ALBERT

Description: African elephants, the largest land animal, face particular physiological challenges in captivity and the wild. Captive elephants can become over- or under-conditioned with inadequate exercise and diet management. Few studies have quantified body composition or water turnover in elephants, and none to date have examined longitudinal responses to changes in diet or air temperature. Using the stable isotope deuterium oxide ( 2 H 2 O), we investigated changes in body mass, estimated fat-free mass (FFM, including fat-free gut content) and body fat in response to a multi-year intervention that reduced dietary energy density for adult African elephants housed at the North Carolina Zoo. We also examined the relationship between air temperature and water turnover. Deuterium dilution and depletion rates were assayed via blood samples and used to calculate body composition and water turnover in two male and three female African elephants at six intervals over a 3-year period. Within the first year after the dietary intervention, there was an increase in overall body mass, a reduction in body fat percentage and an increase in FFM. However, final values of both body fat percentage and FFM were similar to initial values. Water turnover (males: 359 ± 9 l d −1 ; females: 241 ± 28 l d −1 ) was consistent with the allometric scaling of water use in other terrestrial mammals. Water turnover increased with outdoor air temperature. Our study highlights the physiological water dependence of elephants and shows that individuals have to drink every 2–3 days to avoid critical water loss of approximately 10% body mass in hot conditions.

Description: The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard–Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo , possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

Description: The ability to distinguish between erratic and systematic patterns of change in case count data is crucial for assessing and projecting the course of disease outbreaks. Here, it is shown that measuring the strength of trends can provide information that is not readily captured by commonly used descriptive indicators. In combination with the 7-day moving average, Bandt and Pompe's permutation entropy and Wilder's relative strength index were found to support the timely detection of coronavirus epidemic trends and transitions in data from various countries. The results demonstrate that measuring the strength of epidemic growth trends in addition to their magnitude can significantly enhance disease surveillance.

Description: Star and planet formation are inextricably linked. In the earliest phases of the collapse of a protostar, a disc forms around the young star and such discs are observed for the first several million years of a star’s life. It is within these circumstellar, or protoplanetary, discs that the first stages of planet formation occur. Recent observations from the Atacama large millimetre array (ALMA) suggest that planet formation may already be underway after only 1 Myr of a star’s life. However, stars do not form in isolation; they form from the collapse and fragmentation of giant molecular clouds several parsecs in size. This results in young stars forming in groups—often referred to as ‘clusters’. In these star-forming regions, the stellar density is much higher than the location of the Sun and other stars in the Galactic disc that host exoplanets. As such, the environment where stars form has the potential to influence the planet formation process. In star-forming regions, protoplanetary discs can be truncated or destroyed by interactions with passing stars, as well as photoevaporation from the radiation fields of very massive stars. Once formed, the planets themselves can have their orbits altered by dynamical encounters—either directly from passing stars or through secondary effects such as the Kozai–Lidov mechanism. In this contribution, I review the different processes that can affect planet formation and stability in star-forming regions. I discuss each process in light of the typical range of stellar densities observed for star-forming regions. I finish by discussing these effects in the context of theories for the birth environment of the Solar System.

Description: Recognising the nature of the predation risk, and responding to it accurately, is crucial to fitness. Yet, even the most accurate adaptive responses to predation risk usually entail costs, both immediate and lifelong. Rooting in life-history theory, we hypothesize that an animal can perceive the nuances of prey size and age selectivity by the predator and modulate its life history accordingly. We test the prediction that—contrary to the faster or earlier senescence under predation risk that increases with prey size and age—under predation risk that decreases with prey size and age either no senescence acceleration or even its deceleration is to be observed. We use two species of indeterminate growers, small crustaceans of the genus Daphnia , Daphnia Pulex and Daphnia magna , as the model prey, and their respective gape-limited invertebrate predators, a dipteran, midge larva Chaoborus flavicans , and a notostracan, tadpole shrimp Triops cancriformis . We analyse age-specific survival, mortality and fertility rates, and find no senescence acceleration, as predicted. With this study, we complete the picture of the expected non-consumptive phenotypic effects of perceived predation pressure of different age-dependence patterns.

Description: ET-26-HCl, a novel anaesthetic agent with promising pharmacological properties, lacks extensive studies on pharmacokinetics and disposition in vitro and in vivo . In this study, we investigated the metabolic stability, metabolite production and plasma protein binding (PPB) of ET-26-HCl along with its tissue distribution, excretion and pharmacokinetics in animals after intravenous administration. Ultra-high performance liquid chromatography–tandem quadrupole time-of-flight mass spectrometry identified a total of eight new metabolites after ET-26-HCl biotransformation in liver microsomes from different species. A hypothetical cytochrome P450-metabolic pathway including dehydrogenation, hydroxylation and demethylation was proposed. The PPB rate was highest in mouse and lowest in human. After intravenous administration, ET-26-HCl distributed rapidly to all tissues in rats and beagle dogs, with the highest concentrations in fat and liver. High concentrations of ET-26-acid, a major hydroxylation metabolite of ET-26-HCl, were found in liver, plasma and kidney. Almost complete clearance of ET-26-HCl from plasma occurred within 4 h after administration. Only a small fraction of the parent compound and its acid form were excreted via the urine and faeces. Taken together, the results added to a better understanding of the metabolic and pharmacokinetic properties of ET-26-HCl, which may contribute to the further development of this drug.

Description: Aggression in territorial social systems is easy to interpret because the benefits of territorial defence mostly accrue to the territorial holder. However, in non-territorial systems, high aggression seems puzzling and raises intriguing evolutionary questions. We describe extreme rates of despotism between age classes in a passerine bird, the painted bunting ( Passerina ciris ), during the pre-moulting period. Aggressive encounters were not associated with aggressors gaining immediate access to resources. Instead, conspecifics, and even other species, were pursued as though being harassed; this aggression generated an ideal despotic habitat distribution such that densities of adult males were higher in high-quality sites. Aggression was not a by-product of elevated testosterone carried over from the breeding season but, rather, appeared associated with dehydroepiandrosterone, a hormone that changes rates of aggression in non-breeding birds without generating the detrimental effects of high testosterone titres that control aggression in the breeding season. This extraordinary pre-moult aggression seems puzzling because individual buntings do not hold defined territories during their moult. We speculate that this high aggression evolved as a means of regulating the number of conspecifics that moulted in what were historically small habitat patches with limited food for supporting the extremely rapid moults of painted buntings.

Description: Chickens ( Gallus gallus domesticus ) from the Americas have long been recognized as descendants of European chickens, transported by early Europeans since the fifteenth century. However, in recent years, a possible pre-Columbian introduction of chickens to South America by Polynesian seafarers has also been suggested. Here, we characterize the mitochondrial control region genetic diversity of modern chicken populations from South America and compare this to a worldwide dataset in order to investigate the potential maternal genetic origin of modern-day chicken populations in South America. The genetic analysis of newly generated chicken mitochondrial control region sequences from South America showed that the majority of chickens from the continent belong to mitochondrial haplogroup E. The rest belongs to haplogroups A, B and C, albeit at very low levels. Haplogroup D, a ubiquitous mitochondrial lineage in Island Southeast Asia and on Pacific Islands is not observed in continental South America. Modern-day mainland South American chickens are, therefore, closely allied with European and Asian chickens. Furthermore, we find high levels of genetic contributions from South Asian chickens to those in Europe and South America. Our findings demonstrate that modern-day genetic diversity of mainland South American chickens appear to have clear European and Asian contributions, and less so from Island Southeast Asia and the Pacific Islands. Furthermore, there is also some indication that South Asia has more genetic contribution to European chickens than any other Asian chicken populations.

Description: We monitored northern bat Eptesicus nilssonii (Keyserling & Blasius, 1839) acoustically along a 27 km road transect at weekly intervals in 1988, 1989 and 1990, and again in 2016 and 2017. The methodology of data collection and the transect were the same throughout, except that the insect-attracting mercury-vapour street-lights along parts of the road were replaced by sodium lights between the two survey periods. Counts along sections of the transect with and without street-lights were analysed separately. The frequency of bat encounters in unlit sections showed an average decline of 3.0% per year, corresponding to a reduction of 59% between 1988 and 2017. Sections with street-lights showed an 85% decline over the same period (6.3% per year). The decline represents a real reduction in the abundance of bats rather than an artefact of changed distribution of bats away from roads. Our study conforms with another long-term survey of the same species on the Baltic island of Gotland. Our results agree with predictions based on climate change models. They also indicate that the decline was caused directly by the disuse of the insect-attracting mercury-vapour street-lights, which may have resulted in lower availability of preferred prey (moths). In the 1980s, E. nilssonii was considered the most common bat in Sweden, but the subsequent decline would rather qualify it for vulnerable or endangered status in the national Red List of Threatened Species.

Description: We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal–peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict a priori possible binding modes as a precursor to longer, atomistic simulations.

Description: The absence of genome complexity in prokaryotes, being the evolutionary precursors to eukaryotic cells comprising all complex life (the prokaryote–eukaryote divide), is a long-standing question in evolutionary biology. A previous study hypothesized that the divide exists because prokaryotic genome size is constrained by bioenergetics (prokaryotic power per gene or genome being significantly lower than eukaryotic ones). However, this hypothesis was evaluated using a relatively small dataset due to lack of data availability at the time, and is therefore controversial. Accordingly, we constructed a larger dataset of genomes, metabolic rates, cell sizes and ploidy levels to investigate whether an energetic barrier to genome complexity exists between eukaryotes and prokaryotes while statistically controlling for the confounding effects of cell size and phylogenetic signals. Notably, we showed that the differences in bioenergetics between prokaryotes and eukaryotes were less significant than those previously reported. More importantly, we found a limited contribution of power per genome and power per gene to the prokaryote–eukaryote dichotomy. Our findings indicate that the prokaryote–eukaryote divide is hard to explain from the energetic perspective. However, our findings may not entirely discount the traditional hypothesis; in contrast, they indicate the need for more careful examination.

Description: Compounds including non-canonical amino acids (ncAAs) or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the ncAAs can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by a six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved minimizing harmful consequences of mutations or mistranslations of encoded proteins.

Description: The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

Description: Migratory flight is physiologically highly demanding and has been shown to negatively affect multiple parameters of constitutive immune function (CIF), an animal's first line of physiological defence against infections. In between migratory flights, most birds make stopovers, periods during which they accumulate fuel for the next flight(s). Stopovers are also commonly thought of as periods of rest and recovery, but what this encompasses is largely undefined. Here, we show that during stopover, northern wheatears Oenanthe oenanthe, a long-distance migratory bird, can rapidly increase constitutive innate immune function. We caught and temporarily caged birds under ad libitum food conditions at a stopover site in autumn. Within 2 days, most birds significantly increased complement activity and their ability to kill microbes. Changes in immune function were not related to the birds' food intake or extent of fuel accumulation. Our study suggests that stopovers may not only be important to refuel but also to restore immune function. Additionally, the increase in CIF could help migrating birds to deal with novel pathogens they may encounter at stopover sites.

