215 research outputs found
On Aggregation in Ensembles of Multilabel Classifiers
While a variety of ensemble methods for multilabel classification have been
proposed in the literature, the question of how to aggregate the predictions of
the individual members of the ensemble has received little attention so far. In
this paper, we introduce a formal framework of ensemble multilabel
classification, in which we distinguish two principal approaches: "predict then
combine" (PTC), where the ensemble members first make loss minimizing
predictions which are subsequently combined, and "combine then predict" (CTP),
which first aggregates information such as marginal label probabilities from
the individual ensemble members, and then derives a prediction from this
aggregation. While both approaches generalize voting techniques commonly used
for multilabel ensembles, they allow to explicitly take the target performance
measure into account. Therefore, concrete instantiations of CTP and PTC can be
tailored to concrete loss functions. Experimentally, we show that standard
voting techniques are indeed outperformed by suitable instantiations of CTP and
PTC, and provide some evidence that CTP performs well for decomposable loss
functions, whereas PTC is the better choice for non-decomposable losses.Comment: 14 pages, 2 figure
Heterogeneous Aspirations Promote Cooperation in the Prisoner's Dilemma Game
To be the fittest is central to proliferation in evolutionary games. Individuals
thus adopt the strategies of better performing players in the hope of successful
reproduction. In structured populations the array of those that are eligible to
act as strategy sources is bounded to the immediate neighbors of each
individual. But which one of these strategy sources should potentially be
copied? Previous research dealt with this question either by selecting the
fittest or by selecting one player uniformly at random. Here we introduce a
parameter that interpolates between these two extreme options.
Setting equal to zero returns the random selection of the
opponent, while positive favor the fitter
players. In addition, we divide the population into two groups. Players from
group select their opponents as dictated by the parameter
, while players from group
do so randomly irrespective of
. We denote the fraction of players contained in groups
and by
and , respectively. The
two parameters and
allow us to analyze in detail how aspirations in the
context of the prisoner's dilemma game influence the evolution of
cooperation. We find that for sufficiently positive values of
there exist a robust intermediate
for which cooperation thrives best. The robustness of
this observation is tested against different levels of uncertainty in the
strategy adoption process and for different
interaction networks. We also provide complete phase diagrams depicting the
dependence of the impact of and
for different values of , and contrast the
validity of our conclusions by means of an alternative model where individual
aspiration levels are subject to evolution as well. Our study indicates that
heterogeneity in aspirations may be key for the sustainability of cooperation in
structured populations
Structure of bryozoan communities in an Antarctic glacial fjord (Admiralty Bay, South Shetlands)
Bryozoans are among the most important groups of the Southern Ocean benthic macrofauna, both in terms of species richness and abundance. However, there is a considerable lack of ecological research focused on their distribution patterns and species richness on smaller scale, especially in the soft bottom habitats of Antarctic glacial fjords. The aim of this study was to describe those patterns in the Admiralty Bay. Forty-nine Van Veen grab samples were collected at the depth range from 15 to 265 m, in the summer season of 1979/1980, at three sites distributed along the main axis of the fjord. Among 53 identified species of bryozoans, 32 were recorded in the Admiralty Bay for the first time. The most common and abundant species were Himantozoum antarcticum, Inversiula nutrix and Nematoflustra flagellata. Genera such as Arachnopusia, Cellarinella and Osthimosia were the most speciose taxa. It was demonstrated that depth was important for the distribution of the bryozoans. More than half of the recorded species were found only below 70 m. An influence of glacial disturbance was reflected in the dominance structure of colony growth-forms. The inner region of the fjord was dominated almost entirely by encrusting species, while the diversity of bryozoan growth-forms in less disturbed areas was much higher. In those sites the highest percentage of branched, tuft like species represented by buguliform and flustriform zoaria was observed.The study was supported by a grant of Polish Ministry of Science and Higher Education No. 51/N-IPY/2007/0 as well as Census of Antarctic Marine Life Project. Krzysztof Pabis was also partially supported by University of Lodz internal funds. This research was also supported by the Polish Geological Institute-National Research Institute during the realization of the project numbered 40.2900.0903.18.0 titled âBryozoan assemblage of Admiralty Bayârichness, diversity and abundance.â Urszula Hara is deeply grateful to Leszek Giro (Micro-area Analyses Laboratory at the Polish Geological Institute-National Research Institute, Warsaw), for providing SEM assistance during the project. We also want to thank two anonymous reviewers for their suggestions that helped us improve this article. Thanks are also due to Magdalena BĆaĆŒewicz-Paszkowycz for language correction and polishing the final version of the manuscript
Acidic Digestion in a Teleost: Postprandial and Circadian Pattern of Gastric pH, Pepsin Activity, and Pepsinogen and Proton Pump mRNAs Expression
