3D Convolutional Neural Networks for the diagnosis of 6 unique pathologies on head CT

Introduction: Head CT scans are a standard first-line tool used by physicians in the diagnosis of neurological pathologies. Recently, the development of deep learning models such as convolutional neural networks (CNNs) has allowed the rapid identification of bleeds and other pathologies on CT scans. This study aims to show that by training 3D CNNs with a larger, curated dataset, a more comprehensive list of potential diagnoses can be included in the detailed model. Methods: A retrospective study was performed using a dataset of 66,000 head CT studies from the Thomas Jefferson University health system. Studies were acquired using a natural language processor that searched for 60 different diagnoses, and the scans were then grouped into six distinct classes. Images were preprocessed by converting CT Hounsfield Units to greyscale, cropping to remove negative area, normalizing pixel values, and resizing to fit the input dimensions of the neural network. To automatically classify the studies, a three-dimensional residual neural network (3D-ResNet), was trained using 80% of the dataset as a training set and 20% of the dataset as a test set. Results: To achieve the most accurate results, a 3D-ResNet with 34 residual layers was used. Following the training of the 3D-RESNET, the model achieved an accuracy of 0.47 on the test set and 0.915 on the training set. Discussion: These results show a promising initial step toward machine-assisted diagnosis of head CT scans. As more potential diagnoses are added to models, the utility of the models increases, and more studies can be quickly processed. Going forward, neural networks could potentially be used to prioritize radiology worklists and perform automatic diagnosis of urgent scans

Ethnobiology : the missing link in ecology and evolution

Evolutionary biologists and ecologists increasingly appreciate the value of local knowledge of human communities for research into the past, present, and future of biodiversity. However, there are often significant problems accessing and interpreting this knowledge. Here, we argue that closer interaction with ethnobiologists, who study the relation between humans and the natural world, will enable local knowledge to be better applied in ecological and evolutionary biological research. This will provide more comprehensive answers to the scientific questions being asked, and will result in improved engagement with both academic and non-academic communities

MOTMOT:Models of trait macroevolution on trees (an update)

The disparity in species’ traits arises through variation in the tempo and mode of evolution over time and between lineages. Understanding these patterns is a core goal in evolutionary biology. Here we present the comprehensively updated r package MOTMOT: Models Of Trait Macroevolution On Trees that contains methods to fit and test models of continuous trait evolution on phylogenies of extant and extinct species. MOTMOT provides functions to investigate a range of evolutionary hypotheses, including flexible approaches to investigate heterogeneous rates and modes of evolution, models of trait change under interspecific competition and patterns of trait change across significant evolutionary transitions such as mass extinctions. We introduce and test novel algorithms of heterogeneous tempo and mode of evolution that allow for phylogeny-wide shifts in evolution at specific times on a tree. We use these new MOTMOT functions to highlight an exceptionally high rate of mammalian body mass evolution for 10 million years following the Cretaceous–Palaeogene mass extinction. These methods provide biologists and palaeontologists with the tools to analyse continuous trait data on phylogenies, including large trees of up to thousands of species.</p

Understanding appeals of video games for readers’ advisory and recommendation

Information for original publication: Lee, Jin Ha et al. Understanding Appeals of Video Games for Readers' Advisory and Recommendation. Reference & User Services Quarterly, [S.l.], v. 57, n. 2, p. 127-139, dec. 2017. ISSN 1094-9054. Available at: . doi:http://dx.doi.org/10.5860/rusq.57.2.6529.Despite their increasing popularity and inclusion in library collections, video games are rarely suggested in library advisory or recommendation services. In this work, we use the concept of appeals from existing literature in readers' advisory and media studies to understand what attracts people to play certain games. Based on 1,257 survey responses, we identify sixteen different appeals of video games and elaborate how these appeals are expressed in users' terms. We envision these appeals can serve as an additional access point for video games and will be particularly useful for recommendation and advisory services. In addition, we also examined the correlation between appeals and common game genres. The relationships between appeals and genres observed from our data support our argument that appeals can serve as a complementary access point to result in more diversified sets of recommendations across genres. In our future work, we plan to further investigate individual appeals such as mood and narrative across multiple types of media

