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Journal Cover   F1000Research
  [SJR: 0.219]   [H-I: 3]   [4 followers]  Follow
  This is an Open Access Journal Open Access journal
   ISSN (Online) 2046-1402
   Published by Faculty of 1000 Homepage  [1 journal]
  • ViennaNGS: A toolbox for building efficient next- generation sequencing
           analysis pipelines [v2; indexed,]

    • Authors: Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
      Abstract: Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.
      PubDate: 2015-07-20T10:33:38Z
      DOI: 10.12688/f1000research.6157.2
      Issue No: Vol. 4 (2015)
  • Seeing and believing: recent advances in imaging cell-cell interactions
           [v1; indexed,]

    • Authors: Alpha S. Yap, Magdalene Michael, Robert G. Parton
      Abstract: Advances in cell and developmental biology have often been closely linked to advances in our ability to visualize structure and function at many length and time scales. In this review, we discuss how new imaging technologies and new reagents have provided novel insights into the biology of cadherin-based cell-cell junctions. We focus on three developments: the application of super-resolution optical technologies to characterize the nanoscale organization of cadherins at cell-cell contacts, new approaches to interrogate the mechanical forces that act upon junctions, and advances in electron microscopy which have the potential to transform our understanding of cell-cell junctions.
      PubDate: 2015-07-17T15:11:47Z
      DOI: 10.12688/f1000research.6435.1
      Issue No: Vol. 4 (2015)
  • A developmental biologist’s journey to rediscover the Zen of plant
           physiology [v1; indexed,]

    • Authors: José R. Dinneny
      Abstract: Physiology, which is often viewed as a field of study distinct from development, is technically defined as the branch of biology that explores the normal function of living organisms and their parts. Because plants normally develop continuously throughout their life, plant physiology actually encompasses all developmental processes. Viewing plant biology from a physiologist’s perspective is an attempt to understand the interconnectedness of development, form, and function in the context of multidimensional complexity in the environment. To meet the needs of an expanding human population and a degrading environment, we must understand the adaptive mechanisms that plants use to acclimate to environmental change, and this will require a more holistic approach than is used by current molecular studies. Grand challenges for studies on plant physiology require a more sophisticated understanding of the environment that plants grow in, which is likely to be at least as complex as the plant itself. Moving the lab to the field and using the field for inspiration in the lab need to be expressly promoted by the community as we work to apply the basic concepts learned through reductionist approaches toward a more integrated and realistic understanding of the plant.
      PubDate: 2015-07-16T15:14:16Z
      DOI: 10.12688/f1000research.6167.1
      Issue No: Vol. 4 (2015)
  • Case Report: melanoma and melanocytic nevus differentiation with
           reflectance confocal microscopy. [v1; indexed,]

    • Authors: Joanna Łudzik, Alexander M Witkowski, Giovanni Pellacani
      Abstract: Historically, melanoma has been typically diagnosed by naked-eye examination and confirmed with invasive biopsy. However, recently the use of reflectance confocal microscopy enables non-invasive bedside diagnosis of clinically equivocal lesions. We present a case in which reflectance confocal microscopy was used to evaluate two skin lesions in the same patient confirming the diagnosis of a melanoma and potentially avoiding invasive biopsy in the second benign melanocytic lesion.  Clinicians should be aware of the availability of new non-invasive technologies that can aid in early diagnosis of malignant skin tumors and potentially reduce the number of benign lesion excisions.
      PubDate: 2015-07-15T15:14:15Z
      DOI: 10.12688/f1000research.6793.1
      Issue No: Vol. 4 (2015)
  • Problematizing Digital Research Evaluation using DOIs in
           Practice-Based Arts, Humanities and Social Science Research [v1; indexed,

    • Authors: Muriel Swijghuisen Reigersberg
      Abstract: This paper explores emerging practices in research data management in the arts, humanities and social sciences (AHSS). It will do so vis-à-vis current citation conventions and impact measurement for research in AHSS. Case study findings on research data inventoried at Goldsmiths’, University of London will be presented. Goldsmiths is a UK research-intensive higher education institution which specialises in arts, humanities and social science research. The paper’s aim is to raise awareness of the subject-specific needs of AHSS scholars to help inform the design of future digital tools for impact analysis in AHSS. Firstly, I shall explore the definition of research data and how it is currently understood by AHSS researchers. I will show why many researchers choose not to engage with digital dissemination techniques and ORCID. This discussion must necessarily include the idea that practice-based and applied AHSS research are processes which are not easily captured in numerical ‘sets’ and cannot be labelled electronically without giving careful consideration to what a group or data item ‘represents’ as part of the academic enquiry, and therefore how it should be cited and analysed as part of any impact assessment. Then, the paper will explore: the role of the monograph and arts catalogue in AHSS scholarship; how citation practices and digital impact measurement in AHSS currently operate in relation to authorship and how digital identifiers may hypothetically impact on metrics, intellectual property (IP), copyright and research integrity issues in AHSS. I will also show that, if we are to be truly interdisciplinary, as research funders and strategic thinkers say we should, it is necessary to revise the way we think about digital research dissemination. This will involve breaking down the boundaries between AHSS and other types of research.
      PubDate: 2015-07-07T14:38:53Z
      DOI: 10.12688/f1000research.6506.1
      Issue No: Vol. 4 (2015)
  • Recent scientific advances in leiomyoma (uterine fibroids) research
           facilitates better understanding and management [v1; indexed,

