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F1000Research    [5 followers]  Follow    
  This is an Open Access Journal Open Access journal
     ISSN (Online) 2046-1402
     Published by Faculty of 1000 Homepage  [1 journal]
  • The reproductive season of Acropora in Socotra, Yemen [v2; indexed,
    • Authors: Andrew H. Baird, David Abrego, Emily J. Howells, Vivian R. Cumbo
      Abstract: Determining when corals reproduce has clear management and economic implications. Here we document the reproductive condition of corals in the genus Acropora on the island of Socotra in Yemen during February 2014. Twenty percent of colonies (n = 143) contained mature gametes and 28% had immature gametes indicating that spawning will occur in both February and March in 2014, confirming previous anecdotal reports of coral spawning at this time in Socotra. Acropora typically reproduce in synchrony with many other broadcast spawning scleractinian corals, and we therefore predict that many other species are reproductively active at this time of year.
      PubDate: 2014-04-09
      DOI: 10.12688/f1000research.4214
      Issue No: Vol. 3 (2014)
  • FeatureViewer, a BioJS component for visualization of position-based
           annotations in protein sequences [v2; indexed,]
    • Authors: Leyla Garcia, Guy Yachdav, Maria-Jesus Martin
      Abstract: Summary: FeatureViewer is a BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This component is highly flexible and customizable, allowing the presentation of annotations by rows, all centered, or distributed in non-overlapping tracks. It uses either lines or shapes for sites and rectangles for regions. The result is a powerful visualization tool that can be easily integrated into web applications as well as documents as it provides an export-to-image functionality. Availability:;
      PubDate: 2014-04-09
      DOI: 10.12688/f1000research.3-47.v2
      Issue No: Vol. 3 (2014)
  • Fiberoptic monitoring of central venous oxygen saturation (PediaSat) in
           small children undergoing cardiac surgery: continuous is not continuous
           [v2; indexed,]
    • Authors: Francesca G. Iodice, Zaccaria Ricci, Roberta Haiberger, Isabella Favia, Paola Cogo
      Abstract: Background: Monitoring of superior vena cava saturation (ScvO2) has become routine in the management of pediatric patients undergoing cardiac surgery. The objective of our study was to evaluate the correlation between continuous ScvO2 by the application of a fiber-optic oximetry catheter (PediaSat) and intermittent ScvO2 by using standard blood gas measurements. These results were compared to those obtained by cerebral near infrared spectroscopy (cNIRS). Setting: Tertiary pediatric cardiac intensive care unit (PCICU). Methods and main results: A retrospective study was conducted in consecutive patients who were monitored with a 4.5 or 5.5 F PediaSat catheter into the right internal jugular vein. An in vivo calibration was performed once the patient was transferred to the PCICU and re-calibration took place every 24 hours thereafter. Each patient had a NIRS placed on the forehead. Saturations were collected every 4 hours until extubation. Ten patients with a median age of 2.2 (0.13-8.5) years and a weight of 12.4 (3.9-24) kg were enrolled. Median sampling time was 32 (19-44) hours: 64 pairs of PediaSat and ScVO2 saturations showed a poor correlation (r=0.62, 95% CI 44-75; p
      PubDate: 2014-04-09
      DOI: 10.12688/f1000research.3-23.v2
      Issue No: Vol. 3 (2014)
  • Validation of predicted mRNA splicing mutations using high-throughput
           transcriptome data [v2; indexed,]
    • Authors: Coby Viner, Stephanie N. Dorman, Ben C. Shirley, Peter K. Rogan
      Abstract: Interpretation of variants present in complete genomes or exomes reveals numerous sequence changes, only a fraction of which are likely to be pathogenic. Mutations have been traditionally inferred from allele frequencies and inheritance patterns in such data. Variants predicted to alter mRNA splicing can be validated by manual inspection of transcriptome sequencing data, however this approach is intractable for large datasets. These abnormal mRNA splicing patterns are characterized by reads demonstrating either exon skipping, cryptic splice site use, and high levels of intron inclusion, or combinations of these properties. We present, Veridical, an in silico method for the automatic validation of DNA sequencing variants that alter mRNA splicing. Veridical performs statistically valid comparisons of the normalized read counts of abnormal RNA species in mutant versus non-mutant tissues. This leverages large numbers of control samples to corroborate the consequences of predicted splicing variants in complete genomes and exomes.
