Advances in methods for determining fecundity: application of the new methods to some marine fishes

Estimation of individual egg production (realized fecundity) is a key step either to understand the stock and recruit relationship or to carry out fisheries-independent assessment of spawning stock biomass using egg production methods. Many fish are highly fecund and their ovaries may weigh over a kilogram; therefore the work time can be consuming and require large quantities of toxic fixative. Recently it has been shown for Atlantic cod (Gadus morhua) that image analysis can automate fecundity determination using a power equation that links follicles per gram ovary to the mean vitellogenic follicular diameter (the autodiametric method). In this article we demonstrate the precision of the autodiametric method applied to a range of species with different spawning strategies during maturation and spawning. A new method using a solid displacement pipette to remove quantitative fecundity samples (25, 50, 100, and 200 milligram [mg]) is evaluated, as are the underlying assumptions to effectively fix and subsample the ovary. Finally, we demonstrate the interpretation of dispersed formaldehyde-fixed ovarian samples (whole mounts) to assess the presence of atretic and postovulatory follicles to replace labor intensive histology. These results can be used to estimate down regulation (production of atretic follicles) of fecundity during maturation

NRG Oncology/RTOG 0921: A phase 2 study of postoperative intensity-modulated radiotherapy with concurrent cisplatin and bevacizumab followed by carboplatin and paclitaxel for patients with endometrial cancer.

BACKGROUND: The current study was conducted to assess acute and late adverse events (AEs), overall survival (OS), pelvic failure, regional failure, distant failure, and disease-free survival in a prospective phase 2 clinical trial of bevacizumab and pelvic intensity-modulated radiotherapy (IMRT) with chemotherapy in patients with high-risk endometrial cancer. METHODS: Patients underwent a hysterectomy and lymph node removal, and had ≥1 of the following high-risk factors: grade 3 carcinoma with \u3e50% myometrial invasion, grade 2 or 3 disease with any cervical stromal invasion, or known extrauterine extension confined to the pelvis. Treatment included pelvic IMRT and concurrent cisplatin on days 1 and 29 of radiation and bevacizumab (at a dose of 5 mg/kg on days 1, 15, and 29 of radiation) followed by adjuvant carboplatin and paclitaxel for 4 cycles. The primary endpoint was grade ≥3 AEs occurring within the first 90 days (toxicity was graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events [version 4.0]). RESULTS: A total of 34 patients were accrued from November 2009 through December 2011, 30 of whom were eligible and received study treatment. Seven of 30 patients (23.3%; 1-sided 95% confidence interval, 10.6%-36.0%) developed grade ≥3 treatment-related nonhematologic toxicities within 90 days; an additional 6 patients experienced grade ≥3 toxicities between 90 and 365 days after treatment. The 2-year OS rate was 96.7% and the disease-free survival rate was 79.1%. No patient developed a within-field pelvic failure and no patients with International Federation of Gynecology and Obstetrics stage I to IIIA disease developed disease recurrence after a median follow-up of 26 months. CONCLUSIONS: Postoperative bevacizumab added to chemotherapy and pelvic IMRT appears to be well tolerated and results in high OS rates at 2 years for patients with high-risk endometrial carcinoma

Acute Respiratory Distress Syndrome Subphenotypes Respond Differently to Randomized Fluid Management Strategy

RationaleWe previously identified two acute respiratory distress syndrome (ARDS) subphenotypes in two separate randomized controlled trials with differential response to positive end-expiratory pressure.ObjectivesTo identify these subphenotypes in a third ARDS cohort, to test whether subphenotypes respond differently to fluid management strategy, and to develop a practical model for subphenotype identification.MethodsWe used latent class analysis of baseline clinical and plasma biomarker data to identify subphenotypes in FACTT (Fluid and Catheter Treatment Trial; n = 1,000). Logistic regression was used to test for an interaction between subphenotype and treatment for mortality. We used stepwise modeling to generate a model for subphenotype identification in FACTT and validated its accuracy in the two cohorts in which we previously identified ARDS subphenotypes.Measurements and main resultsWe confirmed that a two-class (two-subphenotype) model best described the study population. Subphenotype 2 was again characterized by higher inflammatory biomarkers and hypotension. Fluid management strategy had significantly different effects on 90-day mortality in the two subphenotypes (P = 0.0039 for interaction); mortality in subphenotype 1 was 26% with fluid-liberal strategy versus 18% with fluid-conservative, whereas mortality in subphenotype 2 was 40% with fluid-liberal strategy versus 50% in fluid-conservative. A three-variable model of IL-8, bicarbonate, and tumor necrosis factor receptor-1 accurately classified the subphenotypes.ConclusionsThis analysis confirms the presence of two ARDS subphenotypes that can be accurately identified with a limited number of variables and that responded differently to randomly assigned fluid management. These findings support the presence of ARDS subtypes that may require different treatment approaches