    • Authors: Darlene K. Taylor, Kristine Holthouser, James H. Segars, Phyllis C. Leppert
      Abstract: Uterine leiomyomas (fibroids) are the most prevalent medical problem of the female reproductive tract, but there are few non-surgical treatment options. Although many advances in the understanding of the molecular components of these tumors have occurred over the past five years, an effective pharmaceutical approach remains elusive. Further, there is currently no clinical method to distinguish a benign uterine leiomyoma from a malignant leiomyosarcoma prior to treatment, a pressing need given concerns about the use of the power morcellator for minimally invasive surgery. This paper reviews current studies regarding the molecular biology of uterine fibroids, discusses non-surgical approaches and suggests new cutting-edge therapeutic and diagnostic approaches.
      PubDate: 2015-07-06T16:00:44Z
      DOI: 10.12688/f1000research.6189.1
      Issue No: Vol. 4 (2015)
  • Cytochrome P450 enzymes: understanding the biochemical hieroglyphs [v1;

    • Authors: John T. Groves
      Abstract: Cytochrome P450 (CYP) enzymes are the primary proteins of drug metabolism and steroid biosynthesis. These crucial proteins have long been known to harbor a cysteine thiolate bound to the heme iron. Recent advances in the field have illuminated the nature of reactive intermediates in the reaction cycle. Similar intermediates have been observed and characterized in novel heme-thiolate proteins of fungal origin. Insights from these discoveries have begun to solve the riddle of how enzyme biocatalyst design can afford a protein that can transform substrates that are more difficult to oxidize than the surrounding protein architecture.
      PubDate: 2015-07-01T14:23:06Z
      DOI: 10.12688/f1000research.6314.1
      Issue No: Vol. 4 (2015)
  • Characterization of an APC Promoter 1B deletion in a Patient Diagnosed
           with Familial Adenomatous Polyposis via Whole Genome Shotgun Sequencing
           [v1; indexed,]

    • Authors: Ted Kalbfleisch, Pamela Brock, Angela Snow, Deborah Neklason, Gordon Gowans, Jon Klein
      Abstract: Recently, deletions have been identified and published as causal for Familial Adenomatous Polyposis in the 1B promoter region of the APC gene.  Those deletions were measured using multiplex ligation-dependent probe amplification.  Here, we present and characterize an ~11kb deletion identified by whole genome shotgun sequencing.  The deletion occurred in a patient diagnosed with Familial Adenomatous Polyposis, and was located on chr5, between bases 112,034,824 and 112,045,845, fully encompassing the 1B promoter region of the APC gene.   Results are presented here that include the sequence evidence supporting the presence of the deletion as well as base level characterization of the deletion site.  These results demonstrate the capacity of whole genome sequencing for the detection of large structural variants in single individuals.
      PubDate: 2015-06-26T15:27:44Z
      DOI: 10.12688/f1000research.6636.1
      Issue No: Vol. 4 (2015)
  • Comprehensive knowledge base of two- and three-dimensional activity cliffs
           for medicinal and computational chemistry [v1; indexed,

    • Authors: Ye Hu, Norbert Furtmann, Dagmar Stumpfe, Jürgen Bajorath
      Abstract: Activity cliffs are formed by pairs or groups of structurally similar or analogous active compounds with large differences in potency. They can be defined in two or three dimensions by comparing graph-based molecular representations or compound binding modes, respectively. Through systematic analysis of publicly available compound activity data and ligand-target X-ray structures we have in a series of studies determined all currently available two- and three-dimensional activity cliffs (2D- and 3D-cliffs, respectively). Furthermore, we have systematically searched for 2D extensions of 3D-cliffs. Herein, we specify different categories of activity cliffs we have explored and introduce an open access data deposition in ZENODO (doi: 10.5281/zenodo.18490) that makes the entire knowledge base of current activity cliffs freely available in an organized form.
      PubDate: 2015-06-25T09:47:50Z
      DOI: 10.12688/f1000research.6661.1
      Issue No: Vol. 4 (2015)
  • Magnetic Resonance Imaging in Neuropsychiatric Lupus [v1; indexed,

    • Authors: Nicolae Sarbu, Núria Bargalló, Ricard Cervera
      Abstract: Neuropsychiatric lupus is a major diagnostic challenge, and a main cause of morbidity and mortality in patients with systemic lupus erythematosus (SLE). Magnetic resonance imaging (MRI) is, by far, the main tool for assessing the brain in this disease. Conventional and advanced MRI techniques are used to help establishing the diagnosis, to rule out alternative diagnoses, and recently, to monitor the evolution of the disease. This review explores the neuroimaging findings in SLE, including the recent advances in new MRI methods.
      PubDate: 2015-06-23T15:13:10Z
      DOI: 10.12688/f1000research.6522.1
      Issue No: Vol. 4 (2015)
  • CPIRD: A successful Thai programme to produce clinically competent medical
           graduates [v1; indexed,]

