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At least 865 records · Page 48Linked to original sources
PubMed2005

Preferential attachment in the evolution of metabolic networks.

BACKGROUND: Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. Here we have investigated preferential attachment in the context of metabolic networks. RESULTS: The connectivities of the enzymes in the metabolic network of Escherichia coli were determined and representatives for these enzymes were located in 11 eukaryotes, 17 archaea and 46 bacteria. E. coli enzymes which have representatives in eukaryotes have a higher average connectivity while enzymes which are represented only in the prokaryotes, and especially the enzymes only present in betagamma-proteobacteria, have lower connectivities than expected by chance. Interestingly, the enzymes which have been proposed as candidates for horizontal gene transfer have a higher average connectivity than the other enzymes. Furthermore, It was found that new edges are added to the highly connected enzymes at a faster rate than to enzymes with low connectivities which is consistent with preferential attachment. CONCLUSION: Here, we have found indications of preferential attachment in the metabolic network of E. coli. A possible biological explanation for preferential attachment growth of metabolic networks is that novel enzymes created through gene duplication maintain some of the compounds involved in the original reaction, throughout its future evolution. In addition, we found that enzymes which are candidates for horizontal gene transfer have a higher average connectivity than other enzymes. This indicates that while new enzymes are attached preferentially to highly connected enzymes, these highly connected enzymes have sometimes been introduced into the E. coli genome by horizontal gene transfer. We speculate that E. coli has adjusted its metabolic network to a changing environment by replacing the relatively central enzymes for better adapted orthologs from other prokaryotic species.

Bacteria↗
PubMed2000

Different brain networks mediate task performance in normal aging and AD: defining compensation.

OBJECTIVE: To determine whether the pathologic mechanisms of AD alter the brain networks subserving performance of a verbal recognition task. BACKGROUND: Functional imaging studies comparing task-related activation in AD patients and controls generally have not used network analysis and have not controlled for task difficulty. METHODS: H2 15O PET was used to measure regional cerebral blood flow in 14 patients and 11 healthy elders during the performance of a serial verbal recognition task under two conditions: low demand, with study list size (SLS) equal to one; and titrated demand, with SLS adjusted so that each subject recognized words at 75% accuracy. The Scaled Subprofile Model was used to identify networks of regionally covarying activity across these task conditions. RESULTS: In the elders, higher SLS was associated with the recruitment of a network of brain areas involving left anterior cingulate and anterior insula (R2 = 0.94; p < 0.0001). Three patients also expressed this network. In the remaining patients, higher SLS was associated with the recruitment of an alternate network consisting of left posterior temporal cortex, calcarine cortex, posterior cingulate, and the vermis (R2 = 0.81, p < 0.001). Expression of this network was unrelated to SLS in the elders and more intact AD patients. CONCLUSIONS: The patients' use of the alternate network may indicate compensation for processing deficits. The transition from the normal to the alternate network may indicate a point where brain disease has irreversibly altered brain function and thus may have important implications for therapeutic intervention.

Aged↗
PubMed1981

Polygonal networks in living chick embryonic cells.

Regular polygonal networks have been found in explants and dissociated cells of early chick embryos. These networks are readily observable in live cells with phase-contrast optics thus allowing time-lapse cinemicroscopy. They consisted of a regular pattern of nodes and radiating struts found predominantly in the lamelliplasm of the free edges of the cells bordering explants. At the outer edge, the network was terminated by radial struts associated with substrate-attached retraction processes whilst toward the centre of the cells it faded out. The network was also associated with stress fibres running across the cell and with microextensions on the dorsal surface. Even within one cell the network varied in size. Time-lapse films showed that microvilli were protruded from the dorsal surface over the nodes. Although the cells containing the networks were poorly motile the network itself was a mobile structure. Many explants from regions differing in prospective fates developed these networks after 2-4 days in culture. They appeared earlier in the smaller less yolky cells of definitive endoblast and epiblast. Experiments with dissociated and reaggregated cells confirmed their occurrence mainly in free edges of cells. The relationship between these networks seen in living chick embryo cells and those seen in other cell types using immunofluorescent techniques is discussed and a mechanism is proposed for their formation.

