Showing papers by "Dalhousie University published in 2012"
TL;DR: In this paper, the authors estimated deaths and disability-adjusted life years (DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010.
9,324 citations
Daniel J. Klionsky1, Fábio Camargo Abdalla2, Hagai Abeliovich3, Robert T. Abraham4 +1284 more•Institutions (463)
TL;DR: These guidelines are presented for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
4,316 citations
Johns Hopkins University1, University of Alabama at Birmingham2, University of Birmingham3, Oklahoma Medical Research Foundation4, Laval University5, University of Manchester6, University College London7, University of California, Los Angeles8, Lund University9, Northwestern University10, Hanyang University11, Dalhousie University12, University of Toronto13, McGill University14, North Shore-LIJ Health System15, Allegheny General Hospital16, University of California, San Diego17, University of Pennsylvania18, Monklands Hospital19, University of the Basque Country20, St Thomas' Hospital21, University of Copenhagen22, New York University23, University of North Carolina at Chapel Hill24, Karolinska Institutet25, SUNY Downstate Medical Center26, University of Manitoba27, Wake Forest University28, University of Louisville29, Emory University30, Istanbul University31, Medical University of South Carolina32, University of Texas Health Science Center at San Antonio33, Cedars-Sinai Medical Center34, University of Maryland, Baltimore35
TL;DR: The Systemic Lupus International Collaborating Clinics (SLICC) group revised and validated the American College of Rheumatology (ACR) systemic lupus erythematosus (SLE) classification criteria in order to improve clinical relevance, meet stringent methodology requirements, and incorporate new knowledge regarding the immunology of SLE.
Abstract: Objective The Systemic Lupus International Collaborating Clinics (SLICC) group revised and validated the American College of Rheumatology (ACR) systemic lupus erythematosus (SLE) classification criteria in order to improve clinical relevance, meet stringent methodology requirements, and incorporate new knowledge regarding the immunology of SLE. Methods The classification criteria were derived from a set of 702 expert-rated patient scenarios. Recursive partitioning was used to derive an initial rule that was simplified and refined based on SLICC physician consensus. The SLICC group validated the classification criteria in a new validation sample of 690 new expert-rated patient scenarios. Results Seventeen criteria were identified. In the derivation set, the SLICC classification criteria resulted in fewer misclassifications compared with the current ACR classification criteria (49 versus 70; P = 0.0082) and had greater sensitivity (94% versus 86%; P < 0.0001) and equal specificity (92% versus 93%; P = 0.39). In the validation set, the SLICC classification criteria resulted in fewer misclassifications compared with the current ACR classification criteria (62 versus 74; P = 0.24) and had greater sensitivity (97% versus 83%; P < 0.0001) but lower specificity (84% versus 96%; P < 0.0001). Conclusion The new SLICC classification criteria performed well in a large set of patient scenarios rated by experts. According to the SLICC rule for the classification of SLE, the patient must satisfy at least 4 criteria, including at least one clinical criterion and one immunologic criterion OR the patient must have biopsy-proven lupus nephritis in the presence of antinuclear antibodies or antidouble-stranded DNA antibodies. (Less)
3,609 citations
TL;DR: Use of CT scans in children to deliver cumulative doses of about 50 mGy might almost triple the risk of leukaemia and doses ofabout 60 m Gy might triple therisk of brain cancer.
3,044 citations
Harvard University1, University of Cambridge2, Mayo Clinic3, Okayama University4, Technische Universität München5, Dalhousie University6, University of Amsterdam7, Southampton General Hospital8, Tokyo Metropolitan Komagome Hospital9, Shinshu University10, Kanazawa University11, Kanazawa Medical University12, Kansai Medical University13, Seoul National University14, University College London15, Sapporo Medical University16, University of Verona17
TL;DR: This statement proposes a terminology scheme for the diagnosis of IgG4-related disease that is based primarily on the morphological appearance on biopsy, and advocates the use of strict criteria for accepting newly proposed entities or sites as components of the IgG 4- related disease spectrum.
