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Genetic analysis of natural variations in the architecture of Arabidopsis thaliana vegetative leaves.

To ascertain whether intraspecific variability might be a source of information as regards the genetic controls underlying plant leaf morphogenesis, we analyzed variations in the architecture of vegetative leaves in a large sample of Arabidopsis thaliana natural races. A total of 188 accessions from the Arabidopsis Information Service collection were grown and qualitatively classified into 14 phenotypic classes, which were defined according to petiole length, marginal configuration, and overall lamina shape. Accessions displaying extreme and opposite variations in the above-mentioned leaf architectural traits were crossed and their F(2) progeny was found to be not classifiable into discrete phenotypic classes. Furthermore, the leaf trait-based classification was not correlated with estimates on the genetic distances between the accessions being crossed, calculated after determining variations in repeat number at 22 microsatellite loci. Since these results suggested that intraspecific variability in A. thaliana leaf morphology arises from an accumulation of mutations at quantitative trait loci (QTL), we studied a mapping population of recombinant inbred lines (RILs) derived from a Landsberg erecta-0 x Columbia-4 cross. A total of 100 RILs were grown and the third and seventh leaves of 15 individuals from each RIL were collected and morphometrically analyzed. We identified a total of 16 and 13 QTL harboring naturally occurring alleles that contribute to natural variations in the architecture of juvenile and adult leaves, respectively. Our QTL mapping results confirmed the multifactorial nature of the observed natural variations in leaf architecture.

Arabidopsis↗

Alveolar architecture of clear cell renal carcinomas (< or = 5.0 cm) show high attenuation on dynamic CT scanning.

BACKGROUND: To establish the correlation between tumor appearance on CT and tumor histology in renal cell carcinomas. METHODS: The density and attenuation patterns of 96 renal cell carcinomas, each < or = 5 cm in greatest diameter, were studied by non-enhanced CT and early and late after bolus injection of contrast medium using dynamic CT. The density and attenuation patterns and pathological maps of each tumor were individually correlated. RESULTS: High attenuated areas were present in 72 of the 96 tumors on early enhanced dynamic CT scanning. All 72 high attenuated areas were of the clear cell renal cell carcinoma and had alveolar architecture. The remaining 24 tumors that did not demonstrate high attenuated foci on early enhanced scanning included three clear cell, nine granular cell, six papillary, five chromophobe and one collecting duct type. With respect to tumor architecture, all clear cell tumors of alveolar architecture demonstrated high attenuation on early enhanced scanning. CONCLUSION: Clear cell renal cell carcinomas of alveolar architecture show high attenuation on early enhanced dynamic CT scanning. A larger number of patients are indispensable to obtaining clear results. However, these findings seem to be an important clue to the diagnosis of renal cell carcinomas as having an alveolar structure.

Carcinoma, Renal Cell↗

A mechanical analysis of the relationship between free oscillations of Pinus pinaster Ait. saplings and their aerial architecture.

The aim of this study was to investigate the influence of aerial architecture on the dynamic characteristics of young maritime pines (Pinus pinaster Ait.) using a mechanistic approach. For this purpose, three 4-year-old saplings with prominent differences in their branching patterns were submitted to free oscillation tests. The tests were carried out with different methods and directions of mechanical loading in order to initiate the movement of each sapling. The oscillations of the different architectural elements, i.e. stem and branches of different topological order, were measured with inclinometers and strain gauges fixed to saplings. Successive pruning of the architectural elements was carried out to evaluate their relative influence on the dynamic characteristics of the trees. The aerial systems were digitized before the mechanical tests in order to use 3D visualization techniques and to make architectural analyses of the crown structure. Two distinct modes of deformation were detected during free oscillations. The natural swaying frequency ranged from 0.6-0.8 Hz for the saplings tested at the same period of the year. The frequency variations were partly explained by the morphological differences of the experimental subjects. The motions of the axes were found to depend on their topology, i.e. the movement of the axes of a given branching order was forced by the movement of their respective bearing axis. The axes of third branching order had a significant and negative effect on the damping of the natural deformation mode. Results point out the major role played by foliage, qualitatively and quantitatively, on the damping of tree motions and on coupling the motions of the crown components.

