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PubMed1986

The brain as a self-organizing system.

Clinical evidence and numerous results from animal experimentation indicate that cognitive functions have to be learned. Brain structures subserving these functions require sensory experience for their maturation. Genetic instructions are in principle not sufficient to specify neuronal connections with sufficient precision. Self-organization processes are implemented in addition which allow to optimize genetically determined blue prints of connectivity by making use of functional criteria. Thus, neuronal activity becomes an important shaping factor in the development of the structural and functional architecture of the forebrain. To the extent that this neuronal activity is modulated by sensory signals, environmental factors can influence the development of neuronal networks. Recent experiments indicate that these shaping processes are additionally controlled by modulatory systems. Both, the noradrenergic projection from the locus coeruleus and the cholinergic projection from the basal forebrain facilitate activity-dependent long-term changes of neuronal connections during development. The activity of these modulatory systems in turn depends on central states such as arousal, attention, and perhaps also motivation. It is inferred from this evidence that experience-dependent self-organization should not be considered as a passive imprinting process but rather as an active dialogue between the brain and its environment. The hypothesis is discussed that many developmental disturbances which are commonly attributed to deprivation are in fact due to defaults of the CNS which either lead to the formulation of wrong questions or to the reduction of exploratory drive.

Animals↗

PubMed2004

Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods.

The CRF04_cpx strains of HIV-1 accounts for approximately 2-10% of the infected population in Greece, across different transmission risk groups. CRF04_cpx was the lineage documented in an HIV-1 transmission network in Thessalonica, northern Greece. Most of the transmissions occurred through unprotected heterosexual contacts between 1989 and 1993. Blood samples were available for six patients, obtained 6-10 years later, except for one patient sampled in 1991. Our objective was to examine whether the transmission history is compatible with the evolutionary tree of the virus, in partial gag, partial env, and partial gag+env. The inferred phylogenetic tree obtained using maximum likelihood and Bayesian methods in partial gag+env was much closer to the transmission tree than that using either env or gag separately. Our findings suggest that the epidemiological relationships among patients who have been infected by a common source correspond almost exactly to the evolutionary trees of the virus, given that enough phylogenetic signal is present in the alignment. Moreover, we found evidence that recombination is not the most parsimonious explanation for the phylogenetic incongruence between gag and env. For patients with known infection dates, the estimated dates of the coalescent events obtained using molecular clock calculations based on a newly developed Bayesian method in gag + env were in agreement with the actual infection dates.

Bayes Theorem↗

PubMed2006

Low-frequency earthquakes in Shikoku, Japan, and their relationship to episodic tremor and slip.

Non-volcanic seismic tremor was discovered in the Nankai trough subduction zone in southwest Japan and subsequently identified in the Cascadia subduction zone. In both locations, tremor is observed to coincide temporally with large, slow slip events on the plate interface downdip of the seismogenic zone. The relationship between tremor and aseismic slip remains uncertain, however, largely owing to difficulty in constraining the source depth of tremor. In southwest Japan, a high quality borehole seismic network allows identification of coherent S-wave (and sometimes P-wave) arrivals within the tremor, whose sources are classified as low-frequency earthquakes. As low-frequency earthquakes comprise at least a portion of tremor, understanding their mechanism is critical to understanding tremor as a whole. Here, we provide strong evidence that these earthquakes occur on the plate interface, coincident with the inferred zone of slow slip. The locations and characteristics of these events suggest that they are generated by shear slip during otherwise aseismic transients, rather than by fluid flow. High pore-fluid pressure in the immediate vicinity, as implied by our estimates of seismic P- and S-wave speeds, may act to promote this transient mode of failure. Low-frequency earthquakes could potentially contribute to seismic hazard forecasting by providing a new means to monitor slow slip at depth.

Journal Article↗

PubMed2005

Disease gene discovery through integrative genomics.