Local food systems: concepts, impacts, and issues

Consumer demand for food that is locally produced,marketed, and consumed is generating increased interest in local food throughout the United States. As interest grows, so do questions about what constitutes local food and what characterizes local food systems. What Is the Issue? This study provides a comprehensive literature-review-based overview of the current understanding of local food systems, including: alternative defi nitions; estimates of market size and reach; descriptions of the characteristics of local food consumers and producers; and an examination of early evidence on the economic and health impacts of such systems. What Did the Study Find? There is no generally accepted definition of “local” food. Though “local” has a geographic connotation, there is no consensus on a definition in terms of the distance between production and consumption. Definitions related to geographic distance between production and sales vary by regions, companies, consumers, and local food markets. According to the definition adopted by the U.S. Congress in the 2008 Food, Conservation, and Energy Act,the total distance that a product can be transported and still be considered a “locally or regionally produced agricultural food product” is less than 400 miles from its origin, or within the State in which it is produced. Definitions based on market arrangements, including direct-to-consumer arrangements such as regional farmers’ markets, or direct-to-retail/foodservice arrangements such as farm sales to schools, are well-recognized categories and are used in this report to provide statistics on the market development of local foods. Local food markets account for a small but growing share of total U.S. agricultural sales. • Direct-to-consumer marketing amounted to $1.2 billion in current dollar sales in 2007, according to the 2007 Census of Agriculture, compared with$551 million in 1997. • Direct-to-consumer sales accounted for 0.4 percent of total agricultural sales in 2007, up from 0.3 percent in 1997. If nonedible products are excluded from total agricultural sales, direct-to consumer sales accounted for 0.8 percent of agricultural sales in 2007. • The number of farmers’ markets rose to 5,274 in 2009, up from 2,756 in 1998 and 1,755 in 1994, according to USDA’s Agricultural Marketing Service. • In 2005, there were 1,144 community-supported agriculture organizations, up from 400 in 2001 and 2 in 1986, according to a study by the National Center for Appropriate Technology. In early 2010, estimates exceeded 1,400, but the number could be much larger. • The number of farm to school programs, which use local farms as food suppliers for school meals programs and promote relationships between schools and farms, increased to 2,095 in 2009, up from 400 in 2004 and 2 in the 1996-97 school year, according to the National Farm to School Network. Data from the 2005 School Nutrition and Dietary Assessment Survey, sponsored by USDA’s Food and Nutrition Service, showed that 14 percent of school districts participated in Farm to School programs, and 16 percent reported having guidelines for purchasing locally grown produce. Production of locally marketed food is more likely to occur on small farms located in or near metropolitan counties. Local food markets typically involve small farmers, heterogeneous products, and short supply chains in which farmers also perform marketing functions, including storage, packaging, transportation, distribution, and advertising. According to the 2007 U.S. Census of Agriculture, most farms that sell directly to consumers are small farms with less than $50,000 in total farm sales, located in urban corridors of the Northeast and the West Coast. In 2007, direct-to-consumer sales accounted for a larger share of sales for small farms, as defi ned above, than for medium-sized farms (total farm sales of$50,000 to $499,999) and large farms (total farm sales of$500,000 or more). Produce farms engaged in local marketing made 56 percent of total agricultural direct sales to consumers, while accounting for 26 percent of all farms engaged in direct-to-consumer marketing. Direct-to-consumer sales are higher for the farms engaged in other entrepreneurial activities, such as organic production, tourism, and customwork (planting, plowing, harvesting, etc. for others), than for other farms. In 2007, direct sales by all U.S. farms surpassed customwork to become the leading on-farm entrepreneurial activity in terms of farm household participation. Barriers to local food-market entry and expansion include: capacity constraints for small farms and lack of distribution systems for moving local food into mainstream markets; limited research, education, and training for marketing local food; and uncertainties related to regulations that may affect local food production, such as food safety requirements. Consumers who value high-quality foods produced with low environmental impact are willing to pay more for locally produced food. Several studies have explored consumer preferences for locally produced food. Motives for “buying local” include perceived quality and freshness of local food and support for the local economy. Consumers who are willing to pay higher prices for locally produced foods place importance on product quality, nutritional value, methods of raising a product and those methods’ effects on the environment, and support for local farmers. Federal, State, and local government programs increasingly support local food systems. Many existing government programs and policies support local food initiatives, and the number of such programs is growing. Federal policies have grown over time to include the Community Food Project Grants Program, the WIC Farmers’ Market Nutrition Program, Senior Farmers’ Market Nutrition Program, Federal State Marketing Improvement Program, National Farmers’ Market Promotion Program, Specialty Crop Block Grant Program, and the Community Facilities Program. State and local policies include those related to farm-to-institution procurement, promotion of local food markets, incentives for low-income consumers to shop at farmers’ markets, and creation of State Food Policy Councils to discuss opportunities and potential impact of government intervention. (WIC is the acronym for the Special Supplemental Nutrition Program for Women, Infants, and Children). As of early 2010, there were few studies on the impact of local food markets on economic development, health, or environmental quality. • Empirical research has found that expanding local food systems in a community can increase employment and income in that community. • Empirical evidence is insuffi cient to determine whether local food availability improves diet quality or food security. • Life-cycle assessments—analyses of energy use at all stages of the food system including consumption and disposal—suggest that localization can but does not necessarily reduce energy use or greenhouse gas emissions. How Was the Study Conducted? Existing analyses of local food markets by universities, government agencies, national nonprofit organizations, and others of local food markets were synthesized to evaluate the definition of local foods and the effects of local food systems on economic development, health and nutrition, food security, and energy use and greenhouse gas emissions. The report’s content relies on data collected through the 2007 Census of Agriculture, as well as other surveys by USDA’s Agricultural Marketing Service, the National Farm to School Network, university extension departments, and others, to provide a comprehensive picture of types of local food markets, their characteristics, and their importance over time.Local food systems; farmers’ markets; direct-to-consumer marketing; direct-to-retail/foodservice marketing; community supported agriculture; farm to school programs; Farmers’ Market Promotion Program; food miles; ERS; USDA

