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PubMed2005

Adaptive risk group refinement.

We construct interpretable prognostic rules based on a sequence of "box-shaped" regions in the predictor space indexed by the fraction of patients in the prognostic group. In addition, the method can be used as a building block to construct more general prognostic rules based on unions of boxes, or even as a tool to find multiple prognostic groups. Simulations are used to study the properties of the new method and compare it to constructing prognostic groups based on regression trees and linear proportional hazards (PH) models. We consider an example based on data from several completed clinical trials for patients with multiple myeloma.

Algorithms↗

PubMed2005

libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.

BACKGROUND: An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. RESULTS: The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. CONCLUSION: Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

Algorithms↗

PubMed2005

Dipyridamole, an underestimated vascular protective drug.

Dipyridamole, developed almost half a century ago, acts by inhibiting nucleoside transport, which increases adenosine levels leading to inhibition of platelet aggregation and vasodilatation mainly in the coronary tree. It is a vaso-protective drug with proven efficacy in the prevention of strokes. Adenosine receptor 2 inhibitory purines, ubiquitously available in food and drink, inhibit the vasomotor effects of dipyridamole but not its action on platelet aggregation. This and the slow build-up of blood levels of dipyridamole after oral application may explain why incidents of drug-induced angina ("coronary steal") were never reported in the prevention trials. The prevention of arterial thrombosis and the positive remodeling of the arterial system (arteriogenesis) by elevated blood flows suggest that dipyridamole may be able to halt the progression of organ manifestations of atherosclerosis. Clinical trials for the secondary prevention of vascular occlusions in other vascular beds should be encouraged.

Adenosine↗

PubMedDate not supplied

Discovering H-bonding rules in crystals with inductive logic programming.

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Artificial Intelligence↗

PubMed2002

Rainforest endophytes and bioactive products.

An increase in the number of people in the world having health problems caused by certain cancers, drug-resistant bacteria, parasitic protozoans, and fungi has caused alarm. An intensive search for newer and more effective agents to deal with these problems is now underway. Endophytes are a potential source of novel chemistry and biology to assist in helping solve not only human health, but plant and animal health problems also. Endophytes reside in the tissues between living plant cells. The relationship that they establish with the plant varies from symbiotic to bordering on pathogenic. Of all of the world's plants, it seems that only a few grass species have had their complete complement of endophytes studied. As a result, the opportunity to find new and interesting endophytes among the myriad of plants is great. Sometimes extremely unusual and valuable organic substances are produced by these endophytes. These compounds may contribute to the host-microbe relationship. The initial step in dealing with endophytic microorganisms is their successful isolation from plant materials. Then, the isolation and characterization of bioactive substances from culture filtrates is done using bioassay guided fractionation and spectroscopic methods. Some of the more interesting compounds produced by endophytic microbes with which we have dealt are taxol, cryptocin, cryptocandin, jesterone, oocydin, isopestacin, the pseudomycins and ambuic acid. This review discusses an approach for bio-prospecting the rainforests, not only to harvest their endophytic microorganisms, but to eventually build a better understanding of the importance and value they have to humankind.

Anti-Bacterial Agents↗

PubMed2003

Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray crystallographic, molecular modeling, and sequence-based methods.

A major impediment to the use of adenovirus as a gene therapy vector and for vaccine applications is the host immune response to adenovirus hexon-the major protein component of the icosahedral capsid. A solution may lie in novel vectors with modified or chimeric hexons designed to evade the immune response. To facilitate this approach, we have distinguished the portion of hexon that all serotypes have in common from the hypervariable regions that are responsible for capsid diversity and type-specific immunogenicity. The common hexon core-conserved because it forms the viral capsid-sets boundaries to the regions where modifications can be made to produce nonnative hexons. The core has been defined from the large and diverse set of known hexon sequences by an accurate alignment based on the newly refined crystal structures of human adenovirus types 2 (Ad2) and Ad5 hexon. Comparison of the two hexon models, which are the most accurate so far, reveals that over 90% of the residues in each have three-dimensional positions that closely match. Structures for more distant hexons were predicted by building molecular models of human Ad4, chimpanzee adenovirus (AdC68), and fowl adenovirus 1 (FAV1 or CELO). The five structures were then used to guide the alignment of the 40 full-length (>900 residues) hexon sequences in public databases. Distance- and parsimony-based phylogenetic trees are consistent and reveal evolutionary relationships between adenovirus types that parallel those of their animal hosts. The combination of crystallography, molecular modeling, and phylogenetic analysis defines a conserved molecular core that can serve as the armature for the directed design of novel hexons.

