Can CNN-based species classification generalise across variation in habitat within a camera trap survey?

Camera trap surveys are a popular ecological monitoring tool that produce vast numbers of images making their annotation extremely time-consuming. Advances in machine learning, in the form of convolutional neural networks, have demonstrated potential for automated image classification, reducing processing time. These networks often have a poor ability to generalise, however, which could impact assessments of species in habitats undergoing change. Here, we (i) compare the performance of three network architectures in identifying species in camera trap images taken from tropical forest of varying disturbance intensities; (ii) explore the impacts of training dataset configuration; (iii) use habitat disturbance categories to investigate network generalisability and (iv) test whether classification performance and generalisability improve when using images cropped to bounding boxes. Overall accuracy (72.8%) was improved by excluding the rarest species and by adding extra training images (76.3% and 82.8%, respectively). Generalisability to new camera locations within a disturbance level was poor (mean F1-score: 0.32). Performance across unseen habitat disturbance levels was worse (mean F1-score: 0.27). Training the network on multiple disturbance levels improved generalisability (mean F1-score on unseen disturbance levels: 0.41). Cropping images to bounding boxes improved overall performance (F1-score: 0.77 vs. 0.47) and generalisability (mean F1-score on unseen disturbance levels: 0.73), but at a cost of losing images that contained animals which the detector failed to detect. These results suggest researchers should consider using an object detector before passing images to a classifier, and an improvement in classification might be seen if labelled images from other studies are added to their training data. Composition of training data was shown to be influential, but including rarer classes did not compromise performance on common classes, providing support for the inclusion of rare species to inform conservation efforts. These findings have important implications for use of these methods for long-term monitoring of habitats undergoing change, as they highlight the potential for misclassifications due to poor generalisability to impact subsequent ecological analyses. These methods therefore need to be considered as dynamic, in that changes to the study site would need to be reflected in the updated training of the network

Insights into the Function of the CRM1 Cofactor RanBP3 from the Structure of Its Ran-Binding Domain

Proteins bearing a leucine-rich nuclear export signal (NES) are exported from the nucleus by the transport factor CRM1, which forms a cooperative ternary complex with the NES-bearing cargo and with the small GTPase Ran. CRM1-mediated export is regulated by RanBP3, a Ran-interacting nuclear protein. Unlike the related proteins RanBP1 and RanBP2, which promote disassembly of the export complex in the cytosol, RanBP3 acts as a CRM1 cofactor, enhancing NES export by stabilizing the export complex in the nucleus. RanBP3 also alters the cargo selectivity of CRM1, promoting recognition of the NES of HIV-1 Rev and of other cargos while deterring recognition of the import adaptor protein Snurportin1. Here we report the crystal structure of the Ran-binding domain (RBD) from RanBP3 and compare it to RBD structures from RanBP1 and RanBP2 in complex with Ran and CRM1. Differences among these structures suggest why RanBP3 binds Ran with unusually low affinity, how RanBP3 modulates the cargo selectivity of CRM1, and why RanBP3 promotes assembly rather than disassembly of the export complex. The comparison of RBD structures thus provides an insight into the functional diversity of Ran-binding proteins

The Unmet Need for Interpreting Provision in UK Primary Care

Background: With increasing globalisation, the challenges of providing accessible and safe healthcare to all are great. Studies show that there are substantial numbers of people who are not fluent in English to a level where they can make best use of health services. We examined how health professionals manage language barriers in a consultation.Methods and Findings: This was a cross-sectional study in 41 UK general practices. Health professionals completed a proforma for a randomly allocated consultation session. Seventy-seven (63%) practitioners responded, from 41(59%) practices. From 1008 consultations, 555 involved patients who did not have English as a first language; 710 took place in English; 222 were in other languages, the practitioner either communicating with the patient in their own language/using an alternative language. Seven consultations were in a mixture of English/patient's own language. Patients' first languages numbered 37 (apart from English), in contrast to health practitioners, who declared at least a basic level of proficiency in 22 languages other than English. The practitioner's reported proficiency in the language used was at a basic level in 24 consultations, whereas in 21, they reported having no proficiency at all. In 57 consultations, a relative/friend interpreted and in 6, a bilingual member of staff/community worker was used. Only in 6 cases was a professional interpreter booked. The main limitation was that only one random session was selected and assessment of patient/professional fluency in English was subjective.Conclusions: It would appear that professional interpreters are under-used in relation to the need for them, with bilingual staff/family and friends being used commonly. In many cases where the patient spoke little/no English, the practitioner consulted in the patient's language but this approach was also used where reported practitioner proficiency was low. Further research in different setting is needed to substantiate these findings

