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FINEX: a Probabilistic Expert System for forensic identification.

A series of recent papers have shown how to formulate complex problems of forensic DNA identification inference, such as occur in disputed paternity or criminal identification cases, in terms of Probabilistic Expert Systems (PESs). However, at the present time, general purpose PES software is not particularly well suited to the repetitive tasks of: specifying an appropriate set of marker networks for a specific problem; for editing the many local conditional probability tables; and combining evidence from several genetic markers to evaluate likelihoods. Here, I describe a user-friendly prototype software tool called FINEX developed both to automate such tasks and also to evaluate likelihoods of interest. Ease of use is achieved by a graphical specification language that enables a user to quickly specify a range of forensic DNA problems. I describe the algorithms by which FINEX converts the user input in the graphical specification language and data on observed markers to the Bayesian networks used in PES.

Algorithms↗

DAWN: Drug Abuse Warning Network or Data About Worthless Numbers?

This report presents further data about toxicologic results in 1008 "mentions" to the DAWN (Drug Abuse Warning Network) System from Los Angeles County/USC Medical Center in 1977. Details from some of the blood concentrations found in that retrospective study are presented here for the most commonly reported drugs, both alone and in combination with alcohol. The data suggests caution about inferring drug abuse trends from DAWN data is presently collected.

California↗

Role of fluids in faulting inferred from stress field signatures

The stress orientation signature of weak faults containing high-pressure fluids has been observed for segments of the San Andreas fault system in southern California. The inferred lithostatic fluid pressures extend into the surrounding relatively intact rock in a zone scaling with the width of the interseismic strain accumulation. Repeated strain-related fracturing and crack sealing may have created low-permeability barriers that seal fluids into the network of currently active fractures.

Journal Article↗

Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes.

The systematic classification of nematode-trapping fungi is redefined based on phylogenies inferred from sequence analyses of 28S rDNA, 5.8S rDNA and beta-tubulin genes. Molecular data were analyzed with maximum parsimony, maximum likelihood and Bayesian analysis. An emended generic concept of nematode-trapping fungi is provided. Arthrobotrys is characterized by adhesive networks, Dactylellina by adhesive knobs, and Drechslerella by constricting-rings. Phylogenetic placement of taxa characterized by stalked adhesive knobs and non-constricting rings also is confirmed in Dactylellina. Species that produce unstalked adhesive knobs that grow out to form loops are transferred from Gamsylella to Dactylellina, and those that produce unstalked adhesive knobs that grow out to form networks are transferred from Gamsylella to Arthrobotrys. Gamsylella as currently circumscribed cannot be treated as a valid genus. A hypothesis for the evolution of trapping-devices is presented based on multiple gene data and morphological studies. Predatory and nonpredatory fungi appear to have been derived from nonpredatory members of Orbilia. The adhesive knob is considered to be the ancestral type of trapping device from which constricting rings and networks were derived via two pathways. In the first pathway adhesive knobs retained their adhesive material forming simple two-dimension networks, eventually forming complex three-dimension networks. In the second pathway adhesive knobs lost their adhesive materials, with their ends meeting to form nonconstricting rings and they in turn formed constricting rings with three inflated-cells.

Animals↗

Sociocultural and psychopathological study on depressive disorders among Japanese.

In order to find out whether there is a change in depression itself besides the increase of depression, we made a research by two methods. The first method is what we can call a statistical method, and here we made a comparative examination of the symptoms of depression having different sociocultural backgrounds by examining 114 cases of depression in Tokyo and 108 in Nagasaki. By the second method we divided the 24 cases of depression in Tokyo into two groups, "patients grown up during the prewar period" and "patients grown up during the postwar period", according to the date of their birth, and analyzed the precipitating factors (life events) of depression and psychopathology. As a result, we can infer that while the depression in Tokyo is of an urban type, the depression in Nagasaki is of a classical type, and as for the life events, "patients grown up during the prewar period" tend to be involved in the family/household and social network events whereas "patients grown up during the postwar period" tend to be involved in the personal and livelihood events, and here we can observe a significant statistical difference between the two groups. Furthermore, we found out that the life events of the "patients grown up during the postwar period" were limited to the personal interests and that they rarely suffered from self-reproach or feeling of guilt.