Advances in methods for determining fecundity: application of the new methods to some marine fishes

17 pages, 9 figures, 6 tables.Estimation of individual egg production (realized fecundity) is a key step either to understand the stock and recruit relationship or to carry out fisheries-independent assessment of spawning stock biomass using egg production methods. Many f ish are highly fecund and their ovaries may weigh over a kilogram; therefore the work time can be consuming and require large quantities of toxic fixative. Recently it has been shown for Atlantic cod (Gadus morhua) that image analysis can automate fecundity determination using a power equation that links follicles per gram ovary to the mean vitellogenic follicular diameter (the autodiametric method). In this article we demonstrate the precision of the autodiametric method applied to a range of species with different spawning strategies during maturation and spawning. A new method using a solid displacement pipette to remove quantitative fecundity samples (25, 50, 100, and 200 milligram [mg]) is evaluated, as are the underlying assumptions to effectively fix and subsample the ovary. Finally, we demonstrate the interpretation of dispersed formaldehyde-fixed ovarian samples (whole mounts) to assess the presence of atretic and postovulatory follicles to replace labor intensive histology. These results can be used to estimate down regulation (production of atretic follicles) of fecundity during maturation.T his study was jointly funded under Eu ropean Union Frame Work V Q5RS -2002 - 01825 and the Institutes in England (Department of the Environment, Food, and Rural Affairs), Norway (Institute of Marine Research), and Spain (Consejo Superior de Investigaciones Científ icas, and A ZTI Tecnalia (publication number 424))Peer reviewe

Economics of education research: a review and future prospects

In this paper we offer an appraisal of the economics of education research area, charting its history as a field and discussing the ways in which economists have contributed both to education research and to education policy-making. In particular, we highlight the theoretical and methodological contributions that economists have made to the field of education during the last 50 years. Despite the success of the economics of education as a field of inquiry, we argue that some of the contributions made by economists could be limited if the economics of education is seen as quite distinct from the other disciplines working in the field of education. In these areas of common interest, economists need to work side by side with the other major disciplines in the field of education if their contribution to the field is to be maximised, particularly in terms of applying improved methodology. We conclude that the study of education acquisition and its economic and social impact in the economics of education research area is very likely to remain a fertile research ground. Acknowledgement

Two-microphone spatial filtering provides speech reception benefits for cochlear implant users in difficult acoustic environments

This article introduces and provides an assessment of a spatial-filtering algorithm based on two closely-spaced (∼1 cm) microphones in a behind-the-ear shell. The evaluated spatial-filtering algorithm used fast (∼10 ms) temporal-spectral analysis to determine the location of incoming sounds and to enhance sounds arriving from straight ahead of the listener. Speech reception thresholds (SRTs) were measured for eight cochlear implant (CI) users using consonant and vowel materials under three processing conditions: An omni-directional response, a dipole-directional response, and the spatial-filtering algorithm. The background noise condition used three simultaneous time-reversed speech signals as interferers located at 90°, 180°, and 270°. Results indicated that the spatial-filtering algorithm can provide speech reception benefits of 5.8 to 10.7 dB SRT compared to an omni-directional response in a reverberant room with multiple noise sources. Given the observed SRT benefits, coupled with an efficient design, the proposed algorithm is promising as a CI noise-reduction solution.National Institutes of Health (U.S.) (Grant R01 DC 000117)National Institutes of Health (U.S.) (Grant R01 DC DC7152)National Institutes of Health (U.S.) (Grant 2R44DC010524-02

