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A comparative study of the psychosocial assets of adults with cystic fibrosis and their healthy peers.

Psychosocial assets of 37 adults with cystic fibrosis (CF) and 46 of their healthy peers were assessed by mailed questionnaire. Major sociodemographic variables did not differ significantly between the two groups, nor did indices of emotional social support, social network density, self-esteem, or current life satisfaction. This study revealed adults with CF to function on a par with their healthy peers in nearly all respects, a finding at odds with those from uncontrolled studies and which suggests to us that many previous conclusions about the psychosocial health of adults with CF have been unwarranted. Future psychosocial studies involving patients with CF should include control groups and inferences about the effect of these patients' physical illness on their psychosocial health should not be made in the absence of normative data.

Adaptation, Psychological↗

Synergy of the kappa-carrageenan-carob galactomannan blend inferred from rheological studies.

Rheological measurements have been used to investigate kappa-carrageenan-carob galactomannan mixed gels at different ratios, in particular for very low kappa-carrageenan concentrations. The viscoelastic properties of the gels were explored using sinusoidal tests on dynamic rheometers and compression tests between parallel plates. The properties of the binary gels were compared with the kappa-carrageenan gels and with the carob galactomannan solutions. These measurements display significant synergy for very low kappa-carrageenan concentrations. From these data, it appears that the synergy is based on a gel structure defined by a coupled network with specific junction zones. However, above a total polysaccharide concentration of 8-10 g l-1, self-association of galactomannan chains could also take place.

Carrageenan↗

Kinetoplast DNA minicircles of trypanosomatids encode for a protein product.

The major constituent of the trypanosomal kinetoplast DNA network are several thousand duplex DNA minicircles whose biological function is still unknown. The coding capacity and expression of these DNA minicircles, was studied in the trypanosomatid Crithidia fasciculata. Kinetoplast DNA minicircle fragments inserted into bacterial plasmid vectors were expressed in the bacterial cell. Sera elicited in rabbits, by immunization with the translational products of kinetoplast DNA minicircles in E. coli, reacted specifically with Crithidia fasciculata cellular antigens. It is inferred that kinetoplast DNA minicircles contain long open reading frames of nucleotides which are expressed in the trypanosomatid cell.

Animals↗

Proximity of 5.8 S RNA-binding proteins and A-site proteins in yeast ribosomes inferred from cross-linking.

In order to probe the spatial arrangement of proteins within the 5.8 S rRNA domain of the intact ribosomal subunit of Saccharomyces cerevisiae, 60 S ribosomal subunits were treated with 2-iminothiolane. Proteins were extracted from the cross-linked ribosomes, fractionated by Sephadex G-150 column chromatography, and analyzed by diagonal polyacrylamide-sodium dodecyl sulfate gel electrophoresis. Constituent proteins of cross-linked pairs were identified by two-dimensional polyacrylamide gel electrophoresis. Nine cross-links involving five of the 11 5.8 S rRNA-binding proteins were analyzed. A model showing the network of cross-links is presented. Several of the 5.8 S rRNA-binding proteins are in sufficiently close proximity of the ribosomal A-site proteins to be cross-linked.

Carrier Proteins↗

Drug-protein interactions. Refined structures of three sulfonamide drug complexes of human carbonic anhydrase I enzyme.

N-unsubstituted sulfonamide drugs are widely used for opthalmic disorders. Inhibition of carbonic anhydrase enzyme is believed to be the chief reason for their therapeutic effects. Structures of three such sulfonamide drugs complexed to human carbonic anhydrase I enzyme (HCAI) refined crystallographically at 2 A resolution are reported here. The drug molecules are all bound in the active site of the enzyme, but among themselves show differences in the orientations of the sulfamido groups interacting with the essential zinc ion in the active site. The activity linked solvent molecule coordinated to zinc in the native enzyme is displaced by all the three sulfonamides. The active site loop of Leu198, Thr199 and His200 has been identified to be important for binding of the drug molecules due to their appreciable atomic displacements and intra-molecular hydrogen bonds arising out of their interactions with the sulfonamides. These interactions along with active site charge requirements are proposed to be responsible for the orientational differences of the sulfamido groups and also for differences in the inhibitory powers of the drugs. A hydrogen bond network involving solvent molecules and active site residues His200 and His67 amongst others in the native enzyme, is disrupted upon binding of methazolamide but not in the other two sulfonamides. This is the first crystallographic evidence of the possible involvement of His200 in the inhibition of HCAI. An important role of Thr199 in distinguishing between the substrate and inhibitor binding modes of HCO3- to the enzyme at high pH is also inferred.

