Different methods to assess yield temporal stability in rubber

The objective of this work was to assess, during six years, the temporal stability of natural rubber yield of 25 superior Hevea brasiliensis genotypes, using the Wricke, Eberhart & Russell, Lin & Binns, additive main effect and multiplicative interaction (AMMI) analysis, and harmonic mean of the relative performance of the genetic values (HMRPGV) methods. The IAC 40 and IAC 300 genotypes were identified as stable and high yielding by the Eberhart & Russell, Lin & Binns, HMRPGV, and AMMI Biplot methods. The ranking of the other more stable genotypes identified by these analyses was altered. The observed results in the AMMI Biplot agreed with those observed in the Wricke method for identifying stable, but lower yielding genotypes. The simultaneous use of different methods allows a more accurate indication of stable genotypes. Stability analyses based on different principles show agreement in indicating stable genotypes.

Sensitivity of Spring Phenology to Warming Across Temporal and Spatial Climate Gradients in Two Independent Databases

Disparate ecological datasets are often organized into databases post hoc and then analyzed and interpreted in ways that may diverge from the purposes of the original data collections. Few studies, however, have attempted to quantify how biases inherent in these data (for example, species richness, replication, climate) affect their suitability for addressing broad scientific questions, especially in under-represented systems (for example, deserts, tropical forests) and wild communities. Here, we quantitatively compare the sensitivity of species first flowering and leafing dates to spring warmth in two phenological databases from the Northern Hemisphere. One-PEP725-has high replication within and across sites, but has low species diversity and spans a limited climate gradient. The other-NECTAR-includes many more species and a wider range of climates, but has fewer sites and low replication of species across sites. PEP725, despite low species diversity and relatively low seasonality, accurately captures the magnitude and seasonality of warming responses at climatically similar NECTAR sites, with most species showing earlier phenological events in response to warming. In NECTAR, the prevalence of temperature responders significantly declines with increasing mean annual temperature, a pattern that cannot be detected across the limited climate gradient spanned by the PEP725 flowering and leafing data. Our results showcase broad areas of agreement between the two databases, despite significant differences in species richness and geographic coverage, while also noting areas where including data across broader climate gradients may provide added value. Such comparisons help to identify gaps in our observations and knowledge base that can be addressed by ongoing monitoring and research efforts. Resolving these issues will be critical for improving predictions in understudied and under-sampled systems outside of the temperature seasonal mid-latitudes.

Temporal trends in chemical parameters of upland forest soils in southern Finland

Abstract

Aplicação da análise de agrupamento de dados de expressão gênica temporal a dados em painel

O objetivo deste trabalho foi determinar a melhor alternativa, entre os métodos de agrupamento hierárquico (Ward) e de otimização (Tocher), para a formação de grupos homogêneos de séries de expressão gênica, e realizar previsões quanto à expressão gênica dessas séries, a partir de pequeno número de observações temporais. Os dados utilizados referem-se à expressão de genes que atuam sobre o ciclo celular de Saccharomyces cerevisiae e corresponderam a 114 séries de expressão gênica, cada uma com dez valores de "fold-change" (medida da expressão gênica) ao longo do tempo (0, 15, 30, 45, 60, 75, 90, 105, 120 e 135 min). As estimativas dos parâmetros dos modelos autorregressivos AR(p) foram previamente ajustadas a séries individuais (de cada gene) de dados "microarray time series" e utilizadas, como variáveis, no processo de agrupamento. As previsões da expressão gênica foram feitas dentro de cada grupo formado, a partir dos ajustes no modelo AR(p) para dados em painel. O método de Ward foi o mais apropriado para a formação de grupos de genes com séries homogêneas. Uma vez obtidos esses grupos, é possível ajustar o modelo AR(2) para dados em painel e predizer a expressão gênica em um tempo futuro (135 min), a partir de um pequeno número de observações temporais (os outros nove valores de "fold-change").

Pre-stimulus beta oscillations within left posterior sylvian regions impact auditory temporal order judgment accuracy.

Both neural and behavioral responses to stimuli are influenced by the state of the brain immediately preceding their presentation, notably by pre-stimulus oscillatory activity. Using frequency analysis of high-density electroencephalogram coupled with source estimations, the present study investigated the role of pre-stimulus oscillatory activity in auditory spatial temporal order judgments (TOJ). Oscillations within the beta range (i.e. 18-23Hz) were significantly stronger before accurate than inaccurate TOJ trials. Distributed source estimations identified bilateral posterior sylvian regions as the principal contributors to pre-stimulus beta oscillations. Activity within the left posterior sylvian region was significantly stronger before accurate than inaccurate TOJ trials. We discuss our results in terms of a modulation of sensory gating mechanisms mediated by beta activity.