Two different modes for regulation of stomach acid secretion have been described in vertebrates. Some species exhibit a continuous acid secretion maintaining a low gastric pH during fasting. Others, as some teleosts, maintain a neutral gastric pH during fasting while the hydrochloric acid is released only after the ingestion of a meal. Those different patterns seem to be closely related to specific feeding habits. However, our recent observations suggest that this acidification pattern could be modified by changes in daily feeding frequency and time schedule. The aim of this study was to advance in understanding the regulation mechanisms of stomach digestion and pattern of acid secretion in teleost fish. We have examined the postprandial pattern of gastric pH, pepsin activity, and mRNA expression for pepsinogen and proton pump in white seabream juveniles maintained under a light/dark 12/12 hours cycle and receiving only one morning meal. The pepsin activity was analyzed according to the standard protocol buffering at pH 2 and using the actual pH measured in the stomach. The results show how the enzyme precursor is permanently available while the hydrochloric acid, which activates the zymogen fraction, is secreted just after the ingestion of food. Results also reveal that analytical protocol at pH 2 notably overestimates true pepsin activity in fish stomach. The expression of the mRNA encoding pepsinogen and proton pump exhibited almost parallel patterns, with notable increases during the darkness period and sharp decreases just before the morning meal. These results indicate that white seabream uses the resting hours for recovering the mRNA stock that will be quickly used during the feeding process. Our data clearly shows that both daily illumination pattern and feeding time are involved at different level in the regulation of the secretion of digestive juices
Lymphatic vessel density and function in experimental bladder cancer
<p>Abstract</p> <p>Background</p> <p>The lymphatics form a second circulatory system that drains the extracellular fluid and proteins from the tumor microenvironment, and provides an exclusive environment in which immune cells interact and respond to foreign antigen. Both cancer and inflammation are known to induce lymphangiogenesis. However, little is known about bladder lymphatic vessels and their involvement in cancer formation and progression.</p> <p>Methods</p> <p>A double transgenic mouse model was generated by crossing a bladder cancer-induced transgenic, in which SV40 large T antigen was under the control of uroplakin II promoter, with another transgenic mouse harboring a <it>lacZ </it>reporter gene under the control of an NF-ÎșB-responsive promoter (ÎșB-<it>lacZ</it>) exhibiting constitutive activity of ÎČ-galactosidase in lymphatic endothelial cells. In this new mouse model (SV40-<it>lacZ</it>), we examined the lymphatic vessel density (LVD) and function (LVF) during bladder cancer progression. LVD was performed in bladder whole mounts and cross-sections by fluorescent immunohistochemistry (IHC) using LYVE-1 antibody. LVF was assessed by real-time <it>in vivo </it>imaging techniques using a contrast agent (biotin-BSA-Gd-DTPA-Cy5.5; Gd-Cy5.5) suitable for both magnetic resonance imaging (MRI) and near infrared fluorescence (NIRF). In addition, IHC of Cy5.5 was used for time-course analysis of co-localization of Gd-Cy5.5 with LYVE-1-positive lymphatics and CD31-positive blood vessels.</p> <p>Results</p> <p>SV40-<it>lacZ </it>mice develop bladder cancer and permitted visualization of lymphatics. A significant increase in LVD was found concomitantly with bladder cancer progression. Double labeling of the bladder cross-sections with LYVE-1 and Ki-67 antibodies indicated cancer-induced lymphangiogenesis. MRI detected mouse bladder cancer, as early as 4 months, and permitted to follow tumor sizes during cancer progression. Using Gd-Cy5.5 as a contrast agent for MRI-guided lymphangiography, we determined a possible reduction of lymphatic flow within the tumoral area. In addition, NIRF studies of Gd-Cy5.5 confirmed its temporal distribution between CD31-positive blood vessels and LYVE-1 positive lymphatic vessels.</p> <p>Conclusion</p> <p>SV40-<it>lacZ </it>mice permit the visualization of lymphatics during bladder cancer progression. Gd-Cy5.5, as a double contrast agent for NIRF and MRI, permits to quantify delivery, transport rates, and volumes of macromolecular fluid flow through the interstitial-lymphatic continuum. Our results open the path for the study of lymphatic activity <it>in vivo </it>and in real time, and support the role of lymphangiogenesis during bladder cancer progression.</p
RNA metabolism is the primary target of formamide in vivo
The synthesis, processing and function of coding and non-coding RNA molecules and their interacting proteins has been the focus of a great deal of research that has boosted our understanding of key molecular pathways that underlie higher order events such as cell cycle control, development, innate immune response and the occurrence of genetic diseases. In this study, we have found that formamide preferentially weakens RNA related processes in vivo. Using a non-essential Schizosaccharomyces pombe gene deletion collection, we identify deleted loci that make cells sensitive to formamide. Sensitive deletions are significantly enriched in genes involved in RNA metabolism. Accordingly, we find that previously known temperature-sensitive splicing mutants become lethal in the presence of the drug under permissive temperature. Furthermore, in a wild type background, splicing efficiency is decreased and R-loop formation is increased in the presence of formamide. In addition, we have also isolated 35 formamide-sensitive mutants, many of which display remarkable morphology and cell cycle defects potentially unveiling new players in the regulation of these processes. We conclude that formamide preferentially targets RNA related processes in vivo, probably by relaxing RNA secondary structures and/or RNA-protein interactions, and can be used as an effective tool to characterize these processes