Description: Lameness in sheep is the biggest cause of concern regarding poor health and welfare among sheep-producing countries. Best practice for lameness relies on rapid treatment, yet there are no objective measures of lameness detection. Accelerometers and gyroscopes have been widely used in human activity studies and their use is becoming increasingly common in livestock. In this study, we used 23 datasets (10 non-lame and 13 lame sheep) from an accelerometer- and gyroscope-based ear sensor with a sampling frequency of 16 Hz to develop and compare algorithms that can differentiate lameness within three different activities (walking, standing and lying). We show for the first time that features extracted from accelerometer and gyroscope signals can differentiate between lame and non-lame sheep while standing, walking and lying. The random forest algorithm performed best for classifying lameness with an accuracy of 84.91% within lying, 81.15% within standing and 76.83% within walking and overall correctly classified over 80% sheep within activities. Both accelerometer- and gyroscope-based features ranked among the top 10 features for classification. Our results suggest that novel behavioural differences between lame and non-lame sheep across all three activities could be used to develop an automated system for lameness detection.

Description: Apollo 16 soil-like regolith breccia 65745,7 contains two zircon-bearing clasts. One of these clasts is a thermally annealed silica-rich rock, which mineralogically has affinities with the High Alkali Suite (Clast 1), and yields zircon dates ranging from 4.08 to 3.38 Ga. The other clast is a KREEP-rich impact melt breccia (Clast 2) and yields zircon dates ranging from 3.97 to 3.91 Ga. The crystalline cores of both grains, which yield dates of ca 3.9 Ga, have undergone shock pressure modification at less than 20 GPa. We interpret that the U-Pb chronometer in these zircon grains has been partially reset by the Imbrium basin-forming event when the clasts were incorporated into the Cayley Plains ejecta blanket deposit. The zircon grains in Clast 1 have been partially decomposed, resulting in a breakdown polymineralic texture, with elevated U, Pb and Th abundances compared with those in the crystalline zircon. These decomposed areas exhibit younger dates around 3.4 Ga, suggesting a secondary high-pressure, high-temperature event, probably caused by an impact in the local Apollo 16 highlands area.

Description: Based on an electrochemical multiphysical simulation, a method for analysing electrolysis efficiency has been presented that considers the energy consumption required to produce a single kilogram of lithium and for the production of lithium, rather than the voltage in various parts. By adopting them as the criteria for analysing electrolysis efficiency in the lithium cell, several structural parameters have been optimized, such as the anode radius and anode–cathode distance. These parameters strongly affect the cell voltage and the velocity field distribution, which has a significant impact on the concentration distribution. By integrating the concentration distribution, the lithium production and energy consumption per kilogram, lithium is computed. By appointing the minimum of the chlorine and lithium concentration as the secondary reaction intensity, it is clear where the secondary reaction intensity is strong in the cell. The structure of a lithium electrolysis cell has been optimized by applying an orthogonal design approach, with the energy consumption notably decreasing from 35.0 to 28.3 kWh (kg Li) −1 and the lithium production successfully increasing by 0.17 mol.

Description: Secondary contacts can play a major role in the evolutionary histories of species. Various taxa diverge in allopatry and later on come into secondary contact during range expansions. When they meet, their interactions and the extent of gene flow depend on the level of their ecological differentiation and the strength of their reproductive isolation. In this study, we present the multilocus phylogeography of two cryptic whiskered bat species, Myotis mystacinus and M. davidii , with a particular focus on their putative sympatric zone. Our findings suggest that M. mystacinus and M. davidii evolved in allopatry and came into secondary contact during range expansions. Individuals in the area of secondary contact, in Anatolia and the Balkans, have discordant population assignments based on the mitochondrial and the nuclear datasets. These observed patterns suggest that the local M. mystacinus populations hybridized with expanding M. davidii populations, which resulted in mitochondrial introgression from the former. In the introgression area, M. mystacinus individuals with concordant nuclear and mitochondrial genotypes were identified in relatively few locations, suggesting that the indigenous populations might have been largely replaced by invading M. davidii . Changing environmental conditions coupled with ecological competition is the likely reason for this replacement. Our study presents one possible example of a historical population replacement that was captured in phylogeographic patterns.

Description: By the slight adjustment of oxides constituting thin film transistor-liquid crystal display (TFT-LCD) substrate glass, including equal mole fraction substitution of Al 2 O 3 , GeO 2 , B 2 O 3 , P 2 O 5 and ZrO 2 for SiO 2 , as well as the substitution of CaO for SrO with the total contents unchanged, the structural and physico-chemical properties of the glass was investigated by Raman spectroscopy and other measurements. The results showed that the short-range disorder brought by the substitution of GeO 2 , B 2 O 3 and P 2 O 5 for SiO 2 could weaken the stability and compactness of the glass network, and the physico-chemical properties deteriorated, while the process of glass melting would become easier accordingly. The short-range disorder by the substitution of ZrO 2 for SiO 2 with 1% mole fraction showed a little difference with other samples. Finally, the substitution of modified cations, such as CaO and SrO, showed a smaller variation compared with the substitution of network formers. On the condition of 1% mole fraction substitution of oxides investigated, the variation of samples showed a reasonable change and the performance was basically all satisfied for the use of TFT-LCD substrate.

Description: The exceptionally well-preserved holotype of the armoured dinosaur Borealopelta markmitchelli (Ornithischia; Nodosauridae) from the Early Cretaceous (Clearwater Formation) of northern Alberta preserves a distinct mass within the abdominal cavity. Fourteen independent criteria (including: co-allochthony, anatomical position, gastroliths) support the interpretation of this mass as ingested stomach contents—a cololite. Palynomorphs in the cololite are a subset of the more diverse external sample. Analysis of the cololite documents well-preserved plant material dominated by leaf tissue (88%), including intact sporangia, leaf cross-sections and cuticle, but also including stems, wood and charcoal. The leaf fraction is dominated (85%) by leptosporangiate ferns (subclass Polypodiidae), with low cycad–cycadophyte (3%) and trace conifer foliage. These data represent the most well-supported and detailed direct evidence of diet in an herbivorous dinosaur. Details of the dietary palaeoecology of this nodosaur are revealed, including: selective feeding on ferns; preferential ingestion of leptosporangiate ferns to the exclusion of Osmundaceae and eusporangiate ferns such as Marattiaceae; and incidental consumption of cycad–cycadophyte and conifer leaves. The presence of significant (6%) charcoal may represent the dietary use of recently burned conifer forest undergoing fern succession, early evidence of a fire succession ecology, as is associated with many modern large herbivores.

Description: This is the preface to a special issue in the journal Royal Society Open Science, themed around blockchain technology. Since this is still an emergent and interdisciplinary field, we first provide a gentle introduction into that larger topic. Then, we discuss why this technology has been criticized for not being energy-efficient. Next, we provide an analysis of recent developments in blockchain research that may help with making blockchain technology truly sustainable. Finally, we highlight some of the contributions made by papers in this special issue.

Description: Telomeres are repeat sequences of non-coding DNA-protein molecules that cap or intersperse metazoan chromosomes. Interest in telomeres has increased exponentially in recent years, to now include their ongoing dynamics and evolution within natural populations where individuals vary in telomere attributes. Phylogenetic analyses show profound differences in telomere length across non-model taxa. However, telomeres may also differ in length within individuals and between tissues. The latter becomes a potential source of error when researchers use different tissues for extracting DNA for telomere analysis and scientific inference. A commonly used tissue type for assessing telomere length is blood, a tissue that itself varies in terms of nuclear content among taxa, in particular to what degree their thrombocytes and red blood cells (RBCs) contain nuclei or not. Specifically, when RBCs lack nuclei, leucocytes become the main source of telomeric DNA. RBCs and leucocytes differ in lifespan and how long they have been exposed to ‘senescence' and erosion effects. We report on a study in which cells in whole blood from individual Australian painted dragon lizards ( Ctenophorus pictus ) were identified using flow cytometry and their telomere length simultaneously measured. Lymphocyte telomeres were on average 270% longer than RBC telomeres, and in azurophils (a reptilian monocyte), telomeres were more than 388% longer than those in RBCs. If this variation in telomere length among different blood cell types is a widespread phenomenon, and DNA for comparative telomere analyses are sourced from whole blood, evolutionary inference of telomere traits among taxa may be seriously complicated by the blood cell type comprising the main source of DNA.

Description: The identification of sea turtle behaviours is a prerequisite to predicting the activities and time-budget of these animals in their natural habitat over the long term. However, this is hampered by a lack of reliable methods that enable the detection and monitoring of certain key behaviours such as feeding. This study proposes a combined approach that automatically identifies the different behaviours of free-ranging sea turtles through the use of animal-borne multi-sensor recorders (accelerometer, gyroscope and time-depth recorder), validated by animal-borne video-recorder data. We show here that the combination of supervised learning algorithms and multi-signal analysis tools can provide accurate inferences of the behaviours expressed, including feeding and scratching behaviours that are of crucial ecological interest for sea turtles. Our procedure uses multi-sensor miniaturized loggers that can be deployed on free-ranging animals with minimal disturbance. It provides an easily adaptable and replicable approach for the long-term automatic identification of the different activities and determination of time-budgets in sea turtles. This approach should also be applicable to a broad range of other species and could significantly contribute to the conservation of endangered species by providing detailed knowledge of key animal activities such as feeding, travelling and resting.

Description: Recent population growth of the harbour porpoise ( Phocoena phocoena ), grey seal ( Halichoerus grypus ) and common seal ( Phoca vitulina ) in the North Sea has increased potential interaction between these species. Grey seals are known to attack harbour porpoises. Some harbour porpoises survive initially, but succumb eventually, often showing severely infected skin lesions. Bacteria transferred from the grey seal oral cavity may be involved in these infections and eventual death of the animal. In humans, seal bites are known to cause severe infections. In this study, a 16S rRNA-based microbiome sequencing approach is used to identify the oral bacterial diversity in harbour porpoises, grey seals and common seals; detect the potential transfer of bacteria from grey seals to harbour porpoises by biting and provide insights in the bacteria with zoonotic potential present in the seal oral cavity. β-diversity analysis showed that 12.9% (4/31) of the harbour porpoise skin lesion microbiomes resembled seal oral microbiomes, while most of the other skin lesion microbiomes also showed seal-associated bacterial species, including potential pathogens. In conclusion, this study shows that bacterial transmission from grey seals to harbour porpoises by biting is highly likely and that seal oral cavities harbour many bacterial pathogens with zoonotic potential.

Description: Microhaplotype markers have become an important research focus in forensic genetics. However, many reported microhaplotype markers have limited polymorphisms. In this study, we developed a set of highly polymorphic microhaplotype markers based on tri-allelic single-nucleotide polymorphisms. Eleven newly discovered microhaplotypes along with nine previously identified in our laboratory were studied. The microhaplotype genotypes of unrelated individuals and familial samples were generated on the MiSeq PE300 platform. These 20 loci have an average greater than 3.5 effective number of alleles. Over the whole set, the cumulative power of discrimination was 1–3.3 × 10 −18 , the cumulative power of exclusion was 1–1.928 × 10 −7 and the theoretical probability of detecting a mixture was 1–1.427 × 10 −6 . Differentiation comparisons of 26 populations from the 1000 Genomes Project distinguished among East Asian, South Asian, African and European populations. Overall, these markers enrich the current microhaplotype marker databases and can be applied for individual identification, paternity testing and biogeographic ancestry distinction.