Adenoviruses, Human↗

PubMed2005

Microhabitats occupied by Loxosceles intermedia and Loxosceles laeta (Araneae: Sicariidae) in Curitiba, Paraná, Brazil.

A survey was done of the environments and substrata occupied by Loxosceles intermedia Mello-Leitão, 1934 and Loxosceles laeta (Nicolet, 1849) (Araneae: Sicariidae) in urban woods and anthropic constructions in Curitiba. In total, 2,099 trees, 364 decaying logs as well as stones and roots, built-up areas, and wasteland in six urban parks and 60 residences were inspected. In total, 1,775 m2 of vegetation was inspected, but spiders and their vestiges were collected only in and around buildings in urban parks and residences. L. intermedia was more common than L. laeta and occurred both indoors and outdoors, whereas L. laeta was more common indoors in wooden houses. The two species did not occur in the same microhabitats, although both preferred paper, wood, and construction materials. Spiders collected in urban parks were heavier than those collected in residences, although only males collected in urban parks were larger than those from residences. The lack of vestiges indicative of a previous occupation in the urban parks suggested that both species occupied primarily the anthropic environment where they found numerous substrata that offered thermal isolation and suitable conditions for web fixation, ecdysis, and reproduction.

Animals↗

PubMed2006

DivergentSet, a tool for picking non-redundant sequences from large sequence collections.

DivergentSet addresses the important but so far neglected bioinformatics task of choosing a representative set of sequences from a larger collection. We found that using a phylogenetic tree to guide the construction of divergent sets of sequences can be up to 2 orders of magnitude faster than the naive method of using a full distance matrix. By providing a user-friendly interface (available online) that integrates the tasks of finding additional sequences, building and refining the divergent set, producing random divergent sets from the same sequences, and exporting identifiers, this software facilitates a wide range of bioinformatics analyses including finding significant motifs and covariations. As an example application of DivergentSet, we demonstrate that the motifs identified by the motif-finding package MEME (Motif Elicitation by Maximum Entropy) are highly unstable with respect to the specific choice of sequences. This instability suggests that the types of sensitivity analysis enabled by DivergentSet may be widely useful for identifying the motifs of biological significance.

Amino Acid Sequence↗

PubMed2003

Structure data entry using graphical input: recording symptoms for multiple sclerosis.

Structured Data Entry provides flexible and efficient input to the computer-based patient record. We have utilized the SDE approach to build a prototype interface for recording common symptoms associated with Multiple Sclerosis (MS). The software provides both graphical input and output, to facilitate efficient data entry and monitoring of data. Graphical input is transformed to textual information, which is stored in a database in a hierarchical tree structure. Pain management in MS may be achieved by careful monitoring of the symptom in response to treatment. Pain location is selected on a body image and severity and other attributes represented using a graphical visual analog scale, leading to more convenient input and a less ambiguous coding than is achievable with narrative text alone. This approach could provide an objective means of monitoring the progress of the disease and management of the symptoms. The intuitive interface may also facilitate self-monitoring.

Computer Graphics↗

PubMed2005

Monitoring of symptoms and interventions associated with multiple sclerosis.

We have utilized the Structured Data Entry approach to build a prototype interface for the recording of personalized symptoms associated with Multiple Sclerosis (MS). The software provides both graphical input and output, to facilitate efficient data entry and monitoring. Graphical input is transformed to textual information, which is stored in a database in a hierarchical tree structure. Pain management in MS may be achieved by careful monitoring of the symptom in response to treatment. Pain location is selected on a body image and severity and other attributes represented using a graphical visual analog scale, leading to more convenient input and a less ambiguous coding than is achievable with narrative text alone. The Internet can be used to record and provide access to clinical data, assisting the citizen by providing a healthcare professional partnership approach to care. This approach could provide an objective means of monitoring symptoms and hence provide a more personalized approach to MS management.

Biomedical Technology↗

PubMedDate not supplied

[The value of life. Development of an assessment system for therapeutic strategies].