The availability of complete genome sequences and the wealth of large-scale biological data sets now provide an unprecedented opportunity to elucidate the genetic basis of rare and common human diseases. Here we review some of the emerging genomics technologies and data resources that can be used to infer gene function to prioritize candidate genes. We then describe some computational strategies for integrating these large-scale data sets to provide more faithful descriptions of gene function, and how such approaches have recently been applied to discover genes underlying Mendelian disorders. Finally, we discuss future prospects and challenges for using integrative genomics to systematically discover not only single genes but also entire gene networks that underlie and modify human disease.

Databases, Genetic↗

PubMed2006

A fluctuation method to quantify in vivo fluorescence data.

Quantitative in vivo measurements are essential for developing a predictive understanding of cellular behavior. Here we present a technique that converts observed fluorescence intensities into numbers of molecules. By transiently expressing a fluorescently tagged protein and then following its dilution during growth and division, we observe asymmetric partitioning of fluorescence between daughter cells at each division. Such partition asymmetries are set by the actual numbers of proteins present, and thus provide a means to quantify fluorescence levels. We present a Bayesian algorithm that infers from such data both the fluorescence conversion factor and an estimate of the measurement error. Our algorithm works for arbitrarily sized data sets and handles consistently any missing measurements. We verify the algorithm with extensive simulation and demonstrate its application to experimental data from Escherichia coli. Our technique should provide a quantitative internal calibration to systems biology studies of both synthetic and endogenous cellular networks.

Algorithms↗

PubMed2003

Effects of geographical location and land use on atmospheric deposition of nitrogen in the State of Connecticut.

A network of eight monitoring stations was established to study the atmospheric nitrogen concentration and deposition in the State of Connecticut. The stations were classified into urban, rural, coastal and inland categories to represent the geographical location and land use characteristics surrounding the monitoring sites. Nitrogen species including nitrate, ammonium, nitric acid vapor and organic nitrogen in the air and precipitation were collected, analyzed and used to infer nitrogen concentrations and dry and wet deposition flux densities for the sampling period from 1997 through 1999, with independently collected meteorological data. Statistical analyses were conducted to evaluate the spatial variations of atmospheric concentration and deposition fluxes of total nitrogen in Connecticut. A slightly higher atmospheric concentration of total nitrogen was observed along the Connecticut coastline of Long Island Sound compared to inland areas, while the differences of nitrogen deposition fluxes were insignificant between coastal and inland sites. The land use characteristics surrounding the monitoring sites had profound effects on the atmospheric nitrogen concentration and dry deposition flux. The ambient nitrogen concentration over the four urban sites was averaged 38.9% higher than that over the rural sites, resulting a 58.0% higher dry deposition flux in these sites compared to their rural counterparts. The local industrial activities and traffic emissions of nitrogen at urban areas had significant effects on the spatial distribution of atmospheric nitrogen concentration and dry deposition flux in the State. Wet and total deposition fluxes appeared to be invariant between the monitoring sites, except for high flux densities measured at Old Greenwich, a monitoring station near to and downwind of the New York and New Jersey industrial complexes.

Agriculture↗

PubMed2001

Milk protein interfacial layers and the relationship to emulsion stability and rheology.

The properties of milk protein-stabilised, oil-in-water emulsions are determined by the structure and surface rheology of the adsorbed layer at the oil-water interface. Analysis of the segment density profiles normal to the surface show differences in the structure between adsorbed layers of disordered casein and globular whey protein. Systematic studies of stability and rheology of model oil-in-water emulsion systems made with milk proteins as sole emulsifiers give insight into the relation between adsorbed layer properties and bulk emulsion stability. Of particular importance are effects of pH, temperature, calcium ions and protein content. Colloidal interactions between adsorbed layers on different surfaces can be inferred from an analysis of dynamic collisions of protein-coated emulsion droplets in shear flow using the colloidal particle scattering technique. The role of competitive adsorption on emulsion properties can be derived from experiments on systems containing mixtures of milk proteins and small-molecule surfactants. Shear-induced destabilisation is especially influenced by the presence of fat crystals in the emulsion droplets. Aggregated gel network properties are dependent on the balance of weak and strong interparticle interactions. In heat-set whey protein emulsion gels, the rheological behaviour is especially sensitive to surfactant type and concentration. Rearrangements of transient caseinate-based emulsion gels can have a profound influence on the quiesent stability behaviour. Computer simulation provides a general link between particle interactions, microstructure and rheological properties.

