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PubMed2005

Gestational age discrepancies due to acquisition artifact in the forensic fetal osteology collection at the National Museum of Natural History, Smithsonian Institution, USA.

Previously, numerous techniques have been used to assess either lunar or gestational age from fetal remains, such as from the external dimensions of the fetus, presence or absence of external features and ossification centers. One of the largest fetal collections in the U.S. is assessed with regard to errors in its biologic profile (ancestry, sex and age), the nature of the collection process, the methods of collection and the subsequent considerations for usage. Hrdlicka recorded the age, ancestry, sex and external measurements on card catalogs in the early 1900s for future use. For the purpose of this pilot study, measurements on 38 suitable fetuses stored at NMNH were used to calculate lunar age and compare with the recorded age in the card catalog. The differences between the age assessments are as follows: 20 showed no difference, 11 were discrepant by one month, 6 varied by 2 months and 1 diverged by 5 months. The average difference between lunar ages is 0.74 months, reflecting a nearly three-week difference. The purpose of this paper is to demonstrate that such discrepancies exist and to confirm specimens with accurate ages, which can be marked for future research. Moreover, it is also the purpose of this paper to demonstrate that such bias artifact exists in museum collections, and that this artifact needs to be eliminated from the sample materials prior to study.

Age Determination by Skeleton↗
PubMed2002

Diffusion of epicenters of earthquake aftershocks, Omori's law, and generalized continuous-time random walk models.

The epidemic-type aftershock sequence (ETAS) model is a simple stochastic process modeling seismicity, based on the two best-established empirical laws, the Omori law (power-law decay approximately 1/t(1+theta) of seismicity after an earthquake) and Gutenberg-Richter law (power-law distribution of earthquake energies). In order to describe also the space distribution of seismicity, we use in addition a power-law distribution approximately 1/r(1+mu) of distances between triggered and triggering earthquakes. The ETAS model has been studied for the last two decades to model real seismicity catalogs and to obtain short-term probabilistic forecasts. Here, we present a mapping between the ETAS model and a class of CTRW (continuous time random walk) models, based on the identification of their corresponding master equations. This mapping allows us to use the wealth of results previously obtained on anomalous diffusion of CTRW. After translating into the relevant variable for the ETAS model, we provide a classification of the different regimes of diffusion of seismic activity triggered by a mainshock. Specifically, we derive the relation between the average distance between aftershocks and the mainshock as a function of the time from the mainshock and of the joint probability distribution of the times and locations of the aftershocks. The different regimes are fully characterized by the two exponents theta and mu. Our predictions are checked by careful numerical simulations. We stress the distinction between the "bare" Omori law describing the seismic rate activated directly by a mainshock and the "renormalized" Omori law taking into account all possible cascades from mainshocks to aftershocks of aftershock of aftershock, and so on. In particular, we predict that seismic diffusion or subdiffusion occurs and should be observable only when the observed Omori exponent is less than 1, because this signals the operation of the renormalization of the bare Omori law, also at the origin of seismic diffusion in the ETAS model. We present predictions and insights provided by the ETAS to CTRW mapping which suggest different ways for studying seismic catalogs. Finally, we discuss the present evidence for our predicted subdiffusion of seismicity triggered by a main shock, stressing the caveats and limitations of previous empirical works.

Journal Article↗
PubMed2004

Properties of foreshocks and aftershocks of the nonconservative self-organized critical Olami-Feder-Christensen model.

Following Phys. Rev. Lett. 88, 238501 (2002)] who discovered aftershocks and foreshocks in the Olami-Feder-Christensen (OFC) discrete block-spring earthquake model, we investigate to what degree the simple toppling mechanism of this model is sufficient to account for the clustering of real seismicity in time and space. We find that synthetic catalogs generated by the OFC model share many properties of real seismicity at a qualitative level: Omori's law (aftershocks) and inverse Omori's law (foreshocks), increase of the number of aftershocks and of the aftershock zone size with the mainshock magnitude. There are, however, significant quantitative differences. The number of aftershocks per mainshock in the OFC model is smaller than in real seismicity, especially for large mainshocks. We find that foreshocks in the OFC catalogs can be in large part described by a simple model of triggered seismicity, such as the epidemic-type aftershock sequence (ETAS) model. But the properties of foreshocks in the OFC model depend on the mainshock magnitude, in qualitative agreement with the critical earthquake model and in disagreement with real seismicity and with the ETAS model.

Journal Article↗
PubMed2005

Time-decreasing hazard and increasing time until the next earthquake.

