bluuebunny/crossref_metadata_2025 huggingface dataset:
No improved resistance against generalist herbivores found for invasive genotypes: a case study of Senecio vulgaris (Asteraceae) and a generalist snail (Achatina fulica)
Authors: Nguyen Viet Thang , Ndihokubwayo Noel , Cheng Dandan
Published: January 2018

Invasive plants escape from some natural enemies as predictions of Enemy Release Hypothesis (ERH). However, in fact they still have to face the pressure of generalist herbivores in introduced ranges resulting in the maintenance or enhancing of resistance ability to generalist herbivores. In this study, we carried out a general feeding bioassay in a laboratory with leaves of Senecio vulgaris to test the difference in resistance between ranges. White jade land snails (WJLD, Achatina fulica) were fed with the leaves of Pakchoi (Brassica chinensis), Lettuce (Lactuca sativa), native and invasive plants of S. vulgaris. The feeding experiment with S. vulgaris leaves was carried out in two waves. We found that both native and invasive S. vulgaris plant were resistant again to WJLD compared to Pakchoi and Lettuce. However, there were no significant differences between native and invasive plants of S. vulgaris in relation to the resistance against WJLD. The results prove the maintenance of chemical defense against generalist herbivores in invasive plants in introduced range. The success of S. vulgaris to invader China could not be explained by releasing from natural enemies but possessing of defense ability against herbivores before it introduced to China.
The role of Twitter in the life cycle of a scientific publication
Authors: Darling Emily S , Shiffman David , Côté Isabelle M. , Drew Joshua A
Published: January 2018

Twitter is a micro-blogging social media platform for short messages that can have a long-term impact on how scientists create and publish ideas. We investigate the usefulness of twitter in the development and distribution of scientific knowledge. At the start of the 'life cycle' of a scientific publication, twitter provides a large virtual department of colleagues that can help to rapidly generate, share and refine new ideas. As ideas become manuscripts, twitter can be used as an informal arena for the pre-review of works in progress. Finally, tweeting published findings can communicate research to a broad audience of other researchers, decision makers, journalists and the general public that can amplify the scientific and social impact of publications. However, there are limitations, largely surrounding issues of intellectual property and ownership, inclusiveness and misrepresentations of science ‘sound bites’. Nevertheless, we believe twitter is a useful social media tool that can provide a valuable contribution to scientific publishing in the 21st century.
Caribbean Bulimulus revisited: physical moves and molecular traces (Mollusca, Gastropoda, Bulimulidae)
Authors: Breure Abraham SH
Published: January 2018

Twenty-five samples of Bulimulus species are studied, partly from localities within their known distribution range, partly based on interceptions where the material originates from localities where the species seem to be recently introduced and non-native. Molecular study of cytochrome oxidase 1 (CO1) reveals the origin of some of these introductions, but is less conclusive for others. Four different methods for species delimitation were applied, which did not result in unambiguous species hypotheses. For a rapid identification of morphologically indistinct species, a more comprehensive database of sequences is needed.
Adoption of machine learning techniques in Ecology and Earth Science
Authors: Thessen Anne E
Published: January 2018

The natural sciences, such as ecology and earth science, study complex interactions between biotic and abiotic systems in order to infer understanding and make predictions. Machine-learning-based methods have an advantage over traditional statistical methods in studying these systems because the former do not impose unrealistic assumptions (such as linearity), are capable of inferring missing data, and can reduce long-term expert annotation burden. Thus, a wider adoption of machine learning methods in ecology and earth science has the potential to greatly accelerate the pace and quality of science. Despite these advantages, machine learning techniques have not had wide spread adoption in ecology and earth science. This is largely due to 1) a lack of communication and collaboration between the machine learning research community and natural scientists, 2) a lack of easily accessible tools and services, and 3) the requirement for a robust training and test data set. These impediments can be overcome through financial support for collaborative work and the development of tools and services facilitating ML use. Natural scientists who have not yet used machine learning methods can be introduced to these techniques through Random Forest, a method that is easy to implement and performs well. This manuscript will 1) briefly describe several popular ML methods and their application to ecology and earth science, 2) discuss why ML methods are underutilized in natural science, and 3) propose solutions for barriers preventing wider ML adoption.
Decentralized provenance-aware publishing with nanopublications
Authors: Kuhn Tobias , Chichester Christine , Krauthammer Michael , Queralt-Rosinach Núria , Verborgh Ruben , Giannakopoulos George , Ngonga Ngomo Axel-Cyrille , Viglianti Raffaele , Dumontier Michel
Published: January 2018

