bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceived extrinsic mortality risk and health behaviour: Testing a behavioural ecological model
Authors: Pepper Gillian V , Nettle Daniel
Published: January 2018

Purpose: Socioeconomic gradients in health behaviour are pervasive and well documented. Yet, outside the evolutionary literature, there is no consensus on their causes. Our previously presented theoretical behavioural ecological model predicted that people of low socioeconomic position (SEP) should perceive greater personal extrinsic mortality risk than those of higher SEP, leading them to disinvest in their future health. We collected data to test this prediction.

Methods: We surveyed North American adults for measures of SEP, effort in looking after health and perceived extrinsic and intrinsic mortality risks. We examined the relationships between SEP, perceived mortality risks and effort in looking after health. We then tested whether the association between SEP and effort in looking after health was mediated by perceived extrinsic mortality risk.

Results: SEP was associated with effort in looking after health. Lower SEP was also associated with higher perceived extrinsic mortality risk, which in turn predicted effort in looking after health. The effect of SEP on effort in looking after health was completely mediated by perceived extrinsic mortality risk.

Conclusions: Our findings support the predictions of our previously presented theoretical model. They show that SEP gradients in perceptions of extrinsic mortality risk mirror known SEP gradients in actual extrinsic mortality risk. The large effect size for the relationship between perceived extrinsic mortality risk and health effort in our sample indicates that perceived extrinsic mortality risk may be a key predictor of health behaviour.
Automatic Document Classification for Environmental Risk Assessment
Authors: Painter Kyle , Dutton Steven , Owens Elizabeth O , Burgoon Lyle
Published: January 2018

Motivation: In environmental risk assessment, information about potential health risks of chemicals released into the environment is compiled and distilled for use in informing public policy. The U.S. Environmental Protection Agency (EPA) produces Integrated Science Assessments (ISA) that provide a review of literature on air pollutants, including nitrogen oxides (NOx). That review process currently requires much human labor to evaluate thousands of potentially-relevant documents published each year, a problem this study seeks to alleviate by using automated topic classification methods. Results: For this study, abstracts and titles of scientific documents about NOx were labeled by subject matter experts in four domains relevant to ISAs: toxicology, atmospheric science, epidemiology, and exposure science. In addition, documents not relevant to the four domains were included to simulate the background literature that we want to filter out of consideration. The labeled documents were used to train models using a Naive Bayes Multinomial classifier, via the Weka data mining platform. Separate tests were performed using multi-class or single-class models, and including background literature or not including it. For the multi-class models, recall (% of all documents in a class that are classified correctly) for scientific domains ranged between 74% and 94%, with precision (% of classified documents that are in the desired class) between 38% and 93%, with models created with background literature performing worse than models without the background documents. Single-class models had precision that ranged from 31% to 90%, and recall that ranged from 84% to 98%, with better precision for models not using background literature, but better overall recall for models using background literature. Single-class models generally performed better than multi-class models in recall, though multi-class models without the background screen tended to be best for precision.
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
Authors: Silva Pedro J
Published: January 2018

The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe-4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)// B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe-4S], yielding a negatively-charged intermediate. Depending on the rate of Fe-S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer The computed reaction barriers suggest that Fe-S cluster re-reduction should be the rate-limiting stage of the process. Additional comparisons of the energetic features of the intermediates with those of common biochemical redox intermediates suggest a surprisingly simple explanation for the mechanistic differences between the dark-catalyzed and light-dependent enzyme reaction mechanisms.
Biochemical 'Cambrian events': on the evolution of biological codes
Authors: Wallace Rodrick
Published: January 2018

Tlusty's topological analysis of the genetic code suggests ecosystem changes in available metabolic free energy that predated the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators, protein folding codes, and monosaccharide cell-surface codes. These coevolved via various 'Cambrian explosions' until, very early on, the ancestors of the present narrow spectrum of such biological machineries outcompeted other codings and became evolutionarily locked in at surprisingly modest levels of fitness likely reflecting a modest embedding metabolic free energy ecology. Thus biochemical 'Cambrian singularities' must have occurred at different scales and levels of organization on Earth, with competition or chance-selected outcomes frozen at a far earlier period than the physical bauplan Cambrian explosion. Beyond codes, other examples might include explosive variations in mechanisms of photosynthesis, and the subsequent manifold oxygen metabolisms. Intermediate between Cambrian bauplan and genetic code, variants remain today, even after evolutionary pruning, often protected in specialized ecological niches. It is even possible to interpret the most basic biological 'coding' from this perspective, i.e., homochirality. This suggests that, under other astrobiological ecologies, different spectra of biochemical codes and other mechanisms may survive in appropriate niches.
Temporal variability predicts the magnitude of between-group attentional blink differences in developmental dyslexia: a meta-analysis
Authors: Badcock Nicholas A , Kidd Joanna C
Published: January 2018

