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At least 1,063 records · Page 59Linked to original sources
PubMed2003

International NGOs and the role of network centrality in humanitarian aid operations: a case study of coordination during the 2000 Mozambique floods.

In February 2000, Mozambique suffered its worst flooding in almost 50 years: 699 people died and hundreds of thousands were displaced. Over 49 countries and 30 international non-governmental organisations provided humanitarian assistance. Coordination of disaster assistance is critical for effective humanitarian aid operations, but limited attention has been directed toward evaluating the system-wide structure of inter-organisational coordination during humanitarian operations. Network analysis methods were used to examine the structure of inter-organisational relations among 65 non-governmental organisations (NGOs) involved in the flood operations in Mozambique. Centrality scores were used to estimate NGO-specific potential for aid coordination and tested against NGO beneficiary numbers. The average number of relief- and recovery-period beneficiaries was significantly greater for NGOs with high relative to low centrality scores (p < 0.05). This report addresses the significance of these findings in the context of the Mozambican 2000 floods and the type of data required to evaluate system-wide coordination.

Altruism↗
PubMed2005

Development of pontine noradrenergic A5 neurons requires brain-derived neurotrophic factor.

Pontine noradrenergic A5 neurons play a pivotal role in maturation and regulation of the brainstem respiratory rhythm-generating network. Analysis of newborn brain-derived neurotrophic factor (BDNF)-null mice revealed a marked loss of tyrosine hydroxylase-positive A5 neurons compared to wildtype controls that was rescued by null mutation of the proapoptotic gene Bax. In cultures of the A5 region from E12.5 rat embryos, BDNF significantly increased the number and branching of tyrosine hydroxylase-positive neurons. Immunoneutralization of endogenous glial cell line-derived neurotrophic factor partially inhibited the BDNF-dependent increase in the number of tyrosine hydroxylase-positive cells without affecting neurite number. The A5 nucleus is the first brainstem cell group identified at which BDNF is required in vivo for development of neurons critical for cardiorespiratory control.

Analysis of Variance↗
PubMed2006

The development and delivery of a practice-based breastfeeding education package for general practitioners in the UK.

Growing acceptance that measurable improvements in public health, particularly in lower-income groups, could be achieved by increasing the incidence of breastfeeding has focused attention on the current lack of educational provision in breastfeeding issues for many health professionals. An audit of general practitioners in one area of northern England revealed an interest in receiving breastfeeding training. Department of Health funding was obtained by the breastfeeding subgroup of the local Maternity Services Liaison Committee to develop, deliver and evaluate a practice-based educational session supplemented by a resource pack. Over a 12-month period, 22 practices received the session and the project was evaluated using an illuminative evaluation model. Response rates to two evaluation questionnaires of 81% (133/164) and 62.5% (65/104) were achieved and findings indicated high levels of satisfaction with the session and its accompanying resource pack. Qualitative data related to perceived influence on future practice were subjected to thematic network analysis and revealed four main (organizing) themes: the acquisition of greater knowledge, improved access to resources, a proactive approach to breastfeeding support and the creation of a breastfeeding-friendly environment. The illuminative evaluation also identified recurring issues that could impact on any attempt to replicate or adapt this project; these were the influence of personal breastfeeding experiences, the desire for greater interaction during the training session and the wider implications for practice education of multidisciplinary attendance.

Adult↗
PubMed2002

Pathfinder and other tools for analyzing signal transduction networks.

Many electronic design tools are, at their core, tools for analyzing interacting networks of components in which there is a definite causal sense of direction in each interaction: outputs affect inputs, but not vice versa. Simplifying or restricting a network of protein interactions so that this kind of directedness holds makes the same category of software tools applicable. In signal transduction cascades the direction is usually given by "kinase phosphorylates substrate." This paper examines a few kinds of directed network analysis tools in the context of signal transduction.

Algorithms↗
PubMed2025

Multi-Omics insights into OsZFP252-OsGA20ox5 mediated drought tolerance in rice through stomatal and vascular regulation.

