bluuebunny/crossref_metadata_2025 huggingface dataset:
Formulation of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Microbes for environmental research should be cultured in growth media with characteristics (e.g., pH, ionic strength, and organic and ionic composition) as close to their original habitat as possible. Additionally, the medium should also enable high cell density to be obtained - needed for providing sufficient cells in subsequent experiments. This in-progress report describes the formulation of a medium with an environmentally-relevant composition (lack of complex organics), and that allows aerobic high cell density cultivation of Escherichia coli DH5α in shake flasks. The formulated medium comprises four components: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L), vitamins (yeast extract: 12.0 g/L), salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L), and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium were: high capacity phosphate buffer system (89 mM phosphate); 1:1 molar ratio between D-Glucose and NH4Cl; and yeast extract providing trace elements and a secondary carbon and nitrogen source. Growth experiments revealed that an OD600nm of 9 was attained after 24 hours of cultivation at 37 oC. Glucose and NH4Cl serve as primary carbon and nitrogen sources for this phase of growth. After 48 hours, the OD600nm reached 11, where carbohydrates, lipids and proteins in yeast extract provided the nutrients for biomass formation. Broth’s pH varied between 5.5 and 7.8 during cultivation, which was in the range conducive for E. coli growth. In comparison, the OD600nm of E. coli reached 1.4, 3.2, and 9.2 in three commonly used complex media; Nutrient Broth, LB Lennox, and Tryptic Soy Broth, respectively, over 48 hours under identical culture conditions. In addition, the formulated medium was able to maintain a large viable cell population for a longer period of time (three days) compared to Tryptic Soy Broth. Thus, preliminary data suggested that the formulated medium holds potential for use as a high cell density aerobic growth medium for Gram-negative bacteria.
Do modern theories of biodiversity fail to predict commonness and rarity among microbes?
Authors: Shoemaker William R , Locey Kenneth J , Lennon Jay T
Published: January 2018

Ecological theories of biodiversity seek to predict and unify patterns of commonness and rarity across taxa. The maximum entropy theory of ecology (METE) is among the most unifying theories of biodiversity, explaining >90% of variation in abundance among species of plant animal using the total number of individuals (N0) and number of species as empirical inputs. However, METE has not been tested among the most abundant and diverse organisms on Earth, i.e., microorganisms. Using ~20,000 sites of microbial communities, we show that METE often explains <10% of variation in abundance and increasingly fails for larger N0. In contrast, a more uneven distribution with a maximum entropy solution, the Zipf, often explains >90% of variation among microbes and performs better as N0 increases. Our findings suggest that theories of biodiversity could produce accurate predictions across the tree of life and scales of abundance if they capture how disparities in abundance increase with N0.
Do modern theories of biodiversity fail to predict commonness and rarity among microbes?
Authors: Shoemaker William R , Locey Kenneth J , Lennon Jay T
Published: January 2018

Theories of biodiversity seek to predict and unify patterns of commonness and rarity. Maximum entropy theory of ecology (METE) is among the most unifying and powerful theories of biodiversity, explaining >90% of variation in abundance among species of plant and animal using the total number of individuals (N0) and number of species. However, METE has yet been tested among the most abundant and diverse organisms on Earth, i.e., microorganisms. Using 20,456 sites of microbial communities, we show that METE only explains 0 to 60% of variation in abundance and increasingly fails for larger N0. In contrast, a more uneven distribution with a maximum entropy solution, the Zipf, often explains >90% of variation among microbes and performs better as N0 increases. Our findings suggest that theories of biodiversity could produce accurate predictions across the tree of life and scales of abundance if they capture how disparities in abundance increase with N0.
Scaling laws predict global microbial diversity
Authors: Locey Kenneth J , Lennon Jay T
Published: January 2018

Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ~35,000 sites and ~5.6·106 species, we demonstrate similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of species abundance, we predict that Earth is home to ~1012 microbial species. This estimate is also supported by the microbial richness scaling relationship we derive from the largest ever inventory of high-throughput molecular data. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.
Scaling laws predict global microbial diversity
Authors: Locey Kenneth J , Lennon Jay T
Published: January 2018

Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ~35,000 sites and ~5.6·106 species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we demonstrate similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upwards one trillion (1012) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.
Coral reproduction in Western Australia
Authors: Gilmour James , Speed Conrad W , Babcock Russ
Published: January 2018

