Predicting species distributions from museum and herbarium records using multiresponse models fitted with multivariate adaptive regression splines

Current circumstances — that the majority of species distribution records exist as presence‐only data (e.g. from museums and herbaria), and that there is an established need for predictions of species distributions — mean that scientists and conservation managers seek to develop robust methods for using these data. Such methods must, in particular, accommodate the difficulties caused by lack of reliable information about sites where species are absent. Here we test two approaches for overcoming these difficulties, analysing a range of data sets using the technique of multivariate adaptive regression splines (MARS). MARS is closely related to regression techniques such as generalized additive models (GAMs) that are commonly and successfully used in modelling species distributions, but has particular advantages in its analytical speed and the ease of transfer of analysis results to other computational environments such as a Geographic Information System. MARS also has the advantage that it can model multiple responses, meaning that it can combine information from a set of species to determine the dominant environmental drivers of variation in species composition. We use data from 226 species from six regions of the world, and demonstrate the use of MARS for distribution modelling using presence‐only data. We test whether (1) the type of data used to represent absence or background and (2) the signal from multiple species affect predictive performance, by evaluating predictions at completely independent sites where genuine presence–absence data were recorded. Models developed with absences inferred from the total set of presence‐only sites for a biological group, and using simultaneous analysis of multiple species to inform the choice of predictor variables, performed better than models in which species were analysed singly, or in which pseudo‐absences were drawn randomly from the study area. The methods are fast, relatively simple to understand, and useful for situations where data are limited. A tutorial is included.     

Potential impacts of wave‐powered marine renewable energy installations on marine birds

One potential approach to combat the impacts of climate change is the expansion of renewable energy installations, leading to an increase in the number of wave‐powered marine renewable energy installations (MREIs). The consequences of increased use of these devices for birds are unknown. Here we describe the wave‐powered energy‐generating devices currently either operational or in development and review the potential threats and benefits of these to marine birds, their habitats and prey. Direct negative effects include risk of collision, disturbance, displacement and redirection during construction, operation and decommissioning. Above‐water collision is a particular concern with wind‐powered devices, but, because of their low profiles, the collision risk associated with wave‐powered devices is likely to be much lower. Conversely, wave devices also pose the novel threat of underwater collision. Wave‐energy‐generating devices may indirectly impact marine birds by altering oceanographic processes and food availability, with implications for trophic cascades. Through appropriate mitigation, wave‐powered MREIs offer the potential to enhance habitats. Direct positive effects may include provision of roosting sites, and indirect positive effects may include prey aggregation due to suitable substrates for sessile organisms or because they act as de facto protected areas. The cumulative effect of these could be the improvement and protection of foraging opportunities for marine birds. Recent studies have been critical of the methods used in the assessment of wind‐powered MREI impacts, which lack sufficient sample sizes, controls or pre‐development comparisons. Here we suggest solutions for the design of future studies into the effects of MREIs. Wave‐powered MREIs are certain to become part of the marine environment, but with appropriate planning, mitigation and monitoring they have the potential to offer benefits to marine birds in the future.     

A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery

Plasma is the most easily accessible source for biomarker discovery in clinical proteomics. However, identifying potential biomarkers from plasma is a challenge given the large dynamic range of proteins. The potential biomarkers in plasma are generally present at very low abundance levels and hence identification of these low abundance proteins necessitates the depletion of highly abundant proteins. Sample pre-fractionation using immuno-depletion of high abundance proteins using multi-affinity removal system (MARS) has been a popular method to deplete multiple high abundance proteins. However, depletion of these abundant proteins can result in concomitant removal of low abundant proteins. Although there are some reports suggesting the removal of non-targeted proteins, the predominant view is that number of such proteins is small. In this study, we identified proteins that are removed along with the targeted high abundant proteins. Three plasma samples were depleted using each of the three MARS (Hu-6, Hu-14 and Proteoprep 20) cartridges. The affinity bound fractions were subjected to gelC-MS using an LTQ-Orbitrap instrument. Using four database search algorithms including MassWiz (developed in house), we selected the peptides identified at <1% FDR. Peptides identified by at least two algorithms were selected for protein identification. After this rigorous bioinformatics analysis, we identified 101 proteins with high confidence. Thus, we believe that for biomarker discovery and proper quantitation of proteins, it might be better to study both bound and depleted fractions from any MARS depleted plasma sample.     