Publication and archival of scientific results is still commonly considered the responsability of classical publishing companies. Classical forms of publishing, however, which center around printed narrative articles, no longer seem well-suited in the digital age. In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. In this article, we propose to design scientific data publishing as a Web-based bottom-up process, without top-down control of central authorities such as publishing companies. Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data. We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used as a low-level data publication layer to serve the Semantic Web in general. Our evaluation of the current network shows that this system is efficient and reliable.
Identification of bladder cancer biomarkers by genomic approaches
Authors: Majewski Tadeusz , Bondaruk Jolanta , Lee Sangkyou , Lee June Goo , Baggerly Keitg , McConkey David , Czerniak Bogdan
Published: January 2018

Bladder Cancer is one of the most frequent human cancer which develops on two tracks, papillary and non-papillary that correspond to clinically different forms of the disease. Most bladder cancers are chemically induced with tobacco smoking being the leading risk factor. Recent advances of bladder cancer research for which our laboratory has significantly contributed have enhanced the understanding of the origin of bladder cancer from urothelial progenitor cells via field effects along papillary/luminal non-papillary/basal pathways. Here we present the contribution to the development of novel, both diagnostic and therapeutic, biomarkers using genomic high throughput technologies.

The analysis of hits associated with growth advantage of preneoplastic lesions allowed us to identify six chromosomal regions mapping 3q22, 5q22.2-5q23.3, 9q22.12, 10q26.1, 13q14 and 17p13 that may be critical for the development of bladder cancer and contain a distinct class of genes referred to us forerunner (FR) genes involved in the clonal expansion of precursor conditions. We concentrated our efforts on one of these regions; which contain a model tumor suppressor RB1. We used high-resolution whole-organ mapping with SNPs, which facilitated the identification of five positional candidate FR genes (ITM2B, LPAR6, MLNR, CAB39L, and ARL11) mapping contiguously to RB1. We hypothesized that identification of novel forerunner genes and the investigation in early occult phases of human bladder preneoplasia may not only provide important mechanistic clues to the development of human cancer but also identify a novel class of early detection markers capable of detecting the clinically and microscopically occult phases of human cancer development.

We used the whole-organ histologic and genetic mapping strategy coupled with next generation whole exome sequencing using complemented with genotyping using Illumina HumanOmni2.5_8 chips and whole genome methylation analyses to define the molecular alterations that were associated with the progression of muscle-invasive bladder cancer in one surgical specimen.

We identified a total of 18 structurally significant mutations, three of which appeared to be clear "driver" mutations that had been annotated previously. Alterations in chromatin hyper- and hypomethylation predominated in all of the regions that contained normal-appearing urothelium or low-grade dysplasia. In total, 31 genes were hypermethylated and 26 genes were hypomethylated. Copy number alterations were numerous (n=242) in areas that contained high-grade dysplasia suggesting that genomic instability proceeded the emergence of driver mutations in what ultimately emerged as the dominant tumor subclone. Chromosomal gains (n=216) vastly outnumbered losses (n=26).
Sperm removal during copulation confirmed in the oldest extant damselfly, Hemiphlebia mirabilis
Authors: Cordero-Rivera Adolfo
Published: January 2018

Postcopulatory sexual selection may favour mechanisms to reduce sperm competition, like physical sperm removal by males. To investigate the origin of sperm removal, I studied the reproductive behaviour and mechanisms of sperm competition in the only living member of the oldest damselfly family, Hemiphlebia mirabilis, one species that was considered extinct in the 1980s. This species displays scramble competition behaviour, whose males search for females with short flights and both sexes exhibit a conspicuous “abdominal flicking”. This behaviour is used by males during an elaborate precopulatory courtship, unique among the Odonata. Females use a similar display to reject male attempts to form tandem, but eventually signal receptivity by a particular body position. Males immobilise females during courtship using their legs, which, contrarily to other damselflies, never autotomize. Copulation is short (range 4.1-18.7 min), and has two stages. In the first stage, males remove part of the stored sperm, and inseminate during the second stage, at the end of mating. The examination of genitalia indicates that males have two horns covered by back-oriented spines, which match the size and form of female genitalia. The volume of sperm in females after copulation was 2.8 times larger than the volume stored in females whose copulation was interrupted at the end of stage I, indicative of a significant sperm removal. These results point out that sperm removal is an old character in the evolution of odonates, probably dating back to the Permian.
Preventing Zika virus infection during pregnancy by timing conception seasonally
Authors: Martinez-Bakker Micaela E
Published: January 2018

