Stock assessment of protogynous fish: evaluating measures of spawning biomass used to estimate biological reference points

In stock assessments, recruitment is typically modeled as a function of females only. For protogynous stocks, however, disproportionate fishing on males increases the possibility of reduced fertilization rates. To incorporate the importance of males in protogynous stocks, assessment models have been used to predict recruitment not just from female spawning biomass (Sf), but also from that of males (Sm) or both sexes (Sb). We conducted a simulation study to evaluate the ability of these three measures to estimate biological reference points used in fishery management. Of the three, Sf provides best estimates if the potential for decreased fertilization is weak, whereas Sm is best only if the potential is very strong. In general, Sb estimates the true reference points most closely, which indicates that if the potential for decreased fertilization is moderate or unknown, Sb should be used in assessments of protogynous stocks. Moreover, for a broad range of scenarios, relative errors from Sf and Sb occur in opposite directions, indicating that estimates from these measures could be used to bound uncertainty

Re-evaluating the effect of wind on recruitment in Gulf of Maine Atlantic Cod (Gadus morhua) using an environmentally-explicit stock recruitment model

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Fisheries Oceanography 24 (2015): 90-105, doi:10.1111/fog.12095.A previous study documented a correlation between Atlantic Cod (Gadus morhua) recruitment in the Gulf of Maine and an annual index of the north component of May winds. This correlation was supported by modeling studies that indicated unusually strong recruitment of Gulf of Maine Atlantic Cod results from high retention of spring-spawned larvae in years when winds were predominately out of the north, which favor downwelling. We re-evaluated this relationship using updated recruitment estimates and found that the correlation decreased between recruitment and wind. The original relationship was largely driven by two recruitment estimates, one of which (2005 year class) was highly uncertain because it was near the terminal year of the assessment. With additional data, the updated assessment estimated lower recruitment for the 2005 year class, which consequently lowered the correlation between recruitment and wind. We then investigated whether an environmentally-explicit stock recruit function that incorporated an annual wind index was supported by either the original or updated assessment output. Although incorporation of the annual wind index produced a better fitting model, the uncertainty in the estimated parameters and the implied unexploited conditions were not appropriate for providing management advice. These results suggest the need for caution in the development of environmentally-explicit stock recruitment relationships, in particular when basing relationships and hypotheses on recruitment estimates from the terminal years of stock assessment models. More broadly, this study highlights a number of sources of uncertainty that should be considered when analyses are performed on the output of stock assessment models.We also thank the NMFS Fisheries and the Environment program which funded the initial work of Churchill et al. (2011) (FATE Project 08-02) and funded Hare (FATE Project 10-08) to examine environmentally-explicit stock 487 recruitment models

The Millimeter Astronomy Legacy Team 90 GHz (MALT90) Pilot Survey

We describe a pilot survey conducted with the Mopra 22-m radio telescope in preparation for the Millimeter Astronomy Legacy Team Survey at 90 GHz (MALT90). We identified 182 candidate dense molecular clumps using six different selection criteria and mapped each source simultaneously in 16 different lines near 90 GHz. We present a summary of the data and describe how the results of the pilot survey shaped the design of the larger MALT90 survey. We motivate our selection of target sources for the main survey based on the pilot detection rates and demonstrate the value of mapping in multiple lines simultaneously at high spectral resolution.Comment: Accepted to ApJS. 23 pages and 16 figures. Full resolution version with an appendix showing all the data (12.1 MB) is available at http://malt90.bu.edu/publications/Foster_2011_Malt90Pilot.pd

ACVIM consensus statement on the treatment of immune thrombocytopenia in dogs and cats

Management of immune thrombocytopenia (ITP) in dogs and cats is evolving, but there are no evidence-based guidelines to assist clinicians with treatment decisions. Likewise, the overall goals for treatment of ITP have not been established. Immunosuppressive doses of glucocorticoids are the first line treatment, but optimal treatment regimens beyond glucocorticoids remain uncertain. Additional options include secondary immunosuppressive drugs such as azathioprine, modified cyclosporine, and mycophenolate mofetil, usually selected based on clinician preference. Vincristine, human IV immunoglobulin (hIVIg), and transfusion of platelet or red blood cell–containing products are often used in more severe cases. Splenectomy and thrombopoietin receptor agonists are usually reserved for refractory cases, but when and in which patient these modalities should be employed is under debate. To develop evidence-based guidelines for individualized treatment of ITP patients, we asked 20 Population Intervention Comparison Outcome (PICO) format questions. These were addressed by 17 evidence evaluators using a literature pool of 288 articles identified by a structured search strategy. Evidence evaluators, using panel-designed templates and data extraction tools, summarized evidence and created guideline recommendations. These were integrated by treatment domain chairs and then refined by iterative Delphi survey review to reach consensus on the final guidelines. In addition, 19 non-PICO questions covering scenarios in which evidence was lacking or of low quality were answered by expert opinion using iterative Delphi surveys with panelist integration and refinement. Commentary was solicited from multiple relevant professional organizations before finalizing the consensus. The rigorous consensus process identified few comparative treatment studies, highlighting many areas of ITP treatment requiring additional studies. This statement is a companion manuscript to the ACVIM Consensus Statement on the Diagnosis of Immune Thrombocytopenia in Dogs and Cats

Operationalizing ensemble models for scientific advice to fisheries management

This paper explores the possibility of using the ensemble modelling paradigm to fully capture assessment uncertainty and improve the robustness of advice provision. We identify and discuss advantages and challenges of ensemble modelling approaches in the context of scientific advice. There are uncertainties associated with every phase in the stock assessment process: data collection, assessment model choice, model assumptions, interpretation of risk, up to the implementation of management advice. Additionally, the dynamics of fish populations are complex, and our incomplete understanding of those dynamics and limited observations of important mechanisms, necessitate that models are simpler than nature. The aim is for the model to capture enough of the dynamics to accurately estimate trends and abundance, and provide the basis for robust advice about sustainable harvests. The status quo approach to assessment modelling has been to identify the “best” model and generate advice from that model, mostly ignoring advice from other model configurations regardless of how closely they performed relative to the chosen model. We discuss and make suggestions about the utility of ensemble models, including revisions to the formal process of providing advice to management bodies, and recommend further research to evaluate potential gains in modelling and advice performance.publishedVersio

MEG-BIDS, the brain imaging data structure extended to magnetoencephalography.

