bluuebunny/crossref_metadata_2025 huggingface dataset:
Engineering permanence in finite systems
Authors: Bilar Daniel
Published: January 2018

The man-machine integration era (MMIE) is marked by sensor ubiquity, whose readings map human beings to finite numbers. These numbers processed by continuously changing, optimizing/learning, finite precision, closed loop, distributed systems are used to drive decisions such as insurance rates, prison sentencing, health care allocations and probation guidelines. Optimization and system parameter tuning is increasingly left to machine learning and applied AI. One challenge we face is thus: Ensuring the indelibility, the permanence, the infinite value of human beings as optimization-resistant invariants in such system environments. In this challenge paper, we propose developing safeguards, specifically working towards a 'deontological imprimatur' architecture embedding resilient representations of human beings.
The psychometric properties of a Scale for Achievement Motive in Rehabilitation, and the effects of achievement motive on self-efficacy, hopelessness, and economic poverty for community-dwelling elderly people using rehabilitation services
Authors: Sano Nobuyuki , Kyougoku Makoto
Published: January 2018

Background: Achievement motive is expected to prevent lack of self-efficacy and hope, which negatively impact rehabilitation support, health, and psychological well-being. It has been indicated that the factor structure of the Scale for Achievement Motive in Rehabilitation (SAMR), which was developed to evaluate the state of achievement motive in clients, is affected by gender, age, and type of disorder; however, the item responses for the SAMR have not been fully elucidated.

Purpose: This study demonstrates the effects of achievement motive on self-efficacy, hopelessness, and economic poverty. The secondary purpose was to test the psychometric properties for the robustness of factor analysis and the item responses for the SAMR.

Methods: A cross-sectional study was conducted to assess achievement motive, self-efficacy, hopelessness, and economic poverty in 581 community-dwelling elderly people. Data from a self-administered questionnaire were analyzed for structural relationship, using a structural equation modeling approach, multi-group confirmatory factor analysis, and multidimensional item response theory.

Results: For structural relationship, the modified model indicated an adequate model fit level {Comparative Fit Index (CFI) = 0.914, Tucker Lewis Index (TLI) = 0.906, Root Mean Square Error of Approximation (RMSEA) = 0.062, 90% Confidence Interval (CI) [0.058, 0.066]}, with significant effects among achievement motive, self-efficacy, and hopelessness; i.e., the direct and indirect effects of achievement motive on self-efficacy and hopelessness were accepted. For multi-group confirmatory factor analysis, the SAMR factor structure displayed strong measurement invariance across the group for gender, care level, and age. For multidimensional item response theory, the results showed enough item discrimination and difficulty intensity for each SAMR item.

Discussion: This study suggests that achievement motive is important to prevent clients from missing and giving up their goals and to execute support in rehabilitation smoothly. In addition, we suggest that SAMR is a structurally valid scale to measure two-factor structures across different groups, and the item characteristics and total score enable proper understanding of achievement motive.
Cost hurdles to open access publishing: A citizen scientist perspective
Authors: Ng Wenfa
Published: January 2018

Besides offering fun activities for non-scientists to explore the natural world through experiments, simulations or games, the evolving concept of citizen science is increasingly allowing some serious publication quality science to be published by the practitioners (citizen scientists) themselves. The latter is in contrast to the common perception of citizen science, where most citizen science projects such as Foldit are distribution of piecemeal segments of complex projects suitable for solution by individuals, and where the results are pooled together and informs the design and direction of more complex research initiatives. Usually novices in science publishing but nonetheless aware of the importance of journal articles as the primary medium for communicating new research to the wider community (scientific and general public), citizen scientists do encounter significant challenges in science publication. One challenge is in navigating the lengthy and time-consuming peer review process of most journals. But, as benefactors of open access publishing given that most journal articles are within pay walls inaccessible to citizen scientists without any research funding, open access publishing is one platform sought after or exist as an option for citizen scientists. Is the option open? Yes, at the preprint level where figshare, and PeerJ Preprints help provide an avenue for citizen scientists to have a published non peer reviewed article online, but no at the higher end gold (or immediate) open access journal article level where the manuscript needs to be peer reviewed. Even the biological sciences preprint server, bioRxiv, is closed to citizen scientists as publication on the server requires an institution affiliation with either a university or research institute. Most open access publishers charge a publication fee (in the hundreds to thousands of dollars per article) to defray the cost of maintaining an online presence for a peer reviewed manuscript as well as those for copyediting during final stages of journal article production. This is a significant barrier to cost constrained citizen scientists who want to contribute to the scientific discourse. For the scientific enterprise, this represent a loss, whose magnitude or severity cannot be quantified since ideas help seed new research ideas and fields. Thus, can we as a community provide citizen scientists worldwide a chance to publish gold open access peer reviewed articles without significant cost through a competitive publication fee subsidy scheme where each application is reviewed by the national science funding agency? If the above is possible, it would open up another area where ideas from citizen scientists could percolate into the scientific mainstream, where, as always, vibrancy and diversity of ideas power science forward.
Macroecology for microbiology
Authors: Lennon Jay T , Locey Kenneth J
Published: January 2018