Biomechanical Phenomena↗

Genome architecture drives protein evolution in ciliates.

Studies of microbial eukaryotes have been pivotal in the discovery of biological phenomena, including RNA editing, self-splicing RNA, and telomere addition. Here we extend this list by demonstrating that genome architecture, namely the extensive processing of somatic (macronuclear) genomes in some ciliate lineages, is associated with elevated rates of protein evolution. Using newly developed likelihood-based procedures for studying molecular evolution, we investigate 6 genes to compare 1) ciliate protein evolution to that of 3 other clades of eukaryotes (plants, animals, and fungi) and 2) protein evolution in ciliates with extensively processed macronuclear genomes to that of other ciliate lineages. In 5 of the 6 genes, ciliates are estimated to have a higher ratio of nonsynonymous/synonymous substitution rates, consistent with an increase in the rate of protein diversification in ciliates relative to other eukaryotes. Even more striking, there is a significant effect of genome architecture within ciliates as the most divergent proteins are consistently found in those lineages with the most highly processed macronuclear genomes. We propose a model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner. Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution.

Animals↗

Sleep architecture in term and preterm infants beyond the neonatal period: the influence of gestational age, steroids, and ventilatory support.

STUDY OBJECTIVE: To examine (1) sleep architecture of infants at varied risk for sudden infant death syndrome, (2) delays or advances in preterm infants at term postmenstrual age, (3) whether ventilatory support and gestational age alter sleep, (4) whether steroids alter sleep, (5) confounding influences of sex, small for gestational age, and maternal smoking. DESIGN: Overnight polysomnography. DEPENDENT VARIABLES: Percentage of active sleep, quiet sleep, indeterminate, and awake time per total recording time; mean and longest duration of state epochs; number of episodes > or = 10 minutes; and sleep efficiency. SETTING: Collaborative Home Infant Monitoring Evaluation (CHIME). PARTICIPANTS: Two hundred one preterm and 198 term infants between 33 and 58 weeks postmenstrual age during polysomnography. Fifty-one term infants with an apparent life-threatening event without known etiology (apnea of infancy), 59 subsequent siblings of babies who died of sudden infant death syndrome, and 88 healthy term infants. RESULTS: Tracings of infants with apnea of infancy and healthy term infants were similar. Subsequent siblings of babies who died of sudden infant death syndrome spent less time in quiet sleep. Preterm infants (< or = 37 weeks postmenstrual age) exhibited immature architecture compared with infants of term postmenstrual age. The latter exhibited similar sleep except that they had a lower percentage of quiet sleep and longer mean indeterminate and longest indeterminate episodes. Preterm infants with the youngest gestational age lagged behind older preterm infants. Neither sex nor use of steroids affected sleep. Assisted ventilation was associated with a delay in maturation, small-for-gestational age status with increased active sleep, and smoking with increased awake time. CONCLUSION: With few exceptions, asymptomatic premature infants do not exhibit significant delays in sleep architecture compared with term infants at comparable postmenstrual age. The preterm infant with an early gestational age and morbidity exhibited delayed sleep architecture.

Anti-Inflammatory Agents↗

Ammonium and nitrate acquisition by plants in response to elevated CO2 concentration: the roles of root physiology and architecture.

We examined changes in root system architecture and physiology and whole-plant patterns of nitrate reductase (NR) activity in response to atmospheric CO2 enrichment and N source to determine how changes in the form of N supplied to plants interact with rising CO2 concentration ([CO2]). Seedlings of Betula alleghaniensis Britt. and Pinus strobus L., which differ in growth rate, root architecture, and the partitioning of NR activity between leaves (Betula) and roots (Pinus), were grown in ambient (400 microl l(-1)) and elevated (800 microl l(-1)) [CO2] and supplied with either nitrate (NO3-) or ammonium (NH4+) as their sole N source. After 15 weeks of growth, plants were harvested and root system architecture, N uptake kinetics, and NR activity measured. Betula alleghaniensis responded to elevated [CO2] with significant increases in growth, regardless of the source of N. Pinus strobus showed no significant response in biomass production or allocation to elevated [CO2]. Both species exhibited significantly greater growth with NH4+ than with NO3-, along with lower root:shoot biomass ratios. Betula showed significant increases in total root length in response to elevated [CO2]. However, root N uptake rates in Betula (for both NO3- and NH4+) were either reduced or unchanged by elevated [CO2]. Pinus showed the opposite response to elevated [CO2], with no change in root architecture, but an increase in maximal uptake rates in response to elevated [CO2]. Nitrate reductase activity (on a mass basis) was reduced in leaves of Betula in elevated [CO2], but did not change in other tissues. Nitrate reductase activity was unaffected by elevated [CO2] in Pinus. Scaling this response to the whole-plant, NR activity was reduced in elevated [CO2] in Betula but not in Pinus. However, because Betula plants were larger in elevated [CO2], total whole-plant NR activity was unaffected.