Spatio-temporal variability of sugarcane yield efficiency in the state of São Paulo, Brazil

The objective of this work was to assess the spatial and temporal variability of sugarcane yield efficiency and yield gap in the state of São Paulo, Brazil, throughout 16 growing seasons, considering climate and soil as main effects, and socioeconomic factors as complementary. An empirical model was used to assess potential and attainable yields, using climate data series from 37 weather stations. Soil effects were analyzed using the concept of production environments associated with a soil aptitude map for sugarcane. Crop yield efficiency increased from 0.42 to 0.58 in the analyzed period (1990/1991 to 2005/2006 crop seasons), and yield gap consequently decreased from 58 to 42%. Climatic factors explained 43% of the variability of sugarcane yield efficiency, in the following order of importance: solar radiation, water deficit, maximum air temperature, precipitation, and minimum air temperature. Soil explained 15% of the variability, considering the average of all seasons. There was a change in the correlation pattern of climate and soil with yield efficiency after the 2001/2002 season, probably due to the crop expansion to the west of the state during the subsequent period. Socioeconomic, biotic and crop management factors together explain 42% of sugarcane yield efficiency in the state of São Paulo.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

A matter of time: delayed mate encounter postpones mating window initiation and reduces the strength of female choosiness

Reproductive success is determined by the presence and timing of encounter of mates. The latter depends on species-specific reproductive characteristics (e.g. initiation/duration of the mating window), season, and reproductive strategies (e.g. intensity of choosiness) that may potentially mitigate constraints imposed by mating windows. Despite their potentially crucial role for fitness and population dynamics, limited evidence exists about mating window initiation, duration and reproductive strategies. Here, we experimentally tested the mechanisms of initiation and the duration of the common lizard's Zootoca vivipara mating window, by manipulating the timing of mate encounter and analyzing its effect on (re-)mating probability. We furthermore tested treatment effects on female reproductive strategies, by measuring female choosiness. The timing of mate encounter and season did not significantly affect mating probability. However, a longer delay until mate encounter reduced female choosiness. Re-mating probability decreased with re-mating delay and was independent of mating delay. This indicates that mating window initiation depends on mate encounter, that its duration is fixed, and that plastic reproductive strategies exist. These findings contrast with previous beliefs and shows that mating windows per se may not necessarily constrain reproductive success, which is congruent with rapid range expansion and absence of positive density-effects on reproductive success (Allee effects). In summary, our results show that predicting the effect of mating windows on reproduction is complex and that experimental evidence is essential for evaluating their effect on reproduction and reproductive strategies, both being important determinants of population dynamics and the colonization of new habitats.

Análise temporal e controle da mancha-anular e do ácaro vetor do Coffee ringspot virus

O objetivo deste trabalho foi avaliar a flutuação populacional do ácaro Brevipalpus phoenicis, vetor do Coffee ringspot virus (CoRSV) - agente causal da mancha-anular do cafeeiro -, bem como a sua distribuição em plantas de café e o efeito de acaricidas no seu controle em lavouras cafeeiras. O experimento foi realizado no Município de Coromandel, na região do Alto do Paranaíba, MG, durante dois anos. No segundo ano, avaliou-se o progresso da doença, e determinou-se a relação entre o crescimento populacional do ácaro e a incidência da doença. Observou-se que a mancha-anular e o ácaro ocorreram durante todo o ano, com maiores populações e incidência da doença nos meses com menores índices pluviais e temperaturas amenas. As análises de Pearson mostraram correlação negativa entre os parâmetros climáticos e a população do ácaro. Na análise da incidência da doença em diferentes épocas, verificou-se correlação positiva entre a primeira avaliação e as avaliações subsequentes. Quanto à distribuição espacial, foi observada a presença do ácaro em toda a planta; porém, as folhas são preferidas pelos adultos, enquanto os frutos são preferidos para oviposição. Os acaricidas são eficientes para manter a população do ácaro em baixos níveis, com consequente diminuição da incidência da doença.

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution

Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ~13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator.

Population receptive field estimates of human auditory cortex.

Here we describe a method for measuring tonotopic maps and estimating bandwidth for voxels in human primary auditory cortex (PAC) using a modification of the population Receptive Field (pRF) model, developed for retinotopic mapping in visual cortex by Dumoulin and Wandell (2008). The pRF method reliably estimates tonotopic maps in the presence of acoustic scanner noise, and has two advantages over phase-encoding techniques. First, the stimulus design is flexible and need not be a frequency progression, thereby reducing biases due to habituation, expectation, and estimation artifacts, as well as reducing the effects of spatio-temporal BOLD nonlinearities. Second, the pRF method can provide estimates of bandwidth as a function of frequency. We find that bandwidth estimates are narrower for voxels within the PAC than in surrounding auditory responsive regions (non-PAC).