Description: Standard evolutionary theory of ageing predicts weaker purifying selection on genes critical to later life stages. Prolonged post-reproductive lifespan (PPRLS), observed only in a few species like humans, is likely a result of disparate relaxation of purifying selection on survival and reproduction in late life stages. While the exact origin of PPRLS is under debate, many researchers agree on hypotheses like mother-care and grandmother-care, which ascribe PPRLS to investment into future generations—provision to one’s descendants to enhance their overall reproductive success. Here, we simulate an agent-based model, which properly accounts for age-specific selection, to examine how different investment strategies affect the strength of purifying selection on survival and reproduction. We observed in the simulations that investment strategies that allow a female individual to remain contributive to its own descendants (infants and adults) at late life stages may lead to differential relaxation of selection on survival and reproduction, and incur the adaptive evolution of PPRLS.

Description: The critical technical issues for the structure design of three-roller tube expander were first studied and analysed in this paper. Then, the major design parameters of the expansion unit structure and the bearing limit of 12¼″ three-roller tube expander were optimized and investigated by finite-element numerical simulation method. Results from study show that the required expansion force increases when the taper angle of the roller outer surface gets larger, taking the axial expansion force as the quantitative indicators. It is suggested that the roller tape angle of the expansion unit should be in the range of 9–12° considering the proper length of the roller and the non-self-locking tube expansion process. The required expansion force of the bellows first decreases and then increases when the gauge length of the expansion unit becomes longer. The optimal value of the gauge length is 50 mm considering the proper length of the roller. And according to the numerical simulation results, the designed three-roller tube expander meets the strength requirements. The results of this study are of great significance to the expend bellows drilling technology.

Description: Self-assembled peptide scaffolds based on D-RADA16 are an important matrix for controlled drug release and three-dimensional cell culture. In this work, D-RADA16 peptide hydrogels were coated on artificial bone composed of nano-hydroxyapatite/polyamide 66 (nHA/PA66) to obtain a porous drug-releasing structure for treating bone defects. The developed materials were characterized via transmission electron microscopy and scanning electron microscopy. The proliferation and adhesion of bone mesenchymal stem cells (BMSCs) were examined by confocal laser microscopy and CCK-8 experiments. The osteogenic ability of the porous materials towards bone BMSCs was examined in vitro by staining with Alizarin Red S and alkaline phosphatase, and bioactivity was evaluated in vivo . The results revealed that nHA/PA66/D-RADA16/bFGF reduces the degradation rate of D-RADA16 hydrogels and prolongs sustained release of bFGF, which would promote BMSCs proliferation, adhesion and osteogenesis in vitro and bone repair in vivo . Thus, it deserves more attention and is worthy of further research.

Description: Competition for food resources is widespread in nature. The foraging behaviour of social animals should thus be adapted to potential food competition. We conjectured that in the presence of co-foragers, animals would shift their tactics to forage more frequently for smaller food. Because smaller foods are more abundant in nature and allow faster consumption, such tactics should allow animals to consume food more securely against scrounging. We experimentally tested whether such a shift would be triggered automatically in human eating behaviour, even when there was no rivalry about food consumption. To prevent subjects from having rivalry, they were instructed to engage in a ‘taste test' in a laboratory, alone or in pairs. Even though the other subject was merely present and there was no real competition for food, subjects in pairs immediately exhibited a systematic behavioural shift to reaching for smaller food amounts more frequently, which was clearly distinct from their reaching patterns both when eating alone and when simply weighing the same food without eating any. These patterns suggest that behavioural shifts in the presence of others may be built-in tactics in humans (and possibly in other gregarious animals as well) to adapt to potential food competition in social foraging.

Description: Insecticide resistance has become problematic in tropical and subtropical regions, where Aedes mosquitoes and Aedes -borne arboviral diseases thrive. With the recent occurrence of chikungunya and the Zika virus in Jamaica, the Ministry of Health and Wellness, Jamaica, partnered with the United States Agency for International Development to implement multiple intervention activities to reduce the Aedes aegypti populations in seven parishes across the island and to assess the susceptibility of collected samples to various concentrations of temephos, Bacillus thuringiensis subsp. israelensis, (Bti), diflubenzuron and methoprene. Of the insecticides tested, only temephos has been used in routine larviciding activities in the island. The results showed that only temephos at concentrations 0.625 ppm and Bti at concentrations 6–8 ppm were effective at causing 98–100% mortality of local Ae. aegypti at 24 h exposure. Surprisingly, the growth inhibitors diflubenzuron and methoprene had minimal effect at preventing adult emergence in Ae. aegypti larvae in the populations tested. The results demonstrate the need for insecticide resistance testing as a routine part of vector control monitoring activies in order to determine useful tools that may be incorporated to reduce the abundance of Ae. aegypti .

Description: Parasites constitute a major selective pressure which has shaped animal behaviour through evolutionary time. One adaption to parasites consists of recognizing and avoiding substrates or cues that indicate their presence. Among substrates harbouring infectious agents, faeces are known to elicit avoidance behaviour in numerous animal species. However, the function and mechanisms of faeces avoidance in non-human primates has been largely overlooked by scientists. In this study, we used an experimental approach to investigate whether aversion to faeces in a foraging context is mediated by visual and olfactory cues in two cercopithecoid primates: mandrills ( Mandrillus sphinx ) and long-tailed macaques ( Macaca fascicularis ). Visual and olfactory cues of faeces elicited lower food consumption rates in mandrills and higher food manipulation rates in long-tailed macaques. Both results support the infection-avoidance hypothesis and confirm similar tendencies observed in other primate species. More studies are now needed to investigate the divergence of avoidance strategies observed in non-human primates regarding food contamination.

Description: The constraint release (CR) mechanism has important effects on polymer relaxation and the chains will show different relaxation behaviour in conditions of monodisperse, bidisperse and other topological environments. By comparing relaxation data of linear polyisoprene (PI) chains dissolved in very long matrix and monodisperse melts, Matsumiya et al. showed that CR mechanism accelerates both dielectric and viscoelastic relaxation (Matsumiya et al. 2013 Macromolecules 46 , 6067. ( doi:10.1021/ma400606n )). In this work, the experimental data reported by Matsumiya et al. are reproduced using the single slip-spring (SSp) model and the CR accelerating effects on both dielectric and viscoelastic relaxation are validated by simulations. This effect on viscoelastic relaxation is more pronounced. The coincidence for end-to-end relaxation and the viscoelastic relaxation has also been checked using probe version SSp model. A variant of SSp with each entanglement assigning a characteristic lifetime is also proposed to simulate various CR environment flexibly. Using this lifetime version SSp model, the correct relaxation function can be obtained with equal numbers of entanglement destructions by CR and reptation/contour length fluctuation (CLF) for monodisperse melts. Good agreement with published experiment data is also obtained for bidisperse melts, which validates the ability to correctly describe the CR environment of the lifetime version model.

Description: We employ a mathematical model (a phase oscillator model) to describe the deterministic and stochastic features of frog choruses in which male frogs attempt to avoid call overlaps. The mathematical model with a general interaction term is identified using a Bayesian approach, and it qualitatively reproduces the stationary and dynamical features of the empirical data. In addition, we quantify the magnitude of attention paid among the male frogs from the identified model, and then analyse the relationship between attention and behavioural parameters using a statistical approach. Our analysis demonstrates a negative correlation between attention and inter-frog distance, and also suggests a behavioural strategy in which male frogs selectively attend to a less attractive male frog (i.e. a male producing calls at longer intervals) in order to more effectively advertise their superior relative attractiveness to females.

Description: What is the relationship between environment and democracy? The framework of cultural evolution suggests that societal development is an adaptation to ecological threats. Pertinent theories assume that democracy emerges as societies adapt to ecological factors such as higher economic wealth, lower pathogen threats, less demanding climates and fewer natural disasters. However, previous research confused within-country processes with between-country processes and erroneously interpreted between-country findings as if they generalize to within-country mechanisms. We analyse a time-series cross-sectional dataset to study the dynamic relationship between environment and democracy (1949–2016), accounting for previous misconceptions in levels of analysis. By separating within-country processes from between-country processes, we find that the relationship between environment and democracy not only differs by country but also depends on the level of analysis. Economic wealth predicts increasing levels of democracy in between-country comparisons, but within-country comparisons show that democracy declines in years when countries become wealthier. This relationship is only prevalent among historically wealthy countries but not among historically poor countries, whose wealth also increased over time. By contrast, pathogen prevalence predicts lower levels of democracy in both between-country and within-country comparisons. Multi-level modelling also confirms that the within-country effect of pathogen prevalence remains robust even after considering a region-level analysis. Longitudinal analyses identifying temporal precedence reveal that not only reductions in pathogen prevalence drive future democracy, but also democracy reduces future pathogen prevalence and increases future wealth. These nuanced results contrast with previous analyses using narrow, cross-sectional data. Overall, our findings illuminate the dynamic process by which environment and democracy shape each other.

Description: We present in this work an economic analysis of ransomware, a relatively new form of cyber-enabled extortion. We look at how the illegal gains of the criminals will depend on the strategies they use, examining uniform pricing and price discrimination. We also explore the welfare costs to society of such strategies. In addition, we present the results of a pilot survey which demonstrate proof of concept in evaluating the costs of ransomware attacks. We discuss at each stage whether the different strategies we analyse have been encountered already in existing malware, and the likelihood of them being implemented in the future. We hope this work will provide some useful insights for predicting how ransomware may evolve in the future.

Description: Animal–robot studies can inform us about animal behaviour and inspire advances in agriculture, environmental monitoring and animal health and welfare. Currently, experimental results on how fish are affected by the presence of underwater robots are largely limited to laboratory environments with few individuals and a focus on model species. Laboratory studies provide valuable insight, but their results are not necessarily generalizable to larger scales such as marine aquaculture. This paper examines the effects of underwater robots and a human diver in a large fish aggregation within a Norwegian aquaculture facility, with the explicit purpose to improve the use of underwater robots for fish observations. We observed aquaculture salmon's reaction to the flipper-propelled robot U-CAT in a sea cage with 188 000 individuals. A significant difference in fish behaviour was found using U-CAT when compared to a thruster-driven underwater robot, Argus Mini and a human diver. Specifically, salmon were more likely to swim closer to U-CAT at a lower tailbeat frequency. Fish reactions were not significantly different when considering motor noise or when U-CAT's colour was changed from yellow to silver. No difference was observed in the distance or tailbeat frequency as a response to thruster or flipper motion, when actuated and passively floating robots were compared. These results offer insight into how large aggregations of aquaculture salmon respond to underwater robots. Furthermore, the proposed underwater video processing workflow to assess fish's response to underwater robots is simple and reproducible. This work provides a practical method to study fish–robot interactions, which can lead to improved underwater robot designs to provide more affordable, scalable and effective solutions.