Determinants of gait stability while walking on a treadmill: A machine learning approach

Dynamic balance in human locomotion can be assessed through the local dynamic stability (LDS) method. Whereas gait LDS has been used successfully in many settings and applications, little is known about its sensitivity to individual characteristics of healthy adults. Therefore, we reanalyzed a large dataset of accelerometric data measured for 100 healthy adults from 20 to 70 years of age performing 10 min treadmill walking. We sought to assess the extent to which the variations of age, body mass and height, sex, and preferred walking speed (PWS) could influence gait LDS. The random forest (RF) and multiple adaptive regression splines (MARS) algorithms were selected for their good bias-variance tradeoff and their capabilities to handle nonlinear associations. First, through variable importance measure (VIM), we used RF to evaluate which individual characteristics had the highest influence on gait LDS. Second, we used MARS to detect potential interactions among individual characteristics that may influence LDS. The VIM and MARS results indicated that PWS and age correlated with LDS, whereas no associations were found for sex, body height, and body mass. Further, the MARS model detected an age by PWS interaction: on one hand, at high PWS, gait stability is constant across age while, on the other hand, at low PWS, gait instability increases substantially with age. We conclude that it is advisable to consider the participants’ age as well as their PWS to avoid potential biases in evaluating dynamic balance through LDS.     

Stretchable Supercapacitors as Emergent Energy Storage Units for Health Monitoring Bioelectronics

Emerging health monitoring bioelectronics require energy storage units with improved stretchability, biocompatibility, and self‐charging capability. Stretchable supercapacitors hold great potential for such systems due to their superior specific capacitances, power densities, and tissue‐conforming properties, as compared to both batteries and conventional capacitors. Despite the rapid progress that has been made in supercapacitor research, practical applications in health monitoring bioelectronics have yet to be achieved, requiring innovations in materials, device configurations, and fabrications tailored for such applications. In this review, the progress in stretchable supercapacitor‐powered health monitoring bioelectronics is summarized and the required specifications of supercapacitors for different types of application settings with varying demands on biocompatibility are discussed, including nontouching wearables, skin‐touching wearables, skin‐conforming wearables, and implantables. The perspective of this review is then broadened to focus on integration of stretchable supercapacitors in bioelectronics and aspects of energy harvesting and sensing. Finally further insights on the existing challenges in this developing field and potential solutions are provided.     

Production of complex viral glycoproteins in plants as vaccine immunogens

Plant molecular farming offers a cost‐effective and scalable approach to the expression of recombinant proteins which has been proposed as an alternative to conventional production platforms for developing countries. In recent years, numerous proofs of concept have established that plants can produce biologically active recombinant proteins and immunologically relevant vaccine antigens that are comparable to those made in conventional expression systems. Driving many of these advances is the remarkable plasticity of the plant proteome which enables extensive engineering of the host cell, as well as the development of improved expression vectors facilitating higher levels of protein production. To date, the only plant‐derived viral glycoprotein to be tested in humans is the influenza haemagglutinin which expresses at ~50 mg/kg. However, many other viral glycoproteins that have potential as vaccine immunogens only accumulate at low levels in planta. A critical consideration for the production of many of these proteins in heterologous expression systems is the complexity of post‐translational modifications, such as control of folding, glycosylation and disulphide bridging, which is required to reproduce the native glycoprotein structure. In this review, we will address potential shortcomings of plant expression systems and discuss strategies to optimally exploit the technology for the production of immunologically relevant and structurally authentic glycoproteins for use as vaccine immunogens.     

Life Cycle Assessment of Diesel and Electric Public Transportation Buses

The Clean Air Act in the United States identifies diesel‐powered motor vehicles, including transit buses, as significant sources of several criteria pollutants that contribute to ground‐level ozone formation or smog. The effects of air pollution in urban areas are often more significant due to congestion and can lead to respiratory and cardiovascular health impacts. Life cycle assessment (LCA) has been utilized in the literature to compare conventional gasoline‐powered passenger cars with various types of electric and hybrid‐powered alternatives, however, no similarly detailed studies exist for mass transit buses. LCA results from this study indicate that the use phase, consisting of diesel production/combustion for the conventional bus and electricity generation for the electric bus, dominates most impact categories; however, the effects of battery production are significant for global warming, carcinogens, ozone depletion, and eco‐toxicity. There is a clear connection between the mix of power‐generation technologies and the preference for the diesel or electric bus. With the existing U.S. average grid, there is a strong preference for the conventional diesel bus over the electric bus when considering global warming impacts alone. Policy makers must consider regional variations in the electricity grid prior to recommending the use of battery electric buses to reduce carbon dioxide (CO₂) emissions. This study found that the electric bus was preferable in only eight states, including Washington and Oregon. Improvements in battery technology reduce the life cycle impacts from the electric bus, but the electricity grid makeup is the dominant variable.     