Acetazolamide↗

Structural model analysis of multiple quantitative traits.

We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

Adipose Tissue↗

Integrated access to metabolic and genomic data.

The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.

Artificial Intelligence↗

Advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixtures.

In this paper, we review recent advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixing models. After a general introduction to BSS and ICA, we discuss in more detail uniqueness and separability issues, presenting some new results. A fundamental difficulty in the nonlinear BSS problem and even more so in the nonlinear ICA problem is that they provide non-unique solutions without extra constraints, which are often implemented by using a suitable regularization. In this paper, we explore two possible approaches. The first one is based on structural constraints. Especially, post-nonlinear mixtures are an important special case, where a nonlinearity is applied to linear mixtures. For such mixtures, the ambiguities are essentially the same as for the linear ICA or BSS problems. The second approach uses Bayesian inference methods for estimating the best statistical parameters, under almost unconstrained models in which priors can be easily added. In the later part of this paper, various separation techniques proposed for post-nonlinear mixtures and general nonlinear mixtures are reviewed.

Bayes Theorem↗

Postmarital residence and within-sex genetic diversity among the Urubu-Ka'apor Indians, Brazilian Amazon.

The analysis of biologic variation in prehistoric human populations separately by sex has been used as a tool to recover post-marital residential rules. These studies, which focus on the sexual distribution of skeletal traits, assume that the degree of intragroup or intergroup biologic diversity is higher in one sex with regard to unilocality (uxori- or virilocality). Despite a recent attempt to interpret this phenomenon in terms of population genetics (Konigsberg 1988), the main assumption has never been tested in situations in which the real residential practice of an indigenous population is known and in which genetic rather than phenotypic data are available. We investigated the within-group and between-group genetic variability among males and females from 4 villages of an uxorilocal Amazonian tribe, the Urubu-Ka'apor, on the basis of 20 polymorphic loci. The results were only partly concordant with the expected. Individual mean per locus heterozygosities were not different between the sexes, and the analysis of genetic heterogeneity showed similar gene frequencies for males and females in all villages. On the other hand, the intergroup approach detected a level of variation significantly greater among females than among males. The ethnographic evidence shows that three of the four subgroups studied belong to the same gamic unity, with the fourth subgroup belonging to another gamic network. Within-sex differences in intergroup analysis turned out to be more evident; yet, when those 3 villages were investigated separately, the female FST (0.0609) proved to be significantly higher than the male FST (0.0218). Such results suggest that the intergroup analysis is more sensitive to the genetic effects of differential migration rates between the sexes. In prehistoric contexts, therefore, an intergroup genetic approach can provide more reliable grounds for sociocultural inferences.

Brazil↗

Optimization-based framework for inferring and testing hypothesized metabolic objective functions.

An optimization-based framework is introduced for testing whether experimental flux data are consistent with different hypothesized objective functions. Specifically, we examine whether the maximization of a weighted combination of fluxes can explain a set of observed experimental data. Coefficients of importance (CoIs) are identified that quantify the fraction of the additive contribution of a given flux to a fitness (objective) function with an optimization that can explain the experimental flux data. A high CoI value implies that the experimental flux data are consistent with the hypothesis that the corresponding flux is maximized by the network, whereas a low value implies the converse. This framework (i.e., ObjFind) is applied to both an aerobic and anaerobic set of Escherichia coli flux data derived from isotopomer analysis. Results reveal that the CoIs for both growth conditions are strikingly similar, even though the flux distributions for the two cases are quite different, which is consistent with the presence of a single metabolic objective driving the flux distributions in both cases. Interestingly, the CoI associated with a biomass production flux, complete with energy and reducing power requirements, assumes a value 9 and 15 times higher than the next largest coefficient for the aerobic and anaerobic cases, respectively.

Aerobiosis↗

A framework for the application of knowledge technology to the management of diseases.

Medical diagnosis and treatment constitute a network of interrelated processes. The conventional method of medical diagnosis and treatment of diseases involves a state space search of the medical knowledge of diseases and patient history, which could be combinatorially explosive. This paper presents a report on the experimental study of an intelligent, interactive, user-friendly, knowledge-based system which performs a stepwise analysis of a patient's complaints, filtering cognitive and emotional elements to be able to make inferences. It applies both forward and backward chaining in making inferences concerning the management of disease. A case study of the system is carried out using some tropical diseases. It is believed that the system will serve as a useful contribution towards tropical medical informatics.