Background. Here we report on a meta-analysis of the attentional blink (AB) research focussed on specific reading impairment, commonly referred to as developmental dyslexia. The AB effect relates to a limitation in the allocation of attention over time and examined in a dual-target rapid serial visual presentation paradigm. When the second target appears in close temporal proximity to the first target, the second target is reported less accurately.

Method. A Web of Science search with terms 'dyslexia attentional blink' returned 13 AB experiments (11 papers) conducted with developmental dyslexia (9 were included in this meta-analysis). The main pattern of performance was lower overall accuracy in groups of individuals with dyslexia relative to typically reading peers. That is, a between-group main effect. This meta-analysis examined the size of the between-group effect in relation to physical presentation characteristics, which differed between and within experiments.

Results. Four noteworthy variables were related to the between group effect-size; fixation duration (positive relationship, R2 = .89, p <.01, n = 6), maximum temporal position of T2 (negative relationship, R2 = .46, p <.05, n = 9), the difference between the minimum and maximum temporal position of T2 (negative relationship, R2 = .53, p <.05, n = 9), and the stimulus onset asynchrony (negative relationship, R2 = .46, p <.05, n = 9).

Discussion. These are discussed with respect to the preparation of task-set, temporal orienting, and speed of processing, recommending these as considerations for future research.
Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss
Authors: Leamy Larry , Elo Kari , Nielsen Merlyn K , Thorn Stephanie , Valdar William , Pomp Daniel
Published: January 2018

Obesity in human populations, currently a serious health concern, is considered to be the consequence of an energy imbalance in which more energy in calories is consumed than is expended. We used interval mapping techniques to investigate the genetic basis of a number of energy balance traits in an F11 advanced intercross population of mice created from an original intercross of lines selected for increased and decreased heat loss. We uncovered a total of 137 quantitative trait loci (QTLs) for these traits at 41 unique sites on 18 of the 20 chromosomes in the mouse genome, with X-linked QTLs being most prevalent. Two QTLs were found for the selection target of heat loss, one on distal chromosome 1 and another on proximal chromosome 2. The number of QTLs affecting the various traits generally was consistent with previous estimates of heritabilities in the same population, with the most found for two bone mineral traits and the least for feed intake and several body composition traits. QTLs were generally additive in their effects, and some, especially those affecting the body weight traits, were sex-specific. Pleiotropy was extensive within trait groups (body weights, adiposity and organ weight traits, bone traits) and especially between body composition traits adjusted and not adjusted for body weight at sacrifice. Nine QTLs were found for one or more of the adiposity traits, five of which appeared to be unique. The confidence intervals among all QTLs averaged 13.3 Mb, much smaller than usually observed in an F2 cross, and in some cases this allowed us to make reasonable inferences about candidate genes underlying these QTLs. This study combined QTL mapping with genetic parameter analysis in a large segregating population, and has advanced our understanding of the genetic architecture of complex traits related to obesity.
Feeding behaviour of Caenorhabditis elegans is an indicator of Pseudomonas aeruginosa PAO1 virulence
Authors: Lewenza Shawn , Charron-Mazenod Laetitia , Giroux Lauriane , Zamponi Alexandra D
Published: January 2018

