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F1000Research
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  This is an Open Access Journal Open Access journal
     ISSN (Online) 2046-1402
     Published by Faculty of 1000 Homepage  [1 journal]
  • Sub-strains of Drosophila Canton-S differ markedly in their locomotor
           behavior [v1; indexed, http://f1000r.es/3is]

    • Authors: Julien Colomb, Björn Brembs
      Abstract: We collected five sub-strains of the standard laboratory wild-type Drosophila melanogaster Canton Special (CS) and analyzed their walking behavior in Buridan's paradigm using the CeTrAn software. According to twelve different aspects of their behavior, the sub-strains fit into three groups. The group separation appeared not to be correlated with the origin of the stocks. We conclude that founder effects but not laboratory selection likely influenced the gene pool of the sub-strains. The flies’ stripe fixation was the parameter that varied most. Our results suggest that differences in the genome of laboratory stocks can render comparisons between nominally identical wild-type stocks meaningless. A single source for control strains may settle this problem.
      PubDate: 2014-07-30
      DOI: 10.12688/f1000research.4263.1
      Issue No: Vol. 3 (2014)
       
  • Immunoprecipitation and mass spectrometry identify non-cell autonomous
           Otx2 homeoprotein in the granular and supragranular layers of mouse visual
           cortex [v1; indexed, http://f1000r.es/40d]

    • Authors: Namsuk Kim, Dario Acampora, Florent Dingli, Damarys Loew, Antonio Simeone, Alain Prochiantz, Ariel A. Di Nardo
      Abstract: Plasticity in the visual cerebral cortex is regulated by the internalization of Otx2 homeoprotein into parvalbumin neurons in cortical layers II/III and IV. However the Otx2 locus is not active in these neurons and the protein is imported from external sources, including the choroid plexus. Because Otx1 and Otx2 may have redundant functions, we wanted to verify if part of the staining in parvalbumin neurons corresponds to Otx1 transported from cortical layer V neurons. It is demonstrated here that Otx staining in layer IV cells is maintained in Otx1-null mice. The immunoprecipitation of extracts from finely dissected granular and supragranular cortex (layers I-IV) gave immunoblots with a band corresponding to Otx2 and not Otx1. Moreover, high-resolution mass spectrometry analysis after immunoprecipitation identifies two peptides within the Otx2 homeodomain. One of these peptides is specific for Otx2 and is not found in Otx1. These results unambiguously establish that the staining in parvalbumin neurons revealed with the anti-Otx2 antibodies used in our previous studies identifies non-cell autonomous Otx2.
      PubDate: 2014-07-30
      DOI: 10.12688/f1000research.4869.1
      Issue No: Vol. 3 (2014)
       
  • Case Report: Reversible cabergoline-associated cardiac valvulopathy post
           drug discontinuation [v1; indexed, http://f1000r.es/2jm]

    • Authors: Chris G. Yedinak, Shirley McCartney, Troy H. Dillard, Kevin S. Wei, Maria Fleseriu
      Abstract: We present a case of a 21 year old male patient diagnosed with a 2.2 cm prolactin-secreting adenoma in contact with the optic chiasm. The patient was treated with up to 6mg/week of cabergoline (total cumulative dose 814 mg) and developed mild valvulopathy. Valvulopathy was subsequently reversed after discontinuation of cabergoline therapy.
      PubDate: 2014-07-25
      DOI: 10.12688/f1000research.3062.1
      Issue No: Vol. 3 (2014)
       
  • Case Report: Pneumocephalus after labor epidural anesthesia [v1;
           indexed, http://f1000r.es/3va]