Larval production and recruitment underpin the maintenance of coral populations, but these early life history stages are vulnerable to extreme variation in physical conditions. Environmental managers aim to minimise human impacts during significant periods of larval production and recruitment on reefs, but doing so requires knowledge of the modes and timing of coral reproduction. Most corals are hermaphroditic or gonochoric, with a brooding or broadcast spawning mode of reproduction. Brooding corals are a significant component of some reefs and produce larvae over consecutive months. Broadcast spawning corals are more common and display considerable variation in their patterns of spawning among reefs. Highly synchronous spawning can occur on reefs around Australia, particularly on the Great Barrier Reef. On Australia’s remote north-west coast there have been fewer studies of coral reproduction. The recent industrial expansion into these regions has facilitated research, but the associated data are often contained within confidential reports. Here we combine information in this grey-literature with that available publicly to update our knowledge of coral reproduction in WA, for tens of thousands of corals and hundreds of species from over a dozen reefs spanning 20 degrees of latitude. We identified broad patterns in coral reproduction, but more detailed insights were hindered by biased sampling; most studies focused on species of Acropora sampled over a few months at several reefs. Within the existing data, there was a latitudinal gradient in spawning activity among seasons, with mass spawning during autumn occurring on all reefs (but the temperate south-west). Participation in a smaller, multi-specific spawning during spring decreased from approximately one quarter of corals on the Kimberley Oceanic reefs to little participation at Ningaloo. Within these seasons, spawning was concentrated in March and/or April, and October and/or November, depending on the timing of the full moon. The timing of the full moon determined whether spawning was split over two months, which was common on tropical reefs. There were few data available for non-Acropora corals, which may have different patterns of reproduction. For example, the massive Porites seemed to spawn through spring to autumn on Kimberley Oceanic reefs and during summer in the Pilbara region, where other common corals (e.g. Turbinaria & Pavona) also displayed different patterns of reproduction to the Acropora. The brooding corals (Isopora & Seriatopora) on Kimberley Oceanic reefs appeared to planulate during many months, possibly with peaks from spring to autumn; a similar pattern is likely on other WA reefs. Gaps in knowledge were also due to the difficulty in identifying species and issues with methodology. We briefly discuss some of these issues and suggest an approach to quantifying variation in reproductive output throughout a year.
Exploring the chemical space of influenza neuraminidase inhibitors
Authors: Anuwongcharoen Nuttapat , Shoombuatong Watshara , Tantimongcolwat Tanawut , Prachayasittikul Virapong , Nantasenamat Chanin
Published: January 2018

The fight against the emergence of mutant influenza strains has led to the screening of an increasing number of compounds for inhibitory activity against influenza neuraminidase. This study explores the chemical space of neuraminidase inhibitors (NAIs), which provides an opportunity to obtain further molecular insights regarding the underlying basis of their bioactivity. In particular, a large set of 347 and 175 NAIs against influenza A and B, respectively, was compiled from the literature. Molecular and quantum chemical descriptors were obtained from low-energy conformational structures geometrically optimized at the B3LYP/6-31G(d) level. The bioactivities of NAIs were classified as active or inactive according to their half maximum inhibitory concentration (IC50) value in which IC50 < 1 μM and > 10 μM were defined as active and inactive compounds, respectively. Interpretable decision rules were derived from a quantitative structure-activity relationship (QSAR) model established using a set of 13 descriptors via decision tree analysis. Good predictive performance was achieved as deduced from 10-fold cross-validation, in which an accuracy and MCC of 82.46% and 0.649, respectively, were obtained for influenza A NAIs while values of 80.00% and 0.553 were obtained for influenza B NAIs. Both univariate and multivariate analyses revealed the importance of the lowest unoccupied molecular orbital, number of hydrogen bond donors and number of hydrogen bond acceptors in the predictive model of NAIs against influenza A while the number of hydrogen bond acceptors, molecular energy and the energy gap between the highest occupied and lowest unoccupied molecular orbitals were important in the predictive model for influenza B NAIs. Molecular scaffold analysis was performed on both data sets for discriminating important structural features among active and inactive NAIs. Furthermore, molecular docking was employed to investigate the binding modes and their moiety preferences of active NAIs against both influenza A and B neuraminidase. Moreover, novel NAIs with robust binding fitness towards influenza A and B neuraminidase were generated via combinatorial library enumeration and their binding fitness was on par or better than FDA-approved drugs. The results from this study are anticipated to be beneficial for guiding the rational drug design of novel NAIs for treating influenza infections.
Post-graduate scholars can publish Compended-Guides to the literature of their fields using Knowledge-Step Forums
Authors: Jewett Don L
Published: January 2018

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is NOT adequate for a Web-based world.