To microbiologists, the term macroecology may conjure iconic images of wildebeests grazing in African savannahs or hummingbirds pollinating flowers in a tropical rain forest. Contrary to what the name implies, macroecology is not the ecological study of macroscopic organisms. Rather, macroecology is the study of ecological relationships through patterns in abundance, distribution, and diversity. In this paper, we highlight some of the pressing questions, challenges, and opportunities for microbial macroecology.
Genetic analysis of behavior in Drosophila
Authors: Brembs Björn
Published: January 2018

The main function of brains is to generate adaptive behavior. Far from being the stereotypical, robot-like insect, the fruit fly Drosophila exhibits astounding flexibility and chooses different courses of actions even under identical external circumstances. Due to the power of genetics, we now are beginning to understand the neuronal mechanisms underlying this behavioral flexibility. Interestingly, the evidence from studies of disparate behaviors converges on common organizational principles common to many if not all behaviors, such as modified sensory processing, involvement of biogenic amines in network remodeling, ongoing activity and modulation by feedback. Seemingly foreseeing these recent insights, already the first research fields in Drosophila behavioral neurogenetics reflected this constant negotiation between internal and external demands on the animal as the common mechanism underlying adaptive behavioral choice in Drosophila.
Dynamics of resource allocation in biological systems
Authors: Jeff-Eke Imadol V
Published: January 2018

Here we present a single working model that attempts at reconciliation of biological systems. To do this we recognize and emphasize a universal theme of all biological systems: a need for resources. That is, we consider the dynamics of resource allocation as a requirement for actuation of responses to stimuli. In addition, all contemplations are founded on four postulates that are motivated by the homeostatic principle as conceived of by Claude Bernard and Walter Cannon: biological systems exhaust attempts to prevent from reaching the absolute maximum failure potential; biological systems tend in the direction toward the absolute minimum failure potential; biological systems attempt to assume the failure potential of an ideal regulator system; and all biological systems attempt to be in agreement with all four postulates. Finally, we attempt to determine biological manifestations of the stated model.
Catchments catch all in South African coastal lowlands: multilocus phylogeography and distribution modelling of Nymania capensis (Meliaceae) reveal topographic and palaeoclimatic connectivity constraints
Authors: Potts Alastair J
Published: January 2018

Background. This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots).

Methods. A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM).

Results. The results support an ‘evolutionarily distinct catchment’ hypothesis where: 1) diﬀerent catchments contain genetically distinct lineages, 2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and 3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: a) the timing of chloroplast lineage diversiﬁcation is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations.

Discussion. This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers affecting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionary significant units.
Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles
Authors: Peroni Silvio , Osborne Francesco , Di Iorio Angelo , Nuzzolese Andrea Giovanni , Poggi Francesco , Vitali Fabio , Motta Enrico
Published: January 2018

Purpose: this paper introduces the Research Articles in Simplified HTML (or RASH ), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework , i.e. a set tools for interacting with RASH-based articles. The paper also presents an evaluation that involved authors and reviewers of RASH articles, submitted to the SAVE-SD 2015 and SAVE-SD 2016 workshops.

Design: RASH has been developed in order to: be easy to learn and use; share scholarly documents (and embedded semantic annotations) through the Web; support its adoption within the existing publishing workflow

Findings : the evaluation study confirmed that RASH can already be adopted in workshops, conferences and journals and can be quickly learnt by researchers who are familiar with HTML.