    • Authors: Yanhua Yi, Virasakdi Chongsuvivatwong, Hutcha Sriplung, Chulalak Rueanarong
      Abstract: The programme titled “Collaborative Project to Increase Production of Rural Doctors” (CPIRD) is a rural medical education project launched in 1994 in Thailand. This study aimed to compare the academic performances in medical study over five years and the pass rates in national medical license examinations (MLE) between students enrolled in CPIRD and two other tracks. Grade point average (GPA) over five years and results of MLEs for four cohorts of students enrolled from 2003 to 2006 in Prince of Songkla University were collected from the registration department. A longitudinal analysis was used to compare the GPA over time for medical students enrolled in CPIRD and those from the national and direct regional tracks through generalized estimating equation (GEE) models. The MLE pass rates were compared using chi-square and fisher's exact tests as appropriate. Female students dominated the CPIRD group. GPAs in the first three years in the CPIRD group were significantly lower than those of the other two groups, this disparity narrowed in the fourth and fifth years. For step one of the MLE (basic sciences), cohorts 2003 and 2006 of the CPIRD group had a significantly lower pass rate than the other two groups but there was no significant difference in cohort 2004 and cohort 2005. The CPIRD step two and three MLE pass rates were not significantly different from the national track in all cohorts and lower than the direct track only for step two in cohort 2003 and step three in cohort 2006. The step three pass rate of the CPIRD group in cohort 2004 was significantly higher than the other two tracks. Despite weaker competency in basic science, the CPIRD was successful in forming clinical competency.
      PubDate: 2015-06-18T16:01:16Z
      DOI: 10.12688/f1000research.6638.1
      Issue No: Vol. 4 (2015)
  • Drosophila's contribution to stem cell research [v1; indexed,

    • Authors: Gyanesh Singh
      Abstract: The discovery of Drosophila stem cells with striking similarities to mammalian stem cells has brought new hope for stem cell research. A recent development in Drosophila stem cell research is bringing wider opportunities for contemporary stem cell biologists. In this regard, Drosophila germ cells are becoming a popular model of stem cell research. In several cases, genes that controlled Drosophila stem cells were later discovered to have functional homologs in mammalian stem cells. Like mammals, Drosophila germline stem cells (GSCs) are controlled by both intrinsic as well as external signals. Inside the Drosophila testes, germline and somatic stem cells form a cluster of cells (the hub). Hub cells depend on JAK-STAT signaling, and, in absence of this signal, they do not self-renew. In Drosophila, significant changes occur within the stem cell niche that contributes to a decline in stem cell number over time. In case of aging Drosophila, somatic niche cells show reduced DE-cadherin and unpaired (Upd) proteins. Unpaired proteins are known to directly decrease stem cell number within the niches, and, overexpression of upd within niche cells restored GSCs in older males also . Stem cells in the midgut of Drosophila are also very promising. Reduced Notch signaling was found to increase the number of midgut progenitor cells. On the other hand, activation of the Notch pathway decreased proliferation of these cells. Further research in this area should lead to the discovery of additional factors that regulate stem and progenitor cells in Drosophila.
      PubDate: 2015-06-18T15:32:28Z
      DOI: 10.12688/f1000research.6611.1
      Issue No: Vol. 4 (2015)
  • 1-Octen-3-ol – the attractant that repels [v1; indexed,

    • Authors: Pingxi Xu, Fen Zhu, Garrison K. Buss, Walter S. Leal
      Abstract: Since the discovery in the early 1980s that 1-octen-3-ol, isolated from oxen breath, attracts tsetse fly, there has been growing interest in exploring the use of this semiochemical as a possible generic lure for trapping host-seeking mosquitoes. Intriguingly, traps baited with 1-octen-3-ol captured significantly more females of the malaria mosquito, Anopheles gambiae, and the yellow fever mosquito, Aedes aegypti, than control traps, but failed to attract the southern house mosquito, Culex quinquefasciatus. Additionally, it has been demonstrated that this attractant is detected with enantioselective odorant receptors (ORs) expressed only in maxillary palps. On the basis of indoor behavioral assays it has even been suggested that 1-octen-3-ol might be a repellent to the southern house mosquito. Our approach was two-prong, i.e., to isolate 1-octen-3-ol-sensitive ORs expressed in maxillary palps and antennae of southern house female mosquito, and test the hypothesis that this semiochemical is a repellent. An OR with high transcript levels in maxillary palps, CquiOR118b, showed remarkable selectivity towards (R)-1-octen-3-ol, whereas an OR expressed in antennae, CquiOR114b, showed higher preference for (S)-1-octen-3-ol than its antipode. Repellency by a surface landing and feeding assay showed that not only racemic, but enantiopure (R)- and (S)-1-octen-3-ol are repellents at 1% dose thus suggesting the occurrence of other (S)-1-octen-3-ol-sensitive OR(s). Female mosquitoes with ablated maxillary palps were repelled by 1-octen-3-ol, which implies that in addition to OR(s) in the maxillary palps, antennal OR(s) are essential for repellency activity.
      PubDate: 2015-06-18T14:12:45Z
      DOI: 10.12688/f1000research.6646.1
      Issue No: Vol. 4 (2015)
  • Relationships between activation level, knowledge, self-efficacy, and
           self-management behavior in heart failure patients discharged from rural
           hospitals [v1; indexed,]

    • Authors: Van Do, Lufei Young, Sue Barnason, Hoang Tran
      Abstract: Non-adherence to self-management guidelines accounted for 50% of hospital readmissions in heart failure patients. Evidence showed that patient activation affects self-management behaviors in populations living with chronic conditions. The purpose of this study was to describe patient activation level and its relationship with knowledge, self-efficacy and self-management behaviors in heart failure patients discharged from rural hospitals. Our study populations were recruited from two hospitals in rural areas of Nebraska. We found that two-thirds of the participants reported low activation levels (e.g., taking no action to manage their heart failure condition). In addition, low patient activation levels were associated with inadequate heart failure knowledge (p=.005), low self-efficacy (p
      PubDate: 2015-06-11T10:29:00Z
      DOI: 10.12688/f1000research.6557.1
      Issue No: Vol. 4 (2015)
  • Psoriasis is characterized by deficient negative immune regulation
           compared to transient delayed-type hypersensitivity reactions [v1;

