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PubMed1991

Ice crystal damage and radiation effects in relation to microscopy and analysis at low temperatures.

There are several limitations to the low-temperature techniques which are currently being used for the preparation, examination and analysis of biological and organic samples by means of high-energy beam instrumentation. The low thermal conductivity of samples and the inadequacy of rapid cooling techniques means that, with the exception of thin-film suspensions and the surface of impact-cooled bulk specimens which may be vitrified, ice crystals of varying sizes will be present in nearly all samples which are quench cooled. Data are presented which indicate the depth to which adequate cryo-fixation may be achieved for both morphological and analytical studies. Although dynamic processes may be time resolved in the outer parts of quench-cooled samples, the decreased freezing rate below the surface makes resolution of these processes much less certain. The quality of information which may be obtained from quench-cooled samples is limited by radiation damage. Low-dose microscopy of vitrified thin-film suspensions of macromolecules continues to provide valid structural information at the molecular level. The increased doses needed for X-ray microanalysis present serious problems with the high spatial resolution analysis of thin frozen-hydrated sections although much less damage is observed in dried samples. A case is presented for using the outer fracture faces of frozen-hydrated bulk samples for low-resolution analysis of cells and tissues.

Electron Probe Microanalysis↗
PubMed1997

Binocular combination of contrast signals by striate cortical neurons in the monkey.

With the use of microelectrode recording techniques, we investigated how the contrast signals from the two eyes are combined in individual cortical neurons in the striate cortex of anesthetized and paralyzed macaque monkeys. For a given neuron, the optimal spatial frequency, orientation, and direction of drift for sine wave grating stimuli were determined for each eye. The cell's disparity tuning characteristics were determined by measuring responses as a function of the relative interocular spatial phase of dichoptic stimuli that consisted of the optimal monocular gratings. Binocular contrast summation was then investigated by measuring contrast response functions for optimal dichoptic grating pairs that had left- to right-eye interocular contrast ratios that varied from 0.1 to 10. The goal was to determine the left- and right-eye contrast components required to produce a criterion threshold response. For all functional classes of cortical neurons and for both cooperative and antagonistic binocular interactions, there was a linear relationship between the left- and right-eye contrast components required to produce a threshold response. Thus, for example for cooperative binocular interactions, a reduction in contrast to one eye was counterbalanced by an equivalent increase in contrast to the other eye. These results showed that in simple cells and phase-specific complex cells, the contrast signals from the two eyes were linearly combined at the subunit level before nonlinear rectification. In non-phase-specific complex cells, the linear binocular convergence of contrast signals could have taken place either before or after the rectification process, but before spike generation. In addition, for simple cells, vector analysis of spatial summation showed that the inputs from the two eyes were also combined in a linear manner before nonlinear spike-generating mechanisms. Thus simple cells showed linear spatial summation not only within and between subregions in a given receptive field, but also between the left- and right-eye receptive fields. Overall, the results show that the effectiveness of a stimulus in producing a response reflects interocular differences in the relative balance of inputs to a given cell, however, the eye of origin of a light-evoked signal has no specific consequence.

Animals↗
PubMed2006

Mapping and measuring social disparities in premature mortality: the impact of census tract poverty within and across Boston neighborhoods, 1999-2001.

The identification and documentation of health disparities are important functions of public health surveillance. These disparities, typically falling along lines defined by gender, race/ethnicity, and social class, are often made visible in urban settings as geographic disparities in health between neighborhoods. Recognizing that premature mortality is a powerful indicator of disparities in both health status and access to health care that can readily be monitored using routinely available public health surveillance data, we undertook a systematic analysis of spatial variation in premature mortality in Boston (1999-2001) across neighborhoods and sub-neighborhoods in relation to census tract (CT) poverty. Using a multilevel model based framework, we estimated that the incidence of premature mortality was 1.39 times higher (95% credible interval 1.09-1.78) among persons living in the most economically deprived CTs (>/=20% below poverty) compared to those in the least impoverished tracts (<5% below poverty). We present maps of model-based standardized mortality ratios that show substantial within-neighborhood variation in premature mortality and a sizeable decrease in spatial variation after adjustment for CT poverty. Additionally, we present maps of model-based direct standardized rates that can more readily be compared to externally published rates and targets, as well as maps of the population attributable fraction that show that in some of Boston's poorest neighborhoods, the proportion of excess deaths associated with CT poverty reaches 25-30%. We recommend that these methods be incorporated into routine analyses of public health surveillance data to highlight continuing social disparities in premature mortality.