Functionalized nanopipettes: toward label-free, single cell biosensors

Nanopipette technology has been proven to be a label-free biosensor capable of identifying DNA and proteins. The nanopipette can include specific recognition elements for analyte discrimination based on size, shape, and charge density. The fully electrical read-out and the ease and low-cost fabrication are unique features that give this technology an enormous potential. Unlike other biosensing platforms, nanopipettes can be precisely manipulated with submicron accuracy and used to study single cell dynamics. This review is focused on creative applications of nanopipette technology for biosensing. We highlight the potential of this technology with a particular attention to integration of this biosensor with single cell manipulation platforms.     

A more sensitive platform for the detection of low-abundance BRAFV600E mutations

Identifying low-abundance mutations is important for the therapy and diagnose of cancer. Since the potential for tumor heterogeneity, the efficient detection of cancer-relevant mutations largely depends on the sensitivity of the methods employed. To confirm whether the mutation detection platforms affect the perceived prevalence of the BRAF(V600E) and its correlation with clinicopathologic features in papillary thyroid carcinomas (PTC), we compared Sanger Sequencing (SS), Pyrosequencing (PS), and a newly built allele-specific real-time PCR (AS-qPCR) apparatus for the detection of BRAF(V600E) in a Chinese cohort of conventional variant PTC. Accurate plasmid standards were built to assess the limit of detection of the three platforms. In this research, AS-qPCR has been found both the most sensitive and reliable at detecting mutation. The mutations detected by AS-qPCR which were not detected by SS or PS due to low abundance were confirmed by mutation enrichment platform COLD-PCR followed by SS. When analyzed by AS-qPCR, BRAF(V600E) was associated with a more aggressive phenotype. Our results indicate that the reported prevalence of the BRAF(V600E) mutations in PTC has been underestimated and more sensitive methods such as AS-qPCR should be applied in clinical settings.     

Anti-MRSA agent discovery using Caenorhabditis elegans -based high-throughput screening

Staphylococcus aureus is a leading cause of hospital- and community-acquired infections. Despite current advances in antimicrobial chemotherapy, the infections caused by S. aureus remain challenging due to their ability to readily develop resistance. Indeed, antibiotic resistance, exemplified by methicillin-resistant S. aureus (MRSA) is a top threat to global health security. Furthermore, the current rate of antibiotic discovery is much slower than the rate of antibiotic-resistance development. It seems evident that the conventional in vitro bacterial growth-based screening strategies can no longer effectively supply new antibiotics at the rate needed to combat bacterial antibiotic-resistance. To overcome this antibiotic resistance crisis, screening assays based on host–pathogen interactions have been developed. In particular, the free-living nematode Caenorhabditis elegans has been used for drug screening against MRSA. In this review, we will discuss the general principles of the C. elegans-based screening platform and will highlight its unique strengths by comparing it with conventional antibiotic screening platforms. We will outline major hits from high-throughput screens of more than 100,000 small molecules using the C. elegans–MRSA infection assay and will review the mode-of-action of the identified hit compounds. Lastly, we will discuss the potential of a C. elegans-based screening strategy as a paradigm shift screening platform.     

Bio-Inspired Wooden Actuators for Large Scale Applications

Implementing programmable actuation into materials and structures is a major topic in the field of smart materials. In particular the bilayer principle has been employed to develop actuators that respond to various kinds of stimuli. A multitude of small scale applications down to micrometer size have been developed, but up-scaling remains challenging due to either limitations in mechanical stiffness of the material or in the manufacturing processes. Here, we demonstrate the actuation of wooden bilayers in response to changes in relative humidity, making use of the high material stiffness and a good machinability to reach large scale actuation and application. Amplitude and response time of the actuation were measured and can be predicted and controlled by adapting the geometry and the constitution of the bilayers. Field tests in full weathering conditions revealed long-term stability of the actuation. The potential of the concept is shown by a first demonstrator. With the sensor and actuator intrinsically incorporated in the wooden bilayers, the daily change in relative humidity is exploited for an autonomous and solar powered movement of a tracker for solar modules.     