Description: Corn stalk was used as the initial material to prepare a corn stalk matrix-g-polyacrylonitrile-based adsorbent. At first, the corn stalk was treated with potassium hydroxide and nitric acid to obtain the corn stalk-based cellulose (CS), and then the CS was modified by 2-bromoisobutyrylbromide (2-BiBBr) to prepare a macroinitiator. After that, polyacrylonitrile (PAN) was grafted onto the macroinitiator by single-electron transfer living radical polymerization (SET-LRP). A novel adsorbent AO CS-g-PAN was, therefore, obtained by introducing amidoxime groups onto the CS-g-PAN with hydroxylamine hydrochloride (NH 2 OH · HCl). FTIR, SEM and XPS were applied to characterize the structure of AO CS-g-PAN. The adsorbent was then employed to remove Pb(II) and Cu(II), and it exhibited a predominant adsorption performance on Pb(II) and Cu(II). The effect of parameters, such as temperature, adsorption time, pH and the initial concentration of metal ions on adsorption capacity, were examined in detail during its application. Results suggest that the maximum adsorption capacity of Pb(II) and Cu(II) was 231.84 mg g –1 and 94.72 mg g −1 , and the corresponding removal efficiency was 72.03% and 63%, respectively. The pseudo-second order model was more suitable to depict the adsorption process. And the adsorption isotherm of Cu(II) accorded with the Langmuir model, while the Pb(II) conformed better to the Freundlich isotherm model.

Description: Originally considered as large, solely Cambrian apex predators, Radiodonta—a clade of stem-group euarthropods including Anomalocaris— now comprises a diverse group of predators, sediment sifters and filter feeders. These animals are only known from deposits preserving non-biomineralized material, with radiodonts often the first and/or only taxa known from such deposits. Despite the widespread and diverse nature of the group, only a handful of radiodonts are known from post-Cambrian deposits, and all originate from deposits or localities rich in other total-group euarthropods. In this contribution, we describe the first radiodont from the UK, an isolated hurdiid frontal appendage from the Tremadocian (Lower Ordovician) Dol-cyn-Afon Formation, Wales, UK. This finding is unusual in two major aspects: firstly, the appendage (1.8 mm in size) is less than half the size of the next smallest radiodont frontal appendage known, and probably belonged to an animal between 6 and 15 mm in length; secondly, it was discovered in the sponge-dominated Afon Gam Biota, one of only a handful of non-biomineralized total-group euarthropods known from this deposit. This Welsh hurdiid breaks new ground for Radiodonta in terms of both its small size and sponge-dominated habitat. This occurrence demonstrates the adaptability of the group in response to the partitioning of ecosystems and environments in the late Cambrian and Early Ordovician world.

Description: In order to explore the factors affecting coal spontaneous combustion, the fractal characteristics of coal samples are tested, and a pore-scale model for oxygen adsorption in coal porous media is developed based on self-similar fractal model. The liquid nitrogen adsorption experiments show that the coal samples indicate evident fractal scaling laws at both low-pressure and high-pressure sections, and the fractal dimensions, respectively, represent surface morphology and pore structure of coal rock. The pore-scale model has been validated by comparing with available experimental data and numerical simulation. The present numerical results indicate that the oxygen adsorption depends on both the pore structures and temperature of coal rock. The oxygen adsorption increases with increased porosity, fractal dimension and ratio of minimum to maximum pore sizes. The edge effect can be clearly seen near the cavity/pore, where the oxygen concentration is low. The correlation between the oxygen adsorption and temperature is found to obey Langmuir adsorption theory, and a new formula for oxygen adsorption and porosity is proposed. This study may help understanding the mechanisms of oxygen adsorption and accordingly provide guidelines to lower the risk of spontaneous combustion of coal.

Description: With technologies rapidly evolving, many research institutions are now opting to invest in costly, high-quality, specialized microscopes which are shared by many researchers. As a consequence, the user may not have the ability to adapt a microscope to their specific needs and limitations in experimental design are introduced. A flexible work-horse microscopy system is a valuable tool in any laboratory to meet the diverse needs of a research team and promote innovation in experimental design. We have developed the Flexiscope; a multi-functional, adaptable, efficient and high-performance microscopy/electrophysiology system for everyday applications in a neurobiology laboratory. The core optical components are relatively constant in the three configurations described here: an upright configuration, an inverted configuration and an upright/electrophysiology configuration. We have provided a comprehensive description of the Flexiscope. We show that this method is capable of oblique infrared illumination imaging, multi-channel fluorescent imaging and automated three-dimensional scanning of larger specimens. Image quality is conserved across the three configurations of the microscope, and conversion between configurations is possible quickly and easily, while the motion control system can be repurposed to allow sub-micrometre computer-controlled micromanipulation. The Flexiscope provides similar performance and usability to commercially available systems. However, as it can be easily reconfigured for multiple roles, it can remove the need to purchase multiple microscopes, giving significant cost savings. The modular reconfigurable nature allows the user to customize the system to their specific needs and adapt/upgrade the system as challenges arise, without requiring specialized technical skills.

Description: The narrow pillar mining method is widely adopted for working faces in coal mines. However, in cases of an overlying hard roof, a suspended triangle roof plate or a cantilever will be formed near the goaf. At this point, the coal pillar extrusion and serious deformation will occur in the gob-side roadway. In order to mitigate the problem, the roof-cutting technology with a chainsaw arm and its equipment have been developed. In this paper, based on the analysis of deformation and failure characteristics of 2312 roadway, which is close to the goaf of 2311 working face in Tashan Coal, the roof-cutting technology with a chainsaw arm was chosen to be applied in 2311 roadway. Then, the roof-cutting process and the load acting on the coal pillar were discussed and analysed. A numerical model was established to analyse the stress releasing effects after roof cutting. Moreover, the roof-cutting height and the support parameters of the roadway were optimized through numerical analysis and the results manifested that the roof cutting was the most effective when the roof-cutting height was 6.4 m. After roof cutting, the vertical stresses within the coal pillars were lowered by about 25.0%. Finally, the roof-cutting experiment was carried out in the 2311 roadway in Tashan Coal Mine. The on-site roof-cutting depth was 6.4 m and the roof-cutting width was 42 mm guided by the numerical analysis. To verify the stress-relieving effects, the borehole stress meters were applied to monitor the peak advancing stresses of narrow pillars at various depths. The measured results indicated that the peak advancing stresses decreased by 22.8% on average, and therefore, roof cutting and stress releasing effects were achieved.

Description: The sensitization model suggests that paranoia is explained by over-sensitivity to social threat. However, this has been difficult to test experimentally. We report two preregistered social interaction studies that tested (i) whether paranoia predicted overall attribution and peak attribution of harmful intent and (ii) whether anxiety, interpersonal sensitivity and worry predicted the attribution of harmful intent. In Study 1, we recruited a large general population sample ( N = 987) who serially interacted with other participants in multi-round dictator games and matched to fair, partially fair or unfair partners. Participants rated attributions of harmful intent and self-interest after each interaction. In Study 2 ( N = 1011), a new sample of participants completed the same procedure and additionally completed measures of anxiety, worry and interpersonal sensitivity. As predicted, prior paranoid ideation was associated with higher and faster overall harmful intent attributions, whereas attributions of self-interest were unaffected, supporting the sensitization model. Contrary to predictions, neither worry, interpersonal sensitivity nor anxiety was associated with harmful intent attributions. In a third exploratory internal meta-analysis, we combined datasets to examine the effect of paranoia on trial-by-trial attributional changes when playing fair and unfair dictators. Paranoia was associated with a greater reduction in harmful intent attributions when playing a fair but not unfair dictator, suggesting that paranoia may also exaggerate the volatility of beliefs about the harmful intent of others.

Description: Birds are declining in agricultural landscapes around the world. The causes of these declines can be better understood by analysing change in groups of species that share life-history traits. We investigated how land-use change has affected birds of the Tasmanian Midlands, one of Australia's oldest agricultural landscapes and a focus of habitat restoration. We surveyed birds at 72 sites, some of which were previously surveyed in 1996–1998, and tested relationships of current patterns of abundance and community composition to landscape and patch-level environmental characteristics. Fourth-corner modelling showed strong negative responses of aerial foragers and exotics to increasing woodland cover; arboreal foragers were positively associated with projective foliage cover; and small-bodied species were reduced by the presence of a hyperaggressive species of native honeyeater, the noisy miner ( Manorina melanocephala ). Analysis of change suggests increases in large-bodied granivorous or carnivorous birds and declines in some arboreal foragers and nectarivores. Changes in species richness were best explained by changes in noisy miner abundance and levels of surrounding woodland cover. We encourage restoration practitioners to trial novel planting configurations that may confer resistance to invasion by noisy miners, and a continued long-term monitoring effort to reveal the effects of future land-use change on Tasmanian birds.

Description: Chemical cues from predators induce a range of predator-induced morphological defences (PIMDs) observed across fish taxa. However, the mechanisms, consistency, direction and adaptive value of PIMDs are still poorly studied. Here, we have tested if predatory cues can induce changes in the body shape of the juvenile marine fish Sparus aurata reared under controlled conditions without the presence of predators by exposing individuals to the olfactory stimulus of a fish predator. We tested our hypothesis using a nested replicated before-after-control-impact experiment, including recovery (potential reversibility) after the cessation of the predator stimulus. Differences in the size-independent body shape were explored using landmark-based geometric morphometrics and revealed that, on average, individuals exposed to a predatory cue presented deeper bodies and longer caudal regions, according to our adaptive theoretical predictions. These average plastic responses were reversible after withdrawal of the stimulus and individuals returned to average body shapes. We, therefore, provide evidence supporting innate reversible PIMDs in marine naive fish reared under controlled conditions. The effects at the individual level, including fitness and the associated applied implications, deserve further research.

Description: A novel methodology is introduced for quantifying the severity of damage created during testing in composite components. The method uses digital image correlation combined with image processing techniques to monitor the rate at which the strain field changes during mechanical tests. The methodology is demonstrated using two distinct experimental datasets, a ceramic matrix composite specimen loaded in tension at high temperature and nine polymer matrix composite specimens containing fibre-waviness defects loaded in bending. The changes in the strain field owing to damage creation are shown to be a more effective indicator that the specimen has reached its proportional limit than using load-extension diagrams. The technique also introduces a new approach to using experimental data for creating maps indicating the spatio-temporal distribution of damage in a component. These maps indicate where damage occurs in a component, and provide information about its morphology and its time of occurrence. This presentation format is both easier and faster to interpret than the raw data which, for some tests, can consist of tens of thousands of images. This methodology has the potential to reduce the time taken to interpret large material test datasets while increasing the amount of knowledge that can be extracted from each test.