2,041 citations
Dalhousie University1, University of Saskatchewan2, University of Rhode Island3, Sewanee: The University of the South4, Natural History Museum5, New York State Department of Health6, University of British Columbia7, Kaiserslautern University of Technology8, Charles University in Prague9, University of Guelph10, Le Moyne College11, Georgia College & State University12, University of Colorado Boulder13, University of Geneva14, Edinburgh Napier University15, University of Arkansas16, Saint Petersburg State University17
TL;DR: This revision of the classification of eukaryotes retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees.
Abstract: This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.
1,414 citations
TL;DR: For the types of patient recruited in IST-3, despite the early hazards, thrombolysis within 6 h improved functional outcome and benefit did not seem to be diminished in elderly patients.
1,023 citations
University of South Florida1, Medical College of Wisconsin2, Fred Hutchinson Cancer Research Center3, Emory University4, University of Florida5, Harvard University6, Washington University in St. Louis7, Dalhousie University8, Dresden University of Technology9, Stanford University10, Oregon Health & Science University11, University of Utah12, University of Pennsylvania13, University of Michigan14, Virginia Commonwealth University15, Mayo Clinic16, University of Texas MD Anderson Cancer Center17, National Institutes of Health18, Rutgers University19, Ottawa Hospital Research Institute20, National Marrow Donor Program21
TL;DR: A phase 3, multicenter, randomized trial of transplantation of peripheral-blood stem cells versus bone marrow from unrelated donors did not detect significant survival differences, and exploratory analyses of secondary end points indicated that peripheral- Blood stem cells may reduce the risk of graft failure, whereas bone marrow may reduceThe risk of chronic GVHD.
Abstract: BACKGROUND Randomized trials have shown that the transplantation of filgrastim-mobilized peripheral-blood stem cells from HLA-identical siblings accelerates engraftment but increases the risks of acute and chronic graft-versus-host disease (GVHD), as compared with the transplantation of bone marrow. Some studies have also shown that peripheral-blood stem cells are associated with a decreased rate of relapse and improved survival among recipients with high-risk leukemia. METHODS We conducted a phase 3, multicenter, randomized trial of transplantation of peripheral-blood stem cells versus bone marrow from unrelated donors to compare 2-year survival probabilities with the use of an intention-to-treat analysis. Between March 2004 and September 2009, we enrolled 551 patients at 48 centers. Patients were randomly assigned in a 1:1 ratio to peripheral-blood stem-cell or bone marrow transplantation, stratified according to transplantation center and disease risk. The median follow-up of surviving patients was 36 months (interquartile range, 30 to 37). RESULTS The overall survival rate at 2 years in the peripheral-blood group was 51% (95% confidence interval [CI], 45 to 57), as compared with 46% (95% CI, 40 to 52) in the bone marrow group (P = 0.29), with an absolute difference of 5 percentage points (95% CI, −3 to 14). The overall incidence of graft failure in the peripheral-blood group was 3% (95% CI, 1 to 5), versus 9% (95% CI, 6 to 13) in the bone marrow group (P = 0.002). The incidence of chronic GVHD at 2 years in the peripheral-blood group was 53% (95% CI, 45 to 61), as compared with 41% (95% CI, 34 to 48) in the bone marrow group (P = 0.01). There were no significant between-group differences in the incidence of acute GVHD or relapse. CONCLUSIONS We did not detect significant survival differences between peripheral-blood stem-cell and bone marrow transplantation from unrelated donors. Exploratory analyses of secondary end points indicated that peripheral-blood stem cells may reduce the risk of graft failure, whereas bone marrow may reduce the risk of chronic GVHD. (Funded by the National Heart, Lung, and Blood Institute–National Cancer Institute and others; ClinicalTrials.gov number, NCT00075816.)
715 citations
TL;DR: These estimates expand the evaluation of the global health burden associated with outdoor air pollution, highlighted by increased concentrations in East, South, and Southeast Asia and decreases in North America and Europe.
