The z-model — A proposal for spatial and temporal modeling of visual threshold perception

By considering only the modulation transfer functions of stationary, uniformly moved, and time modulated sinusoidal gratings it is possible to derive a simple model, the z-model, for the spatio-temporal frequency behaviour of one-dimensional patterns. The transmission function of this model is a band pass function of a single coordinate z, which is a quadratic form of the spatial and temporal frequencies (rotational symmetry with respect to space and time). The model is determined by only three constants. Optionally a time phase which accounts for delay and phase distortion can be added. This model can also be derived from reaction time measurements for switched on sinusoidal gratings. With this model the response of a wide variety of spatio-temporal patterns have been calculated and compared with measured threshold data. For two-dimensional patterns orientational filtering has to be added to the model leading to a further parameter. This model predicts satisfactorily the threshold modulation for a great variety of arbitrary spatio-temporal patterns. However the absolute threshold value for aperiodic transient patterns differs slightly in direction of smaller sensitivity as compared with periodic stationary patterns. This suggests that the peak detection scheme usually used in threshold detection modeling should be replaced by an integrative mechanism.     

The spatial and temporal patterns of falciparum and vivax malaria in Perú: 1994–2006

Background

Malaria is the direct cause of approximately one million deaths worldwide each year, though it is both preventable and curable. Increasing the understanding of the transmission dynamics of falciparum and vivax malaria and their relationship could suggest improvements for malaria control efforts. Here the weekly number of malaria cases due to Plasmodium falciparum (1994–2006) and Plasmodium vivax (1999–2006) in Perú at different spatial scales in conjunction with associated demographic, geographic and climatological data are analysed.

Methods

Malaria periodicity patterns were analysed through wavelet spectral analysis, studied patterns of persistence as a function of community size and assessed spatial heterogeneity via the Lorenz curve and the summary Gini index.

Results

Wavelet time series analyses identified annual cycles in the incidence of both malaria species as the dominant pattern. However, significant spatial heterogeneity was observed across jungle, mountain and coastal regions with slightly higher levels of spatial heterogeneity for P. vivax than P. falciparum. While the incidence of P. falciparum has been declining in recent years across geographic regions, P. vivax incidence has remained relatively steady in jungle and mountain regions with a slight decline in coastal regions. Factors that may be contributing to this decline are discussed. The time series of both malaria species were significantly synchronized in coastal (ρ = 0.9, P < 0.0001) and jungle regions (ρ = 0.76, P < 0.0001) but not in mountain regions. Community size was significantly associated with malaria persistence due to both species in jungle regions, but not in coastal and mountain regions.

Conclusion

Overall, findings highlight the importance of highly refined spatial and temporal data on malaria incidence together with demographic and geographic information in improving the understanding of malaria persistence patterns associated with multiple malaria species in human populations, impact of interventions, detection of heterogeneity and generation of hypotheses.     

The ontogeny of visual–motor memory and its importance in handwriting and reading: a developing construct

Humans have evolved a remarkable ability to remember visual shapes and use these representations to generate motor activity (from Palaeolithic cave drawings through Jiahu symbols to cursive handwriting). The term visual–motor memory (VMM) describes this psychological ability, which must have conveyed an evolutionary advantage and remains critically important to humans (e.g. when learning to write). Surprisingly, little empirical investigation of this unique human ability exists—almost certainly because of the technological difficulties involved in measuring VMM. We deployed a novel technique for measuring this construct in 87 children (6–11 years old, 44 females). Children drew novel shapes presented briefly on a tablet laptop screen, drawing their responses from memory on the screen using a digitizer stylus. Sophisticated algorithms (using point-registration techniques) objectively quantified the accuracy of the children''s reproductions. VMM improved with age and performance decreased with shape complexity, indicating that the measure captured meaningful developmental changes. The relationship between VMM and scores on nationally standardized writing assessments were explored with the results showing a clear relationship between these measures, even after controlling for age. Moreover, a relationship between VMM and the nationally standardized reading test was mediated via writing ability, suggesting VMM''s wider importance within language development.     

Preaching to the choir or composing new verses? Toward a writerly climate literacy in introductory undergraduate biology

Climate change is one of the most pressing issues facing society today, yet a wide range of misconceptions exist in society about whether or why climate change is happening, what its consequences are, and what can be done to address it. Large introductory biology courses present an opportunity to teach a large number of students—some of whom may never take another course focused on climate, ecology, or the environment—about climate change. However, content knowledge alone may not be enough to prepare students to transform their knowledge into action. To begin understanding how content knowledge interacts with student constructions of climate change solutions, we administered and quantitatively analyzed a survey that examined student views of climate change and how they shifted with instruction during an undergraduate introductory biology course at a large Midwestern university. Almost all participants entered the course agreeing that climate change is occurring, and their certainty about the science of climate change increased after instruction. After taking the course, more participants described climate change as having more immediate impacts, reporting that climate change is already harming people and that climate change will harm them personally. However, both at the beginning and end of the course, participants tended to think that humans would either be unable or unwilling to reduce climate change. They were also more worried about climate change at the end of the course than they were before. Increased concern might result from students becoming more certain of the science and severity of climate change, while remaining pessimistic that humans will effectively act on climate change. This pattern suggests instructors have opportunities to modify curricula in ways that leave students with a greater sense of empowerment and efficacy; we suggest questions that instructors can ask themselves in order to modify their courses with this goal in mind.     

