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PubMed1994

The relationship between occupational form and occupational performance: a kinematic perspective.

OBJECTIVES: This study examined, through kinematic analysis, the effect of occupational form on reaching performance. The hypothesis was that reaching performance would show an enhanced quality of movement in materials-based occupation (i.e., pick up a pencil and prepare to write one's own name) than in imagery-based occupation (i.e., pretend to pick up a pencil and prepare to sign one's own name) and in exercise (i.e., move the arm forward). It was further hypothesized that imagery-based occupation would elicit better performance than exercise. METHOD: The reaching performance was measured, using WATSMART (Waterloo Spatial Motion Analysis & Recording Technique), by the variables including reaction time, movement time, number of movement units, total displacement, the amplitude of peak velocity, and percentage of reach in which peak velocity occurred. A repeated-measures counterbalanced research design was used with 37 female college students. Contrast analysis was used to test the hypotheses. RESULTS: Materials-based occupation elicited enhanced quality of movement performance, as compared with imagery-based occupation and exercise. However, exercise seemed to elicit better performance than imagery-based occupation. CONCLUSION: The practical implication is that materials-based occupation might be used to elicit enhanced quality of reaching movement in occupational therapy intervention.

Adolescent↗
PubMedDate not supplied

[Recording of masticatory cycles by electrognathographic method].

Electrognathographic method of the three-dimensional recording of mandibular movements can be successfully used in the analysis of spatial shifting of interincisal point during mastication. Investigations carried out in the world by a sirognathograph (Sirognathograph, Siemens A.G., Bensheim, W. Germany) resulted in classifications of the masticatory cycles in order to determine types of samples and to establish the basis for comparative studies of patients with or without disorders in the stomatognathic system. Since our preliminary sirognathographic studies also confirmed the existence of the reported types of masticatory cycles, we considered it necessary to present here these classifications and to emphasize the positive results of their use in both scientific research devoted to analysis of function or disfunction of the stomatognathic system, and in estimation of therapeutical effects of prosthetic aids in complete denture wearers, as applied in routine clinical practice.

Denture, Complete↗
PubMed2006

Efficient design and operation of a data acquisition system for pressurized pipeline systems.

The unsteady flow analysis of pipeline systems provides useful guidelines for implementing data acquisition components such as data filtering ranges, sensor locations and sampling frequencies. A theoretical integration among hydraulics, free vibration analysis and signal processing is proposed for a comprehensive approach aiming at enhanced design and operation of data acquisition system. Transient analysis is performed to extract flow variation by a valve modulation in a pipeline system. Frequency transformation analysis is developed to convert pressure variations between time domain and frequency domain. Free vibration analysis provides spatial distribution of impedance characteristics and pressure variation for determining optimum sensor location. A real-time filter can be designed to secure valid signals of any particular unsteady event. Hypothetical and experimental applications show that the proposed method has potentials of the leakage detection of a pipeline system as well as an efficient design of data acquisition system.

Equipment Failure Analysis↗
PubMed2003

Spatial and temporal variation in mortality of newly settled damselfish: patterns, causes and co-variation with settlement.

Local abundance and dynamics of sedentary species with a dispersing life stage reflect factors that influence input and loss rates to patches of suitable habitat. For reef fishes, more attention has focused on sources of variation in input (larval settlement) than on patterns and causes of subsequent losses. We estimated spatial and temporal variation in juvenile mortality of a tropical damselfish, yellow-tail dascyllus (Dascyllus flavicaudus; Pomacentridae), using a fixed density experiment that was repeated 5 times at the same eight mid-lagoon localities at Moorea, French Polynesia. There was little temporal variation in the overall percent of outplanted fish lost in 48 h among five time periods (range: 32-37%), whereas there was substantial variation among the sites in the average percent lost (range: 16-56%). Differences in loss rates among the sites were highly consistent among the time periods. Densities of predators of juvenile dascyllus varied substantially among the eight sites and were highly correlated with loss rate of dascyllus. We used the empirically derived relationship between predator density and damselfish loss rate to predict the loss rate of dascyllus at four additional sites, and there was excellent agreement between the predicted and observed loss rates. There was a strong positive relationship between predator densities at the 12 sites and structural attributes of the reefs that do not change on a fast time scale, suggesting why there was strong spatial and weak temporal variation in mortality rates, with no interaction between spatial and temporal variation. Natural settlement rates of yellow-tail dascyllus and of a close congener (humbug dascyllus, D. aruanus) varied among the sites, and settlement of the two species was inversely correlated (r=-0.68). Settlement of these species was not statistically correlated with variation in mortality rate, but there was a weak trend for settlement of yellow-tail dascyllus to be greater at sites with higher mortality (r=0.27), and for settlement of humbug dascyllus to be greater at sites with lower mortality (r=-0.32). We calculated that even these weak co-variances could reduce (yellow-tail dascyllus) or increase (humbug dascyllus) the spatial variance in density of 48-h-old recruits arising at settlement by 19 and 27% respectively. Taken together, the findings suggest that the interactions between and relative contributions of input and loss processes can differ substantially over a scale of a few kilometers, resulting in a mosaic of local patches characterized by different abundances and dynamics.