Dietary amino acids and risk of stroke subtypes: a prospective analysis of 356,000 participants in seven European countries

Purpose Previously reported associations of protein-rich foods with stroke subtypes have prompted interest in the assessment of individual amino acids. We examined the associations of dietary amino acids with risks of ischaemic and haemorrhagic stroke in the EPIC study. Methods We analysed data from 356,142 participants from seven European countries. Dietary intakes of 19 individual amino acids were assessed using validated country-specific dietary questionnaires, calibrated using additional 24-h dietary recalls. Multivariable-adjusted Cox regression models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) of ischaemic and haemorrhagic stroke in relation to the intake of each amino acid. The role of blood pressure as a potential mechanism was assessed in 267,642 (75%) participants. Results After a median follow-up of 12.9 years, 4295 participants had an ischaemic stroke and 1375 participants had a haemorrhagic stroke. After correction for multiple testing, a higher intake of proline (as a percent of total protein) was associated with a 12% lower risk of ischaemic stroke (HR per 1 SD higher intake 0.88; 95% CI 0.82, 0.94). The association persisted after mutual adjustment for all other amino acids, systolic and diastolic blood pressure. The inverse associations of isoleucine, leucine, valine, phenylalanine, threonine, tryptophan, glutamic acid, serine and tyrosine with ischaemic stroke were each attenuated with adjustment for proline intake. For haemorrhagic stroke, no statistically significant associations were observed in the continuous analyses after correcting for multiple testing. Conclusion Higher proline intake may be associated with a lower risk of ischaemic stroke, independent of other dietary amino acids and blood pressure

Selective pressures on genomes in molecular evolution

We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms.Comment: 16 pages, 3 figures, to be published in J. theor. Biolog

Shape analysis of the StW 578 calotte from Jacovec Cavern, Gauteng (South Africa)

