Matching effort to threat: Strategies to increase the scale and effectiveness of revegetation in southern Australia

The past 30 years of restoration activities in Australia has been mere cautious fiddling in the face of continental‐wide native habitat loss, fragmentation and degradation. A fundamental principle of conservation is to address threats at the scale of the threatening processes. This is still not happening for two reasons: we do not know how to effectively restore at scale, and if we did, there is no demand because it does not pay. The first problem of developing the technologies needed for large‐scale revegetation will largely be solved if we collectively demand revegetation at scale. Such a scale of demand by Australian governments (taxpayers) is only likely if a permanent Natural Heritage Trust is created for long‐term funding complemented by a price on carbon pollution. That will take a lot of political will. The other big opportunity is to create demand for large‐scale revegetation cofunded by farmers to improve their farm's long‐term productivity, resilience and economic viability. This requires sustained R&D supported by novel partnerships with the massive Australian agricultural market. Native vegetation must move from the margins to the mainstream if scale is to be achieved.     

Protein interaction-targeted drug discovery: evaluating critical issues

Employment of the decision strategies outlined in this general discussion should help to pinpoint mode of activity in drug development and validation. Overall, as a paradigm for drug development, a search for small molecules that can interfere with PPIs would seem to have significant long term potential. At present, the level of structural knowledge in databases is not sufficient to predict in toto the protein binding properties of a modeled drug, but as databases improve, this may become generally feasible. A major point that remains to be determined is how much specificity of protein binding can be incorporated into molecules of generally less than 500 Da. Finally, integration of PPI-targeting strategies with other approaches towards drug design will enhance the number of signaling pathways that can effectively be targeted. These points will be particularly pertinent as technologies permit a systematic identification of encoded protein interactions that govern the proteornic complement of cells.     

Closing the translation gap: AI applications in digital pathology

Recent advances in artificial intelligence show tremendous promise to improve the accuracy, reproducibility, and availability of medical diagnostics across a number of medical subspecialities. This is especially true in the field of digital pathology, which has recently witnessed a surge in publications describing state-of-the-art performance for machine learning models across a wide range of diagnostic applications. Nonetheless, despite this promise, there remain significant gaps in translating applications for any of these technologies into actual clinical practice. In this review, we will first give a brief overview of the recent progress in applying AI to digitized pathology images, focusing on how these tools might be applied in clinical workflows in the near term to improve the accuracy and efficiency of pathologists. Then we define and describe in detail the various factors that need to be addressed in order to successfully close the “translation gap” for AI applications in digital pathology.     

R/parallel – speeding up bioinformatics analysis with R

Background  

R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example using high-throughput screening devices, the processing time required to analyze data is often quite long. A solution to reduce the processing time is the use of parallel computing technologies. Because R does not support parallel computations, several tools have been developed to enable such technologies. However, these tools require multiple modications to the way R programs are usually written or run. Although these tools can finally speed up the calculations, the time, skills and additional resources required to use them are an obstacle for most bioinformaticians.     

Information: needs for the future

The four central questions surrounding the use of information are: where to find it; how to find it; how to present it; and how to maintain information availability and information literacy. It is usually assumed that the main source of information for most scientists is the peer-reviewed journal literature. Traditional journal publishing is beset with a number of problems. Although electronic publishing might possibly solve some of these, it in turn introduces new problems. Further problems arise with respect to secondary sources which, in some cases, are being supplemented by electronic archives of full-text documents. One fundamental question that arises when considering any large collection of documents or of records about documents is whether or not to index them, and how to index them. The pros and cons of free-text searching versus the use of controlled vocabularies are discussed, as is the importance of harmonising the Three Rs-related terminology of existing and proposed thesauri. However, there is a further problem that documents pertinent to the Three Rs are not always indexed from this point of view. Authors need to be made aware that, if the information is not provided in the abstract, there is no easy way to identify and retrieve this document from a database. Small specialised databases on the Three Rs in relation to specific subject areas could provide a further solution, especially if they provide references to conference proceedings and book chapters, which are not usually found in the large bibliographical databases. The provision of training in the use of information resources, and the establishment and maintenance of these resources require investment of money and professional skills. Finally, the future of Three Rs information depends on a recognition that this in an important topic which deserves more than lip service.     