Research limitations: the evaluation study also highlighted some issues in the adoption of RASH, and in general of HTML formats, especially by less technical savvy users. Moreover, additional tools are needed, e.g. for enabling additional conversion from/to existing formats such as OpenXML.

Practical implications: RASH (and its Framework) is another step towards enabling the definition of formal representations of the meaning of the content of an article, facilitate its automatic discovery, enable its linking to semantically related articles, provide access to data within the article in actionable form, and allow integration of data between papers.

Social implications: RASH addresses the intrinsic needs related to the various users of a scholarly article: researchers (focussing on its content), readers (experiencing new ways for browsing it), citizen scientists (reusing available data formally defined within it through semantic annotations), publishers (using the advantages of new technologies as envisioned by the Semantic Publishing movement).

Value: RASH focuses strictly on writing the content of the paper (i.e., organisation of text + semantic annotations) and leaves all the issues about it validation, visualisation, conversion, and semantic data extraction to the various tools developed within its Framework.
Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles
Authors: Peroni Silvio , Osborne Francesco , Di Iorio Angelo , Nuzzolese Andrea Giovanni , Poggi Francesco , Vitali Fabio , Motta Enrico
Published: January 2018

Purpose: this paper introduces the Research Articles in Simplified HTML (or RASH ), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework , a set of tools for interacting with RASH-based articles. The paper also presents an evaluation that involved authors and reviewers of RASH articles submitted to the SAVE-SD 2015 and SAVE-SD 2016 workshops.

Design: RASH has been developed aiming to: be easy to learn and use; share scholarly documents (and embedded semantic annotations) through the Web; support its adoption within the existing publishing workflow

Findings : the evaluation study confirmed that RASH is ready to be be adopted in workshops, conferences, and journals and can be quickly learnt by researchers who are familiar with HTML.

Research limitations: the evaluation study also highlighted some issues in the adoption of RASH, and in general of HTML formats, especially by less technically savvy users. Moreover, additional tools are needed, e.g. for enabling additional conversions from/to existing formats such as OpenXML.

Practical implications: RASH (and its Framework) is another step towards enabling the definition of formal representations of the meaning of the content of an article, facilitating its automatic discovery, enabling its linking to semantically related articles, providing access to data within the article in actionable form, and allowing integration of data between papers.

Social implications: RASH addresses the intrinsic needs related to the various users of a scholarly article: researchers (focussing on its content), readers (experiencing new ways for browsing it), citizen scientists (reusing available data formally defined within it through semantic annotations), publishers (using the advantages of new technologies as envisioned by the Semantic Publishing movement).

Value: RASH helps authors to focus on the organisation of their texts, supports them in the task of semantically enriching the content of articles, and leaves all the issues about validation, visualisation, conversion, and semantic data extraction to the various tools developed within its Framework.
SysMIC: A Blueprint for interdisciplinary online training in the life sciences
Authors: Baier Gerold , Barnes Chris , Crowe David , Gilmore Stephen , Grimm Uwe , Lewis Philip , Morse David , Sansom Clare , Saunders Robert D C , Shepherd Adrian , Thomas Geraint
Published: January 2018

‘Big Data’ and a surge in quantitative methodologies increasingly urge bioresearchers to train and improve their mathematical and computational skills. In response to this challenge the Biotechnology and Biological Sciences Research Council in the United Kingdom offered funds to develop web-based training in mathematics and computation for life scientists in all fields. The SysMIC consortium won the bid and implemented a new type of online course, which so far has been delivered to more than 1400 scientists, mostly in the UK. Researchers train self-paced or in cohorts in a media rich environment with materials based around intuitive biological examples. We describe the course, its trainee spectrum, and the modes of trainee engagement. We propose that tailored interactive online training is a scalable model for continuing professional development in the interdisciplinary life sciences in the 21st century.
nanoHUB: Experiences and insights on care and feeding of a successful, engaged science gateway community
Authors: Zentner Lynn , Klimeck Gerhard
Published: January 2018

