Approximate decoding approaches for network coded correlated data

This paper considers a framework where data from correlated sources are transmitted with the help of network coding in ad hoc network topologies. The correlated data are encoded independently at sensors and network coding is employed in the intermediate nodes in order to improve the data delivery performance. In such settings, we focus on the problem of reconstructing the sources at decoder when perfect decoding is not possible due to losses or bandwidth variations. We show that the source data similarity can be used at decoder to permit decoding based on a novel and simple approximate decoding scheme. We analyze the influence of the network coding parameters and in particular the size of finite coding fields on the decoding performance. We further determine the optimal field size that maximizes the expected decoding performance as a trade-off between information loss incurred by limiting the resolution of the source data and the error probability in the reconstructed data. Moreover, we show that the performance of the approximate decoding improves when the accuracy of the source model increases even with simple approximate decoding techniques. We provide illustrative examples showing how the proposed algorithm can be deployed in sensor networks and distributed imaging applications.

A test of genetic association among male nuptial coloration, female mating preference, and male aggression bias within a polymorphic population of cichlid fish

Both inter- and intrasexual selection have been implicated in the origin and maintenance of species-rich taxa with diverse sexual traits. Simultaneous disruptive selection by female mate choice and male-male competition can, in theory, lead to speciation without geographical isolation if both act on the same male trait. Female mate choice can generate discontinuities in gene flow, while male-male competition can generate negative frequency-dependent selection stabilizing the male trait polymorphism. Speciation may be facilitated when mating preference and/or aggression bias are physically linked to the trait they operate on. We tested for genetic associations among female mating preference, male aggression bias and male coloration in the Lake Victoria cichlid Pundamilia. We crossed females from a phenotypically variable population with males from both extreme ends of the phenotype distribution in the same population (blue or red). Male offspring of a red sire were significantly redder than males of a blue sire, indicating that intra-population variation in male coloration is heritable. We tested mating preferences of female offspring and aggression biases of male offspring using binary choice tests. There was no evidence for associations at the family level between female mating preferences and coloration of sires, but dam identity had a significant effect on female mate preference. Sons of the red sire directed significantly more aggression to red than blue males, whereas sons of the blue sire did not show any bias. There was a positive correlation among individuals between male aggression bias and body coloration, possibly due to pleiotropy or physical linkage, which could facilitate the maintenance of color polymorphism.

Female preference for male color is necessary and sufficient for assortative mating in 2 cichlid sister species

A critical step for speciation in the face of gene flow is the origination of reproductive isolation. The evolution of assortative mating greatly facilitates this process. Assortative mating can be mediated by one or multiple cues across an array of sensory modalities. We here explore possible cues that may underlie female mate choice in a sympatric species pair of cichlid fish from Lake Victoria, Pundamilia pundamilia and Pundamilia nyererei. Previous studies identified species-specific female preferences for male coloration, but effects of other cues could not be ruled out. Therefore, we assessed female choice in a series of experiments in which we manipulated visual (color) and chemical cues. We show that the visibility of differences in nuptial hue (i.e., either blue or red) between males of the 2 species is necessary and sufficient for assortative mating by female mate choice. Such assortment mediated by a single cue may evolve relatively quickly, but could make reproductive isolation vulnerable to environmental changes. These findings confirm the important role of female mate choice for male nuptial hue in promoting the explosive speciation of African haplochromine cichlids.

Inheritance of female mating preference in a sympatric sibling species pair of Lake Victoria cichlids: implications for speciation

Female mate choice has often been proposed to play an important role in cases of rapid speciation, in particular in the explosively evolved haplochromine cichlid species flocks of the Great Lakes of East Africa. Little, if anything, is known in cichlid radiations about the heritability of female mating preferences. Entirely sympatric distribution, large ecological overlap and conspicuous differences in male nuptial coloration, and female preferences for these, make the sister species Pundamilia pundamilia and P. nyererei from Lake Victoria an ideally suited species pair to test assumptions on the genetics of mating preferences made in models of sympatric speciation. Female mate choice is necessary and sufficient to maintain reproductive isolation between these species, and it is perhaps not unlikely therefore, that female mate choice has been important during speciation. A prerequisite for this, which had remained untested in African cichlid fish, is that variation in female mating preferences is heritable. We investigated mating preferences of females of these sister species and their hybrids to test this assumption of most sympatric speciation models, and to further test the assumption of some models of sympatric speciation by sexual selection that female preference is a single-gene trait. We find that the differences in female mating preferences between the sister species are heritable, possibly with quite high heritabilities, and that few but probably more than one genetic loci contribute to this behavioural speciation trait with no apparent dominance. We discuss these results in the light of speciation models and the debate about the explosive radiation of cichlid fishes in Lake Victoria.