Adolescent↗
PubMed2002

Statistical analysis of multiplex brain gene expression images.

Analysis of variance (ANOVA) was employed to investigate 9,000 gene expression patterns from brains of both normal mice and mice with a pharmacological model of Parkinson's disease (PD). The data set was obtained using voxelation, a method that allows high-throughput acquisition of 3D gene expression patterns through analysis of spatially registered voxels (cubes). This method produces multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. The ANOVA model was compared to the results from singular value decomposition (SVD) by using the first 42 singular vectors of the data matrix, a number equal to the rank of the ANOVA model. The ANOVA was also compared to the results from non-parametric statistics. Lastly, images were obtained for a subset of genes that emerged from the ANOVA as significant. The results suggest that ANOVA will be a valuable framework for insights into the large number of gene expression patterns obtained from voxelation.

Analysis of Variance↗
PubMed2002

Vestibular information is required for dead reckoning in the rat.

Dead reckoning is an on-line form of spatial navigation used by an animal to identify its present location and return directly to a starting location, even after circuitous outward trips. At present, it is not known which of several self-movement cues (efferent copy from movement commands, proprioceptive information, sensory flow, or vestibular information) are used to compute homeward trajectories. To determine whether vestibular information is important for dead reckoning, the impact of chemical labyrinthectomy was evaluated in a test that demanded on-line computation of a homeward trajectory. Rats were habituated to leave a refuge that was visible from all locations on a circular table to forage for large food pellets, which they carried back to the refuge to eat. Two different probe trials were given: (1) the rats foraged from the same spatial location from a hidden refuge in the light and so were able to use visual cues to navigate; (2) the same procedure took place in the dark, constraining the animals to dead reckon. Although control rats carried food directly and rapidly back to the refuge on both probes, the rats with vestibular lesions were able to do so on the hidden refuge but not on the dark probe. The scores of vestibular reflex tests predicted the dead reckoning deficit. The vestibular animals were also impaired in learning a new piloting task. This is the first unambiguous demonstration that vestibular information is used in dead reckoning and also contributes to piloting.

Animals↗
PubMed2001

A large outdoor radial maze for comparative studies in birds and mammals.

For a comparative neurobiological analysis of spatial learning and memory, a large outdoor eight-arm radial maze was constructed which permits behavioral assessment of many avian and mammalian species both from the laboratory or the wild, using the same metric space and session schedules. It consists of a central part of 250cm diameter, and has arms of 650cm length, 170cm height and 80cm width. In order to determine appropriate training schedules for comparison of different species, we tested four mammalian and two avian species during 9-15 sessions: 18 albino rats (Rattus norvegicus), nine outdoors and nine in a conventional small indoor maze; six guinea pigs (Cavia porcellus); six rabbits (Oryctolagus cuniculus); five hedgehogs (Erinaceus europaeus); seven hooded crows (Corvus corone cornix) and six chickens (Gallus domesticus). Rats learned fast in both mazes yet significantly better in the large one. Good-to-excellent learning was also observed in juvenile rabbits and wild-caught crows, although the latter tended to avoid arms in the vicinity of the observer. Hedgehogs and chickens did not show significant learning as a group, but some individuals appeared to learn the task. Guinea pigs remained continuously passive and could not be trained. Thus, in spite of species-specific demands for reward, adaptation and pre-training, this type of radial maze permits to directly compare a wide variety of species. Such comparability is essential for an analysis of underlying neurobiological mechanisms.

Animals↗
PubMed2006

Exposure of inner-shelf reefs to nutrient enriched runoff entering the Great Barrier Reef Lagoon: post-European changes and the design of water quality targets.