In 2006, an estimated 3,700 peer-reviewed scientific articles were published per day (Bjork2009)! This totals about 1.35 million articles per year. A similar estimate for 2011 was 1.8 million (Outsell2013), which is almost 5,000 per day. The total number of English-language scholarly documents accessible on the Web was estimated in 2014 to be at least 114 million (Khabsa2014). The methods and features described here are clearly needed now, and will be absolutely necessary in the future, when even more articles are available.

In this context of an overload of information from scientific articles, described here is the idea of Knowledge-Step Forums as the basis for creating new peer-reviewed, compended "Literature-Guides", each on a very narrow topic and in a MultiLevel Format (Knowledge-Step Compendia). A multitude of Forum-Compendors, who need not be a senior faculty member (as is the case in traditional literature-reviews), but can be pre-docs, post-docs, and senior medical/surgical residents, will be aided by their mentors and online experts to create these Knowledge-Step Compendia. All participants (students and faculty) will be motivated by their own self-interest and thus each gains from the activity, it being a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.

The Software for Knowledge-Step Forums will also be useful to speed publication on the Web because it will easily support Publication Preprints with online "peer-review" comments.
Post-graduate scholars can publish Compended-Guides to the literature of their fields using Knowledge-Step Forums
Authors: Jewett Don L
Published: January 2018

ABSTRACT "Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is NOT adequate for a Web-based world.

In 2006, an estimated 3,700 peer-reviewed scientific articles were published per day (Bjork2009)! This totals about 1.35 million articles per year. A similar estimate for 2011 was 1.8 million (Outsell2013), which is almost 5,000 per day. The total number of English-language scholarly documents accessible on the Web was estimated in 2014 to be at least 114 million (Khabsa2014). The methods and features described here are clearly needed now, and will be absolutely necessary in the future, when even more articles are available.

In this context of an overload of information from scientific articles, described here is the idea of Knowledge-Step Forums as the basis for creating new peer-reviewed, compended "Literature-Guides", each on a very narrow topic and in a MultiLevel Format (Knowledge-Step Compendia). A multitude of Forum-Compendors, who need not be a senior faculty member (as is the case in traditional literature-reviews), but can be pre-docs, post-docs, and senior medical/surgical residents, will be aided by their mentors and online experts to create these Knowledge-Step Compendia. All participants (students and faculty) will be motivated by their own self-interest and thus each gains from the activity, it being a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.

The Software for Knowledge-Step Forums will also be useful to speed publication on the Web because it will easily support Publication of Preprints with automatic collection of online "peer-review" comments.
Post-graduate scholars can publish Compended-Guides to the literature of their fields using Knowledge-Step Forums
Authors: Jewett Don L
Published: January 2018

ABSTRACT

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is NOT adequate for a Web-based world.

In 2006, an estimated 3,700 peer-reviewed scientific articles were published per day (Bjork2009)! This totals about 1.35 million articles per year. A similar estimate for 2011 was 1.8 million (Outsell2013), which is almost 5,000 per day. The total number of English-language scholarly documents accessible on the Web was estimated in 2014 to be at least 114 million (Khabsa2014). The methods and features described here are clearly needed now, and will be absolutely necessary in the future, when even more articles are available.

In this context of an overload of information from scientific articles, described here is the idea of Knowledge-Step Forums as the basis for creating new peer-reviewed, compended "Literature-Guides", each on a very narrow topic and in a MultiLevel Format (Knowledge-Step Compendia). A multitude of Forum-Compendors, who need not be a senior faculty member (as is the case in traditional literature-reviews), but can be pre-docs, post-docs, and senior medical/surgical residents, will be aided by their mentors and online experts to create these Knowledge-Step Compendia. All participants (students and faculty) will be motivated by their own self-interest and thus each gains from the activity, it being a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.

The Software for Knowledge-Step Forums will also be useful to speed publication on the Web because it will easily support Publication of Preprints with automatic collection of online "peer-review" comments.
When scholars use Knowledge-Step Forums to create Web-Compended Guides to the literature of their fields, paradigm-shifts will occur in the processes of knowledge creation and in graduate education.
Authors: Jewett Don L
Published: January 2018

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication" is still paper-based in its style and methods. As will become painfully obvious, such a paper-based "publishing model" is NOT adequate for a Web-based world.