The wide therapeutic supply which a present is available for diverse disorders, together with a excess of indiscriminate scientific information, occasionally complicates the possibility of acquiring a wide experience in the treatment of certain patients (limited experience). To acquire genuinely useful experience, it is necessary to accumulate simiular experiences from our environment, with it being necessary to precisely define, in an objective manner, concepts which until now are difficult to quantify (risk of mortality or morbidity, survival, quality of life, etc.). The definition of these parameters, shall favor the creation of homogenous groups (isoseverity indices), which is the first step in the evaluation of more complex conceps, such as; quality of life, increase of life expectancy, quality adjusted life years (QALY's), and beneficial application, all of which validated in diverse hospital media. Based on the previous, we would obtain other calculated parameters; the benefit (of the patient), the use (of the procedure), and the efficacy (of the physician or the unit). Once these parameters have been standarized, it shall be possible to compare them with the results published in other media, considered to be standards, with the aim of establishing the corresponding self-evaluation. The evaluation of the cost of each process, is a compulsory procedure, to produce, if possible, based on the previous results, a better distribution of the means without a decrease in the quality of assistance. With the aim of evaluating the results in an objective and quantifiable manner, we have worked these last years on developing assessment applied to the evaluation of predictive and isoseverity indices, such as the cost/benefit evaluation in critical, geriatric, and oncological patients, and in those with artificial nutrition in the home. The fruit of this labor has come together in the production of a computerized information system (SAETA), which builds de previously validated modules into is structure, thus permiting the storage and subsequent multifactoral analysis of the results.

Decision Theory↗

PubMed2000

The structure and gene repertoire of an ancient red algal plastid genome.

Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, a unicellular red alga (AF022186). The analysis revealed that this genome shows several unusual structural features, such as a hypothetical hairpin structure in a gene-free region and absence of large repeat units. We provide evidence that this structural organization of the cp-genome of C. caldarium may be that of the most ancient cp-genome so far described. We also compared the cp-genome of C. caldarium to the other known cp-genomes of the red lineage. The cp-genome of C. caldarium cannot be readily aligned with that of Porphyra purpurea, a multicellular red alga, or Guillardia theta due to a displacement of a region of the cp-genome. The phylogenetic tree reveals that the secondary endosymbiosis, through which G. theta evolved, took place after the separation of the ancestors of C. caldarium and P. purpurea. We found several genes unique to the cp-genome of C. caldarium. Five of them seem to be involved in the building of bacterial cell envelopes and may be responsible for the thermotolerance of the chloroplast of this alga. Two additional genes may play a role in stabilizing the photosynthetic machinery against salt stress and detoxification of the chloroplast. Thus, these genes may be unique to the cp-genome of C. caldarium and may be required for the endurance of the extreme living conditions of this alga.

Adaptation, Physiological↗

PubMed2003

The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes.

Genome analyses and the resolution of three-dimensional structures have provided evidence in recent years for hitherto unexpected family relationships between redox proteins of very diverse enzymes involved in bioenergetic electron transport. Many of these enzymes appear in fact to be constructed from only a limited set of building blocks. Phylogenetic analysis of selected units from this "redox enzyme construction kit" indicates an origin for several prominent bioenergetic enzymes that is very early, lying before the divergence of Bacteria and Archaea. Possible scenarios for the early evolution of selected complexes are proposed based on the obtained tree topologies.

Archaea↗

PubMed2006

Meteorological variation effect on aerobiology--new tools on pollen forecasting.

Spanish Aerobiology Network (REA) includes 22 research groups implied in the biological analysis of the air from 50 observation sites extended over the Iberian Peninsula and Baleares Islands. To offer in-advance information for pollen allergy sufferers, doctors and health authorities is one of REA priorities. One of our objectives is the study of the influence of meteorological variations on the quantity and occurrence of pollen in the atmosphere. Nevertheless, to include only weather parameters is not enough for build accurate forecasts. Field phenology data, vegetation land cover, topography data and previous aerobiological data should be included in the models. Meteorological conditions control the start, duration, intensity and end of the pollen season, but their effect depends on the different types of vegetation. The biological response of tree pollination is highly differentiated from the herbaceous one. Another important point is the adaptation of a given species phetnology to different climatic areas. We showed the different phenoclimatic variables determining tree flowering in the Mediterranean climate areas and in the Atlantic climate ones of the Iberian Peninsula, and the consequences on the development of our forecasting models. Finally we comment our more recent studies that use geostatistic algorithms as a tool for including all the cited parameters and also space variables as altitude, latitude and orientation to sun.