Immunostaining of a heterodimeric dermatan sulphate proteoglycan is correlated with smooth muscles and some basement membranes.

A heterodimeric 760-kDa dermatan sulphate proteoglycan tentatively named PG-760 was characterized as a product of keratinocytes, endothelial cells, and fibroblasts. The two core proteins of 460 kDa and 300 kDa are linked by disulphide bridges, and both carry one or only very few dermatan sulphate chains. Different antisera against PG-760 were used in the present study to investigate the distribution in selected murine tissues by light and electron microscopy. PG-760 immunostaining was observed in cornea (epithelium including basement membrane, stroma, and Descemet's membrane), skin, mucosa of the small intestine, Engelbreth-Holm-Swarm (EHS)-tumour (matrix and cells), and the smooth muscle layers of uterus, small intestine, and blood vessels. No staining was observed in capillaries, striated muscles, and liver parenchyma including the central vein. The expression of PG-760 in EHS-tumour was also demonstrated after extraction with 4 M guanidine and partial purification by diethylaminoethyl (DEAE)-chromatography. We conclude that this novel proteoglycan exhibits a unique tissue distribution being a constituent of some but not all basement membranes, of some other extracellular matrices, and additionally, of all investigated smooth muscle layers.

EVOLUTION OF DOMINANCE UNDER FREQUENCY-DEPENDENT INTRASPECIFIC COMPETITION IN AN ASSORTATIVELY MATING POPULATION

We study the evolution of higher levels of dominance as a response to negative frequency-dependent selection. In contrast to previous studies, we focus on the effect of assortative mating on the evolution of dominance under frequency-dependent intraspecific competition. We analyze a two-locus two-allele model, in which the primary locus has a major effect on a quantitative trait that is under a mixture of frequency-independent stabilizing selection, density-dependent selection, and frequency-dependent selection caused by intraspecific competition for a continuum of resources. The second (modifier) locus determines the degree of dominance at the trait level. Additionally, the population mates assortatively with respect to similarities in the ecological trait. Our analysis shows that the parameter region in which dominance can be established decreases if small levels of assortment are introduced. In addition, the degree of dominance that can be established also decreases. In contrast, if assortment is intermediate, sexual selection for extreme types can be established, which leads to evolution of higher levels of dominance than under random mating. For modifiers with large effects, intermediate levels of assortative mating are most favorable for the evolution of dominance. For large modifiers, the speed of fixation can even be higher for intermediate levels of assortative mating than for random mating.

Tritrichomonas foetus: Prevalence study in naturally mating bulls in Switzerland

Switzerland is officially free from bovine Tritrichomonas foetus. While bulls used for artificial insemination (AI) are routinely examined for this pathogen, bulls engaged in natural mating, as well as aborted fetuses, are only very sporadically investigated, indicating that the disease awareness for bovine tritrichomoniasis is low. Natural mating in cattle is becoming increasingly popular in Switzerland. Accordingly, a re-introduction/re-occurrence of T. foetus in cattle seems possible either via resurgence from a yet unknown bovine reservoir, or via importation of infected cattle. The low disease awareness for bovine tritrichomoniasis might favor an unnoticed re-establishment of T. foetus in the Swiss cattle population. The aim of our study was thus to search for the parasite, and if found, to assess the prevalence of bovine T. foetus in Switzerland. We included (1) bulls over two years of age used in natural mating and sent to slaughter, (2) bulls used for natural service in herds with or without fertility problems and (3) aborted fetuses. Furthermore, the routinely examined bulls used for AI (4) were included in this study. In total, 1362 preputial samples from bulls and 60 abomasal fluid samples of aborted fetuses were analyzed for the presence of T. foetus by both in vitro cultivation and molecular analyses. The parasite could not be detected in any of the samples, indicating that the maximal prevalence possibly missed was about 0.3% (95% confidence). Interestingly, in preputial samples of three bulls of category 1, apathogenic Tetratrichomonas sp. was identified, documenting a proof-of-principle for the methodology used in this study.

