Maturation-Induced Cloaking of Neutralization Epitopes on HIV-1 Particles

To become infectious, HIV-1 particles undergo a maturation process involving proteolytic cleavage of the Gag and Gag-Pol polyproteins. Immature particles contain a highly stable spherical Gag lattice and are impaired for fusion with target cells. The fusion impairment is relieved by truncation of the gp41 cytoplasmic tail (CT), indicating that an interaction between the immature viral core and gp41 within the particle represses HIV-1 fusion by an unknown mechanism. We hypothesized that the conformation of Env on the viral surface is regulated allosterically by interactions with the HIV-1 core during particle maturation. To test this, we quantified the binding of a panel of monoclonal antibodies to mature and immature HIV-1 particles by immunofluorescence imaging. Surprisingly, immature particles exhibited markedly enhanced binding of several gp41-specific antibodies, including two that recognize the membrane proximal external region (MPER) and neutralize diverse HIV-1 strains. Several of the differences in epitope exposure on mature and immature particles were abolished by truncation of the gp41 CT, thus linking the immature HIV-1 fusion defect with altered Env conformation. Our results suggest that perturbation of fusion-dependent Env conformational changes contributes to the impaired fusion of immature particles. Masking of neutralization-sensitive epitopes during particle maturation may contribute to HIV-1 immune evasion and has practical implications for vaccine strategies targeting the gp41 MPER

Flexible prey handling, preference and a novel capture technique in invasive, sub-adult Chinese mitten crabs

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Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota

Infection by gastrointestinal helminths of humans, livestock and wild animals is common, but the impact of such endoparasites on wild hosts and their gut microbiota represents an important overlooked component of population dynamics. Wild host gut microbiota and endoparasites occupy the same physical niche spaces with both affecting host nutrition and health. However, associations between the two are poorly understood. Here we used the commonly parasitized European shag (Phalacrocorax aristotelis) as a model wild host. Forty live adults from the same colony were sampled. Endoscopy was employed to quantify helminth infection in situ. Microbiota from the significantly distinct proventriculus (site of infection), cloacal and faecal gastrointestinal tract microbiomes were characterised using 16S rRNA gene-targeted high-throughput sequencing. We found increasingly strong associations between helminth infection and microbiota composition progressing away from the site of infection, observing a pronounced dysbiosis in microbiota when samples were partitioned into high- and low-burden groups. We posit this dysbiosis is predominately explained by helminths inducing an anti-inflammatory environment in the proventriculus, diverting host immune responses away from themselves. This study, within live wild animals, provides a vital foundation to better understand the mechanisms that underpin the three-way relationship between helminths, microbiota and hosts

Patchiness and Co-Existence of Indigenous and Invasive Mussels at Small Spatial Scales: The Interaction of Facilitation and Competition

Ecological theory predicts that two species with similar requirements will fail to show long-term co-existence in situations where shared resources are limiting, especially at spatial scales that are small relative to the size of the organisms. Two species of intertidal mussels, the indigenous Perna perna and the invasive Mytilus galloprovincialis, form mixed beds on the south coast of South Africa in a situation that has been stable for several generations of these species, even though these populations are often limited by the availability of space. We examined the spatial structure of these species where they co-exist at small spatial scales in the absence of apparent environmental heterogeneity at two sites, testing: whether conspecific aggregation of mussels can occur (using spatial Monte-Carlo tests); the degree of patchiness (using Korcak B patchiness exponent), and whether there was a relationship between percent cover and patchiness. We found that under certain circumstances there is non-random conspecific aggregation, but that in other circumstances there may be random distribution (i.e. the two species are mixed), so that spatial patterns are context-dependent. The relative cover of the species differed between sites, and within each site, the species with higher cover showed low Korcak B values (indicating low patchiness, i.e. the existence of fewer, larger patches), while the less abundant species showed the reverse, i.e. high patchiness. This relationship did not hold for either species within sites. We conclude that co-existence between these mussels is possible, even at small spatial scales because each species is an ecological engineer and, while they have been shown to compete for space, this is preceded by initial facilitation. We suggest that a patchy pattern of co-existence is possible because of a balance between direct (competitive) and indirect (facilitative) interactions