Rice growth is highly dependent on water availability, and drought stress significantly impacts its entire life cycle. However, previous studies lack systematic investigations into drought-responsive candidate genes across the full life cycle of rice. This study integrates transcriptomic and phenotypic data from two rice lines, IR64 (drought-sensitive) and DK151 (drought-tolerant), under varied environmental conditions at distinct growth stages. Using k-means clustering, 13&#x2009;369 genes were categorized into 17 distinct expression patterns, revealing drought-responsive genes specifically upregulated or downregulated under drought stress. Weighted co-expression network analysis (WGCNA) further identified four gene modules strongly correlated with drought-related phenotypes, co-localizing 2859 drought-responsive genes through both approaches. Proteomics and metabolomics were supplemented at the booting stage, where phenotypic and transcriptomic differences under drought were most pronounced. Integrated omics results demonstrate gibberellin (GA) and abscisic acid (ABA) pathways play a key role during drought tolerance in rice, and 79 high-confidence drought-resistant candidate genes were prioritized from the 2859 drought-responsive genes. Among these, Gibberellin 20-oxidase 5 (OsGA20ox5) was identified as a key negative regulator of drought tolerance. Furthermore, the transcription factor zinc finger protein 252 (OsZFP252) directly binds to the OsGA20ox5 promoter, repressing its expression and enhancing ABA biosynthesis, thereby improving drought tolerance by increasing stomatal closure and expanding vascular bundle water transport capacity. Notably, the drought-tolerant haplotype 2-4 (Hap2-4) of OsGA20ox5 provides valuable insights for drought-resistant breeding.

Oryza↗
PubMed2025

Historical introgression as a driver of diversification of diploid Picris (Compositae) in the Mediterranean Basin.

The Mediterranean Basin is recognized as one of the world's most prominent biodiversity hotspots, where past climatic changes have driven range shifts, secondary contact between populations, and gene exchange. This study investigates the impact of historical introgression on the diversification of diploid members of the genus Picris (Compositae). Using nuclear and plastid genome data obtained through the Hyb-Seq approach, we assess whether introgression contributed to the evolution of the Mediterranean Picris, potentially giving rise to multiple regional endemics. We also test whether introgression was associated with the transfer of traits such as life strategy and fruit morphology, which are involved in habitat-specific adaptation. Phylogenetic network analysis revealed two major introgression events that shaped evolutionary trajectories within the genus. The earliest and most complex events involved the Turkish endemic P.&#xa0;campylocarpa, which hybridized with the most recent common ancestor (MRCA) of the P. cyprica-P. pauciflora lineage and with the MRCA of the B1 subclade, comprising the P. hieracioides group and the P.&#xa0;scaberrima-P.&#xa0;strigosa lineage. The latter introgression preceded shifts from iteroparity to semelparity and from heterocarpy to homocarpy, ruling out an adaptive introgression origin for these traits. Nevertheless, all detected historical introgression events contributed to the diversification of diploid Picris taxa.

Diploidy↗
PubMed1999

Quantifying complex patterns of bioacoustic variation: use of a neural network to compare killer whale (Orcinus orca) dialects.

A quantitative measure of acoustic similarity is crucial to any study comparing vocalizations of different species, social groups, or individuals. The goal of this study was to develop a method of extracting frequency contours from recordings of pulsed vocalizations and to test a nonlinear index of acoustic similarity based on the error of an artificial neural network at classifying them. Since the performance of neural networks depends on the amount of consistent variation in the training data, this technique can be used to assess such variation from samples of acoustic signals. The frequency contour extraction and the neural network index were tested on samples of one call type shared by nine social groups of killer whales. For comparison, call similarity was judged by three human subjects in pairwise classification tasks. The results showed a significant correlation between the neural network index and the similarity ratings by the subjects. Both measures of acoustic similarity were significantly correlated with the groups' association patterns, indicating that both methods of quantifying acoustic similarity are biologically meaningful. An index based on neural network analysis therefore represents an objective and repeatable means of measuring acoustic similarity, and allows comparison of results across studies, species and time.

Acoustics↗
PubMed2006

Reassortment and concerted evolution in banana bunchy top virus genomes.

The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.

Asia↗
PubMedDate not supplied

The structure of medical informatics journal literature.