Myoglobin expression in prostate cancer is correlated to androgen receptor expression and markers of tumor hypoxia.

Recent studies identified unexpected expression and transcriptional complexity of the hemoprotein myoglobin (MB) in human breast cancer but its role in prostate cancer is still unclear. Expression of MB was immunohistochemically analyzed in three independent cohorts of radical prostatectomy specimens (n = 409, n = 625, and n = 237). MB expression data were correlated with clinicopathological parameters and molecular parameters of androgen and hypoxia signaling. Expression levels of novel tumor-associated MB transcript variants and the VEGF gene as a hypoxia marker were analyzed using qRT-PCR. Fifty-three percent of the prostate cancer cases were MB positive and significantly correlated with androgen receptor (AR) expression (p < 0.001). The positive correlation with CAIX (p < 0.001) and FASN (p = 0.008) as well as the paralleled increased expression of the tumor-associated MB transcript variants and VEGF suggest that hypoxia participates in MB expression regulation. Analogous to breast cancer, MB expression in prostate cancer is associated with steroid hormone signaling and markers of hypoxia. Further studies must elucidate the novel functional roles of MB in human carcinomas, which probably extend beyond its classic intramuscular function in oxygen storage.

Competitive fitness in coronaviruses is not correlated with size or number of double-membrane vesicles under reduced-temperature growth conditions.

Positive-stranded viruses synthesize their RNA in membrane-bound organelles, but it is not clear how this benefits the virus or the host. For coronaviruses, these organelles take the form of double-membrane vesicles (DMVs) interconnected by a convoluted membrane network. We used electron microscopy to identify murine coronaviruses with mutations in nsp3 and nsp14 that replicated normally while producing only half the normal amount of DMVs under low-temperature growth conditions. Viruses with mutations in nsp5 and nsp16 produced small DMVs but also replicated normally. Quantitative reverse transcriptase PCR (RT-PCR) confirmed that the most strongly affected of these, the nsp3 mutant, produced more viral RNA than wild-type virus. Competitive growth assays were carried out in both continuous and primary cells to better understand the contribution of DMVs to viral fitness. Surprisingly, several viruses that produced fewer or smaller DMVs showed a higher fitness than wild-type virus at the reduced temperature, suggesting that larger and more numerous DMVs do not necessarily confer a competitive advantage in primary or continuous cell culture. For the first time, this directly demonstrates that replication and organelle formation may be, at least in part, studied separately during infection with positive-stranded RNA virus. IMPORTANCE The viruses that cause severe acute respiratory syndrome (SARS), poliomyelitis, and hepatitis C all replicate in double-membrane vesicles (DMVs). The big question about DMVs is why they exist in the first place. In this study, we looked at thousands of infected cells and identified two coronavirus mutants that made half as many organelles as normal and two others that made typical numbers but smaller organelles. Despite differences in DMV size and number, all four mutants replicated as efficiently as wild-type virus. To better understand the relative importance of replicative organelles, we carried out competitive fitness experiments. None of these viruses was found to be significantly less fit than wild-type, and two were actually fitter in tests in two kinds of cells. This suggests that viruses have evolved to have tremendous plasticity in the ability to form membrane-associated replication complexes and that large and numerous DMVs are not exclusively associated with efficient coronavirus replication.

