Gross Brain Morphology in the Yellow Stingray, Urobatis jamaicensis

The yellow stingray, Urobatis jamaicensis (family Urolophidae), a short-lived, relatively small elasmobranch species (35--40 cm total length), is a common inhabitant of hard bottom and coral reef communities in southeastern Florida and many parts of the Caribbean. A paucity of published studies deal with the yellow stingray, none however on the gross morphology of its nervous system. The gross brain structure of the yellow stingray is compared with previously published studies on other batoid elasmobranchs. The external brain structure of Urobatis jamaicensis was similar to that reported for other Dasyatids, including presence of an asymmetric cerebellum. The bilaterally symmetric brain is well developed and quite large in proportion to body size (≈1--2% bw). Stingrays generally possess a brain three to 10 times the size of their sister groups, the electric rays, guitarfish, and skates (Northcutt, 1989), the yellow stingray is no exception

Authors' opinions on publication in relation to annual performance assessment

<p>Abstract</p> <p>Background</p> <p>In the past 50 years there has been a substantial increase in the volume of published research and in the number of authors per scientific publication. There is also significant pressure exerted on researchers to produce publications. Thus, the purpose of this study was to survey corresponding authors in published medical journals to determine their opinion on publication impact in relation to performance review and promotion.</p> <p>Methods</p> <p>Cross-sectional survey of corresponding authors of original research articles published in June 2007 among 72 medical journals. Measurement outcomes included the number of publications, number of authors, authorship order and journal impact factor in relation to performance review and promotion.</p> <p>Results</p> <p>Of 687 surveys, 478 were analyzed (response rate 69.6%). Corresponding authors self-reported that number of publications (78.7%), journal impact factor (67.8%) and being the first author (75.9%) were most influential for their annual performance review and assessment. Only 17.6% of authors reported that the number of authors on a manuscript was important criteria for performance review and assessment. A higher percentage of Asian authors reported that the number of authors was key to performance review and promotion (41.4% versus 7.8 to 22.2%). compared to authors from other countries.</p> <p>Conclusions</p> <p>The number of publications, authorship order and journal impact factor were important factors for performance reviews and promotion at academic and non-academic institutes. The number of authors was not identified as important criteria. These factors may be contributing to the increase in the number of authors per publication.</p

New approach combining food value with nutrient budgeting provides insights into the value of alternative farming systems

Sustainable farming systems provide food for humans while balancing nutrient management. Inclusion or exclusion of livestock has nutrient management implications, as livestock produce food from otherwise inedible crops and their manure is a valuable soil conditioner. However, plant-based diets are becoming more widespread due to perceived environmental benefits. We measure both food production in terms of nourishment to humans (in this study measured by protein, fat, starch and sugar production) and nutrient sustainability in terms of fertiliser use of six rotational farming systems with differences in nutrient management approaches. The arable practices included were the application of synthetic fertilisers, a range of organic amendments, incorporation of crop residues and legume cultivation. Livestock and associated products were included in some systems but excluded in others. The production of protein, fat, starch and sugar was combined with the balance of nitrogen (N), phosphorus (P) and potassium (K) into an overall measure of nutrient use efficiency of human macronutrient production. Across all systems considered, N use efficiency (5-13 kg protein/kg applied N) was lower than P (84-772 kg protein/kg applied P) or K (63-2060 kg protein/kg applied K), and combining synthetic fertiliser use with organic amendment applications raised production significantly while balancing P and K management, regardless of which organic amendment was used. Legume-supported rotations without livestock produced more protein, starch and sugar per unit area than those with livestock. Nutrient balances and nutrient use efficiencies were more sensitive to management changes than purely food production. Using this approach allowed us to identify areas for improvement in food production based on the specific nutritional value of offtakes as opposed to yield overall

New approach combining food value with nutrient budgeting provides insights into the value of alternative farming systems