Caenorhabditis elegans is commonly used as an infection model for pathogenesis studies in Pseudomonas aeruginosa. While the standard virulence assays rely on the slow and fast killing or paralysis of nematodes, here we developed a behaviour assay to monitor the preferred bacterial food sources of C. elegans. The type III secretion system is a well-conserved virulence trait that is not required for slow or fast killing of C. elegans. However, ΔexsE mutants that are competent for hypersecretion of ExoS, ExoT and ExoY effectors were avoided as food sources in binary assays. Conversely, mutants lacking the secretion machinery or type III effectors were preferred food sources for PAO1. In binary feeding assays, both food sources were ingested and observed in the gastrointestinal tract, but non-preferred food sources were ultimately avoided. Next we developed a high throughput feeding behaviour assay to test a library of 2370 transposon mutants in order to identify preferred food sources. After primary and secondary screens, 37 mutants were identified as preferred food sources, which included mutations in many known virulence genes and that showed reduced virulence in the slow killing assay. We propose that C. elegans feeding behaviour can be used as a sensitive indicator of virulence for bacterial strains that have moderate worm killing activity.
Extended consciousness as revealed by the angular gyrus model of consciousness
Authors: Smith Graeme E
Published: January 2018

The Extended Consciousness builds on the strengths of the proto conscious and the core consciousness to add a sense of experience onto the basic alertness provided by core consciousness. The Angular Gyrus Model of Consciousness provides some hints as to how the experential image is built. In this article I explore the role of the Temporal-Parietal Fiber Intersection Area in providing links between other parts of the brain and the Angular Gyrus that encourage the formation of the experential image.
Toxicity of ciprofloxacin and sulfamethoxazole to marine periphytic algae and bacteria
Authors: Johansson Henrik , Janmar Lisa , Backhaus Thomas
Published: January 2018

Ciprofloxacin and sulfamethoxazole are two antibiotics commonly detected in the aquatic environment, but information on their toxicity towards natural microbial communities is largely absent. In particular no data are available for marine microorganisms. Aim of the current study was therefore to evaluate the chronic toxicity of ciprofloxacin and sulfamethoxazole on natural marine biofilms (periphyton), a complex ecological community comprising a variety of bacterial and algal species. The biofilms were sampled along the Swedish west coast and subsequently exposed over 4 days in a semi-static system to a concentration series of each antibiotic. Effects on the bacterial part of the periphyton community were assessed using Biolog Ecoplates, reflecting total respiration and functional diversity of the bacterial community. Exposure to either antibiotic resulted in a clear concentration-response relationship with EC10 and EC50 values for the inhibition of total carbon source utilization of 46.1 nmol/L and 490.7 nmol/L for ciprofloxacin, respectively 56 and 1073 nmol/L for sulfamethoxazole. The NOEC for ciprofloxacin was 26 nmol/L, with a minimum significant difference of 19.24%, for sulfamethoxazole it was 140 nmol/L with a minimum significant difference of 14%. Multivariate data exploration of the whole carbon source utilization pattern confirmed these results. The data indicate that sulfamethoxazole leads to a general decrease in carbon source utilization, while ciprofloxacin exposure leads to a re-arrangement of the carbon-utilization pattern in the region of 20-50% effect. This corresponds with the higher specificity of ciprofloxacin for certain bacterial species. Effects on the algal part of the communities were evaluated by analyzing the amount and composition of photosynthetic pigments, and neither ciprofloxacin nor sulfamethoxazole caused any inhibitory effects up to the maximum tested concentration of 9 000 nmol/L. However, sulfamethoxazole exposure did lead to a significant stimulation (75% above control level) of the total pigment content of the biofilm already at the lowest tested concentration of 5 nmol/L. The stimulation then decreased with increasing concentrations to finally return to control level at 3 000 nmol/L. No shifts in the relative pigment composition were observed, indicating a generally increased algal biomass without major shifts in community composition.
Psychometric properties of the Children's Revised Impact of Events Scale (CRIES) with Bangladeshi children and adolescents
Authors: Deeba Farah , Rapee Ronald M , Prvan Tania
Published: January 2018