    • Authors: Beatriz Nistal-Nuño, Manuel Ángel Gómez-Ríos
      Abstract: Lumbar epidural anesthesia is commonly used for labor analgesia. The 'loss-of- resistance' to air technique (LORA) is generally employed for recognition of the epidural space. One of the rare complications of this technique is pneumocephalus (PC). Here we describe the case of a parturient who developed a frontal headache when locating the epidural space using LORA. On the second day after epidural injection, the patient exhibited occipital headaches with gradual worsening. Computed tomography scans of the brain indicated PC. Following symptomatic treatment, our patient was discharged on the 13th day. We concluded that the amount of air used to identify the epidural space in LORA should be minimized, LORA should not be used after dural puncture and the use of saline avoids PC complications.
      PubDate: 2014-07-22
      DOI: 10.12688/f1000research.4693.1
      Issue No: Vol. 3 (2014)
       
  • The effects of extremes of pH on the growth and transcriptomic profiles of
           three haloarchaea [v1; indexed, http://f1000r.es/3y1]

    • Authors: Aida Moran-Reyna, James A. Coker
      Abstract: The halophilic archaea (haloarchaea) live in saline environments which are found across the globe.  In addition to salinity, these niches can be quite dynamic and experience extreme conditions such as low oxygen content, radiation (gamma and UV), pH and temperature.  However, of all the naturally occurring stresses faced by the haloarchaea, only one, pH, has not been previously reported on. Therefore, we endeavored to determine the responses of the transcriptomes of three haloarchaea (Hla, Hvo, and NRC-1) to growth under acidic and alkaline pH. Our observations showed that the transcriptomes of Hvo and NRC-1 respond in a similar manner to each other as well as other prokaryotes when grown in an acidic environment, while the pattern for Hla was dissimilar. For alkaline stress, all three haloarchaea responded in a manner similar to well-studied archaea and bacteria and had four-times more significantly regulated transcripts in common, compared to acidic growth. Additionally, we performed an analysis on the changes in the transcriptomes of the three haloarchaea when shifting from one pH extreme to the other. The results showed that the transcriptomes of all three haloarchaea respond more similarly when moving from alkaline to acidic conditions compared to moving from an acidic to alkaline environment. Interestingly, our studies also showed that individual genes of multiple paralogous gene families (tbp, tfb, orc/cdc6, etc.) found in the haloarchaea were regulated under specific stresses thereby providing evidence that they modulate the response to various environmental stresses. The studies described here are the first to catalog the changes in the haloarchaeal transcriptomes under growth in extreme pH and help us understand how life is able to thrive under all conditions present on Earth and, if present, on extraterrestrial bodies as well.
      PubDate: 2014-07-22
      DOI: 10.12688/f1000research.4789.1
      Issue No: Vol. 3 (2014)
       
  • The need for antibiotic stewardship and treatment standardization in the
           care of cirrhotic patients with spontaneous bacterial peritonitis –
           a retrospective cohort study examining the effect of ceftriaxone dosing
           [v2; indexed, http://f1000r.es/3se]

    • Authors: Laura Mazer, Elliot B. Tapper, Gail Piatkowski, Michelle Lai
      Abstract: Background: Spontaneous bacterial peritonitis (SBP) is a common, often fatal affliction for cirrhotic patients. Despite all clinical trials of ceftriaxone for SBP using 2g daily, it is often given at 1g daily. Aim: We evaluated survival after SBP as a function of ceftriaxone dosage. Methods:  A retrospective cohort of all patients who received ceftriaxone for SBP (greater than 250 neutrophils in the ascites). Results: As opposed to 1 gram, median survival is longer for patients receiving 2 grams (228 days vs. 102 days (p = 0.26) and one year survival is significantly higher (p = 0.0034).  After adjusting for baseline Model for End Stage Liver Disease (MELD) score, however, this difference was no longer significant.  Similarly, there was a significantly shorter length of intensive care for patients receiving 2 g (0.59 ± 1.78 days vs. 3.26 ± 6.9, p = 0.034), odds ratio 0.11 (95% CI 0.02 - 0.65). This difference, too, was no longer significant after controlling for the MELD score - odds ratio 0.21 (95% CI 0.04 - 1.07). Additionally, 70% of patients received at least one additional antibiotic; over 25 different medications were used in various combinations. Conclusions:  Patients receiving 2 g of ceftriaxone may require fewer intensive care days and may enjoy an improved survival compared to those receiving 1 g daily. The complexity of antibiotic regimens to which cirrhotic patients are exposed must be studied further and rationalized.  We recommend fastidious antibiotic stewardship for patients with cirrhosis. Efforts should be made to craft local standards for the treatment of SBP that include appropriate antibiotic selection and dose.
      PubDate: 2014-07-14
      DOI: 10.12688/f1000research.3-57.v2
      Issue No: Vol. 3 (2014)
       