    • Authors: Nicholas Gulati, Mayte Suárez-Fariñas, Joel Correa da Rosa, James G. Krueger
      Abstract: Diphencyprone (DPCP) is a hapten that causes delayed-type hypersensitivity (DTH) reactions in human skin, and is used as a topical therapeutic for alopecia areata, warts, and cutaneous melanoma metastases.  We examined peak DTH reactions induced by DPCP (3 days post-challenge) by comprehensive gene expression and histological analysis.  To better understand how these DTH reactions naturally resolve, we compared our DPCP biopsies to those from patients with psoriasis vulgaris, a chronic inflammatory disease that does not resolve.  By both microarray and qRT-PCR, we found that psoriasis lesional skin has significantly lower expression of many negative immune regulators compared to peak DPCP reactions.  These regulators include: interleukin-10, cytotoxic T lymphocyte-associated 4 (CTLA4), programmed cell death 1 (PD1), programmed cell death 1 ligand 1 (PDL1), programmed cell death 1 ligand 2 (PDL2), and indoleamine 2,3-dioxygenase (IDO1).  Their decreased expression was confirmed at the protein level by immunohistochemistry.  To more completely determine the balance of positive vs. negative immune regulators in both DPCP reactions and psoriasis, we developed one comprehensive gene list for positive regulatory (inflammatory) genes, and another for negative regulatory (immunosuppressive) genes, through Gene Ontology terms and literature review.  With this approach, we found that DPCP reactions have a higher ratio of negative to positive regulatory genes (both in terms of quantity and expression levels) than psoriasis lesional skin.  These data suggest that the disease chronicity that distinguishes psoriasis from transient DTH reactions may be related to absence of negative immune regulatory pathways, and induction of these is therefore of therapeutic interest.  Further study of these negative regulatory mechanisms that are present in DPCP reactions, but not in psoriasis, could reveal novel players in the pathogenesis of chronic inflammation.  The DPCP system used here thus provides a tractable model for primary discovery of pathways potentially involved in immune regulation in peripheral tissues.
      PubDate: 2015-06-11T09:39:02Z
      DOI: 10.12688/f1000research.6581.1
      Issue No: Vol. 4 (2015)
  • Immunoblotting validation of research antibodies generated against
           HS1-associated protein X-1 in the human neutrophil model cell line
           PLB-985. [v1; indexed,]

    • Authors: Inman Kristina, Peter Cavnar
      Abstract: HS1-associated protein X-1 (Hax1) is a 32 kDa protein that is ubiquitously expressed. Hax1 is an anti-apoptotic protein with additional roles in cell motility, and autosomal recessive loss of Hax1 results in Kostmann syndrome, a form of severe congenital neutropenia. Because of the important role of Hax1 in neutrophils we demonstrate here validation of two research antibodies directed against human Hax1 in the human neutrophil model cell line PLB-985 cells. We show that both the mouse anti-Hax1 monoclonal IgG directed against amino acids 10-148 of Hax1 and a rabbit anti-Hax1 polyclonal IgG antibody directed against full-length Hax1 reliably and consistently detect Hax1 during immunoblotting of three different PLB-985 cell densities. Using shRNA mediated Hax1 knockdown, we demonstrate the specificity of both Hax1 antibodies. In addition, our results suggest that the rabbit anti-Hax1 polyclonal antibody is provides a stronger intensity in detecting Hax1 protein, with detection in as few as 0.1 x 106 cells in 6 total replicates we have performed.
      PubDate: 2015-06-10T14:13:59Z
      DOI: 10.12688/f1000research.6516.1
      Issue No: Vol. 4 (2015)
  • Understanding carbon regulation in aquatic systems - Bacteriophages as a
           model [v1; indexed,]

    • Authors: Swapnil Sanmukh, Krishna Khairnar, Waman Paunikar, Satish Lokhande
      Abstract: The bacteria and their phages are the most abundant constituents of the aquatic environment, and so represent an ideal model for studying carbon regulation in an aquatic system. The microbe-mediated interconversion of bioavailable organic carbon (OC) into dissolved organic carbon (DOC) by the microbial carbon pump (MCP) has been suggested to have the potential to revolutionize our view of carbon sequestration. It is estimated that DOC is the largest pool of organic matter in the ocean and, though a major component of the global carbon cycle, its source is not yet well understood. A key element of the carbon cycle is the microbial conversion of DOC into inedible forms. The primary aim of this study is to understand the phage conversion from organic to inorganic carbon during phage-host interactions. Time studies of phage-host interactions under controlled conditions reveal their impact on the total carbon content of the samples and their interconversion of organic and inorganic carbon compared to control samples. A total organic carbon (TOC) analysis showed an increase in inorganic carbon content by 15-25 percent in samples with bacteria and phage compared to samples with bacteria alone. Compared to control samples, the increase in inorganic carbon content was 60-70-fold in samples with bacteria and phage, and 50-55-fold for samples with bacteria alone. This study indicates the potential impact of phages in regulating the carbon cycle of aquatic systems.
      PubDate: 2015-06-01T15:38:44Z
      DOI: 10.12688/f1000research.6031.1
      Issue No: Vol. 4 (2015)
  • An open ecosystem engagement strategy through the lens of global food
           safety [v1; indexed,]

