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PubMed1996

Spontaneous architectural organization of mammalian epidermis from random cell packing.

The cells of the stratum corneum in the epidermis of some mammalian species are precisely stacked in columns in a honeycomb fashion. The epidermis constantly loses surface cells, which are replaced by basal cells that have differentiated during migration to the surface. The path of this migration is seen as precisely defined columns of cells that are in compressed Kelvin's tetrakaidecahedral form. We present a computer simulation of this architectural organization based on the assumption that the cells that migrate upward occupy less crowded regions. The simulation not only explained the mechanism by which the architecture is maintained during the process of cell replacement, but also showed that the architecture was spontaneously organized from initial cells supplied at random. Living organisms consist of self-organizing systems at various levels; however, self-organizing systems have been investigated mostly at the molecular level. The present computer simulation clarified the self-organizing system at the cellular level.

Animals↗
PubMed2004

Proliferation patterns reflect architectural dedifferentiation: a study of nodular basal cell carcinoma.

The distribution of proliferating cells in basal cell carcinoma (BCC) may be related to lesion type and architecture. Single proliferation indexes may not be representative. We aimed to establish the distribution of cell proliferation in BCC as related to architecture. We studied an unselected, consecutive series of 45 resection specimens of nodular BCC from patients in the age range of 25-95 years using MIB-1 staining and systematically reviewed the cases. These lesions included nodular (n=32) and non-nodular (n=9) BCC. Within the nodular BCC, two patterns were recognised, not related to age or gender. In small nodular patterns with well developed peripheral palisading and central parallel streaming of small, elongated nuclei, proliferation is limited to the basal palisading cells in a clustered distribution. In large nodular patterns, proliferation is absent at the basal membrane (BM) and distributed in single random cells throughout the lesion. Both patterns preclude accurate quantitation. Many lesions contained both patterns in a side-by-side, unmixed manner. These pattern differences suggest a loss of differentiation in nodular BCC. Perhaps a single mutation results in the loss of BM associated cell architecture and proliferation control related to tumor-stroma interactions. As a result, the lesion reverts to a low frequency, non-regulated proliferation, diffusely distributed throughout the lesion. The two patterns may exist side-by-side in a single lesion, further supporting the concept of polyclonality. This hypothesis explains perilesional clefting and previously reported variations in intra-lesional laminin synthesis. Based on our findings, representation of tumor cell proliferation activity by a single value is not justified. Nodular BCC exists in one of two dedifferentiation-mutation-determined patterns of cell proliferation; many lesions clearly demonstrate bi-clonality.

Adult↗
PubMed2005

Intrinsic and environmental response pathways that regulate root system architecture.

Root system development is an important agronomic trait. The right architecture in a given environment allows plants to survive periods of water of nutrient deficit, and compete effectively for resources. Root systems also provide an optimal system for studying developmental plasticity, a characteristic feature of plant growth. This review proposes a framework for describing the pathways regulating the development of complex structures such as root systems: intrinsic pathways determine the characteristic architecture of the root system in a given plant species, and define the limits for plasticity in that species. Response pathways co-ordinate environmental cues with development by modulating intrinsic pathways. The current literature describing the regulation of root system development is summarized here within this framework. Regulatory pathways are also organized based on their specific developmental effect in the root system. All the pathways affect lateral root formation, but some specifically target initiation of the lateral root, while others target the development and activation of the lateral root primordium, or the elongation of the lateral root. Finally, we discuss emerging approaches for understanding the regulation of root system architecture.

Cell Cycle↗
PubMed2006

The proximal neurovascular plate and the tri-zonal neural architecture around the prostate gland: importance in the athermal robotic technique of nerve-sparing prostatectomy.