  • An explanatory evo-devo model for the developmental hourglass [v1;
           indexed, http://f1000r.es/3s6]

    • Authors: Saamer Akhshabi, Shrutii Sarda, Constantine Dovrolis, Soojin Yi
      Abstract: The "developmental hourglass'' describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the "phylotypic stage''). Recent studies have found evidence in support of the hourglass effect at the genomic level. For instance, the phylotypic stage expresses the oldest and most conserved transcriptomes. However, the regulatory mechanism that causes the hourglass pattern remains an open question. Here, we use an evolutionary model of regulatory gene interactions during development to identify the conditions under which the hourglass effect can emerge in a general setting. The model focuses on the hierarchical gene regulatory network that controls the developmental process, and on the evolution of a population under random perturbations in the structure of that network. The model predicts, under fairly general assumptions, the emergence of an hourglass pattern in the structure of a temporal representation of the underlying gene regulatory network. The evolutionary age of the corresponding genes also follows an hourglass pattern, with the oldest genes concentrated at the hourglass waist. The key behind the hourglass effect is that developmental regulators should have an increasingly specific function as development progresses. Analysis of developmental gene expression profiles from Drosophila melanogaster and Arabidopsis thaliana provide consistent results with our theoretical predictions.
      PubDate: 2014-07-08
      DOI: 10.12688/f1000research.4583.1
      Issue No: Vol. 3 (2014)
       
  • KEGGscape: a Cytoscape app for pathway data integration [v1; indexed,
           http://f1000r.es/3qe]

    • Authors: Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi
      Abstract: In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape (http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.
      PubDate: 2014-07-01
      DOI: 10.12688/f1000research.4524.1
      Issue No: Vol. 3 (2014)
       
  • GeneMANIA: Fast gene network construction and function prediction for
           Cytoscape [v1; indexed, http://f1000r.es/3rv]

    • Authors: Jason Montojo, Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
      Abstract: The GeneMANIA Cytoscape app enables users to construct a composite gene-gene functional interaction network from a gene list. The resulting network includes the genes most related to the original list, and functional annotations from Gene Ontology. The edges are annotated with details about the publication or data source the interactions were derived from. The app leverages GeneMANIA’s database of 1800+ networks, containing over 500 million interactions spanning 8 organisms: A. thaliana, C. elegans, D. melanogaster, D. rerio, H. sapiens, M. musculus, R. norvegicus, and S. cerevisiae. Users may also import their own organisms, networks, and expression profiles. The app is compatible with Cytoscape versions 2 and 3.
      PubDate: 2014-07-01
      DOI: 10.12688/f1000research.4572.1
      Issue No: Vol. 3 (2014)
       
  • Cytoscape: the network visualization tool for GenomeSpace workflows [v1;
           indexed, http://f1000r.es/3ph]

    • Authors: Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael Smoot, Trey Ideker, Jill P. Mesirov
      Abstract: Modern genomic analysis often requires workflows incorporating multiple best-ofbreed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded it over 850 times since the release of its first version in September, 2013.
      PubDate: 2014-07-01
      DOI: 10.12688/f1000research.4492.1
      Issue No: Vol. 3 (2014)
       
  • WikiPathways App for Cytoscape: Making biological pathways amenable to
           network analysis and visualization [v1; indexed, http://f1000r.es/3ij]