Journal Article↗

PubMed1998

Rethinking eliminative connectionism.

Humans routinely generalize universal relationships to unfamiliar instances. If we are told "if glork then frum," and "glork," we can infer "frum"; any name that serves as the subject of a sentence can appear as the object of a sentence. These universals are pervasive in language and reasoning. One account of how they are generalized holds that humans possess mechanisms that manipulate symbols and variables; an alternative account holds that symbol-manipulation can be eliminated from scientific theories in favor of descriptions couched in terms of networks of interconnected nodes. Can these "eliminative" connectionist models offer a genuine alternative? This article shows that eliminative connectionist models cannot account for how we extend universals to arbitrary items. The argument runs as follows. First, if these models, as currently conceived, were to extend universals to arbitrary instances, they would have to generalize outside the space of training examples. Next, it is shown that the class of eliminative connectionist models that is currently popular cannot learn to extend universals outside the training space. This limitation might be avoided through the use of an architecture that implements symbol manipulation.

Humans↗

PubMed2005

The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.

During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudogenization) and deletion. Here, we examine the evolutionary sequence of gene-death events during the process of genome miniaturization in three bacterial species that have experienced extensive genome reduction: Mycobacterium leprae, Shigella flexneri, and Salmonella typhi. We infer that in all three lineages, the distribution of functional categories is similar in pseudogenes and genes but different from that of absent genes. Based on an analysis of evolutionary distances, we propose a two-step "domino effect" model for reductive genome evolution. The process starts with a gradual gene-by-gene-death sequence of events. Eventually, a crucial gene within a complex pathway or network is rendered nonfunctional triggering a "mass gene extinction" of the dependent genes. In contrast to published reports according to which genes belonging to certain functional categories are prone to nonfunctionalization more frequently and earlier than genes belonging to other functional categories, we could discern no characteristic regularity in the temporal order of function loss.

Bacteria↗

PubMed2005

Detecting a currency's dominance or dependence using foreign exchange network trees.

In a system containing a large number of interacting stochastic processes, there will typically be many nonzero correlation coefficients. This makes it difficult to either visualize the system's interdependencies, or identify its dominant elements. Such a situation arises in foreign exchange (FX), which is the world's biggest market. Here we develop a network analysis of these correlations using minimum spanning trees (MSTs). We show that not only do the MSTs provide a meaningful representation of the global FX dynamics, but they also enable one to determine momentarily dominant and dependent currencies. We find that information about a country's geographical ties emerges from the raw exchange-rate data. Most importantly from a trading perspective, we discuss how to infer which currencies are "in play" during a particular period of time.

Journal Article↗

PubMed1985

A case of elliptocytosis associated with a truncated spectrin chain.