Established in 2002, nanoHUB.org continues to attract a large community of users for computational tools and learning materials related to nanotechnology [1, 2]. Over the last 12 months, nanoHUB has engaged over 1.4 million visitors and 13,000 simulation users with over 5,000 items of content, making it a premier example of an established science gateway. The nanoHUB team tracks references to nanoHUB in the scientific literature and have found nearly 1,600 vetted citations to nanoHUB, with over 19,000 secondary citations to the primary papers, supporting the concept that nanoHUB enables quality research. nanoHUB is also used extensively for both informal and formal education [3,4], with automatic algorithms detecting use in 1,501 classrooms reaching nearly 30,000 students. During 14 years of operation, the nanoHUB team has had an opportunity to study the behaviors of its user base, evaluate mechanisms for success, and learn when and how to make adjustments to better serve the community and stakeholders. We have developed a set of success criteria for a science gateway such as nanoHUB, for attracting and growing an active community of users. Outstanding science content is necessary and that content must continue to expand or the gateway and community will grow stagnant. A large challenge is to incentivize a community to not only use the site, but more importantly, to contribute [5,6]. There is often a recruitment and conversion process that involves, first, attracting users, giving them reason to stay, use, and share increasingly complex content, and then go on to become content authors themselves. This process requires a good understanding of the user community and its needs as well as an active outreach program, led by a user-oriented content steward with a technical background sufficient to understand the work and needs of the community. A reliable infrastructure is a critical key to maintaining an active, participatory community. Using underlying HUBzero® technology, nanoHUB is able to leverage infrastructure developments from across a wide variety of hubs, and by utilizing platform support from the HUBzero team, access development and operational expertise from a team of 25 professionals that one scientific project would be hard-pressed to support on its own. nanoHUB has found that open assessment and presentation of stats and impact metrics not only inform development and outreach activities but also incentivize users and provide transparency to the scientific community at large.
Containerization and wrapping of a mass spectra prediction workflow
Authors: Krüger Jens , Kohlbacher Oliver
Published: January 2018

Practical experiences are reported about implementing a workflow for the prediction of mass spectra. QCEIMS is used to simulate the fragmentation trajectories consequently leading to predicted mass spectra for small molecules, such as metabolites. The individual calculations are embedded into UNICORE workflow nodes using Docker containerization for the applications themselves. Challenges, caveats, but also advantages are discussed, providing guidance for the deployment of a scientific protocol on high performance computing resources.
Hypothesis on Serenoa repens (Bartram) small extract inhibition of prostatic 5α-reductase through an in silico approach on 5β-reductase x-ray structure
Authors: Governa Paolo , Giachetti Daniela , Biagi Marco , Manetti Fabrizio , De Vico Luca
Published: January 2018

Benign prostatic hyperplasia is a common disease in men aged over 50 years old, with an incidence increasing to more than 80% over the age of 70, that is increasingly going to attract pharmaceutical interest. Within conventional therapies, such as α-adrenoreceptor antagonists and 5α-reductase inhibitor, there is a large requirement for treatments with less adverse events on, e.g., blood pressure and sexual function: phytotherapy may be the right way to fill this need. Serenoa repens standardized extract has been widely studied and its ability to reduce lower urinary tract symptoms related to benign prostatic hyperplasia is comprehensively described in literature. An innovative investigation on the mechanism of inhibition of 5α-reductase by Serenoa repens extract active principles is proposed in this work through computational methods, performing molecular docking simulations on the crystal structure of human liver 5β-reductase. The results confirm that both sterols and fatty acids can play a role in the inhibition of the enzyme, thus, suggesting a competitive mechanism of inhibition. This work proposes a further confirmation for the rational use of herbal products in the management of benign prostatic hyperplasia, and suggests computational methods as an innovative, low cost, and non-invasive process for the study of phytocomplex activity toward proteic targets.
Multiple stressors threaten the imperiled coastal foundation species eelgrass (Zostera marina) in Chesapeake Bay, USA
Authors: Lefcheck Jonathan S , Wilcox David J , Murphy Rebecca R , Marion Scott R , Orth Robert J
Published: January 2018