Consider that in 2011, an estimated 5,000 peer-reviewed scientific articles were published per day (Outsell2013), and that in 2014 just the English-language scholarly publications on the Web were about 4,900 per day.

In 1980, the distinguished scientist Garrett Hardin wrote [Hardin1980]:"Who can keep up with such a torrent? When I was young and foolish I vowed that I would read all the articles in my small field of science. Discovering that this was impossible, I tried to read all the abstracts. That, too, proved too much. Now I know that I cannot even read all the titles."

To help reduce scholarly information-overload, this article proposes using Knowledge-Step Forums for the purpose of creating a new type scholarly publication, Web-based Compendia. Each Compendium is about a very narrow topic and is presented in a MultiLevel Format. When all these features are combined, the scholarly article is called a Knowledge-Step Compendium, and it is posted on the Web by the scholar, either on an institutional server, or on one of many web-hosting servers. Web-search engines will be automatically notified about the new posting (and later changes, too).

Forum-Compendors need not be a senior faculty member (as is the case in traditional literature-reviews), but can be pre-docs, post-docs, and senior medical/surgical residents. These graduate-students will be aided by their mentors and online experts to create these Knowledge-Step Compendia. All participants (students and faculty) will be motivated by their own self-interest and everyone gains from the activity, which self-organizes groups of like-minded scholars. Such groups can be the basis for early reviews of new data, for discovering new ideas, and for finding jobs.

Knowledge-Step Forums will speed publication on the Web because it will easily support Publication of Preprints using the software's automatic collection of online "peer-review" comments.

In order for the Internet to be an efficient searchable repository of current and developing knowledge, one additional feature will be needed: ForwardLinks must be available in any given publication to those articles that, in the future, cite the given publication, as fully described in a Supplement to this article. Open-source software for this functionality should be on all Web-servers that contain scholarly articles, so as to make the WWW a distributed web full of linkages, of both ForwardLinks and RetroLinks.
Post-graduate scholars can publish Compended-Guides to the literature of their field using Knowledge-Step-Forums
Authors: Jewett Don L
Published: January 2018

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of many activities, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is not adequate for a Web-based world!

In 2006, an estimated 3,700 peer-reviewed articles were published per day (Bjork2009)! As will become apparent, the methods and features described here are needed now, and will be absolutely necessary in the future, when even more articles are published.

A New Knowledge-Tool is proposed that is in addition to those already available. The new Knowledge-Tool is a new Literature-Guide called a "Knowledge-Step Compendium" which will be on a very-narrow topic, will be organized in a new MultiLevel-Format, and will be created in a Compending-Forum on the Internet.

This New Knowledge-Tool will, in turn, be the basis for a change in academic careers of the timing of when a scholar "Compends" Knowledge. A "Knowledge-Compendor" need not be a senior faculty member (as is the case in traditional literature-reviews), but can be a Post-Graduate Student new to a field. Because a Knowledge-Step Compendium is based on a very-narrow topic and created with the aid of an Internet Forum, for a Graduate Student Compendor this activity will be a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.

To learn what these new names describe, read on.
The essential need for research misconduct allegation audits
Authors: Loikith Lisa , Bauchwitz Robert P
Published: January 2018

The percentage of allegations of biomedical research misconduct in the United States that are dismissed by responsible institutions without any faculty assessment or auditable record is near 90%. Recently, members of the U.S. Congress have complained that the penalties for those against whom findings of research misconduct are made are too light and that too few grant funds associated with research misconduct have been recovered for use by other researchers and taxpayers. Here we describe the laws that empower federal agencies which can oversee investigations of biomedical research misconduct: the Office of Research Integrity (ORI) and Office of the Inspector General (OIG), both located within the Department of Health and Human Services (HHS). Research misconduct pertaining to U.S. physical sciences funded through the National Science Foundation (NSF) is overseen by the NSF's OIG. While OIGs may provide some improvement over ORI in the handling of research misconduct, we have found that a much more serious flaw exists which undermines an ability to conduct performance audits as to the effectiveness by which allegations of research misconduct are handled in the United States. Federal audit standards (GAGAS/Yellow Book), if applied to the handling of research misconduct, would allow a determination as to whether the handling of allegations of biomedical research misconduct actually functions adequately, and if not, how it might be improved. Specifically, we propose that independent, external peer review under GAGAS audit standards should be instituted without delay in assessing the performance of ORI, or any other similarly tasked federal agency, in handling allegations of research misconduct.
Biodiversity collapse in a phase transition between neutral and niche communities
Authors: Saravia Leonardo A , Momo Fernando R
Published: January 2018