It has come to light that ZIKV infection during pregnancy can result in fetal death, damage to the central nervous system, and growth restrictions. In 2016 there are expected to be >8,600,000 births in countries with ongoing ZIKV transmission. In response to the ZIKV threat, the WHO is strategically targeting prevention of infection in pregnant women and funding contraception use in epidemic regions. I propose that the damaging effects of ZIKV can be curtailed by timing pregnancy seasonally to minimize maternal exposure to ZIKV. The ZIKV mosquito vector has seasonal changes in its abundance and flavivirus transmission competence. By seasonally planning pregnancy, this aspect of vector ecology can be leveraged to align sensitive periods of gestation with the low-transmission season.
Expressed and understood gestural repertoires of wild bonobos (Pan paniscus)
Authors: Graham Kirsty E , Hobaiter Catherine , Byrne Richard W
Published: January 2018

Research on great ape gestural communication has hitherto prioritised the signaller, focusing on the expressed repertoire, the set of gesture types that an individual deploys. In this study of wild bonobos (Pan paniscus), we also examine the understood repertoire, the set of gesture types that a recipient understands: a recipient understands a gesture if they respond to the signaller with an Apparently Satisfactory Outcome (ASO). Combining the understood and expressed repertoires substantially expands an individual’s overall repertoire. Hence, we propose that including the understood repertoire better represents an individual’s actual communicative repertoire, and may for the first time reveal gesture types received exclusively by specific subsets of individuals. Significant differences between expressed and understood repertoires might result from two things: (1) gestures are ritualised between signallers and recipients and may therefore be unidirectional in some cases, or (2) the circumstances of use differ among age-sex groups, limiting the need for an individual to use a certain gesture type. In the latter, we expect consistency in particular age-sex groups whereas unidirectional comprehension as a result of ritualization would predict random distribution among individuals. We further compare our dataset with and without gesture instances occurring in play, as play may be a context in which individuals deploy gestures that they rarely or never use otherwise. Assessing the understood repertoire is a useful tool for animal communication researchers, not only allowing shorter study-periods, but also to discover gesture types specific to subsets of individuals, which may reveal much about a species’ social behaviour.
Microbes in deionized water: Implications for maintenance of laboratory water production system
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Microbes, with their vast metabolic capabilities and great adaptability, occupy almost every conceivable ecological niche on Earth – thus, could they survive in the oligotrophic (i.e., nutrient poor) deionized (DI) water that we use for experiments? Observations of white cauliflower-like lumps and black specks in salt solutions after months of storage in plastic bottles prompted the inquisition concerning the origin and nature of the “contaminants”. Hypothesizing that the “contaminants” may be microbes from DI water, a series of growth experiments was conducted to detect and profile the diversity of microbes in fresh DI water - produced on a just-in-time basis by a filter cum ion exchange system with tap water as feed. While microbes could also be present on the surfaces and headspace of the unsterilized polyethylene bottles, investigating whether microbes are present in freshly produced DI water provides a more stringent performance test of the production system. Inoculation of DI water on R2A agar followed by multi-day aerobic cultivation revealed the presence of a wide variety of microbes (total viable cell concentration of ~103 colony forming units (CFU) per mL) with differing pigmentations, growth rates as well as colony sizes and morphologies. In addition, greater abundance and diversity of microorganisms was recovered at 30 oC compared to 25 and 37 oC; most probably due to adaptation of microbes to tropical ambient water temperatures of 25 to 30 oC. Comparative experiments with tap water as inoculum recovered a significantly smaller number and diversity of microorganisms; thus, suggesting that monochloramine residual disinfectant in tap water was effective in inhibiting cell viability. In contrast, possible removal of monochloramine by adsorption onto ion exchange resins – and thus, alleviation of a source of environment stress - might explain the observed greater diversity and abundance of viable microbes in DI water. Collectively, this study confirmed the presence of microbes in fresh DI water – and suggested a possible source of the “contaminants” in prepared salt solutions. Propensity of microbes in forming biofilm on various surfaces suggested that intermittent flow in just-in-time DI water production provided opportunities for cell attachment and biofilm formation during water stagnation, and subsequent dislodgement and resuspension of cells upon water flow. Thus, regular maintenance and cleaning of the production system should help reduce DI water’s microorganism load. In addition, simple and low cost culture experiments on solid medium can provide a qualitative and semi-quantitative estimate of microbe diversity and viable cell concentration in DI water, respectively. The above, together with regular monitoring of water resistivity or conductivity, comprise a trio of tests useful for detecting possible contamination, or deterioration of DI water’s chemical and microbiological quality.
Beyond p-values in the evaluation of brain-computer interfaces
Authors: Melinscak Filip , Montesano Luis
Published: January 2018