      PubDate: 2014-04-07
      DOI: 10.12688/f1000research.3-8.v2
      Issue No: Vol. 3 (2014)
  • Two fatal cases of melioidosis on the Thai-Myanmar border [v2; indexed,
    • Authors: Cindy S. Chu, Stuart Winearls, Clare Ling, Miriam Beer Torchinsky, Aung Phae Phyo, Warat Haohankunnathum, Paul Turner, Vanaporn Wuthiekanun, François Nosten
      Abstract: Melioidosis is endemic in areas of Southeast Asia, however, there are no published reports from the Thai-Myanmar border. We report the first two documented cases of fatal melioidosis in this region. This is of great public health importance and highlights the need to both increase clinical awareness of melioidosis on the Thai-Myanmar border, and to assess the true burden of disease in the area through improved case detection and Burkholderia pseudomallei prevalence studies.
      PubDate: 2014-03-31
      DOI: 10.12688/f1000research.3-4.v2
      Issue No: Vol. 3 (2014)
  • Drugs acting on central nervous system (CNS) targets as leads for non-CNS
           targets [v2; indexed,]
    • Authors: Prashant S. Kharkar
      Abstract: Innovative drug discovery approaches are currently needed to rejuvenate the shrinking product pipelines of the pharmaceutical companies across the globe. Here a theme is presented – the use of central nervous system (CNS) drugs as leads for non-CNS targets. The approach is related to the use of existing drugs for new indications. Suitable chemical modifications of the CNS drugs abolish their CNS penetration. These novel analogs may then be screened for activity against non-CNS targets. Careful selection of the appropriate structural modifications remains the key to success.
      PubDate: 2014-03-21
      DOI: 10.12688/f1000research.3-40.v2
      Issue No: Vol. 3 (2014)
  • Advancing the activity cliff concept, part II [v1; indexed,
    • Authors: Dagmar Stumpfe, Antonio de la Vega de León, Dilyana Dimova, Jürgen Bajorath
      Abstract: We present a follow up contribution to further complement a previous commentary on the activity cliff concept and recent advances in activity cliff research. Activity cliffs have originally been defined as pairs of structurally similar compounds that display a large difference in potency against a given target. For medicinal chemistry, activity cliffs are of high interest because structure-activity relationship (SAR) determinants can often be deduced from them. Herein, we present up-to-date results of systematic analyses of the ligand efficiency and lipophilic efficiency relationships between activity cliff-forming compounds, which further increase their attractiveness for the practice of medicinal chemistry. In addition, we summarize the results of a new analysis of coordinated activity cliffs and clusters they form. Taken together, these findings considerably add to our evaluation and current understanding of the activity cliff concept. The results should be viewed in light of the previous commentary article.
      PubDate: 2014-03-18
      DOI: 10.12688/f1000research.4057
      Issue No: Vol. 3 (2014)
  • Postoperative visual loss following cerebral arteriovenous malformation
           surgery: a case report [v2; indexed,]
    • Authors: Nicolai Goettel, Jayati Ghosh, Michael Tymianski, Pirjo H Manninen
      Abstract: We report the case of a 46 year-old woman presenting with unilateral postoperative visual loss after right frontal craniotomy for resection of an arteriovenous malformation in the supine position. The intraoperative course was uneventful with maintenance of hemodynamic stability. Blood loss was 300 ml; postoperative hemoglobin was 12.4 g/dl. In the recovery room, the patient reported loss of vision in her right eye. Ophthalmologic examination revealed decreased visual acuity, color vision, and visual field. Assessment of the retina was normal, but the patient showed a relative afferent pupillary defect consistent with the clinical diagnosis of ischemic optic neuropathy. Postoperative computer tomogram showed normal perfusion of ophthalmic artery and vein, no hemorrhage or signs of cerebral ischemia or edema. The patient recovered most of her vision 3 months after surgery. Anesthesiologists should be aware that this condition may follow uncomplicated intracranial surgeries in the supine position, and should obtain prompt ophthalmologic consultation when a patient develops postoperative visual loss.