Digital game design-based STEM activity: Biodiversity example

Abstract

The purpose of this study is to design a digital game design-based STEM activity for fifth-grade students learning about endangered organisms and significance of biodiversity for living. This activity was carried out with twenty students in a public school in Eastern Black Sea Region of Turkey during academic year of 2018–2019 spring term. This study planned as eight-lesson time (8?×?40?minutes) and completed at this lesson time. The students were given the digital game design challenge in real-life problem context that has been created based on design-based science learning and for which they shall use their knowledge and skills in each of the STEM disciplines. During this design challenge, students worked like a scientist and an engineer. They carried out scientific research and inquiry process in the science discipline, understood the engineering design process in the engineering discipline, established mathematical relations in the mathematics discipline, learned how to make coding in the technology discipline, and used this knowledge and skills thus acquired in their suggested solutions for the design challenge. They designed a digital game by coding and presented science knowledge and skills that acquired from inquiry process.     

The challenge of challenge: Can problem solving opportunities enhance animal welfare?

Cognitive mechanisms are an important part of the organization of the behavior systems of animals. In the wild, animals regularly face problems that they must overcome in order to survive and thrive. Solving such problems often requires animals to process, store, retrieve, and act upon information from the environment—in other words, to use their cognitive skills. For example, animals may have to use navigational, tool-making or cooperative social skills in order to procure their food. However, many enrichment programs for captive animals do not include the integration of these types of cognitive challenges. Thus, foraging enrichments typically are designed to facilitate the physical expression of feeding behaviors such as food-searching and food consumption, but not to facilitate complex problem solving behaviors related to food acquisition. Challenging animals by presenting them with problems is almost certainly a source of frustration and stress. However, we suggest here that this is an important, and even necessary, feature of an enrichment program, as long as animals also possess the skills and resources to effectively solve the problems with which they are presented. We discuss this with reference to theories about the emotional consequences of coping with challenge, the association between lack of challenge and the development of abnormal behavior, and the benefits of stress (arousal) in facilitating learning and memory of relevant skills. Much remains to be done to provide empirical support for these theories. However, they do point the way to a practical approach to improving animal welfare—to design enrichments to facilitate the cognitive mechanisms which underlie the performance of complex behaviors that cannot be performed due to the restrictions inherent to the captive environment.     

Dynamics of an age‐structured population drawn from a random numbers table

I constructed age‐structured populations by drawing numbers from a random numbers table, the constraints being that within a cohort each number be smaller than the preceding number (indicating that some individuals died between one year and the next) and that the first two‐digit number following 00 or 01 ending one cohort’s life be the number born into the next cohort. Populations constructed in this way showed prolonged existence with total population numbers fluctuating about a mean size and with long‐term growth rate (r) ≈ 0. The populations’ birth rates and growth rates and the females’ per capita fecundity decreased significantly with population size, whereas the death rates showed no significant relationship to population size. These results indicate that age‐structured populations can persist for long periods of time with long‐term growth rates of zero in the absence of negative‐feedback loops between a population’s present or prior density and its birth rate, growth rate, and fecundity, contrary to the assumption of density‐dependent regulation hypotheses. Thus, a long‐term growth rate of zero found in natural populations need not indicate that a population’s numbers are regulated by density‐dependent factors.     

Electronic waste—a modern form of risk? On the consequences of the delay between the increasing generation of electronic waste and regulations to manage this increase

This article addresses the relation between the current proliferation of Information and Communication Technology (ICT) goods and services and the development of different kinds of risk assessments and policy documents. The ambition is to shed light on a, hithertho, less-discussed aspect of the development of risk assessments and policy documents, namely the time span between the development of new technologies and the development of regulatory frameworks. The concept of risk and danger can be seen as a potential means through which we can start to think about the consequences of the delay between the increased generation of electronic waste (e-waste) and the regulations to manage this increase. By using e-waste as a case study, this article provides the basis for a more general understanding of the relation between the development of new technologies and the development of regulatory frameworks. While it might be difficult to pin down the effects that this delay had/has for the subsequent development of ICTs, this article highlights the importance of taking into account not only how and by whom risk assessments and policy documents are developed, but also when they are developed in relation to the technologies that they serve to regulate.     

Mitigation of ruminant methane production: current strategies,constraints and future options

Mitigating methane losses from cattle has economic as well as environmental benefits. The aim of this paper is to review the current approaches in relation to associated advantages and disadvantages and future options to reduce enteric methane emission from cattle. Current technologies can be broadly grouped into those that increase productivity of the animal (improved nutrition strategies) so that less methane is produced per unit of meat or milk, and those that directly modify the rumen fermentation so that less methane is produced in total. Data suggest that many of these practices are not appropriate for long term mitigation of methane emissions in ruminants because of their constraints. So it is necessity to develop long term strategies in suppressing methane production. An integrated research investigating animal, plant, microbe and nutrient level strategies would offer a long term solution of methane production. Genetic selection of animals, vaccination, probiotics, prebiotics and plant improvement are the most promising options of all the future approaches discussed. These approaches will reduce enteric methane production without any hazard to animal or environment.     