Analysis of Variance↗
PubMed2006

Wnt signaling activation during bone regeneration and the role of Dishevelled in chondrocyte proliferation and differentiation.

Wnt signaling is intrinsically involved in diverse cellular activities during cell differentiation, early embryonic development and organogenesis. Although much is known regarding the effects of Wnt signaling in the developing skeletal system, its role during regeneration remains unclear. Herein, we show transcriptional activation of specific members and target genes of the Wnt signaling pathway. Specifically, all of the Wnt signaling members and target genes analyzed were found to be upregulated during the early stages of fracture repair, with the exception of LEF1 whose expression was downregulated. In addition, spatial expression analysis of Dishevelled (Dvl) and beta-catenin in the fracture callus revealed an identical pattern of expression with both proteins localizing in osteoprogenitor cells of the periosteum, osteoblasts and proliferating/pre-hypertrophic chondrocytes. Further, in vitro knockdown of all three Dvl isoforms in chondrocytes using small interfering RNAs (siRNA) leads to partial inhibition of cell proliferation and differentiation, decreased expression of chondrogenic markers (ColII, ColX, Sox9) and suppressed nuclear accumulation of unphosphorylated beta-catenin. Taken together, these data verify our previous finding that the Wnt signaling pathway is activated during bone regeneration, by characterizing the temporal and spatial expression of a broad spectrum of Wnt-signaling molecules. Our data also suggest that all three Dvl isoforms, acting through the Wnt canonical pathway, are critical regulatory molecules for chondrocyte proliferation and differentiation.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Characterization of high explosive particles using cluster secondary ion mass spectrometry.

The use of secondary ion mass spectrometry (SIMS) for the detection and spatially resolved analysis of individual high explosive particles is described. A C(8) (-) carbon cluster primary ion beam was used in a commercial SIMS instrument to analyze samples of high explosives dispersed as particles on silicon substrates. In comparison with monatomic primary ion bombardment, the carbon cluster primary ion beam was found to greatly enhance characteristic secondary ion signals from the explosive compounds while causing minimal beam-induced degradation. The resistance of these compounds to degradation under ion bombardment allows explosive particles to be analyzed under high primary ion dose bombardment (dynamic SIMS) conditions, facilitating the rapid acquisition of spatially resolved molecular information. The use of cluster SIMS combined with computer control of the sample stage position allows for the automated identification and counting of explosive particle distributions on silicon surfaces. This will be useful for characterizing the efficiency of transfer of particulates in trace explosive detection portal collectors and/or swipes utilized for ion mobility spectrometry applications.

Journal Article↗
PubMed2006

Ecological and reproductive character displacement on an environmental gradient.

Character displacement, in which coevolution of similar species alters their phenotypes, can be difficult to identify on the basis of observational data alone. In two-species systems, the most commonly identified (i.e., classic) resulting pattern is greater phenotypic difference between species in sympatry than allopatry. We show that restricting studies to this pattern may exclude many instances of character displacement, particularly in the presence of spatial environmental gradients. We present four spatial models of character displacement in quantitative traits affecting competition and hybridization between the species. Our models highlight the connections between range limits and character displacement in continuous space. We conclude that the classic pattern is less likely to occur for a trait affecting resource acquisition than for a trait affecting mate choice. We also show that interspecific hybridization (when hybrids are inviable), even in very small amounts, has marked effects on the shape and stability of borders between species and the nature of character displacement. A survey of the empirical literature shows that character displacement studies often lack analysis of spatial phenotype and abundance data. We recommend more careful spatial sampling in character displacement studies, and we illustrate how comparison of clines in mean phenotype in sympatry and allopatry can be used to suggest the action of character displacement.

Animals↗
PubMed2003

Stereologic characterization and spatial distribution patterns of Betz cells in the human primary motor cortex.