Identification of possible cases suffering post-traumatic stress disorder (PTSD) is important, especially in developing countries where traumatic events are typically prevalent. The Children’s Revised Impact of Events Scale is a reliable and valid measure that has two brief versions (13 items and 8 items) to assess reactions to traumatic events among young people. The current study evaluated the psychometric properties of both versions of the CRIES in a sample of 1342 children and adolescents aged 9-17 years (M=12.3 years, SD=2.12) recruited from six districts of Bangladesh. A sub-group of 120 children from four schools was re-tested on the measures within 3.5 weeks. Confirmatory factor analysis supported factor structures similar to those found in other studies for both versions of the CRIES. Multiple group confirmatory factor analysis showed gender and age-group differences within the sample, supporting established age and gender differences in prevalence of PTSD symptoms. Analyses also indicated moderate to excellent internal consistency and test-retest reliability and clear discriminant and convergent validity. These data support use of both the CRIES-13 and CRIES-8 to provide quick and psychometrically sound assessment of symptoms of PTSD among children and adolescents from Bangla-speaking communities.
No association between autistic traits and contextual influences on eye-movements during reading
Authors: Caruana Nathan , Brock Jon
Published: January 2018

Individuals with autism spectrum disorders are claimed to show a local cognitive bias, termed “weak central coherence”, which manifests in a reduced influence of contextual information on linguistic processing. Here, we investigated whether this bias might also be demonstrated by individuals who exhibit sub-clinical levels of autistic traits, as has been found for other aspects of autistic cognition. The eye-movements of 71 university students were monitored as they completed a reading comprehension task. Consistent with previous studies, participants made shorter fixations on words that were highly predicted on the basis of preceding sentence context. However, contrary to the weak central coherence account, this effect was not reduced amongst individuals with high levels of autistic traits, as measured by the Autism Spectrum Quotient (AQ). Further exploratory analyses revealed that participants with high AQ scores fixated longer on words that resolved the meaning of an earlier homograph. However, this was only the case for sentences where the two potential meanings of the homograph result in different pronunciations. The results provide tentative evidence for differences in reading style that are associated with autistic traits, but fail to support the notion of weak central coherence extending into the non-autistic population.
Curculio Curculis lupus: biology, behavior and morphology of immatures of the cannibal weevil Anchylorhynchus eriospathae G. G. Bondar, 1943
Authors: de Medeiros Bruno A S , Bená Daniela C , Vanin Sergio A
Published: January 2018

Weevils are one of the largest groups of living organisms, with more than 60,000 species feeding mostly on plants. With only one exception, their described larvae are typical plant-feeders, with mouthparts adapted to chewing plant material. Here we describe the second case of a weevil with early-instar larvae adapted to killing conspecifics. We have studied the life history of Anchylorhynchus eriospathae G. G. Bondar, 1943, a species whose immatures feed internally on palm flowers and fruits. We provide detailed descriptions of all immature stages, including the extremely modified first-instar larva. Unlike other weevils and later instars, this stage exhibits a flat body with very long ventropedal lobe setae, a large and prognathous head with a gula, and falciform mandibles, each with a serrate retinaculum, that are used to fight with and eventually kill other first-instar larvae. We also provide biological notes on all stages and the results of behavioral tests that showed that larval aggression occurs only among early life stages. Finally we show that adult size is highly dependent on timing of oviposition. This specialized killer first instar probably evolved independently from the one other case known in weevils (in Revena rubiginosa). Interestingly, both lineages inhabit the same hosts, raising the possibility that both intra- and inter-specific competition shaped those phenotypes. Given the scarcity of knowledge on early larval stages of concealed insect herbivores, it is possible that our findings represent an instance of a much broader phenomenon. Our observations also allowed us to conclude that Anchylorhynchus eriospathae and A. hatschbachi G. G. Bondar, 1943 are actually the same species, which we synonymize here by considering the latter as a junior synonym (new synonymy).
Anatomical and biomechanical traits of broiler chickens across ontogeny. Part II. Body segment inertial properties and muscle architecture of the pelvic limb
Authors: Paxton Heather , Tickle Peter G , Rankin Jeffery W , Codd Jonathan R , Hutchinson John R
Published: January 2018