Hybrid FMS control architectures based on holonic principles

The escalation in processor technologies and the corresponding reduction in costs have enabled alternative FMS control architectures to be developed without the restrictions of “fixed machine controller boundaries”. These new architectures can be based upon the use of intelligent servo axes, which are desccribed in this article, as flexible numerical control (FNC). In current parlance, the FNC is a “part movement holon” within a manufacturing cell. The control architectures that can be derived from the FNC concept are referred to as hybrid architectures and share the emerging attributes of holonics. This article details the problems that arise in the scheduling and control of FMSs in the light of hybrid control architectures. A number of traditional scheduling approaches have been devised to cope with the scheduling of parts to discrete machines, but the problem here is to ascribe the processing (machining) of part features to axis groups. This article documents how two research programs, undertaken at the CIM Centre at Swinburne University of Technology in Hawthorn, Victoria, Australia, have endeavored to address the problem of hybrid architectures and their associated scheduling.     

Long term effects of ART: What do animals tell us?

Early stages of mammalian embryonic development are now known to be very sensitive to their microenvironment, with long term effects on fetal, postnatal, and adult health, thus extending to these early stages the concept of Developmental Origin of Health and Disease (DoHaD). In this scientific context, and with 3% of births in developed countries, safety of Assisted Reproductive Techniques procedures becomes a matter of concern. Besides, embryo technologies in domestic mammals, using huge number of embryos, do not seem to evidence heavy impacts on adult phenotypes. This paper first discusses what can or cannot be concluded from farm animal data, then develops long term effects of ART procedures (ovarian stimulation, in vitro fertilization and embryo culture) evidenced in model species (mainly mouse model). Recent literature demonstrates both individual and cumulative effects of each ART procedure on fetal and postnatal phenotypes. In a second part, because they are sources for further perturbations, immediate effects of ART on early embryo phenotypes at the cellular and molecular levels are described in both farm animals and model species. Mechanistic hypotheses supporting these ART induced phenotypic alterations are subsequently considered. Finally, taking into account interspecies differences in the mechanisms likely to be involved, the relevance of results obtained in animal models for human ART are discussed.     

Document image binarisation using a supervised neural network

Advances in digital technologies have allowed us to generate more images than ever. Images of scanned documents are examples of these images that form a vital part in digital libraries and archives. Scanned degraded documents contain background noise and varying contrast and illumination, therefore, document image binarisation must be performed in order to separate foreground from background layers. Image binarisation is performed using either local adaptive thresholding or global thresholding; with local thresholding being generally considered as more successful. This paper presents a novel method to global thresholding, where a neural network is trained using local threshold values of an image in order to determine an optimum global threshold value which is used to binarise the whole image. The proposed method is compared with five local thresholding methods, and the experimental results indicate that our method is computationally cost-effective and capable of binarising scanned degraded documents with superior results.     

De-extinction and the conception of species

Developments in genetic engineering may soon allow biologists to clone organisms from extinct species. The process, dubbed “de-extinction,” has been publicized as a means to bring extinct species back to life. For theorists and philosophers of biology, the process also suggests a thought experiment for the ongoing “species problem”: given a species concept, would a clone be classified in the extinct species? Previous analyses have answered this question in the context of specific de-extinction technologies or particular species concepts. The thought experiment is given more comprehensive treatment here. Given the products of three de-extinction technologies, twenty-two species concepts are “tested” to see which are consistent with the idea that species may be resurrected. The ensuing discussion considers whether or not de-extinction is a conceptually coherent research program and, if so, whether or not its development may contribute to a resolution of the species problem. Ultimately, theorists must face a choice: they may revise their commitments to species concepts (if those concepts are inconsistent with de-extinction) or they may recognize de-extinction as a means to make progress in the species problem.     