The dynamics of ecological communities can be described by two contrasting models: the first assumes that the individuals of all species are identical and do not have competitive interactions. The second assumes that species are different, adapted to particular habitat conditions, and have strong interactions. These represent extremes of a continuum: the neutral and the niche models of community organization. Real communities are actually a mixture of both types of dynamics. Here we study the simplest model of neutral-niche communities where niche dynamics is represented as a competitive hierarchy. The competition intensity is defined as a parameter that modulates the transition between these extremes. We use a stochastic cellular automata to show that there is a phase transition between the neutral and niche model with a spanning patch formed by the most abundant species. We measure the diversity as the Shannon index and the richness as the number of species. The transition implies a sharp fall of species diversity but the richness shows a gentle decline with increasing competitive intensity. As this kind of multi-species critical transition have not been described previously, we suggest new early warning signals: the rate of exponential decay in the patch distribution of the non-dominant species. This rate decreases when the community approaches the critical point and increases when the community crosses it. As an example we apply the early warnings to the Barro Colorado Tropical forest, which as expected, appear to be far from a critical transition. The model shows that the critical point occur at a very low value of competitive intensity. Low values of competitive intensity were also reported for different high diversity real communities suggesting the possibility that these kind of communities are located near the critical point. This transition could happen before habitat destruction or degradation affect the community in response to changes in environmental conditions like the ones produced by climate change or exotic species invasions.
Enriching scientific publications with interactive 3D PDF figures: A complete toolbox
Authors: Newe Axel
Published: January 2018

Three-dimensional (3D) data of many kinds is produced at an increasing rate throughout all scientific disciplines. The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents and allows for embedding three-dimensional models. Therefore, it is a well suited medium for the visualization and the publication of this kind of data. The generation of the appropriate files has been cumbersome so far. This article presents the first release of a software toolbox which integrates the complete workflow for generating 3D model files and ready-to-publish 3D PDF documents for scholarly publications in a consolidated working environment. It can be used as a simple working tool or as a basis for specifically tailored solutions. It is available royalty-free and for Windows, MacOS and Linux.
An approach to cognitive evaluation using games on TV
Authors: Rivas Costa Carlos , Fernández Iglesias Manuel José , Anido Rifón Luis Eulogio , Gómez Carballa Miguel , Valladares Rodríguez Sonia
Published: January 2018

Introduction: The recent advances in consumer electronics paved the way for new approaches to neurophysiological evaluation at home. More specifically, the computing capabilities of state-of-the-art television sets and media centres facilitate the introduction of computer-assisted evaluation at home. This approach helps to overcome the drawbacks of traditional pen-and-paper evaluations administered in clinical facilities, as they can be performed in a more comfortable environment, the subject’s home, and they are more flexible to elaborate complex environments for the evaluation of neuropsychological constructs that are difficult to evaluate through traditional testing. The objective of this work was to develop a collection of games to be played on the TV to obtain some initial evidence about the convenience of this approach for the cognitive evaluation of senior adults.

Materials and methods: We developed a collection of games to be deployed on a smart TV environment. These games were tried by a group of senior adults at their homes. Perception surveys were performed to study their usability and acceptability as a means for cognitive evaluation.

Results: More than 90% perceive cognitive games on TV as easy or very easy to interact with, and this result correlates with the number of participants perceiving them as usable or very usable.

Limitations: Although participating users were carefully selected to obtain a representative sample of the Galician population. A larger and more diverse user sample may be needed to obtain significant results for a wider population profile.

Conclusion: The study confirmed the usability and acceptance of games as a means of cognitive evaluation. Nevertheless, more research is needed in order to implement serious games in a way that they are widely accepted by the medical community as a valid, reliable way to perform cognitive evaluation at home.
Students’ and professionals’ perceptions of test-driven development: a focus group study
Authors: Scanniello Giuseppe , Romano Simone , Fucci Davide , Turhan Burak , Juristo Natalia
Published: January 2018