Interactions among global change stressors and their effects at large scales are often proposed, but seldom evaluated. This situation is primarily due to lack of comprehensive, sufficiently long-term, and spatially-extensive datasets. Seagrasses, which provide nursery habitat, improve water quality, and constitute a globally-important carbon sink, are among the most vulnerable habitats on the planet. Here, we unite 31-years of high-resolution aerial monitoring and water quality data to elucidate the patterns and drivers of eelgrass (Zostera marina) abundance in Chesapeake Bay, USA, one of the largest and most valuable estuaries in the world with an unparalleled history of regulatory efforts. We show that eelgrass area has declined 29% in total since 1991, with wide-ranging and severe ecological and economic consequences. We go on to identify an interaction between decreasing water clarity and warming temperatures as the primary driver of this trend. Declining clarity has gradually reduced eelgrass over the past two decades, primarily in deeper beds where light is already limiting. In shallow beds, however, reduced visibility exacerbates the physiological stress of acute warming, leading to recent instances of decline approaching 80%. While degraded water quality has long been known to influence underwater grasses worldwide, we demonstrate a clear and rapidly emerging interaction with climate change. We highlight the urgent need to integrate a broader perspective into local water quality management, in the Chesapeake Bay and in the many other coastal systems facing similar stressors.
Eurasian jays do not copy the choices of conspecifics, but they do show evidence of stimulus enhancement
Authors: Miller Rachael , Logan Corina J , Lister Katherine , Clayton Nicola S
Published: January 2018

Corvids (birds in the crow family) are hypothesised to have a general cognitive tool-kit because they show a wide range of transferrable skills across social, physical and temporal tasks, despite differences in socioecology. However, it is unknown whether relatively asocial corvids differ from social corvids in their use of social information in the context of copying the choices of others, because only one such test has been conducted in a relatively asocial corvid. We investigated whether relatively asocial Eurasian jays (Garrulus glandarius) use social information (i.e., information made available by others). Previous studies have indicated that jays attend to social context in their caching and mate provisioning behaviour; however, it is unknown whether jays copy the choices of others. We tested the jays in two different tasks varying in difficulty, where social corvid species have demonstrated social information use in both tasks. Firstly, an object-dropping task was conducted requiring objects to be dropped down a tube to release a food reward from a collapsible platform, which corvids can learn through explicit training. Only one rook and one New Caledonian crow have learned the task using social information from a demonstrator. Secondly, we tested the birds on a simple colour discrimination task, which should be easy to solve, because it has been shown that corvids can make colour discriminations. Using the same colour discrimination task in a previous study, all common ravens and carrion crows copied the demonstrator. After observing a conspecific demonstrator, none of the jays solved the object-dropping task, though all jays were subsequently able to learn to solve the task in a non-social situation through explicit training, and jays chose the demonstrated colour at chance levels. Our results suggest that social and relatively asocial corvids differ in social information use, indicating that relatively asocial species may have secondarily lost this ability due to lack of selection pressure from an asocial environment.
Elementary cellular automata as conditional Boolean formulæ
Authors: Fleeman y Garcia Trace
Published: January 2018

I show that any elementary cellular automata -- a class of 1-dimensional, 2-state cellular automata originally formulated by Stephen Wolfram -- can be deconstructed into a set of two Boolean operators; I also present a conjecture concerning the relationship between the set of computationally complete elementary cellular automata rules (such as rule 110, shown in section 2 to be composed of a NAND gate) and the set of elementary cellular automata rules that contain universal Boolean operators (such as rule 52, shown in section 3.1 to contain a universal Boolean operator yet has not been shown as of 2016 to be computationally complete.)
Modelling environmental drivers of black band disease outbreaks in populations of foliose corals in the genus Montipora
Authors: Chen Carla C.M , Bourne David G , Drovandi Chris , Mengersen Kerrie , Willis Bette L , Caley M. Julian , Sato Yui
Published: January 2018