OBJECTIVE: Medical informatics is an emergent interdisciplinary field described as drawing upon and contributing to both the health sciences and information sciences. The authors elucidate the disciplinary nature and internal structure of the field. DESIGN: To better understand the field's disciplinary nature, the authors examine the intercitation relationships of its journal literature. To determine its internal structure, they examined its journal cocitation patterns. MEASUREMENTS: The authors used data from the Science Citation Index (SCI) and Social Science Citation Index (SSCI) to perform intercitation studies among productive journal titles, and software routines from SPSS to perform multivariate data analyses on cocitation data for proposed core journals. RESULTS: Intercitation network analysis suggests that a core literature exists, one mark of a separate discipline. Multivariate analyses of cocitation data suggest that major focus areas within the field include biomedical engineering, biomedical computing, decision support, and education. The interpretable dimensions of multidimensional scaling maps differed for the SCI and SSCI data sets. Strong links to information science literature were not found. CONCLUSION: The authors saw indications of a core literature and of several major research fronts. The field appears to be viewed differently by authors writing in journals indexed by SCI from those writing in journals indexed by SSCI, with more emphasis placed on computers and engineering versus decision making by the former and more emphasis on theory versus application (clinical practice) by the latter.

Abstracting and Indexing↗
PubMed2005

Abridged 5S rDNA units in sea beet (Beta vulgaris subsp. maritima).

Amplification by polymerase chain reaction of the 5S rDNA repeat units of Beta vulgaris subsp. maritima resulted in a 350-bp product corresponding to the full-length 5S unit, but also revealed 4 abridged unit classes, each with a deletion that removed most of the spacer and 12-76 bp of the coding sequence. Each abridged type lacks at least 1 of the conserved elements involved in transcription of the 5S gene, and so appear to be nonfunctional. Network analysis revealed that the abridged units are evolving in the same manner as the full-length versions.

Beta vulgaris↗
PubMed2004

Analyzing cellular biochemistry in terms of molecular networks.

One way to understand cells and circumscribe the function of proteins is through molecular networks. These networks take a variety of forms including webs of protein-protein interactions, regulatory circuits linking transcription factors and targets, and complex pathways of metabolic reactions. We first survey experimental techniques for mapping networks (e.g., the yeast two-hybrid screens). We then turn our attention to computational approaches for predicting networks from individual protein features, such as correlating gene expression levels or analyzing sequence coevolution. All the experimental techniques and individual predictions suffer from noise and systematic biases. These problems can be overcome to some degree through statistical integration of different experimental datasets and predictive features (e.g., within a Bayesian formalism). Next, we discuss approaches for characterizing the topology of networks, such as finding hubs and analyzing subnetworks in terms of common motifs. Finally, we close with perspectives on how network analysis represents a preliminary step toward a systems approach for modeling cells.

Biochemical Phenomena↗
PubMed2004

Molecular networks in model systems.

Model organisms, especially the budding yeast, are leading systems in the transformation of biology into an information science. With the availability of genome sequences and genome-scale data generation technologies, the extraction of biological insight from complex integrated molecular networks has become a major area of research. Here I examine key concepts and review research developments. I propose specific areas of research effort to drive network analysis in directions that will promote modeling with increasing predictive power.

Computational Biology↗
PubMed1999

Nonlinear kinetics and new approaches to complex reaction mechanisms.

This paper reviews recent developments in the field of nonlinear chemical kinetics. Five topics are dealt with: (a) new approaches to complex reaction mechanisms, stoichiometric network analysis, classification of chemical oscillators and formulation of their mechanisms by deduction from experiments, and correlation metric construction of reaction pathways from measurements; (b) thermodynamic and stochastic theory of nonequilibrium processes, the eikonal approximation, the evaluation of stochastic potentials, experimental tests of the thermodynamic and stochastic theory of relative stability, and fluctuation-dissipation relations in nonequilibrium chemical systems; (c) chemical kinetics and cellular automata and lattice gas automata; (d) theoretical approaches and experimental studies of stochastic resonance in chemical kinetics; and (e) rate processes in disordered systems, stochastic Liouville equations, stretched exponential relaxation in disordered systems, and universality classes for rate processes in systems with static or dynamic disorder.

Journal Article↗
PubMed2007

Abnormal muscle and hematopoietic gene expression may be important for clinical morbidity in primary hyperparathyroidism.