    • Authors: Martina Kutmon, Samad Lotia, Chris T Evelo, Alexander R Pico
      Abstract: In this paper we present the open-source WikiPathways app for Cytoscape (http://apps.cytoscape.org/apps/wikipathways) that can be used to import biological pathways for data visualization and network analysis. WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services. The WikiPathways app allows users to load pathways in two different views: as an annotated pathway ideal for data visualization and as a simple network to perform computational analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps. More than 2000 downloads between its first release in August 2013 and the submission of the paper in May 2014 highlight the importance and adoption of the app in the network biology field.
      PubDate: 2014-07-01
      DOI: 10.12688/f1000research.4254.1
      Issue No: Vol. 3 (2014)
       
  • BridgeDb app: unifying identifier mapping services for Cytoscape [v1;
           indexed, http://f1000r.es/3qb]

    • Authors: Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico
      Abstract: The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app greatly simplifies the identifier mapping process in Cytoscape by providing a unified interface to different mapping resources and services. The app also provides a programming interface via Cytoscape Commands that can be utilized for identifier mapping by other Cytoscape apps. In this article we provide a technical guide to the BridgeDb app for mapping identifiers in Cytoscape.
      PubDate: 2014-07-01
      DOI: 10.12688/f1000research.4521.1
      Issue No: Vol. 3 (2014)
       
  • An evolutionarily significant unicellular strategy in response to
           starvation stress in Dictyostelium social amoebae [v1; indexed,
           http://f1000r.es/3hg]

    • Authors: Darja Dubravcic, Minus van Baalen, Clément Nizak
      Abstract: The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation and constitutes a model of choice in microbial cooperation studies. Aggregates of up to 106 cells form fruiting bodies containing two cell types: (i) dormant spores (~80%) that can persist for months in the absence of nutrients, and (ii) dead stalk cells (~20%) that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus regulate population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. D. discoideum thus constitutes a model system lying at the intersection of microbial cooperation and bet hedging, defining a new frontier in microbiology and evolution studies
      PubDate: 2014-06-24
      DOI: 10.12688/f1000research.4218.1
      Issue No: Vol. 3 (2014)
       
  • CETP inhibitors and cardiovascular disease: Time to think again [v1;
           indexed, http://f1000r.es/3mp]

    • Authors: Norman E Miller
      Abstract: Inhibition of cholesteryl ester transfer protein (CETP) lowers plasma low-density lipoprotein cholesterol concentration and raises high-density lipoprotein (HDL) cholesterol, suggesting it might prevent cardiovascular disease (CVD). From the outset, however, the concept has been controversial owing to uncertainty about its effects on HDL function and reverse cholesterol transport (RCT). Although there has long been good evidence that CETP inhibition reduces atherosclerosis in rabbits, the first information on CETP as a CVD risk factor in a prospectively followed cohort was not published until after the first Phase 3 trial of a CETP inhibitor had begun. The worrying finding that CVD incidence was related inversely to plasma CETP has since been reproduced in each of five further prospective cohort studies. Similar results were obtained in subjects on or off statin therapy, for first and second CVD events, and for mortality as well as CVD morbidity. Additionally, two recent studies have found alleles of the CETP gene that lower hepatic CETP secretion to be associated with an increased risk of myocardial infarction. Meanwhile, CETP gene transfer in mice was found to increase RCT from peripheral macrophages in vivo, and human plasma with high CETP activity was shown to have a greater capacity to remove cholesterol from cultured cells than plasma with low activity. This mounting evidence for a protective function of CETP has been given remarkably little attention, and indeed was not mentioned in several recent reviews.  It appears to show that CETP inhibition does not test the HDL hypothesis as originally hoped, and raises a pressing ethical issue regarding two Phase 3 trials of inhibitors, involving more than forty thousand subjects, which are currently in progress. As the weight of evidence now clearly supports an adverse effect of CETP inhibition on CVD, an urgent review is needed to determine if these trials should be discontinued.
      PubDate: 2014-06-10
      DOI: 10.12688/f1000research.4396.1
      Issue No: Vol. 3 (2014)
       
  • Epiphyte response to drought and experimental warming in an Andean cloud
           forest [v2; indexed, http://f1000r.es/3le]