OBJECTIVE: To review the neural architecture around the prostate gland, as it is relevant for nerve-sparing robotic prostatectomy, including in particular the anatomy of the proximal neurovascular tissue, the neurovascular bundle (NVB), and accessory neural pathways (ANPs). MATERIALS AND METHODS: The aims of this study were achieved in collaboration between the Cornell Institute of Robotic Surgery, New York, NY, USA and the Institute of Urology at the University of Innsbruck, Austria. The broad steps were: (i) anatomical studies of 10 fresh and two fixed male cadavers; and (ii) collection of videotape and still image data from 200 men undergoing radical prostatectomy by the athermal robotic technique at the Cornell Institute. RESULTS: From a surgical standpoint there was a tri-zonal neural architecture including the proximal neurovascular plate (PNP), the predominant NVB (PNB) and ANPs. The PNP was a mean (range) of 5 (3-10) mm lateral to the seminal vesicles, was 3 (2-7) mm thick, 7 (5-25) mm wide and 9 (4-30) mm long. It was within 6 (4-15) mm of the bladder neck, 5 (2-7) mm of the endopelvic fascia and overlapped 5 (0-7) mm of the proximal prostate. The PNB varied in shape and size from the proximal to distal end, was thickest at the base and most variable near the apex. In eight of 12 cases, there was a medial extension behind the prostate, which converged medially at the apex in four cases. ANPs were noted within the layers of levator fascia and/or lateral pelvic fascia on the anterolateral aspect in five cases and in three on the posterior aspect of the prostate. In nine cadavers, the proximal third of the prostate was covered by the PNP where these ANPs were most prominent. The ANPs formed a plexus on the posterolateral aspect of the apex in four cases. CONCLUSION: We have created an anatomical map of neurovascular tissue relevant to robotic prostatectomy. A tri-zonal neural architecture is described which has helped in standardizing the steps of robotic prostatectomy.

Adult↗
PubMed2005

Towards a generic architectural model of tillering in Gramineae, as exemplified by spring wheat (Triticum aestivum).

This paper presents an architectural model of wheat (Triticum aestivum), designed to explain effects of light conditions at the individual leaf level on tillering kinetics. Various model variables, including blade length and curvature, were parameterized for spring wheat, and compared with winter wheat and other Gramineae species. The architectural model enables simulation of plant properties at the level of individual organs. Parameterization was based on data derived from an outdoor experiment with spring wheat cv. Minaret. Final organ dimensions of tillers could be modelled using the concept of relative phytomer numbers. Various variables in spring wheat showed marked similarities to winter wheat and other species, suggesting possibilities for a general Gramineae architectural model. Our descriptive model is suitable for our objective: investigating light effects on tiller behaviour. However, we plan to replace the descriptive modelling solutions by physiological, mechanistic solutions, starting with the localized production and partitioning of assimilates as affected by abiotic growth factors.

Models, Structural↗
PubMed2006

Disruptions in sleep time and sleep architecture in a mouse model of repeated ethanol withdrawal.

BACKGROUND: Insomnia and other sleep difficulties are perhaps the most common and enduring symptoms reported by alcoholics undergoing detoxification, especially those alcoholics with a history of multiple detoxifications. While some studies have reported sleep disruptions in animal models after chronic ethanol exposure, the reports are inconsistent and few address sleep architecture across repeated ethanol exposures and withdrawals. The present study evaluated sleep time and architecture in a well-characterized mouse model of repeated chronic ethanol exposure and withdrawal. METHODS: C57BL6/J mice were fitted with electrodes in frontal cortex, hippocampus, and nuchal muscle for collection of continuous electroencephalogram (EEG)/electromyogram (EMG) data. Baseline data were collected, after which mice received 4 cycles of 16-hour exposure to alcohol (ethanol: EtOH) vapor separated by 8-hour periods of withdrawal or similar handling in the absence of EtOH vapor. Ethanol-exposed mice attained a blood ethanol concentration of 165 mg%. Upon completion of vapor exposure, EEG/EMG data were again collected across 4 days of acute withdrawal. Data were subjected to automated analyses classifying 10-second epochs into wake, non-rapid eye movement (REM) sleep, or REM sleep states. RESULTS: Mice in withdrawal after chronic EtOH exposure showed profound disruptions in the total time asleep, across the acute withdrawal period. Sleep architecture, the composition of sleep, was also disrupted with a reduction in non-REM sleep concomitant with a profound increase in REM sleep. While altered sleep time and non-REM sleep loss resolved by the fourth day of withdrawal, the increase in REM sleep ("REM rebound") persisted. CONCLUSIONS: These results mirror those reported for the human alcoholic and demonstrate that EtOH withdrawal-induced sleep disruptions are evident in this mouse model of alcohol withdrawal-induced sensitization. This mouse model may provide mechanisms to investigate fully the high correlation between unremitting sleep problems and increased risk of relapse documented clinically.

Animals↗
PubMed2006

Architectural patterns in cytology: correlation with histology.