The singular fate of genetics in the history of French biology, 1900–1940

In this study we have examined the reception of Mendelism in France from 1900 to 1940, and the place of some of the extra-Mendelian traditions of research that contributed to the development of genetics in France after World War II. Our major findings are:

The untold story of IFN-γ in cancer biology

Interferon (IFN)-γ is the uppermost cytokine implicated in anti-tumor immunity. With its cytostatic, pro-apoptotic and immune-provoking effects, IFN-γ plays a central role in the recognition and elimination of transformed cells. Considering well-characterized anti-tumor effects of this cytokine, many clinical trials and immunotherapy approaches have been designed to reinforce IFN-γ-mediated immunity for different types of cancer. However, the outcomes were not satisfactory and leaded to questioning of alternative actions of IFN-γ. Many regulatory pathways can be induced by IFN-γ to protect the normal tissues from collateral damage and to facilitate the re-establishment of homeostasis. Nevertheless, malignant cells can take the advantage of IFN-γ as an inducer of mediators inhibiting anti-tumor immune reactions. In addition, under the influence of tumor-derived factors, certain types of immune cells are also licensed by IFN-γ to perform regulatory actions. This review focuses on the immune modulatory functions of IFN-γ in cancer as an alternative story to be told.     

The strategy of “The strategy of model building in population biology”

In this essay, I argue for four related claims. First, Richard Levins’ classic “The Strategy of Model Building in Population Biology” was a statement and defense of theoretical population biology growing out of collaborations between Robert MacArthur, Richard Lewontin, E. O. Wilson, and others. Second, I argue that the essay served as a response to the rise of systems ecology especially as pioneered by Kenneth Watt. Third, the arguments offered by Levins against systems ecology and in favor of his own methodological program are best construed as “pragmatic”. Fourth, I consider limitations of Levins’ arguments given contemporary population biology.

The histochemistry and cell biology vade mecum: a review of 2005–2006

The procurement of new knowledge and understanding in the ever expanding discipline of cell biology continues to advance at a breakneck pace. The progress in discerning the physiology of cells and tissues in health and disease has been driven to a large extent by the continued development of new probes and imaging techniques. The recent introduction of semi-conductor quantum dots as stable, specific markers for both fluorescence light microscopy and electron microscopy, as well as a virtual treasure-trove of new fluorescent proteins, has in conjunction with newly introduced spectral imaging systems, opened vistas into the seemingly unlimited possibilities for experimental design. Although it oftentimes proves difficult to predict what the future will hold with respect to advances in disciplines such as cell biology and histochemistry, it is facile to look back on what has already occurred. In this spirit, this review will highlight some advancements made in these areas in the past 2 years.     

The influence of abiotic and spatial variables on woody and herbaceous species abundances in a woodland–grassland system in the Eastern Terai of India

印度特莱东部林地-草地系统中非生物和空间变量对木本和草本物种丰度的影响 目前尚不清楚哪些环境因素决定了热带稀树草原特别是在潮湿地带的林地和草地镶嵌处的林地和草地的物种多度。基于此,本研究探究了非生物和空间变量对印度东北部的台拉河生态系统木本和草本物种分布的影响,评估了气候和非气候因素在整个景观中保持可变的树草比和空间连通性和分散性的相对重要性。在519 km²的受保护的特莱栖息地中随机建立了134个30 m × 30 m的抽样样方,并调查了每个样方的木本和草本植物的物种多度和气候,以及非气候环境因素。基于不同的地点空间连通性模型,通过构建变量检验气候和非气候环境因素对物种多度的影响。使用冗余分析和方差分解定量解析环境变量和空间结构对林地和草地物种多度的相对重要性。研究结果表明,降雨、火灾、水分胁迫、地形和土壤养分在内的环境变量对物种多度和林草比有显著的影响。空间结构显著,最佳空间模型为反距离加权模型(inverse distance-weighted model), 而且显示最大的空间扩散距离可以达到23.5 km,表明扩散限制较弱。约21%的物种多度变化能够被环境和空间因素解释。这些结果揭示了植物群落动态的决定因素,即环境因子的时空变化可能驱动物种分布和多度的随机性,并对植被镶嵌产生主导影响。     

Measurement of visual acuity and crowding effect in 3–9-year-old children

Visual acuity was measured in 140 3–9-year-old children using Landolt’s rins with a gap in one of four orientations. The influence of surrounding additional contours on the detection of orientation of rings of a minimal visible size was studied in the same children, depending on the distance between the rings and the surrounding. The latter consisted of four bands, located symmetrically with reference to the ring. Visual acuity increased with age, reaching the adult level by approximately seven years. A deterioration of the orientation recognition was detected in all children when the surrounding was close to a ring. The distance that caused a perception deterioration decreased with age, reaching the adult level by nine years. The obtained data are discussed from the viewpoint of a possible influence of individual visual areas formed during ontogeny on task performance.     