Betula↗

Clinical significance of skeletal muscle architecture.

Skeletal muscle architecture is one of the most important properties that determines a muscle's force and excursion capability. In the current review, basic architectural terms first are reviewed and then specific examples relevant to upper extremity anatomy are presented. Specific examples of anatomic considerations required for surgical reconstruction after radial nerve palsy also are detailed. Together, these data show not only the wide variety of architectural designs in human muscles, but the importance of considering architectural design when making surgical decisions.

Biomechanical Phenomena↗

The prognostic value of nuclear versus architectural grading in endometrial adenocarcinoma: a Gynecologic Oncology Group study.

The pathologic grade of endometrial adenocarcinoma is widely recognized as an important prognostic and therapeutic indicator. However, disagreement persists about the optimal method of determining grade. The pathology committee of the Gynecologic Oncology Group employs a system based on the proportion of tumor in glandular array; this system is both reproducible and predictive of outcome. Others have suggested that grading based on nuclear pleomorphism and the size of nucleoli provides better prognostication. We compared the three-level architectural grading system (AG) with a two-level nuclear grading system (NG) to determine reproducibility and prognostic value in 88 cases of stage 1 endometrial adenocarcinoma. Three pathologists made independent assessments of grade by each method. The division of tumors by architectural arrangement was superior for predicting survival (83%, 73%, and 44%, AG, p = 0.005; vs. 79% and 61%, NG, p = 0.14) and equivalent to nuclear grading for prediction of recurrence. Both systems were moderately reproducible (k = 0.49, AG; k = 0.57, NG). Assessment of NG was more tedious than that of AG. Subdivision of architectural grade based on high nuclear atypia, as recommended in current, International Federation of Gynecology and Obstetrics guidelines, did not improve prognostication. Because grading based on nuclear pleomorphism does not provide prognostic information superior to that resulting from architectural grading, we do not advocate its use in routine surgical pathology practice.

Adenocarcinoma↗

High-resolution three-dimensional micro-computed tomography detects bone loss and changes in trabecular architecture early: comparison with DEXA and bone histomorphometry in a rat model of disuse osteoporosis.

RATIONALE AND OBJECTIVES: The ability of three-dimensional micro-computed tomography (3D-microCT) to detect changes in a rat model of disuse osteoporosis was evaluated and compared with two reference techniques: dual x-ray absorptiometry (DEXA) for bone mass, and bone histomorphometry (BHM) for bone mass and trabecular micro-architecture. METHODS: Forty-two rats were divided into controls or were hindlimb unloaded for 7, 13, and 23 days. DEXA bone mineral density measurements were performed on right tibiae. Then, after plastic embedding, bone volume (BV/TV) and trabecular (Tb)-derived parameters of trabecular bone architecture (Tb Th, thickness; Tb N, number) were measured with BHM. 3D-microCT measurements of BV/TV, Tb Th, and Tb N were carried out on left tibiae. RESULTS: Unloaded rats lost bone in a time-dependent manner. DEXA and 3D-microCT detected bone loss earlier than BHM. The decreases in Tb Th and Tb N were observed at day 13 only with 3D-microCT (P < 0.05 and P < 0.01, respectively). All bone mass and architectural parameters measured with the three techniques correlated significantly (0.59, 0.89, P < 0.001), except Tb Th. CONCLUSIONS: 3D-microCT is a valid technique for bone mass and micro-architecture measurements in this rat model of disuse osteoporosis.

Absorptiometry, Photon↗

Polysomnography in newborns and young infants: sleep architecture.