To statistically evaluate the performance of brain-computer interfaces (BCIs), researchers usually rely on null hypothesis significance testing (NHST), i.e. p-values. However, over-reliance on NHST is often identified as one of the causes of the recent reproducibility crisis in psychology and neuroscience. In this paper we propose Bayesian estimation as an alternative to NHST in the analysis of BCI performance data. For the three most common experimental designs in BCI research - which would usually be analyzed using a t-test, a linear regression, or an ANOVA - we develop hierarchical models and estimate their parameters using Bayesian inference. Furthermore, we show that the described models are special cases of the hierarchical generalized linear model (HGLM), which we propose as a general framework for the analysis of BCI performance. The HGLM framework allows the analysis of complex experimental designs with multiple levels of hierarchy (e.g. multiple sessions, multiple subjects, multiple groups) and can accommodate different types of non-normal data (e.g. classification accuracy), which are often analyzed under inappropriate assumptions with NHST. We demonstrate the effectiveness of the proposed models on three real datasets and show how the results obtained with Bayesian estimation can give a more nuanced insight into BCI performance data, compared to NHST. Therefore we believe that a wider adoption of the Bayesian estimation approach in BCI studies could bring about greater transparency in data analysis, allow accumulation of knowledge across studies, and reduce questionable practices such as "p-hacking". To achieve this goal, we provide all the data and code necessary to reproduce the presented results, allowing BCI researchers to use Bayesian estimation in their own work.
Adult neurobehavioral outcome of hyperbilirubinemia in full term neonates – a 30 year prospective follow-up study
Authors: Hokkanen Laura , Launes Jyrki , Michelsson Katarina
Published: January 2018

Background. Neonatal hyperbilirubinemia (HB) may cause severe neurological damage, but serious consequences are effectively controlled by phototherapy and blood exchange transfusion. HB is still a serious health problem in economically compromised parts of the world. The long term outcome has been regarded favorable based on epidemiological data, but has not been confirmed in prospective follow-up studies extending to adulthood.Methods. We studied the long term consequences of HB in a prospective birth cohort of 128 HB cases and 82 controls. The cases are part of a neonatal at-risk cohort (n=1196) that has been followed up to 30 years of age. HB cases were newborns ≥ 2500 g birth weight and ≥ 37 weeks of gestation who had bilirubin concentrations > 340µmol/l or required blood exchange transfusion. Subjects with HB were divided into subgroups based on the presence (affected HB) or absence (unaffected HB) of diagnosed neurobehavioral disorders in childhood, and compared with healthy controls. Subjects were seen at discharge, 5, 9 and 16 years of life and parent’s and teacher’s assessments were recorded. At 30 years they filled a questionnaire about academic and occupational achievement, life satisfaction, somatic and psychiatric symptoms including a ADHD self-rating score. Cognitive functioning was tested using ITPA, WISC, and reading and writing tests at 9 years of life. Results. Compared to controls, the odds for a child with HB having neurobehavioral symptoms at 9 years was elevated (OR=4.68). Fortyfive per cent of the HB group were affected by cognitive abnormalities in childhood and continued to experience problems in adulthood. This was apparent in academic achievement (p<0.0001) and the ability to complete secondary (p<0.0001) and tertiary (p<0.004) education. Also, the subgroup of affected HB reported persisting cognitive complaints e.g. problems with reading, writing and mathematics. Childhood symptoms of hyperactivity/impulsivity (p<0.0001) and inattention (p<0.02) were more common in HB groups, but in adulthood the symptoms were equal. The affected HB had lower scores in parameters reflecting life satisfaction, less controlled drinking, but not increased substance abuse. Discussion. Our results indicate that neonatal HB has negative consequences in adult age. A prospectively collected cohort with strict inclusion criteria enables to control most of the bias factors involved with retrospective data. The control and HB groups were remarkably similar at birth in terms of medical data, and the growth environment of the children, as well as the parents’ social groups, education, size of family, type of housing at birth and at 9 years of age. Our findings bear resemblance to disorders of the fronto-striatal network, and also symptoms of the ADHD spectrum were frequent in the HB group suggesting a link of HB to other neurodevelopmental disorders.
Food and nutritional security require adequate protein as well as energy, delivered from whole-year crop production
Authors: Coles Graeme D , Wratten Stephen D , Porter John R
Published: January 2018

Human food security requires the production of sufficient quantities of both high-quality protein and dietary energy. In a series of case-studies from New Zealand, we show that while production of food ingredients from crops on arable land can meet human dietary energy requirements effectively, requirements for high-quality protein are met more efficiently by animal production from such land. We present a model that can be used to assess dietary energy and quality-corrected protein production from various crop and crop/animal production systems, and demonstrate its utility. We extend our analysis with an accompanying economic analysis of commercially-available, pre-prepared or simply-cooked foods that can be produced from our case-study crop and animal products. We calculate the per-person, per-day cost of both quality-corrected protein and dietary energy as provided in the processed foods. We conclude that mixed dairy/cropping systems provide the greatest quantity of high-quality protein per unit price to the consumer, have the highest food energy production and can support the dietary requirements of the highest number of people, when assessed as all-year-round production systems. Global food and nutritional security will largely be an outcome of national or regional agro-economies addressing their own food needs. We hope that our model will be used for similar analyses of food production systems in other countries, agro-ecological zones and economies.
Results from an ethnographically-informed study in the context of test-driven development
Authors: Romano Simone , Fucci Davide Davide , Scanniello Giuseppe , Turhan Burak , Juristo Natalia
Published: January 2018