Existence and non-existence of spatial patterns in a ratio-dependent predator–prey model

In this paper, first we consider the global dynamics of a ratio-dependent predator–prey model with density dependent death rate for the predator species. Analytical conditions for local bifurcation and numerical investigations to identify the global bifurcations help us to prepare a complete bifurcation diagram for the concerned model. All possible phase portraits related to the stability and instability of the coexisting equilibria are also presented which are helpful to understand the global behaviour of the system around the coexisting steady-states. Next we extend the temporal model to a spatiotemporal model by incorporating diffusion terms in order to investigate the varieties of stationary and non-stationary spatial patterns generated to understand the effect of random movement of both the species within their two-dimensional habitat. We present the analytical results for the existence of globally stable homogeneous steady-state and non-existence of non-constant stationary states. Turing bifurcation diagram is prepared in two dimensional parametric space along with the identification of various spatial patterns produced by the model for parameter values inside the Turing domain. Extensive numerical simulations are performed for better understanding of the spatiotemporal dynamics. This work is an attempt to make a bridge between the theoretical results for the spatiotemporal model of interacting population and the spatial patterns obtained through numerical simulations for parameters within Turing and Turing–Hopf domain.     

Whither Pst? The approximation of Qst by Pst in evolutionary and conservation biology

Local adaptation through natural selection can be inferred in case the additive genetic divergence in a quantitative trait across populations (Q(st)) exceeds the neutral expectation based on differentiation of neutral alleles across these populations (e.g. F(st)). As such, measuring Q(st) in relation to neutral differentiation presents a first-line investigation applicable in evolutionary biology (selection on functional genes) and conservation biology (identification of locally adapted coding genes). However, many species, especially those in need of conservation actions, are not amenable for the kind of breeding design required to estimate either narrow- or broad-sense Q(st). In such cases, Q(st) has been approximated by the phenotypic divergence in a trait across populations (P(st)). I here argue that the critical aspect for how well P(st) approximates Q(st) depends on the extent that additive genetic effects determine variation between populations relative to within populations. I review how the sensitivity of conclusions regarding local adaptation based on P(st) have been evaluated in the literature and find that many studies make a anticonservative null assumption in estimating P(st) and/or use a nonconservative approach to explore sensitivity of their conclusions. Data from two studies that have provided a second, independent assessment of selection in their system suggest that P(st)-F(st) comparisons should be interpreted very conservatively. I conclude with recommendations for improving the robustness of the inferences drawn from comparing P(st) with neutral differentiation.     

The spatial variability of methane emission from subtaiga and forest–steppe grass–moss fens of Western Siberia

Methane emission from the grass–moss fens of the Western Siberia subtaiga was studied using a static chamber method. It was established that CH₄ flux median ± half of the interquartile range in the studied wetland ecosystems constituted 4.9 ± 2.9 mg of CH₄/(m² h). It was shown that such a high spatial variability of emission is caused mainly by the difference in the water table level. It was found that, in these observations, a higher water table level correlates with lower emission values. The causes of this phenomenon are discussed, and recommendations for conducting field studies for estimating the regional flux are given.     

The aerobiome–health axis: a paradigm shift in bioaerosol thinking

Historically, a primary aim of bioaerosol research has been to understand and prevent ‘unhealthy’ human exposures to pathogens and allergens. However, there has been a recent paradigm shift in thinking about bioaerosols. Exposure to a diverse aerobiome – the microbiome of the air – is now considered necessary to be healthy.     

The spatial pattern and dispersion of Lygodium microphyllum in the Everglades wetland ecosystem

Since 1958, L. microphyllum (Old World Climbing Fern), which originated from the Old World Tropics, has become a nuisance exotic and has rapidly spread and is being established system-wide in extremely remote and undisturbed areas such as the Florida Everglades. Of particular concern is that L. microphyllum is disrupting, at an alarming rate, the flora and fauna of the native ecosystem at the same time that a major 8.4 billion dollar Everglades restoration program is trying to enhance these same attributes. This research utilized IKONOS satellite data to map L. microphyllum within the 58,000-ha Loxahatchee National Wildlife Refuge wetland in south Florida. Results show that approximately 11.6% of the tree/shrub vegetation within the impoundment has been infected by L. microphyllum. These data were then utilized to explore the spatial spread patterns of L. microphyllum within the Refuge. Results suggest that L. microphyllum is more likely to establish on the southeast side of a tree/shrub island and then spread to the northwest, which corresponds to the prevailing wind direction in south Florida. Spatial pattern analysis of L. microphyllum spread indicated that it is correlated with the density and spatial distribution of tree/shrub island vegetation. It appears that the dispersion of L. microphyllum is density dependent, which can be expressed as a logistic function and has a catastrophic threshold of 160 m of mean distance between tree/shrub islands in the Everglades. It is predicted that 38% (or 1910 ha) of tree/shrub islands in the Refuge will be invaded by L. microphyllum by 2012. Tree islands in the Everglades wetland could be considered similar to oceanic islands throughout the world that are notoriously vulnerable to biological invasions.