Abstract: Ambient air pollution is associated with numerous adverse health impacts. Previous assessments of global attributable disease burden have been limited to urban areas or by coarse spatial resolution of concentration estimates. Recent developments in remote sensing, global chemical-transport models, and improvements in coverage of surface measurements facilitate virtually complete spatially resolved global air pollutant concentration estimates. We combined these data to generate global estimates of long-term average ambient concentrations of fine particles (PM2.5) and ozone at 0.1° × 0.1° spatial resolution for 1990 and 2005. In 2005, 89% of the world’s population lived in areas where the World Health Organization Air Quality Guideline of 10 μg/m3 PM2.5 (annual average) was exceeded. Globally, 32% of the population lived in areas exceeding the WHO Level 1 Interim Target of 35 μg/m3, driven by high proportions in East (76%) and South (26%) Asia. The highest seasonal ozone levels were found in North and Latin...
668 citations
TL;DR: Acute cannabis consumption is associated with an increased risk of a motor vehicle crash, especially for fatal collisions, and could be used as the basis for campaigns against drug impaired driving, developing regional or national policies to control acute drug use while driving, and raising public awareness.
Abstract: Objective To determine whether the acute consumption of cannabis (cannabinoids) by drivers increases the risk of a motor vehicle collision. Design Systematic review of observational studies, with meta-analysis. Data sources We did electronic searches in 19 databases, unrestricted by year or language of publication. We also did manual searches of reference lists, conducted a search for unpublished studies, and reviewed the personal libraries of the research team. Review methods We included observational epidemiology studies of motor vehicle collisions with an appropriate control group, and selected studies that measured recent cannabis use in drivers by toxicological analysis of whole blood or self report. We excluded experimental or simulator studies. Two independent reviewers assessed risk of bias in each selected study, with consensus, using the Newcastle-Ottawa scale. Risk estimates were combined using random effects models.
637 citations
Harvard University1, Dalhousie University2, University of Amsterdam3, Kobe University4, Mayo Clinic5, Technische Universität München6, Tokyo Metropolitan Komagome Hospital7, Shinshu University8, Kanazawa University9, Kanazawa Medical University10, Kansai Medical University11, Seoul National University12, Okayama University13, University College London14, Sapporo Medical University15, University of Verona16, King's College London17
TL;DR: John H. Stone, Arezou Khosroshahi, Vikram Deshpande, John K.Stone, Masayuki Takahira, Hisanori Umehara, George Webster, Motohisa Yamamoto, Eunhee Yi, Tadashi Yoshino, Giuseppe Zamboni, Yoh Zen, and Suresh Chari.
Abstract: John H. Stone, Arezou Khosroshahi, Vikram Deshpande, John K. C. Chan, J. Godfrey Heathcote, Rob Aalberse, Atsushi Azumi, Donald B. Bloch, William R. Brugge, Mollie N. Carruthers, Wah Cheuk, Lynn Cornell, Carlos Fernandez-Del Castillo, Judith A. Ferry, David Forcione, Gunter Kloppel, Daniel L. Hamilos, Terumi Kamisawa, Satomi Kasashima, Shigeyuki Kawa, Mitsuhiro Kawano, Yasufumi Masaki, Kenji Notohara, Kazuichi Okazaki, Ji Kon Ryu, Takako Saeki, Dushyant Sahani, Yasuharu Sato, Thomas Smyrk, James R. Stone, Masayuki Takahira, Hisanori Umehara, George Webster, Motohisa Yamamoto, Eunhee Yi, Tadashi Yoshino, Giuseppe Zamboni, Yoh Zen, and Suresh Chari
TL;DR: A comprehensive reference for clinicians which may facilitate optimal material/device selection for peripheral nerve repair and for materials scientists, this review highlights predicate devices and evaluation methodologies, offering an insight into current deficiencies associated with state-of-the-art materials.
Abstract: Several nerve guidance conduits (NGCs) and nerve protectant wraps are approved by the US Food and Drug Administration (FDA) for clinical use in peripheral nerve repair. These devices cover a wide range of natural and synthetic materials, which may or may not be resorbable. This review consolidates the data pertaining to all FDA approved materials into a single reference, which emphasizes material composition alongside pre-clinical and clinical safety and efficacy (where possible). This article also summarizes the key advantages and limitations for each material as noted in the literature (with respect to the indication considered). In this context, this review provides a comprehensive reference for clinicians which may facilitate optimal material/device selection for peripheral nerve repair. For materials scientists, this review highlights predicate devices and evaluation methodologies, offering an insight into current deficiencies associated with state-of-the-art materials and may help direct new technology developments and evaluation methodologies thereof.