A case of haemolytic anaemia with elliptocytosis is described, in which a large part of the smaller (beta) subunit of the spectrin is truncated, and has an apparent molecular weight of about 214 000 compared with about 230 000 for the normal chain. It is shown that this is not a product of adventitious proteolysis during lysis or extraction. At the same time about 35% of the total spectrin in the cells is liberated from the membrane as the dimer (which is present in normal cells to the extent of less than 10%). The truncated (beta') chain appears exclusively in this dimer fraction. The beta'-chain is incapable of phosphorylation by the endogenous cAMP-independent membrane kinase, and it may be inferred that the deleted segment of the chain contains both the spectrin self-association site and the residues normally phosphorylated. The alpha beta'-dimer is active with respect to participation in a ternary complex with its partnering proteins in the membrane cytoskeleton, F-actin and 4.1, confirming that the phosphorylation sites are not involved in the primary interaction with the other cytoskeletal proteins at the network junctions. The spectrin alpha-chain generates the terminal tryptic fragment of molecular weight 80 000 characteristic of normal spectrin, rather than the 74 000 molecular weight peptide derived from the alpha-chain in cases of hereditary elliptocytosis and pyropoikilocytosis, associated with anomalous self-association of spectrin dimer. Membrane cytoskeletons, extracted from the patient's red cells, undergo normal gelation on incubation with cAMP-independent kinase and ATP, and thus do not resemble those derived from hereditary spherocytosis cells. The properties of the anomalous spectrin resemble in most respects that described in a French family by Dhermy et al (1982).

Adolescent↗

PubMed2002

Seismic detection of sonic booms.

The pressure signals from a sonic boom will produce a small, but detectable, ground motion. The extensive seismic network in southern California, consisting of over 200 sites covering over 50000 square kilometers, is used to map primary and secondary sonic boom carpets. Data from the network is used to analyze three supersonic overflights in the western United States. The results are compared to ray-tracing computations using a realistic model of the stratified atmospheric at the time of the measurements. The results show sonic boom ground exposure under the real atmosphere is much larger than previously expected or predicted by ray tracing alone. Finally, seismic observations are used to draw some inferences on the origin of a set of "mystery booms" recorded in 1992-1993 in southern California.

Acoustics↗

PubMed1999

Patterns of gene flow inferred from genetic distances in the Mediterranean region.

The analysis of population structure may lead to inferences about demographic phenomena. In particular, regions of sharp genetic differentiation suggest the existence of factors that impaired gene flow and increased the evolutionary role of genetic drift. Here, we present an analysis of a data set of 10 allele frequencies in 39 populations of the Mediterranean region. As a preliminary step, we describe spatial patterns of allele frequencies using spatial autocorrelation analysis. We then construct a network connecting localities and estimate genetic distances along the edges of the network. By applying specific algorithms, we locate on the map the areas of sharpest genetic differentiation, or genetic boundaries. The main boundaries separate the northern and the southern coasts, especially in their western portions; in addition, several localities appear genetically isolated. The comparatively high genetic differentiation across the western Mediterranean, where the sea distances between localities are shorter, strongly suggests that the sea distance by itself can hardly be regarded as a major isolating factor among these populations. On the contrary, the decrease in genetic resemblance between populations of the 2 coasts as one proceeds westward may reflect an increased genetic exchange in the eastern Mediterranean basin or independent human dispersal along the 2 coasts or both.

Algorithms↗

PubMed2026

A transcription factor regulatory atlas for activity inference and perturbation prediction.

Inferring transcription factor (TF) activity from transcriptomes and predicting transcriptome-wide responses to TF perturbations remain challenging, in part because available TF-mRNA resources often face a trade-off between precision and coverage and typically lack signed regulatory information. Here, we present TFActProfiler, a TF-mRNA resource and computational framework that learns signed, quantitative TF-mRNA regulatory coefficients by integrating heterogeneous prior evidence (ChIP-based, motif-based, and curated TF-mRNA annotations) with large-scale bulk and single-cell RNA-seq atlases. TFActProfiler contains 2 606 176 signed TF-mRNA interactions and improves TF activity inference in TF knockdown benchmarks relative to widely used regulon resources while retaining broad TF and target coverage. In addition, because the same learned regulatory coefficients can be used to model downstream transcriptional effects, TFActProfiler enables prediction of transcriptome-wide gene expression responses to TF knockdown without training on task-matched perturbation data. When perturbation datasets are available, TFActProfiler can be further refined to achieve performance comparable to state-of-the-art machine-learning baselines. By providing a direction-aware representation of TF-mRNA regulation for both activity inference and perturbation-response modeling, TFActProfiler supports systematic dissection of gene regulatory programs across diverse cellular contexts.