In broiler chickens, genetic success for desired production traits is often shadowed by welfare concerns related to musculoskeletal health. Whilst these concerns are clear, a viable solution is still elusive. Part of the solution lies in knowing how anatomical changes in afflicted body systems that occur across ontogenyinfluence standing and moving. Here, to demonstrate these changes we quantify the segment inertial properties of the whole body, trunk (legs removed) and the right pelvic limb segments of five broilers at three different age groups across development. We also consider how muscle architecture (mass, fascicle length and other properties related to mechanics) changes for selected muscles of the pelvic limb. Wholelimb morphology is not uniform relative to body size, with broilers obtaining large thighs and feet between four and six weeks of age. This implies that the energetic cost of swinging the limbs is markedly increased across this growth period, perhaps contributing to reduced activity levels. Hindlimb bone length does not change during this period, which may be advantageous for increased stability despite the increased energetic costs. Increased pectoral muscle growth appears to move the centre of mass cranio-dorsally in the last two weeks of growth. This has direct consequences for ventilation (heavier sterna apparatus must be moved with each breath) and locomotion (potentially greater limb muscle stresses during standing andmoving). Our study is the first to measure these changes in the musculoskeletal system across growth in chickens, and reveals how artificially selected changes of the morphology of the pectoral apparatus may cause deficits in locomotion, as well as breathing.
Evidence of conditional strategies in human friendship
Authors: Arter Jennifer
Published: January 2018

Many species employ conditional strategies for reproduction or survival. In other words, each individual “chooses” one of two or more possible phenotypes to maximize survival or reproductive advantage given specific ecological niche conditions (e.g., Moran, 1992). Humans seem to employ at least one conditional reproductive strategy, choosing between a more short-term or a more long-term mating strategy (Gangestad & Simpson, 2000), and as with non-human animals, their choices relate in part to an assessment of their own traits (Belsky, 1997; Schmitt, 2005). However, the selection pressures that individuals of a species can exert on each other are not restricted to mate selection; they can arise from many forms of social interaction (West-Eberhard, 1983; Wolf, Brodie, & Moore, 1999). Evidence suggests that individuals are sensitive to characteristics of the self, friend, and environmental conditions when choosing friends (Fehr, 1996; Rose, 1985; Verbrugge, 1977), and that a person’s economic, social, and environmental circumstances influence how they form and organize their friendships (Adams & Allan, 1998; Feld & Carter, 1998). Thus, in this paper I hypothesize that humans have evolved a coherent range of conditional friendship strategies: that we vary predictably in terms of the friendships we form, based on an assessment of our own traits, others’ traits, and our own current needs. I propose a continuum of individual differences in friendship strategy, anchored on one end by those who use friendships for exploration (e.g., skill-building and networking) and on the other end by those who use friendships for intimate exchange (e.g., emotional support and intimacy). I created a measure assessing this continuum, and found that men tended to report a stronger exploration strategy than women. I also found that people with a stronger exploration strategy also had a more short-term mating strategy and were more extroverted, and that people with a stronger intimate exchange strategy reported themselves to be more kind and generous; these results remained when controlling for gender. However, friendship strategy did not relate to socioeconomic status, age, attachment avoidance, relationship status, or presence of kin relationships. There was some evidence that friendship strategy was related to the number of friends an individual reported having and how close they felt to their friends.
SKIMMR: Facilitating knowledge discovery in life sciences by machine-aided skim reading
Authors: Novacek Vit , Burns Gully APC
Published: January 2018

Background: Unlike full reading, 'skim-reading' involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles that are being published ongoingly in life sciences. Methods: To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used to construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed. Last but not least, we describe a methodology for automated experimental evaluation of the presented approach. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. Results: We provide a web-based prototype (called `SKIMMR') that generates a network of inter-related entities from a set of documents which a user may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are the most relevant to those entities of interest currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson's Disease. Finally, we report on the results of experimental evaluation using the two domains and one additional dataset based on the TREC challenge. The results show that the presented method for machine-aided skim reading outperforms tools like PubMed regarding focused browsing and informativeness of the browsing context.
Within country differences of the association between parity and overnutrition in Peruvian women
Authors: Poterico Julio A. , Huayanay-Espinoza Carlos A. , Carrillo-Larco Rodrigo , Miranda J. Jaime
Published: January 2018