We have conducted a qualitative investigation on test-driven development (TDD) with focus groups in order to develop insights on the opinions of developers using TDD regarding the unintuitive process involved, its claimed effects, as well as the context factors that can facilitate (or hinder) its application. In particular, we conducted two focus group sessions: one with professional developers and another with Master students in Computer Science at the University of Basilicata. We used thematic analysis template (TAT) method for iden- tifying patterns, themes, and interpretations in the gathered data. The application of this qualitative method allowed us to obtain a number of results that can provide directions for future research. Our main results can be summarized as follows: (i) applying TDD without knowing advanced unit testing techniques can be difficult; (ii) refactoring (one of the phases of TDD) is not done as often as the process re- quires; (iii) there is a need for live feedback to let developers understand if TDD is being applied correctly; and (iv) the usefulness of TDD hinges on task and domain to which it is applied to.
Selenium uptake, toxicity and reduction in Flammulina velutipes supplied with selenite
Authors: Wang Jipeng , Wang Bo , Zhang Dan , Wu Yanhong
Published: January 2018

Recently, selenium (Se) enriched mushrooms have been exploited as diary Se supplements, but our knowledge of the metabolism process during the Se enrichment process is far from complete. In this study, the uptake, toxicity and reduction of selenite in a widely cultivated mushroom, Flammulina velutipes, was investigated. The results showed that pH variation (from 5.5 to 7.5), metabolic inhibitor (0.1 mM 2,4-DNP) and P or S starvation led to 11%-26% decreases in the selenite uptake rate of F. velutipes. This indicates that a minor portion of the selenite uptake was metabolism dependent, whereas a carrier-facilitated passive transport may be crucial. Growth inhibition of F. velutipes initiated at 0.1 mM selenite (11% decrease in the growth rate) and complete growth inhibition occurred at 3 mM selenite. A selenite concentration of 0.03-0.1 mM was recommended to maintain the balance between mycelium production and Se enrichment. F. velutipes was capable of reducing selenite to Se(0) nanoparticles, possibly as a detoxification mechanism. This process depended on both selenite concentration and metabolism activity. Overall, the data obtained provided some basic information for the cultivation of the selenized F. velutipes, and highlighted the opportunity of using mushrooms for the production of Se(0) nanoparticles.
Advertisement call and genetic structure conservatism : good news for an endangered Neotropical frog
Authors: Forti Lucas R , Costa William P , Martins Lucas B , Nunes-de-Almeida Carlos H L , Toledo Luís Felipe
Published: January 2018

Background. Many amphibian species are negatively affected by anthropogenic habitat change. Populations distributed over modified landscapes may be subject to local extinction or may be relegated to remaining, likely isolated and possibly degraded, patches of available habitat. Isolation without gene flow can lead to variability in phenotypic traits due to differences in local selective pressures, such as environmental structure, microclimate or site-specific species assemblages. Methods. Here we tested this microevolution hypothesis by evaluating the acoustic parameters of 349 advertisement calls from 15 males representing six populations of the endangered species Proceratophrys moratoi. In addition, we analyzed the genetic distance between populations and the genetic diversity by haplotype network. We carried out a cluster analysis by Bray-Curtis index of similarity using acoustic data by UPGMA method. We correlated acoustic dissimilarities (calculated by Euclidean distance) with geographic and genetic distances among populations. Results. Spectral traits of the advertisement call of P. moratoi presented lower coefficients of variation than did temporal traits both within and among males. Cluster analyses placed individuals without population and geographical distance congruence, but recovered the species topology in relation to sister species. The genetic distance was low among populations: it did not exceed 0.4% for the most distant populations, and was not correlated with acoustic distance. Discussion. Both acoustic features and genetic sequences are highly conserved, suggesting that populations may be connected by recent migrations or that they are subject to stabilizing selective forces. Although future studies are needed, these findings contribute to a growing body of literature suggesting that this species would be a good candidate for a reintroduction program without negative effects on communication or even genetic heritage.
Sexing a gender-role-reversed species based on plumage: potential challenges in the red phalarope
Authors: Giroux Marie-Andrée , Ditlecadet Delphine , Martin Luc J , Lanctot Richard B. , Lecomte Nicolas
Published: January 2018