    • Authors: Joshua M. Rapp, Miles R. Silman
      Abstract: The high diversity and abundance of vascular epiphytes in tropical montane cloud forest is associated with frequent cloud immersion, which is thought to protect plants from drought stress. Increasing temperature and rising cloud bases associated with climate change may increase epiphyte drought stress, leading to species and biomass loss. We tested the hypothesis that warmer and drier conditions associated with a lifting cloud base will lead to increased mortality and/or decreased recruitment of epiphyte ramets, altering species composition in epiphyte mats. By using a reciprocal transplant design, where epiphyte mats were transplanted across an altitudinal gradient of increasing cloud immersion, we differentiated between the effects of warmer and drier conditions from the more general prediction of niche theory that transplanting epiphytes in any direction away from their home elevation should result in reduced performance. Effects differed among species, but effects were generally stronger and more negative for epiphytes in mats transplanted down slope from the highest elevation, into warmer and drier conditions, than for epiphyte mats transplanted from other elevations. In contrast, epiphytes from lower elevations showed greater resistance to drought in all treatments. Epiphyte community composition changed with elevation, but over the timescale of the experiment there were no consistent changes in species composition. Our results suggest some epiphytes may show resistance to climate change depending on the environmental and evolutionary context. In particular, sites where high rainfall makes cloud immersion less important for epiphyte water-balance, or where occasional drought has previously selected for drought-resistant taxa, may be less adversely affected by predicted climate changes.
      PubDate: 2014-06-06
      DOI: 10.12688/f1000research.3-7.v2
      Issue No: Vol. 3 (2014)
       
  • Lung transplantation in an intensive care patient with pulmonary alveolar
           microlithiasis - a case report [v1; indexed, http://f1000r.es/3c2]

    • Authors: Bülent Güçyetmez, Aylin Ogan, Aylin Çimet Ayyıldız, Berrin Yalçın Güder, Walter Klepetko
      Abstract: Introduction: Pulmonary alveolar microlithiasis (PAM) is an autosomal recessive disease characterized by the deposition of phosphate and calcium in the alveoli. The disease progresses asymptomatically until later stages. When it becomes symptomatic, lung transplantations performed before the onset of right heart failure may improve life expectancy and quality. Here we present a case report concerning the very first Turkish PAM patient to have undergone lung transplantation surgery. Patient information: A 52 year-old female, Caucasian patient, already diagnosed with PAM in infancy, was admitted to the intensive care unit, diagnosed with pneumonia and hospitalized for 20 days. We decided to refer the patient to a specialized center for lung transplantation. Bilateral lung transplantation was performed in Vienna 14 months later and no recurrence was observed during the first postoperative year. Conclusion: Bilateral lung transplantation may improve both the life expectancy and the quality of life of PAM diagnosed patients with severe respiratory failure who do not suffer from right heart failure. The risk of recurrence should not be considered as a justifying reason to avoid transplantation as a treatment method.
      PubDate: 2014-05-28
      DOI: 10.12688/f1000research.4035.1
      Issue No: Vol. 3 (2014)
       
  • A 13 year-old boy with post-transplantation lymphoproliferative disorder
           presenting with obscure gastrointestinal bleeding: a case report [v1;
           indexed, http://f1000r.es/2p0]

    • Authors: Edith Y. Ho, Vijay George, Marjorie McCracken, James W. Ostroff
      Abstract: One well recognized and potentially serious complication of chronic immunosuppression in organ transplant recipients is post-transplantation lymphoproliferative disorders (PTLD). This accounts for 20% of all malignancies in transplant recipients, which is four times higher than the general population1,2. The diagnosis of PTLD is often difficult, due to various manifestations resulting in late diagnosis. We report an unusual presentation of PTLD in a pediatric patient where the diagnosis was achieved only after extensive investigation.
      PubDate: 2014-04-07
      DOI: 10.12688/f1000research.3252.1
      Issue No: Vol. 3 (2014)
       
  • Nigrostriatal dynein changes in A53T alpha-synuclein transgenic mice [v1;
           indexed, http://f1000r.es/2wb]