The existence of a slowly always decreasing probability density for the recurrence times of earthquakes in the stationary case implies that the occurrence of an event at a given instant becomes more unlikely as time since the previous event increases. Consequently, the expected waiting time to the next earthquake increases with the elapsed time, that is, the event moves away fast to the future. We have found direct empirical evidence of this counterintuitive behavior in two worldwide catalogs as well as in diverse regional catalogs. Universal scaling functions describe the phenomenon well.

Journal Article↗
PubMed2004

Do earthquakes exhibit self-organized criticality?

If earthquakes are phenomena of self-organized criticality (SOC), statistical characteristics of the earthquake time series should be invariant after the sequence of events in an earthquake catalog are randomly rearranged. In this Letter we argue that earthquakes are unlikely phenomena of SOC because our analysis of the Southern California Earthquake Catalog shows that the first-return-time probability PM(T) is apparently changed after the time series is rearranged. This suggests that the SOC theory should not be used to oppose the efforts of earthquake prediction.

Journal Article↗
PubMed2004

In silico screening of a saturated mutation library of tomato.

A comprehensive mutant population is a basic resource for exploring gene function. We developed an isogenic tomato 'mutation library' in the genetic background of the inbred variety M82. A total of 13 000 M(2) families, derived from EMS (ethyl methane sulfonate) and fast-neutron mutagenesis, were visually phenotyped in the field and categorized into a morphological catalog that includes 15 primary and 48 secondary categories. Currently, 3417 mutations have been cataloged; among them are most of the previously described phenotypes from the monogenic mutant collection of The Tomato Genetics Resource Center, and over a thousand new mutants, with multiple alleles per locus. The phenotypic database indicates that most mutations fall into more than a single category (pleiotropic), with some organs such as leaves more prone to alterations than others. All data and images can be searched and accessed in the Solanaceae Genome Network (SGN) on a site called 'The Genes That Make Tomatoes' (http://zamir.sgn.cornell.edu/mutants/).

Crosses, Genetic↗
PubMed2005

Comparative study of apoptosis-related gene loci in human, mouse and rat genomes.

Many genes are involved in mammalian cell apoptosis pathway. These apoptosis genes often contain characteristic functional domains, and can be classified into at least 15 functional groups, according to previous reports. Using an integrated bioinformatics platform for motif or domain search from three public mammalian proteomes (International Protein Index database for human, mouse, and rat), we systematically cataloged all of the proteins involved in mammalian apoptosis pathway. By localizing those proteins onto the genomes, we obtained a gene locus centric apoptosis gene catalog for human, mouse and rat. Further phylogenetic analysis showed that most of the apoptosis related gene loci are conserved among these three mammals. Interestingly, about one-third of apoptosis gene loci form gene clusters on mammal chromosomes, and exist in the three species, which indicated that mammalian apoptosis gene orders are also conserved. In addition, some tandem duplicated gene loci were revealed by comparing gene loci clusters in the three species. All data produced in this work were stored in a relational database and may be viewed at http://pcas.cbi.pku.edu.cn/database/apd.php.

Animals↗
PubMed2004

Direct analysis of molybdenum target generated x-ray spectra with a portable device.

In routine applications, information about the photon flux of x-ray tubes is obtained from exposure measurements and cataloged spectra. This approach relies mainly on the assumption that the real spectrum is correctly approximated by the cataloged one, once the main characteristics of the tube such as voltage, target material, anode angle, and filters are taken account of. In practice, all this information is not always available. Moreover, x-ray tubes with the same characteristics may have different spectra. We describe an apparatus that should be useful for quality control in hospitals and for characterizing new radiographic systems. The apparatus analyzes the spectrum generated by an x-ray mammographic unit. It is based on a commercial CZT produced by AMPTEK Inc. and a set of tungsten collimator disks. The electronics of the CZT are modified so as to obtain a faster response. The signal is digitized using an analog to digital converter with a sampling frequency of up to 20 MHz. The whole signal produced by the x-ray tube is acquired and analyzed off-line in order to accurately recognize pile-up events and reconstruct the emitted spectrum. The energy resolution has been determined using a calibrated x-ray source. Spectra were validated by comparison of the HVL measured using an ionization chamber.

Algorithms↗
PubMed2005

International Union of Pharmacology. XLVI. G protein-coupled receptor list.