Sex-role reversal, in which males care for offspring, can occur when mate competition is stronger between females than males. Secondary sex traits and mate attracting displays in sex-role-reversed species are usually more pronounced in females than in males. The red phalarope is a textbook example of a sex-role-reversed species. It is generally agreed that males are responsible for all incubation and parental care duties, whereas females typically desert males after having completed a clutch and may pair with new males to lay additional clutches. Breeding plumage of female red phalaropes is usually more brightly colored than male plumage, a reversed sexual dichromatism usually associated with sex-role reversal. Here, we confirm with PCR-based sexing that male red phalaropes can exhibit both the red body plumage typical of a female and the incubation behaviour typical of a male in this sex-role-reversed species. Our result, combined with previous observations of brightly coloured red phalaropes incubating nests at the same arctic location (Igloolik Island, Nunavut, Canada), suggests that plumage dichromatism alone may not be sufficient to distinguish males from females in this breeding population of red phalaropes. This stresses the need for more systematic genetic sexing combined with standardized description of intersexual differences in red phalarope plumages. Determining whether such female-like plumage on males is a result of phenotypic plasticity or genetic variation could contribute to further understanding sex-role reversal strategies in the short Arctic summer.
Data Rate Theorem perspectives on the contribution of extrinsic risk factors to cancer development
Authors: Wallace Rodrick
Published: January 2018

We explore environmentally-induced tumors in the context of the ongoing conflict between long-evolved cancer control mechanisms and the central flaw of multicellularity, using a number of convergent necessary conditions statistical models based on the Data Rate Theorem linking control and information theories. Multicellular cancer suppression is an inherently unstable dynamic process that can fail through sufficient environmental insult, in particular for humans, involving the synergism of chemical exposures with the chronic inflammation of 'social' exposures that may be seen as accelerated aging.
High non publication rate from publication professionals hinders evidence-based publication practices
Authors: Carey Luke C , Stretton Serina , Kenreigh Charlotte A , Wagner Linda T , Woolley Karen L
Published: January 2018

Background. The need for timely, ethical, and high-quality reporting of clinical trial results has seen a rise in demand for publication professionals. These publication experts, who are not ghostwriters, work with leading medical researchers and funders around the world to plan and prepare thousands of publications each year. Despite the involvement of publication professionals in an increasing number of peer-reviewed publications, especially those that affect patient care, there is limited evidence-based guidance in the peer-reviewed literature on their publication practices. Similar to the push for editors and the peer-review community to conduct and publish research on publication ethics and the peer-review process, the International Society for Medical Publication Professionals (ISMPP) has encouraged members to conduct and publish research on publication planning and practices. Our primary objective was to investigate the publication rate of research presented at ISMPP Annual Meetings. Methods. ISMPP Annual Meeting abstract lists (April 2009 to April 2014) were searched in November 2014 and data were extracted into a pilot-tested spreadsheet. MEDLINE was searched in December 2014 to determine the publication rate (calculated as the % of presented abstracts published as full papers in peer-reviewed journals). Data were analyzed using the Cochran-Armitage trend test (significance: P <.05) by an independent academic statistician. Results. From 2009 to 2014, there were 220 abstracts submitted, 185 accepted, and 164 presented. There were only four corresponding publications (publication rate 2.4%). Over time, ISMPP’s abstract acceptance rate (overall: 84.1%) did not change, but the number of abstracts presented increased significantly (P = .02). Most abstracts were presented as posters (81.1%) and most research was observational (72.6%). Most researchers came from the US (78.0%), followed by Europe (17.7%), and the Asia-Pacific region (11.2%). Discussion. Research presented at ISMPP Annual Meetings has rarely been published in peer-reviewed journals. The high-rate of non publication by publication professionals has now been quantified and is of concern. Publication professionals should do more to contribute to evidence‑based publication practices, including, and especially, their own. Unless the barriers to publication are identified and addressed, the practices of publication professionals, which affect thousands of peer-reviewed publications each year, will remain hidden and unproven.
Microgeographic variation in locomotor traits among lizards in a human-built environment
Authors: Donihue Colin
Published: January 2018

Microgeographic variation in fitness-relevant traits may be more common than previously appreciated. The fitness of many vertebrates is directly related to their locomotor capacity, a whole-organism trait integrating behavior, morphology, and physiology. Because locomotion is inextricably related to context, I hypothesized that it might vary with habitat structure in a wide-ranging lizard, Podarcis erhardii, found in the Greek Cyclade Islands. I compared lizard populations living on human-built rock walls, a novel habitat with complex vertical structure, with nearby lizard populations that are naive to human-built infrastructure and live in flat, loose-substrate habitat. I tested for differences in morphology, behavior, and performance. Lizards from built sites were larger and had significantly (and relatively) longer forelimbs and hindlimbs. The differences in hindlimb morphology were especially pronounced for distal components – the foot and longest toe. These morphologies facilitated a significant behavioral shift in jumping propensity across a rocky experimental substrate. I found no difference in maximum velocity between these populations, however females originating from wall sites potentially accelerated faster over the rocky experimental substrate. The variation between these closely neighboring populations suggests that the lizards inhabiting walls have experienced a suite of trait changes enabling them to take advantage of the novel habitat structure created by humans.
The analysis of the canid mitochondrial genome studied in Morocco shows that it is neither wolf (Canis lupus) nor Eurasian jackal (Canis aureus)
Authors: Urios Moliner Vicente , Donat-Torres Maria P , Ramírez Castillo Carlos A , Monroy-Vilchis Octavio , Rguibi Idrissi Hamid
Published: January 2018

