Top-down Hypotheses Research Articles

Transdisciplinary method for exploration and visualization of neuroimaging papers and databases: Application to PTSD

A major improvement in MRI techniques has led to an exponential increase in data acquisition and, consequently, in the number of published articles reporting brain impairments and cognitive deficits underlying a disorder. Meta-analysis offers a means of synthesizing the available literature, testing existing models in the light of scientific advances, and revealing unexpected information. However, article selection, author specialization and top-down hypotheses can mask some results and introduce bias into interpretations. LinkRdata is a platform for automated, data-driven, meta-analytical methods suitable for processing large numbers of MRI articles, that can reduce selection and interpretation biases, thereby allowing scientists to review neurocognitive correlates of disorders in relation to their own corpus of articles. To validate our method, we applied it to fMRI studies of post-traumatic stress disorder. Results confirmed LinkRdata's power to uncover findings hidden by the top-down hypothesis approach.

The power of large-scale community science in addressing anthropogenic change.

The human imprint on the global environment has become so pervasive that it rivals the forces of nature in its impact on ecosystem function. We are now living in the Anthropocene with increased air, light, noise, and heavy metal pollution (Foley et al., 2005). Understanding the link between anthropogenic stressors and functional trait characteristics will be vital to predict species response and adaptability to environmental change. Especially as urban areas increase, where anthropogenic changes are highly concentrated and overlapping, investigating how multiple stressors interact to affect individuals and populations is a current research priority. Wilson et al. (this issue) levy the power of human interest in wildlife to study the effects of human-generated pollution (2021). The authors provide a timely and novel continent-level study that addresses the interaction of light and noise pollution on species abundance and response using community science.

Are all patches worth exploring? Foraging desert birds do not rely on environmental indicators of seed abundance at small scales

BackgroundConsumers should show strong spatial preferences when foraging in environments where food availability is highly heterogeneous and predictable. Postdispersal granivores face this scenario in most arid areas, where soil seed bank abundance and composition associates persistently with vegetation structure at small scales (decimetres to metres). Those environmental features should be exploited as useful pre-harvest information, at least to avoid patches predicted to be poor. However, we did not find the expected spatial association in the algarrobal of the central Monte desert by observing foraging seed-eating birds, a field technique influenced by how much they exploit visited patches. In this work we tested if the first stage of foraging by granivorous birds (patch visit, encounter or exploration) is positively associated with environmental indicators of patch quality by recording the removal of single seeds from 300 scattered experimental devices during seasonal trials. Spatial selectivity was analysed by comparing the structural characteristics of used vs. available microhabitats, and evaluated against bottom-up and top-down hypotheses based on our previous knowledge on local seed bank abundance, composition and dynamics. Their foraging activity was also explored for spatial autocorrelation and environmental correlates at bigger scales.ResultsPostdispersal granivorous birds were less selective in their use of foraging space than expected if microhabitat appearance were providing them relevant information to guide their search for profitable foraging patches. No microhabitat type, as defined by their vegetation structure and soil cover, remained safe from bird exploration. Analyses at bigger temporal and spatial scales proved more important to describe heterogeneity in seed removal.ConclusionsCloseness to tall trees, probably related to bird territoriality and reproduction or to their perception of predation risk, seemed to determine a first level of habitat selection, constraining explorable space. Then, microhabitat openness (rather than seed abundance) exerted some positive influence on which patches were more frequently visited among those accessible. Selective patterns by birds at small scales were closer to our predictions of a top-down spatial effect, with seed consumption creating or strengthening (and not responding to) the spatial pattern and dynamics of the seed bank.

LSD modulates effective connectivity and neural adaptation mechanisms in an auditory oddball paradigm