Seawater temperature anomalies associated with warming climate have been linked to increases in coral disease outbreaks that have contributed to coral reef declines globally. However, little is known about how seasonal scale variations in environmental factors influence disease dynamics at the level of individual coral colonies. In this study, we applied a multi-state Markov model (MSM) to investigate the dynamics of black band disease (BBD) developing from apparently healthy corals and/or a precursor-stage, termed ‘cyanobacterial patches’ (CP), in relation to seasonal variation in light and seawater temperature at two reef sites around Pelorus Island in the central sector of the Great Barrier Reef. The model predicted returning rate from BBD to Healthy in three months was approximately 57%, but 5.6% of BBD cases resulted in whole colony mortality. Healthy coral colonies were more susceptible to BBD during summer months when light levels were at their maxima and seawater temperatures were either rising or at their maxima. In contrast, CP mostly occurred during spring, when both light and seawater temperatures were rising. This suggests that environmental drivers for healthy coral colonies transitioning into a CP state are different from those driving transitions into BBD. Our model predicts that (1) the transition from healthy to CP state is best explained by rising light, (2) the transition between healthy to BBD occurs more frequently from early to late summer, (3) 20% of CP infected corals developed BBD, although light and temperature appeared to have limited impact on this state transition, and (4) the number of transitions from healthy to BBD differed significantly between the two study sites, potentially reflecting differences in localised wave action regimes.
Scientific data science and the case for Open Access
Authors: Sarma Gopal P
Published: January 2018

“Open access” has become a central theme of journal reform in academic publishing. In this article, I examine the consequences of an important technological loophole in which publishers can claim to be adhering to the principles of open access by releasing articles in proprietary or “locked” formats that cannot be processed by automated tools, whereby even simple copy and pasting of text is disabled. These restrictions will prevent the development of an important infrastructural element of a modern research enterprise, namely, scientific data science, or the use of data analytic techniques to conduct meta-analyses and investigations into the scientific corpus. I give a brief history of the open access movement, discuss novel journalistic practices, and an overview of data-driven investigation of the scientific corpus. I argue that particularly in an era where the veracity of many research studies has been called into question, scientific data science should be one of the key motivations for open access publishing. The enormous benefits of unrestricted access to the research literature should prompt scholars from all disciplines to reject publishing models whereby articles are released in proprietary formats or are otherwise restricted from being processed by automated tools as part of a data science pipeline.
Counting complete? Finalising the plant inventory of a global biodiversity hotspot
Authors: Treurnicht Martina , Colville Jonathan F , Joppa Lucas N , Huyser Onno , Manning John
Published: January 2018

The Cape Floristic Region – the world’s smallest, but third richest hotspot – experienced sustained levels of taxonomic effort and exploration for almost three centuries resulting in a near-complete plant species inventory. Here we analyse, for a core component of this flora, trends over a 250 year period in taxonomic effort and species discovery linked to ecological and conservation attributes. We show that >40% of species were described within the initial 100 years, followed by a steady rate of description, culminating in <1% of the flora estimated still to be described. A relatively constant cohort of taxonomists working at their ‘taxonomic maximum’ was seen across 250 years, while rates of description remained independent of plant growth-form. Since 1950, narrow-range taxa constituted significantly greater proportions of species discoveries, highlighting the fraction of undiscovered species which exist as localised endemics and thus of high conservation value. In the context of initiated global strategic plans for biodiversity, our dataset provides real world insights for other hotspots to consider the effort required for attaining set targets of comprehensive plant inventories.
OncoRank: A pan-cancer method of combining survival correlations and its application to mRNAs, miRNAs, and lncRNAs
Authors: Anaya Jordan
Published: January 2018

OncoRank adopts a method for finding recurrent miRNA-target interactions to find genes with consistent relationships to patient survival across cancers. Genes are first ranked in each cancer by their Cox coefficients, and these ranks are then combined by applying Fisher's method. Using ranks instead of the raw coefficients or p-values allows each cancer to be weighted equally and prevents bias from cancers with large numbers of patients. OncoLnc (http://www.oncolnc.org) is a newly available resource for Cox coefficients and utilizes data from 21 cancers in The Cancer Genome Atlas. Using this resource I applied OncoRank to mRNAs, miRNAs, and lncRNAs and in each case found consistently harmful or protective genes. These genes may be members of central cancer pathways and should be of interest to cancer researchers.
A connect-approach in high-grade glioma management; Position statement from the Neuro-Oncology Scientific Club (NOSC), Shiraz, Iran
Authors: Ansari Mansour , Mosalaei Ahmad , Ahmadloo Niloofar , Rasekhi Alireza , Geramizadeh Bita , Razmkon Ali , Afarid Mohammad , Dadras Ali , Nafarieh Leila , Mohammadianpanah Mohammad , Nasrolahi Hamid , Hamedi Seyed Hasan , Omidvari Shapour , Nami Mohammad
Published: January 2018