Description: Sperm whales interact with commercially important groundfish fisheries offshore in the Gulf of Alaska (GOA). This study aims to use stable isotope analysis to better understand the trophic variability of sperm whales and their potential prey, and to use dietary mixing models to estimate the importance of prey species to sperm whale diets. We analysed tissue samples from sperm whales and seven potential prey (five groundfish and two squid species). Samples were analysed for stable carbon and nitrogen isotope ratios, and diet composition was estimated using Bayesian isotopic mixing models. Mixing model results suggest that an isotopically combined sablefish/dogfish group, skates and rockfish make up the largest proportion of sperm whale diets (35%, 28% and 12%) in the GOA. The top prey items of whales that interact more frequently with fishing vessels consisted of skates (49%) and the sablefish/dogfish group (24%). This is the first known study to provide an isotopic baseline of adult male sperm whales and these adult groundfish and offshore squid species, and to assign contributions of prey to whale diets in the GOA. This study provides information to commercial fishermen and fisheries managers to better understand trophic connections of important commercial species.

Description: Young children learn selectively from others based on the speakers' prior accuracy. This indicates that they recognize the models’ (in)competence and use it to predict who will provide the most accurate and useful information in the future. Here, we investigated whether 5-year-old children are also able to use speaker reliability retrospectively, once they have more information regarding their competence. They first experienced two previously unknown speakers who provided conflicting information about the referent of a novel label, with each speaker using the same novel label to refer exclusively to a different novel object. Following this, children learned about the speakers' differing labelling accuracy. Subsequently, children selectively endorsed the object–label link initially provided by the speaker who turned out to be reliable significantly above chance. Crucially, more than half of these children justified their object selection with reference to speaker reliability, indicating the ability to explicitly reason about their selective trust in others based on the informants’ individual competences. Findings further corroborate the notion that young children are able to use advanced, metacognitive strategies (trait reasoning) to learn selectively. By contrast, since learning preceded reliability exposure and gaze data showed no preferential looking toward the more reliable speaker, findings cannot be accounted for by attentional bias accounts of selective social learning.

Description: The animal purpose questionnaire (APQ) is a new instrument to measure human attitudes to animal use systematically across both species and purpose of use. This offers a more fine-grained approach to our understanding of how the belief in a specific animal's mental capacities relates to (dis-)agreement with their use for different human purposes. In the present study, 317 participants completed an online survey containing the APQ and the belief in animal mind (BAM) scale in a species-specific format, to test the prediction that levels of (dis-)agreement with animal use should mirror participants' judgements of animal sentience. The results obtained with the APQ confirmed that attitudes to animal use differed significantly across both purpose and species. Key findings included a relatively greater concern for dolphins and dogs over chimpanzees (suggesting that phylogenetic position is not the only determinant of attitudes to animal use). Across the purposes examined, respondents were largely negative about animal usage, with the exception that there was less disagreement if this was for medical research. Participants were also asked to provide demographic details such as gender and dietary preference. Regression analyses revealed high predictive power for species-specific BAM across five different kinds of animal use. General BAM scores, non-meat-eating and being female accounted for 31.5% of the total variability in APQ scores. The results indicate that BAM is a strong predictor of self-reported attitudes for using particular animals. However, the results showed some exceptions in the case of culturally typical ‘produce’ animals.

Description: We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of atomic orbitals ( N ∼ 10 10 ). KITE’s core is written in C++, with a versatile Python-based interface, and is fully optimized for shared memory multi-node CPU architectures, thus scalable, efficient and fast. At the core of KITE is a seamless spectral expansion of lattice Green’s functions, which enables large-scale calculations of generic target functions with uniform convergence and fine control over energy resolution. Several functionalities are demonstrated, ranging from simulations of local density of states and photo-emission spectroscopy of disordered materials to large-scale computations of optical conductivity tensors and real-space wave-packet propagation in the presence of magneto-static fields and spin–orbit coupling. On-the-fly calculations of real-space Green’s functions are carried out with an efficient domain decomposition technique, allowing KITE to achieve nearly ideal linear scaling in its multi-threading performance. Crystalline defects and disorder, including vacancies, adsorbates and charged impurity centres, can be easily set up with KITE’s intuitive interface, paving the way to user-friendly large-scale quantum simulations of equilibrium and non-equilibrium properties of molecules, disordered crystals and heterostructures subject to a variety of perturbations and external conditions.

Description: The intestinal epithelium is a selectively permeable barrier for nutrients, electrolytes and water, while maintaining effective protection against pathogens. Combinations of stressors throughout an animal's life, especially in agriculture and aquaculture settings, may affect the regular operativity of this organ with negative consequences for animal welfare. In the current study, we report the effects of a three-week unpredictable chronic stress (UCS) period on the intestinal morphology and transcriptome response of Atlantic salmon ( Salmon salar ) parr midgut and hindgut. Midgut and hindgut from both control and UCS fish were collected for histology and RNA-sequencing analysis to identify respective changes in the membrane structures and putative genes and pathways responding to UCS. Histological analysis did not show any significant effect on morphometric parameters. In the midgut, 1030 genes were differentially expressed following UCS, resulting in 279 genes which were involved in 13 metabolic pathways, including tissue repair pathways. In the hindgut, following UCS, 591 differentially expressed genes were detected with 426 downregulated and 165 upregulated. A total of 53 genes were related to three pathways. Downregulated genes include cellular senescence pathways, p53 signalling and cytokine–cytokine receptor pathways. The overall results corroborate that salmon parr were at least partly habituating to the UCS treatment. In midgut, the main upregulation was related to cell growth and repair, while in the hindgut there were indications of the activated apoptotic pathway, reduced cell repair and inhibited immune/anti-inflammatory capacity. This may be the trade-off between habituating to UCS and health resilience. This study suggests possible integrated genetic regulatory mechanisms that are tuned when farmed Atlantic salmon parr attempt to cope with UCS.

Description: It is of interest to fabricate curved surfaces in three dimensions from homogeneous material in the form of flat sheets. The aim is not just to obtain a surface which has a desired intrinsic Riemannian metric, but to get the desired embedding in R 3 up to translations and rotations. In this paper, we demonstrate three generic methods of moulding a flat sheet of thermo-responsive plastic by selective contraction induced by targeted heating. These methods do not involve any cutting and gluing, which is a property they share with origami. The first method is inspired by tailoring, which is the usual method for making garments out of plain pieces of cloth. Unlike usual tailoring, this method produces the desired embedding in R 3 . The second method just aims to bring about the desired new Riemannian metric via an appropriate pattern of local contractions, without directly controlling the embedding. The third method is based on triangulation, and seeks to induce the desired local distances. This results in getting the desired embedding in R 3 . The second and the third methods, and also the first method for the special case of surfaces of revolution, are algorithmic in nature. We explain these methods and show examples.

Description: We described an instrument-free method for quantitative analysis of the total content of tea polyphenols by measurement of the length of a coloured band. Polyphenols react with ferrous ions to form a colourless ferrous-polyphenols complex on cotton threads, which could be adsorbed on the threads. The complex was then oxidized to form a blue-black ferric-polyphenols complex, generating a blue-black band on the cotton thread. The length of this blue-black band was then measured to detect the total content of polyphenols. The advantages of this method include low cost, rapid analysis, low consumption, easy fabrication and operation. Furthermore, the digital instrument (scanner or camera) as well as the image processing software are not required. This proposed method was used to detect polyphenols in tea leaf extracts with an analytical result agreeing well with that obtained by a standard method, which demonstrates its potential in monitoring of tea leaf quality, especially in resource-limited regions and settings.

Description: The critical micelle concentration (CMC) is an important parameter of widely used surfactants and needs to be measured in the application and development of surfactants. Fluorometric method is a widely used method determining CMC values owing to the advantages of highly sensitivity, fast response and wide application range. There are two common methods (I and II) of preparing samples for CMC fluorometric determination. In the process of developing CMC probes with aggregation-induced emission (AIE) characteristics, we found that methods I and II were not suitable for CMC probes with AIE charateristics and developed a new sample preparation method (III), which is not only suitable for CMC probes with AIE characteristic but also decreases operation procedures and errors owing to omitting the addition of micro amount of dyes into each sample. To ascertain if method III is also suitable for other CMC probes without AIE characteristics, the CMC values of surfactants were determined by fluorometric method using widely used pyrene without AIE charateristic as probe and methods I–III to prepare samples. The obtained experimental results proved that method III not only was suitable for preparation of samples for CMC determination of surfactants using pyrene as probe but also led to the least average deviation (methods I–III led to ±0.13, ±0.34 and ±0.05 mM deviation for the CMC determination of sodium dodecyl sulfate (SDS), respectively). The CMC determination using pyrene as probe is based on its change in the ratio ( I FIII / I FI ) of its emission peaks I and III with surfactant concentration. Unexpectedly, it was found that the I FIII / I FI value of pyrene in surfactant solutions is sensitive to the measurement conditions changing exciting light energy, such as slit widths and sample-measured number. In addition, it was found that surfactant SDS or cetrimonium bromide from different suppliers not only has significantly different CMC values but also leads to very different I FIII / I FI values of pyrene in a certain concentration of surfactant, which can be used as a simple method to distinguish the same surfactant with different CMC values.

Description: The recruitment and biomass of a fish stock are influenced by their environmental conditions and anthropogenic pressures such as fishing. The variability in the environment often translates into fluctuations in recruitment, which then propagate throughout the stock biomass. In order to manage fish stocks sustainably, it is necessary to understand their dynamics. Here, we systematically explore the dynamics and sensitivity of fish stock recruitment and biomass to environmental noise. Using an age-structured and trait-based model, we explore random noise (white noise) and autocorrelated noise (red noise) in combination with low to high levels of harvesting. We determine the vital rates of stocks covering a wide range of possible body mass (size) growth rates and asymptotic size parameter combinations. Our study indicates that the variability of stock recruitment and biomass are probably correlated with the stock's asymptotic size and growth rate. We find that fast-growing and large-sized fish stocks are likely to be less vulnerable to disturbances than slow-growing and small-sized fish stocks. We show how the natural variability in fish stocks is amplified by fishing, not just for one stock but for a broad range of fish life histories.

Description: Snakes can move through almost any terrain. Although their locomotion on flat surfaces using planar gaits is inherently stable, when snakes deform their body out of plane to traverse complex terrain, maintaining stability becomes a challenge. On trees and desert dunes, snakes grip branches or brace against depressed sand for stability. However, how they stably surmount obstacles like boulders too large and smooth to gain such ‘anchor points’ is less understood. Similarly, snake robots are challenged to stably traverse large, smooth obstacles for search and rescue and building inspection. Our recent study discovered that snakes combine body lateral undulation and cantilevering to stably traverse large steps. Here, we developed a snake robot with this gait and snake-like anisotropic friction and used it as a physical model to understand stability principles. The robot traversed steps as high as a third of its body length rapidly and stably. However, on higher steps, it was more likely to fail due to more frequent rolling and flipping over, which was absent in the snake with a compliant body. Adding body compliance reduced the robot's roll instability by statistically improving surface contact, without reducing speed. Besides advancing understanding of snake locomotion, our robot achieved high traversal speed surpassing most previous snake robots and approaching snakes, while maintaining high traversal probability.