Sleep architecture derived from long-term polysomnographic recordings during the first year of life is characterized by clear developmental trends against a backdrop of variability. Variability is due to differences in state definitions and data collection and analysis strategies but probably also to an intrinsic characteristic of the maturing central nervous system (functional plasticity). Changes in sleep and wakefulness probably constitute nonspecific responses to a variety of stimuli. The variability has frustrated efforts to use specific features of sleep architecture for diagnostic or prognostic purposes. At present, polysomnographic studies of sleep architecture independent from EEG and cardiorespiratory studies are not indicated for diagnosing specific medical conditions or prognoses of good/adverse outcomes. For accurate interpretation for cardio-respiratory data, however, studies of sleep and wakefulness are indispensable. Furthermore, the study of neonatal seizures, in particular the coherence of state-defining variables or the evolution of sleep morphology, may benefit from attention to sleep architecture. Initial findings from some laboratories suggest that the very feature of excessive instability, which can be measured by repetitive long-term polysomnographic monitoring, signals a poor prognosis. In addition, fragmented sleep and the evolving interrelationship between ultradian and circadian rhythms may contain useful information that has yet to be mined. The advent of computer technologies can make the clinical laboratory into a setting where both research and clinical studies contribute to an elucidation of risk for sudden infant death syndrome and sequelae of neonatal seizures.

Circadian Rhythm↗

Changes in bone architecture during spinal fusion: three years follow-up and the role of cage stiffness.

STUDY DESIGN: A morphometrical analysis of microcomputed tomography-based reconstructions of bone from the fusion zone in spinal cages. OBJECTIVE: To describe the architectural changes of the fusing bone tissue in time and to study the effect of cage stiffness on the development of the bone architecture within the cage. SUMMARY OF BACKGROUND DATA: Interbody fusion within spinal cages is routinely evaluated as either successful or not successful. The quality of the fusion, however, strongly depends on the architecture (i.e., structure and density) of the bone tissue within the cage. Bone architecture obviously changes during the fusion process, and cage stiffness is known to play a pivotal role. METHODS: Nine bone samples were available from a long-term in vivo study on resorbable spinal cages in Dutch milk goats described elsewhere. Follow-up periods of 3, 6, 12, 24, 30, and 36 months were considered for cages made of titanium or Poly L-Lactic Acid. The specimens were scanned with a resolution of 13 microm in a microcomputed tomography system. From the resulting reconstructions, the bone density; trabecular thickness, spacing, and number; connectivity density; and structure model index were assessed. RESULTS: We found a homogenization of all bone structure indexes along the spinal axis with time, and remarkably faster in the Poly L-Lactic Acid cages than in the titanium cages. After longer follow-up periods, a coarser bone structure with larger trabecular thickness and intertrabecular spacing was found. The structure model index appeared to be sensitive for nonunions. CONCLUSIONS: More "mature" spinal fusions showed a coarser and more homogeneous bone structure. High cage stiffness had a deteriorating effect on the fusion rate. The structure model index appears to be an interesting parameter for quantifying the quality of bone in the fusion zone.

Animals↗

Trabecular architecture of lumbar vertebral pedicle.

STUDY DESIGN: Investigation on architecture of lumbar pedicle. OBJECTIVE: To determine morphological properties of pedicular cancellous bone. SUMMARY OF BACKGROUND DATA: Many researchers have been stimulated to study trabecular architecture by improvements in stereological technology. Although the structure of vertebral cancellous bone has been well studied in the literature, no information is available about the architecture of pedicular cancellous bone. METHODS: Eight cadaveric L3 lumbar vertebrae were harvested. After collecting the bone mineral density (BMD) data on the vertebrae, pedicle isthmuses were removed from the vertebral bodies using a reciprocal hand saw. The BMD measurements were done on the dissected pedicle isthmus specimens. All the specimens were then analyzed using a micro-computed tomography unit. Morphologic parameters of trabecular bone were calculated. RESULTS: Bone volume was found as 0.209 +/- 0.046, whereas Tb.Th, Tb.Sp, and Tb.N were found to be 0.201 +/- 0.035 mm, 0.930 +/- 0.123 mm, and 1.098 +/- 0.136 mm(-1), respectively. Connectivity density and structure model index were observed to be 3.135 +/- 0.918 mm(-3), 0.37, whereas degree of anisotropy value was 1.241 +/- 0.093. Vertebral BMD could explain 63% of variance in bone density of a pedicle isthmus. CONCLUSIONS: The structure of the pedicular cancellous bone is somewhat different from that of vertebral body. The trabecular architecture within the pedicle isthmus is isotropic and plate-like. The thickness and number of the trabeculae were greater than those of vertebral trabeculae. Decrease in the bone volume with age is mainly by thinning of the trabeculae and increasing in trabecular spacing, but not by loss of mass.