‘What are you going to do, confiscate their passports?’ Professional perspectives on cross-border reproductive travel

Objective: This article reports findings from a UK-based study which explored the phenomenon of overseas travel for fertility treatment. The first phase of this project aimed to explore how infertility clinicians and others professionally involved in fertility treatment understand the nature and consequences of cross-border reproductive travel. Background: There are indications that, for a variety of reasons, people from the UK are increasingly travelling across national borders to access assisted reproductive technologies. While research with patients is growing, little is known about how ‘fertility tourism’ is perceived by health professionals and others with a close association with infertility patients. Methods: Using an interpretivist approach, this exploratory research included focussed discussions with 20 people professionally knowledgeable about patients who had either been abroad or were considering having treatment outside the UK. Semi-structured interviews were recorded, transcribed verbatim and subjected to a thematic analysis. Results: Three conceptual categories are developed from the data: ‘the autonomous patient’; ‘cross-border travel as risk’, and ‘professional responsibilities in harm minimisation’. Professionals construct nuanced, complex and sometimes contradictory narratives of the ‘fertility traveller’, as vulnerable and knowledgeable; as engaged in risky behaviour and in its active minimisation. Conclusions: There is little support for the suggestion that states should seek to prevent cross-border treatment. Rather, an argument is made for less direct strategies to safeguard patient interests. Further research is required to assess the impact of professional views and actions on patient choices and patient experiences of treatment, before, during and after travelling abroad

Border skirmishes and the question of belonging: An authoethnographic account of everyday exclusion in multicultural society

Transnational migration has transformed most European countries, making the problem of how to 'integrate' an increasingly popular topic in public debates and social policy. It is assumed that as long as the newcomer learns the language, adapts to the local customs and finds work, s/he will be integrated and welcomed with open arms as a full-fledged member of society. Based on an autoethnography of our experiences as US-born, long-term and fully 'integrated' residents of the Netherlands, one of Europe's most multicultural societies, we have explored some of the subtle, well-intentioned practices of distancing and exclusion that are part of the fabric of everyday life. We will show how, contrary to the official discourse of integration, 'Dutch-ness' as a white/ethnic national identity is continuously constructed as a 'we', which excludes all 'others'. And, indeed, we have discovered that, paradoxically, the closer the 'other' comes to being completely assimilated into Dutch society, the more the symbolic borders of national belonging may need to be policed and tightened. © The Author(s) 2011

Joining the conspiracy? Negotiating ethics and emotions in researching (around) AIDS in southern Africa

AIDS is an emotive subject, particularly in southern Africa. Among those who have been directly affected by the disease, or who perceive themselves to be personally at risk, talking about AIDS inevitably arouses strong emotions - amongst them fear, distress, loss and anger. Conventionally, human geography research has avoided engagement with such emotions. Although the ideal of the detached observer has been roundly critiqued, the emphasis in methodological literature on 'doing no harm' has led even qualitative researchers to avoid difficult emotional encounters. Nonetheless, research is inevitably shaped by emotions, not least those of the researchers themselves. In this paper, we examine the role of emotions in the research process through our experiences of researching the lives of 'Young AIDS migrants' in Malawi and Lesotho. We explore how the context of the research gave rise to the production of particular emotions, and how, in response, we shaped the research, presenting a research agenda focused more on migration than AIDS. This example reveals a tension between universalised ethics expressed through ethical research guidelines that demand informed consent, and ethics of care, sensitive to emotional context. It also demonstrates how dualistic distinctions between reason and emotion, justice and care, global and local are unhelpful in interpreting the ethics of research practice

Reproducible protocols for metagenomic analysis of human faecal phageomes

peer-reviewedAll sequence data used in the analyses were deposited in the Sequence read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA407341. Sample IDs, meta data and corresponding accession numbers are summarised in Additional file 2: Table S2. All raw count tables, 16S taxonomic assignments, BLAST top hits for viral contigs and R code used for the analysis are available at (https://figshare.com/s/71163558b4f78e3e7ed6).Background Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing. Results Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples. Conclusions The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results