We used historical flood plume extent data (modelled) to quantify the typical spatial extent of the summer runoff-seawater mixing zone of the Great Barrier Reef (GBR) lagoon. Spatially explicit analysis of the variability of in situ chlorophyll a concentrations (observed) across the runoff-seawater mixing zone, then allowed us to explore regional differences in the nutrient enrichment impact of runoff events from the various river systems that drain the GBR catchment. We demonstrate the existence of a discernable north-south gradient along the length of the GBR, such that for equivalent runoff:seawater dilutions ratios, lower levels of nutrient enrichment (as indicated by chlorophyll alpha observations) result from the river systems that drain the relatively undisturbed northern areas of the GBR catchment, compared to more human-impacted central and south areas. We identify a strong correlation between this north-south enrichment gradient and the flood concentration of dissolved inorganic nitrogen (DIN) entrained by the various river systems. By substituting the nutrient enrichment characteristics of the human-impacted river discharges with those of the undisturbed northern rivers, we provide a means to compare the short-term enriching 'footprint' for existing runoff intrusions with those that are likely to have occurred under pre-European catchment conditions. We demonstrate that under pre-European conditions, the nutrient enriching impact from river runoff was likely to have been largely constrained within 1-2 km of the coast, whereas existing conditions support the impact of reefs some 20-30 km off the coast. By using the developed spatial relations, we show that for the heavily human-impacted river systems, reductions in the end-of-river concentrations of DIN in the order 50-80% are needed in order to restore parity with pre-European conditions. We discuss these results in regard to developing end-of-catchment water quality targets for the region.

Animals↗
PubMed2006

Object perception impairments predict instrumental activities of daily living dependence in Alzheimer's disease.

This study examined the contribution of object perception and spatial localization to functional dependence among Alzheimer's disease (AD) patients. Forty patients with probable AD completed measures assessing verbal recognition memory, working memory, object perception, spatial localization, semantic knowledge, and global cognition. Primary caregivers completed a measure of activities of daily living (ADLs) that included instrumental and basic self-care subscales (i.e., IADLs and BADLs, respectively). Stepwise multiple regressions revealed that global cognition accounted for significant portions of variance among the ADL total, IADL, and BADL scores. However, when global cognition was removed from the model, object perception was the only significant cognitive predictor of the ADL total and IADL subscale scores, accounting for 18.5% and 19.3% of the variance, respectively. When considering multiple cognitive components simultaneously, object perception and the integrity of the inferotemporal cortex is important in the completion of functional abilities in general and IADLs in particular among AD patients.

Activities of Daily Living↗
PubMed2003

Selective spatial information from surface EMG after temporal filtering: the application to interference EMG using cross-covariance analysis.

OBJECTIVE: An increased spatial resolution in multichannel surface EMG recordings would provide new possibilities for the investigation of intermuscular and intramuscular coordination. A known analytical solution for volume conduction allows the conclusion that a high pass filtered surface electromyography (SEMG) signal contains information from a smaller environment near the recording electrode and therefore provides a higher spatial resolution. METHODS: The present paper concerns experiments on 9 subjects to measure, from the human biceps brachii muscle during static isometric contraction, using multichannel surface EMG. Cross-correlation functions between bipolar SEMG channels were calculated and high pass filtered. RESULTS: The correlation peaks showed the signs of propagating action potentials. The spatial width in the direction perpendicular to the muscle fibres decreased with increasing cut-off frequency. There exists an optimal cut-off frequency, which provides the best spatial resolution. It correlates with the thickness of the subcutaneous fat layer which causes a minimum depth of the active muscle fibres measured. CONCLUSIONS: High pass filtered cross-covariance functions of bipolar SEMG channels have an increased spatial resolution perpendicular to the muscle fibre direction and the frequency content of the signals can potentially give an indication of the depth of the active muscle fibres.

Action Potentials↗
PubMed1999

Hippocampectomized rats are impaired in homing by path integration.