Adult↗

Vertebral endplate architecture and vascularization: application of micro-computerized tomography, a vascular tracer, and immunocytochemistry in analyses of disc degeneration in the aging sand rat.

STUDY DESIGN: Lower lumbar vertebral endplates from young and old sand rats were assessed in an Institutional Animal Care and Use Committee approved study for architectural endplate features using micro-computerized tomography (CT) 3-dimensional (3D) models and vascularization studies by an in vivo vascular tracer or immunocytochemical identification of blood vessels. OBJECTIVE: To assess endplate porosity and vascularization using microCT architectural analysis, an in vivo vascular tracer, and immunocytochemical identification of blood vessels in the endplate. SUMMARY OF THE BACKGROUND DATA: The vertebral endplates, also called cartilage endplates, form the superior and inferior, or cranial and caudal, boundaries of the disc. In the human being and sand rat, the cartilaginous endplate undergoes calcification with aging and is replaced by bone. Endplate sclerosis has long been thought to play a role in disc degeneration by decreasing nutrient availability to the disc, but this is still poorly understood. Previous work has identified increasing bone mineral density with aging and disc degeneration in the sand rat model. METHODS: microCT models of the lower lumbar endplates of vertebrae at L5-6 and L6-7 were constructed from 6 younger (mean age 11 months) and 21 older (mean age 25.6 months) sand rats. Architectural features were scored on a semiquantitative scale for smoothness of the endplate face, irregularities on the endplate margin, and endplate thickness. There were 2 smaller sets of animals (n = 18) evaluated for endplate vascularity following in vivo injection of a fluorescent vascular tracer or by the use of immunocytochemistry to identify blood vessels. RESULTS: microCT revealed a solid bony surface to the endplate, which was not penetrated by vasculature; with aging/disc degeneration, there was roughening and pitting of the plate surface, and the development of irregular margins. In L5-6 and L6-7, sites of prominent disc degeneration evident on radiographs, the proportion of abnormalities in surface smoothness, margin irregularity, and endplate thickening were all statistically significant in both younger and older animals (P < or = 0.0027). More severe changes were evident in the caudal versus cranial endplate surfaces. Histologic study of vascular tracer showed that there was no penetration of the disc by vascular supply from the endplate; this was verified by immunocytochemical identification of blood vessels. The canal system within the endplate was a complex 3D interconnected network. CONCLUSIONS: Findings show that disc degeneration in the sand rat occurs concomitantly with marked architectural bony changes on the endplate face, including loss of smoothness and development of irregular bony margins. Vascular connections were not present between the endplate and disc; this was verified with microCT studies, in vivo vascular tracers, and traditional immunocytochemistry. The canal system within the imaged endplate was revealed to consist of a complex 3D interconnected network.

Aging↗

Sexual reproduction reshapes the genetic architecture of digital organisms.

Modularity and epistasis, as well as other aspects of genetic architecture, have emerged as central themes in evolutionary biology. Theory suggests that modularity promotes evolvability, and that aggravating (synergistic) epistasis among deleterious mutations facilitates the evolution of sex. Here, by contrast, we investigate the evolution of different genetic architectures using digital organisms, which are computer programs that self-replicate, mutate, compete and evolve. Specifically, we investigate how genetic architecture is shaped by reproductive mode. We allowed 200 populations of digital organisms to evolve for over 10 000 generations while reproducing either asexually or sexually. For 10 randomly chosen organisms from each population, we constructed and analysed all possible single mutants as well as one million mutants at each mutational distance from 2 to 10. The genomes of sexual organisms were more modular than asexual ones; sites encoding different functional traits had less overlap and sites encoding a particular trait were more tightly clustered. Net directional epistasis was alleviating (antagonistic) in both groups, although the overall strength of this epistasis was weaker in sexual than in asexual organisms. Our results show that sexual reproduction profoundly influences the evolution of the genetic architecture.

