grain Data Access Scheme
This paper addresses the problem of efficiently storing and accessing massive
data blocks in a large-scale distributed environment, while providing efficient
fine-grain access to data subsets. This issue is crucial in the context of
applications in the field of databases, data mining and multimedia. We propose
a data sharing service based on distributed, RAM-based storage of data, while
leveraging a DHT-based, natively parallel metadata management scheme. As
opposed to the most commonly used grid storage infrastructures that provide
mechanisms for explicit data localization and transfer, we provide a
transparent access model, where data are accessed through global identifiers.
Our proposal has been validated through a prototype implementation whose
preliminary evaluation provides promising results
Human phosphodiesterase 4D7 (PDE4D7) expression is increased in TMPRSS2-ERG positive primary prostate cancer and independently adds to a reduced risk of post-surgical disease progression
background: There is an acute need to uncover biomarkers that reflect the molecular pathologies, underpinning prostate cancer progression and poor patient outcome. We have previously demonstrated that in prostate cancer cell lines PDE4D7 is downregulated in advanced cases of the disease. To investigate further the prognostic power of PDE4D7 expression during prostate cancer progression and assess how downregulation of this PDE isoform may affect disease outcome, we have examined PDE4D7 expression in physiologically relevant primary human samples.
methods: About 1405 patient samples across 8 publically available qPCR, Affymetrix Exon 1.0 ST arrays and RNA sequencing data sets were screened for PDE4D7 expression. The TMPRSS2-ERG gene rearrangement status of patient samples was determined by transformation of the exon array and RNA seq expression data to robust z-scores followed by the application of a threshold >3 to define a positive TMPRSS2-ERG gene fusion event in a tumour sample.
results: We demonstrate that PDE4D7 expression positively correlates with primary tumour development. We also show a positive association with the highly prostate cancer-specific gene rearrangement between TMPRSS2 and the ETS transcription factor family member ERG. In addition, we find that in primary TMPRSS2-ERG-positive tumours PDE4D7 expression is significantly positively correlated with low-grade disease and a reduced likelihood of progression after primary treatment. Conversely, PDE4D7 transcript levels become significantly decreased in castration resistant prostate cancer (CRPC).
conclusions: We further characterise and add physiological relevance to PDE4D7 as a novel marker that is associated with the development and progression of prostate tumours. We propose that the assessment of PDE4D7 levels may provide a novel, independent predictor of post-surgical disease progression
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Defect production and electronic stopping for light ions in metals
A method for determining effective electronic stopping powers in metals is presented. The method involves measuring damage rates in thin films as a function of ion energy. The experimental results are compared with predictions based on Monte Carlo computer simulations. Results are presented for H, D, He, and Li projectiles on Cu, Ag, and Ni. The implication of these results for defect production is discussed
Archiving and referencing source code with Software Heritage
Software, and software source code in particular, is widely used in modern
research. It must be properly archived, referenced, described and cited in
order to build a stable and long lasting corpus of scientic knowledge. In this
article we show how the Software Heritage universal source code archive
provides a means to fully address the first two concerns, by archiving
seamlessly all publicly available software source code, and by providing
intrinsic persistent identifiers that allow to reference it at various
granularities in a way that is at the same time convenient and effective. We
call upon the research community to adopt widely this approach.Comment: arXiv admin note: substantial text overlap with arXiv:1909.1076
Local forage fish abundance influences foraging effort and offspring condition in an endangered marine predator
This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.All data will be archived in the Dryad Digital Repository and BirdLife Seabird Tracking
Database.1. Understanding the functional relationship between marine predators and their prey is vital
to inform ecosystem-based management. However, collecting concurrent data on predator
behaviour and their prey at relevant scales is challenging. Moreover, opportunities to study
these relationships in the absence of industrial fishing are extremely rare.
2. We took advantage of an experimental fisheries closure to study how local prey abundance
influences foraging success and chick condition of Endangered African penguins Spheniscus
demersus in the Benguela Ecosystem.
3. We tracked 75 chick-provisioning penguins with GPS-time-depth devices, measured body
condition of 569 chicks, quantified the diet of 83 breeding penguins and conducted 12 forage
fish hydro-acoustic surveys within a 20 km radius of Robben Island, South Africa, over three
years (2011â2013). Commercial fishing for the penguinsâ main prey, sardine Sardinops sagax
and anchovy Engraulis encrasicolus, was prohibited within this 20 km radius during the study
period.