Theoretical, behavioral, and electrophysiologic evidence suggests that the hippocampal formation may play a role in path integration, a form of spatial navigation in which an animal can return to a starting point by integrating self-movement cues generated on its outward journey. The present study examined whether the hippocampus (Ammon's horn and the dentate gyrus) is involved in this form of spatial behavior. Control rats and rats with selective ibotenic acid lesions of the hippocampus were tested in a foraging task in which they retrieved large food pellets from an open field, which when found, they carried to a refuge for consumption. The experiments measured the rats' homing accuracy, returning to the starting location, under conditions in which visual, surface, and self-movement cues; surface and self-movement cues; or only self-movement cues were available. Although both control rats and rats without a hippocampus could use visual and surface cues, only control rats appeared to be able to use self-movement cues. The finding that hippocampal rats are impaired under conditions requiring the use of self-movement cues suggests that the hippocampus plays an essential role in path integration.

Animals↗
PubMed2006

Effects of industrial outfalls on tropical macrobenthic sediment communities in Reunion Island (Southwest Indian Ocean).

Temporal changes in the composition of soft bottom macrobenthic assemblages at Reunion Island (Southwest Indian Ocean) were studied in the context of a long-term environmental monitoring programme studying the impacts of effluents of industrial sugar cane refineries that are transferred to shallow and deep coastal environments by different pathways: surface discharge and deep underground injection. Seven stations (between 20 and 160 m depth) were surveyed between 1994 and 2003 on the industrial zone. One additional station was surveyed on a reference site. Spatio-temporal changes in the composition of macrobenthic communities were assessed using several diversity indices, ABC curves, MDS and associated ANOSIM tests and biotic indices. Among the 171 taxa recorded, polychaetes were dominant (89 species), followed by crustaceans and molluscs. The analysis of spatial changes in the composition of macrobenthos showed the existence of distinct benthic communities along the depth gradient. Temporal changes in macrobenthos composition were most prominent at the shallowest station. They mainly corresponded to the decline of several initially dominant taxa and the increase of the Eunicid polychaete Diopatra cuprea. This station further showed increasing macrofaunal abundance, biomass and sediment organic content over time, concomitant with decreasing sediment grain sizes. In deeper environments, temporal changes were much smaller. Macrofaunal abundance and species richness increased progressively, suggesting a moderate impact on benthic ecosystems resulting from slight enrichments due to effluents rich in organic matter. Our results highlight an original response to disturbance pattern involving opportunistic Eunicidae species (D. cuprea) not previously described. Moreover, they allow for the comparison of the impact on macrofauna caused by industrial effluents exported by two distinct and different pathways in a tropical coastal high-energy marine environment.

Analysis of Variance↗
PubMedDate not supplied

[Multiple parameter comparative EEG analysis in alcoholism and narcotic dependence].

Multiparametric comparative analysis of spatial organization of EEG was carried out in 137 alcoholics and 131 heroin addicts. Common and different deviations from normal EEG (105 control subjects) were found. Global alterations of EEG spatial organization were observed in drug addicts (as compared to alcoholics). Such changes characterized increasing synchronizing effects of mesolimbic and brainstem structures on the brain cortex. The ethanol effects were more specific and asymmetric. Changes in EEG spectral-coherence characteristics were revealed in all frequency band, however, maximal changes took place in the high-frequency theta in drug addicts and in narrow-frequency alpha subranges in alcoholics. Different effects on the high-frequency EEG component (19.00-21.25 Hz) and information-energy index (coherence-to-spectral power ratio) suggest the difference influence of ethanol and heroin on emotional-motivational and cognitive processes as well as the level of consciousness. The obtained data on EEG discrimination of alcoholism and drug addiction (the inverse problem solution) on the basis of "specific" EEG patterns appear to have considerable promise in development of systems of occupational selection.

Adolescent↗
PubMed1997

Switching of gene expression: analysis of the factors that spatially and temporally regulate plant gene expression.