TL;DR: It is found that the frequency of airline flights between the two parties is the best predictor of Twitter ties, highlighting the importance of looking at pre-existing ties between places and people.
TL;DR: Lysosomal storage diseases (LSDs) as mentioned in this paper are a family of disorders that result from inherited gene mutations that perturb lysosome homeostasis, which leads to abnormal storage of macromolecular substrates.
Abstract: Lysosomal storage diseases (LSDs) are a family of disorders that result from inherited gene mutations that perturb lysosomal homeostasis. LSDs mainly stem from deficiencies in lysosomal enzymes, but also in some non-enzymatic lysosomal proteins, which lead to abnormal storage of macromolecular substrates. Valuable insights into lysosome functions have emerged from research into these diseases. In addition to primary lysosomal dysfunction, cellular pathways associated with other membrane-bound organelles are perturbed in these disorders. Through selective examples, we illustrate why the term “cellular storage disorders” may be a more appropriate description of these diseases and discuss therapies that can alleviate storage and restore normal cellular function.
TL;DR: Understanding the molecular details of quorum sensing mechanisms and their controlled social activities may open a new avenue for controlling bacterial infections.
Abstract: Many bacteria are known to regulate their cooperative activities and physiological processes through a mechanism called quorum sensing (QS), in which bacterial cells communicate with each other by releasing, sensing and responding to small diffusible signal molecules. The ability of bacteria to communicate and behave as a group for social interactions like a multi-cellular organism has provided significant benefits to bacteria in host colonization, formation of biofilms, defense against competitors, and adaptation to changing environments. Importantly, many QS-controlled activities have been involved in the virulence and pathogenic potential of bacteria. Therefore, understanding the molecular details of quorum sensing mechanisms and their controlled social activities may open a new avenue for controlling bacterial infections.
TL;DR: The progression of food-web ecology and the challenges in using the food- web approach are summarized and five areas of research are identified where advances can continue, and be applied to global challenges.
Abstract: The global biodiversity crisis concerns not only unprecedented loss of species within communities, but also related consequences for ecosystem function. Community ecology focuses on patterns of species richness and community composition, whereas ecosystem ecology focuses on fluxes of energy and materials. Food webs provide a quantitative framework to combine these approaches and unify the study of biodiversity and ecosystem function. We summarise the progression of food-web ecology and the challenges in using the food-web approach. We identify five areas of research where these advances can continue, and be applied to global challenges. Finally, we describe what data are needed in the next generation of food-web studies to reconcile the structure and function of biodiversity.
University of Washington1, Cleveland Clinic2, University of Pittsburgh3, Children's Memorial Hospital4, North York General Hospital5, University of Louisville6, Sacred Heart Hospital7, Boston Children's Hospital8, Rutgers University9, Dalhousie University10, University of Michigan11, Group Health Cooperative12, Izaak Walton Killam Health Centre13, Rush University Medical Center14, State University of New York Upstate Medical University15, Memorial Hospital of South Bend16, Rhode Island Hospital17, Carolinas Medical Center18, Nemours Foundation19, University of New Mexico20
TL;DR: It is found that syndromic disorders could be distinguished from those with extreme phenotypic heterogeneity on the basis of the total number of copy-number variants and whether the variants are inherited or de novo.
Abstract: Background Some copy-number variants are associated with genomic disorders with extreme phenotypic heterogeneity. The cause of this variation is unknown, which presents challenges in genetic diagnosis, counseling, and management. Methods We analyzed the genomes of 2312 children known to carry a copy-number variant associated with intellectual disability and congenital abnormalities, using array comparative genomic hybridization. Results Among the affected children, 10.1% carried a second large copy-number variant in addition to the primary genetic lesion. We identified seven genomic disorders, each defined by a specific copy-number variant, in which the affected children were more likely to carry multiple copy-number variants than were controls. We found that syndromic disorders could be distinguished from those with extreme phenotypic heterogeneity on the basis of the total number of copy-number variants and whether the variants are inherited or de novo. Children who carried two large copy-number variant...