Cultural Characteristics↗

Real time monitoring and analysis via the medical information bus, Part II.

The complexity of the monitored data available in modern intensive care units suggests that they may be best processed, for presentation to medical staff, by expert system techniques. However, standard expert system shells are ill-fitted to either the basic sequential monitoring tasks of data acquisition and storage, or to handling the temporal considerations inherent in monitoring and in the recognition and processing of sporadic alarm signals. A solution to this dilemma is described: an expert system that has an appropriately designed inference engine and manages data acquisition via a medical information bus (MIB). Use of this MIB standard allows great flexibility as regards the monitoring apparatuses employed; in particular, the connection or disconnection of any apparatus is recognised and triggers the automatic reconfiguration of the network.

Computer Systems↗

A Raman spectroscopic study of the uranyl phosphate mineral threadgoldite.

Raman spectra of threadgoldite at 298 and 77K are measured and interpreted for the first time. Bands related the (UO(2))(2+) and (PO(4))(3-) stretching and bending vibrations are tenatively attributed together with the bands assigned to the stretching a and bending vibrations of water molecules and hydroxyls. Hydrogen-bonding network and H(2)O and (OH)(-1) libration modes are mentioned. U-O bond lengths in uranyls are calculated via empirical relations R(U-O)=f[nu(1) and nu(3)(UO(2))(2+)]A. They are comparable to the values inferred from the single crystal structure analysis of threadgoldite.

Hydrogen Bonding↗

Ribosomal ITS sequences and plant phylogenetic inference.

One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.

DNA, Ribosomal Spacer↗

Graphical-Model-based Morphometric Analysis.

We propose a novel method for voxel-based morphometry (VBM), which we call Graphical-Model-based Morphometric Analysis (GAMMA), to identify morphological abnormalities automatically, and to find complex probabilistic associations among voxels in magnetic-resonance images and clinical variables. GAMMA is a fully automatic, nonparametric morphometric-analysis algorithm, with high sensitivity and specificity. It uses a Bayesian network to represent the associations among voxels and the function variable, and uses a contextual-clustering method based on a Markov random field to find clusters in which all voxels have similar associations with the function variable. We use loopy belief propagation to infer the unobserved label field and belief map. As opposed to voxel-based morphometric methods based on general linear models, GAMMA is capable of identifying nonlinear associations among the function variable and voxels. Compared with our previous approach, a Bayesian morphometry algorithm, GAMMA has greater sensitivity, specificity, and computational efficiency.

Algorithms↗

Melt segregation and strain partitioning: implications for seismic anisotropy and mantle flow.

One of the principal means of understanding upper mantle dynamics involves inferring mantle flow directions from seismic anisotropy under the assumption that the seismic fast direction (olivine a axis) parallels the regional flow direction. We demonstrate that (i) the presence of melt weakens the alignment of a axes and (ii) when melt segregates and forms networks of weak shear zones, strain partitions between weak and strong zones, resulting in an alignment of a axes 90 degrees from the shear direction in three-dimensional deformation. This orientation of a axes provides a new means of interpreting mantle flow from seismic anisotropy in partially molten deforming regions of Earth.

Journal Article↗

Representation of cooperative firing activity among simultaneously recorded neurons.