Biological Evolution↗

Phosphate availability alters architecture and causes changes in hormone sensitivity in the Arabidopsis root system.

The postembryonic developmental program of the plant root system is plastic and allows changes in root architecture to adapt to environmental conditions such as water and nutrient availability. Among essential nutrients, phosphorus (P) often limits plant productivity because of its low mobility in soil. Therefore, the architecture of the root system may determine the capacity of the plant to acquire this nutrient. We studied the effect of P availability on the development of the root system in Arabidopsis. We found that at P-limiting conditions (<50 microM), the Arabidopsis root system undergoes major architectural changes in terms of lateral root number, lateral root density, and primary root length. Treatment with auxins and auxin antagonists indicate that these changes are related to an increase in auxin sensitivity in the roots of P-deprived Arabidopsis seedlings. It was also found that the axr1-3, axr2-1, and axr4-1 Arabidopsis mutants have normal responses to low P availability conditions, whereas the iaa28-1 mutant shows resistance to the stimulatory effects of low P on root hair and lateral root formation. Analysis of ethylene signaling mutants and treatments with 1-aminocyclopropane-1-carboxylic acid showed that ethylene does not promote lateral root formation under P deprivation. These results suggest that in Arabidopsis, auxin sensitivity may play a fundamental role in the modifications of root architecture by P availability.

2,4-Dichlorophenoxyacetic Acid↗

A three-dimensional architecture for a parallel processing photosensing array.

A three-dimensional architecture for a photosensing array has been developed. This silicon based architecture consists of a 10 x 10 array of photosensors with 80 microns diameter, through chip interconnects to the back side of a 500 microns thick silicon wafer. Each photosensor consists of a 300 x 300 microns pn-junction photodiode. The following processes were used to create this photosensing architecture: 1) thermomigration of aluminum pads through an n-type silicon wafer; 2) creation of pn-junction photosensors on one side of the wafer; and 3) creation of aluminum pad ohmic contacts to the thermomigrated, through chip interconnects and the substrate on the back side of the wafer. The electrical and optical characteristics of the three-dimensional architecture indicates that it should be well suited as a photosensing framework around which a "silicon retina" could be built.

Artificial Organs↗

A characterization of the geometric architecture of the peritalar joint complex via MRI: an aid to the classification of foot type.

The purpose of this work is to study the architecture of the rearfoot using in vivo MR image data. Each data set used in this study is made of sixty sagittal slices of the foot acquired in a 1.5-T commercial GE MR system. We use the live-wire method to delineate boundaries and form the surfaces of the bones. In the first part of this work, we describe a new method to characterize the three-dimensional (3-D) relationships of four bones of the peritalar complex and apply this description technique to data sets from ten normal subjects and from seven pathological cases. In the second part, we propose a procedure to classify feet, based on the values of these new architectural parameters. We conclude that this noninvasive method offers a unique tool to characterize the 3-D architecture of the feet in live patients, based on a set of new architectural parameters. This can be integrated into a set of tools to improve diagnosis and treatment of foot malformations.

Algorithms↗

Workflow-enabled distributed component-based information architecture for digital medical imaging enterprises.

Few information systems today offer a flexible means to define and manage the automated part of radiology processes, which provide clinical imaging services for the entire healthcare organization. Even fewer of them provide a coherent architecture that can easily cope with heterogeneity and inevitable local adaptation of applications and can integrate clinical and administrative information to aid better clinical, operational, and business decisions. We describe an innovative enterprise architecture of image information management systems to fill the needs. Such a system is based on the interplay of production workflow management, distributed object computing, Java and Web techniques, and in-depth domain knowledge in radiology operations. Our design adapts the approach of "4+1" architectural view. In this new architecture, PACS and RIS become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, the workflow-enabled digital radiology system would provide powerful query and statistical functions for managing resources and improving productivity. This paper will potentially lead to a new direction of image information management. We illustrate the innovative design with examples taken from an implemented system.

Computer Communication Networks↗