TL;DR: These findings confirm previous single-centre studies showing that the CTA spot sign is a predictor of haematoma expansion, and is recommended as an entry criterion for future trials ofHaemostatic therapy in patients with acute ICH.
Abstract: Summary Background In patients with intracerebral haemorrhage (ICH), early haemorrhage expansion affects clinical outcome. Haemostatic treatment reduces haematoma expansion, but fails to improve clinical outcomes in many patients. Proper selection of patients at high risk for haematoma expansion seems crucial to improve outcomes. In this study, we aimed to prospectively validate the CT-angiography (CTA) spot sign for prediction of haematoma expansion. Methods PREDICT (predicting haematoma growth and outcome in intracerebral haemorrhage using contrast bolus CT) was a multicentre prospective observational cohort study. We recruited patients aged 18 years or older, with ICH smaller than 100 mL, and presenting at less than 6 h from symptom onset. Using two independent core laboratories, one neuroradiologist determined CTA spot-sign status, whereas another neurologist masked for clinical outcomes and imaging measured haematoma volumes by computerised planimetry. The primary outcome was haematoma expansion defined as absolute growth greater than 6 mL or a relative growth of more than 33% from initial CT to follow-up CT. We reported data using standard descriptive statistics stratified by the CTA spot sign. Mortality was assessed with Kaplan-Meier survival analysis. Findings We enrolled 268 patients. Median time from symptom onset to baseline CT was 135 min (range 22–470), and time from onset to CTA was 159 min (32–475). 81 (30%) patients were spot-sign positive. The primary analysis included 228 patients, who had a follow-up CT before surgery or death. Median baseline ICH volume was 19·9 mL (1·5–80·9) in spot-sign-positive patients versus 10·0 mL (0·1–102·7) in spot-sign negative patients (p Interpretation These findings confirm previous single-centre studies showing that the CTA spot sign is a predictor of haematoma expansion. The spot sign is recommended as an entry criterion for future trials of haemostatic therapy in patients with acute ICH. Funding Canadian Stroke Consortium and NovoNordisk Canada.
TL;DR: Participatory Action Research (PAR) is a qualitative research methodology option that requires further understanding and consideration as mentioned in this paper, which is considered democratic, equitable, liberating, and life-enhancing qualitative inquiry that remains distinct from other qualitative methodologies.
Abstract: Participatory Action Research (PAR) is a qualitative research methodology option that requires further understanding and consideration. PAR is considered democratic, equitable, liberating, and life-enhancing qualitative inquiry that remains distinct from other qualitative methodologies (Kach & Kralik, 2006). Using PAR, qualitative features of an individual’s feelings, views, and patterns are revealed without control or manipulation from the researcher. The participant is active in making informed decisions throughout all aspects of the research process for the primary purpose of imparting social change; a specific action (or actions) is the ultimate goal. The following paper will contextualize PAR in terms of its history, principles, definitions, and strengths, as well as discuss challenges and practical suggestions for using PAR. In addition, it will examine focus groups and interviews as methods for data collection, the role of PAR in education, and the types of research for which PAR is best suited.
TL;DR: Shared immuno-inflammatory pathways underpin the physiology of sickness behavior and the pathophysiology of clinical depression explaining their partially overlapping phenomenology.
Abstract: It is of considerable translational importance whether depression is a form or a consequence of sickness behavior. Sickness behavior is a behavioral complex induced by infections and immune trauma and mediated by pro-inflammatory cytokines. It is an adaptive response that enhances recovery by conserving energy to combat acute inflammation. There are considerable phenomenological similarities between sickness behavior and depression, for example, behavioral inhibition, anorexia and weight loss, and melancholic (anhedonia), physio-somatic (fatigue, hyperalgesia, malaise), anxiety and neurocognitive symptoms. In clinical depression, however, a transition occurs to sensitization of immuno-inflammatory pathways, progressive damage by oxidative and nitrosative stress to lipids, proteins, and DNA, and autoimmune responses directed against self-epitopes. The latter mechanisms are the substrate of a neuroprogressive process, whereby multiple depressive episodes cause neural tissue damage and consequent functional and cognitive sequelae. Thus, shared immuno-inflammatory pathways underpin the physiology of sickness behavior and the pathophysiology of clinical depression explaining their partially overlapping phenomenology. Inflammation may provoke a Janus-faced response with a good, acute side, generating protective inflammation through sickness behavior and a bad, chronic side, for example, clinical depression, a lifelong disorder with positive feedback loops between (neuro)inflammation and (neuro)degenerative processes following less well defined triggers.