NC-IUPHAR (International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification) and its subcommittees provide authoritative reports on the nomenclature and pharmacology of G protein-coupled receptors (GPCRs) that summarize their structure, pharmacology, and roles in physiology and pathology. These reports are published in Pharmacological Reviews (http://www.iuphar.org/nciuphar_arti.html) and through the International Union of Pharmacology (IUPHAR) Receptor Database web site (http://www.iuphar-db.org/iuphar-rd). The essentially complete sequencing of the human genome has allowed the cataloging of all of the human gene sequences potentially encoding GPCRs. The IUPHAR Receptor List (http://www.iuphar-db.org/iuphar-rd/list/index.htm) presents this catalog giving IUPHAR-approved nomenclature (where available), known ligands, and gene names for all of these potential receptors (excluding sensory receptors and pseudogenes) together with links to curated sequence, descriptive information, and additional links in the Entrez Gene database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene). This list is a major new initiative of NC-IUPHAR that, through continuing curation, defines the target of our ongoing receptor classification and invites further input from the scientific community.

Animals↗
PubMed2006

The breakup of a main-belt asteroid 450 thousand years ago.

Collisions in the asteroid belt frequently lead to catastrophic breakups, where more than half of the target's mass is ejected into space. Several dozen large asteroids have been disrupted by impacts over the past several billion years. These impact events have produced groups of fragments with similar orbits called asteroid families. Here we report the discovery of a very young asteroid family around the object 1270 Datura. Our work takes advantage of a method for identification of recent breakups in the asteroid belt using catalogs of osculating (i.e., instantaneous) asteroid orbits. The very young families show up in these catalogs as clusters in a five-dimensional space of osculating orbital elements.

Journal Article↗
PubMed2026

Toxoplasma gondii infection disrupts secondary bile acid transformation in feline gut microbiota.

UNLABELLED: Bile acid (BA) transformation relies on gut microbiota and is vulnerable to Toxoplasma gondii infection, yet feline microbial BA-transforming capacity upon toxoplasmosis remains unclear. Here, we constructed a catalog of 2,474 nonredundant feline gut microbial genomes and integrated serum metabolomic data to verify BA transformation alterations. The results revealed that the feline gut microbiome harbored widespread genetic potential for BA transformation but lacked a complete 7α-dehydroxylation pathway due to the absence of the key gene baiE. The BA transformation-related genomes (2,045 in total) were predominantly from the phyla Bacillota_A and Actinomycetota, among which only 37 encoded baiB, all belonging to Bacillota_A. The distribution of BA transformation-related genes varied across intestinal regions: genes encoding 7α-HSDH were primarily enriched in the small intestine, whereas genes encoding 3α-HSDH, baiCD, and baiH were more abundant in the large intestine. Additionally, the abundance of genes encoding BSH and 3α-HSDH increased significantly in the small intestine on day 3 post-infection, accompanied by increases in the phylum Bacillota_C and genera such as Blautia_A, Enterococcus_E, and Ligilactobacillus. Serum metabolomics revealed a significant increase in cholesterol levels post-infection, supporting the impact of T. gondii infection on intestinal BA transformation. These findings illustrated that the feline gut microbiota played an important role in BA transformation and that T. gondii infection disrupted the microbial potential for secondary BA transformation. This study provided new insights into gut microbiota-associated metabolic perturbations during feline toxoplasmosis. IMPORTANCE: Bile acid (BA) transformation plays a critical role in host metabolism and immune regulation. Although studies on BA transformation are increasing, the capacity for BA transformation within the feline gut microbiota and the impact of Toxoplasma gondii infection on this capacity remain unclear. To bridge this gap, we constructed a catalog of 2,474 nonredundant feline gut microbial genomes and integrated serum metabolomic data to verify BA transformation alterations. Our findings revealed that the feline gut microbiome lacked a complete 7α-dehydroxylation pathway, and the specific functions involved in BA transformation may differ between the small and large intestines. Furthermore, integrated metagenomic and serum metabolomic analyses suggested that T. gondii infection disrupted BA transformation capacity in the small intestine. This study provided new insights into gut microbiota-associated metabolic perturbations during feline toxoplasmosis.

Toxoplasma gondii↗
PubMed2006

Distribution of monocarboxylate transporters MCT1-MCT8 in rat tissues and human skeletal muscle.