Cellular arrangements are highly relevant in the evaluation of histologic sections, but cytologic specimens are not thought to accurately reflect the same patterns. Only occasionally do cytologic descriptions comprise, apart from cytoplasmic and nuclear features, architectural patterns. Architectural arrangement of cells in cytologic specimens, however, may mirror the corresponding arrangement of cells in histologic specimens provided the cytologic preparations are collected and prepared appropriately. Recognition and understanding of the different types of cell arrangements that may be seen in cytologic specimens can provide important information for obtaining a definitive diagnosis, particularly for neoplastic lesions. The goal of this review is to describe the most common architectural patterns observed in cytologic specimens and to draw correlations with similar histologic arrangements.

Animals↗
PubMed1996

Repressive coping style and the architecture of emotion-related memories: is their relationship that simple?

The present study re-examines the relationship between repressive coping style and the architecture of emotion-related memories by introducing methodological improvements in the elicitation of these memories. Participants were classified into four repressive coping groups according to the Taylor Manifest Anxiety scale and the Marlowe-Crowne Social Desirability scale. They were then asked to recall personal experiences related to five core relational themes attempting to elicit positive and negative emotions and to rate how they felt in each situation. Results indicated that differences in the architecture of emotion-related memories among the four repressive coping groups depended on the type of the elicited memory. The discussion emphasizes the complexity of the relationship between repressive coping style and the architecture of emotion-related memories and suggests an expansion of the concept of repression.

Adaptation, Psychological↗
PubMed2026

Establishment of a CRISPR-Cas9 Library for Indica Rice and Identification of OsOPR5 (LOC_Os06g11210) as a Regulator of Root Architecture.

Functional characterization of a large number of rice genes remains a major challenge despite the availability of genome sequences and large-scale transcriptomic datasets. CRISPR-Cas9 library is a powerful approach for high-throughput targeted mutagenesis; however, its application in indica rice cultivars remains limited due to low transformation and regeneration efficiencies. In this study, we developed a CRISPR-Cas9 library targeting 12,000 rice genes and evaluated its utility for functional genomics in the indica cultivar MTU-1010. Sanger sequencing and NGS analysis of the plasmid library revealed high sgRNA coverage and more than 80% accuracy. Transformation of the developed library into the indica cultivar MTU-1010 resulted in a high target editing efficiency, with 90% of analyzed transgenic plants carrying mutations at the intended target site. Functional analysis of one homozygous mutant identified a previously uncharacterized role for OsOPR5 (LOC_Os06g11210), a member of the 12-oxophytodienoate reductase family in root architecture. The opr5 mutants exhibited significant reductions in lateral root number, seminal and crown root number, and root length, demonstrating that OsOPR5 positively regulates root system architecture in rice. Notably, endogenous jasmonic acid (JA) and JA-isoleucine levels were not significantly altered in the mutant, suggesting potential functional specialization or redundancy among rice OPR family members for JA accumulation. The root system architecture is a key determinant of water and nutrient acquisition; our results suggest that OsOPR5 may play an important role in adaptation under adverse environmental conditions. Collectively, this study establishes an efficient genome-editing platform for indica rice and identifies OsOPR5 as a novel regulator of root development.

Oryza↗
PubMed1996

In vivo human gastrocnemius architecture with changing joint angle at rest and during graded isometric contraction.

1. Human gastrocnemius medialis architecture was analysed in vivo, by ultrasonography, as a function of joint angle at rest and during voluntary isometric contractions up to the maximum force (MCV). maximum force (MVC). 2. At rest, as ankle joint angle increased from 90 to 150 deg, pennation increased from 15.8 to 27.7 deg, fibre length decreased from 57.0 to 34.0 mm and the physiological cross-sectional area (PCSA) increased from 42.1 to 63.5 cm2. 3. From rest to MVC, at a fixed ankle joint angle of 110 deg, pennation angle increased from 15.5 to 33.6 deg and fibre length decreased from 50.8 to 32.9 mm, with no significant change in the distance between the aponeuroses. As a result of these changes the PCSA increased by 34.8%. 4. Measurements of pennation angle, fibre length and distance between the aponeuroses of the gastrocnemius medialis were also performed by ultrasound on a cadaver leg and found to be in good agreement with direct anatomical measurements. 5. It is concluded that human gastrocnemius medialis architecture is significantly affected both by changes of joint angle at rest and by isometric contraction intensity. The remarkable shortening observed during isometric contraction suggests that, at rest, the gastrocnemius muscle and tendon are considerably slack. The extrapolation of muscle architectural data obtained from cadavers to in vivo conditions should be made only for matching muscle lengths.

Adult↗
PubMed2006

The effect of the loading condition corresponding to functional shoulder activities on trabecular architecture of glenoid.