Background: Evidence denotes a direct association between parity and overnutrition in developing societies. This work aims to assess the relationship between them in Peruvian women, and to investigate whether this association varies by place of residence and socioeconomic status. Methods: We used secondary data from the National Health and Demographic Survey 2011 of Peru (ENDES 2011). Parity was the independent variable, defined as the number of children ever born to a woman. The outcome variable was the body mass index (BMI), with cut-off points of 25-30 kg/m2 and ≥30 kg/m2, for overweight and obesity; respectively. We included other variables due to their potential confounding or modification effect, such as: age, place of residence, wealth index, education, and frequency of watching television. We used a significance level of 5%. Results: We analyzed information of 18262 women. The mean BMI was 25.9 Kg/m2 (SD±4.6). The overall prevalence of obesity and overweight was of 17.2% and 35.0%, respectively. Rural and urban women reported having had 2.5 (95%CI: 2.4-2.6) and 1.5 (95%CI: 1.4-1.5) ever born children, respectively. We found a positive association between parity and overnutrition, and identified the effect modification of place of residence and wealth. The relationship between parity with overweight or obesity was stronger in urban than in rural areas. Women in the bottom and top groups of wealth index showed stronger associations than the other categories of socioeconomic status. Conclusion: Our findings suggest that the more childbirths a woman has, the more likely she is of being overweight or obese. This relationship varies by socioeconomic status and area of residence. Identification of increased BMI in women, especially after the first childbirth, should be evaluated in primary care to establish adequate public health policies to tackle obesity in Peruvian women.
Soil carbon research and global environmental challenges
Authors: Hartemink Alfred E , Lal Rattan , Gerzabek Martin H. , Jama Bashir , McBratney Alex , Six Johan , Tornquist Carlos G.
Published: January 2018

The role of soil organic carbon (SOC) in maintaining soil conditions and its resulting services is well established. Currently, over 1,000 articles per year are being published in peer-reviewed journals, and increasing at about 10% per year. It was not until the 1980s when the relation between soils and climate change was noted, and it was realized that soils play a key role as a sink and source of greenhouse gases (GHGs) ( Bouwman 1990, Scharpenseel, Ayoub and Schomaker 1990, Jenny 1980). A large number of research projects have been initiated globally in which soil C is a key component, and there have been some excellent reviews ( Lal 2004, Stockmann et al. 2013, Melillo et al. 2011). Yet, there is a lack of focus in soil C research in relation to current environmental challenges. Here we recommend research priorities to advance the knowledge base and use of soil C in relation to global human and environmental challenges: food and fiber production, water scarcity and purification, energy production, climate change, biodiversity, recycling waste, and environmental degradation. We have listed the priorities under three themes: (i) Soil C in space and time, (ii) Soil C properties and processes, and (ii) Soil C depletion and management.
Primary memory is priming memory seen through the working memory viewpoint
Authors: Smith Graeme E
Published: January 2018

There are two streams of thought about memory that don't seem to jibe with each other, one thought stream works with implicit and explicit memory and one stream works with working memory. The problem is that the theories are not visible each within the other. In this article I attempt to combine the two threads of thought by pointing out a simple but overlooked identity between priming memory and primary memory, explaining why they look so different when looked at from their own particular threads of interpretation, and showing how the difference is really one of the interface between priming and working memory, not an incompatibility in design as first seems obvious.
Migratory bottlenecks as integrators of species- and population-level diversity: the Skeena River estuary, its salmon, and industrial development
Authors: Carr-Harris Charmaine N , Gottesfeld Allen S. , Moore Jonathan
Published: January 2018

We quantify how an estuarine migratory bottleneck supports population- and species- level diversity of salmon. The estuary of the Skeena River is under pressure from industrial development, with two gas liquefaction terminals and a potash loading facility in various stages of environmental review processes at the same time as recent changes to Canadian environmental laws have reduced the timeframe for federal environmental assessments. We conducted a juvenile salmonid sampling program throughout the Skeena River estuary in 2007 and 2013. We captured all species of juvenile salmonids throughout the estuary in both years, and found that areas proposed for development support some of the highest abundances of some species of salmonids. Specifically, the highest abundances of sockeye (both years) Chinook in 2007, and coho salmon in 2013 were captured in areas proposed for development. For example, juvenile sockeye salmon were 2-8 times more abundant in the proposed development areas. Genetic stock assignment demonstrated that the Chinook salmon and most of the sockeye salmon that were captured originated from throughout the Skeena watershed, while some sockeye salmon came from the Nass, Stikine, Southeast Alaska, and coastal systems on the northern and central coasts of British Columbia. These fish support extensive commercial, recreational, and First Nations fisheries throughout the Skeena River and beyond. Our results demonstrate that estuary habitats integrate species and population diversity of salmon, and that proposed development in these areas will threaten the fisheries that depend on these fishes.
Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives
Authors: Strickler Susan R , Bombarely Aureliano , Munkvold Jesse D , Menda Naama , Martin Gregory B , Mueller Lukas A
Published: January 2018