Description: The ecological success of ants relies on their ability to discover and collectively exploit available resources. In this process, the nest entrances are key locations at which foragers transfer food and information about the surrounding environment. We assume that the number of nest entrances regulates social exchanges between foragers and inner-nest workers, and hence influences the foraging efficiency of the whole colony. Here, we compared the foraging responses of Myrmica rubra colonies settled in either one-entrance or two-entrance nests. The total outflows of workers exploiting a sucrose food source were similar regardless of the number of nest entrances. However, in the two-entrance nests, the launching of recruitment was delayed, a pheromone trail was less likely to emerge between the nest and the food source, and recruits were less likely to reach the food target. As a result, an additional entrance through which information could transit decreased the efficiency of social foraging and ultimately led to a lower amount of retrieved food. Our study confirms the key-role of nest entrances in the transfer of information from foragers to potential recruits. The influence of the number of entrances on the emergence of a collective trail also highlights the spatially extended impact of the nest architecture that can shape foraging patterns outside the nest.

Description: This research work designed a novel mud-cake solidification method to improve the zonal isolation of oil and gas wells. The calculation methodology of mud-cake compressive strength was proposed. The optimal formula of activator and solid precursors, the proper activating time and the best activator concentration were determined by the compressive strength test. The effects of solid precursors on the properties of drilling fluid were evaluated. Test results show that the respective percentage of bentonite, metakaolin, slag and activator is 1 : 1 : 0.3 : 0.8, as well as the optimum ratio of Na 2 SiO 3 /NaOH is 40 : 1. The optimum concentration of activator is 0.21 and the activating time should be more than 10 min. The solid precursors did not show any bad influence on the rheological property of drilling fluids. Even though the compressive strength decreased when the solid precursors blended with barite, the strength values can still achieve 8 MPa. The reaction of metakaolin and activator formed cross-link structure in the mud-cake matrix, which enhanced the connection of the loose bentonite particles, lead to the significant enhancement of shear bonding strength and hydraulic bonding strength. This mud-cake solidification method provides a new approach to improve the quality of zonal isolation.

Description: Sexual reproduction is not always synonymous with the existence of two morphologically different sexes; isogamous species produce sex cells of equal size, typically falling into multiple distinct self-incompatible classes, termed mating types. A long-standing open question in evolutionary biology is: what governs the number of these mating types across species? Simple theoretical arguments imply an advantage to rare types, suggesting the number of types should grow consistently; however, empirical observations are very different. While some isogamous species exhibit thousands of mating types, such species are exceedingly rare, and most have fewer than 10. In this paper, we present a mathematical analysis to quantify the role of fitness variation—characterized by different mortality rates—in determining the number of mating types emerging in simple evolutionary models. We predict that the number of mating types decreases as the variance of mortality increases.

Description: Every now and then the cultural paradigm of a society changes. While current models of cultural shifts usually require a major exogenous or endogenous change, we propose that the mechanism underlying many paradigm shifts may just be an emergent feature of the inherent congruence among different cultural traits. We implement this idea through a population dynamics model in which individuals are defined by a vector of cultural traits that changes mainly through cultural contagion, biased by a ‘cultural fitness’ landscape, between contemporary individuals. Cultural traits reinforce or hinder each other (through a form of cultural epistasis) to prevent cognitive dissonance. Our main result is that abrupt paradigm shifts occur, in response to weak changes in the landscape, only in the presence of epistasis between cultural traits, and regardless of whether horizontal transmission is biased by homophily. A relevant consequence of this dynamics is the irreversible nature of paradigm shifts: the old paradigm cannot be restored even if the external changes are undone. Our model puts the phenomenon of paradigm shifts in cultural evolution in the same category as catastrophic shifts in ecology or phase transitions in physics, where minute causes lead to major collective changes.

Description: Leaf nitrogen concentration (LNC) is a major indicator in the estimation of the crop growth status which has been diffusely applied in remote sensing. Thus, it is important to accurately obtain LNC by using passive or active technology. Laser-induced fluorescence can be applied to monitor LNC in crops through analysing the changing of fluorescence spectral information. Thus, the performance of fluorescence spectrum (FS) and first-derivative fluorescence spectrum (FDFS) for paddy rice (Yangliangyou 6 and Manly Indica) LNC estimation was discussed, and then the proposed FS + FDFS was used to monitor LNC by multivariate analysis. The results showed that the difference between FS ( R 2 = 0.781, s.d. = 0.078) and FDFS ( R 2 = 0.779, s.d. = 0.097) for LNC estimation by using the artificial neural network is not obvious. The proposed FS + FDFS can improved the accuracy of LNC estimation to some extent ( R 2 = 0.813, s.d. = 0.051). Then, principal component analysis was used in FS and FDFS, and extracted the main fluorescence characteristics. The results indicated that the proposed FS + FDFS exhibited higher robustness and stability for LNC estimation ( R 2 = 0.851, s.d. = 0.032) than that only using FS ( R 2 = 0.815, s.d. = 0.059) or FDFS ( R 2 = 0.801, s.d. = 0.065).

Description: Inter-event times of various human behaviour are apparently non-Poissonian and obey long-tailed distributions as opposed to exponential distributions, which correspond to Poisson processes. It has been suggested that human individuals may switch between different states, in each of which they are regarded to generate events obeying a Poisson process. If this is the case, inter-event times should approximately obey a mixture of exponential distributions with different parameter values. In the present study, we introduce the minimum description length principle to compare mixtures of exponential distributions with different numbers of components (i.e. constituent exponential distributions). Because these distributions violate the identifiability property, one is mathematically not allowed to apply the Akaike or Bayes information criteria to their maximum-likelihood estimator to carry out model selection. We overcome this theoretical barrier by applying a minimum description principle to joint likelihoods of the data and latent variables. We show that mixtures of exponential distributions with a few components are selected, as opposed to more complex mixtures in various datasets, and that the fitting accuracy is comparable to that of state-of-the-art algorithms to fit power-law distributions to data. Our results lend support to Poissonian explanations of apparently non-Poissonian human behaviour.

Description: In order to accurately grasp the timing for the prevention and control of diseases, we established an artificial neural network model to issue early warning signals. The real-time recurrent learning (RTRL) and extended Kalman filter (EKF) methods were performed to analyse four types of respiratory infectious diseases and four types of digestive tract infectious diseases in China to comprehensively determine the epidemic intensities and whether to issue early warning signals. The numbers of new confirmed cases per month between January 2004 and December 2017 were used as the training set; the data from 2018 were used as the test set. The results of RTRL showed that the number of new confirmed cases of respiratory infectious diseases in September 2018 increased abnormally. The results of the EKF showed that the number of new confirmed cases of respiratory infectious diseases increased abnormally in January and February of 2018. The results of these two algorithms showed that the number of new confirmed cases of digestive tract infectious diseases in the test set did not have any abnormal increases. The neural network and machine learning can further enrich and develop the early warning theory.

Description: Sewage sludge is an organic matter-rich material with abundant fractions of nitrogen and other macro and micronutrients, essential for plant growth and development such as Acacia mangium Willd. (Fabales: Fabaceae) used in recovering actions of degraded areas. The objective of this study was to evaluate over 24 months the abundance and diversity of chewing and pollinator insects and arthropod predators on A. mangium plants and the mass production and soil coverage by this plant, fertilized with dehydrated sewage sludge, in a degraded area. The experimental design was in randomized blocks with two treatments (with and without dehydrated sewage sludge) and 24 replications. The number of leaves per branch and branches per plant, defoliation percentage by chewing insects, soil cover and abundance of chewing and pollinator insects and arthropod predators were higher on A. mangium plants fertilized with dehydrated sewage sludge. Nasutitermes sp. (Blattodea: Termitidae) and Trigona spinipes F. (Hymenoptera: Apidae) were the most observed insects on trunks and leaves, respectively, of A. mangium plants fertilized with dehydrated sewage sludge. The A. mangium fertilization increases the populations of different insect and spider groups on this plant.

Description: Compartmental equations are primary tools in the study of disease spreading processes. They provide accurate predictions for large populations but poor results whenever the integer nature of the number of agents is evident. In the latter instance, uncertainties are relevant factors for pathogen transmission. Starting from the agent-based approach, we investigate the role of uncertainties and autocorrelation functions in the susceptible–infectious–susceptible (SIS) epidemic model, including their relationship with epidemiological variables. We find new differential equations that take uncertainties into account. The findings provide improved equations, offering new insights on disease spreading processes.

Description: Killer whales ( Orcinus orca ) are top marine predators occurring globally. In Antarctic waters, five ecotypes have been described, with Type C being the smallest form of killer whale known. Acoustic recordings of nine encounters of Type C killer whales were collected in 2012 and 2013 in McMurdo Sound, Ross Sea. In a combined 3.5 h of recordings, 6386 killer whale vocalizations were detected and graded based on their signal-to-noise ratio. Spectrograms of the highest-quality calls were examined for characteristic patterns yielding a catalogue of 28 call types (comprising 1250 calls). Acoustic parameters of each call were measured and summarized by call type. Type C killer whales produced complex calls, consisting of multiple frequency-modulated, amplitude-modulated and pulsed components. Often, two components occurred simultaneously, forming a biphonation; although the biphonic components did not necessarily start and end together, with one component lasting over several others. The addition and deletion of components yielded call subtypes. Call complexity appears stable over time and may be related to feeding ecology. Characterization of the Type C acoustic repertoire is an important step for the development of passive acoustic monitoring of the diverse assemblage of killer whale ecotypes in Antarctica's rapidly changing marine ecosystems.

Description: Serious concerns about research quality have catalysed a number of reform initiatives intended to improve transparency and reproducibility and thus facilitate self-correction, increase efficiency and enhance research credibility. Meta-research has evaluated the merits of some individual initiatives; however, this may not capture broader trends reflecting the cumulative contribution of these efforts. In this study, we manually examined a random sample of 250 articles in order to estimate the prevalence of a range of transparency and reproducibility-related indicators in the social sciences literature published between 2014 and 2017. Few articles indicated availability of materials (16/151, 11% [95% confidence interval, 7% to 16%]), protocols (0/156, 0% [0% to 1%]), raw data (11/156, 7% [2% to 13%]) or analysis scripts (2/156, 1% [0% to 3%]), and no studies were pre-registered (0/156, 0% [0% to 1%]). Some articles explicitly disclosed funding sources (or lack of; 74/236, 31% [25% to 37%]) and some declared no conflicts of interest (36/236, 15% [11% to 20%]). Replication studies were rare (2/156, 1% [0% to 3%]). Few studies were included in evidence synthesis via systematic review (17/151, 11% [7% to 16%]) or meta-analysis (2/151, 1% [0% to 3%]). Less than half the articles were publicly available (101/250, 40% [34% to 47%]). Minimal adoption of transparency and reproducibility-related research practices could be undermining the credibility and efficiency of social science research. The present study establishes a baseline that can be revisited in the future to assess progress.