      PubDate: 2014-03-14
      DOI: 10.12688/f1000research.3-27.v2
      Issue No: Vol. 3 (2014)
  • The beauty of being (label)-free: sample preparation methods for SWATH-MS
           and next-generation targeted proteomics [v2; indexed,
    • Authors: Jakob Vowinckel, Floriana Capuano, Kate Campbell, Michael J. Deery, Kathryn S. Lilley, Markus Ralser
      Abstract: The combination of qualitative analysis with label-free quantification has greatly facilitated the throughput and flexibility of novel proteomic techniques. However, such methods rely heavily on robust and reproducible sample preparation procedures. Here, we benchmark a selection of in gel, on filter, and in solution digestion workflows for their application in label-free proteomics. Each procedure was associated with differing advantages and disadvantages. The in gel methods interrogated were cost effective, but were limited in throughput and digest efficiency. Filter-aided sample preparations facilitated reasonable processing times and yielded a balanced representation of membrane proteins, but led to a high signal variation in quantification experiments. Two in solution digest protocols, however, gave optimal performance for label-free proteomics. A protocol based on the detergent RapiGest led to the highest number of detected proteins at second-best signal stability, while a protocol based on acetonitrile-digestion, RapidACN, scored best in throughput and signal stability but came second in protein identification. In addition, we compared label-free data dependent (DDA) and data independent (SWATH) acquisition on a TripleTOF 5600 instrument. While largely similar in protein detection, SWATH outperformed DDA in quantification, reducing signal variation and markedly increasing the number of precisely quantified peptides.
      PubDate: 2014-04-07
      DOI: 10.12688/f1000research.2-272.v2
      Issue No: Vol. 2 (2014)
  • The Human dsRNA binding protein PACT is unable to functionally substitute
           for the Drosophila dsRNA binding protein R2D2 [v2; indexed,
    • Authors: Benjamin K Dickerman, Jocelyn A McDonald, Ganes C Sen
      Abstract: The dsRNA binding protein (dsRBP) PACT was first described as an activator of the dsRNA dependent protein kinase PKR in response to stress signals.  Additionally, it has been identified as a component of the small RNA processing pathway.  A role for PACT in this pathway represents an important interplay between two modes of post-transcriptional gene regulation.  The function of PACT in this context is poorly understood.  Thus, additional approaches are required to clarify the mechanism by which PACT functions.  In this study, the genetic utility of Drosophila melanogaster was employed to identify dsRNA-binding proteins that are functionally orthologous to PACT.  Transgenic Drosophila expressing human PACT were generated to determine whether PACT is capable of functionally substituting for the Drosophila dsRBP R2D2, which has a well-defined role in small RNA biogenesis.  Results presented here indicate that PACT is unable to substitute for R2D2 at the whole organism level.