    • Authors: Yan Liu, Yu-He Yuan, Jian-Dong Sun, Jing Li, Zhi-Peng Li, Nai-Hong Chen
      Abstract: The accumulation of misfolded a-synuclein is mechanistically linked to neurodegeneration in Parkinson’s disease (PD) and other alpha-synucleinopathies. However, how alpha-synuclein causes neurodegeneration is unresolved. Several studies have supported the involvement of dynein, the major motor for retrograde axonal transport in alpha-synuclein-dependent neurodegeneration, especially in the nigrostriatal system. Therefore, we examined the nigrostriatal dyneins in transgenic mice that overexpress human A53T alpha-synuclein and recapitulate key features of a PD-like neuronal synucleinopathy. Age-matched nontransgenic littermates were used as controls. The results demonstrated that the protein level of dynein was decreased in the striatum, whereas it was elevated in the substantia nigra. Double immunostaining results revealed that the reduction in dynein level was associated with aggregation of A53T a-synuclein in the striatum. Furthermore, we performed a quantitative analysis of motor behaviors in A53T alpha-synuclein transgenic mice and controls using a modified open field test. We demonstrated that the protein level of dynein in the striatum was significantly correlated with the motor behaviors. Together, our data indicate that dynein changes in the nigrostriatal system of A53T alpha-synuclein transgenic mice may contribute to their severe movement disorder.
      PubDate: 2014-03-11
      DOI: 10.12688/f1000research.3507.1
      Issue No: Vol. 3 (2014)
       
  • Improved performance of sequence search approaches in remote homology
           detection [v2; indexed, http://f1000r.es/3qo]

    • Authors: Adwait Govind Joshi, Upadhyayula Surya Raghavender, Ramanathan Sowdhamini
      Abstract: The protein sequence space is vast and diverse, spanning across different families. Biologically meaningful relationships exist between proteins at superfamily level. However, it is highly challenging to establish convincing relationships at the superfamily level by means of simple sequence searches. It is necessary to design a rigorous sequence search strategy to establish remote homology relationships and achieve high coverage. We have used iterative profile-based methods, along with constraints of sequence motifs, to specify search directions. We address the importance of multiple start points (queries) to achieve high coverage at protein superfamily level. We have devised strategies to employ a structural regime to search sequence space with good specificity and sensitivity. We employ two well-known sequence search methods, PSI-BLAST and PHI-BLAST, with multiple queries and multiple patterns to enhance homologue identification at the structural superfamily level. The study suggests that multiple queries improve sensitivity, while a pattern-constrained iterative sequence search becomes stringent at the initial stages, thereby driving the search in a specific direction and also achieves high coverage. This data mining approach has been applied to the entire structural superfamily database.
      PubDate: 2014-07-16
      DOI: 10.12688/f1000research.2-93.v2
      Issue No: Vol. 2 (2014)
       
  • Density but not climate affects the population growth rate of guanacos
           (Lama guanicoe) (Artiodactyla, Camelidae) [v2; indexed,
           http://f1000r.es/3h1]

    • Authors: María Zubillaga, Oscar Skewes, Nicolás Soto, Jorge E Rabinovich
      Abstract: We analyzed the effects of population density and climatic variables on the rate of population growth in the guanaco (Lama guanicoe), a wild camelid species in South America. We used a time series of 36 years (1977-2012) of population sampling in Tierra del Fuego, Chile. Individuals were grouped in three age-classes: newborns, juveniles, and adults; for each year a female population transition matrix was constructed, and the population growth rate (λ) was estimated for each year as the matrix highest positive eigenvalue. We applied a regression analysis with finite population growth rate (λ) as dependent variable, and total guanaco population, sheep population, annual mean precipitation, and winter mean temperature as independent variables, with and without time lags. The effect of population size was statistically significant, but the effects of the sheep population and the climatic variables on guanaco population growth rate were not statistically significant.
      PubDate: 2014-05-28
      Issue No: Vol. 2 (2014)
       
 
 
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