In this chapter, we have reviewed the present research and understanding of several families of transcription factors in plants. From this information, it appears there is good conservation between the types of transcription factors in plants and animals. However, there are several types of factors which have been isolated in plants that remain to be documented in animals (e.g., HD-Zip and GT). These as well as the presence of two types of TATA-binding proteins (TBPs) in plants suggest that although transcription in eukaryotes is highly conserved, fundamental differences may exist. Despite the differences, the modes of regulating transcription are well conserved. Figure 3 summarizes these modes of regulation. In recent years, the role of chromatin structure as well as subcellular localization have been the focus of a vast amount of research in mammals, Drosophila and yeast. However, very little research in these areas has been done in plants. Isolation of genes such as Curly leaf suggest a conservation of genes that influence the formation of heterochromatin-like structures. Whether or not this gene influences chromatin/heterochromatin structure in plants, however, remains to be tested. The study of nuclear localization of factors such as COP1 and KN1 is now leading to models for regulating nuclear transport as well as intercellular transport of transcription factors. Further study of the inter- and intracellular movement of these and other transcription factors may provide information on new modes of regulating transcription. In addition to understanding the role chromatin structure and subcellular localization of transcription factors may have on transcription initiation, the biological role of many plant transcription factors remains to be identified. Several approaches may be taken to understand the mechanisms by which transcription factors influence biochemical and physiological processes in the plant. These steps include 1) identification of the DNA-binding sites of the factors as well as the promoter regions which contain these sites. Presently, this approach is limiting in that not many non-coding regions have been sequenced and characterized in detail. Furthermore, the presence of a putative binding site within a promoter does not necessarily indicate that the factor will bind to the site in vivo. 2) Analysis of the binding affinity for a particular factor to a binding site in comparison to other related factors, via in vitro competition assays and quantitative titrations. This will provide information on how strongly these factors are binding to the sites, but without knowledge of all the factors present in a single cell it is difficult to recreate the in vivo conditions. 3) Generation of transgenic plants or microinjection of DNA/RNA to express a particular factor ectopically, reduce expression of the factor via antisense expression, and creation of dominant negative mutants by overexpression of key dimerization domains may provide information concerning what biological pathways these factors influence. 4) Isolation of mutations in particular transcription factors has been extremely informative in floral development. However, this approach usually entails isolation of a mutant due to a phenotype and eventual mutated locus. The cloning of the locus may or may not involve a transcription factor. 5) Many plant transcription factors have been isolated via sequence similarity to other previously identified and/or characterized transcription factors. However, the biological role of may of these factors is not known. In addition to ectopic expression of these factors by creating transgenic plants, isolation of a loss-of-function mutation may provide valuable information concerning the role of this factor in vivo. Many loss-of-function mutations in MADS box genes have led to a better understanding of how the MADS domain proteins interact with one another as well as how they influence floral development. (ABSTRACT TRUNCATED)

Cell Compartmentation↗
PubMed2004

Strategies and determinants for selection of alternate foot placement during human locomotion: influence of spatial and temporal constraints.

During locomotion in a cluttered terrain, certain terrain surfaces such as an icy one are not appropriate for foot placement; an alternate choice is required. In a previous study we showed that the selection of foot placement is not random but systematic; the dominant choices made are not uniquely defined by the available or predicted sensory inputs. We argued that selection is guided by specific rules and involves minimal displacement of the foot from its normal landing spot. The experimental protocol involved implicit spatial constraint by requiring individuals to step on the force plate that could trigger a lighted area to be avoided, thereby requiring individuals to respond within one step-cycle. Alternate foot placement was visually identified, but not measured. The purpose of this study was to directly measure foot placement, validate and/or refine the rules used to guide selection, and identify whether the alternate foot placement choices are influenced by spatial and temporal constraints on response selection. The area to be avoided was visible from the start and therefore individuals could plan and implement appropriate avoidance strategies without any temporal constraint. Spatial constraint introduced in this experiment included requirement both to step on a specific location and to avoid stepping on a specific location on the next step. The results provide support for the rules previously identified in guiding foot placement to an alternate location. Minimal displacement of the foot from its normal landing spot was validated as an important factor for selecting alternate foot placement. When several choices satisfied this factor, additional factors guide alternate foot placement. Modifications in the plane of progression are preferred while stepping wide is avoided. When no temporal constraints are imposed on the response selection, enhancing forward progression of the body becomes the dominant determinant followed by stability and lastly by energy costs associated with the modifications. A decision algorithm for selecting foot placement is proposed based on these findings. It is clear that while visual input plays a critical role in guiding foot placement, it is not entirely based on reactive control. This has implications for implementing visually guided adaptive locomotion in legged robots.

Adolescent↗
PubMed2004

Anatomical methods for voxelation of the mammalian brain.

