wild birds in Serbia during 2012: first isolation and characterisation of WNV strains from Serbia

Monitoring West Nile virus (WNV) infection i

Scaling Agile Beyond Organizational Boundaries: Coordination Challenges in Software Ecosystems

The shift from sequential to agile software development originates from relatively small and co-located teams but soon gained prominence in larger organizations. How to apply and scale agile practices to fit the needs of larger projects has been studied to quite an extent in previous research. However, scaling agile beyond organizational boundaries, for instance in a software ecosystem context, raises additional challenges that existing studies and approaches do not yet investigate or address in great detail. For that reason, we conducted a case study in two software ecosystems that comprise several agile actors from different organizations and, thereby, scale development across organizational boundaries, in order to elaborate and understand their coordination challenges. Our results indicate that most of the identified challenges are caused by long communication paths and a lack of established processes to facilitate these paths. As a result, the participants in our study, among others, experience insufficient responsivity, insufficient communication of prioritizations and deliverables, and alterations or loss of information. As a consequence, agile practices need to be extended to fit the identified needs

Induction of neutralizing antibody response against koala retrovirus (KoRV) and reduction in viral load in koalas following vaccination with recombinant KoRV envelope protein

Koala retrovirus (KoRV) infects the majority of Australia's koalas (Phascolarctos cinereus) and has been linked to several life-threatening diseases such as lymphoma and leukemia, as well as Chlamydia and thus poses a threat to the continued survival of this species. While quarantine and antiretroviral drug treatment are possible control measures, they are impractical, leaving vaccination as the only realistic option. In this study, we examined the effect of a recombinant envelope protein-based anti-KoRV vaccine in two groups of South Australian koalas: KoRV infected or KoRV free. We report a successful vaccination response in the koalas with no vaccine-associated side effects. The vaccine induced a significant humoral immune response as well as the production of neutralizing antibodies in both groups of koalas. We also identified B-cell epitopes that were differentially recognized in KoRV-infected versus KoRV-free koalas following vaccination. Importantly, we also showed that vaccination had a therapeutic effect on koalas infected exogenously with KoRV by reducing their circulating viral load. Together, this study highlights the possibility of successfully developing a vaccine against KoRV infection in koalas.O Olagoke, D Miller, F Hemmatzadeh, T Stephenson, J Fabijan, P Hutt, S Finch, N Speight and P Timm

Pathological Findings in Koala Retrovirus-positive Koalas (Phascolarctos cinereus) from Northern and Southern Australia

© 2020 Elsevier Ltd Koala retrovirus (KoRV) infection shows differences in prevalence and load between northern and southern Australian koala populations; however, the effect of this on diseases such as lymphoma and chlamydial disease is unclear. This study compared clinicopathological findings, haematology and splenic lymphoid area of KoRV-positive koalas from northern (Queensland [Qld], n = 67) and southern (South Australia [SA], n = 92) populations in order to provide further insight into KoRV pathogenesis. Blood was collected for routine haematology and for measurement of KoRV proviral load by quantitative polymerase chain reaction (qPCR). Plasma samples were assessed for KoRV viral load by reverse transcriptase qPCR and conjunctival and cloacal swabs were collected for measurement of the load of Chlamydia pecorum (qPCR). During necropsy examination, spleen was collected for lymphoid area analysis. Lymphoma was morphologically similar between the populations and occurred in koalas with the highest KoRV proviral and viral loads. Severe ocular chlamydial disease was observed in both populations, but urinary tract disease was more severe in Qld, despite similar C. pecorum loads. No associations between KoRV and chlamydial disease severity or load were observed, except in SA where viral load correlated positively with chlamydial disease severity. In both populations, proviral and viral loads correlated positively with lymphocyte and metarubricyte counts and correlated negatively with erythrocyte and neutrophil counts. Splenic lymphoid area was correlated positively with viral load. This study has shown further evidence for KoRV-induced oncogenesis and highlighted that lymphocytes and splenic lymphoid tissue may be key sites for KoRV replication. However, KoRV infection appears to be highly complex and continued investigation is required to fully understand its pathogenesis

Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population

© 2021, The Author(s). Historical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future

Hypotheses Elicitation in Early-Stage Software Startups Based on Cognitive Mapping

Software startups develop innovative products for which there are typically no customers to refer to elicit requirements. Often, these companies develop a set of features without a better understanding of customer needs. An experiment-based approach to validate hypotheses about the customer and market could increase their chance of success or, at least, accelerate their realization of the product worthlessness. The first step of an experiment-based approach is to elicit hypotheses to guide experiments. Software startups base their products on business assumptions, but there is a lack of understanding of how these assumptions are formed and how teams could elicit hypotheses systematically. To fill this gap, we performed an empirical study consisted of two steps. First, we explored based on which assumptions startups define their products using a multiple case study. The results indicate that these companies developed their products based on founders' assumptions derived from their previous experience. Second, we investigated cognitive mapping as a tool to elicit hypotheses systematically with two software startups. The results indicate that this approach can serve as the basis of a method to elicit hypotheses in early-stage software startups

Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: identification and modelling of a population free from infection

Chlamydia pecorum is an established and prevalent infection that produces severe clinical disease in many koala populations, contributing to dramatic population declines. In wild South Australian koala populations, C. pecorum occurrence and distribution is unknown. Here, C. pecorum-specific real-time quantitative PCR (qPCR) was applied to ocular and urogenital swabs from targeted surveys of wild koalas from the mainland Mount Lofty Ranges (MLR) (n = 75) and Kangaroo Island (KI) (n = 170) populations. Historical data from 13,081 KI koalas (1997-2018) provided additional evidence for assessing the absence of C. pecorum infection. In the MLR population, 46.7% (CI: 35.1-58.6%) of koalas were C. pecorum positive by qPCR but only 4% had grade 3 clinical disease. MLR koala fertility was significantly reduced by C. pecorum infection; all reproductively active females (n = 16) were C. pecorum negative, whereas 85.2% of inactive females (n = 23) were positive (P < 0.001). KI koalas were C. pecorum negative and the population was demonstrated to be free of C. pecorum infection with 95% confidence. C. pecorum is a real threat for the sustainability of the koala and KI is possibly the last isolated, large C. pecorum-free population remaining in Australia. These koalas could provide a safeguard against this serious disease threat to an iconic Australian species.Jessica Fabijan, Charles Caraguel, Martina Jelocnik, Adam Polkinghorne, Wayne S.J. Boardman, Elisa Nishimoto, Greg Johnsson, Robyn Molsher, Lucy Woolford, Peter Timms, Greg Simmons, Farhid Hemmatzadeh, Darren J. Trott, Natasha Speigh

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Geostatistical evaluation of lead and zinc concentration in soils of an old mining area with complex land management

This study is aimed at detailed statistical and geostatistical investigation of lead and zinc concentration in an old mining area located in the eastern part of the Upper Silesian Industrial Region. This area is rich in lead and zinc ores whose intense extraction dates back to the tenth century ad. The complexity of the area results from historical and current mining activities, as well as from a variety of different types of land management and complex geological conditions. Almost 1,000 collected soil cores were divided into two subsets: those collected at the depth of up to 20 cm and the those collected at the depth from 40 to 60 cm. Extensive analyses considered geological substrata in terms of spatial variability and spatial distributions, the type of land management, geoaccumulation indexes and enrichment factors. Lead and zinc concentration was several times higher on depths ranging from 40 to 60 cm beneath the soil surface than in the 20-cm topsoil. The results showed that clearer spatial dependence was observed for deeper soil layers then for the topmost ones, especially near mines where anthropogenic factors predominated over lithogenic ones. Weak spatial dependence was accompanied by high values of the geoaccumulation index. The lowest concentrations of pollution with geoaccumulation index below 0 and enrichment factor up to 5 observed in the forest were caused by low anthropogenic pressure and the presence of sandy soils, less capable of accumulating heavy metals