Betz cells are giant motoneurons located in layer Vb of the primate primary motor cortex. We conducted stereological analyses of Betz cells and neighboring pyramidal cells from the brains of six neurologically normal elderly humans to determine their volume, total number, and spatial distribution, and to relate these data to functional localization. The distribution of cellular volumes exhibits a bimodal pattern, delineating two different subpopulations. Betz cell volumes follow a mediolateral gradient, the largest Betz cells being located on the most medial part of the motor cortex. Additionally, the shape of Betz cells varies between the rostral and caudal parts of the primary motor cortex, supporting the notion that there are anatomically distinct zones in primary motor cortex. The total number of Betz cells per hemisphere accounts for about one-tenth of the total number of pyramidal cells in layer Vb. Analysis of spatial distribution using Voronoi tessellation revealed maximal clustering of Betz cells in a zone situated two-thirds from the midline along the mediolateral axis of the primary motor cortex. These data suggest that Betz cells have a discrete subregional distribution that may correspond to certain aspects of the functional parcellation of area 4. These results may offer a histological correlate of functional imaging studies and are relevant in the context of neurodegenerative diseases such as amyotrophic lateral sclerosis, progressive supranuclear palsy, and Guamanian amyotrophic lateral sclerosis/Parkinsonism-dementia, and in studies of normal brain aging.

Aged↗
PubMed2026

Uncovering hub genes and key pathways responsive to drought stress in rice via meta-analysis of transcriptomic data.

Drought stress presents a formidable threat to global rice cultivation, triggering complex molecular responses that impact plant growth and productivity. To decipher the underlying gene expression dynamics, we performed a comprehensive meta-analysis of transcriptomic datasets derived from drought-tolerant rice genotypes. Via microarray data from three independent studies, we identified a set of consistently expressed differentially expressed genes (DEGs) under drought conditions. Integration of functional annotation tools, including GO and KEGG pathway enrichment, revealed key biological processes and signaling cascades involved in stress mitigation, such as ABA signaling, protein folding, and photosynthesis suppression. Protein-protein interaction (PPI) network construction, followed by hub gene identification via maximal clique centrality (MCC), highlighted pivotal regulators including LEA proteins, dehydrins, HSP70, and several transcription factors. Machine learning approaches further prioritize potential biomarkers, with Random Forest models achieving high classification accuracy and pinpointing key predictive genes. Chromosomal localization analysis provided spatial insights into the distribution of these hub genes, whose expression patterns were further compared against qRT-PCR data from previously published studies. This integrative approach identifies candidate genomic markers and mechanistic insights that may support future breeding strategies for drought-tolerant rice, pending experimental validation.

Cytoscape↗
PubMed2002

Analyses of genotypic diversity among North, South, and Central American isolates of sugarcane yellow leaf virus: evidence for Colombian origins and for intraspecific spatial phylogenetic variation.

We have analyzed the genotypic diversity of sugarcane yellow leaf virus (SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the family Luteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156-171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a "partial likelihoods assessed through optimization" (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.

Central America↗
PubMed2025

High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties.

INTRODUCTION: The epigenetic silencing of O6-methylguanine DNA methyltransferase (MGMT) is associated with reduced DNA repair capacity, carcinogenesis and increased sensitivity to alkylating chemotherapy. However, the biological role and clinical significance of MGMT overexpression in cancer remains poorly understood. METHODS: Using multiplexed quantitative immunofluorescence we measured the localized levels of MGMT protein, γH2AX and CD8+ T cells in multiple retrospective colorectal cancer (CRC) cohorts. Genomic and transcriptomic features of selected cases were also studied with whole exome DNA sequencing and genome-wide methylation analysis. MGMT-methylated human CRC cells SW620 were transfected with an MGMT-containing plasmid and co-cultured with allogeneic peripheral blood mononuclear cells. RESULTS: A subset of CRCs showed MGMT protein upregulation associated with lower γH2AX, reduced CD8+ tumor infiltrating lymphocytes (TILs), mismatch repair proficient (pMMR) status and shorter survival. CD8+ TILs were more distant from MGMT-expressing cells than MGMT-negative cells and the MGMT promoter methylation status did not highly correlate with MGMT protein levels in CRC. In genomic/transcriptomic analysis, high MGMT expression was associated with a lower nonsynonymous somatic mutational burden, higher transition-to-transversion mutation ratio, increased deleterious TP53 variants and distinct transcriptomic profiles. The exogenous expression of MGMT in SW620 CRC cells reduced the number of spontaneous nonsynonymous mutations, reproduced mutational features of MGMT-high CRC and limited the in vitro T-cell-mediated killing of malignant cells induced by proinflammatory cytokines in tumor/immune cell co-cultures. CONCLUSIONS: MGMT overexpression identifies a previously undescribed subset of CRCs with distinct biological and clinical properties including reduced mutagenesis, adaptive immune evasion, predominantly pMMR phenotype and aggressive clinical course. Direct, quantitative assessment of MGMT protein expression using spatially resolved analysis is more reliable than inference of MGMT expression by promoter methylation status in CRC.