Description: Community compositions of ectomycorrhizal (ECM) fungi are similar within the same host taxa. However, careful interpretation is required to determine whether the combination of ECM fungi and plants is explained by the host preference for ECM fungi, or by the influence of neighbouring heterospecific hosts. In the present study, we aimed to evaluate the effects of host species on the ECM community compositions in a forested landscape (approx. 10 km) where monodominant forest stands of six ECM host species belonging to three families were patchily distributed. A total of 180 ECM operational taxonomic units (OTUs) were detected with DNA metabarcoding. Quantitative multivariate analyses revealed that the ECM community compositions were primarily structured by host species and families, regardless of the soil environments and spatial arrangements of the sampling plots. In addition, 38 ECM OTUs were only detected from particular host tree species. Furthermore, the neighbouring plots harboured similar fungal compositions, although the host species were different. The relative effect of the spatial factors on the ECM compositions was weaker than that of host species. Our results suggest that the host preference for ECM fungi is the primary determinant of ECM fungal compositions in the forested landscape.

Description: Ulcerative colitis is a chronic disease in which the mucosa of the colon or rectum becomes inflamed. An objective biomarker of inflammation will provide quantitative measures to support qualitative assessment during an endoscopic examination. Previous studies show that transmural electrical impedance is a quantifiable biomarker of inflammation. Here, we hypothesize that impedance detects spatially restricted areas of inflammation, thereby allowing the distinction between regions that differ in their severity of inflammation. A platinum ball electrode was placed into minimally inflamed (i.e. normal) or 2,4,6-trinitrobenzene sulphonic acid (TNBS)-inflamed colonic regions of rats and impedance measurements obtained by passing current between the intraluminal and subcutaneous return electrode. Histology of the colon was correlated with impedance measurements. The impedance of minimally inflamed (normal) tissue was 1.5–1.9 kΩ. Following TNBS injection, impedance significantly decreased within the inflammatory penumbra ( p 〈 0.05), and decreased more in the inflammatory epicentre ( p = 0.02). Histological damage correlated with impedance values ( p 〈 0.05). Thus, impedance values of 1.5–1.9, 1.3–1.4 and 0.9–1.1 kΩ corresponded to minimally inflamed, mildly inflamed and moderately inflamed tissue, respectively. In conclusion, transmural impedance is an objective, spatially localized biomarker of mucosal integrity, and distinguishes between severities of intestinal inflammation.

Description: In the present article, we explore the influence of undisclosed flexibility in the analysis of reaction times (RTs). RTs entail some degrees of freedom of their own, due to their skewed distribution, the potential presence of outliers and the availability of different methods to deal with these issues. Moreover, these degrees of freedom are usually not considered part of the analysis itself, but preprocessing steps that are contingent on data. We analysed the impact of these degrees of freedom on the false-positive rate using simulations over real and simulated data. When several preprocessing methods are used in combination, the false-positive rate can easily rise to 17%. This figure becomes more concerning if we consider that more degrees of freedom are awaiting down the analysis pipeline, potentially making the final false-positive rate much higher.

Description: Abnormal fluid dynamics at the ascending aorta may be at the origin of aortic aneurysms. This study was aimed at comparing the performance of computational fluid dynamics (CFD) and fluid–structure interaction (FSI) simulations against four-dimensional (4D) flow magnetic resonance imaging (MRI) data; and to assess the capacity of advanced fluid dynamics markers to stratify aneurysm progression risk. Eight Marfan syndrome (MFS) patients, four with stable and four with dilating aneurysms of the proximal aorta, and four healthy controls were studied. FSI and CFD simulations were performed with MRI-derived geometry, inlet velocity field and Young's modulus. Flow displacement, jet angle and maximum velocity evaluated from FSI and CFD simulations were compared to 4D flow MRI data. A dimensionless parameter, the shear stress ratio (SSR), was evaluated from FSI and CFD simulations and assessed as potential correlate of aneurysm progression. FSI simulations successfully matched MRI data regarding descending to ascending aorta flow rates ( R 2 = 0.92) and pulse wave velocity ( R 2 = 0.99). Compared to CFD, FSI simulations showed significantly lower percentage errors in ascending and descending aorta in flow displacement (−46% ascending, −41% descending), jet angle (−28% ascending, −50% descending) and maximum velocity (−37% ascending, −34% descending) with respect to 4D flow MRI. FSI- but not CFD-derived SSR differentiated between stable and dilating MFS patients. Fluid dynamic simulations of the thoracic aorta require fluid–solid interaction to properly reproduce complex haemodynamics. FSI- but not CFD-derived SSR could help stratifying MFS patients.

Description: Walking on different grades becomes challenging on energetic and muscular levels compared to level walking. While it is not possible to eliminate the cost of raising or lowering the centre of mass (COM), it could be possible to minimize the cost of distal joints with shoes that offset downhill or uphill grades. We investigated the effects of shoe outsole geometry in 10 participants walking at 1 m s −1 on downhill, level and uphill grades. Level shoes minimized metabolic rate during level walking ( P second-order effect 〈 0.001). However, shoes that entirely offset the (overall) treadmill grade did not minimize the metabolic rate of walking on grades: shoes with a +3° (upward) inclination minimized metabolic rate during downhill walking on a −6° grade, and shoes with a −3° (downward) inclination minimized metabolic rate during uphill walking on a +6° grade ( P interaction effect = 0.023). Shoe inclination influenced (distal) ankle joint parameters, including soleus muscle activity, ankle moment and work rate, whereas treadmill grade influenced (whole-body) ground reaction force and COM work rate as well as (distal) ankle joint parameters including tibialis anterior and plantarflexor muscle activity, ankle moment and work rate. Similar modular footwear could be used to minimize joint loads or assist with walking on rolling terrain.

Description: We hypothesized that the mitogenome of Gammarus lacustris (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of Gammarus pisinnus (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% atp8 to 76.1% cox1 ). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, GP and Gammarus fossarum exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in atp8 ) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining Gammarus species populating the same geographical range as GP.

Description: The application of machine learning to inference problems in biology is dominated by supervised learning problems of regression and classification, and unsupervised learning problems of clustering and variants of low-dimensional projections for visualization. A class of problems that have not gained much attention is detecting outliers in datasets, arising from reasons such as gross experimental, reporting or labelling errors. These could also be small parts of a dataset that are functionally distinct from the majority of a population. Outlier data are often identified by considering the probability density of normal data and comparing data likelihoods against some threshold. This classical approach suffers from the curse of dimensionality, which is a serious problem with omics data which are often found in very high dimensions. We develop an outlier detection method based on structured low-rank approximation methods. The objective function includes a regularizer based on neighbourhood information captured in the graph Laplacian. Results on publicly available genomic data show that our method robustly detects outliers whereas a density-based method fails even at moderate dimensions. Moreover, we show that our method has better clustering and visualization performance on the recovered low-dimensional projection when compared with popular dimensionality reduction techniques.

Description: The optimum conditions to produce palm fatty acid distillate (PFAD)-derived-methyl esters via esterification have been demonstrated with the aid of the response surface methodology (RSM) with central composite rotatable design in the presence of heterogeneous acid catalyst. The effect of four reaction variables, reaction time (30–110 min), reaction temperature (30–70°C), catalyst concentration (1–3 wt.%) and methanol : PFAD molar ratio (3 : 1–11 : 1), were investigated. The reaction time had the most influence on the yield response, while the interaction between the reaction time and the catalyst concentration, with an F -value of 95.61, contributed the most to the esterification reaction. The model had an R 2 -value of 0.9855, suggesting a fit model, which gave a maximum yield of 95%. The fuel properties of produced PFAD methyl ester were appraised based on the acid value, iodine value, cloud and pour points, flash point, kinematic viscosity, density, ash and water contents and were compared with biodiesel EN 14214 and ASTM D-6751 standard limits. The PFAD methyl ester was further blended with petro-diesel from B0, B3, B5, B10, B20 and B100, on a volumetric basis. The blends were characterized by TGA, DTG and FTIR. With an acid value of 0.42 (mg KOH g −1 ), iodine value of 63 (g.I 2 /100 g), kinematic viscosity of 4.31 (mm 2 s −1 ), the PFAD methyl ester has shown good fuel potential, as all of its fuel properties were within the permissible international standards for biodiesel.

Description: In the area of computer vision, deep learning techniques have recently been used to predict whether urban scenes are likely to be considered beautiful: it turns out that these techniques are able to make accurate predictions. Yet they fall short when it comes to generating actionable insights for urban design. To support urban interventions, one needs to go beyond predicting beauty, and tackle the challenge of recreating beauty. Unfortunately, deep learning techniques have not been designed with that challenge in mind. Given their ‘black-box nature’, these models cannot be directly used to explain why a particular urban scene is deemed to be beautiful. To partly fix that, we propose a deep learning framework (which we name FaceLift 1 ) that is able to both beautify existing urban scenes (Google Street Views) and explain which urban elements make those transformed scenes beautiful. To quantitatively evaluate our framework, we cannot resort to any existing metric (as the research problem at hand has never been tackled before) and need to formulate new ones. These new metrics should ideally capture the presence (or absence) of elements that make urban spaces great. Upon a review of the urban planning literature, we identify five main metrics: walkability, green spaces, openness, landmarks and visual complexity. We find that, across all the five metrics, the beautified scenes meet the expectations set by the literature on what great spaces tend to be made of. This result is further confirmed by a 20-participant expert survey in which FaceLift has been found to be effective in promoting citizen participation. All this suggests that, in the future, as our framework’s components are further researched and become better and more sophisticated, it is not hard to imagine technologies that will be able to accurately and efficiently support architects and planners in the design of the spaces we intuitively love.

Description: Urban resource models increasingly rely on implicit network formulations. Resource consumption behaviours documented in the existing empirical studies are ultimately by-products of the network abstractions underlying these models. Here, we present an analytical formulation and examination of a generic demand-driven network model that accounts for the effectiveness of resource utilization and its implications for policy levers in addressing resource management in cities. We establish simple limiting boundaries to systems' resource effectiveness. These limits are found not to be a function of system size and to be simply determined by the system's average ability to maintain resource quality through its transformation processes. We also show that resource utilization in itself does not enjoy considerable size efficiencies with larger and more diverse systems only offering increased chances of finding matching demand and supply between existing sectors in the system.

Description: Evidence for compression, or minimization of code length, has been found across biological systems from genomes to human language and music. Two linguistic laws—Menzerath's Law (which states that longer sequences consist of shorter constituents) and Zipf's Law of abbreviation (a negative relationship between signal length and frequency of use)—are predictions of compression. It has been proposed that compression is a universal in animal communication, but there have been mixed results, particularly in reference to Zipf's Law of abbreviation. Like songbirds, male gibbons ( Hylobates muelleri ) engage in long solo bouts with unique combinations of notes which combine into phrases. We found strong support for Menzerath's Law as the longer a phrase, the shorter the notes. To identify phrase types, we used state-of-the-art affinity propagation clustering, and were able to predict phrase types using support vector machines with a mean accuracy of 74%. Based on unsupervised phrase type classification, we did not find support for Zipf's Law of abbreviation. Our results indicate that adherence to linguistic laws in male gibbon solos depends on the unit of analysis. We conclude that principles of compression are applicable outside of human language, but may act differently across levels of organization in biological systems.