Vitamin D supplementation and breast cancer prevention : a systematic review and meta-analysis of randomized clinical trials

In recent years, the scientific evidence linking vitamin D status or supplementation to breast cancer has grown notably. To investigate the role of vitamin D supplementation on breast cancer incidence, we conducted a systematic review and meta-analysis of randomized controlled trials comparing vitamin D with placebo or no treatment. We used OVID to search MEDLINE (R), EMBASE and CENTRAL until April 2012. We screened the reference lists of included studies and used the “Related Article” feature in PubMed to identify additional articles. No language restrictions were applied. Two reviewers independently extracted data on methodological quality, participants, intervention, comparison and outcomes. Risk Ratios and 95% Confident Intervals for breast cancer were pooled using a random-effects model. Heterogeneity was assessed using the I2 test. In sensitivity analysis, we assessed the impact of vitamin D dosage and mode of administration on treatment effects. Only two randomized controlled trials fulfilled the pre-set inclusion criteria. The pooled analysis included 5372 postmenopausal women. Overall, Risk Ratios and 95% Confident Intervals were 1.11 and 0.74–1.68. We found no evidence of heterogeneity. Neither vitamin D dosage nor mode of administration significantly affected breast cancer risk. However, treatment efficacy was somewhat greater when vitamin D was administered at the highest dosage and in combination with calcium (Risk Ratio 0.58, 95% Confident Interval 0.23–1.47 and Risk Ratio 0.93, 95% Confident Interval 0.54–1.60, respectively). In conclusions, vitamin D use seems not to be associated with a reduced risk of breast cancer development in postmenopausal women. However, the available evidence is still limited and inadequate to draw firm conclusions. Study protocol code: FARM8L2B5L

Vitamin D and the hepatitis B vaccine response: a prospective cohort study and a randomized, placebo-controlled oral vitamin D3 and simulated sunlight supplementation trial in healthy adults.

PURPOSE: To determine serum 25(OH)D and 1,25(OH)2D relationship with hepatitis B vaccination (study 1). Then, to investigate the effects on hepatitis B vaccination of achieving vitamin D sufficiency (serum 25(OH)D ≥ 50 nmol/L) by a unique comparison of simulated sunlight and oral vitamin D3 supplementation in wintertime (study 2). METHODS: Study 1 involved 447 adults. In study 2, 3 days after the initial hepatitis B vaccination, 119 men received either placebo, simulated sunlight (1.3 × standard-erythema dose, 3 × /week for 4 weeks and then 1 × /week for 8 weeks) or oral vitamin D3 (1000 IU/day for 4 weeks and 400 IU/day for 8 weeks). We measured hepatitis B vaccination efficacy as percentage of responders with anti-hepatitis B surface antigen immunoglobulin G ≥ 10 mIU/mL. RESULTS: In study 1, vaccine response was poorer in persons with low vitamin D status (25(OH)D ≤ 40 vs 41-71 nmol/L mean difference [95% confidence interval] - 15% [- 26, - 3%]; 1,25(OH)2D ≤ 120 vs ≥ 157 pmol/L - 12% [- 24%, - 1%]). Vaccine response was also poorer in winter than summer (- 18% [- 31%, - 3%]), when serum 25(OH)D and 1,25(OH)2D were at seasonal nadirs, and 81% of persons had serum 25(OH)D < 50 nmol/L. In study 2, vitamin D supplementation strategies were similarly effective in achieving vitamin D sufficiency from the winter vitamin D nadir in almost all (~ 95%); however, the supplementation beginning 3 days after the initial vaccination did not effect the vaccine response (vitamin D vs placebo 4% [- 21%, 14%]). CONCLUSION: Low vitamin D status at initial vaccination was associated with poorer hepatitis B vaccine response (study 1); however, vitamin D supplementation commencing 3 days after vaccination (study 2) did not influence the vaccination response. CLINICAL TRIAL REGISTRY NUMBER: Study 1 NCT02416895; https://clinicaltrials.gov/ct2/show/study/NCT02416895; Study 2 NCT03132103; https://clinicaltrials.gov/ct2/show/NCT03132103

Second Generation Leptoquark Search in p\bar{p} Collisions at s\sqrt{s} = 1.8 TeV

We report on a search for second generation leptoquarks with the D\O\ detector at the Fermilab Tevatron $p\bar{p}$ collider at $\sqrt{s}$ = 1.8 TeV. This search is based on 12.7 pb$^{-1}$ of data. Second generation leptoquarks are assumed to be produced in pairs and to decay into a muon and quark with branching ratio $\beta$ or to neutrino and quark with branching ratio $(1-\beta)$. We obtain cross section times branching ratio limits as a function of leptoquark mass and set a lower limit on the leptoquark mass of 111 GeV/c$^{2}$ for $\beta = 1$ and 89 GeV/c$^{2}$ for $\beta = 0.5$ at the 95%\ confidence level.Comment: 18 pages, FERMILAB-PUB-95/185-