Humans↗
PubMed2025

Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology.

Characterizing cancer presents a delicate challenge as it involves deciphering complex biological interactions within the tumor's microenvironment. Clinical trials often provide histology images and molecular profiling of tumors, which can help understand these interactions. Despite recent advances in representing multimodal data for weakly supervised tasks in the medical domain, achieving a coherent and interpretable fusion of whole slide images and multi-omics data is still a challenge. Each modality operates at distinct biological levels, introducing substantial correlations between and within data sources. In response to these challenges, we propose a novel deep-learning-based approach designed to represent multi-omics & histopathology data for precision medicine in a readily interpretable manner. While our approach demonstrates superior performance compared to state-of-the-art methods across multiple test cases, it also deals with incomplete and missing data in a robust manner. It extracts various scores characterizing the activity of each modality and their interactions at the pathway and gene levels. The strength of our method lies in its capacity to unravel pathway activation through multimodal relationships and to extend enrichment analysis to spatial data for supervised tasks. We showcase its predictive capacity and interpretation scores by extensively exploring multiple TCGA datasets and validation cohorts. The method opens new perspectives in understanding the complex relationships between multimodal pathological genomic data in different cancer types and is publicly available on Github.

Deep Learning↗
PubMed2004

ISSR and AFLP analysis of the temporal and spatial population structure of the post-fire annual, Nicotiana attenuata, in SW Utah.

BACKGROUND: The native annual tobacco, Nicotiana attenuata, is found primarily in large ephemeral populations (typically for less than 3 growing seasons) after fires in sagebrush and pinyon-juniper ecosystems and in small persistent populations (for many growing seasons) in isolated washes typically along roadsides throughout the Great Basin Desert of the SW USA. This distribution pattern is due to its unusual germination behavior. Ephemeral populations are produced by the germination of dormant seeds from long-lived seed banks which are stimulated to germinate by a combination of unidentified positive cues found in wood smoke and the removal of inhibitors leached from the unburned litter of the dominant vegetation. Persistent populations may result where these inhibitors do not exist, as in washes or along disturbed roadsides. To determine if this germination behavior has influenced population structure, we conducted an AFLP (244 individuals), ISSR (175 individuals) and ISSR+ AFLP (175 individuals) analysis on plants originating from seed collected from populations growing in 11 wash and burns over 11 years from the SW USA. RESULTS: Genetic variance as measured by both ISSR and AFLP markers was low among sites and comparatively higher within populations. Cluster analysis of the Utah samples with samples collected from Arizona, California, and Oregon as out-groups also did not reveal patterns. AMOVA analysis of the combined AFLP and ISSR data sets yielded significantly low genetic differentiation among sites (Phict), moderate among populations within sites (Phisc) and higher genetic differentiation within populations (Phist). CONCLUSIONS: We conclude that the seed dormancy of this post-fire annual and its resulting age structure in conjunction with natural selection processes are responsible for significantly low among sites and comparatively high within-population genetic variation observed in this species.

Analysis of Variance↗
PubMed2001

KH domain: one motif, two folds.

The K homology (KH) module is a widespread RNA-binding motif that has been detected by sequence similarity searches in such proteins as heterogeneous nuclear ribonucleoprotein K (hnRNP K) and ribosomal protein S3. Analysis of spatial structures of KH domains in hnRNP K and S3 reveals that they are topologically dissimilar and thus belong to different protein folds. Thus KH motif proteins provide a rare example of protein domains that share significant sequence similarity in the motif regions but possess globally distinct structures. The two distinct topologies might have arisen from an ancestral KH motif protein by N- and C-terminal extensions, or one of the existing topologies may have evolved from the other by extension, displacement and deletion. C-terminal extension (deletion) requires ss-sheet rearrangement through the insertion (removal) of a ss-strand in a manner similar to that observed in serine protease inhibitors serpins. Current analysis offers a new look on how proteins can change fold in the course of evolution.

Amino Acid Motifs↗
PubMed1999

mtDNA analysis of Nile River Valley populations: A genetic corridor or a barrier to migration?