Algorithms↗

PubMed1996

WWW-query: an on-line retrieval system for biological sequence banks.

We have developed a World Wide Web (WWW) version of the sequence retrieval system Query: WWW-Query. This server allows to query nucleotide sequence banks in the EMBL/GenBank/DDBJ formats and protein sequence banks in the NBRF/PIR format. WWW-Query includes all the features of the on-line sequences browsers already available: possibility to build complex queries, integration of cross-references with different data banks, and access to the functional zones of biological interest. It also provides original services not available elsewhere: introduction of the notion of re-usable sequence lists, integration of dedicated helper applications for visualizing alignments and phylogenetic trees and links with multivariate methods for studying codon usage or for complementing phylogenies.

Amino Acid Sequence↗

PubMedDate not supplied

Successful public/private donation programs: a review of the Diflucan Partnership Program in South Africa.

A review of the partnership between Pfizer Inc. and the South African Ministry of Health to distribute free Diflucan (fluconazole) in the Diflucan Partnership Program (DPP) demonstrates that product donations may be a useful response to AIDS if they are coupled with efforts to build means of drug distribution and enhance professional healthcare capacity to treat patients. Equally important is the creation of a new set of productive working relationships between stakeholders who came to the project with different backgrounds and perspectives, as well as a frankly disparate set of objectives. A decision tree illustrates how these relationships were built into the DPP. This review concludes with a few lessons learned in providing medicines not only to South Africa, but also to the 77 other African countries now participating in the DPP. As the search for new treatments and vaccines continues, increasing access to existing medicines through targeted donations--including training and infrastructure support--is the most practical way for the health community to address the problem of ill health among the poor. In addition to a detailed analysis of the DPP, there is also a discussion of the benefits of a donation program that addresses the AIDS crises on a global scale. This review may serve as a blueprint for establishing programs that are successful in fighting AIDS and improving the lives of millions of people.

AIDS-Related Opportunistic Infections↗

PubMed1995

Identification and molecular evolution of new dynein-like protein sequences in rat brain.

RT-PCR cloning was performed to find unknown members of the dynein superfamily expressed in rat brain. Six kinds of degenerate primers designed for the dynein catalytic domain consensuses were used for extensive PCR amplifications. We have sequenced 550 plasmid clones which turned out to include 13 kinds of new dynein-like sequences (DLP1-8, 9A/B, 10-12) and cytoplasmic dynein heavy chain. In these clones, alternative splicing was detected for a 105 nt-domain containing the CFDEFNRI consensus just downstream of the most N-terminal P-loop (DLP9A and 9B). By using these obtained sequences, initial hybridization studies were performed. Genomic Southern blotting showed each sequence corresponds to a single copy of the gene, while northern blotting of adult brain presented more than one band for some subtypes. We further accomplished molecular evolutionary analysis to recognize their phylogenetic origins for the axonemal and non-axonemal (cytoplasmic) functions. Different methods (UPGMA, NJ and MP) presented well coincident phylogenetic trees from 44 partial amino acid sequences of dynein heavy chain from various eukaryotes. The trunk for all the cytoplasmic dynein heavy chain homologues diverged directly from the root of the phylogenetic tree, suggesting that the first dynein gene duplication defined two distinct functions as respective subfamilies. Of particular interest, we found a duplication event of the cytoplasmic dynein heavy chain gene giving rise to another subtype, DLP4, located between the divergence of yeast and that of Dictyostelium. Such evolutionary topology builds up an inceptive hypothesis that there are at least two non-axonemal dynein heavy chains in mammals.

Amino Acid Sequence↗

PubMed2006

Light harvesting dendrimers.

Tree-like dendrimers with decreasing number of chromophores from periphery to core is an attractive candidate for light-harvesting applications. Numerous dendritic designs with different kinds of light-collecting chromophores at periphery and an energy-sink at the core have been demonstrated with high energy transfer efficiency. These building blocks are now being developed for several applications such as light-emitting diodes, frequency converters and other photonic devices. This review outlines the efforts that are based on both conjugated and non-conjugated dendrimers.

Dendrimers↗