Continent‐scale global change attribution in European birds ‐ combining annual and decadal time scales

Species attributes are commonly used to infer impacts of environmental change on multiyear species trends, e.g. decadal changes in population size. However, by themselves attributes are of limited value in global change attribution since they do not measure the changing environment. A broader foundation for attributing species responses to global change may be achieved by complementing an attributes‐based approach by one estimating the relationship between repeated measures of organismal and environmental changes over short time scales. To assess the benefit of this multiscale perspective, we investigate the recent impact of multiple environmental changes on European farmland birds, here focusing on climate change and land use change. We analyze more than 800 time series from 18 countries spanning the past two decades. Analysis of long‐term population growth rates documents simultaneous responses that can be attributed to both climate change and land‐use change, including long‐term increases in populations of hot‐dwelling species and declines in long‐distance migrants and farmland specialists. In contrast, analysis of annual growth rates yield novel insights into the potential mechanisms driving long‐term climate induced change. In particular, we find that birds are affected by winter, spring, and summer conditions depending on the distinct breeding phenology that corresponds to their migratory strategy. Birds in general benefit from higher temperatures or higher primary productivity early on or in the peak of the breeding season with the largest effect sizes observed in cooler parts of species' climatic ranges. Our results document the potential of combining time scales and integrating both species attributes and environmental variables for global change attribution. We suggest such an approach will be of general use when high‐resolution time series are available in large‐scale biodiversity surveys.     

Reconstructing DNA copy number by joint segmentation of multiple sequences

ABSTRACT: BACKGROUND: Variations in DNA copy number carry information on the modalities of genome evolution and mis-regulation of DNA replication in cancer cells. Their study can help localize tumor suppressor genes, distinguish different populations of cancerous cells, and identify genomic variations responsible for disease phenotypes. A number of different high throughput technologies can be used to identify copy number variable sites, and the literature documents multiple effective algorithms. We focus here on the specific problem of detecting regions where variation in copy number is relatively common in the sample at hand. This problem encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual. RESULTS: We present a segmentation method named generalized fused lasso (GFL) to reconstruct copy number variant regions, that is based on penalized estimation and is capable of processing multiple signals jointly. Our approach is computationally very attractive and leads to sensitivity and specificity levels comparable to those of state-of-the-art specialized methodologies. We illustrate its applicability with simulated and real data sets. CONCLUSIONS: The flexibility of our framework makes it applicable to data obtained with a wide range of technology. Its versatility and speed make GFL particularly useful in the initial screening stages of large data sets.     

Comparison of intravenous infusions of iloprost and oral nifedipine in treatment of Raynaud's phenomenon in patients with systemic sclerosis: a double blind randomised study.

OBJECTIVE--To compare the long term effects of short term intravenous infusions of iloprost with those of oral nifedipine in patients with Raynaud''s phenomenon associated with systemic sclerosis. DESIGN--Double blind, placebo controlled, randomised group comparison. SETTING--Dermatology outpatient clinic. PATIENTS--Twenty three patients with Raynaud''s phenomenon associated with well documented systemic sclerosis (American Rheumatism Association criteria) and with typical abnormalities in fingernail folds on capillaroscopy. INTERVENTIONS--Twelve patients were randomised to receive intravenous infusions of iloprost starting at 0.5 ng/kg/min and increased by 0.5 ng/kg/min every 15 minutes to a maximum of 2.0 ng/kg/min for eight hours on three consecutive days with a further single infusion at week 8. Placebo capsules were given concurrently. Eleven patients were randomised to receive nifedipine, starting at 30 mg daily and increased to 60 mg daily after four weeks for another 12 weeks. Infusions of placebo were given in the same manner as the infusions of iloprost. One patient from each group withdrew because of social reasons and three patients receiving nifedipine withdrew because of side effects. END POINT--Reduction in number, duration, and severity of attacks of Raynaud''s phenomenon, reduction in number of digital lesions, increase in digital blood flow. MEASUREMENTS AND MAIN RESULTS--Measurements were taken at 0, 4, 8, 12, and 16 weeks. Both regimens produced a reduction in the number, duration, and severity of attacks of Raynaud''s phenomenon. The mean (SE) number of digital lesions was reduced with iloprost (from 3.5 (1.6) to 0.6 (0.3] and with nifedipine (from 4.3 (0.8) to 1.4 (0.5] after 16 weeks. Hand temperature and digital and microcirculatory blood flow were increased with iloprost but not with nifedipine. CONCLUSION--Both iloprost and nifedipine are beneficial in the treatment of Raynaud''s phenomenon. With nifedipine, however, side effects are common. Short term infusions of iloprost provide longlasting relief of symptoms, and side effects occur only during the infusions and are dose dependent.