Simultaneous and separable extracellular recording of substantial populations of neurons under chronic and behavioral conditions is becoming experimentally feasible. We have recently described a conceptual transformation of such multiple spike train data that allows the experimenter to analyze the entire network of observed neurons as an entity rather than as a summation of neuron pairs. The basic transformation represents each of N neurons as a particle in an N-space. Each particle is given a "charge" that is related to the spike train of the corresponding neuron. The resulting forces on the N particles cause aggregation of those particles that represent neurons with time-related firing. The present paper extends the visualization and possibilities of this way of analyzing properties of neuronal assemblies. Data are taken from computer-simulated neuronal networks in order to provide known properties. We demonstrate projection of particle positions from the N space to a plane. Under the right conditions the spatial arrangement of the particles forms a Venn diagram of functional relationships in the entire neural network. We introduce revised force rules in the transformation that allow detection and study of inhibitory connections among the observed neurons. Sensitivity is lower than for excitatory connections. We introduce revised "charge" rules that improve "signal-to-noise" properties and in addition allow inference of directed connectivity. The original transformation only allows identification of neurons with time-related firing. The two-charge transformation allows explicit identification of presynaptic and postsynaptic neurons. Finally we examine sensitivity of the transformation to individual and near-coincident firing rates. Some criteria are presented for choice of charge normalization rules in the transformation.

Action Potentials↗

[Pathophysiology of the "hibernating" myocardium].

Myocardial ischemia has traditionally been viewed as an imbalance between energy supply and demand. Within the first few seconds following an acute reduction of myocardial blood flow, energy demand of the hypoperfused myocardium clearly exceeds the reduced energy supply. However, this imbalance between energy supply and demand is an inherently unstable condition since ischemia induces mechanisms which are not yet understood, but reduce contractile function and thus energy demand. In the subsequent steady-state condition, the amount of contractile dysfunction is in proportion to the reduction of myocardial blood flow. A situation of persistent ischemic contractile dysfunction in viable myocardium which normalizes upon reperfusion has been termed myocardial hibernation. The metabolic status of such hibernating myocardium improves over the first few hours as myocardial lactate production is attenuated and creatine phosphate, after an initial reduction, returns towards control values. The hibernating myocardium can respond to an inotropic stimulation by dobutamine 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 hibernating myocardium. The development of such delicate balance between regional myocardial blood flow and function during early ischemia is disturbed by unfavorable alterations in supply and demand. When after 5 min of ischemia, at a blood flow reduction compatible with the development of myocardial hibernation over 90 min, energy supply is further reduced by a further reduction of myocardial blood flow, necroses develop. Likewise, increasing energy demand by continuous inotropic stimulation with dobutamine induces necroses. Thus, both the further reduction in energy supply by an increasing severity of ischemia and an enhanced energy expenditure by continuous inotropic stimulation impair the development of myocardial hibernation and precipitate myocardial infarction. Hibernation over the first few hours of ischemia (short-term hibernation) is well characterized in animal experiments. Increased release of endogenous adenosine and activation of ATP-dependent potassium channels as the underlying mechanisms have been ruled out. The existence of hibernation over weeks or months (long-term hibernation) can only be inferred from clinical studies. In long-term hibernating myocardium morphological alterations occur. In myocardial biopsies from patients with prolonged contractile dysfunction which was reversible after bypass surgery, myofibrils are reduced in number and disorganized. 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 can therefore require weeks or even months.

Animals↗

Is short-term odour recognition predictable from odour profile?

Smelling an odour induces a pattern of sensations, images and memories which participate in identification. It was proposed that perceptual memory performances for odours could be inferred from the description of these olfactory representations. The subject was asked to elaborate an odour descriptor profile, and a short-term odour recognition memory task was chosen to test the individual perceptual memory performance. Two pattern-recognition methods based on artificial neural networks and discriminant analysis were carried out and allowed odour profile and perceptual memory performance to be related. Insofar as the subjects gave dichotomic responses in the recognition memory task, each response could be evaluated in terms of correct or incorrect responses. Simulations indicated that the olfactory recognition memory performance can be predicted in man from odour-elicited semantic profiles by using artificial neural networks. It was also shown that all semantic descriptors do not participate in olfactory recognition to the same degree. Low-level information, such as intensity, familiarity and hedonic judgements, did not allow the artificial neural network to predict the olfactory performance. By contrast, high-level information, such as gustatory, olfactory and visual evocations, allowed artificial networks to make such predictions.

Adult↗

Modeling other minds.