In the past decade, a family of monocarboxylate transporters (MCTs) have been identified that can potentially transport lactate, pyruvate, ketone bodies, and branched-chain ketoacids. Currently, 14 such MCTs are known. However, many orphan transporters exist that have transport capacities that remain to be determined. In addition, the tissue distribution of many of these MCTs is not well defined. Such a cataloging can, at times, begin to suggest the metabolic role of a particular MCT. Recently, a number of antibodies against selected MCTs (MCT1, -2, -4, and -5 to -8) have become commercially available. Therefore, we examined the protein expression of these MCTs in a large number of rat tissues (heart, skeletal muscle, skin, brain, testes, vas deferens, adipose tissue, liver, kidney, spleen, and pancreas), as well as in human skeletal muscle. Unexpectedly, many tissues coexpressed 4-5 MCTs. In particular, in rat skeletal muscle MCT1, MCT2, MCT4, MCT5, and MCT6 were observed. In human muscle, these same MCTs were present. We also observed a pronounced MCT7 signal in human muscle, whereas a very faint signal occurred for MCT8. In rat heart, which is an important metabolic sink for lactate, we confirmed that MCT1 and -2 were expressed. In addition, MCT6 and -8 were also prominently expressed in this tissue, although it is known that MCT8 does not transport aromatic amino acids or lactate. This catalog of MCTs in skeletal muscle and other tissues has revealed an unexpected complexity of coexpression, which makes it difficult to associate changes in monocarboxylate transport with the expression of a particular MCT. The differences in transport kinetics for lactate and pyruvate are only known for MCT1, -2 and -4. Transport kinetics remain to be established for many other MCTs. In conclusion, this study suggests that in skeletal muscle, as well as other tissues, lactate and pyruvate transport rates may not only involve MCT1 and -4, as other monocarboxylate transporters are also expressed in rat (MCT2, -5, -6) and human skeletal muscle (MCT2, -5, -6, -7).

Animals↗
PubMed1976

Calcium-binding proteins.

Calcium binding, which appears to be either specific or physiologically significant, has been reported for 70 norminally "different" proteins. First, I catalog these proteins. Only a few recent or general references can be cited. Those proteins that serve critical physiological functions or that may be regarded as chemical prototypes are discussed in more detail. Second, I present several generalizations. Inevitably the logic here is cyclic in that the generalizations dictate which data from all those available are actually presented. In order to focus our attention in the catalog, I outline these generalizations: 1. An examination of the five calcium-binding proteins of known structure does not reveal a correlation between ligand type and/or geometry and Ca2+ affinity or selectivity. 2. For many of the enzymes supposedly activated or stabilized by Ca2+ the available data dot not allow one to judge the physiological significance of the calcium binding or its contribution of the enzymic mechanism. 3. Of the enzymes requiring Ca2 and concanavalin A, only the nuclease of Staphylococcus and possibly phospholipase appear to bind Ca2 at the active site. 4. The calcium affinities of most of the extracellular enzymes are low, pKd = 3 to 4. This is consistent with the fact that the Ca2+ concentration of the extracellular environment is about 10(-3) M. 5. The cytosol concentration of free Ca2+ in most if not all eukaryotic cells is from 10(-6) to 10(-8) M. Following a stimulus to the cell after which Ca2+ functions as a second messenger, the free Ca2+ may rise to 10(-6) to 10(-5) M. The reported affinities of most enzymes of the cytosol are too low to be physiologically significant. 6. Several intracellular enzymes or enzyme activators have pKd values between 5 and 8. These enzymes therefore may be turned on and off or "modulated" in response to extracellular stimuli. 7. There is a distinct conceptual difference between extracellular enzymes that are "activated" by Ca2+ and those intracellular enzymes that are modulated by Ca2+. The activated proteins bind Ca2+ upon secretion or upon incorporation into a secretory vesicle and retain it throughout their functional lifetimes. The modulated proteins may bind and release Ca2+ many times in response to varying concentrations of this second messenger. 8. Several of the calcium-modulated proteins contain a characteristic conformation, consisting of a helix, calcium-binding loop, and second helix, referred to as the "EF hand". These proteins are homologous, that is, evolutionarily related.

Adenosine Triphosphatases↗
PubMed1999

GIST: A web tool for collecting gene information.

As the human genome is sequenced and annotated, an important step in future genetic studies of complex traits and diseases will be the identification of relevant candidate genes. To enable such compilations, it would be useful to collate all necessary and available genetic information for each candidate gene. To this end, we have created a web tool (http://genome.cwru.edu/gist/gist.html+ ++) to allow the rapid cataloging of currently available genetic data. This tool, called GIST (or "Gene Information Search Tool"), allows an investigator to search the major genomic databases containing gene and marker information from a single query point. To prove the utility of GIST, a catalog of 150 hypertension candidate genes was created. This resource collates all available nucleotide and amino acid sequence data, expression data, chromosomal map location, and genetic marker interval for each gene, collected from on-line databases. These data can be used to guide genetic studies of hypertension.