We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG measures brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS was a solution to organise magnetic resonance imaging (MRI) data. The nature and acquisition parameters of MRI and MEG data are strongly dissimilar. Although there is no standard data format for MEG, we propose MEG-BIDS as a principled solution to store, organise, process and share the multidimensional data volumes produced by the modality. The standard also includes well-defined metadata, to facilitate future data harmonisation and sharing efforts. This responds to unmet needs from the multimodal neuroimaging community and paves the way to further integration of other techniques in electrophysiology. MEG-BIDS builds on MRI-BIDS, extending BIDS to a multimodal data structure. We feature several data-analytics software that have adopted MEG-BIDS, and a diverse sample of open MEG-BIDS data resources available to everyone

The Vaginal Microbiome: Disease, Genetics and the Environment

The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect the vagina from infectious or non-infectious diseases, or it may enhance its susceptibility to them. Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora. Specific interactions dictated by the genetics of both the host and microbes are likely responsible for maintaining both the environment and the microbiome. However, the genetic basis of these interactions in both the host and the bacterial colonizers is currently unknown. _Lactobacillus_ species are associated with vaginal health, but the role of these species in the maintenance of health is not yet well defined. Similarly, other species, including those representing minor components of the overall flora, undoubtedly influence the ability of potential pathogens to thrive and cause disease. Gross alterations in the vaginal microbiome are frequently observed in women with bacterial vaginosis, but the exact etiology of this disorder is still unknown. There are also implications for vaginal flora in non-infectious conditions such as pregnancy, pre-term labor and birth, and possibly fertility and other aspects of women’s health. Conversely, the role of environmental factors in the maintenance of a healthy vaginal microbiome is largely unknown. To explore these issues, we have proposed to address the following questions:

*1.	Do the genes of the host contribute to the composition of the vaginal microbiome?* We hypothesize that genes of both host and bacteria have important impacts on the vaginal microbiome. We are addressing this question by examining the vaginal microbiomes of mono- and dizygotic twin pairs selected from the over 170,000 twin pairs in the Mid-Atlantic Twin Registry (MATR). Subsequent studies, beyond the scope of the current project, may investigate which host genes impact the microbial flora and how they do so.
*2.	What changes in the microbiome are associated with common non-infectious pathological states of the host?* We hypothesize that altered physiological (e.g., pregnancy) and pathologic (e.g., immune suppression) conditions, or environmental exposures (e.g., antibiotics) predictably alter the vaginal microbiome. Conversely, certain vaginal microbiome characteristics are thought to contribute to a woman’s risk for outcomes such as preterm delivery. We are addressing this question by recruiting study participants from the ~40,000 annual clinical visits to women’s clinics of the VCU Health System.
*3.	What changes in the vaginal microbiome are associated with relevant infectious diseases and conditions?* We hypothesize that susceptibility to infectious disease (e.g. HPV, _Chlamydia_ infection, vaginitis, vaginosis, etc.) is impacted by the vaginal microbiome. In turn, these infectious conditions clearly can affect the ability of other bacteria to colonize and cause pathology. Again, we are exploring these issues by recruiting participants from visitors to women’s clinics in the VCU Health System.

Three kinds of sequence data are generated in this project: i) rDNA sequences from vaginal microbes; ii) whole metagenome shotgun sequences from vaginal samples; and iii) whole genome shotgun sequences of bacterial clones selected from vaginal samples. The study includes samples from three vaginal sites: mid-vaginal, cervical, and introital. The data sets also include buccal and perianal samples from all twin participants. Samples from these additional sites are used to test the hypothesis of a per continuum spread of bacteria in relation to vaginal health. An extended set of clinical metadata associated with these sequences are deposited with dbGAP. We have currently collected over 4,400 samples from ~100 twins and over 450 clinical participants. We have analyzed and deposited data for 480 rDNA samples, eight whole metagenome shotgun samples, and over 50 complete bacterial genomes. These data are available to accredited investigators according to NIH and Human Microbiome Project (HMP) guidelines. The bacterial clones are deposited in the Biodefense and Emerging Infections Research Resources Repository ("http://www.beiresources.org/":http://www.beiresources.org/). 

In addition to the extensive sequence data obtained in this study, we are collecting metadata associated with each of the study participants. Thus, participants are asked to complete an extensive health history questionnaire at the time samples are collected. Selected clinical data associated with the visit are also obtained, and relevant information is collected from the medical records when available. This data is maintained securely in a HIPAA-compliant data system as required by VCU’s Institutional Review Board (IRB). The preponderance of these data (i.e., that judged appropriate by NIH staff and VCU’s IRB are deposited at dbGAP ("http://www.ncbi.nlm.nih.gov/gap":http://www.ncbi.nlm.nih.gov/gap). Selected fields of this data have been identified by NIH staff as ‘too sensitive’ and are not available in dbGAP. Individuals requiring access to these data fields are asked to contact the PI of this project or NIH Program Staff. 
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