‘Sub-Prime’ Water, Low-Security Entitlements and Policy Challenges in Over-Allocated River Basins: the Case of the Murray–Darling Basin

Environmental policy is often implemented using market instruments. In some cases, including carbon taxing, the links between financial products and the environmental objectives, are transparent. In other cases, including water markets, the links are less transparent. In Australia’s Murray–Darling Basin (MDB), financial water products are known as ‘entitlements’, and are similar to traditional financial products, such as shares. The Australian water market includes ‘Low Security’ entitlements, which are similar to ‘sub-prime’ mortgage bonds because they are unlikely to yield an amount equal to their financial worth. Nearly half the water purchased under the Murray–Darling Basin Plan for environmental purposes is ‘Low Security’. We suggest that the current portfolio of water held by the Australian Government for environmental purposes reflects the mortgage market in the lead-up to the global financial crisis. Banks assumed that the future value of the mortgage market would reflect past trends. Similarly, it is assumed that the future value of water products will reflect past trends, without considering climate change. Historic records of allocations to ‘Low Security’ entitlements in the MDB suggest that, in the context of climate change, the Basin Plan water portfolio may fall short of the target annual average yield of 2075 GL by 511 GL. We recommend adopting finance sector methods including ‘hedging’ ‘Low Security’ entitlements by purchasing an additional 322–2755 GL of ‘Low Security’, or 160–511 GL of ‘High Security’ entitlements. Securing reliable environmental water is a global problem. Finance economics present opportunities for increasing the reliability of environmental flows

Jet Production via Strongly-Interacting Color-Singlet Exchange in ppˉp\bar{p} Collisions

A study of the particle multiplicity between jets with large rapidity separation has been performed using the D{\O}detector at the Fermilab Tevatron $p\bar{p}$ Collider operating at $\sqrt{s}=1.8$ TeV. A significant excess of low-multiplicity events is observed above the expectation for color-exchange processes. The measured fractional excess is $1.07 \pm 0.10({\rm stat})^{+ 0.25}_{- 0.13}({\rm syst})$, which is consistent with a strongly-interacting color-singlet (colorless) exchange process and cannot be explained by electroweak exchange alone. A lower limit of 0.80% (95% C.L.) is obtained on the fraction of dijet events with color-singlet exchange, independent of the rapidity gap survival probability.Comment: 15 pages (REVTeX), 3 PS figs (uuencoded/tar compressed, epsf.sty) Complete postscript available at http://d0sgi0.fnal.gov/d0pubs/journals.html Submitted to Physical Review Letter

Migration of myogenic cells in the rat extensor digitorum longus muscle studied with a split autograft model

The ability of myogenic cells to migrate perpendicular to the long axis of freely autografted muscles was examined. Rat extensor digitorum longus muscles were divided, and one half was devitalized by repeated freezing in liquid nitrogen while the other half was kept viable in physiologic saline. The halves were reunited with sutures and grafted back into the original muscle bed. At intervals between 5 and 25 days the grafts were removed and examined histologically for the presence of myotubes within the devitalized region. Myotubes were first seen in the devitalized half 10 days postgrafting with the maximum number of myotubes observed after 12 to 15 days. These results indicate that myogenic cells are capable of migration perpendicular to the long axis of the muscle fibers in an autograft.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47687/1/441_2004_Article_BF00327748.pd

Anaphylatoxin C3a receptors in asthma

The complement system forms the central core of innate immunity but also mediates a variety of inflammatory responses. Anaphylatoxin C3a, which is generated as a byproduct of complement activation, has long been known to activate mast cells, basophils and eosinophils and to cause smooth muscle contraction. However, the role of C3a in the pathogenesis of allergic asthma remains unclear. In this review, we examine the role of C3a in promoting asthma. Following allergen challenge, C3a is generated in the lung of subjects with asthma but not healthy subjects. Furthermore, deficiency in C3a generation or in G protein coupled receptor for C3a abrogates allergen-induced responses in murine models of pulmonary inflammation and airway hyperresponsiveness. In addition, inhibition of complement activation or administration of small molecule inhibitors of C3a receptor after sensitization but before allergen challenge inhibits airway responses. At a cellular level, C3a stimulates robust mast cell degranulation that is greatly enhanced following cell-cell contact with airway smooth muscle (ASM) cells. Therefore, C3a likely plays an important role in asthma primarily by regulating mast cell-ASM cell interaction