Under the predictive coding framework, perceptual learning and inference are dependent on the interaction between top-down predictions and bottom-up sensory signals both between and within regions in a network. However, how such feedback and feedforward connections are modulated in the state induced by lysergic acid diethylamide (LSD) is poorly understood. In this study, an auditory oddball paradigm was presented to healthy participants (16 males, 4 female) under LSD and placebo, and brain activity was recorded using magnetoencephalography (MEG). Scalp level Event Related Fields (ERF) revealed reduced neural adaptation to familiar stimuli, and a blunted neural ‘surprise’ response to novel stimuli in the LSD condition. Dynamic causal modelling revealed that both the presentation of novel stimuli and LSD modulate backward extrinsic connectivity within a task-activated fronto-temporal network, as well as intrinsic connectivity in the primary auditory cortex. These findings show consistencies with those of previous studies of schizophrenia and ketamine but also studies of reduced consciousness – suggesting that rather than being a marker of conscious level per se, backward connectivity may index modulations of perceptual learning common to a variety of altered states of consciousness, perhaps united by a shared altered sensitivity to environmental stimuli. Since recent evidence suggests that the psychedelic state may correspond to a heightened ‘level’ of consciousness with respect to the normal waking state, our data warrant a re-examination of the top-down hypotheses of conscious level and suggest that several altered states may feature this specific biophysical effector.This article is part of the Special Issue entitled ‘Psychedelics: New Doors, Altered Perceptions’.

Carry-over effect between diet and physical activity: the bottom-up and top-down hypotheses of hierarchical self-efficacy

Healthy diet and physical activity have consistently been found to be positively correlated; however, most health behavior theories are focused on regulation of changes in single, rather than multiple, behaviors. Thus, this study explored the mechanism of the carry-over effect between diet and physical activity by conducting a longitudinal study with 706 participants to test the bottom-up and top-down hypotheses of hierarchical self-efficacy (SE). At Time 1 (baseline) and Time 3 (4 weeks after baseline), dietary behavior, physical activity, and self-efficacies of these behaviors (at the contextual level) were measured, while at Time 2 (2 weeks after baseline), general SE (at the general level) was assessed. Mediation analysis and structural equation models supported both the bottom-up and top-down hypotheses for different levels of self-efficacies, suggesting that hierarchical SE is an important factor underlying the carry-over mechanism between diet and physical activity.

Testing the nutritional-limitation, predator-avoidance, and storm-avoidance hypotheses for restricted sea otter habitat use in the Aleutian Islands, Alaska.

Sea otters (Enhydra lutris) inhabiting the Aleutian Islands have stabilized at low abundance levels following a decline and currently exhibit restricted habitat-utilization patterns. Possible explanations for restricted habitat use by sea otters can be classified into two fundamentally different processes, bottom-up and top-down forcing. Bottom-up hypotheses argue that changes in the availability or nutritional quality of prey resources have led to the selective use of habitats that support the highest quality prey. In contrast, top-down hypotheses argue that increases in predation pressure from killer whales have led to the selective use of habitats that provide the most effective refuge from killer whale predation. A third hypothesis suggests that current restricted habitat use is based on a need for protection from storms. We tested all three hypotheses for restricted habitat use by comparing currently used and historically used sea otter foraging locations for: (1) prey availability and quality, (2) structural habitat complexity, and (3) exposure to prevailing storms. Our findings suggest that current use is based on physical habitat complexity and not on prey availability, prey quality, or protection from storms, providing further evidence for killer whale predation as a cause for restricted sea otter habitat use in the Aleutian Islands.

Does climate limit species richness by limiting individual species' ranges?

Broad-scale geographical variation in species richness is strongly correlated with climate, yet the mechanisms underlying this correlation are still unclear. We test two broad classes of hypotheses to explain this pattern. Bottom-up hypotheses propose that the environment determines individual species' ranges. Ranges then sum up to yield species richness patterns. Top-down hypotheses propose that the environment limits the number of species that occur in a region, but not which ones. We test these two classes of hypotheses using a natural experiment: seasonal changes in environmental variables and seasonal range shifts of 625 migratory birds in the Americas. We show that richness seasonally tracks the environment. By contrast, individual species' geographical distributions do not. Rather, species occupy different sets of environmental conditions in two seasons. Our results are inconsistent with extant bottom-up hypotheses. Instead, a top-down mechanism appears to constrain the number of species that can occur in a given region.