The mitochondrial genome of three Moroccan canids has been analysed. Two of them complete and one partial. The sequences are included in GenBank with the accession number KT378605 (16721 bp), KT378606 (16734bp) and KT378607 (27809bp) Theses results have been compared with the results currently available in GenBank. In the phylogenetic analysis of the of cytochrome b regions and control region the three are grouped together with Canis lupus lupaster and the Senegalese golden jackal Canis aureus and separate from the wolf Canis lupus and the Eurasian golden jackal Canis aureus. The comparison of the complete mitochondrial genomes with Canis lupus confirms the distance between the two groups. We conclude that they belong to a different species to the wolf Canis lupus and the Eurasian golden jackal. We propose in agreement with (Koepfli et al., 2015) that it´s scientific name be Canis anthus by merit of being the name by which it was classified and published for the first time as a different species by Cuvier in 1824.

The preprint is a translation of a Spanish document published in Altorero journal on the 15th August 2015.
­A practical application of reduced-copper antifouling paint in marine biological research
Authors: Jerabek Andrea S. , Wall Kara R. , Stallings Christopher D.
Published: January 2018

Predator exclusion cages are commonly used to enclose settlement tiles to distinguish between pre- and post-recruitment processes. Biofouling of experimental cages and other field apparatuses can be problematic, and has traditionally been addressed using frequent manual removal (e.g., scrubbing twice per week). However, such intense efforts can be both labor intensive and costly, especially with apparatuses in remote locations, and may also have unintended effects on study results. Recent environmental restrictions and legislative changes have driven the development of less hazardous antifouling products, making antifouling paint a potential alternative option to manual removal. The viability of using these newly developed products as a replacement for the manual cleaning of exclusion cages was experimentally investigated. Six treatment levels were tested, three with and three without antifouling paints. The three antifouling treatments consisted of two reduced-copper paints (21% Cu2O and 40% Cu2O) and one copper-free, Econea®-based paint (considered “ecofriendly”). Antifouling paints were assessed for performance on the cages and whether they elicited local effects on settlement tiles contained within them. The community compositions, biomass, and percent cover of tiles inside cages treated with the copper-based paints were indistinguishable from those inside manually scrubbed cages, while the “ecofriendly” paint resulted in reduced local settlement. The results of this study suggest that the reduced-copper paints tested have the potential to serve as a viable replacement for manual maintenance.
Communication styles in bonobos and chimpanzees: Same same but different?
Authors: Fröhlich Marlen , Kuchenbuch Paul H , Müller Gudrun , Fruth Barbara , Furuichi Takeshi , Wittig Roman M , Pika Simone
Published: January 2018

Comparative studies in relation to language origins have mainly focused on our closest living relatives, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Direct comparisons however are still lacking and/or concerned individuals living in captive environments only. Here, we carried out a systematic, quantitative comparison of communicative abilities of bonobos and chimpanzees living in four different communities in the wild with a special focus on within- and between-species variability. The analyses focused on communicative exchanges between mother-infant dyads to initiate joint travel. The communicative behavior of twelve bonobo (LuiKotale, Wamba; DRC) and thirteen chimpanzee mother-infant dyads (Taï South, Côte d’Ivoire; Kanyawara, Uganda) was filmed during a total of 1033 (bonobos) and 1189 (chimpanzees) hours of observation. We analyzed ‘signal-response’ structures (e.g. response waiting, gestural sequences, temporal relationships) in 316 bonobo and 415 chimpanzee carry initiations, while taking into account dyadic role, infant age and site. Differences in behavior could not be attributed to within-species variability. Bonobos solicited carries more frequently from shorter distances and via coordinated responses. Chimpanzees used a higher frequency of response waiting and sequences, showing overall more persistence. Our findings suggest that interactional intelligence paved the way to language with communication styles being influenced by social matrices.