Animals↗
PubMed1996

Morphology and biomechanics of the microfibrillar network of sea cucumber dermis

The principal component of the body wall of the sea cucumber Cucumaria frondosa is a dermis consisting of collagen fibrils, microfibrils, proteoglycans and other soluble and insoluble components. A major structural constituent of the dermis is a network of 10&shy;14 nm diameter microfibrils, which surrounds and penetrates bundles of collagen fibrils. This network has been extracted and purified using guanidine and bacterial collagenase. Tensile testing of the microfibrillar network in artificial sea water demonstrates that it is reversibly extensible up to approximately 300 % of its initial length. It behaves like a viscoelastic solid, having a long-range elastic component as well as a time-dependent viscous component. Reduction and alkylation of the cysteine residues in the network do not change its breaking strain or strength, but greatly increase the compliance of the network until, near the breaking strain, the tensile resistance rapidly increases. These data suggest that the strength of the network is due to non-reducible crosslinks, while its elasticity is dependent upon disulfide bonds. In deionized water, the network becomes swollen and, although it remains elastic, is much more compliant than when tested in artificial sea water. Examination of whole tissues and purified networks with the electron microscope reveals structures similar to vertebrate fibrillin-containing microfibrils. Considering that the dermis of C. frondosa is a mechanically mutable tissue in which elongation is accompanied by the sliding of collagen fibrils past one another, the microfibrillar network may act to maintain the orientation of fibrillar components during movement and may also provide a long-range restoring force.

Journal Article↗
PubMed2005

Functional alignment of regulatory networks: a study of temperate phages.

The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can provide insights into how network architecture is constrained by the functions it directs. Here, we discuss methods of network comparison based on network architecture and signaling logic. Introducing local and global signaling scores for the difference between two networks, we quantify similarities between evolutionarily closely and distantly related bacteriophages. Despite the large evolutionary separation between phage lambda and 186, their networks are found to be similar when difference is measured in terms of global signaling. We finally discuss how network alignment can be used to pinpoint protein similarities viewed from the network perspective.

Bacteriophages↗
PubMed2025

Balanced state of networks of winner-take-all units.

Irregularly timed action potentials, or spikes, are pervasively observed in the brain activity of awake mammals. However, the role of this temporal irregularity in neural computation is still not well understood. In canonical network models irregular spiking emerges via balanced, fluctuating input currents, leading to collective responses that track inputs linearly. How networks characterized by irregular spiking could support flexible nonlinear dynamics needed for general-purpose computation remains under ongoing debate. Here we characterize the dynamics of networks whose elementary unit is not a single neuron but a small group of neurons, with distinct tunings, that compete at each timestep via a winner-take-all (WTA) interaction. While WTA has long been proposed as an elementary functional motif in the brain and represents a powerful computational primitive, how large networks of such units behave has received less investigation. We show that these networks, like classic excitatory-inhibitory balanced networks, exhibit a chaotic fluctuation-driven regime characterized by sustained irregular activity resembling realistic cortical spiking, which we interpret as a multidimensional balance spread over several competing neural populations with different tunings. We develop a mean-field theory for the network, which shows how irregular spiking sustained by time-varying input fluctuations can support flexible nonlinear collective dynamics. Using the theory we predict and verify network regimes in which input fluctuations alone yield multistability, stable sequence generation, or complex heterogeneous firing rate dynamics-three core dynamical primitives thought to underlie memory-dependent neural computation-via consistent Poisson-like spiking produced through chaos. Thus, networks of WTA units support a chaotic fluctuation-driven regime characterized by irregular spiking that can power complex nonlinear collective dynamics. This represents a new model of brain activity capable of simultaneously reproducing realistic spike trains and diverse nonlinear firing rate patterns well posed for flexible computation, and which can be trained or fit to data.

Models, Neurological↗
PubMed2006

Do recent-onset schizophrenia patients experience a "social network crisis"?