Temporal issues in e-learning research: A literature review

Peer-reviewed

A multi-temporal approach to model endangered species distribution in Europe: the case of the Eurasian otter in Italy

We analysed the relationship between changes in land cover patterns and the Eurasian otter occurrence over the course of about 20 years (1985-2006) using multi-temporal Species Distribution Models (SDMs). The study area includes five river catchments covering most of the otter's Italian range. Land cover and topographic data were used as proxies of the ecological requirements of the otter within a 300-m buffer around river courses. We used species presence, pseudo-absence data, and environmental predictors to build past (1985) and current (2006) SDMs by applying an ensemble procedure through the BIOMOD modelling package. The performance of each model was evaluated by measuring the area under the curve (AUC) of the receiver-operating characteristic (ROC). Multi-temporal analyses of species distribution and land cover maps were performed by comparing the maps produced for 1985 and 2006. The ensemble procedure provided a good overall modelling accuracy, revealing that elevation and slope affected the otter's distribution in the past; in contrast, land cover predictors, such as cultivations and forests, were more important in the present period. During the transition period, 20.5% of the area became suitable, with 76% of the new otter presence data being located in these newly available areas. The multi-temporal analysis suggested that the quality of otter habitat improved in the last 20 years owing to the expansion of forests and to the reduction of cultivated fields in riparian belts. The evidence presented here stresses the great potential of riverine habitat restoration and environmental management for the future expansion of the otter in Italy

Neural plasticity associated with recently versus often heard objects.

In natural settings the same sound source is often heard repeatedly, with variations in spectro-temporal and spatial characteristics. We investigated how such repetitions influence sound representations and in particular how auditory cortices keep track of recently vs. often heard objects. A set of 40 environmental sounds was presented twice, i.e. as prime and as repeat, while subjects categorized the corresponding sound sources as living vs. non-living. Electrical neuroimaging analyses were applied to auditory evoked potentials (AEPs) comparing primes vs. repeats (effect of presentation) and the four experimental sections. Dynamic analysis of distributed source estimations revealed i) a significant main effect of presentation within the left temporal convexity at 164-215ms post-stimulus onset; and ii) a significant main effect of section in the right temporo-parietal junction at 166-213ms. A 3-way repeated measures ANOVA (hemisphere×presentation×section) applied to neural activity of the above clusters during the common time window confirmed the specificity of the left hemisphere for the effect of presentation, but not that of the right hemisphere for the effect of section. In conclusion, spatio-temporal dynamics of neural activity encode the temporal history of exposure to sound objects. Rapidly occurring plastic changes within the semantic representations of the left hemisphere keep track of objects heard a few seconds before, independent of the more general sound exposure history. Progressively occurring and more long-lasting plastic changes occurring predominantly within right hemispheric networks, which are known to code for perceptual, semantic and spatial aspects of sound objects, keep track of multiple exposures.

Temporal dynamics of auditory what and where processing in humans

Recent evidence suggests the human auditory system is organized,like the visual system, into a ventral 'what' pathway, devoted toidentifying objects and a dorsal 'where' pathway devoted to thelocalization of objects in space w1x. Several brain regions have beenidentified in these two different pathways, but until now little isknown about the temporal dynamics of these regions. We investigatedthis issue using 128-channel auditory evoked potentials(AEPs).Stimuli were stationary sounds created by varying interaural timedifferences and environmental real recorded sounds. Stimuli ofeach condition (localization, recognition) were presented throughearphones in a blocked design, while subjects determined theirposition or meaning, respectively.AEPs were analyzed in terms of their topographical scalp potentialdistributions (segmentation maps) and underlying neuronalgenerators (source estimation) w2x.Fourteen scalp potential distributions (maps) best explained theentire data set.Ten maps were nonspecific (associated with auditory stimulationin general), two were specific for sound localization and two werespecific for sound recognition (P-values ranging from 0.02 to0.045).Condition-specific maps appeared at two distinct time periods:;200 ms and ;375-550 ms post-stimulus.The brain sources associated with the maps specific for soundlocalization were mainly situated in the inferior frontal cortices,confirming previous findings w3x. The sources associated withsound recognition were predominantly located in the temporal cortices,with a weaker activation in the frontal cortex.The data show that sound localization and sound recognitionengage different brain networks that are apparent at two distincttime periods.References1. Maeder et al. Neuroimage 2001.2. Michel et al. Brain Research Review 2001.3. Ducommun et al. Neuroimage 2002.