    • Authors: Paul Stacey, Garin Fons, Theresa M Bernardo
      Abstract: The Global Food Safety Partnership (GFSP) is a public/private partnership established through the World Bank to improve food safety systems through a globally coordinated and locally-driven approach. This concept paper aims to establish a framework to help GFSP fully leverage the potential of open models.   In preparing this paper the authors spoke to many different GFSP stakeholders who asked questions about open models such as: what is it' what’s in it for me' why use an open rather than a proprietary model' how will open models generate equivalent or greater sustainable revenue streams compared to the current “traditional” approaches'  This last question came up many times with assertions that traditional service providers need to see opportunity for equivalent or greater revenue dollars before they will buy-in. This paper identifies open value propositions for GFSP stakeholders and proposes a framework for creating and structuring that value.   Open Educational Resources (OER) were the primary open practice GFSP partners spoke to us about, as they provide a logical entry point for collaboration. Going forward, funders should consider requiring that educational resources and concomitant data resulting from their sponsorship should be open, as a public good. There are, however, many other forms of open practice that bring value to the GFSP. Nine different open strategies and tactics (Appendix A) are described, including: open content (including OER and open courseware), open data, open access (research), open government, open source software, open standards, open policy, open licensing and open hardware. It is recommended that all stakeholders proactively pursue "openness" as an operating principle.   This paper presents an overall GFSP Open Ecosystem Engagement Strategy within which specific local case examples can be situated. Two different case examples, China and Colombia, are presented to show both project-based and crowd-sourced, direct-to-public paths through this ecosystem.
      PubDate: 2015-05-27T14:54:05Z
      DOI: 10.12688/f1000research.6123.1
      Issue No: Vol. 4 (2015)
  • Unexpected lack of specificity of a rabbit polyclonal TAP-L (ABCB9)
           antibody [v1; indexed,]

    • Authors: Peter van Endert, Myriam Lawand
      Abstract: In this article, we describe the surprising non-specific reactivity in immunoblots of a rabbit polyclonal antibody (ref. Abcam 86222) expected to recognize the transporter associated with antigen processing like (TAP-L, ABCB9) protein. Although this antibody, according to company documentation, recognizes a band with the expected molecular weight of 84 kDa in HeLa, 293T and mouse NIH3T3 whole-cell lysates, we found that this band is also present in immunoblots of TAP-L deficient bone marrow-derived dendritic cell (BMDC) whole-cell lysates in three independent replicates. We performed extensive verification by multiple PCR tests to confirm the complete absence of the ABCB9 gene in our TAP-L deficient mice. We conclude that the antibody tested cross-reacts with an unidentified protein present in TAP-L knockout cells, which coincidentally runs at the same molecular weight as TAP-L. These findings underline the pitfalls of antibody specificity testing in the absence of cells lacking expression of the target protein.
      PubDate: 2015-05-22T16:06:26Z
      DOI: 10.12688/f1000research.6535.1
      Issue No: Vol. 4 (2015)
  • Case Report: Pre- and postnatal management of an allantoic cyst with
           patent urachus and single umbilical artery [v1; indexed,

    • Authors: Than Trong Thach, Vo Duy Quan, Tran Diem Nghi, Nguyen Hoang Anh, Le Phi Hung, Nguyen Thien Luan, Nguyen Phuoc Long
      Abstract: Patent urachus is a rare congenital abnormality. Since its first description by Cabriolus in 1550, few cases have been reported. A 26-year-old Vietnamese primigravida presented at 20 weeks of gestation for evaluation of a cystic mass in the umbilical cord, which was first discovered at week 13 of pregnancy by ultrasound scan. The cystic mass originated from the root of the umbilical cord, connected to the urinary bladder, and no intestinal contents were enclosed within. Doppler ultrasound assessment showed that the single umbilical artery existed within the normal range. The progression of the umbilical cyst continued to be screened, but the mass disappeared on ultrasound images at 27 weeks of gestation. This led to the consideration of the cyst’s rupture. After 38 gestational weeks, the pregnant woman delivered a 3350g male infant via cesarean section because of an obstructed vaginal labor. The following days, a stream of urine was recorded leaking out from the umbilical mass whenever he cried. Seven weeks after delivery, an open surgical approach was successfully performed. The baby is now 43 months of age, growing and developing normally. Since an allantoic cyst with patent urachus is a rare clinical entity, early discovery, close monitoring and accurate diagnosis through ultrasound in the prenatal period may consequently allow clinicians to have suitable attitudes towards management when the infant is born.
      PubDate: 2015-05-22T12:44:30Z
      DOI: 10.12688/f1000research.6546.1
      Issue No: Vol. 4 (2015)
  • Neutrophil Lymphocyte Ratio as a predictor of systemic inflammation - A
           cross-sectional study in a pre-admission setting. [v1; indexed,