It has been proposed that the onset of schizophrenia creates a social network crisis, resulting in a dramatic deterioration of social resources during the period immediately following a first hospitalization from essentially normal pre-hospitalization levels. To evaluate this proposal, recent onset patients (n = 89) completed comprehensive assessments that examined their social networks in the 12 months prior to first hospitalization and, in a subset of patients (n = 34), at a 15-month follow-up. Cross-sectional relationships to social functioning and symptoms were examined at both time points. Compared to existing research, at the initial assessment patients were characterized by several network disturbances, including small network size, a high proportion of family members, and highly dense interconnections among network members; these disturbances generally remained moderately to highly stable at follow-up. Smaller social networks were related to poor current and premorbid social functioning and aspects of clinical functioning, particularly at the 15-month follow-up assessment. Thus, this first repeated assessment of social network characteristics in the early course of schizophrenia does not support the social network crisis concept. Instead, results suggest that functionally relevant social network disturbances often exist by the time of first hospitalization in schizophrenia.

Adult↗
PubMed2005

Activation of early silent synapses by spontaneous synchronous network activity limits the range of neocortical connections.

During the early development of neocortical networks, many glutamatergic synapses lack AMPA receptors and are physiologically silent. We show in neocortical cultures that spontaneous synchronous network activity is able to convert silent synapses to active synapses by the incorporation of AMPA receptors into synaptic complexes throughout the network within a few minutes. To test the effect of synaptic activation on the connectivity of neuronal populations, we created separated neuronal networks that could innervate each other. We allowed outgrowing axons to invade the neighboring network either before or after the onset of synchronous network activity. In the first case, both subnetworks connected to each other and synchronized their activity, whereas in the second case, axonal connections failed to form and network activity did not synchronize between compartments. We conclude that early spontaneous synchronous network activity triggers a global AMPAfication of immature synapses, which in turn prevents later-arriving axons from forming afferent connections. This activity-dependent process may set the range of corticocortical connections during early network development before experience-dependent mechanisms begin elaborating the mature layout of the neocortical connections and modules.

2-Amino-5-phosphonovalerate↗
PubMed2004

The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.

Large-scale models of signaling networks are beginning to be reconstructed and corresponding analysis frameworks are being developed. Herein, a reconstruction of the JAK-STAT signaling system in the human B-cell is described and a scalable framework for its network analysis is presented. This approach is called extreme signaling pathway analysis and involves the description of network properties with systemically independent basis vectors called extreme pathways. From the extreme signaling pathways, emergent systems properties of the JAK-STAT signaling network have been characterized, including 1), a mathematical definition of network crosstalk; 2), an analysis of redundancy in signaling inputs and outputs; 3), a study of reaction participation in the network; and 4), a delineation of 85 correlated reaction sets, or systemic signaling modules. This study is the first such analysis of an actual biological signaling system. Extreme signaling pathway analysis is a topologically based approach and assumes a balanced use of the signaling network. As large-scale reconstructions of signaling networks emerge, such scalable analyses will lead to a description of the fundamental systems properties of signal transduction networks.

B-Lymphocytes↗
PubMed2006

Using the topology of metabolic networks to predict viability of mutant strains.

Understanding the relationships between the structure (topology) and function of biological networks is a central question of systems biology. The idea that topology is a major determinant of systems function has become an attractive and highly disputed hypothesis. Although structural analysis of interaction networks demonstrates a correlation between the topological properties of a node (protein, gene) in the network and its functional essentiality, the analysis of metabolic networks fails to find such correlations. In contrast, approaches utilizing both the topology and biochemical parameters of metabolic networks, e.g., flux balance analysis, are more successful in predicting phenotypes of knockout strains. We reconcile these seemingly conflicting results by showing that the topology of the metabolic networks of both Escherichia coli and Saccharomyces cerevisiae are, in fact, sufficient to predict the viability of knockout strains with accuracy comparable to flux balance analysis on large, unbiased mutant data sets. This surprising result is obtained by introducing a novel topology-based measure of network transport: synthetic accessibility. We also show that other popular topology-based characteristics such as node degree, graph diameter, and node usage (betweenness) fail to predict the viability of E. coli mutant strains. The success of synthetic accessibility demonstrates its ability to capture the essential properties of the metabolic network, such as the branching of chemical reactions and the directed transport of material from inputs to outputs. Our results strongly support a link between the topology and function of biological networks and, in agreement with recent genetic studies, emphasize the minimal role of flux rerouting in providing robustness of mutant strains.