Background: Test-driven development (TDD) is an iterative software development technique where unit-tests are defined before production code. Previous studies fail to analyze the values, beliefs, and assumptions that inform and shape TDD. Aim: We designed and conducted a qualitative study to understand the values, beliefs, and assumptions of TDD. In particular, we sought to understand how novice and professional software developers, arranged in pairs (a driver and a pointer), perceive and apply TDD. Method: 14 novice software developers, i.e., graduate students in Computer Science at the University of Basilicata, and six professional software developers with work one to 10 years work experience participated in our ethnographically-informed study. We asked the participants to implement a new feature for an existing software written in Java. We immersed ourselves in the context of the study, and collected data by means of contemporaneous field notes, audio recordings, and other artifacts. Results: A number of insights emerge from our analysis of the collected data, the main ones being: (i) refactoring (one of the phases of TDD) is not performed as often as the process requires and it is considered less important than other phases, (ii) the most important phase is implementation, (iii) unit tests for unimplemented functionalities or behaviors are almost never up-to-date, (iv) participants first build a sort of mental model of the source code to be implemented and only then write test cases on the basis of this model; and (v) apart from minor differences, professional developers and students applied TDD in a similar fashion. Conclusions: Developers write quick-and-dirty production code to pass the tests and ignore refactoring.
Depression, anxiety, and stress in partners of Australian combat veterans and military personnel: A comparison with Australian population norms
Authors: MacDonell Gail V , Bhullar Navjot , Thorsteinsson Einar B
Published: January 2018

Partners of Australian combat veterans are at an increased risk of experiencing mental health problems. For a comparative analysis of mental health of partners of veterans with that of their non-military counterparts, the study sample comprised female partners of (a) Australian combat veterans (Sample 1: n = 282, age M = 60.79, SD = 5.05), (b) a random sub-sample of partners of Australian combat veterans from the previous sample (Sample 2: n = 50; M = 60.06, SD = 4.80), (c) partners of Special Air Services Regiment (SASR) personnel (Sample 3: n = 41, age M = 34.39 SD = 7.01), and (d) partners of current serving military (non-SASR) personnel (Sample 4: n = 38, age M = 32.37, SD= [i]6.20). Respondents completed measures to assess their reported levels of depression, anxiety, and stress. The two samples (Samples 1 and 2) for partners of Australian combat veterans reported significantly poorer symptoms of depression, anxiety, and stress than the comparative population norms. The sample of SASR personnel partners reported significantly greater levels of depression and anxiety, while the sample with non‑SASR personnel partners reported a significantly poorer symptomatology in stress than the comparative norms. Lessons and protective factors can be learnt from groups within the current military as to what may assist partners and families to maintain a better level of psychosocial health.
Impact of climate change and human activity on the runoff in the upper reaches of the Shiyang River, Northwest China
Authors: Li Peng , Xu Jianhua , Chen Zhongsheng , Zhao Benfu
Published: January 2018

Based on the hydrological and meteorological data of the upper reaches of Shiyang River basin in Northwest China from 1960 to 2009, this paper analyzed the change in runoff and its related climatic factors, and estimated the contribution of climate change and human activity to runoff change by using the moving T test, cumulative analysis of anomalies and multiple regression analysis. The results showed that temperature revealed a significant increasing trend, and potential evaporation capacity decreased significantly, while precipitation increased insignificantly in the past recent 50 years. Although there were three mutations in 1975, 1990 and 2002 respectively, runoff presented a slight decreasing trend in the whole period. The contributions of climate change and human activity to runoff change during the period of 1976-2009 were 45% and 55% respectively.
Isolation and characterization of halophilic soil fungi from the salt desert of Little Rann of Kutch, India
Authors: Rajpal Kartikeya , Prasad Ram , Gupta Vijai Kumar , Varma Ajit
Published: January 2018