      PubDate: 2014-03-28
      DOI: 10.12688/f1000research.2-220.v2
      Issue No: Vol. 2 (2014)
  • Thermoregulation strategies in ants in comparison to other social insects,
           with a focus on red wood ants (Formica rufa group) [v2; indexed,
    • Authors: Štěpánka Kadochová, Jan Frouz
      Abstract: Temperature influences every aspect of ant biology, especially metabolic rate, growth and development. Maintenance of high inner nest temperature increases the rate of sexual brood development and thereby increases the colony fitness. Insect societies can achieve better thermoregulation than solitary insects due to the former’s ability to build large and elaborated nests and display complex behaviour. In ants and termites the upper part of the nest, the mound, often works as a solar collector and can also have an efficient ventilation system. Two thermoregulatory strategies could be applied. Firstly the ants use an increased thermal gradient available in the mound for brood relocation. Nurse workers move the brood according to the thermal gradients to ensure the ideal conditions for development. A precise perception of temperature and evolution of temperature preferences are needed to make the correct choices. A second thermoregulatory strategy used by mound nesting ants is keeping a high temperature inside large nests. The unique thermal and insulation properties of the nest material help to maintain stable conditions, which is the case of the Wood ant genus Formica. Ants can regulate thermal loss by moving nest aggregation and alternating nest ventilation. Metabolic heat produced by ant workers or associated micro organisms is an important additional source of heat which helps to maintain thermal homeostasis in the nest.
      PubDate: 2014-03-21
      DOI: 10.12688/f1000research.2-280.v2
      Issue No: Vol. 2 (2014)
  • A novel variable delay Go/No-Go task to study attention, motivation and
           working memory in the head-fixed rodent [v2; indexed,
    • Authors: Samuel D Dolzani, Shinya Nakamura, Donald C Cooper
      Abstract: In order to parse the causal elements underlying complex behaviors and decision-making processes, appropriate behavioral methods must be developed and used in concurrence with molecular, pharmacological, and electrophysiological approaches. Presented is a protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Pharmacological and viral manipulation of various brain regions via targeted guide cannula; (2) Optogenetic cell-type specific activation and silencing with simultaneous electrophysiological recording and; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior. The task consists of three components. The subject first makes an observing response by initiating a trial by lever pressing in response to distinctive Go or No-Go tones.  Then, after a variable delay period, the subject is presented with a challenge period cued by white noise during which they must respond with a lever press for the Go condition or withhold from lever pressing for the duration of the cue in the No-Go condition. After correctly responding during the challenge period (Challenge) and a brief delay, a final reward tone of the same frequency as the initiation tone is presented and sucrose reward delivery is available and contingent upon lever pressing. Here, we provide a novel procedure and validating data set that allows researchers to study and manipulate components of behavior such as attention, motivation, impulsivity, and reward-related working memory during an ongoing operant behavioral task while limiting interference from non task-related behaviors.
      PubDate: 2014-03-19
      DOI: 10.12688/f1000research.2-125.v2
      Issue No: Vol. 2 (2014)
  • Modeling enzootic raccoon rabies from land use patterns - Georgia (USA)
           2006-2010 [v2; indexed,]
    • Authors: John E. Duke, Jesse D. Blanton, Melissa Ivey, Charles Rupprecht
      Abstract: We analyzed how land-use patterns and changes in urbanization influence reported rabid raccoons in Georgia from 2006 - 2010.  Using Geographical Information Systems and rabies surveillance data, multivariate analysis was conducted on 15 land-use variables that included natural topography, agricultural development, and urbanization to model positive raccoon rabies cases while controlling for potential raccoon submission bias associated with higher human population densities.  Low intensity residential development was positively associated with reported rabid raccoons while a negative association was found with evergreen forest.  Evergreen forests may offer a barrier effect where resources are low and raccoon populations are not supported.  Areas with pure stands of upland evergreen forest might be utilized in baiting strategies for oral rabies vaccination programs where fewer or no baits may be needed.  Their use as a barrier should be considered carefully in a cost-effective strategy for oral rabies vaccination (ORV) programs to contain the western spread of this important zoonotic disease.
      PubDate: 2014-03-18
      DOI: 10.12688/f1000research.2-285.v2
      Issue No: Vol. 2 (2014)
School of Mathematical and Computer Sciences
Heriot-Watt University
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