Algorithms↗
PubMed2001

[Public, decentralized and community health networks in Bolivia].

Health sector reform in Bolivia is based primarily on the principles of decentralization and equity, and with the objectives of improving quality and of expanding health services coverage in rural and low-income areas of the country. As an experiment in reform, the Bolivian Ministry of Health and Social Welfare, the department of La Paz, and the municipality of El Alto signed an agreement with a nongovernmental organization (NGO), transferring to the NGO the overall management of one of the health services networks in El Alto. The transfer was based on a management contract that had process and outcome indicators for the network. A year after implementation began, the preliminary results suggest that through the agreement the quality of management and services has improved, health services coverage has expanded, and the network's primary care services have been strengthened. Bed occupancy rates are generally very low in secondary hospitals in Bolivia, with that figure being just 43% in the department of La Paz in 1999. However, in the second 6 months of operation of the El Alto network the occupancy rate for the network's hospital reached 84%. Between the first 6 months of 1999 and the same period in 2000, outpatient consultations increased by 55% in the network (83% in the hospital and 18% in the network's primary care centers). Over that same period, institutional deliveries increased by 41% and the percentage of deliveries in the primary care centers grew from 5% of the total to 9%. A recent user survey found that 87% of the people receiving care in the network felt highly satisfied with the service they had received, and 75% of the persons surveyed said they would recommend the service to others. These are not typical data for health services in Bolivia. This pilot effort suggests that a change in the organization and management of a health services network, with a separation of the roles of purchaser and provider, combined with management based on results and with community participation in the process, can improve the quality and efficiency of those health services, stimulate demand for them, and increase user satisfaction.

Adolescent↗
PubMedDate not supplied

The significance of red cell surface area to the permeability of fibrin network.

Thrombus formed under low shear conditions in the intravascular compartment consists of red cells enmeshed within a fibrin network framework. The permeability of the network determines the rate of molecular transport by convection. The effect of red cells on the permeability of the fibrin network was examined in networks developed from red cell suspensions in platelet-rich (PRP) and platelet-poor plasma (PPP). Red cell-rich networks developed in PRP were significantly more permeable than those developed in PPP. Network permeability decreased linearly with increase in hematocrit due to volume exclusion and cell surface hydraulic drag. The hydraulic resistance of the red cells was similar in order of magnitude to that of the fibrin fibers. The hydraulic resistance was calculated to be dependent on the surface area of the red cells, as well as on red cell concentration. Calculation of red cell surface area from permeability (45-90 microns2) was found to be lower than the known surface area (145 microns2). From these studies, it is suggested that red cells entrapped within the network are aggregated. Aggregation is promoted by low shear plasma conditions during fibrin polymerization and by fibrin polymerization intermediaries. The degree of red cell aggregation regulates the hydraulic resistivity of the red cells, and the fibrin fiber structure regulates the hydraulic resistivity of the fibrin network. Both are significant determinants of the network permeability and, therefore, of molecular transport in thrombi.

Blood Platelets↗
PubMed1996

Gender differences in the support networks of caregivers.

Nurses in home care and long-term care settings play an important role in assisting family caregivers of elders who are cognitively impaired to sustain personal support while caregiving. Research has shown that such support is associated with positive health status. The characteristics of the caregiver's social network provide information about the potential for support. The purpose of this study was to describe and compare the social networks of men and women caregivers in terms of the composition of the social network and the size of the available, utilized and conflicted social networks. The possible relationship between the demographic characteristics of caregivers and the size and composition of their social networks was also examined. In comparison to men, the conflicted social networks of women were larger and comprised of more family members. For women, age, years of caregiving and socioeconomic status were not significantly related to the size of their social network. However, younger men and men of higher socioeconomic status reported significantly larger available social networks than other men. Knowledge of the gender differences in network size and composition that were identified in this study contributes to nurses' ability to identify caregivers who may be at risk for inadequate social support. In conjunction with the findings from related studies these results have implications for nursing assessment and intervention in home care and long-term care settings.

Adult↗
PubMed2000

Improving adequacy of hemodialysis in Northern California ESRD patients: a final project report. Provider Participants and Medical Review Board of the TransPacific Renal Network.