Computer Systems↗

Multivariate autoregressive modeling of fMRI time series.

We propose the use of multivariate autoregressive (MAR) models of functional magnetic resonance imaging time series to make inferences about functional integration within the human brain. The method is demonstrated with synthetic and real data showing how such models are able to characterize interregional dependence. We extend linear MAR models to accommodate nonlinear interactions to model top-down modulatory processes with bilinear terms. MAR models are time series models and thereby model temporal order within measured brain activity. A further benefit of the MAR approach is that connectivity maps may contain loops, yet exact inference can proceed within a linear framework. Model order selection and parameter estimation are implemented by using Bayesian methods.

Algorithms↗

Introgression among maternal lineages inferred from complete mitogenomes and molecular dating helps resolve phylogeography of European roe deer.

BACKGROUND: The European roe deer (Capreolus capreolus) is one of the most widespread ungulates in Europe, with a phylogeographic structure mainly shaped by Pleistocene glacial cycles and secondary contacts with the Siberian roe deer (C. pygargus). METHODS: We sequenced 52 complete mitogenomes of C. capreolus from Slovenia, Poland and France, and combined them with 24 publicly available sequences of C. capreolus and C. pygargus, yielding an alignment of 76 genomes representing 59 haplotypes (42 from C. capreolus and 17 from C. pygargus). Phylogeographic structure was assessed using a median-joining network, and divergence times were estimated using a time-calibrated Bayesian phylogeny based on mitochondrial coding regions, incorporating published ancient C. pygargus mitogenomes. We additionally screened mitochondrial protein-coding genes for selection. RESULTS: The haplotype network recovered the three major European roe deer clades (Eastern, Central, and Western) and detected Central-clade haplotypes in France. Two Polish haplotypes (Cp9 and Cp10), detected in C. capreolus, clustered within the C. pygargus mitochondrial lineage, supporting mitochondrial introgression. Time-calibrated phylogenies placed introgressed haplotypes within established C. pygargus lineages. Selection analyses provided limited evidence for episodic positive selection restricted to a small number of codons. CONCLUSIONS: Whole mitogenomes improve resolution of roe deer phylogeography and reveal introgressed maternal lineages, while time-calibrated phylogenies and selection tests add evolutionary context for interpreting mtDNA diversity in genus Capreolus.

Animals↗

Hibernating myocardium: a review.

Within a few seconds after a sudden reduction of coronary blood flow regional contractile dysfunction ensues. The mechanisms responsible for the rapid reduction in contractile function during acute myocardial ischemia remain unclear, but may involve a rise in inorganic phosphate. When severe ischemia, such as resulting from a sudden and complete coronary artery occlusion, is prolonged for more than 20-40 min, myocardial infarction develops, and there is irreversible loss of contractile function. When myocardial ischemia is less severe but nevertheless prolonged, the myocardium is dysfunctional but can remain viable. In such ischemic and dysfunctional myocardium, contractile function is reduced in proportion to the reduction in regional myocardial blood flow; i.e. a state of "perfusion-contraction matching" exists. The metabolic status of such myocardium improves over the first few hours, as myocardial lactate production is attenuated and creatine phosphate, after an initial reduction, returns towards control values. Ischemic myocardium, characterized by perfusion-contraction matching, metabolic recovery and lack of necrosis, has been termed "short-term hibernating myocardium". Short-term hibernating myocardium can respond to an inotropic stimulation with increased contractile function, however, at the expense of a renewed worsening of the metabolic status. This situation of an increased regional contractile function at the expense of metabolic recovery during inotropic stimulation can be used to identify short-term hibernating myocardium. When inotropic stimulation is prolonged, the development of short-term hibernation is impaired and myocardial infarction develops. The mechanisms responsible for the development of short-term myocardial hibernation remain unclear at present; a significant involvement of adenosine and of activation of ATP-dependent potassium channels has been excluded. Whereas short-term hibernation is well characterized in animal experiments, the existence of hibernation over weeks or months (long-term hibernation) can only be inferred from clinical studies. Hibernation, as defined by Rahimtoola, is a state of chronic contractile dysfunction which is fully reversible upon reperfusion. Clinical syndromes consistent with the existence of myocardial hibernation include unstable and stable angina, acute myocardial infarction and left ventricular dysfunction and/or congestive heart failure. In long-term hibernating myocardium morphological alterations occur; the myofibrils are reduced in number and disorganized and myocardial glycogen content as well as the extracellular collagen network are increased. Thus, despite the fact that the myocardium remains viable during persistent ischemia and contractile dysfunction is reversible upon reperfusion, there are severe morphological alterations. Understandably, full functional recovery following reperfusion might therefore require weeks or even months.