Nine normal volunteers performed a 'theory of mind' task while their regional brain blood flow pattern was recorded using the PET [15O]H2O technique. Control conditions induced subjects to attend to the visual and semantic attributes of known objects. In a third condition, subjects had to infer the function of an unfamiliar object from its form. In the 'theory of mind' condition, subjects had to infer function based on the form of both familiar and unfamiliar objects and in addition, model the knowledge and rationality of another mind about the function of these objects. Performance during the 'theory of mind' condition evoked the activation of a distributed set of neural networks with prominent activation of the left medial frontal lobe (Brodmann area 9) and left temporal lobe (Brodmann areas 21, 39/19, 38). This result suggests that when inferential reasoning depends on constructing a mental model about the beliefs and intentions of others, the participation of the prefrontal cortex is required. When access to such knowledge is affected by central nervous system dysfunction, such as that found in autism, modeling other minds may prove difficult.

Adolescent↗

Life sign decision support algorithms.

There is a pressing need in the military for a system that interprets data from a suite of wearable physiological sensors to infer a soldier's current clinical state on the battlefield. The Warfighter Physiological Status Monitoring (WPSM) concept is envisioned by the US Army to address this need. Life sign detection is a key component. The future WPSM system will consist of a body-worn network of biosensors with a central processing control unit containing firmware for assessing the soldier's physiological status. In the present application, the system will diagnose a Dead, Alive, or Unknown (DAU) physiological state, and this information will be made available to field medics and others over separate communication channels. This paper describes the various modules in the DAU determination algorithms and how they interact with each other, as well as a simulator system built for parametric studies of the overall system.

Algorithms↗

On selecting features from splice junctions: an analysis using information theoretic and machine learning approaches.

The computational recognition of precise splice junctions is a challenge faced in the analysis of newly sequenced genomes. This is challenging due to the fact that the distribution of sequence patterns in these regions is not always distinct. Our objective is to understand the sequence signatures at the splice junctions, not simply to create an artificial recognition system. We use a combination of a neural network based calliper randomization approach and an information theoretic based feature selection approach for this purpose. This has been done in an effort to understand regions that harbor information content and to extract features relevant for the prediction of splice junctions. The analysis using the neural network based calliper randomization approach revealed regions important in the internal representation of the network model. The calliper approach captured both correlated as well as independently important features. The feature selection approach captures features that are independently informative. The two different methods can capture features with different properties. Comparative analysis of the results using both the methods help to infer about the kind of information present in the region.

Alternative Splicing↗

UMLS knowledge for biomedical language processing.

This paper describes efforts to provide access to the free text in biomedical databases. The focus of the effort is the development of SPECIALIST, an experimental natural language processing system for the biomedical domain. The system includes a broad coverage parser supported by a large lexicon, modules that provide access to the extensive Unified Medical Language System (UMLS) Knowledge Sources, and a retrieval module that permits experiments in information retrieval. The UMLS Metathesaurus and Semantic Network provide a rich source of biomedical concepts and their interrelationships. Investigations have been conducted to determine the type of information required to effect a map between the language of queries and the language of relevant documents. Mappings are never straightforward and often involve multiple inferences.

Humans↗

Serial distribution of airway diameters from input impedance and computed tomography.

Indirect measures of airway diameter such as respiratory system input impedance (Zin) have been widely used to infer or quantify bronchoconstriction, or bronchodilation. One such measure, Zin above 100 Hz has been shown to be primarily influenced by airway geometry and airway walls but not by lung and chest wall tissues. We used a recently developed method based on a complex asymmetrically branched network of tubes with nonrigid walls to analyze Zin from 100 to 2,000 Hz in control and bronchoconstricted (histamine injection) dogs. The resulting estimates of airway diameters indicated that peripheral airways were constricted far more (approximately 30% of their control diameters) than central airways (i.e., 0% in the trachea). Separate measurements of changes in airway diameters were made in an excised dog lung using high resolution computed tomography. The observed changes in airway diameter between lung volumes of total lung capacity (TLC) and functional residual capacity (FRC) were quantitatively consistent with those obtained from Zin data in our control dogs at FRC. We conclude that this systems identification method can be used to estimate the distribution of airway diameters from Zin.

Airway Resistance↗