The National Core Indicators Project, initiated in 1994, has brought progressive changes in adequacy of dialysis for end-stage renal disease (ESRD) patients in the TransPacific Renal Network and across the United States. The 1998 Core Indicator Project showed each Network's standing for percentage of patients with urea reduction ratio (URR) > or = 0.65 and average URR. The TransPacific Renal Network ranked 12(th) among the 18 Networks for this adequacy measure. The goals of this project were to improve the Network standing in the United States for the percent of patients with URR > or = 0.65, eliminate or reduce the barriers to achieving adequate dialysis, and evaluate URR versus KT/V data and the variances occurring with these measures. In January 1999, data were collected from all 113 Northern California hemodialysis facilities for quarter 4, 1998, to evaluate adequacy. Each facility provided patient population (N) for KT/V and URR samples, facility averages for KT/V and URR, number of patients with KT/V > or = 1.2 and URR > or = 0.65, and data on post-blood-urea-nitrogen (BUN) sampling methods. A random selection of 10% (12) providers with data below the US and Network standards was selected for an intensive assessment. Using baseline measurements, on-site data were collected from a random selection of the patient population. Chart data were reviewed, analyzed, and discussed in an exit interview with the facility management. On-site visits were performed in July/June 1999. The primary focus included adequacy data and process of care that affect adequacy outcomes, concurrent review of patients receiving treatment at the time of the site visit, and general medical record review. In Phase I, only 12 facilities showed an average URR below 0.65. All facilities reported an average KT/V greater than the DOQI target of 1.2. Forty-two facilities had their percentage of patients with a URR below the national benchmark; only 18 facilities had their percentage of patients with a KT/V below the national benchmark. Only 9% (n = 8) of the 113 providers had a variance in post-BUN sampling methodologies that could be related to the clinical measure of adequacy. In Phase II, a random selection of 12 providers with data below US and Network standards was made for an intensive assessment. A total of 217 patient records were reviewed from a population of 1,027. In addition to comparison of baseline data, each facility was assessed for barriers to achieving adequacy outcomes. The number of problems was extensive and specific to each facility; however, a common reoccurring theme in the majority of events was the lack of supporting documentation for changes to the plan of care when variances occur. The most common occurrences were incorrect blood flow and dialysate flow with no supporting documentation on record for the prescription not being met. In Phase III, Network interventions for facilities not meeting US and Network standards for adequacy as measured by URR and KT/V included required quarterly reporting on their facility-specific quality improvement programs for adequacy. In addition the 12 facilities that participated in the intensive assessment had additional interventions that included an educational "tool box" focused on documentation, legal implications of charting, and general medical records management, and an educational program to review information to be shared with facility staff. All on-site facilities reported ongoing quality improvement programs. In some facilities they did provide a focus on processes and not only a measurement of an indicator. All facilities reported a team concept of some type used in their program. Although there were similarities in the facilities, each facility presented with a unique combination of barriers. In addition to a large patient-to-RN ratio, the lack of technical education for the unlicensed assistive personnel on processes and outcomes appears to play a significant role in the achievement of

Ambulatory Care Facilities↗
PubMedDate not supplied

[Correlations between some features of social networks and treatment outcome in patients with schizophrenia three years after initial hospitalization].

There were studied correlations between some features of social networks of 56 DSM-III schizophrenic patients and "specific aims of treatment": insight, satisfaction of the treatment, compliance, motivation for the treatment and "outcome of treatment" in psychopathological and social level three years from the first admission. There were used Fallow-up Chart, Bizoń's Social Support Questionnaire, BPRS-LA scale and Social Assessment Scale (SAS). There were obtained statistically significant results concerning correlations between the type of support (concentrated, dispersed, and mixed) and the size of the extra-familiar network and the "specific aims" of treatment. This means that patients who have a mixed type of social support and a extended extra-familiar social network obtain better specific treatment aims as: motivation for treatment, co-operation in treatment, insight and a subjective satisfaction of treatment. There exists also significant correlation between some features of social network such as the range of network, the amount and localisation of support and the size of the extra-familiar network and the psychopathology level. The patients who get little support and those whose whole support is localised in family have higher level of negative symptoms measured with BPRS sub-scale. Patients of little range of the social network, including extra-familiar network show more positive symptoms three years after the first hospitalisation. There were found no correlations between the social network features and profession.