    • Authors: Lashmi Venkatraghavan, Tze Ping Tan, Jigesh Mehta, Anil Arekapudi, Arun Govindarajulu, Eric Siu
      Abstract: Abstract: Background: Neutrophil:lymphocyte ratio (NLR)  is an emerging biomarker that is used to predict postoperative mortality and morbidity in cardiac and cancer surgeries. The association of this biomarker with systemic illness and its usefulness in risk assessment of preoperative patients has not been fully elucidated. Objectives: To determine the prevalence of elevated NLR in preoperative patients and to examine the relationship between elevated NLR and the presence of systemic illnesses as well as anaesthesia risk indices such as American Society of Anesthesia (ASA) and the revised cardiac risk index (RCRI) scores.  Design: Cross-sectional study Setting: Anaesthesia pre-admission clinic, Toronto Western Hospital, Toronto, Canada Patients: We evaluated 1117 pre-operative patients seen at an anesthesia preadmission clinic. Results: NLR was elevated (>3.3) in 26.6% of target population. In multivariate analysis, congestive cardiac failure, diabetes mellitus and malignancy were independent risk factors predicting raised NLR. After regression analysis, a relationship between NLR and ASA score (Odds Ratio 1.78; 95% CI: 1.42-2.24) and revised cardiac risk index (RCRI, odds ratio 1.33; 95% CI: 1.09-1.64, p-value: 0.0063) was observed. Conclusions:  NLR was elevated (> 3.3) in 26.6% of patients. Congestive cardiac failure and malignancy were two constant predictors of elevated NLR at >3.3 and > 4.5. There was a strong association between NLR and anesthesia risk scoring tools of ASA and RCRI.
      PubDate: 2015-05-22T09:58:04Z
      DOI: 10.12688/f1000research.6474.1
      Issue No: Vol. 4 (2015)
  • A bioinformatics insight to rhizobial globins: gene identification and
           mapping, polypeptide sequence and phenetic analysis, and protein modeling.
           [v1; indexed,]

    • Authors: Reinier Gesto-Borroto, Miriam Sánchez-Sánchez, Raúl Arredondo-Peter
      Abstract: Globins (Glbs) are proteins widely distributed in organisms. Three evolutionary families have been identified in Glbs: the M, S and T Glb families. The M Glbs include flavohemoglobins (fHbs) and single-domain Glbs (SDgbs); the S Glbs include globin-coupled sensors (GCSs), protoglobins and sensor single domain globins, and the T Glbs include truncated Glbs (tHbs). Structurally, the M and S Glbs exhibit 3/3-folding whereas the T Glbs exhibit 2/2-folding. Glbs are widespread in bacteria, including several rhizobial genomes. However, only few rhizobial Glbs have been characterized. Hence, we characterized Glbs from 62 rhizobial genomes using bioinformatics methods such as data mining in databases, sequence alignment, phenogram construction and protein modeling. Also, we analyzed soluble extracts from Bradyrhizobium japonicum USDA38 and USDA58 by (reduced + carbon monoxide (CO) minus reduced) differential spectroscopy. Database searching showed that only fhb, sdgb, gcs and thb genes exist in the rhizobia analyzed in this work. Promoter analysis revealed that apparently several rhizobial glb genes are not regulated by a -10 promoter but might be regulated by -35 and Fnr (fumarate-nitrate reduction regulator)-like promoters. Mapping analysis revealed that rhizobial fhbs and thbs are flanked by a variety of genes whereas several rhizobial sdgbs and gcss are flanked by genes coding for proteins involved in the metabolism of nitrates and nitrites and chemotaxis, respectively. Phenetic analysis showed that rhizobial Glbs segregate into the M, S and T Glb families, while structural analysis showed that predicted rhizobial SDgbs and fHbs and GCSs globin domain and tHbs fold into the 3/3- and 2/2-folding, respectively. Spectra from B. japonicum USDA38 and USDA58 soluble extracts exhibited peaks and troughs characteristic of bacterial and vertebrate Glbs thus indicating that putative Glbs are synthesized in B. japonicum USDA38 and USDA58.
      PubDate: 2015-05-13T10:32:04Z
      DOI: 10.12688/f1000research.6392.1
      Issue No: Vol. 4 (2015)
  • Case Report: Pulmonary Alveolar Calcification as a Result of Severe
           Hypercalcemia due to Acute Lymphoblatic Leukemia. [v1; indexed,

    • Authors: Jose Colleti Junior, Eliana Carla Armelin Benites, Gustavo Spadaccia dos Santos Fernandes, Norberto Antonio Freddi, Walter Koga, Werther Brunow de Carvalho
      Abstract: Severe hypercalcemia is a rare metabolic disorder in pediatric medicine. This report describes a rare case of severe hypercalcemia and its clinical manifestations in a 2-year-old toddler. The radiological findings caused by hypercalcemia and osteolysis were emblematic of the osteolytic lesions. Hypercalcemia led to massive pulmonary alveolar calcification. The hypercalcemia was successfully treated with pamidronate, a bisphosphonate drug class. Further investigation resulted in a diagnosis of acute lymphoblastic leukemia (ALL). The patient is currently on chemotherapy and has a favorable prognosis. Although severe hypercalcemia alone is an unusual finding as the first sign for ALL, this should be considered, not to mention the radiological images resulted from calcium deposits.
      PubDate: 2015-05-11T11:15:27Z
      DOI: 10.12688/f1000research.6393.1
      Issue No: Vol. 4 (2015)
  • Photoperiodic and circadian bifurcation theories of depression and mania
           [v1; indexed,]