In primary hyperparathyroidism (PHPT), excess PTH secretion by adenomatous or hyperplastic parathyroid glands leads to elevated serum [Ca(2+)]. Patients present complex symptoms of muscular fatigue, various neuropsychiatric, neuromuscular, and cardiovascular manifestations, and, in advanced disease, kidney stones and metabolic bone disease. Our objective was to characterize changes in muscle and hematopoietic gene expression in patients with reversible mild PHPT after parathyroidectomy and possibly link molecular pathology to symptoms. Global mRNA profiling using Affymetrix gene chips was carried out in biopsies obtained before and 1 yr after parathyroidectomy in seven patients discovered by routine blood [Ca(2+)] screening. The tissue distribution of PTH receptor (PTHR1 and PTHR2) mRNAs were quantitated using real-time RT-PCR in unrelated persons to define PTH target tissues. Of about 10,000 expressed genes, 175 muscle, 169 hematological, and 99 bone-associated mRNAs were affected. Notably, the major part of muscle-related mRNAs was increased whereas hematological mRNAs were predominantly decreased during disease. Functional and molecular network analysis demonstrated major alterations of several tissue characteristic groups of mRNAs as well as those belonging to common cell signaling and major metabolic pathways. PTHR1 and PTHR2 mRNAs were more abundantly expressed in muscle and brain than in hematopoietic cells. We suggest that sustained stimulation of PTH receptors present in brain, muscle, and hematopoietic cells have to be considered as one independent, important cause of molecular disease in PHPT leading to profound alterations in gene expression that may help explain symptoms like muscle fatigue, cardiovascular pathology, and precipitation of psychiatric illness.

Aged↗
PubMed2005

Functional hierarchy of coronary circulation: direct evidence of a structure-function relation.

The heart muscle is nourished by a complex system of blood vessels that make up the coronary circulation. Here we show that the design of the coronary circulation has a functional hierarchy. A full anatomic model of the coronary arterial tree, containing millions of blood vessels down to the capillary vessels, was simulated based on previously measured porcine morphometric data. A network analysis of blood flow through every vessel segment was carried out based on the laws of fluid mechanics and appropriate boundary conditions. Our results show an abrupt change in cross-sectional area that demarcates the transition from epicardial (EPCA) to intramyocardial (IMCA) coronary arteries. Furthermore, a similar pattern of blood flow was observed with a corresponding transition from EPCA to IMCA. These results suggest functional differences between the two types of vessels. An additional abrupt change occurs in the IMCA in relation to flow velocity. The velocity is fairly uniform proximal to these vessels but drops significantly distal to those vessels toward the capillary branches. This finding suggests functional differences between large and small IMCA. Collectively, these observations suggest a novel functional hierarchy of the coronary vascular tree and provide direct evidence of a structure-function relation.

Blood Flow Velocity↗
PubMed1979

Photoreceptor coupling in retina of the toad, Bufo marinus. II. Physiology.

1. Intracellular recordings were made from red rods in the isolated toad retina in order to measure the extent of the rod coupling. 2. The network space constant, lambda, was determined from edge-response profile measurements on single cells (lambda = 19 +/- 7 micrometer). 3. The network input resistance was estimated to be between 45 and 100 M omega. 4. Both discrete and continuous resistance networks, which were based on the anatomical observations, were analyzed. For lambda/D greater than 1, a continuous network provides an accurate description of the discrete network (D, cell spacing for a square grid). 5. The network analysis was used to estimate the specific resistance of junction membrane (0.75--1.5 omega.cm2) and the conductance provided by a single junctional channel (2.0--3.9 X 10(-12) mho). 6. The anatomical and physiological results provide strong evidence that the rods are electrically coupled. It is concluded that photoreceptor coupling provides averaging of the voltages in adjacent cells. The consequences of this averaging are discussed.

Animals↗
PubMed2002

Exploring genetic regulatory networks in metazoan development: methods and models.

One of the foremost challenges of 21st century biological research will be to decipher the complex genetic regulatory networks responsible for embryonic development. The recent explosion of whole genome sequence data and of genome-wide transcriptional profiling methods, such as microarrays, coupled with the development of sophisticated computational tools for exploiting and analyzing genomic data, provide a significant starting point for regulatory network analysis. In this article we review some of the main methodological issues surrounding genome annotation, transcriptional profiling, and computational prediction of cis-regulatory elements and discuss how the power of model genetic organisms can be used to experimentally verify and extend the results of genomic research.

Animals↗
PubMed2000

Mechanisms of Modulation of a Neural Network.

Neural networks form the basis for the generation and control of various patterns of behavior. Such networks are subjected to modulatory systems that influence their operation and, thereby, the behavior. In the lamprey locomotor network, analysis on the ion channel, synaptic, and cellular levels has given new insights into the organization of such modulatory systems.

Journal Article↗