Extremophiles are considered a cornucopian source of chemically diverse and often novel metabolites. Determination of their growth and distribution pattern and their chemical nature is therefore vital to fully gauge their existential uniqueness and potential as a fount of novel compounds. Present study deals with growth characterization and chemoprofiling of halophilic fungi inhabiting a hitherto unexplored terrain of Little Rann of Kutch, India. Thirty five morphologically discrete fungi, primarily belonging to phylum Ascomycota, were isolated from the soil, suggestive of the region’s low microbial diversity. Calculation of fungal salt tolerance index identified one isolate as a halophile with the remaining being halotolerant. Morphological characteristics and 18S rDNA sequencing established the halophile’s identity as Aspergillus versicolor. A. versicolor was further characterized for its salt tolerance potential and degree of halophily. The fungus grew optimally at 7.5% NaCl, thereby classifying it as a moderate halophile. Macro-morphology of the fungus corresponded well with its micro-morphology. At 0% and 10% NaCl, fungal specimen exhibited mycelial distortions, loss of cytoplasm and sparse conidiation; healthy growth features were observed at 7.5% NaCl. For chemoprofiling, A. versicolor was cultured on Czapek Dox broth and Malt Extract broth and the crude extract was analysed by liquid chromatography mass spectrometry (LC-MS). A comparative chemoprofile analysis determined Czapek Dox broth to be a better choice for profiling of this particular strain as it exhibited higher compound diversity. The rich chemical contour of A. versicolor suggests the fungus to be a potential source of novel bioactive molecules of pharmaceutical significance.
Strong Stackelberg Reasoning in Symmetric Games: An Experimental Replication and Extension
Authors: Pulford Briony D , Colman Andrew M. , Lawrence Catherine L.
Published: January 2018

In common interest games in which players are motivated to coordinate their strategies to achieve a jointly optimal outcome, orthodox game theory provides no general reason or justification for choosing the required strategies. In the simplest cases, where the optimal strategies are intuitively obvious, human decision makers generally coordinate without difficulty, but how they achieve this is poorly understood. Most theories seeking to explain strategic coordination have limited applicability, or require changes to the game specification, or introduce implausible assumptions or radical departures from fundamental game-theoretic assumptions. The theory of strong Stackelberg reasoning, according to which players choose strategies that would maximize their own payoffs if their co-players could invariably anticipate any strategy and respond with a best reply to it, avoids these problems and explains strategic coordination in all dyadic common interest games. Previous experimental evidence has provided evidence for strong Stackelberg reasoning in asymmetric games. Here we report evidence from two experiments consistent with players being influenced by strong Stackelberg reasoning in a wide variety of symmetric 3 × 3 games but tending to revert to other choice criteria when strong Stackelberg reasoning generates small payoffs.
Animal-oriented Virtual Environments: illusion, dilation, and discovery
Authors: Alicea Bradly
Published: January 2018

As a research tool, virtual environments hold immense promise for brain scientists. Yet to fully realize this potential in non-human systems, theoretical and conceptual perspectives must be developed. When selectively coupled to nervous systems, virtual environments can help us better understand the functional architecture of animals’ brains during naturalistic behaviors. While this will no doubt allow us to further our understanding of the neural basis of behavior, there is also an opportunity to uncover the diversity inherent in brain activity and behavior. This is due to two properties of virtual environments: the ability to create sensory illusions, and the ability to dilate space and/or time. These and other potential manipulations will be characterized as the effects of virtuality. In addition, the systems-level outcomes of virtual environment-enhanced perception will be discussed in the context of the uncanny valley and other expected relationships between emotional valence, cognition, and training. These effects and their usefulness for brain science will be understood in the context of three types of neurobehavioral phenomena: sensorimotor integration, spatial navigation, and interactivity. For each of these behaviors, a combination of illusory and space/time dilation examples will be reviewed. Once these examples are presented, the implications for improving upon virtual models for more directly inducing the mental phenomena of illusion and space/time dilation will be considered. To conclude, future directions for integrating this research area into a strategy of broader biological inquiry will be presented.
Estimation of wolf population density using spatial capture-recapture: refining methods for monitoring cryptic species
Authors: Roffler Gretchen H , Waite Jason N , Flynn Rodney W , Larson Kristian R
Published: January 2018