I2T: Image Parsing to Text Description

In this paper, we present an image parsing to text description (I2T) framework that generates text descriptions of image and video content based on image understanding. The proposed I2T framework follows three steps: 1) input images (or video frames) are decomposed into their constituent visual patterns by an image parsing engine, in a spirit similar to parsing sentences in natural language; 2) the image parsing results are converted into semantic representation in the form of Web ontology language (OWL), which enables seamless integration with general knowledge bases; and 3) a text generation engine converts the results from previous steps into semantically meaningful, human readable, and query-able text reports. The centerpiece of the I2T framework is an and-or graph (AoG) visual knowledge representation, which provides a graphical representation serving as prior knowledge for representing diverse visual patterns and provides top-down hypotheses during the image parsing. The AoG embodies vocabularies of visual elements including primitives, parts, objects, scenes as well as a stochastic image grammar that specifies syntactic relations (i.e., compositional) and semantic relations (e.g., categorical, spatial, temporal, and functional) between these visual elements. Therefore, the AoG is a unified model of both categorical and symbolic representations of visual knowledge. The proposed I2T framework has two objectives. First, we use semiautomatic method to parse images from the Internet in order to build an AoG for visual knowledge representation. Our goal is to make the parsing process more and more automatic using the learned AoG model. Second, we use automatic methods to parse image/video in specific domains and generate text reports that are useful for real-world applications. In the case studies at the end of this paper, we demonstrate two automatic I2T systems: a maritime and urban scene video surveillance system and a real-time automatic driving scene understanding system.

Mendel's Impact

ArgumentI wish to propose that the history of genetics reflects the history of the concept of reductionism in the life sciences. Reductionism is the thesis that explanation of laws or phenomena in one realm by those of another realm are always likely to be successful as explanations. By 1900 reduction of biology to the laws of chemistry and physics was not self evident: Although bottom-up preformationist explanations were largely inadequate for development, top-down epigenetic hypotheses often adopted metaphysical assumptions. Similarly, top-down theories of evolution as dependent on the accumulated impact of the past confronted those of bottom-up notions of fitness of specific traits that are relevant for future evolution. Mendel's 1865 methodological reductionist study of inheritance of traits was embraced in 1900 as evidence for reduction at the conceptual level. With the achievements of research of the mechanisms of inheritance, genetics became increasingly genocentric in its explanatory arsenal of development, and accordingly it was in conflict with the top-down, life-as-organized-systems' notions of embryology. Similarly, evolution was conceptually reduced to changes of gene-frequencies in populations. It was, however, precisely the increasing attempts to ground the bottom-up approach at the molecular level that eventually pushed conceptual reductionism to its crisis. Modern developments of molecular and computational methods finally forced, or allowed, researchers to apply bottom-up methodologies to top-down systems' analyses.

The Ecological Effects of Fishing and Implications for Coastal Management in San Miguel Bay, the Philippines

This article uses ecological theory to explore the interactions between fishing and the ecosystem and to examine the implications for fisheries assessment and management in San Miguel Bay, the Philippines. The fishery is modeled using a trophodynamic multispecies model, Ecopath with Ecosim. The impacts of fishing by a multisector fishery on a multispecies resource were dynamically explored under top-down and bottom-up trophic hypotheses. The results demonstrated that the interplay of fishing mortality, species interactions and flow dynamics can have profound implications for fisheries assessment and management. Top-down control is more precautionary than bottom-up control. The uncertainties concerning the resource dynamics were explored using an adaptive management approach. Four models of the San Miguel Bay were analyzed: top-down, bottom-up, immigration plus top-down and immigration plus bottom-up. Results showed that there was no value in learning more about the uncertainty or distinguishing between the different resource models. It was concluded that although an active experimental adaptive management was not worthwhile, adaptive management, using feedback information from the response of the resource to management actions, was recommended.

A unified quantitative approach to trophic cascade and bottom-up: top-down hypotheses

A general analytic approach is developed to predict how perturbing one level of a food chain affects the stocks in other levels. (The comparison is between initial and final steady states.) This yields qualitative and quantitative predictions of the trophic cascade hypothesis and the bottom-up: top-down hypothesis, respectively. For a wide range of reasonable ratio-dependent functional relationships between trophic levels in a food chain, the quantitative approach predicts that perturbation effects should propagate up the chain with the same sign and roughly constant strength, but down the chain with alternating sign and diminishing strength. There is less diminishment for the case of trophic levels with a low ratio of energy losses (metabolism, mortality) to input. The trophic cascade model’s prediction of the sign of compartmental stock changes is based on a linear food chain model and does not necessarily hold for food webs. Both points are illustrated by simulating perturbation responses in models of two ecosystems (one representing a chain and one a web). The approach can be used for a wide range of functional responses connecting trophic levels besides ratio dependence.