Background Studies of ancestry are difficult in tomato because it crosses with many wild relatives and species in the tomato clade have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using coding sequence from Solanum lycopericum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and genomic sequence from two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, as well as an heirloom line, S. lycopersicum ‘Yellow Pear’, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results Divergence date estimates suggest divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 29 genes in our analysis showed evidence of selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these accessions, likely as a result of incomplete lineage sorting and introgression, a primary phylogenetic history was strongly supported. Conclusions Based on analysis of these accessions, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.
Error estimates for the analysis of differential expression from RNA-seq count data
Authors: Burden Conrad , Qureshi Sumaira , Wilson Susan R
Published: January 2018

A number of algorithms exist for analysing RNA-sequencing data to infer profiles of differential gene expression. Problems inherent in building algorithms around statistical models of over dispersed count data are formidable and frequently lead to non-uniform p-value distributions for null-hypothesis data and to inaccurate estimates of false discovery rates (FDRs). This can lead to an inaccurate measure of significance and loss of power to detect differential expression.

We use synthetic and real biological data to assess the ability of several available R packages to accurately estimate FDRs. The packages surveyed are based on statistical models of overdispersed Poisson data and include edgeR, DESeq, DESeq2, PoissonSeq and QuasiSeq. Also tested is an add-on package to edgeR and DESeq which we introduce called Polyfit. Polyfit aims to address the problem of a non-uniform null p-value distribution for two-class datasets by adapting the Storey-Tibshirani procedure.

We find the best performing package in the sense that it achieves a low FDR which is accurately estimated over the full range of p-values, albeit with a very slow run time, is the QLSpline implementation of QuasiSeq. This finding holds provided the number of biological replicates in each condition is at least 4. The next best performing packages are edgeR and DESeq2. When the number of biological replicates is sufficiently high, and within a range accessible to multiplexed experimental designs, the Polyfit extension improves the performance DESeq (for approximately 6 or more replicates per condition), making its performance comparable with that of edgeR and DESeq2 in our tests with synthetic data.
Bird-window collisions in the summer breeding season
Authors: Hager Stephen B. , Craig Matthew E.
Published: January 2018

Birds that reside in urban settings face numerous human-related threats to survival, including mortality from bird-window collisions (BWCs). Our current understanding of this issue has largely been driven by data collected during spring and fall migration, and patterns of collision mortality during the summer breeding season remain relatively unexplored. We assessed BWCs during four breeding seasons (2009- 2012) at a site in northwestern Illinois, USA, by comparing the abundance, richness, migratory class, and age of the species living around buildings to species mortally wounded by window collisions. We also systematically assessed the daily timing of BWCs throughout the breeding season. We documented BWCs in 4 of 25 (16%) species and 7 of 21 (33%) species in 2009 and 2010, respectively. The relationship between BWCs and abundance depended on age. For adults, BWCs were highest in the least abundant species, e.g., Red-eyed Vireo (Vireo olivaceus), and lowest in species with high abundance values, e.g., House Sparrow (Passer domesticus). For juveniles, mortality was greatest for the most abundant species, and the American Robin (Turdus migratorius) accounted for 62% of all juvenile carcasses. Early in the breeding season, collision mortality was restricted to adults of Long- distance Migrants, whereas juveniles of all three migratory guilds (Long-distance and Short-distance Migrants and Permanent Residents) died at windows from late June through early August. Daily mortality for all species was highest between sunrise - 1600 h and lowest from 1600 h - sunrise the next day. Generally, the species observed as carcasses matched birds considered a ‘high risk’ for BWCs, e.g., Ruby-throated Hummingbird (Archilochus colubris), and those considered ‘low risk’ were not observed as carcasses, e.g., Blue-gray Gnatcatcher (Polioptila caerulea). Our results suggest that the number of BWCs during the breeding season does not necessarily increase with abundance, but rather appears related to variation among species and age classes, which may have important implications on the population health of affected species. The mechanisms driving these differences are unknown, but may be related reproductive behavior, flight speed, distance movements, and dispersal patterns.
A case study demonstrates a democratic methodology for making risk based decisions
Authors: Corin Steve , Atapattu Asela
Published: January 2018