Sustainable farming systems provide food for humans while balancing nutrient management. Inclusion or exclusion of livestock has nutrient management implications, as livestock produce food from otherwise inedible crops and their manure is a valuable soil conditioner. However, plant-based diets are becoming more widespread due to perceived environmental benefits. We measure both food production in terms of nourishment to humans (in this study measured by protein, fat, starch and sugar production) and nutrient sustainability in terms of fertiliser use of six rotational farming systems with differences in nutrient management approaches. The arable practices included were the application of synthetic fertilisers, a range of organic amendments, incorporation of crop residues and legume cultivation. Livestock and associated products were included in some systems but excluded in others. The production of protein, fat, starch and sugar was combined with the balance of nitrogen (N), phosphorus (P) and potassium (K) into an overall measure of nutrient use efficiency of human macronutrient production. Across all systems considered, N use efficiency (5-13 kg protein/kg applied N) was lower than P (84-772 kg protein/kg applied P) or K (63-2060 kg protein/kg applied K), and combining synthetic fertiliser use with organic amendment applications raised production significantly while balancing P and K management, regardless of which organic amendment was used. Legume-supported rotations without livestock produced more protein, starch and sugar per unit area than those with livestock. Nutrient balances and nutrient use efficiencies were more sensitive to management changes than purely food production. Using this approach allowed us to identify areas for improvement in food production based on the specific nutritional value of offtakes as opposed to yield overall.Peer reviewe

Soil health metrics reflect yields in long-term cropping system experiments

Soil health metrics with strong links to ecological function and agricultural productivity are needed to ensure that future management of agricultural systems meets sustainability goals. While ecological metrics and crop yields are often considered separately from one another, our work sought to assess the links between the two in an agricultural context where productivity is a key consideration. Here, we investigated the value of soil health tests in terms of their relevance to agricultural management practices and crop yields at contrasting long term cropping systems experiments. One site was on a sandy loam Leptic Podzol and the other on a sandy clay loam Endostagnic Luvisol. Furthermore, the experiments had different management systems. One contained legume-supported rotations with different grass-clover ley durations and organic amendment usage, while the other compared a range of nutrient input options through fertiliser and organic amendments on the same rotation without ley periods. Metrics included field tests (earthworm counts and visual evaluation of soil structure scores) with laboratory analysis of soil structure, chemistry and biology. This analysis included bulk density, macroporosity, pH, available phosphorus, exchangeable potassium, soil organic matter and potentially mineralizable nitrogen. Using a novel combination of long-term experiments, management systems and distinctive soil types, we demonstrated that as well as providing nutrients, agricultural management which resulted in better soil organic matter, pH, potassium and bulk density was correlated with higher crop yields. The importance of ley duration and potentially mineralizable nitrogen to yield in legume-supported systems showed the impact of agricultural management on soil biology. In systems with applications of synthetic fertiliser, earthworm counts and visual evaluation of soil structure scores were correlated with higher yields. We concluded that agricultural management altered yields not just through direct supply of nutrients to crops, but also through the changes in soil health measured by simple metrics

A low surface brightness halo surrounding the globular cluster NGC 5694

We report on the discovery of an extended stellar halo surrounding the distant Galactic globular cluster NGC 5694, based on new deep (V ~ 24.5) wide-field (24' * 20') photometry acquired with VIMOS at VLT. Stars with colour and magnitude consistent with the Main Sequence of the cluster are clearly identified out to r ~ 9'(~ 93 pc) from the cluster center, much beyond the tidal radius of the King model that best fits the inner profile (r_t=3.15'). We do not find a clear end of the structure within our field. The overall observed profile cannot be properly fitted with either a King (1966) model, an Elson et al. (1987) model, or a Wilson (1975) model; however it is very smooth and does not show any sign of the break near the tidal radius that is typically observed in stellar systems with tidal tails. The density map we derived does not show evidence of tidal tails, within the considered field. The extra-tidal component contains ~ 3.5% of the cluster light (mass) and has a surface density profile falling as ~ r^{-3.2}. The possible origin of the detected structure is discussed, as a clear-cut conclusion cannot be reached with the available data.Comment: 7 pages, 4 figures, accepted for publication in MNRA