Crop Updates 2002 - Cereals

This session covers thirty one papers from different authors: VARIETIES AND BREEDING 1. Agronomic evaluation of wheat and barley in the central wheatbelt of Western Australia, Peter Burgess1and Gary Fawell2, 1Agritech and 2Farmanco Management 2. Evaluating stress tolerance to terminal drought by Western Australian wheats, Dean Diepeveen and Dr Tim Setter, Department of Agriculture 3. Broadscale wheat variety comparisons featuring Wyalkatchem, Jeff Russell, Department of Agriculture 4. Australian crop accreditation system variety selector, Tony Seymour, Australian Crop Accreditation System 5. Future wheat varieties, Robin Wilson, Iain Barclay,Robyn McLean, Robert Loughman, Jenny Garlinge, Bill Lambe, Neil Venn and Peter Clarke, Department of Agriculture AGRONOMY 6. Beware of wheat variety interactions with row spacing and seed rate, Mohammad Amjad and Wal Anderson, Department of Agriculture 7. Yield and falling numbers of wheat varieties on the South Coast, Mohammad Amjad and Wal Anderson, Department of Agriculture 8. Maximising wheat variety performance through agronomic management, Wal Anderson, Raffaele Del Cima, James Bee, Darshan Sharma, Sheena Lyon, Melaine Kupsch, Mohammad Amjad, Pam Burgess, Veronika Reck, Brenda Shackley, Ray Tugwell, BindiWebb and Steve Penny Jr, Department of Agriculture 9. High impact of soil type and seasonal rainfall on optimum wheat seed rate , Raffaele Del Cima and Wal Anderson Department of Agriculture 10. 101 seasons in one day: Using the ‘WA Wheat’ database to predict wheat yield, James Fisher1, Bill Bowden1, Craig Scanlan1, Senthold Asseng2and Michael Robertson2 1Department of Agriculture, 2CSIRO 11. Economics of improving compact soils, M.A. Hamza1, G. McConnell2and W.K. Anderson1, 1Department of Agriculture, 2Planfarm 12. Reducing the risks in producing durum wheat in Western Australia, Md Shahajahan Miyan and Wal Anderson, Department of Agriculture 13. Taking the Why out of Wyalkatchem – the new widely adopted wheat variety, Steve Penny, Department of Agriculture 14. Influence of nutrition and environmental factors on seed vigour in wheat, Darshan Sharma, Wal Anderson and Daya Patabendige, Department of Agriculture NUTRITION 15. N and K are important for oat yield and quality, Patrick Gethin, Stephen Loss, Tim O’Dea, Ryan Guthrie and Lisa Leaver, CSBP Futurefarm 16. Effects of nitrogen and phosphorus on the grain yield and quality of noodle wheat, Tyrone Henning1, Lionel Martin1and Wal Anderson2 1Muresk Institute of Agriculture, 2Department of Agriculture 17. Assessment of a high input fertiliser regime on the yield and quality of Gairdner barley, Narelle Hill1, Simon Wallwork2and Laurence Carslake2 1Department of Agriculture, 2Wesfarmers Landmark 18. The use of Flexi-N to achieve high yielding, high protein wheat, Darren Hughes1, Lionel Martin1, Wal Anderson2and Stephen Loss3 1Muresk Institute of Agriculture, 2Department of Agriculture, 3CSBP Futurefarm 19. Are liquid phosphorus fertilisers more efficient than solid fertilisers in Western Australia?Stephen Loss, Lisa Leaver, Ryan Guthrie, Patrick Gethin and Tim O’Dea, CSBP Futurefarm 20. Oats respond to phosphorus and potassium, Glenn McDonald, Department of Agriculture PESTS AND DISEASES 21. Cereal disease diagnostics and rust monitoring, Nichole Burges and Dominie Wright, Department of Agriculture 22. Distribution and incidence of aphids and barley yellow dwarf virus in over-summering grasses in the Western Australian wheatbelt, Jenny Hawkes and Roger Jones, Centre for Legumes in Mediterranean Agriculture and Department of Agriculture 23. Spring sprays for powdery mildew control in cereals, Kith Jayasena1, Kazue Tanaka1, Vanessa Johnson1, Robert Loughman1and Josh Jury2 1Department of Agriculture, 2Wesfarmers Landmark 24. Impact of root lesion nematodes on wheat and triticale in Western Australia, Sean Kelly and Shashi Sharma, Department of Agriculture 25. Cropping options for the management of root lesion nematodes in Western Australia, Sean Kelly, Shashi Sharma and Robert Loughman, Department of Agriculture 26. Cereal rust update 2002 – new stem rust on Camm wheat, Robert Loughman1and Robert Park2 1Department of Agriculture, 2University of Sydney 27. Cereal aphids and direct feeding damage to cereals, Phil Michael, Department of Agriculture 28. A decision support system for control of aphids and BYDV in cereal crops, Debbie Thackray, Jenny Hawkes and Roger Jones, Department of Agriculture and Centre for Legumes in Mediterranean Agriculture STORAGE 29. Aeration – opportunity for profit, Christopher Newman, Department of Agriculture CLIMATE 30. Financial impact of frost on the Western Australian grains industry, Garren Knell and Kim Povey, ConsultAg 31. Summary of 2001 weather and seasonal prospects for 2002, David Stephens, Department of Agricultur

Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: a report of the international immuno‐oncology biomarker working group

The clinical significance of the tumor-immune interaction in breast cancer (BC) has been well established, and tumor-infiltrating lymphocytes (TILs) have emerged as a predictive and prognostic biomarker for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2 negative) breast cancer (TNBC) and HER2-positive breast cancer. How computational assessment of TILs can complement manual TIL-assessment in trial- and daily practices is currently debated and still unclear. Recent efforts to use machine learning (ML) for the automated evaluation of TILs show promising results. We review state-of-the-art approaches and identify pitfalls and challenges by studying the root cause of ML discordances in comparison to manual TILs quantification. We categorize our findings into four main topics; (i) technical slide issues, (ii) ML and image analysis aspects, (iii) data challenges, and (iv) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns, or design choices in the computational implementation. To aid the adoption of ML in TILs assessment, we provide an in-depth discussion of ML and image analysis including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial- and routine clinical management of patients with TNBC

From Sea to Sea: Canada's Three Oceans of Biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada's natural heritage

Measurements of Higgs bosons decaying to bottom quarks from vector boson fusion production with the ATLAS experiment at √=13TeV

The paper presents a measurement of the Standard Model Higgs Boson decaying to b-quark pairs in the vector boson fusion (VBF) production mode. A sample corresponding to 126 fb−1 of s√=13TeV proton–proton collision data, collected with the ATLAS experiment at the Large Hadron Collider, is analyzed utilizing an adversarial neural network for event classification. The signal strength, defined as the ratio of the measured signal yield to that predicted by the Standard Model for VBF Higgs production, is measured to be 0.95+0.38−0.36 , corresponding to an observed (expected) significance of 2.6 (2.8) standard deviations from the background only hypothesis. The results are additionally combined with an analysis of Higgs bosons decaying to b-quarks, produced via VBF in association with a photon

Dijet Resonance Search with Weak Supervision Using root S=13 TeV pp Collisions in the ATLAS Detector

This Letter describes a search for narrowly resonant new physics using a machine-learning anomaly detection procedure that does not rely on signal simulations for developing the analysis selection. Weakly supervised learning is used to train classifiers directly on data to enhance potential signals. The targeted topology is dijet events and the features used for machine learning are the masses of the two jets. The resulting analysis is essentially a three-dimensional search A → BC, for mA ∼ OðTeVÞ, mB; mC ∼ Oð100 GeVÞ and B, C are reconstructed as large-radius jets, without paying a penalty associated with a large trials factor in the scan of the masses of the two jets. The full run 2 ffiffi s p ¼ 13 TeV pp collision dataset of 139 fb−1 recorded by the ATLAS detector at the Large Hadron Collider is used for the search. There is no significant evidence of a localized excess in the dijet invariant mass spectrum between 1.8 and 8.2 TeV. Cross-section limits for narrow-width A, B, and C particles vary with mA, mB, and mC. For example, when mA ¼ 3 TeV and mB ≳ 200 GeV, a production cross section between 1 and 5 fb is excluded at 95% confidence level, depending on mC. For certain masses, these limits are up to 10 times more sensitive than those obtained by the inclusive dijet search. These results are complementary to the dedicated searches for the case that B and C are standard model boson

Measurement of the tt¯tt¯ production cross section in pp collisions at √s=13 TeV with the ATLAS detector

A measurement of four-top-quark production using proton-proton collision data at a centre-of-mass energy of 13 TeV collected by the ATLAS detector at the Large Hadron Collider corresponding to an integrated luminosity of 139 fb−1 is presented. Events are selected if they contain a single lepton (electron or muon) or an opposite-sign lepton pair, in association with multiple jets. The events are categorised according to the number of jets and how likely these are to contain b-hadrons. A multivariate technique is then used to discriminate between signal and background events. The measured four-top-quark production cross section is found to be 26+17−15 fb, with a corresponding observed (expected) significance of 1.9 (1.0) standard deviations over the background-only hypothesis. The result is combined with the previous measurement performed by the ATLAS Collaboration in the multilepton final state. The combined four-top-quark production cross section is measured to be 24+7−6 fb, with a corresponding observed (expected) signal significance of 4.7 (2.6) standard deviations over the background-only predictions. It is consistent within 2.0 standard deviations with the Standard Model expectation of 12.0 ± 2.4 fb