There is little information on bone morphology as it relates to shoulder activities. This study investigated how loads corresponding to functional shoulder activities affect the trabecular architecture of the glenoid. Two different protocols were used. Protocol 1 investigated the material and morphological characteristics of the glenoid by analyzing digitized trabecular bone images obtained from 12 cadaver scapula specimens. Protocol 2 used a finite element analysis (FEA) to compute the principal stress trajectories acting within the glenoid. The principal stresses were derived for five loading conditions, which represent typical functional shoulder activities. The study showed that shoulder activity involved in carrying a light load makes the greatest contribution to the trabecular architecture compared with other shoulder activities considered in this study (p<0.05). With all of the activities considered in this study, the lateral region, particularly in the anterior and posterior portions, showed greater deviation and greater sensitivity to variation under loading conditions than did the other regions (p<0.05). These results suggest that owing to the extra sensitivity of the anterior and posterior parts of the lateral region, these regions may be more informative in the analysis of the trabecular architecture following shoulder musculoskeletal injuries. These results may provide essential design information for shoulder prostheses and contribute to an understanding of morphological changes resulting from injury.

Activities of Daily Living↗
PubMed2004

Implementation of the DPM Monte Carlo code on a parallel architecture for treatment planning applications.

We have parallelized the Dose Planning Method (DPM), a Monte Carlo code optimized for radiotherapy class problems, on distributed-memory processor architectures using the Message Passing Interface (MPI). Parallelization has been investigated on a variety of parallel computing architectures at the University of Michigan-Center for Advanced Computing, with respect to efficiency and speedup as a function of the number of processors. We have integrated the parallel pseudo random number generator from the Scalable Parallel Pseudo-Random Number Generator (SPRNG) library to run with the parallel DPM. The Intel cluster consisting of 800 MHz Intel Pentium III processor shows an almost linear speedup up to 32 processors for simulating 1 x 10(8) or more particles. The speedup results are nearly linear on an Athlon cluster (up to 24 processors based on availability) which consists of 1.8 GHz+ Advanced Micro Devices (AMD) Athlon processors on increasing the problem size up to 8 x 10(8) histories. For a smaller number of histories (1 x 10(8)) the reduction of efficiency with the Athlon cluster (down to 83.9% with 24 processors) occurs because the processing time required to simulate 1 x 10(8) histories is less than the time associated with interprocessor communication. A similar trend was seen with the Opteron Cluster (consisting of 1400 MHz, 64-bit AMD Opteron processors) on increasing the problem size. Because of the 64-bit architecture Opteron processors are capable of storing and processing instructions at a faster rate and hence are faster as compared to the 32-bit Athlon processors. We have validated our implementation with an in-phantom dose calculation study using a parallel pencil monoenergetic electron beam of 20 MeV energy. The phantom consists of layers of water, lung, bone, aluminum, and titanium. The agreement in the central axis depth dose curves and profiles at different depths shows that the serial and parallel codes are equivalent in accuracy.

Algorithms↗
PubMed2000

Comparison of trabecular bone architecture in young and old bones.

In this study, different parameters currently applied for the description of trabecular bone architecture in young and old subjects are compared. Moreover, new parameters are proposed and assessed. For the investigations, the two-dimensional images of vertebral body sections are acquired with the use of a low-magnification digital camera. The parameters were calculated both for the skeleton and for the bone/marrow interface distinguished in the images of the trabecular network. The following methods of the descriptions of the trabecular bone architecture were considered: histomorphometric analysis (BV/TV, asymmetry, mean trabeculae length), fractal geometry technique, Euler characteristic, star volume of the marrow cavity, the mean distance between two points of the trabecular network, and the probability of disconnection (is straightforwardly connected with the number of separated parts of the network). Moreover, bone mineral density (BMD) was determined for comparative purposes. The quantities directly extracted form the images are also combined to produce new indexes, which better differentiate young and old bones. It was found that the BMD, the BV/TV, the star volume, the Euler number, and the probability of disconnection might be used as indicators of the age-related changes of trabecular bone. The parameters could be measured with the precision comparable to that of the BMD. The only exception is the probability of disconnection. Highly significant correlations were demonstrated between bone density (BMD, BV/TV) and trabecular architecture (SV/GV, probability of disconnection).

Adult↗
PubMed2002

Dynamics of genome architecture in Rhizobium sp. strain NGR234.

Bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. Nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. To address these issues, we have studied the dynamics of the genome architecture in Rhizobium sp. strain NGR234 and analyzed its biological significance. NGR234 genome consists of three replicons: the symbiotic plasmid pNGR234a (536,165 bp), the megaplasmid pNGR234b (>2,000 kb), and the chromosome (>3,700 kb). Here we report that genome analyses of cell siblings showed the occurrence of large-scale DNA rearrangements consisting of cointegrations and excisions between the three replicons. As a result, four new genomic architectures have emerged. Three consisted of the cointegrates between two replicons: chromosome-pNGR234a, chromosome-pNGR234b, and pNGR234a-pNGR234b. The other consisted of a cointegrate of the three replicons (chromosome-pNGR234a-pNGR234b). Cointegration and excision of pNGR234a with either the chromosome or pNGR234b were studied and found to proceed via a Campbell-type mechanism, mediated by insertion sequence elements. We provide evidence showing that changes in the genome architecture did not alter the growth and symbiotic proficiency of Rhizobium derivatives.

DNA Transposable Elements↗
PubMed2003

Rhamnolipid surfactant production affects biofilm architecture in Pseudomonas aeruginosa PAO1.

In response to certain environmental signals, bacteria will differentiate from an independent free-living mode of growth and take up an interdependent surface-attached existence. These surface-attached microbial communities are known as biofilms. In flowing systems where nutrients are available, biofilms can develop into elaborate three-dimensional structures. The development of biofilm architecture, particularly the spatial arrangement of colonies within the matrix and the open areas surrounding the colonies, is thought to be fundamental to the function of these complex communities. Here we report a new role for rhamnolipid surfactants produced by the opportunistic pathogen Pseudomonas aeruginosa in the maintenance of biofilm architecture. Biofilms produced by mutants deficient in rhamnolipid synthesis do not maintain the noncolonized channels surrounding macrocolonies. We provide evidence that surfactants may be able to maintain open channels by affecting cell-cell interactions and the attachment of bacterial cells to surfaces. The induced synthesis of rhamnolipids during the later stages of biofilm development (when cell density is high) implies an active mechanism whereby the bacteria exploit intercellular interaction and communication to actively maintain these channels. We propose that the maintenance of biofilm architecture represents a previously unrecognized step in the development of these microbial communities.

Biofilms↗
PubMedDate not supplied

CDC WONDER: a cooperative processing architecture for public health.

CDC WONDER is an information management architecture designed for public health. It provides access to information and communications without the user's needing to know the location of data or communication pathways and mechanisms. CDC WONDER users have access to extractions from some 40 databases; electronic mail (e-mail); and surveillance data processing. System components include the Remote Client, the Communications Server, the Queue Managers, and Data Servers and Process Servers. The Remote Client software resides in the user's machine; other components are at the Centers for Disease Control and Prevention (CDC). The Remote Client, the Communications Server, and the Applications Server provide access to the information and functions in the Data Servers and Process Servers. The system architecture is based on cooperative processing, and components are coupled via pure message passing, using several protocols. This architecture allows flexibility in the choice of hardware and software. One system limitation is that final results from some subsystems are obtained slowly. Although designed for public health, CDC WONDER could be useful for other disciplines that need flexible, integrated information exchange.

Centers for Disease Control and Prevention, U.S.↗
PubMed2000

Features selection and architecture optimization in connectionist systems.

In this paper, we propose a features selection measure and an architecture optimization procedure for Multi-Layer Perceptrons (MLP). The algorithm presented in this contribution employs a heuristic measure named HVS (Heuristic for Variable Selection). This new measure allows us to identify and select important variables in the features space. This can be achieved by eliminating redundant features and those which do not contain enough relevant information. The proposed measure is used in a new procedure aimed at selecting the "best" MLP architecture given an initial structure. Application results for two generic problems: regression and discrimination, demonstrates the proposed selection algorithm's effectiveness in identifying optimized connectionist models with higher accuracy. Finally, an extension of HVS, named epsilonHVS, is proposed for discriminative features detection and architecture optimization for Time Delay Neural Networks models (TDNN).

Algorithms↗
PubMed2001

A neural network architecture for data classification.

This article aims at showing an architecture of neural networks designed for the classification of data distributed among a high number of classes. A significant gain in the global classification rate can be obtained by using our architecture. This latter is based on a set of several little neural networks, each one discriminating only two classes. The specialization of each neural network simplifies their structure and improves the classification. Moreover, the learning step automatically determines the number of hidden neurons. The discussion is illustrated by tests on databases from the UCI machine learning database repository. The experimental results show that this architecture can achieve a faster learning, simpler neural networks and an improved performance in classification.

Computer Systems↗