CAManim: Animating end-to-end network activation maps

Deep neural networks have been widely adopted in numerous domains due to their high performance and accessibility to developers and application-specific end-users. Fundamental to image-based applications is the development of Convolutional Neural Networks (CNNs), which possess the ability to automatically extract features from data. However, comprehending these complex models and their learned representations, which typically comprise millions of parameters and numerous layers, remains a challenge for both developers and end-users. This challenge arises due to the absence of interpretable and transparent tools to make sense of black-box models. There exists a growing body of Explainable Artificial Intelligence (XAI) literature, including a collection of methods denoted Class Activation Maps (CAMs), that seek to demystify what representations the model learns from the data, how it informs a given prediction, and why it, at times, performs poorly in certain tasks. We propose a novel XAI visualization method denoted CAManim that seeks to simultaneously broaden and focus end-user understanding of CNN predictions by animating the CAM-based network activation maps through all layers, effectively depicting from end-to-end how a model progressively arrives at the final layer activation. Herein, we demonstrate that CAManim works with any CAM-based method and various CNN architectures. Beyond qualitative model assessments, we additionally propose a novel quantitative assessment that expands upon the Remove and Debias (ROAD) metric, pairing the qualitative end-to-end network visual explanations assessment with our novel quantitative "yellow brick ROAD" assessment (ybROAD). This builds upon prior research to address the increasing demand for interpretable, robust, and transparent model assessment methodology, ultimately improving an end-user's trust in a given model's predictions

MetaCAM: Ensemble-Based Class Activation Map

The need for clear, trustworthy explanations of deep learning model predictions is essential for high-criticality fields, such as medicine and biometric identification. Class Activation Maps (CAMs) are an increasingly popular category of visual explanation methods for Convolutional Neural Networks (CNNs). However, the performance of individual CAMs depends largely on experimental parameters such as the selected image, target class, and model. Here, we propose MetaCAM, an ensemble-based method for combining multiple existing CAM methods based on the consensus of the top-k% most highly activated pixels across component CAMs. We perform experiments to quantifiably determine the optimal combination of 11 CAMs for a given MetaCAM experiment. A new method denoted Cumulative Residual Effect (CRE) is proposed to summarize large-scale ensemble-based experiments. We also present adaptive thresholding and demonstrate how it can be applied to individual CAMs to improve their performance, measured using pixel perturbation method Remove and Debias (ROAD). Lastly, we show that MetaCAM outperforms existing CAMs and refines the most salient regions of images used for model predictions. In a specific example, MetaCAM improved ROAD performance to 0.393 compared to 11 individual CAMs with ranges from -0.101-0.172, demonstrating the importance of combining CAMs through an ensembling method and adaptive thresholding.Comment: 9 page

Land restitution, traditional leadership and belonging: defining Barokologadi identity

How do government policies and practices affect struggles over collective identity and struggles over land? Examining the interconnections among collective identity struggles, land struggles and state policies and practices in post-apartheid South Africa, this paper argues that the government\u27s contradictory policies and ambivalent practices have aggravated collective struggles over the boundaries of belonging. Specifically, the differing definitions of community set forth in traditional leadership, land tenure and land restitution policies exacerbate existing divisions among ‘communities’ concurrently subject to these policies and create practical policy dilemmas for decision-makers. This paper illustrates the interplay between public policies and collective identity struggles through close examination of struggles among the Barokologadi ba ga Maotwe, a so-called traditional community. The Barokologadi case underscores the necessity of attending to these interactions

Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania

SummaryThis study was part of a larger cross-sectional survey that was evaluating tuberculosis (TB) infection in humans, livestock and wildlife in the Serengeti ecosystem in Tanzania. The study aimed at evaluating the genetic diversity of Mycobacterium tuberculosis isolates from TB patients attending health facilities in the Serengeti ecosystem. DNA was extracted from 214 sputum cultures obtained from consecutively enrolled newly diagnosed untreated TB patients aged ≥18 years. Spacer oligonucleotide typing (spoligotyping) and Mycobacterium Interspersed Repetitive Units and Variable Number Tandem Repeat (MIRU-VNTR) were used to genotype M. tuberculosis to establish the circulating lineages. Of the214 M. tuberculosis isolates genotyped, 55 (25.7%) belonged to the Central Asian (CAS) family, 52 (24.3%) were T family (an ill-defined family), 38 (17.8%) belonged to the Latin American Mediterranean (LAM) family, 25 (11.7%) to the East-African Indian (EAI) family, 25 (11.7%) comprised of different unassigned (‘Serengeti’) strain families, while 8 (3.7%) belonged to the Beijing family. A minority group that included Haarlem, X, U and S altogether accounted for 11 (5.2%) of all genotypes. MIRU-VNTR typing produced diverse patterns within and between families indicative of unlinked transmission chains. We conclude that, in the Serengeti ecosystem only a few successful families predominate namely CAS, T, LAM and EAI families. Other types found in lower prevalence are Beijing, Haarlem, X, S and MANU. The Haarlem, EAI_Somalia, LAM3 and S/convergent and X2 subfamilies found in this study were not reported in previous studies in Tanzania