Transcription Factors↗

PubMed2000

Irregularity and asynchrony in biologic network signals.

The principal focus of this chapter has been the description of both ApEn, a quantification of serial irregularity, and of cross-ApEn, a thematically similar measure of two-variable asynchrony (conditional irregularity). Several properties of ApEn facilitate its utility for biological time series analysis: (1) ApEn is nearly unaffected by noise of magnitude below a de facto specified filter level; (2) ApEn is robust to outliers; (3) ApEn can be applied to time series of 50 or more points, with good reproducibility; (4) ApEn is finite for stochastic, noisy deterministic, and composite (mixed) processes, these last of which are likely models for complicated biological systems; (5) increasing ApEn corresponds to intuitively increasing process complexity in the settings of (4); and (6) changes in ApEn have been shown mathematically to correspond to mechanistic inferences concerning subsystem autonomy, feedback, and coupling, in diverse model settings. The applicability to medium-sized data sets and general stochastic processes is in marked contrast to capabilities of "chaos" algorithms such as the correlation dimension, which are properly applied to low-dimensional iterated deterministic dynamical systems. The potential uses of ApEn to provide new insights in biological settings are thus myriad, from a complementary perspective to that given by classical statistical methods. ApEn is typically calculated by a computer program, with a FORTRAN listing for a "basic" code referenced above. It is imperative to view ApEn as a family of statistics, each of which is a relative measure of process regularity. For proper implementation, the two input parameters m (window length) and r (tolerance width, de facto filter) must remain fixed in all calculations, as must N, the data length, to ensure meaningful comparisons. Guidelines for m and r selection are indicated above. We have found normalized regularity to be especially useful, as in the growth hormone studies discussed above; "r" is chosen as a fixed percentage (often 20%) of the subject's SD. This version of ApEn has the property that it is decorrelated from process SD--it remains unchanged under uniform process magnification, reduction, and translation (shift by a constant). Cross-ApEn is generally applied to compare sequences from two distinct yet interwined variables in a network. Thus we can directly assess network, and not just nodal, evolution, under different settings--e.g., to directly evaluate uncoupling and/or changes in feedback and control. Hence, cross-ApEn facilitates analyses of output from myriad complicated networks, avoiding the requirement to fully model the underlying system. This is especially important, since accurate modeling of (biological) networks is often nearly impossible. Algorithmically and insofar as implementation and reproducibility properties are concerned, cross-ApEn is thematically similar to ApEn. Furthermore, cross-ApEn is shown to be complementary to the two most prominent statistical means of assessing multivariate series, correlation and power spectral methodologies. In particular, we highlight, both theoretically and by case study examples, the many physiological feedback and/or control systems and models for which cross-ApEn can detect significant changes in bivariate asynchrony, yet for which cross-correlation and cross-spectral methods fail to clearly highlight markedly changing features of the data sets under consideration. Finally, we introduce spatial ApEn, which appears to have considerable potential, both theoretically and empirically, in evaluating multidimensional lattice structures, to discern and quantify the extent of changing patterns, and for the emergence and dissolution of traveling waves, throughout multiple contexts within biology and chemistry.

Adrenocorticotropic Hormone↗

PubMed2005

Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana.

BACKGROUND: Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds. RESULTS: We have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation. CONCLUSION: The presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.

Arabidopsis↗

PubMed2025

Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011-23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study.