Age and date for early arrival of the Acheulian in Europe (Barranc de la Boella, la Canonja, Spain)
The first arrivals of hominin populations into Eurasia during the Early Pleistocene are currently considered to have occurred
as short and poorly dated biological dispersions. Questions as to the tempo and mode of these early prehistoric settlements
have given rise to debates concerning the taxonomic significance of the lithic assemblages, as trace fossils, and the
geographical distribution of the technological traditions found in the Lower Palaeolithic record. Here, we report on the
Barranc de la Boella site which has yielded a lithic assemblage dating to ,1 million years ago that includes large cutting
tools (LCT). We argue that distinct technological traditions coexisted in the Iberian archaeological repertoires of the late
Early Pleistocene age in a similar way to the earliest sub-Saharan African artefact assemblages. These differences between
stone tool assemblages may be attributed to the different chronologies of hominin dispersal events. The archaeological
record of Barranc de la Boella completes the geographical distribution of LCT assemblages across southern Eurasia during
the EMPT (Early-Middle Pleistocene Transition, circa 942 to 641 kyr). Up to now, chronology of the earliest European LCT
assemblages is based on the abundant Palaeolithic record found in terrace river sequences which have been dated to the
end of the EMPT and later. However, the findings at Barranc de la Boella suggest that early LCT lithic assemblages appeared
in the SW of Europe during earlier hominin dispersal episodes before the definitive colonization of temperate Eurasia took
place.The research at Barranc de la Boella has been carried out with the financial support of the Spanish Ministerio de EconomıŽa y Competitividad (CGL2012-
36682; CGL2012-38358, CGL2012-38434-C03-03 and CGL2010-15326; MICINN project HAR2009-7223/HIST), Generalitat de Catalunya, AGAUR agence (projects
2014SGR-901; 2014SGR-899; 2009SGR-324, 2009PBR-0033 and 2009SGR-188) and Junta de Castilla y LeoÂŽn BU1004A09. Financial support for Barranc de la Boella
field work and archaeological excavations is provided by the Ajuntament de la Canonja and Departament de Cultura (Servei dâArqueologia i Paleontologia) de la
Generalitat de Catalunya. A. Carranchoâs research was funded by the International Excellence Programme, Reinforcement subprogramme of the Spanish Ministry
of Education. I. Lozano-FernaÂŽndez acknowledges the pre-doctoral grant from the FundacioÂŽn Atapuerca. The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript
ErbB2, EphrinB1, Src Kinase and PTPN13 Signaling Complex Regulates MAP Kinase Signaling in Human Cancers
In non-cancerous cells, phosphorylated proteins exist transiently, becoming de-phosphorylated by specific phosphatases that terminate propagation of signaling pathways. In cancers, compromised phosphatase activity and/or expression occur and contribute to tumor phenotype. The non-receptor phosphatase, PTPN13, has recently been dubbed a putative tumor suppressor. It decreased expression in breast cancer correlates with decreased overall survival. Here we show that PTPN13 regulates a new signaling complex in breast cancer consisting of ErbB2, Src, and EphrinB1. To our knowledge, this signaling complex has not been previously described. Co-immunoprecipitation and localization studies demonstrate that EphrinB1, a PTPN13 substrate, interacts with ErbB2. In addition, the oncogenic V660E ErbB2 mutation enhances this interaction, while Src kinase mediates EphrinB1 phosphorylation and subsequent MAP Kinase signaling. Decreased PTPN13 function further enhances signaling. The association of oncogene kinases (ErbB2, Src), a signaling transmembrane ligand (EphrinB1) and a phosphatase tumor suppressor (PTPN13) suggest that EphrinB1 may be a relevant therapeutic target in breast cancers harboring ErbB2-activating mutations and decreased PTPN13 expression
An ultrahot Neptune in the Neptune desert
About one out of 200 Sun-like stars has a planet with an orbital period
shorter than one day: an ultra-short-period planet (Sanchis-ojeda et al. 2014;
Winn et al. 2018). All of the previously known ultra-short-period planets are
either hot Jupiters, with sizes above 10 Earth radii (Re), or apparently rocky
planets smaller than 2 Re. Such lack of planets of intermediate size (the "hot
Neptune desert") has been interpreted as the inability of low-mass planets to
retain any hydrogen/helium (H/He) envelope in the face of strong stellar
irradiation. Here, we report the discovery of an ultra-short-period planet with
a radius of 4.6 Re and a mass of 29 Me, firmly in the hot Neptune desert. Data
from the Transiting Exoplanet Survey Satellite (Ricker et al. 2015) revealed
transits of the bright Sun-like star \starname\, every 0.79 days. The planet's
mean density is similar to that of Neptune, and according to thermal evolution
models, it has a H/He-rich envelope constituting 9.0^(+2.7)_(-2.9)% of the
total mass. With an equilibrium temperature around 2000 K, it is unclear how
this "ultra-hot Neptune" managed to retain such an envelope. Follow-up
observations of the planet's atmosphere to better understand its origin and
physical nature will be facilitated by the star's brightness (Vmag=9.8)
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