Wolves (Canis lupus) in Southeast Alaska have been proposed for listing under the U.S. Endangered Species Act first in 1993, and more recently in 2011. Reports of declining wolf populations sparked concern, in addition to high rates of logging and broad-scale succession patterns predicted to negatively impact Sitka black-tailed deer (Odocoileus hemionus sitkensis), the primary ungulate prey species of wolves in Southeast Alaska. Given the recurring interest of wolf viability in the region, and in order to manage wolves and their prey sustainably, it is imperative to obtain regular and reliable population estimates. However, monitoring wolves in temperate rainforests is challenging because the landscape obscures visibility and lowers success of traditional methods such as aerial surveys and radio collar mark-recapture. We used hair snares to collect DNA samples and spatially-explicit capture-recapture (SECR) models to estimate fall wolf density during 2012–2015 on northcentral Prince of Wales Island (POW), Alaska. We incorporated covariates including sex, behavioral responses, and site-specific changes in effectiveness of detection probability by fitting hybrid mixture models to the data. We also incorporated into our models landscape variables including forest habitats in various management conditions and succession stages to relate to wolf habitat selection. We concurrently implemented a traditional approach for comparison to the DNA-based SECR method using radiocollared wolf data to estimate population abundance with minimum counts and the size of wolf packs and pack territories. The results of the DNA-based SECR method proved to be more reliable, efficient, cost-effective, and robust than the traditional method, which was sensitive to violations of model assumptions. Our efforts to improve SECR density estimate precision by increasing the hair sampling intensity and area resulted in more wolf hair detections and redetections, and increased the number of unique wolves redetected. Based on multiple lines of evidence, we report a decline in wolf population abundance over the past 2 decades in northcentral POW. We conclude that DNA-based SECR is an effective tool for regular population monitoring, as is required in situations of elevated concern for the persistence of a population, and may simultaneously provide information on heterogeneous landscape use, an important wildlife management consideration in fragmented forests.
The influence of physical exercise and sports on telomere length - A model for telomere length and telomerase activity regulation based on a comparative assessment of literature
Authors: Lang Paul F , Fröhlich Kai-Uwe
Published: January 2018

Based upon a comprehensive analysis of current literature and by combining a molecular biology and a sports science perspective, this review examines (1) if a correlation between physical activity load and telomere length (TL) exists, and (2) comprehensively analyses and integrates molecular pathways regulating exercise dependent TL dynamics. The focus is on TL in leukocytes and muscle tissue in middle to advanced aged subjects. Regarding item (1), a strong tendency for an increase in mean leukocyte TL was found for exercise energy expenditures up to about 2∙103 kcal/week, while for higher activity levels no conclusive statement can be made. Conversely, research on skeletal muscle TL so far is quite limited but suggests that physical exercise with prolonged eccentric muscle contractions rather acts to shorten telomeres, while sports with little eccentric contractions might rather act to lengthen telomeres. As to item (2), a model for hypothetical pathways for exercise dependent telomerase activity regulation is proposed by consolidating findings of different studies in different cells. Consistent with this pathway model, various studies report increased telomerase transcription or activation by exercise. Moreover, a qualitative overall model for endurance exercise related TL dynamics is presented. It considers telomeres as dynamic structures in equilibrium between telomere shortening (e.g., cellular turnover, oxidative stress, inflammation) and telomere lengthening (e.g., telomerase activity, telomerase recruitment) effects. A negative feedback-loop mediated by enhanced telomerase recruitment to short telomeres is assumed to counteract too excessive TL alterations. Finally, a proposal is put forth for future research on exercise dependent telomere dynamics by adopting a systems biology approach to develop mathematical models that properly integrate the complexity of the interacting variables.
Coral reef baselines: how much macroalgae is natural?
Authors: Bruno John F , Precht William F , Vroom Peter S , Aronson Richard B.
Published: January 2018

Identifying the baseline or natural state of an ecosystem is a critical step in effective conservation and restoration. Like most marine ecosystems, coral reefs are being degraded by human activities: corals and fish have declined in abundance and seaweeds, or macroalgae, have become more prevalent. The challenge for resource managers is to reverse these trends, but by how much? Based on surveys of Caribbean reefs in the 1970s, most reef scientists believe that the average cover of seaweed was very low in the natural state. On the other hand, evidence from remote Pacific reefs, ecological theory, and impacts of over-harvesting in other systems all suggest that, historically, macroalgal biomass may have been higher than assumed. Uncertainties about the natural state of coral reefs illustrate the difficulty of determining the baseline condition of even well-studied systems.
Data reuse and the open data citation advantage
Authors: Piwowar Heather , Vision Todd J
Published: January 2018

BACKGROUND: Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain estimates of the “citation boost”. Furthermore, little is known about patterns in data reuse over time and across datasets.

METHOD AND RESULTS: Here, we look at citation rates while controlling for many known citation predictors, and investigate the variability of data reuse. In a multivariate regression on 10,555 studies that created gene expression microarray data, we found that studies that made data available in a public repository received 9% (95% confidence interval: 5% to 13%) more citations than similar studies for which the data was not made available. Date of publication, journal impact factor, open access status, number of authors, first and last author publication history, corresponding author country, institution citation history, and study topic were included as covariates. The citation boost varied with date of dataset deposition: a citation boost was most clear for papers published in 2004 and 2005, at about 30%. Authors published most papers using their own datasets within two years of their first publication on the dataset, whereas data reuse papers published by third-party investigators continued to accumulate for at least six years. To study patterns of data reuse directly, we compiled 9,724 instances of third party data reuse via mention of GEO or ArrayExpress accession numbers in the full text of papers. The level of third-party data use was high: for 100 datasets deposited in year 0, we estimated that 40 papers in PubMed reused a dataset by year 2, 100 by year 4, and more than 150 data reuse papers had been published by year 5. Data reuse was distributed across a broad base of datasets: a very conservative estimate found that 20% of the datasets deposited between 2003 and 2007 had been reused at least once by third parties.