4. Local forage fish abundance explained 60% of the variation in time spent diving for 14
penguins at sea within 2 days of a hydro-acoustic survey. Penguin foraging effort (time spent
diving, number of wiggles per trip, number of foraging dives and the maximum distance
travelled) increased and offspring body condition decreased as forage fish abundance
declined. In addition, quantile regression revealed that variation in foraging effort increased as
prey abundance around the colony declined.
5. Policy implications. Our results demonstrate that local forage fish abundance influences
seabird foraging and offspring fitness. They also highlight the potential for offspring condition
and the mean-variance relationship in foraging behaviour to act as leading indicators of poor
prey abundance. By rapidly indicating periods where forage resources are scarce, these
metrics could help limit seabird-fisheries competition and aid the implementation of dynamic
ocean managemen
Breakdown of the Landauer bound for information erasure in the quantum regime
A known aspect of the Clausius inequality is that an equilibrium system
subjected to a squeezing \d S of its entropy must release at least an amount
|\dbarrm Q|=T|\d S| of heat. This serves as a basis for the Landauer
principle, which puts a lower bound for the heat generated by erasure
of one bit of information. Here we show that in the world of quantum
entanglement this law is broken. A quantum Brownian particle interacting with
its thermal bath can either generate less heat or even {\it adsorb} heat during
an analogous squeezing process, due to entanglement with the bath. The effect
exists even for weak but fixed coupling with the bath, provided that
temperature is low enough. This invalidates the Landauer bound in the quantum
regime, and suggests that quantum carriers of information can be much more
efficient than assumed so far.Comment: 13 pages, revtex, 2 eps figure
In vivo 1H NMR spectroscopy of the human brain at 7 T
In vivo 1H NMR spectra from the human brain were measured at 7 T. Ultrashort echo-time STEAM was used to minimize J-modulation and signal attenuation caused by the shorter T2 of metabolites. Precise adjustment of higher-order shims, which was achieved with FASTMAP, was crucial to benefit from this high magnetic field. Sensitivity improvements were evident from single-shot spectra and from the direct detection of glucose at 5.23 ppm in 8-ml volumes. The linewidth of the creatine methyl resonance was at best 9 Hz. In spite of the increased linewidth of singlet resonances at 7 T, the ability to resolve overlapping multiplets of J-coupled spin systems, such as glutamine and glutamate, was substantially increased. Characteristic spectral patterns of metabolites, e.g., myo-inositol and taurine, were discernible in the in vivo spectra, which facilitated an unambiguous signal assignment. © 2001 Wiley-Liss, Inc
Human phosphodiesterase 4D7 (PDE4D7) expression is increased in TMPRSS2-ERG-positive primary prostate cancer and independently adds to a reduced risk of post-surgical disease progression
Background:There is an acute need to uncover biomarkers that reflect the molecular pathologies, underpinning prostate cancer progression and poor patient outcome. We have previously demonstrated that in prostate cancer cell lines PDE4D7 is downregulated in advanced cases of the disease. To investigate further the prognostic power of PDE4D7 expression during prostate cancer progression and assess how downregulation of this PDE isoform may affect disease outcome, we have examined PDE4D7 expression in physiologically relevant primary human samples.Methods:About 1405 patient samples across 8 publically available qPCR, Affymetrix Exon 1.0 ST arrays and RNA sequencing data sets were screened for PDE4D7 expression. The TMPRSS2-ERG gene rearrangement status of patient samples was determined by transformation of the exon array and RNA seq expression data to robust z-scores followed by the application of a threshold >3 to define a positive TMPRSS2-ERG gene fusion event in a tumour sample.Results:We demonstrate that PDE4D7 expression positively correlates with primary tumour development. We also show a positive association with the highly prostate cancer-specific gene rearrangement between TMPRSS2 and the ETS transcription factor family member ERG. In addition, we find that in primary TMPRSS2-ERG-positive tumours PDE4D7 expression is significantly positively correlated with low-grade disease and a reduced likelihood of progression after primary treatment. Conversely, PDE4D7 transcript levels become significantly decreased in castration resistant prostate cancer (CRPC).Conclusions:We further characterise and add physiological relevance to PDE4D7 as a novel marker that is associated with the development and progression of prostate tumours. We propose that the assessment of PDE4D7 levels may provide a novel, independent predictor of post-surgical disease progression
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