Androgen receptors: Relationship to growth response and to intracellular androgen transport in nine variant lines of the shionogi mouse mammary carcinoma

Aspects of the biological significance of androgen receptors have been studied in nine variant lines of the Shionogi carcinoma, two of which are androgen dependent and seven of which are autonomous. The dependent lines, and two of the seven autonomous lines, contain androgen receptors; this finding demonstrates that the presence of receptors is not an accurate marker of hormonal dependence in vivo. Since the ability to transport androgens into the nucleus, as judged from the relative maximal rates of transport, is virtually restricted to dependent and autonomous lines which possess cytoplasmic receptors, it is clear that such receptors may play a role in regulating the intranuclear concentration of androgens. The absence of cytoplasmic receptors and the comparative lack of perceptible transper of androgens across the nuclear membrane are features peculiar to the autonomous condition.     

Androgen receptors: relationship to growth response and to intracellular androgen transport in nine variant lines of the Shionogi mouse mammary carcinoma.

Aspects of the biological significance of androgen receptors have been studied in nine variant lines of the Shionogi carcinoma, two of which are androgen dependent and seven of which are autonomous. The dependent lines, and two of the seven autonomous lines, contain androgen receptors; this finding demonstrates that the presence of receptors is not an accurate marker of hormonal dependence in vivo. Since the ability to transport androgens into the nucleus, as judged from the relative maximal rates of transport, is virtually restricted to dependent and autonomous lines which possess cytoplasmic receptors, it is clear that such receptors may play a role in regulating the intranuclear concentration of androgens. The absence of cytoplasmic receptors and the comparative lack of perceptible transfer of androgens across the nuclear membrane are features peculiar to the autonomous condition.     

Integrated Assessment of Large-Scale Biofuel Production

This paper proposes a different framework for discussing the possibility of replacing a significant fraction of fossil energy consumption of modern economies with biofuels. The proposed analysis is not based on the two classic feasibility checks—land availability and output/input energy ratio—debated in the majority of the literature in this field. Rather, the focus is on the desirability of an energy sector powered by biomass energy. Discussing of desirability requires introducing a multicriteria approach, that in turn requires a definition of a set of criteria of performance for such an energy sector. The concepts of societal metabolism and ecosystem metabolism are introduced to define five criteria of performance for an energy sector powered by alternative sources.

This paper does not tell the society whether or not biofuels should be used to replace fossil energy. Rather, it proposes a method of characterization of pros and cons for the option biofuel which can be used to make more informed choices. An analysis of three systems of production—corn-ethanol, sunflower-biodiesel, and SRWC-methanol—is provided to indicate the existence of systemic characteristics associated with an energy sector powered by biofuels. These characteristics are likely to persist even when different technical coefficients will be achieved. The conclusion is that, at the moment, it is not possible to replace the actual performance of an energy sector based on fossil energy with an energy sector running on biofuel. Biomass energy can and will have to play an important role in the sustainability of humankind, but this will require a better understanding of (i) the role that an energy sector plays within a given structure of societal metabolism; and (ii) the impact generated on ecosystem metabolism by societal metabolism, plus a lot of wisdom.     

Crop improvement in the 21st century

Crop yields increased dramatically in the 20th century as recorded on Broadbalk or in world averages. The vast majority of that increase has occurred since the last world war and has been powered by changes in the genetic potential of the crop and in the way in which it has been managed. Nevertheless, the challenge to feed a world population that is likely to rise to 8 billion is formidable, particularly since recent analyses suggest that the rate of increase in yields of several crops may have dropped over the last decade. What are the opportunities to meet this challenge and to continue to improve the yields of our crops? Improvements in agronomy are likely to be more concerned with efficiency and elegance rather than in major breakthroughs. More sophisticated crop protection chemicals designed on the basis of vastly increased screening potentials and (at last?) possibilities of rational design will be supplemented by a battery of decision support systems to aid management choices which can be precisely implemented. Genetic improvement is the area in which to-look for the major breakthroughs. The broad potential of recombinant DNA technology will provide the possibility of both molecular analyses of crop productivity and ways in which it may be possible to improve that productivity. The goal of analysis may be approached in three ways: starting at the beginning by generating complete sequences of the plant genome; starting at the end by genetic analysis of phenotypes using genetic marker technology; or, starting in the middle, by metabolic analysis. Improvements may be obtained by re-assorting what has been achieved through enhanced breeding technologies, by randomly induced change, and by generation of totally new possibilities through biochemical engineering. Examples of all approaches will be given. The onset of genomics will provide massive amounts of information, but the success will depend on using that to improve crop phenotypes. The ability to meet the challenges of the 21st century will depend on the ability to close that 'phenotype gap'.     