Voxelation allows high-throughput acquisition of three-dimensional gene expression patterns in the brain through analysis of spatially registered voxels (cubes). The method results in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging techniques. An important issue for voxelation is the development of approaches to anchor correctly harvested voxels to the underlying anatomy. Here, we describe experiments to identify fixation and cryopreservation protocols for improved registration of harvested voxels with neuroanatomical structures. Paraformaldehyde fixation greatly reduced RNA recovery as judged by ribosomal RNA abundance. However, gene expression signals from paraformaldehyde-fixed samples were not appreciably diminished as judged by average signal-noise ratios from microarrays, highlighting the difficulties of accurate quantitation of cross-linked RNA. Additional use of cryoprotection helped to improve further RNA recovery and signal from fixed tissue. It appears that the best protocol to provide the necessary resolution of neuroanatomical information in voxelation entails a controlled dose of fixation and thorough cryoprotection, complemented by histological staining.

Animals↗
PubMed2026

Distinct cellular phenotypes of language and executive decline in amyotrophic lateral sclerosis.

Cognitive manifestations, including impairments in language and executive functions, are seen in amyotrophic lateral sclerosis (ALS), but the underlying mechanisms remain unclear. We mapped prefrontal cortex regions from ALS patients by integrating spatial and single-nucleus transcriptomics in a cognitively stratified patient cohort. We uncover that cognitive impairment in ALS is associated with distinct patterns of neuronal dysfunction and glial-vascular dysregulation that vary by region and cognitive subtype. Executive dysfunction is linked to reduced mitochondrial and synaptic activity in deep-layer dorsolateral prefrontal cortex neurons, whereas language-related deficits track with a diffuse pan-regional response involving glial and vascular abnormalities. Our analyses, validated by multiplexed imaging, further identify signatures in the prefrontal cortex that span both motor and cognitive phenotypes, including a multicellular gliosis response. The findings reveal that clinical heterogeneity in ALS is driven by phenotype-specific cellular interactions in motor and non-motor regions of the brain.

Amyotrophic Lateral Sclerosis↗
PubMed1998

Extrapolating species abundance across spatial scales

The analysis, measurement, and management of species abundance is central to ecology and conservation biology, but it has proved difficult to find a single index that adequately reflects the commonness or rarity of species across a range of spatial scales. Here, a scale-independent measure of species abundance is developed, using presence-absence maps at varying spatial resolutions. By extrapolating such "scale-area" curves, species abundance can be estimated accurately even at scales finer than those used to parameterize the model, a task that had previously been deemed impossible in principle.

Journal Article↗
PubMed2024

Geospatial Analysis of Multilevel Socioenvironmental Factors Impacting the Campylobacter Burden among Infants in Rural Eastern Ethiopia: A One Health Perspective.

Increasing attention has focused on health outcomes of Campylobacter infections among children younger than 5 years in low-resource settings. Recent evidence suggests that colonization by Campylobacter species contributes to environmental enteric dysfunction, malnutrition, and growth faltering in young children. Campylobacter species are zoonotic, and factors from humans, animals, and the environment are involved in transmission. Few studies have assessed geospatial effects of environmental factors along with human and animal factors on Campylobacter infections. Here, we leveraged Campylobacter Genomics and Environmental Enteric Dysfunction project data to model multiple socioenvironmental factors on Campylobacter burden among infants in eastern Ethiopia. Stool samples from 106 infants were collected monthly from birth through the first year of life (December 2020-June 2022). Genus-specific TaqMan real-time polymerase chain reaction was performed to detect and quantify Campylobacter spp. and calculate cumulative Campylobacter burden for each child as the outcome variable. Thirteen regional environmental covariates describing topography, climate, vegetation, soil, and human population density were combined with household demographics, livelihoods/wealth, livestock ownership, and child-animal interactions as explanatory variables. We dichotomized continuous outcome and explanatory variables and built logistic regression models for the first and second halves of the infant's first year of life. Infants being female, living in households with cattle, reported to have physical contact with animals, or reported to have mouthed soil or animal feces had increased odds of higher cumulative Campylobacter burden. Future interventions should focus on infant-specific transmission pathways and create adequate separation of domestic animals from humans to prevent potential fecal exposures.

Humans↗