Portraying a robust working-team model in the practice of neuro-oncology requires continued interdisciplinary efforts. The Neuro-Oncology Scientific Club (NOSC) initiative is an interdisciplinary clinical forum promoting the connect-approach across involved disciplines in the management of CNS malignancies. With its provincial founding-panels and national steering board; NOSC has been operational in Iran since 2011. This initiative has pursued its mission through interval strategic meetings, tumor-boards, case-discussions as well as publishing neuro-oncology updates, case study periodicals and newsletters. A provincial meeting of NOSC in Shiraz, put together insights from international practice guidelines, emerging evidence and expert opinions to draw a position statement on high-grade glioma management in adults. The present report summarizes key highlights from the above clinical forum.
Endocrine disruption: where are we with hazard and risk assessment?
Authors: Coady Katherine , Matthiessen Peter , Zahner Holly M , Staveley Jane , Caldwell Daniel J , Levine Steven L , Gray, Jr. Leon Earl , Borgert Christopher J
Published: January 2018

Approaches to assessing endocrine disruptors (EDs) differ across the globe, with some regulatory environments using a hazard-based approach, while others employ risk-based analyses. In session four of the Society of Environmental Toxicology and Chemistry (SETAC) North America Focused Topic Meeting: Endocrine Disruption Chemical Testing: Risk Assessment Approaches and Implications (February 4 – 6, 2014), various aspects related to the hazard and/or risk assessment of EDs were explored. The presentations in the session included an overview of the regulatory environments for assessing and managing endocrine disruptors, and scenarios whereby a hazard-based approach might be most appropriate were discussed. Three case studies for ED assessment, one for an industrial chemical, one for a pharmaceutical, and one for a pesticide, were presented. The topics of non-monotonic dose response relationships as well as potency and threshold effects were also presented in this session, since these concepts are important for determining whether a risk or hazard based approach to ED regulation is most appropriate. Session four concluded with an open discussion concerning the issue of hazard and risk as a basis for regulating EDCs. An outcome of session four was the drafting of an outreach statement that summarizes the overarching themes of this session.
Three-dimensional printing for device selection in cardiology: Several key points should not be neglected
Authors: Luo Hongxing , Wang Zhongmin
Published: January 2018

We comment on the recent developments and problems of three-dimensional printing in cardiology. Since there are currently no standards or consensuses for 3D printing in clinical medicine and the technology is at its infancy in cardiology, it’s very important to detail the procedures to allow more similar studies to further our understandings of this novel technology. Most studies have employed computed tomography to obtain source data for 3D printing, the use of real-time 3D transesophageal echocardiography for data acquisition remains rare, so it would be very valuable and inspiring to detail the image postprocessing steps, or the reliability of the study results will be doubtful.
An updated assessment of Symbiodinium that associate with common scleractinian corals from Moorea (French Polynesia) reveals high diversity among background symbionts and a novel finding of clade B.
Authors: Rouzé Héloïse , Lecellier Gaël J , Saulnier Denis , Planes Serge , Gueguen Yannick , Wirshing Herman H , Berteaux-Lecellier Véronique
Published: January 2018

The adaptative bleaching hypothesis (ABH) states that depending on the symbiotic flexibility of coral hosts (i.e., the ability of corals to “switch” or “shuffle” their algal symbionts), coral bleaching can lead to a change in the composition of their associated Symbiodinium community, and, thus, contribute to the coral’s overall survival. In order to determine the flexibility of corals, molecular tools are required to provide accurate species delineations, and to detect low levels of coral-associated Symbiodinium. Here, we used highly sensitive quantitative (real-time) PCR (qPCR) technology to analyse five common coral species from Moorea (French Polynesia), previously screened using only traditional conventional molecular methods, to assess the presence of low-abundance (background) Symbiodinium. Similar to other studies, each coral species exhibited a strong specificity to a particular clade, irrespective of the environment. In addition, however, each of the five species harboured at least one additional Symbiodinium clade, among clades A-D, at background levels. Unexpectedly, and for the first time in French Polynesia, clade B was detected as a coral symbiont. These results increase the number of known coral-Symbiodinium associations from corals found in French Polynesia, and likely indicate an underestimation of the ability of the corals in this region to associate with and/or “shuffle” different Symbiodinium clades. Altogether our data suggest that corals from French Polynesia may manage a trade-off between optimizing symbioses with a specific Symbiodinium clade(s), and maintaining associations with particular background clades that may play a role in the ability of corals to respond to environmental change.
Exploiting opportunistic observations to estimate changes in seasonal site use: an example with wetland birds
Authors: Ruete Alejandro , Pärt Tomas , Berg Åke , Knape Jonas
Published: January 2018