TL;DR: In this large national cohort of nonimmigrant Canadians, mortality was associated with long-term exposure to PM2.5 and cardiovascular mortality in nonimmigrant Canadian adults.
Abstract: Background: Few cohort studies have evaluated the risk of mortality associated with long-term exposure to fine particulate matter [≤ 2.5 μm in aerodynamic diameter (PM2.5)]. This is the first natio...
TL;DR: The process used for a realist review and synthesis to answer the question ‘what interventions and strategies are effective in enabling evidence-informed healthcare?’ is described.
Abstract: Realist synthesis is an increasingly popular approach to the review and synthesis of evidence, which focuses on understanding the mechanisms by which an intervention works (or not). There are few published examples of realist synthesis. This paper therefore fills a gap by describing, in detail, the process used for a realist review and synthesis to answer the question ‘what interventions and strategies are effective in enabling evidence-informed healthcare?’ The strengths and challenges of conducting realist review are also considered. The realist approach involves identifying underlying causal mechanisms and exploring how they work under what conditions. The stages of this review included: defining the scope of the review (concept mining and framework formulation); searching for and scrutinising the evidence; extracting and synthesising the evidence; and developing the narrative, including hypotheses. Based on key terms and concepts related to various interventions to promote evidence-informed healthcare, we developed an outcome-focused theoretical framework. Questions were tailored for each of four theory/intervention areas within the theoretical framework and were used to guide development of a review and data extraction process. The search for literature within our first theory area, change agency, was executed and the screening procedure resulted in inclusion of 52 papers. Using the questions relevant to this theory area, data were extracted by one reviewer and validated by a second reviewer. Synthesis involved organisation of extracted data into evidence tables, theming and formulation of chains of inference, linking between the chains of inference, and hypothesis formulation. The narrative was developed around the hypotheses generated within the change agency theory area. Realist synthesis lends itself to the review of complex interventions because it accounts for context as well as outcomes in the process of systematically and transparently synthesising relevant literature. While realist synthesis demands flexible thinking and the ability to deal with complexity, the rewards include the potential for more pragmatic conclusions than alternative approaches to systematic reviewing. A separate publication will report the findings of the review.
University of Geneva1, Centre national de la recherche scientifique2, University of Saskatchewan3, Natural History Museum4, New York State Department of Health5, Charles University in Prague6, Kaiserslautern University of Technology7, University of Greifswald8, Dalhousie University9, Free University of Berlin10, Academy of Sciences of the Czech Republic11, University of British Columbia12, Sewanee: The University of the South13, Saint Petersburg State University14, Royal Botanic Garden Edinburgh15, University of Cologne16, Uppsala University17, University of New Brunswick18, Halifax19, National Institutes of Health20, University of Giessen21, National Museum of Natural History22
TL;DR: A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial Eukaryotes.
Abstract: Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.
TL;DR: Combining FA analysis with other lines of evidence, such as sta- ble isotope analysis, offers a more reliable approach to examining trophic interactions in benthic systems.
Abstract: Fatty acid (FA) analysis is a well- established tool for studying trophic interactions in marine habitats. However, its application to benthic food webs poses 2 particular challenges. First, unlike pelagic zooplankton, benthic con- sumers have access to different sizes and func- tional groups of primary producers and may con- sume a highly mixed diet. Classes of benthic primary producers are distinct in their overall FA composition, but most do not possess unique marker FAs that can be used to identify their con- tribution to higher trophic levels. Second, unlike mammalian predators, benthic invertebrates have the capacity to significantly modify their dietary FAs and thereby obscure markers for food sources. Controlled feeding studies have been used to dis- tinguish dietary tracer FAs from those that are modified by the consumer in several benthic invertebrates, but more such studies are needed. Despite these challenges, FAs have been used to study trophic structure in a variety of benthic habitats including the deep sea, polar regions, estuaries, and the rocky subtidal zone. However, the complexity of benthic food webs and lack of unique markers impose uncertainties in the inter- pretation of FA data from field studies. Multivari- ate analyses are necessary for analyzing FA datasets, although univariate tests can be useful for comparing levels of informative FAs among food sources and consumers. Combining FA analysis with other lines of evidence, such as sta- ble isotope analysis, offers a more reliable approach to examining trophic interactions in benthic systems.