CONCLUSION: After accounting for other factors affecting citation rate, we find a robust citation benefit from open data, although a smaller one than previously reported. We conclude there is a direct effect of third-party data reuse that persists for years beyond the time when researchers have published most of the papers reusing their own data. Other factors that may also contribute to the citation boost are considered. We further conclude that, at least for gene expression microarray data, a substantial fraction of archived datasets are reused, and that the intensity of dataset reuse has been steadily increasing since 2003.
Performance of finite mixture distribution models to estimate nursery habitat contributions to fish stocks
Authors: Niklitschek Edwin J , Darnaude Audrey M
Published: January 2018

Background. Otolith microchemistry applications of finite mixture distribution models (FMDM) describe mixed stocks using three sets of parameters: proportional contributions (pi), baseline parameters (θi) and number of contributing nursery origins (c#). Under ideal scenarios, c# is known and all potential sources are sampled to produce source-based ^θi estimates. Hence, ^pi is the only parameter vector estimated by FMDM from the mixed-data. If some/all nursery areas are unknown or not sampled, some or all θi and c# need to be also estimated from the mixed-data. Our goal here was to assess bias and variability in ^pi, ^θi and ^c# when estimated by FMDM, under a range of data availability scenarios. Methods. We used a comprehensive Sparus aurata dataset, tat contained otolith elemental ratios from 301 young of the year, sampled at four nursery origins, in three highly contrasting years. Using bootstrap resampling (n=1000) we produced artificial source- and mixed-samples. Source-samples simulated different scenarios where KU=0-4 nursery sources were excluded. We evaluated bias (BI) and variability (VI) in ^pi by fitting FMDM to mixed-samples with true pi=0.1-0.4. Bias and variability in ^θi and ^c# were, instead, assessed on balanced mixed stock-samples (pi=0.25). Estimations of ^c# were obtained by fitting and comparing multiple FMDMs with c#=1-9. Results. Accurate and precise ^pi estimates (BI<0.03, VI<0.07) were produced by FMDM when samples from all origins were available (KU=0). BI and VI in ^pi tended to increase rapidly as KU increased, yielding unreliable results for KU>1. BI and VI in ^θi were highly heterogeneous among cohorts and less sensitive to KU. Relatively accurate ^θi estimates (BI<0.3) were produced for cohorts 2008 and 2010, but highly biased ones for cohort 2011 (VI>0.53), at all scenarios. Variability in ^θi was relatively low (VI<0.3) and insensitive to KU, across all cohorts. While ^c# tended to underestimate c# (BI=0.05 to -2.06), its variability was relatively high (VI=0.24-1.14) across scenarios and cohorts. Both bias and variability in ^c# were highly sensitive to KU. Discussion. FMDM estimated accurate and unbiased ^pi and ^θi parameters when all origins were known and sampled. FMDM performance decreased rapidly and all three set of estimated parameters became unreliable when ≥2 origins were missing from nursery-samples. Large differences in BI and VI among cohorts emphasized the need for extensive sampling of nursery origins. Being FMDM one default method for mixed stock analysis, we strongly recommend exploring alternative FMDM implementations and extreme caution when using results from FMDM, under incomplete sampling scenarios.
Impact of migration on child health in urban India: Evidence from NFHS-3
Authors: Narayan Raj , Singh Aditya
Published: January 2018

Using data from the third round of National Family Health Survey (NFHS, 2005-06), the present study examined the effect of quality of housing on the risk of anthropometric failure and child health status among migrant and non-migrant children in urban India. It is very urgent to from the policy and program perspective to understand whether source of safe drinking water, type of toilet facilities, and type of housing and cooking fuel really make a difference when it comes to the health and nutritional status of Indian children, particularly the urban poor. The main findings from the present studies indicate the poor nutritional and health status of migrant and non-migrant children in urban India. There were also large interstate disparities in anthropometric failures and ARI & diarrhea among migrant and non-migrant children across various Indian states. Result from the multivariate analysis suggest that poor source of sanitation facilities and poor quality of housing significantly raised the risk of stunting and diarrhea, whereas use of safe cooking fuel reduces the likelihood of ARI among children in urban India. However, we do not find any significant effect of quality of housing on the risk of underweight and wasting. Furthermore, few of the findings from the analysis appear in opposite directions that should be interpreted with caution which might be possible due to small sample size in few categories. Therefore, we need further in-depth research at micro-level to explore the plausible mechanism of how does housing quality influence child health and nutritional status in urban India.