Adult↗
PubMed1975

Application of network analysis to the study of the branching patterns of dendritic fields.

The technique of network analysis has been used to define the connectivity and growth of networks generated by monochotomous, dichotomous, and trichotomous branching. The number of distinct topologic branching patterns exhibited by networks with a given number of pendant arcs is defined mathematically; when all types are represented, a complete pendant arc series is formed. The frequency of occurrence of topologic types in these series is unique for a given hypothesis of growth. The growth of the small dendritic arrays such as the basal dendritic fields of neocortical pyramids may be studied by comparing the actual frequency of topologic types with those computed according to given hypotheses. For larger dendritic networks such as those of Purkinje cells in the cerebellum it is only practicable to use the topologic types formed by the peripheral parts of the tree as a basis for comparison. Individual dendritic segments can be ordered sequentially to define their hierarchical arrangement; the frequency of orders in a given network always forms an inverse geometric series. The ratio between orders is called the "bifurcation ratio," and the relationship in a given large series between adjacent orders becomes stabilized to a fixed or "established" bifurcation ratio at the periphery of the tree only. This "established ratio" characterizes the pattern of growth of the network. In the proximal part of the tree the ratio between adjacent orders is unstable and accounts for the variability of the overall bifurcation ratio exhibited by different networks with the same fundamental growth pattern and for the deviation of the overall from the established bifurcation ratio. For a given size of network the overall bifurcation ratio may be similar regardless of the mode of growth. It is concluded that the precise definition of branching structures afforded by network analysis makes this technique well suited for the study of the connectivity, growth, and morphology of dendritic trees.

Computers↗
PubMed2002

Quality of relationships and structural properties of social support networks of female survivors of abuse.

The purposes of this study were to examine the structural properties of the social support networks of female survivors of violence and abuse and to investigate the quality of the relationship, and specific level of satisfaction, survivors have with their social support networks. Participants averaged 5.8 persons in their social support networks. Their levels of satisfaction with the emotional, practical, financial, guidance, and socializing support they received from members of their social support networks were higher with respect to close friends and coworkers than with respect to family members and professionals (e.g., attorneys and social workers). The most common type of support provided by close friends who were themselves victims of abuse was emotional, guidance, and socializing support, and the most satisfying support was the financial and practical help that came from parents or family. An interesting finding was the significant presence of men in the survivors' social support networks. Overall satisfaction with the quality of support from the social support networks was high, and satisfaction with support from men was comparable, if not higher, than support from women. Multiple regression models revealed that satisfaction with support networks was a potent predictor of self-esteem, emotional health, and loneliness. Intimacy, especially in terms of exclusiveness and trust or loyalty, with at least a few members of the support network contributed significantly to the variance in self-esteem, emotional health, and loneliness among the abused women. The size of the support network also emerged as a limited contributor to well-being. Implications and applications are discussed for professionals working with female survivors of abuse.

Activities of Daily Living↗
PubMed2002

Increasing social capital via local networks: analysis in the context of a surgical practice.

The relationship between social capital (support, trust, patient awareness, and increased practice revenue) and local networks (university hospital) in communities has received little attention. The development of computer-based communication networks (social networks) has added a new dimension to the argument, posing the question of whether local networks can (re-)create social capital in local communities. This relationship is examined through a review of the literature on local networks and social capital and a surgeon's practice management from 1990 to 2001 with respect to repair of pectus chest deformities. With respect to pectus repair there was a consistent but small number of new referrals (15-20 new patients/year), lack of patient awareness (eight to 12 self-referred patients/year), and modest practice revenue. Since the inception of an Internet website (social network) dedicated to pectus repair in 1996 there has been increased social participation (n = 630 hits/year to the website); facilitation of spread of information through E-mail messages (n = 430 messages/year); and a greater participation of groups such as women, minorities, adults, and those with disability (n = 120 patients/year). The dissemination of information via the local network has also allowed an "outward movement" with increased participation by interconnecting communities (n = 698,300 global Internet participants based on statistical ratios). We conclude that local networks have enhanced social networks providing new grounds for the development of relationships based on choice and shared interest.

Adult↗