Databases, Factual↗
PubMed2006

Development and characterization of a normalized canine retinal cDNA library for genomic and expression studies.

PURPOSE: Identification of causative mutations for retinal blinding disorders is often limited by restricted understanding of gene expression and underlying molecular mechanisms that trigger degenerative processes. This study was conducted to develop a catalog of canine retina-expressed genes that would provide a unique tool to investigate normal and altered function in the adult retina. Because of the conserved syntenies between the dog and human, this approach would identify new potential disease candidate genes for both species. METHODS: A canine normalized retinal cDNA library was produced and analyzed by using a modified PhredPhrap algorithm. Computerized annotation provided gene homology and chromosomal location for individual clones and contigs in a Web-accessible database. RESULTS: From 6316 cDNA clones, 3980 retinal expressed sequence tags (ESTs) were derived. Homology to the canine genome draft sequence was found for more than 99% of all ESTs, but only for 32% when compared with annotated canine cDNAs. Functional analysis suggests an enrichment of this library for genes involved with eye function and development, chaperone, or ribosomal functions when compared with mouse and human National Center for Biotechnology Information (NCBI) RefSeq entries. CONCLUSIONS: A combination of annotation approaches with ongoing mapping and expression studies provide functional data covering at least 27% to 30% of the currently proposed canine catalog of genes expressed in the retina. This is an essential first step toward establishing an integrated network for gene identification and expression patterns suitable for functional genetics, comparative genomics and evolutionary analysis of genes and gene families with respect to the developmental and degenerative processes of the retina.

Animals↗
PubMed1990

The Carolina Nosology of Destructive Behavior (CNDB).

This article sets forth a multiaxial system for cataloging individuals who manifest destructive behavior toward themselves, others, or property. An initial codification to describe the characteristics of the destructive behavior of the individual is presented, followed by a description of a quaternary axial system which catalogs in a clinically relevant manner, individuals engaging in destructive behavior. The four axes presented and developed are Axis A--a medical diagnosis axis, Axis B--an axis of psychological correlates, Axis C--an axis of biological correlates, and Axis D--an axis of moral/cultural correlates. This nosology is proposed in order to standardize the coding of human destructive behavior. It is intended to be used by members of the clinical and research communities in order to compare patient types and their relationship to treatment interventions.

Aggression↗
PubMed2001

The Adaptive Evolution Database (TAED).

BACKGROUND: Developing an understanding of the molecular basis for the divergence of species lies at the heart of biology. The Adaptive Evolution Database (TAED) serves as a starting point to link events that occur at the same time in the evolutionary history (tree of life) of species, based upon coding sequence evolution analyzed with the Master Catalog. The Master Catalog is a collection of evolutionary models, including multiple sequence alignments, phylogenetic trees, and reconstructed ancestral sequences, for all independently evolving protein sequence modules encoded by genes in GenBank [1]. RESULTS: We have estimated from these models the ratio of nonsynonymous to synonymous nucleotide substitution (Ka/Ks), for each branch in their respective evolutionary trees of every subtree containing only chordata or only embryophyta proteins. Branches with high Ka/Ks values represent candidate episodes in the history of the family where the protein may have undergone positive selection, a phenomenon in molecular evolution where the mutant form of a gene must have conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. We have found that an unexpectedly large number of families (between 10 and 20% of those families examined) have at least one branch with a notably high Ka/Ks value (putative adaptive evolution). As a resource for biologists wishing to understand the interaction between protein sequences and the Darwinian processes that shape these sequences, we have collected these into The Adaptive Evolution Database (TAED). CONCLUSIONS: Placed in a phylogenetic perspective, candidate genes that are undergoing evolution at the same time in the same lineage can be viewed together. This framework based upon coding sequence evolution can be readily expanded to include other types of evolution. In its present form, TAED provides a resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.

Animals↗
PubMed2001

The adaptive evolution database (TAED).

BACKGROUND: The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (KA/KS values) on branches of an evolutionary tree between nodes representing reconstructed ancestral sequences. RESULTS: Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. Branches with high KA/KS values were identified. These represent candidate episodes in the history of the protein family when the protein may have undergone positive selection, where the mutant form conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. An unexpectedly large number of families (between 10% and 20% of those families examined) were found to have at least one branch with high KA/KS values above arbitrarily chosen cut-offs (1 and 0.6). Most of these survived a robustness test and were collected into TAED. CONCLUSIONS: TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study. It can be expanded to include other evolutionary information (for example changes in gene regulation or splicing) placed in a phylogenetic perspective.

Adaptation, Physiological↗