Evaluating semi-supervision methods for medical image segmentation: applications in cardiac magnetic resonance imaging

PURPOSE: Purpose Neural networks have potential to automate medical image segmentation but require expensive labeling efforts. While methods have been proposed to reduce the labeling burden, most have not been thoroughly evaluated on large, clinical datasets or clinical tasks. We propose a method to train segmentation networks with limited labeled data and focus on thorough network evaluation. APPROACH: We propose a semi-supervised method that leverages data augmentation, consistency regularization, and pseudolabeling and train four cardiac magnetic resonance (MR) segmentation networks. We evaluate the models on multiinstitutional, multiscanner, multidisease cardiac MR datasets using five cardiac functional biomarkers, which are compared to an expert’s measurements using Lin’s concordance correlation coefficient (CCC), the within-subject coefficient of variation (CV), and the Dice coefficient. RESULTS: The semi-supervised networks achieve strong agreement using Lin’s CCC (>0.8), CV similar to an expert, and strong generalization performance. We compare the error modes of the semi-supervised networks against fully supervised networks. We evaluate semi-supervised model performance as a function of labeled training data and with different types of model supervision, showing that a model trained with 100 labeled image slices can achieve a Dice coefficient within 1.10% of a network trained with 16,000+ labeled image slices. CONCLUSION: We evaluate semi-supervision for medical image segmentation using heterogeneous datasets and clinical metrics. As methods for training models with little labeled data become more common, knowledge about how they perform on clinical tasks, how they fail, and how they perform with different amounts of labeled data is useful to model developers and users

Reader and author gender and genre in Goodreads

This is an accepted manuscript of an article published by SAGE Publishing in Journal of Librarianship & Information Science on 01/05/2017, available online: https://doi.org/10.1177/0961000617709061 The accepted version of the publication may differ from the final published version.There are known gender differences in book preferences in terms of both genre and author gender but their extent and causes are not well understood. It is unclear whether reader preferences for author genders occur within any or all genres and whether readers evaluate books differently based on author genders within specific genres. This article exploits a major source of informal book reviews, the Goodreads.com website, to assess the influence of reader and author genders on book evaluations within genres. It uses a quantitative analysis of 201,560 books and their reviews, focusing on the top 50 user-specified genres. The results show strong gender differences in the ratings given by reviewers to books within genres, such as female reviewers rating contemporary romance more highly, with males preferring short stories. For most common book genres, reviewers give higher ratings to books authored by their own gender, confirming that gender bias is not confined to the literary elite. The main exception is the comic book, for which male reviewers prefer female authors, despite their scarcity. A word frequency analysis suggested that authors wrote, and reviewers valued, gendered aspects of books within a genre. For example, relationships and romance were disproportionately mentioned by women in mystery and fantasy novels. These results show that, perhaps for the first time, it is possible to get large scale evidence about the reception of books by typical readers, if they post reviews online

Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure

BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage

The prevalence of common mental disorders and PTSD in the UK military: using data from a clinical interview-based study

<p>Abstract</p> <p>Background</p> <p>The mental health of the Armed Forces is an important issue of both academic and public interest. The aims of this study are to: a) assess the prevalence and risk factors for common mental disorders and post traumatic stress disorder (PTSD) symptoms, during the main fighting period of the Iraq War (TELIC 1) and later deployments to Iraq or elsewhere and enlistment status (regular or reserve), and b) compare the prevalence of depression, PTSD symptoms and suicidal ideation in regular and reserve UK Army personnel who deployed to Iraq with their US counterparts.</p> <p>Methods</p> <p>Participants were drawn from a large UK military health study using a standard two phase survey technique stratified by deployment status and engagement type. Participants undertook a structured telephone interview including the Patient Health Questionnaire (PHQ) and a short measure of PTSD (Primary Care PTSD, PC-PTSD). The response rate was 76% (821 participants).</p> <p>Results</p> <p>The weighted prevalence of common mental disorders and PTSD symptoms was 27.2% and 4.8%, respectively. The most common diagnoses were alcohol abuse (18.0%) and neurotic disorders (13.5%). There was no health effect of deploying for regular personnel, but an increased risk of PTSD for reservists who deployed to Iraq and other recent deployments compared to reservists who did not deploy. The prevalence of depression, PTSD symptoms and subjective poor health were similar between regular US and UK Iraq combatants.</p> <p>Conclusion</p> <p>The most common mental disorders in the UK military are alcohol abuse and neurotic disorders. The prevalence of PTSD symptoms remains low in the UK military, but reservists are at greater risk of psychiatric injury than regular personnel.</p