Geographic variation in floral allometry suggests repeated transitions between selfing and outcrossing in a mixed mating plant

• Premise of the study: Isometric and allometric scaling of a conserved floral plan could provide a parsimonious mechanism for rapid and reversible transitions between breeding systems. This scaling may occur during transitions between predominant autogamy and xenogamy, contributing to the maintenance of a stable mixed mating system. • Methods: We compared nine disjunct populations of the polytypic, mixed mating species Oenothera flava (Onagraceae) to two parapatric relatives, the obligately xenogamous species O. acutissima and the mixed mating species O. triloba. We compared floral morphology of all taxa using principal component analysis (PCA) and developmental trajectories of floral organs using ANCOVA homogeneity of slopes. • Key results: The PCA revealed both isometric and allometric scaling of a conserved floral plan. Three principal components (PCs) explained 92.5% of the variation in the three species. PC1 predominantly loaded on measures of floral size and accounts for 36% of the variation. PC2 accounted for 35% of the variation, predominantly in traits that influence pollinator handling. PC3 accounted for 22% of the variation, primarily in anther–stigma distance (herkogamy). During O. flava subsp. taraxacoides development, style elongation was accelerated relative to anthers, resulting in positive herkogamy. During O. flava subsp. flava development, style elongation was decelerated, resulting in zero or negative herkogamy. Of the two populations with intermediate morphology, style elongation was accelerated in one population and decelerated in the other. • Conclusions: Isometric and allometric scaling of floral organs in North American Oenothera section Lavauxia drive variation in breeding system. Multiple developmental paths to intermediate phenotypes support the likelihood of multiple mating system transitions.

Implicit probabilistic sequence learning: Correlated streams and sequence length matter

We investigated whether a pure perceptual stream is sufficient for probabilistic sequence learning to occur within a single session or whether correlated streams are necessary, whether learning is affected by the transition probability between sequence elements, and how the sequence length influences learning. In each of three experiments, we used six horizontally arranged stimulus displays which consisted of randomly ordered bigrams xo and ox. The probability of the next possible target location out of two was either .50/.50 or .75/.25 and was marked by an underline. In Experiment 1, a left vs. right key response was required for the x of a marked bigram in the pure perceptual learning condition and a response key press corresponding to the marked bigram location (out of 6) was required in the correlated streams condition (i.e., the ring, middle, or index finger of the left and right hand, respectively). The same probabilistic 3-element sequence was used in both conditions. Learning occurred only in the correlated streams condition. In Experiment 2, we investigated whether sequence length affected learning correlated sequences by contrasting the 3-elements sequence with a 6-elements sequence. Significant sequence learning occurred in all conditions. In Experiment 3, we removed a potential confound, that is, the sequence of hand changes. Under these conditions, learning occurred for the 3-element sequence only and transition probability did not affect the amount of learning. Together, these results indicate that correlated streams are necessary for probabilistic sequence learning within a single session and that sequence length can reduce the chances for learning to occur.

Correlated cosmogenic W and Os isotopic variations in Carbo and implications for Hf-W chronology

An obstacle for establishing the chronology of iron meteorite formation using 182Hf-182W systematics (t1/2 = 8.9 Myr) is to find proper neutron fluence monitors to correct for cosmic ray modification of W isotopic composition. Recent studies showed that siderophile elements such as Pt and Os could serve such a purpose. To test and calibrate these neutron dosimeters, the isotopic compositions of W and Os were measured in a slab of the IID iron meteorite Carbo. This slab has a well-characterized noble gas depth profile reflecting different degrees of shielding to cosmic rays. The results show that W and Os isotopic ratios correlate with distance from the pre-atmospheric center. Negative correlations, barely resolved within error, were found between epsilo190Os-epsilo189Os and epsilo186Os-epsilo189Os with slopes of -0.64 ± 0.45 and -1.8(+1.9/-2.1), respectively. These Os isotope correlations broadly agree with model predictions for capture of secondary neutrons produced by cosmic ray irradiation and results reported previously for other groups of iron meteorites. Correlations were also found between epsilo182W-epsilo189Os (slope = 1.02 ± 0.37) and epsilo182W-epsilo190Os (slope = -1.38 ± 0.58). Intercepts of these two correlations yield pre-exposure epsilo182W values of -3.32 ± 0.51 and -3.62 ± 0.23, respectively (weighted average epsilo182W = -3.57 ± 0.21). This value relies on a large extrapolation leading to a large uncertainty but gives a metal-silicate segregation age of -0.5 ± 2.4 Myr after formation of the solar system. Combining the iron meteorite measurements with simulations of cosmogenic effects in iron meteorites, equations are presented to calculate and correct for cosmogenic effects on 182W using Os isotopes.