    • Authors: Daniel F. Kripke, Jeffrey A. Elliott, David K. Welsh, Shawn D. Youngstedt
      Abstract: Seasonal effects on mood have been observed throughout much of human history.  Seasonal changes in animals and plants are largely mediated through the changing photoperiod (i.e., the photophase or duration of daylight).  We review that in mammals, daylight specifically regulates SCN (suprachiasmatic nucleus) circadian organization and its control of melatonin secretion.  The timing of melatonin secretion interacts with gene transcription in the pituitary pars tuberalis to modulate production of TSH (thyrotropin), hypothalamic T3 (triiodothyronine), and tuberalin peptides which modulate pituitary production of regulatory gonadotropins and other hormones.  Pituitary hormones largely mediate seasonal physiologic and behavioral variations.  As a result of long winter nights or inadequate illumination, we propose that delayed morning offset of nocturnal melatonin secretion, suppressing pars tuberalis function, could be the main cause for winter depression and even cause depressions at other times of year.  Irregularities of circadian sleep timing and thyroid homeostasis contribute to depression.  Bright light and sleep restriction are antidepressant and conversely, sometimes trigger mania.  We propose that internal desynchronization or bifurcation of SCN circadian rhythms may underlie rapid-cycling manic-depressive disorders and perhaps most mania.  Much further research will be needed to add substance to these theories.
      PubDate: 2015-05-06T13:52:03Z
      DOI: 10.12688/f1000research.6444.1
      Issue No: Vol. 4 (2015)
  • Case Report: Bone fragment in the third ventricle of a 22 year-old woman
           [v2; indexed,]

    • Authors: Sunil Munakomi, Balaji Srinivas, Iype Cherian
      Abstract: Here we present a very rare case of a woman with a bone fragment in the third ventricle of the brain following compound-depressed skull fractures due to a road traffic accident. There are only few case reports of bullets and textiloma being removed from the third ventricle. Following operative removal of the fragment, the patient was started on cortisol, mineralocorticoid and thyroid hormone replacement. However, the patient eventually died of the severe traumatic hypothalamic insult.
      PubDate: 2015-03-31T11:28:07Z
      DOI: 10.12688/f1000research.6180.2
      Issue No: Vol. 4 (2015)
  • Tweets from the forest: using Twitter to increase student engagement in an
           undergraduate field biology course [v1; indexed,]

    • Authors: Lauren Soluk, Christopher M. Buddle
      Abstract: Twitter is a cold medium that allows users to deliver content-rich but small packets of information to other users, and provides an opportunity for active and collaborative communication. In an education setting, this social media tool has potential to increase active learning opportunities, and increase student engagement with course content. The effects of Twitter on learning dynamics was tested in a field biology course offered by a large Canadian University: 29 students agreed to take part in the Twitter project and quantitative and qualitative data were collected, including survey data from 18 students. Students published 200% more public Tweets than what was required, and interacted frequently with the instructor and teaching assistant, their peers, and users external to the course. Almost 80% of students stated that Twitter increased opportunities for among-group communication, and 94% of students felt this kind of collaborative communication was beneficial to their learning. Although students did not think they would use Twitter after the course was over, 77% of the students still felt it was a good learning tool, and 67% of students felt Twitter had a positive impact on how they engaged with course content. These results suggest social media tools such as Twitter can help achieve active and collaborative learning in higher education.
      PubDate: 2015-03-31T09:50:48Z
      DOI: 10.12688/f1000research.6272.1
      Issue No: Vol. 4 (2015)
  • Resources, challenges and way forward in rare mitochondrial diseases
           research [v1; indexed,]

    • Authors: Anshu Bhardwaj, Neeraj Kumar Rajput, Vipin Singh
      Abstract: Over 300 million people are affected by about 7000 rare diseases globally. There are tremendous resource limitations and challenges in driving research and drug development for rare diseases. Hence, innovative approaches are needed to identify potential solutions. This review focuses on the resources developed over the past years for analysis of genome data towards understanding disease biology especially in the context of mitochondrial diseases, given that mitochondria are central to major cellular pathways and their dysfunction leads to a broad spectrum of diseases. Platforms for collaboration of research groups, clinicians and patients and the advantages of community collaborative efforts in addressing rare diseases are also discussed. The review also describes crowdsourcing and crowdfunding efforts in rare diseases research and how the upcoming initiatives for understanding disease biology including analyses of large number of genomes are also applicable to rare diseases.
      PubDate: 2015-03-16T17:29:15Z
      DOI: 10.12688/f1000research.6208.1
      Issue No: Vol. 4 (2015)
  • Biological network analysis with CentiScaPe: centralities and experimental
           dataset integration [v2; indexed,]

    • Authors: Giovanni Scardoni, Gabriele Tosadori, Mohammed Faizan, Fausto Spoto, Franco Fabbri, Carlo Laudanna
      Abstract: The growing dimension and complexity of the available experimental data generating biological networks have increased the need for tools that help in categorizing nodes by their topological relevance. Here we present CentiScaPe, a Cytoscape app specifically designed to calculate centrality indexes used for the identification of the most important nodes in a network. CentiScaPe is a comprehensive suite of algorithms dedicated to network nodes centrality analysis, computing several centralities for undirected, directed and weighted networks. The results of the topological analysis can be integrated with data set from lab experiments, like expression or phosphorylation levels for each protein represented in the network. Our app opens new perspectives in the analysis of biological networks, since the integration of topological analysis with lab experimental data enhance the predictive power of the bioinformatics analysis.
      PubDate: 2015-07-07T15:34:15Z
      DOI: 10.12688/f1000research.4477.2
      Issue No: Vol. 3 (2015)
  • Detecting miRNA Mentions and Relations in Biomedical Literature [v2;