Nonsteroidal anti-inflammatory drugs (NSAIDs), cyxlooxygenase-2 selective inhibitors (coxibs) and gastrointestinal harm: review of clinical trials and clinical practice

BACKGROUND: Gastrointestinal harm, known to occur with NSAIDs, is thought to be lower with NSAID and gastroprotective agent, and with inhibitors selective to cyclooxygenase-2 (coxibs) at usual plasma concentrations. We examine competing strategies for available evidence of reduced gastrointestinal bleeding in clinical trials and combine this evidence with evidence from clinical practice on whether the strategies work in the real world, whether guidance on appropriate prescribing is followed, and whether patients adhere to the strategies. METHODS: We used a series of systematic literature searches to find full publications of relevant studies for evidence about the efficacy of these different gastroprotection strategies in clinical trials, and for evidence that they worked and were adhered to in clinical practice – whether they were effective. We chose to use good quality systematic reviews and meta-analyses when they were available. RESULTS: Evidence of efficacy of coxibs compared to NSAIDs for upper gastrointestinal bleeding was strong, with consistent reductions in events of about 50% in large randomised trials (34,460 patients), meta-analyses of randomised trials (52,474 patients), and large observational studies in clinical practice (3,093 bleeding events). Evidence on the efficacy of NSAID plus gastroprotection with acid suppressants (proton pump inhibitors, PPIs, and histamine antagonists, H2As) was based mainly on the surrogate measure of endoscopic ulcers. The limited information on damage to the bowel suggested that NSAID plus PPI was more damaging than coxibs. Eleven observational studies studied 1.6 million patients, of whom 911,000 were NSAID users, and showed that 76% (range 65% to 90%) of patients with at least one gastrointestinal risk factor received no prescription for gastroprotective agent with an NSAID. The exception was a cohort of US veterans with previous gastrointestinal bleeding, where 75% had gastroprotection with an NSAID. When gastroprotection was prescribed, it was often described as inadequate. A single study suggested that patient adherence to prescribed gastroprotection was low. CONCLUSION: Evidence for efficacy of gastroprotection strategies with NSAIDs is limited. In clinical practice few patients who need gastroprotection get it, and those who get it may not take it. For coxibs, gastroprotection is inherent, although probably not complete

Combined effects of precipitation and nitrogen deposition on native and invasive winter annual production in California deserts

Primary production in deserts is limited by soil moisture and N availability, and thus is likely to be influenced by both anthropogenic N deposition and precipitation regimes altered as a consequence of climate change. Invasive annual grasses are particularly responsive to increases in N and water availabilities, which may result in competition with native forb communities. Additionally, conditions favoring increased invasive grass production in arid and semi-arid regions can increase fire risk, negatively impacting woody vegetation that is not adapted to fire. We conducted a seeded garden experiment and a 5-year field fertilization experiment to investigate how winter annual production is altered by increasing N supply under a range of water availabilities. The greatest production of invasive grasses and native forbs in the garden experiment occurred under the highest soil N (inorganic N after fertilization = 2.99 g m−2) and highest watering regime, indicating these species are limited by both water and N. A classification and regression tree (CART) analysis on the multi-year field fertilization study showed that winter annual biomass was primarily limited by November–December precipitation. Biomass exceeded the threshold capable of carrying fire when inorganic soil N availability was at least 3.2 g m−2 in piñon-juniper woodland. Due to water limitation in creosote bush scrub, biomass exceeded the fire threshold only under very wet conditions regardless of soil N status. The CART analyses also revealed that percent cover of invasive grasses and native forbs is primarily dependent on the timing and amount of precipitation and secondarily dependent on soil N and site-specific characteristics. In total, our results indicate that areas of high N deposition will be susceptible to grass invasion, particularly in wet years, potentially reducing native species cover and increasing the risk of fire