TL;DR: Habitat compression and associated potential habitat loss was validated using electronic tagging data from 47 blue marlin and may be associated with a 10–50% worldwide decline of pelagic predator diversity and further expansion of the Atlantic OMZ along with overfishing may threaten the sustainability of these valuable pelagic fisheries and marine ecosystems.
Abstract: Climate model predictions1, 2 and observations3, 4 reveal regional declines in oceanic dissolved oxygen, which are probably influenced by global warming5. Studies indicate ongoing dissolved oxygen depletion and vertical expansion of the oxygen minimum zone (OMZ) in the tropical northeast Atlantic Ocean6, 7. OMZ shoaling may restrict the usable habitat of billfishes and tunas to a narrow surface layer8, 9. We report a decrease in the upper ocean layer exceeding 3.5 ml l−1 dissolved oxygen at a rate of ≤1 m yr−1 in the tropical northeast Atlantic (0–25° N, 12–30° W), amounting to an annual habitat loss of ~5.95×1013 m3, or 15% for the period 1960–2010. Habitat compression and associated potential habitat loss was validated using electronic tagging data from 47 blue marlin. This phenomenon increases vulnerability to surface fishing gear for billfishes and tunas8, 9, and may be associated with a 10–50% worldwide decline of pelagic predator diversity10. Further expansion of the Atlantic OMZ along with overfishing may threaten the sustainability of these valuable pelagic fisheries and marine ecosystems.
TL;DR: Evidence is provided that species diversity evolved in response to ecological opportunity, and that eutrophication, by diminishing this opportunity, has driven extinctions through speciation reversal and demographic decline, and it is argued that extinction by Speciation reversal may be more widespread than currently appreciated.
Abstract: Species diversity can be lost through two different but potentially interacting extinction processes: demographic decline and speciation reversal through introgressive hybridization. To investigate the relative contribution of these processes, we analysed historical and contemporary data of replicate whitefish radiations from 17 pre-alpine European lakes and reconstructed changes in genetic species differentiation through time using historical samples. Here we provide evidence that species diversity evolved in response to ecological opportunity, and that eutrophication, by diminishing this opportunity, has driven extinctions through speciation reversal and demographic decline. Across the radiations, the magnitude of eutrophication explains the pattern of species loss and levels of genetic and functional distinctiveness among remaining species. We argue that extinction by speciation reversal may be more widespread than currently appreciated. Preventing such extinctions will require that conservation efforts not only target existing species but identify and protect the ecological and evolutionary processes that generate and maintain species.
TL;DR: When choosing to use probiotics in the treatment or prevention of gastrointestinal disease, the type of disease and probiotic species (strain) are the most important factors to take into consideration.
Abstract: Background
Meta-analyses on the effects of probiotics on specific gastrointestinal diseases have generally shown positive effects on disease prevention and treatment; however, the relative efficacy of probiotic use for treatment and prevention across different gastrointestinal diseases, with differing etiology and mechanisms of action, has not been addressed.
TL;DR: The RAM Legacy Stock Assessment Database as mentioned in this paper provides a new insight into the status of exploited populations: 58% of stocks with reference points (n = 214) were estimated to be below the biomass resulting in maximum sustainable yield (BMSY) and 30% had exploitation levels above the exploitation rate resulting in UMSY.