To assess the extent to which the Nile River Valley has been a corridor for human migrations between Egypt and sub-Saharan Africa, we analyzed mtDNA variation in 224 individuals from various locations along the river. Sequences of the first hypervariable segment (HV1) of the mtDNA control region and a polymorphic HpaI site at position 3592 allowed us to designate each mtDNA as being of "northern" or "southern" affiliation. Proportions of northern and southern mtDNA differed significantly between Egypt, Nubia, and the southern Sudan. At slowly evolving sites within HV1, northern-mtDNA diversity was highest in Egypt and lowest in the southern Sudan, and southern-mtDNA diversity was highest in the southern Sudan and lowest in Egypt, indicating that migrations had occurred bidirectionally along the Nile River Valley. Egypt and Nubia have low and similar amounts of divergence for both mtDNA types, which is consistent with historical evidence for long-term interactions between Egypt and Nubia. Spatial autocorrelation analysis demonstrates a smooth gradient of decreasing genetic similarity of mtDNA types as geographic distance between sampling localities increases, strongly suggesting gene flow along the Nile, with no evident barriers. We conclude that these migrations probably occurred within the past few hundred to few thousand years and that the migration from north to south was either earlier or lesser in the extent of gene flow than the migration from south to north.

DNA Mutational Analysis↗
PubMed1997

Geographic analysis of pertussis infection in an urban area: a tool for health services planning.

OBJECTIVE: This study examined whether incident cases of pertussis cluster in urban census tracts and identified community characteristics that predict high-incidence areas. METHODS: An ecological study design was used. The study population included all persons diagnosed with pertussis from January 1, 1986, through December 31, 1994. Maps of rates were constructed via a geographic information system and clustering was statistically confirmed. Associations between pertussis rates and community characteristics were tested. RESULTS: Mapping and statistical analysis revealed spatial clustering of pertussis. Higher age-adjusted rates of pertussis infection were associated with higher proportions of residents below poverty level. CONCLUSIONS: In urban areas pertussis infection clusters in areas of poverty.

Age Distribution↗
PubMed2000

Spatial distribution of in-patient service use of psychiatric patients: somatic departments versus psychiatric units.

BACKGROUND: It has long been recognized that a high proportion of psychiatric patients are admitted to emergency, medical and surgical wards. However, until now no assessment has been made of which urban general hospitals would be most appropriate for the establishment of specific psychiatric facilities. METHOD: Our study concerned Germany's second largest city, Hamburg (population 1.7 million), and involved an evaluation of psychiatric principal diagnoses in general and psychiatric hospitals. The research was based on data collected between 1988 and 1994 embracing approximately 77% of all psychiatric patients (n = 64,000) in 41 hospitals. The evaluation was carried out using the statistics programs SPSS and DismapWin. RESULTS: We established that the proportion of male patients discharged from somatic wards, mainly internal medicine, with alcohol and drug abuse as well as with neuroses and personality disorders or illegal drug abuse was surprisingly high (70%, 34% and 24% respectively). For female patients the figures were 67%, 40% and 35% respectively. A geographical analysis of spatial heterogeneity of hospitalization risks showed that general hospitals admit a disproportionately high number of patients from areas of lower social status - both male and female from the above-mentioned diagnostic categories. A rank correlation between the classification of areas based on the heterogeneity model and the social status of the areas supports this hypothesis, at least for males. CONCLUSION: Our findings lead us to the conclusion that the establishment of new psychiatric services should focus on internal wards in hospitals located in areas of low social status.

Adult↗
PubMed1996

Microstates in language-related brain potential maps show noun-verb differences.

Brain processing of grammatical word class was studied analyzing event-related potential (ERP) brain fields. Normal subjects observed a randomized sequence of single German nouns and verbs on a computer screen, while 20-channel ERP field map series were recorded separately for both word classes. Spatial microstate analysis was applied, based on the observation that series of ERP maps consist of epochs of quasi-stable map landscapes and based on the rationale that different map landscapes must have been generated by different neural generators and thus suggest different brain functions. Space-oriented segmentation of the mean map series identified nine successive, different functional microstates, i.e., steps of brain information processing characterized by quasi-stable map landscapes. In the microstate from 116 to 172 msec, noun-related maps differed significantly from verb-related maps along the left-right axis. The results indicate that different neural populations represent different grammatical word classes in language processing, in agreement with clinical observations. This word class differentiation as revealed by the spatial-temporal organization of neural activity occurred at a time after word input compatible with speed of reading.

Adult↗