Tremor in multiple sclerosis

Tremor is estimated to occur in about 25 to 60 percent of patients with multiple sclerosis (MS). This symptom, which can be severely disabling and embarrassing for patients, is difficult to manage. Isoniazid in high doses, carbamazepine, propranolol and gluthetimide have been reported to provide some relief, but published evidence of effectiveness is very limited. Most trials were of small size and of short duration. Cannabinoids appear ineffective. Tremor reduction can be obtained with stereotactic thalamotomy or thalamic stimulation. However, the studies were small and information on long-term functional outcome is scarce. Physiotherapy, tremor reducing orthoses, and limb cooling can achieve some functional improvement. Tremor in MS remains a significant challenge and unmet need, requiring further basic and clinical research

The Nature Index: A General Framework for Synthesizing Knowledge on the State of Biodiversity

The magnitude and urgency of the biodiversity crisis is widely recognized within scientific and political organizations. However, a lack of integrated measures for biodiversity has greatly constrained the national and international response to the biodiversity crisis. Thus, integrated biodiversity indexes will greatly facilitate information transfer from science toward other areas of human society. The Nature Index framework samples scientific information on biodiversity from a variety of sources, synthesizes this information, and then transmits it in a simplified form to environmental managers, policymakers, and the public. The Nature Index optimizes information use by incorporating expert judgment, monitoring-based estimates, and model-based estimates. The index relies on a network of scientific experts, each of whom is responsible for one or more biodiversity indicators. The resulting set of indicators is supposed to represent the best available knowledge on the state of biodiversity and ecosystems in any given area. The value of each indicator is scaled relative to a reference state, i.e., a predicted value assessed by each expert for a hypothetical undisturbed or sustainably managed ecosystem. Scaled indicator values can be aggregated or disaggregated over different axes representing spatiotemporal dimensions or thematic groups. A range of scaling models can be applied to allow for different ways of interpreting the reference states, e.g., optimal situations or minimum sustainable levels. Statistical testing for differences in space or time can be implemented using Monte-Carlo simulations. This study presents the Nature Index framework and details its implementation in Norway. The results suggest that the framework is a functional, efficient, and pragmatic approach for gathering and synthesizing scientific knowledge on the state of biodiversity in any marine or terrestrial ecosystem and has general applicability worldwide

Dietary Protein and Blood Pressure: A Systematic Review

Background - Elevated blood pressure (BP), which is a major risk factor for cardiovascular disease, is highly prevalent worldwide. Recently, interest has grown in the role of dietary protein in human BP. We performed a systematic review of all published scientific literature on dietary protein, including protein from various sources, in relation to human BP. Methodology/Principal Findings - We performed a MEDLINE search and a manual search to identify English language studies on the association between protein and blood pressure, published before June 2010. A total of 46 papers met the inclusion criteria. Most observational studies showed no association or an inverse association between total dietary protein and BP or incident hypertension. Results of biomarker studies and randomized controlled trials indicated a beneficial effect of protein on BP. This beneficial effect may be mainly driven by plant protein, according to results in observational studies. Data on protein from specific sources (e.g. from fish, dairy, grain, soy, and nut) were scarce. There was some evidence that BP in people with elevated BP and/or older age could be more sensitive to dietary protein. Conclusions/Significance - In conclusion, evidence suggests a small beneficial effect of protein on BP, especially for plant protein. A blood pressure lowering effect of protein may have important public health implications. However, this warrants further investigation in randomized controlled trials. Furthermore, more data are needed on protein from specific sources in relation to BP, and on the protein-BP relation in population subgroup