The fossiliferous deposits within the lower-lying Jacovec Cavern in the locality of Sterkfontein yielded valuable hominin remains, including the StW 578 specimen. Because StW 578 mainly preserves the calotte, the taxonomic status of this specimen has been a matter of discussion. Within this context, here we employed high-resolution microtomography and a landmark-free registration method to explore taxonomically diagnostic features in the external surface of the StW 578 calotte. Our comparative sample included adult humans and common chimpanzees as well as one Australopithecus africanus specimen (Sts 5). We partially restored the StW 578 calotte digitally and compared it to extant specimens and Sts 5 using a landmark-free registration based on smooth and invertible surface deformation. Our comparative shape analysis reveals morphological differences with extant humans, especially in the frontal bones, and with extant chimpanzees, as well as intriguing specificities in the morphology of the StW 578 parietal bones. Lastly, our study suggests morphological proximity between StW 578 and Sts 5. Given the intimate relationship between the brain and the braincase, as well as the integration of the hominin face and neurocranium, we suggest that cranial vault shape differences between StW 578 and extant humans, if confirmed by further analyses, could be either explained by differences in brain surface morphology or in the face. Besides providing additional information about the morphology of the Jacovec calotte that will be useful in future taxonomic discussion, this study introduces a new protocol for the landmark-free analysis of fossil hominin cranial shape.Significance:• We provide further information on the enigmatic fossil specimen StW 578.• We introduce a new approach for the morphological study of fossil hominin crania.• We highlight morphological similarities between StW 578 and ‘Mrs Ples’

METRIC-EF: magnetic resonance enterography to predict disabling disease in newly diagnosed Crohn's disease-protocol for a multicentre, non-randomised, single-arm, prospective study

INTRODUCTION: Crohn's disease (CD) is characterised by discontinuous, relapsing enteric inflammation. Instituting advanced therapies at an early stage to suppress inflammation aims to prevent future complications such as stricturing or penetrating disease, and subsequent surgical resection. Therapeutics are effective but associated with certain side-effects and relatively expensive. There is therefore an urgent need for robust methods to predict which newly diagnosed patients will develop disabling disease, to identify patients who are most likely to benefit from early, advanced therapies. We aim to determine if magnetic resonance enterography (MRE) features at diagnosis improve prediction of disabling CD within 5 years of diagnosis. METHODS AND ANALYSIS: We describe the protocol for a multicentre, non-randomised, single-arm, prospective study of adult patients with newly diagnosed CD. We will use patients already recruited to the METRIC study and extend their clinical follow-up, as well as a separate group of newly diagnosed patients who were not part of the METRIC trial (MRE within 3 months of diagnosis), to ensure an adequate sample size. Follow-up will extend for at least 4 years. The primary outcome is to evaluate the comparative predictive ability of prognostic models incorporating MRE severity scores (Magnetic resonance Enterography Global Score (MEGS), simplified MAgnetic Resonance Index of Activity (sMaRIA) and Lémann Index) versus models using standard characteristics alone to predict disabling CD (modified Beaugerie definition) within 5 years of new diagnosis. ETHICS AND DISSEMINATION: This study protocol achieved National Health Service Research Ethics Committee (NHS REC), London-Hampstead Research Ethics Committee approval (IRAS 217422). Our findings will be disseminated via conference presentations and peer-reviewed publications. TRIAL REGISTRATION NUMBER: ISRCTN76899103

A systematic review of compositional data analysis studies examining associations between sleep, sedentary behaviour, and physical activity with health outcomes in adults

This systematic review determined if the composition of time spent in movement behaviours (i.e., sleep, sedentary behaviour (SED), light physical activity, and moderate-to-vigorous physical activity (MVPA)) is associated with health in adults. Five electronic databases were searched in August 2019. Studies were eligible for inclusion if they were peer-reviewed, examined community-dwelling adults, and used compositional data analysis to examine the associations between the composition of time spent in movement behaviours and health outcomes. Eight studies (7 cross-sectional, 1 prospective cohort) of >12 000 unique participants were included. Findings indicated that the 24-h movement behaviour composition was associated with all-cause mortality (1 of 1 analyses), adiposity (4 of 4 analyses), and cardiometabolic biomarkers (8 of 15 analyses). Reallocating time into MVPA from other movement behaviours was associated with favourable changes to most health outcomes and taking time out of SED and reallocating it into other movement behaviours was associated with favourable changes to all-cause mortality. The quality of evidence was very low for all health outcomes. In conclusion, these findings support the notion that the composition of movement across the entire 24-h day matters, and that recommendations for sleep, SED, and physical activity should be combined into a single public health guideline. (PROSPERO registration no.: CRD42019121641.) Novelty The 24-h movement behaviour composition is associated with a variety of health outcomes. Reallocating time into MVPA is favourably associated with health. Reallocating time out of SED is associated with favourable changes to mortality risk