Fluorescence detection methods for microfluidic droplet platforms

The development of microfluidic platforms for performing chemistry and biology has in large part been driven by a range of potential benefits that accompany system miniaturisation. Advantages include the ability to efficiently process nano- to femoto- liter volumes of sample, facile integration of functional components, an intrinsic predisposition towards large-scale multiplexing, enhanced analytical throughput, improved control and reduced instrumental footprints.¹In recent years much interest has focussed on the development of droplet-based (or segmented flow) microfluidic systems and their potential as platforms in high-throughput experimentation.^2-4 Here water-in-oil emulsions are made to spontaneously form in microfluidic channels as a result of capillary instabilities between the two immiscible phases. Importantly, microdroplets of precisely defined volumes and compositions can be generated at frequencies of several kHz. Furthermore, by encapsulating reagents of interest within isolated compartments separated by a continuous immiscible phase, both sample cross-talk and dispersion (diffusion- and Taylor-based) can be eliminated, which leads to minimal cross-contamination and the ability to time analytical processes with great accuracy. Additionally, since there is no contact between the contents of the droplets and the channel walls (which are wetted by the continuous phase) absorption and loss of reagents on the channel walls is prevented.Once droplets of this kind have been generated and processed, it is necessary to extract the required analytical information. In this respect the detection method of choice should be rapid, provide high-sensitivity and low limits of detection, be applicable to a range of molecular species, be non-destructive and be able to be integrated with microfluidic devices in a facile manner. To address this need we have developed a suite of experimental tools and protocols that enable the extraction of large amounts of photophysical information from small-volume environments, and are applicable to the analysis of a wide range of physical, chemical and biological parameters. Herein two examples of these methods are presented and applied to the detection of single cells and the mapping of mixing processes inside picoliter-volume droplets. We report the entire experimental process including microfluidic chip fabrication, the optical setup and the process of droplet generation and detection.     

Small-angle X-ray Solution Scattering Study of the Multi-aminoacyl-tRNA Synthetase Complex Reveals an Elongated and Multi-armed particle

In animal cells, nine aminoacyl-tRNA synthetases are associated with the three auxiliary proteins p18, p38, and p43 to form a stable and conserved large multi-aminoacyl-tRNA synthetase complex (MARS), whose molecular mass has been proposed to be between 1.0 and 1.5 MDa. The complex acts as a molecular hub for coordinating protein synthesis and diverse regulatory signal pathways. Electron microscopy studies defined its low resolution molecular envelope as an overall rather compact, asymmetric triangular shape. Here, we have analyzed the composition and homogeneity of the native mammalian MARS isolated from rabbit liver and characterized its overall internal structure, size, and shape at low resolution by hydrodynamic methods and small-angle x-ray scattering in solution. Our data reveal that the MARS exhibits a much more elongated and multi-armed shape than expected from previous reports. The hydrodynamic and structural features of the MARS are large compared with other supramolecular assemblies involved in translation, including ribosome. The large dimensions and non-compact structural organization of MARS favor a large protein surface accessibility for all its components. This may be essential to allow structural rearrangements between the catalytic and cis-acting tRNA binding domains of the synthetases required for binding the bulky tRNA substrates. This non-compact architecture may also contribute to the spatiotemporal controlled release of some of its components, which participate in non-canonical functions after dissociation from the complex.     

Issues and developments on the consumer recovery construct

The consumer recovery model has had increasing influence on mental health practices in the United States, Western Europe, and several other countries. However, adoption of the model has reflected political decisions rather than empirical evidence of the validity of the model or its value for treatment services. The recovery construct is poorly defined, and until recently there has been no reliable and valid measure with which to base a research program. We have developed an empirical measure that is well-suited for both research and clinical applications: the Maryland Assessment of Recovery in Serious Mental Ill-ness (MARS). We briefly describe the MARS and present preliminary data demonstrating that recovery is not a simple by-product of traditional outcome do-mains, but seems to be a distinct construct that may have important implications for understanding consumers with serious mental illness and for evaluating the outcome of treatment programs.