Abstract: Meta-analyses of stock assessments can provide novel insight into marine population dynamics and the status of fished species, but the world’s main stock assessment database (the Myers Stock-Recruitment Database) is now outdated. To facilitate new analyses, we developed a new database, the RAM Legacy Stock Assessment Database, for commercially exploited marine fishes and invertebrates. Time series of total biomass, spawner biomass, recruits, fishing mortality and catch/landings form the core of the database. Assessments were assembled from 21 national and international management agencies for a total of 331 stocks (295 fish stocks representing 46 families and 36 invertebrate stocks representing 12 families), including nine of the world’s 10 largest fisheries. Stock assessments were available from 27 large marine ecosystems, the Caspian Sea and four High Seas regions, and include the Atlantic, Pacific, Indian, Arctic and Antarctic Oceans. Most assessments came from the USA, Europe, Canada, New Zealand and Australia. Assessed marine stocks represent a small proportion of harvested fish taxa (16%), and an even smaller proportion of marine fish biodiversity (1%), but provide high-quality data for intensively studied stocks. The database provides new insight into the status of exploited populations: 58% of stocks with reference points (n = 214) were estimated to be below the biomass resulting in maximum sustainable yield (BMSY) and 30% had exploitation levels above the exploitation rate resulting in maximum sustainable yield (UMSY). We anticipate that the database will facilitate new research in population dynamics and fishery management, and we encourage further data contributions from stock assessment scientists.
TL;DR: In this article, the authors evaluated air pollution-related health impacts on the Chinese economy by using an expanded version of the Emissions Prediction and Policy Analysis model, and found that marginal welfare losses from air pollution decreased from 14% of the historical welfare level to 5% during the same period because the total size of the economy grew much faster than air pollution damages.
Abstract: A B S T R A C T This study evaluates air pollution-related health impacts on the Chinese economy by using an expanded version of the Emissions Prediction and Policy Analysis model. We estimated that marginal welfare impact to the Chinese economy of ozone and particulate-matter concentrations above background levels increased from 1997 US$22 billion in 1975 to 1997 US$112 billion in 2005, despite improvements in overall air quality. This increase is a result of the growing urban population and rising wages that thus increased the value of lost labor and leisure. In relative terms, however, welfare losses from air pollution decreased from 14% of the historical welfare level to 5% during the same period because the total size of the economy grew much faster than the absolute air pollution damages. In addition, we estimated that particulate-matter pollution alone led to a gross domestic product loss of 1997 US$64 billion in 1995. Given that the World Bank’s comparable estimate drawn from a static approach was only 1997 US$34 billion, this result suggests that conventional static methods neglecting the cumulative impact of pollution-caused welfare damage are likely to underestimate pollution-health costs substantially. However, our analysis of uncertainty involved in exposure–response functions suggests that our central estimates are susceptible to significantly large error bars of around � 80%.
TL;DR: In subjects aged 50-59 years, the ZV significantly reduced the incidence of HZ and was well tolerated, with the difference primarily due to higher rates of injection-site AEs and headache.
Abstract: Background. Herpes zoster (HZ) adversely affects individuals aged 50‐59, but vaccine efficacy has not been assessed in this population. This study was designed to determine the efficacy, safety, and tolerability of zoster vaccine for preventing HZ in persons aged 50‐59 years. Methods. This was a randomized, double-blind, placebo-controlled study of 22 439 subjects aged 50‐59 years conducted in North America and Europe. Subjects were given 1 dose of licensed zoster vaccine (ZV) (Zostavax; Merck) and followed for occurrence of HZ for $1 year (mean, 1.3 years) postvaccination until accrual of $96 confirmed HZ cases (as determined by testing lesions swabs for varicella zoster virus DNA by polymerase chain reaction). Subjects were followed for all adverse events (AEs) from day 1 to day 42 postvaccination and for serious AEs (SAEs) through day 182 postvaccination. Results. The ZV reduced the incidence of HZ (30 cases in vaccine group, 1.99/1000 person-years vs 99 cases in placebo group, 6.57/1000 person-years). Vaccine efficacy for preventing HZ was 69.8% (95% confidence interval, 54.1‐80.6). AEs were reported by 72.8% of subjects in the ZV group and 41.5% in the placebo group, with the difference primarily due to higher rates of injection-site AEs and headache. The proportion of subjects reporting SAEs occurring within 42 days postvaccination (ZV, 0.6%; placebo, 0.5%) and 182 days postvaccination (ZV, 2.1%; placebo, 1.9%) was similar between groups. Conclusions. In subjects aged 50‐59 years, the ZV significantly reduced the incidence of HZ and was well tolerated.