Risk is a subjective notion, but the limits between our role as risk practitioners and decision makers can become blurred. A belief that the public misunderstands risk and the need to control the process are two barriers to effective engagement. We believe that a lack of engagement and the ability to enable citizens to decide their own future can contribute to the controversy we see on important public debates. In our study, using an existing risk assessment and decision, we survey four stakeholder groups in New Zealand in order to determine how they rate the costs and benefits. Our survey methodology incorporates a continuous scale along three axes that represent the biophysical outcomes of economic, environmental and human health. This design enables costs and benefits to be traded-off between individuals, giving them a representative voice. We use these results to investigate whether or not it would be feasible to use such an approach in order to make decisions, and what this may mean. Our results indicate that public decision making is possible, and in this case broadly the public view broadly agrees with the official decision. Such an approach holds promise for expanding the role in the risk assessment process.
Effects of deuterium oxide on cell growth and vesicle speed in RBL-2H3 cells
Authors: Kalkur Roshni S , Ballast Andrew C , Triplett Ashley R , Spendier Kathrin
Published: January 2018

For the first time we show the effects of deuterium oxide on the cell growth and vesicle transport in rat basophilic leukemia (RBL-2H3) cells. RBL-2H3 cells cultured with 15 moles/L deuterium showed decreased cell growth which was attributed to cells not doubling their DNA content. Experimental observations also showed an increase in vesicle speed for cells cultured in deuterium oxide. This increase in vesicle speed was not observed in deuterium oxide cultures treated with a microtubule-destabilizing drug suggesting that deuterium oxide affects microtubule-dependent vesicle transport.
An ontogenetic perspective on the evolution of shell size and shell shape in the land snail genus Plectostoma
Authors: Liew Thor-Seng , Schilthuizen Menno
Published: January 2018

The rampant convergent and parallel evolution in shell form in the Gastropoda is well known. Many studies focus on the functional drivers which have been regarded as a major force in shell evolution. There is, however, a scarcity in studies that aim at understanding shell form evolution with respect to their ontogeny. Hence, we investigated the evolution of shell form in the micro-landsnail genus Plectostoma (Diplommatinidae) from the viewpoint of shell ontogeny. We examined the aperture ontogeny profiles that describe how aperture form and growth trajectory change along the shell ontogeny, and how the aperture ontogeny profiles relate to the observed shell forms. We also estimated the phylogeny of Plectostoma species, and examined patterns of character evolution for shell form. Our study revealed a general issue in the characterisation of shell shape and demonstrated how shell shape differences can be expressed as differences in the ontogeny of morphospace. It is clear that in Plectostoma the phylogenetic history does not prevent the course of shell ontogeny, and the resultant form. Finally, each species has a unique aperture ontogeny profile that determines its shell shape while retaining a conserved developmental program that maintains shell size.
The pupillary light response reflects exogenous attention and inhibition of return
Authors: Mathôt Sebastiaan , Dalmaijer Edwin S. , Grainger Jonathan , Van der Stigchel Stefan
Published: January 2018

Here we show that the pupillary light response reflects exogenous (involuntary) shifts of attention and inhibition of return. Participants fixated in the center of a display that was divided into a bright and a dark half. An exogenous cue attracted attention to the bright or dark side of the display. Initially, the pupil constricted when the bright, as compared to the dark side of the display was cued, reflecting a shift of attention towards the exogenous cue. Crucially, this pattern reversed about one second after cue presentation. This later-occurring, relative dilation (when the bright side was cued) reflected disengagement from the previously attended location, analogous to the behavioral phenomenon of inhibition of return. Indeed, we observed a strong correlation between 'pupillary inhibition' and behavioral inhibition of return. We conclude that the pupillary light response is a complex eye movement that reflects how we selectively parse and interpret visual input.
What’s for dinner?: Undescribed species in commercial porcini from China
Authors: Dentinger Bryn TM , Suz Laura M
Published: January 2018

Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species in the food chain, leading to an improved ability to regulate their harvest and trade, and to monitor potential adverse health effects from their consumption.