Non-systematically collected, a.k.a. opportunistic, species observations are accumulating at a high rate in biodiversity databases. Occupancy models have arisen as the main tool to reduce effects of limited knowledge about effort in analyses of opportunistic data. These models are generally using long closure periods (e.g. breeding season) for the estimation of probability of detection and occurrence. Here we use the fact that multiple opportunistic observations in biodiversity databases may be available even within days (e.g. at popular birding localities) to reduce the closure period to one day in order to estimate daily occupancies within the breeding season. We use a hierarchical dynamic occupancy model for daily visits to analyse opportunistic observations of 71 species from nine wetlands during 10 years. Our model of daily colonization-extinction dynamics of species estimates within-season dynamics in occupancy at sites. We use the model to derive estimates of site use within seasons, in contrast to an annual occupancy estimates as produced in previous analyses of opportunistic data. Comparing results from our “seasonal site use model” to results from a traditional annual occupancy model (using a closure criterion of two months or more) showed that our model provide more detailed biologically relevant information. For example, when the aim is to analyse occurrences of breeding species, an annual occupancy model will over-estimate site use of species with temporary occurrences (e.g. migrants passing by, single itinerary prospecting individuals) as even a single observation during the closure period will be viewed as an occupancy. On the other hand, an occupancy model with within-season dynamics, such as our seasonal site use model will produce estimates of the extent to which sites are actually used. Model validation based on simulated data confirmed that our model is robust to certain changes and variability in sampling effort and species detectability. We conclude that for opportunistic data with many records (e.g. several reports per day almost every day), more information can be gained by reducing the time window of the closure criterion to acquire estimates of occupancies within seasons.
Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity
Authors: Enquist Brian J , Condit Rick , Peet Robert K , Schildhauer Mark , Thiers Barbara M.
Published: January 2018

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within a local area or even a few hundred square meters. Understanding ecological patterns and how plants respond to global warming and human alteration of landscapes and ecosystems necessitates a holistic approach. Such an approach must be conducted at a scale that is commensurate with the breadth of the questions being asked. Further, it requires identification, retrieval, and integration of diverse data from a global confederation of collaborating scientists across a broad range of disciplines. We propose to network core databases and data networks to create a novel resource for quantitative plant biodiversity science. The grand challenge is to assemble and share the world’s rapidly accumulating botanical information from plots and collections to create a distributed, web-accessible, readily analyzable data resource. With such a resource, we will answer major questions of direct relevance to plant ecology, plant evolution, plant geography, conservation, global change biology, and protection of biodiversity and ecosystem services. In particular, how does climate influence the distribution and abundance of plant species, how does the phylogenetic diversity of plants vary across broad environmental and climatic gradients, and how are plants assembled into ecological communities? While these and associated questions are at the core of many research endeavors in comparative botany and ecology, our past collective inability to integrate data on a large scale has significantly limited our ability to address these questions head on. This proposed Grand Challenge team will create a data resource of unprecedented size and scope together with the tools for its use, thereby empowering botanists and the general public to better address fundamental issues in plant ecology and global change biology. Although we will focus on plants of the New World, the infrastructure and protocols developed will be scalable to all geographic regions and all types of organisms. Future steps will enable cross-cutting linkages to emerging networks on plant genomics, physiology, and phylogeny, allowing us to address fundamental genetic and evolutionary questions at unprecedented spatial and temporal scales.
Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California
Authors: Gurfield Nikos , Grewal Saran , Cua Lynnie S , Torres Pedro J , Kelley Scott T
Published: January 2018

The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D.Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species.We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren’t infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results also raise interesting possibilities about the effects of putative vertebrate hosts on the tick microbiome.