    • Authors: Shweta Bagewadi, Tamara Bobić, Martin Hofmann-Apitius, Juliane Fluck, Roman Klinger
      Abstract: Introduction: MicroRNAs (miRNAs) have demonstrated their potential as post-transcriptional gene expression regulators, participating in a wide spectrum of regulatory events such as apoptosis, differentiation, and stress response. Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases. Dissection of miRNA-related associations are valuable for contemplating their mechanism in diseases, leading to the discovery of novel miRNAs for disease prognosis, diagnosis, and therapy. Motivation: Apart from databases and prediction tools, miRNA-related information is largely available as unstructured text. Manual retrieval of these associations can be labor-intensive due to steadily growing number of publications. Additionally, most of the published miRNA entity recognition methods are keyword based, further subjected to manual inspection for retrieval of relations. Despite the fact that several databases host miRNA-associations derived from text, lower sensitivity and lack of published details for miRNA entity recognition and associated relations identification has motivated the need for developing comprehensive methods that are freely available for the scientific community. Additionally, the lack of a standard corpus for miRNA-relations has caused difficulty in evaluating the available systems. We propose methods to automatically extract mentions of miRNAs, species, genes/proteins, disease, and relations from scientific literature. Our generated corpora, along with dictionaries, and miRNA regular expression are freely available for academic purposes. To our knowledge, these resources are the most comprehensive developed so far. Results: The identification of specific miRNA mentions reaches a recall of 0.94 and precision of 0.93.  Extraction of miRNA-disease and miRNA-gene relations lead to an F1 score of up to 0.76. A comparison of the information extracted by our approach to the databases miR2Disease and miRSel for the extraction of Alzheimer's disease related relations shows the capability of our proposed methods in identifying correct relations with improved sensitivity. The published resources and described methods can help the researchers for maximal retrieval of miRNA-relations and generation of miRNA-regulatory networks. Availability: The training and test corpora, annotation guidelines, developed dictionaries, and supplementary files are available at
      PubDate: 2014-12-23T11:25:19Z
      DOI: 10.12688/f1000research.4591.2
      Issue No: Vol. 3 (2014)
  • Methodological framework to identify possible adverse drug reactions using
           population-based administrative data [v1; indexed,]

    • Authors: Brian Sauer, Jonathan Nebeker, Shuying Shen, Randall Rupper, Suzanne West, Judith A. Shinogle, Wu Xu, Kathleen N. Lohr, Matthew Samore
      Abstract: Purpose: We present a framework for detecting possible adverse drug reactions (ADRs) using the Utah Medicaid administrative data. We examined four classes of ADRs associated with treatment of dementia by acetylcholinesterase inhibitors (AChEIs): known reactions (gastrointestinal, psychological disturbances), potential reactions (respiratory disturbance), novel reactions (hepatic, hematological disturbances), and death. Methods: Our cohort design linked drug utilization data to medical claims from Utah Medicaid recipients. We restricted the analysis to 50 years-old and older beneficiaries diagnosed with dementia-related diseases. We compared patients treated with AChEI to patients untreated with anti-dementia medication therapy. We attempted to remove confounding by establishing propensity-score-matched cohorts for each outcome investigated; we then evaluated the effects of drug treatment by conditional multivariable Cox-proportional-hazard regression. Acute and transient effects were evaluated by a crossover design using conditional logistic regression. Results: Propensity-matched analysis of expected reactions revealed that AChEI treatment was associated with gastrointestinal episodes (Hazard Ratio [HR]: 2.02; 95%CI: 1.28-3.2), but not psychological episodes, respiratory disturbance, or death. Among the unexpected reactions, the risk of hematological episodes was higher (HR: 2.32; 95%CI: 1.47-3.6) in patients exposed to AChEI. AChEI exposure was not associated with an increase in hepatic episodes. We also noted a trend, identified in the case-crossover design, toward increase odds of experiencing acute hematological events during AChEI exposure (Odds Ratio: 3.0; 95% CI: 0.97 - 9.3). Conclusions: We observed an expected association between AChEIs treatment and gastrointestinal disturbances and detected a signal of possible hematological ADR after treatment with AChEIs in this pilot study. Using this analytic framework may raise awareness of potential ADEs and generate hypotheses for future investigations. Early findings, or signal detection, are considered hypothesis generating since confirmatory studies must be designed to determine if the signal represents a true drug safety problem.
      PubDate: 2014-10-29T11:42:15Z
      DOI: 10.12688/f1000research.4816.1
      Issue No: Vol. 3 (2014)
  • Differential recolonization of Atlantic intertidal habitats after
           disturbance reveals potential bottom-up community regulation [v1; indexed,

    • Authors: Willy Petzold, Ricardo A. Scrosati
      Abstract: In the spring of 2014, abundant sea ice that drifted out of the Gulf of St. Lawrence caused extensive disturbance in rocky intertidal habitats on the northern Atlantic coast of mainland Nova Scotia, Canada. To monitor recovery of intertidal communities, we surveyed two wave-exposed locations in the early summer of 2014. Barnacle recruitment and the abundance of predatory dogwhelks were low at one location (Tor Bay Provincial Park) but more than 20 times higher at the other location (Whitehead). Satellite data indicated that the abundance of coastal phytoplankton (the main food source for barnacle larvae) was consistently higher at Whitehead just before the barnacle recruitment season, when barnacle larvae were in the water column. These observations suggest bottom-up forcing of intertidal communities. The underlying mechanisms and their intensity along the NW Atlantic coast could be investigated through studies done at local and regional scales.
      PubDate: 2014-10-20T13:57:10Z
      DOI: 10.12688/f1000research.5545.1
      Issue No: Vol. 3 (2014)
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