BACKGROUND: Streptococcus dysgalactiae subspecies equisimilis (SDSE) is closely related to Streptococcus pyogenes, with overlapping disease manifestations. We compared the clinical and genomic epidemiology of invasive SDSE with invasive S pyogenes across different settings in Australia and phylogenetically contextualised the SDSE sequences within a global cohort of genomes. METHODS: In this retrospective clinical and genomic epidemiology study, cases of invasive SDSE isolated from normally sterile sites were identified and whole-genome sequenced across five hospital networks in temperate southeast Australia (Melbourne and Sydney) and the tropical Top End of the Northern Territory. SDSE disease incidence, case demographics, clinical outcomes, and longitudinal lineage dynamics were compared between southeast Australia and the Top End and to co-collected invasive S pyogenes cases in each region. SDSE genomes and lineages were also contextualised within 1166 global SDSE sequences. Genomic transmission clusters (not necessarily direct transmission) were inferred between isolates from different individuals by single-linkage clustering at a single nucleotide polymorphism threshold of less than or equal to seven for SDSE and less than or equal to five for S pyogenes based on previous transmission analyses. FINDINGS: Between Jan 1, 2011, and Feb 28, 2023, there were 693 invasive SDSE cases and 995 invasive S pyogenes cases. Invasive SDSE occurred almost exclusively in adults. The overall invasive SDSE incidence in southeast Australia was similar to invasive S pyogenes (incidence rate ratio [IRR] 1·15, 95% CI 0·91-1·46; p=0·26) and increased over the study period (IRR 1·06 per year, 95% CI 1·05-1·08; p<0·0001) from 1·30 cases per 10 000 admissions in 2011 to 3·72 cases per 10 000 admissions in the first 2 months of 2023 (95% CI 2·13-6·07). In southeast Australia, where stringent COVID-19 non-pharmaceutical interventions (NPIs) were implemented between 2020 and 2021, the SDSE incidence plateaued during 2020-21 but did not significantly decline (IRR 1·09 compared with 2017-19, 95% CI 0·88-1·35; p=0·47). By contrast, S pyogenes incidence substantially declined in 2020-21 in southeast Australia (IRR 0·35 compared to 2017-19, 95% CI 0·22-0·52; p=0·017). In the Top End, SDSE incidence was lower than S pyogenes (IRR 0·24, 95% CI 0·19-0·31; p<0·0001). However, crude incidence remained higher than southeast Australia (crude IRR 1·24, 95% CI 1·07-1·42; p=0·0037) and disproportionately affected First Nations Australians in the Top End compared with non-First Nations individuals (IRR 3·36, 95% CI 2·33-4·85; p<0·0001). Comparing 2020-21 with 2017-19, there was no decline in SDSE (IRR 1·27, 95% CI 0·73-2·24; p=0·45) or S pyogenes (IRR 0·97, 95% CI 0·80-1·18; p=0·81) incidence in the Top End, which did not implement prolonged stringent COVID-19 NPIs. Analysing the available genomes of invasive cases and in lineages for which more than or equal to five invasive cases occurred, only 24 (6%) of 384 SDSE cases were assigned to genomic transmission clusters, compared with 271 (52%) of 524 S pyogenes cases. An stG62647 lineage encompassed 113 (26%) of 436 sequenced SDSE genomes. Analysis of available SDSE sequences from Australia, western Europe, and North America inferred concurrent international expansion of the stG62647 lineage in all three regions between 1990 and 2005. INTERPRETATION: We identified a substantial burden of invasive SDSE, dominated by the emergent stG62647 lineage. The contrasting epidemiology between species in the different Australian regions, during COVID-19 NPIs, and genomic infection patterns indicates transmission dynamic, pathogen population, and host-pathogen interaction differences between SDSE and S pyogenes and indicates implications for disease control measures. FUNDING: Australian National Health and Medical Research Council.

Humans↗

PubMed2003

IPPRED: server for proteins interactions inference.

SUMMARY: IPPRED is a web based server to infer protein-protein interactions through homology search between candidate proteins and those described as interacting. This simple inference allows to propose or to validate potential interactions. AVAILABILITY: IPPRED is freely available at http://cbi.labri.fr/outils/ippred/.

Algorithms↗