Description: Stem cells are important to generate all specialized tissues at an early life stage, and in some systems, they also have repair functions to replenish the adult tissues. Repeated cell divisions lead to the accumulation of molecular damage in stem cells, which are commonly recognized as drivers of ageing. In this paper, a novel model is proposed to integrate stem cell proliferation and differentiation with damage accumulation in the stem cell ageing process. A system of two structured PDEs is used to model the population densities of stem cells (including all multiple progenitors) and terminally differentiated (TD) cells. In this system, cell cycle progression and damage accumulation are modelled by continuous dynamics, and damage segregation between daughter cells is considered at each division. Analysis and numerical simulations are conducted to study the steady-state populations and stem cell damage distributions under different damage segregation strategies. Our simulations suggest that equal distribution of the damaging substance between stem cells in a symmetric renewal and less damage retention in stem cells in the asymmetric division are favourable strategies, which reduce the death rate of the stem cells and increase the TD cell populations. Moreover, asymmetric damage segregation in stem cells leads to less concentrated damage distribution in the stem cell population, which may be more robust to the stochastic changes in the damage. The feedback regulation from stem cells can reduce oscillations and population overshoot in the process, and improve the fitness of stem cells by increasing the percentage of cells with less damage in the stem cell population.

Description: Understanding the failure modes of curved hollow tree trunks is essential from both safety and conservation perspectives. Despite extensive research, the underlying mechanism that determines the cracking failure of curved hollow tree trunks remains unclear due to the lack of theoretical analysis that considers both the initial curvature and orthotropic material properties. Here we derive new mathematical expressions for predicting the bending moment, M crack , at which the cracking failure occurs. The failure mode of a tree species is then determined, as a function of t / R and cR , by comparing M crack with M bend , where t , R and c are, respectively, the trunk wall thickness, outer radius and initial curvature; M bend is the bending moment for conventional bending failure. Our equation shows that M crack is proportional to the tangential tensile strength of wood σ T , increases with t / R , and decreases with the final cR . We analyse 11 tree species and find that hardwoods are more likely to fail in conventional bending, whereas softwoods tend to break due to cracking. This is due to the softwoods' much smaller tangential tensile strength, as observed from the data of 66 hardwoods and 43 softwoods. For larger cR , cracking failure is easier to occur in curvature-decreasing bending than curvature-increasing due to additional normal tensile force F acting on the neutral cross-section; on the other hand, for smaller cR , bending failure is easier to occur due to decreased final curvature. Our formulae are applicable to other natural and man-made curved hollow beams with orthotropic material properties. Our findings provide insights for those managing trees in urban situations and those managing for conservation of hollow-dependent fauna in both urban and rural settings.

Description: With polyol-synthesized silver nanoparticles (AgNPs) as raw materials, the silver electrodes with high conductivity were fabricated via a dip-coating method followed by sintering process, and the effects of the dip-coating and sintering process on the conductivity and surface roughness of silver electrodes were investigated in detail. The silver film with a thickness of 1.97 µm and a roughness of about 2 nm can be prepared after dip-coating at a pulling rate of 500 µm s −1 for 40 coating times. The non-conductive dip-coated silver films are transformed into conductive silver electrodes after conventional sintering in a muffle oven, infrared sintering and microwave sintering, respectively. Compared with high sintering temperature and long sintering time of conventional sintering and infrared sintering, microwave sintering can achieve quick sintering of silver films to fabricate high conductive silver electrodes. The silver electrodes with a sheet resistance of 0.75 Ω sq −1 and a surface roughness of less than 1 nm can be obtained after microwave sintering at 500 W for 50 s. The adjustable dip-coating method followed by quick microware sintering is an appropriate approach to prepare high conductive AgNPs-based electrodes for organic light-emitting diodes or other devices.

Description: Nitrogen (N) uptake in response to its availability and effective N-use are important for determining plant fitness, as N is a major limiting resource and its availability changes both seasonally and annually. Storage organs such as bulbs are considered an adaptive trait with respect to plant N-use strategies. It is well known that N is remobilized from storage organs to satisfy the high demand for new growth that is not completely satisfied by external uptake alone. However, little is known about how this N absorbed during different seasons contributes to plant performance. By manipulating seasonal N availability in potted Lycoris radiata var. radiata (Amaryllidaceae), a winter-green perennial, we found that the N absorbed during different seasons had different effects on leaf growth and leaf N concentrations, effectively increasing the growth and survival of the plants. N absorbed during the summer (leafless period; N was thus stored in the bulb) enhanced plant growth by increasing leaf growth. Compared with the plants supplied with N during autumn (leaf flush period), the leafy plants also showed greater growth per unit leaf area despite the lower area-based photosynthetic capacity of the latter. By contrast, N absorbed during the autumn increased the leaf N concentration and thus the photosynthetic capacity, which was considered to enhance survival and growth of the plant during winter by reducing the potentially fatal risk caused by the absorption of photons under low temperature. Our findings have important implications for estimating plant responses to environmental changes. We predict that changes in seasonal N availability impact the performance of plants, even that of perennials that have large storage organs, via an altered relative investment of N into different functions.

Description: Anticipatory looking on mindreading tasks can indicate our expectation of an agent's action. The challenge is that social situations are often more complex, involving instances where we need to track an agent's false belief to successfully identify the outcome to which an action is directed. If motor processes can guide how action goals are understood, it is conceivable—where that kind of goal ascription occurs in false-belief tasks—for motor representations to account for someone's belief-like state. Testing adults ( N = 42) in a real-time interactive helping scenario, we discovered that participants' early mediolateral motor activity (leftwards–rightwards leaning on balance board) foreshadowed the agent's belief-based action preparation. These results suggest fast belief-tracking can modulate motor representations generated in the course of one's interaction with an agent. While adults' leaning, and anticipatory looking, revealed the contribution of fast false-belief tracking, participants did not correct the agent's mistake in their final helping action. These discoveries suggest that adults may not necessarily use another's belief during overt social interaction or find reflecting on another's belief as being normatively relevant to one's own choice of action. Our interactive task design offers a promising way to investigate how motor and mindreading processes may be variously integrated.

Description: Chromatin remodelling and transcription factors play important roles in lineage commitment and development through control of gene expression. Activation of selected lineage-specific genes and repression of alternative lineage-affiliated genes result in tightly regulated cell differentiation transcriptional programmes. However, the complex functional and physical interplay between transcription factors and chromatin-modifying enzymes remains elusive. Recent evidence has implicated histone demethylases in normal haematopoietic differentiation as well as in malignant haematopoiesis. Here, we report an interaction between H3K4 demethylase JARID1A and the haematopoietic-specific master transcription proteins SCL and GATA1 in red blood cells. Specifically, we observe a direct physical contact between GATA1 and the second PHD domain of JARID1A. This interaction has potential implications for normal and malignant haematopoiesis.

Description: Serial and parallel processing in visual search have been long debated in psychology, but the processing mechanism remains an open issue. Serial processing allows only one object at a time to be processed, whereas parallel processing assumes that various objects are processed simultaneously. Here, we present novel neural models for the two types of processing mechanisms based on analysis of simultaneously recorded spike trains using electrophysiological data from prefrontal cortex of rhesus monkeys while processing task-relevant visual displays. We combine mathematical models describing neuronal attention and point process models for spike trains. The same model can explain both serial and parallel processing by adopting different parameter regimes. We present statistical methods to distinguish between serial and parallel processing based on both maximum likelihood estimates and decoding the momentary focus of attention when two stimuli are presented simultaneously. Results show that both processing mechanisms are in play for the simultaneously recorded neurons, but neurons tend to follow parallel processing in the beginning after the onset of the stimulus pair, whereas they tend to serial processing later on.

Description: A novel hydrophobic and cationic cyclodextrin-based acrylamide flocculant (AM-β-CD-DMDAAC) was prepared by chemical oxidative polymerization to adsorb water-soluble dyes in dye wastewater. Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscope and thermogravimetric (TG) measurements results demonstrated that the AM-β-CD-DMDAAC was successfully synthesized. The effects of pH, contact time, initial dye concentration, temperature and adsorbent dose on dye removal efficiency for AM-β-CD-DMDAAC flocculants were investigated. The kinetic data were found to follow the pseudo-second-order kinetic model. The equilibrium adsorption data were fitted to the Langmuir isotherm model, with the maximum adsorption capacity of 147.1 mg g −1 . The adsorbent retained about 60% of the adsorption efficiency after three adsorption/desorption cycles, which implied a promising application as the dye adsorbent.

Description: In this study, a novel signal-increase electrochemiluminescence (ECL) biosensor has been developed for the detection of glucose based on graphene quantum dot/glucose oxidase (GQD/GO x ) on Ti foil. The proposed GQD with excellent ECL ability is synthesized through a green one-step strategy by the electrochemical reduction of graphene oxide quantum dot. Upon the addition of glucose, GO x can catalytically oxidize glucose and the direct electron transfer between the redox centre of GO x and the modified electrode also has been realized, which results in the bio-generated H 2 O 2 for ECL signal increase in GQD and realizes the direct ECL detection of glucose. The signal-increase ECL biosensor enables glucose detection with high sensitivity reaching 5 × 10 −6 mol l −1 in a wide linear range from 5 × 10 −6 to 1.5 × 10 −3 mol l −1 . Additionally, the fabrication process of such GQD-based ECL biosensor is also suitable to other biologically produced H 2 O 2 system, suggesting the possible applications in the sensitive detection of other biologically important targets (e.g. small molecules, protein, DNA and so on).

Description: In ecological systems, heterogeneous interactions between pathogens take place simultaneously. This occurs, for instance, when two pathogens cooperate, while at the same time, multiple strains of these pathogens co-circulate and compete. Notable examples include the cooperation of human immunodeficiency virus with antibiotic-resistant and susceptible strains of tuberculosis or some respiratory infections with Streptococcus pneumoniae strains. Models focusing on competition or cooperation separately fail to describe how these concurrent interactions shape the epidemiology of such diseases. We studied this problem considering two cooperating pathogens, where one pathogen is further structured in two strains. The spreading follows a susceptible-infected-susceptible process and the strains differ in transmissibility and extent of cooperation with the other pathogen. We combined a mean-field stability analysis with stochastic simulations on networks considering both well-mixed and structured populations. We observed the emergence of a complex phase diagram, where the conditions for the less transmissible, but more cooperative strain to dominate are non-trivial, e.g. non-monotonic boundaries and bistability. Coupled with community structure, the presence of the cooperative pathogen enables the coexistence between strains by breaking the spatial symmetry and dynamically creating different ecological niches. These results shed light on ecological mechanisms that may impact the epidemiology of diseases of public health concern.