Animals↗

Inverse and predictive modeling of seepage into underground openings.

We discuss the development and calibration of a model for predicting seepage into underground openings. Seepage is a key factor affecting the performance of the potential nuclear-waste repository at Yucca Mountain, Nevada. Three-dimensional numerical models were developed to simulate field tests in which water was released from boreholes above excavated niches. Data from air-injection tests were geostatistically analyzed to infer the heterogeneous structure of the fracture permeability field. The heterogeneous continuum model was then calibrated against the measured amount of water that seeped into the opening. This approach resulted in the estimation of model-related, seepage-specific parameters on the scale of interest. The ability of the calibrated model to predict seepage was examined by comparing calculated with measured seepage rates from additional experiments conducted in different portions of the fracture network. We conclude that an effective capillary strength parameter is suitable to characterize seepage-related features and processes for use in a prediction model of average seepage into potential waste-emplacement drifts.

Calibration↗

The transformation of consequential functions in accordance with the relational frames of more-than and less-than.

Across three experiments, the transformation of consequential functions in accordance with a seven-member relational network (A-B-C-D-E-F-G) was investigated. In this network, the relational rankings ranged from A, ranked the least, to G, ranked the most. In the first phase, contextual cues for more-than and less-than were established by training participants across multiple exemplars to select comparisons containing larger quantities in the presence of the former cue, and fewer quantities in the presence of the latter cue. Participants then were trained in six conditional discriminations (i.e., A D, F>E, and G>F) with the contextual cues as samples and nonsense words as comparisons, and all possible derived relations were tested (e.g., B<F). In a subsequent phase, the D stimulus was paired with the delivery of points. Next, a test for a transformation of consequential functions was presented in either simultaneous discrimination tasks (Experiments 1 and 2) or a free-operant schedule task (Experiment 3), each of which employed members of the relational network as consequences. In all experiments, participants consistently emitted the response that produced the derived consequential stimulus that was ranked higher in the relational network, thus demonstrating a transformation of consequential functions. In Experiment 2, the baseline conditional discriminations were altered in a reversal design, and Experiment 3 examined generalization of the derived performance to a schedule-based task, with and without detailed instructions. Overall, the study demonstrated a transformation and generalization of consequential functions in accordance with the relational frames of More-than and Less-than, and bears relevance to the literature on transitive inference.

Adolescent↗

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

Networks are proving to be central to the study of gene function, protein-protein interaction, and biochemical pathway data. Visualization of networks is important for their study, but visualization tools are often inadequate for working with very large biological networks. Here, we present an algorithm, called large graph layout (LGL), which can be used to dynamically visualize large networks on the order of hundreds of thousands of vertices and millions of edges. LGL applies a force-directed iterative layout guided by a minimal spanning tree of the network in order to generate coordinates for the vertices in two or three dimensions, which are subsequently visualized and interactively navigated with companion programs. We demonstrate the use of LGL in visualizing an extensive protein map summarizing the results of approximately 21 billion sequence comparisons between 145579 proteins from 50 genomes. Proteins are positioned in the map according to sequence homology and gene fusions, with the map ultimately serving as a theoretical framework that integrates inferences about gene function derived from sequence homology, remote homology, gene fusions, and higher-order fusions. We confirm that protein neighbors in the resulting map are functionally related, and that distinct map regions correspond to distinct cellular systems, enabling a computational strategy for discovering proteins' functions on the basis of the proteins' map positions. Using the map produced by LGL, we infer general functions for 23 uncharacterized protein families.

Algorithms↗

Migration patterns among global populations of the pathogenic fungus Mycosphaerella graminicola.

DNA sequences from five nuclear loci and data from three microsatellites were collected from 360 isolates representing 14 globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Haplotype networks were constructed for the five sequence loci and population subdivision was assessed using Hudson's permutation test. Migration estimates were calculated using six regional populations for both the sequence and microsatellite loci. While subdivision was detected among the six regional populations, significant gene flow was indicated among some of the populations. The European and Israeli populations contributed the majority of historical immigrants to the New World. Migration estimates for microsatellite loci were used to infer more recent migration events among specific New World populations. We conclude that gene flow was an important factor in determining the demographic history of Mycosphaerella graminicola.

Ascomycota↗