bluuebunny/crossref_metadata_2025 huggingface dataset:
The skin microbiome of cow-nose rays (Rhinoptera bonasus) in an aquarium touch-tank exhibit
Authors: Kearns Patrick J , Bowen Jennifer L , Tlusty Michael F
Published: January 2018

Public aquarium exhibits offer numerous educational opportunities for visitors while touch tank exhibits offer guests the ability to directly interact with marine life. However, despite the popularity of these exhibits, the effect of human interactions on the host-associated microbiome or the habitat microbiome remains unclear. Microbial communities, both host-associated and habitat associated can have great implications for host health and habitat function. To better understand the link between human interactions and the microbiome of a touch tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as its environment in a frequently visited touch tank exhibit at the New England Aquarium. Our analyses revealed a distinct microbial community associated with the skin of the ray that had lower diversity than the surrounding habitat. The ray skin was dominated by three orders: Burkholderiales (~55%), Flavobacteriales (~19%) and Pseudomonadales (~12%), suggesting a potentially important role of these taxa in ray health. Further, there was no difference between dorsal and ventral surface of the ray in terms of microbial composition or diversity, and a very low presence of common human-associated microbial taxa (<1.5%). Our results suggest that human contact has a minimal effect on the skin and habitat microbiome of the cow-nose ray and that the ray skin harbors a distinct and lower diversity microbial community than its environment.
Quantitative assessment of Fgfr1 expression in neurons and glia
Authors: Choubey Lisha , Collette Jantzen C , Smith Karen Muller
Published: January 2018

Fibroblast growth factors (FGFs) and their receptors (FGFRs) have numerous functions in the developing and adult CNS. For example, the FGFR1 receptor is important for proliferation of radial glial cells in the cortex and hippocampus, oligodendrocyte proliferation and regeneration, midline glia morphology and soma translocation, Bergmann glia morphology, and cerebellar morphogenesis. In addition, FGFR1 signaling in astrocytes is required for postnatal maturation of interneurons expressing parvalbumin (PV). FGFR1 is implicated in synapse formation in the hippocampus, and alterations in the expression of Fgfr1 and its ligand, Fgf2 accompany major depression. Understanding which cell types express Fgfr1 during development may elucidate its roles in normal development of the brain as well as illuminate possible causes of certain neuropsychiatric disorders. Here, we used a BAC transgenic reporter line to trace Fgfr1 expression in the developing murine CNS. The specific transgenic line employed was created by the GENSAT project, tgFGFR1-EGFPGP338Gsat, and includes a gene encoding enhanced green fluorescent protein (EGFP) under the regulation of the Fgfr1 promoter, to trace Fgfr1 expression in the developing CNS. This model reveals that Fgfr1 is primarily expressed in glial cells, in both astrocytes and oligodendrocytes, along with some neurons. Dual labeling experiments indicate that the proportion of GFP+ (Fgfr1+) cells that are also GFAP+ increases from postnatal day 7 (P7) to 1 month, illuminating dynamic changes in Fgfr1 expression during postnatal development of the cortex. In postnatal neurogenic areas, GFP expression was also observed in SOX2, doublecortin (DCX), and brain lipid-binding protein (BLBP) expressing cells. Fgfr1 is also highly expressed in DCX positive cells of the dentate gyrus, but not in the rostral migratory stream. Fgfr1 driven GFP was also observed in tanycytes and GFAP+ cells of the hypothalamus, as well as in Bergmann glia and astrocytes of the cerebellum. Understanding which cell types express Fgfr1 may elucidate its role in neuropsychiatric disorders and brain development.
Predator management and species at risk in Alberta
Authors: Hervieux Dave
Published: January 2018

Alberta has employed lethal techniques to reduce predator populations in several wildlife-management situations, particularly in attempts to achieve goals and objectives for threatened or endangered species. Annual wolf populations reductions within and adjacent to woodland caribou population ranges in West Central Alberta are a notable example of this management approach. Almost all woodland caribou populations in Alberta are exhibiting ongoing population declines, with some populations declining at rapid rates. Current knowledge indicates that these declines are from apparent competition due to anthropogenic habitat changes, with resulting unsustainably high levels of wolf predation on woodland caribou populations. Delivery of annual wolf population reductions for two woodland caribou populations has resulted in stable or slightly increasing caribou population growth; in the absence of the wolf program at least one of the caribou populations would now be extirpated. The delivery of lethal wolf management for woodland caribou conservation and recovery in Alberta is enabled by a variety of provincial government approved management plans and policies. It is fully recognized that predator management for woodland caribou recovery must be predicated on management approaches and actions to improve caribou habitat conservation and recovery and thereby address the ultimate factors influencing apparent competition and unsustainably high levels of predation. Considerable effort is now being devoted to planning, policy revisions, regulatory adjustments, and management actions to address fundamental considerations related to caribou habitat. Progress on woodland caribou habitat will have little relevance; however, if the resident caribou population becomes extirpated before sufficient habitat recovery is achieved. Effective reductions in predation rates are needed immediately.
CartograTree: Enabling Landscape Genomics for Forest Trees
Authors: Herndon Nic , Grau Emily S , Batra Iman , Demurjian Jr. Steven A , Vasquez-Gross Hans A , Staton Margaret E , Wegrzyn Jill L
Published: January 2018

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated for hundreds of species. These long-lived and immobile individuals serve as ideal models to assess population structure and adaptation to environment. Despite the availability of comprehensive data, researchers are challenged to integrate genotype, phenotype, and environment in one place. Towards this goal, CartograTree was designed and implemented as a repository and analytic framework for genomic, phenotypic, and environmental data for forest trees. One of key components, the integration of geospatial data, allows the display of environmental layers and acquisition of environmental metrics relative to the positions of georeferenced individuals.
CartograTree: Enabling landscape genomics for forest trees
Authors: Herndon Nic , Grau Emily S , Batra Iman , Demurjian Jr. Steven A , Vasquez-Gross Hans A , Staton Margaret E , Wegrzyn Jill L
Published: January 2018

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated for hundreds of species. These long-lived and immobile individuals serve as ideal models to assess population structure and adaptation to environment. Despite the availability of comprehensive data, researchers are challenged to integrate genotype, phenotype, and environment in one place. Towards this goal, CartograTree was designed and implemented as an open repository and open-source analytic framework for genomic, phenotypic, and environmental data for forest trees. One of its key components, the integration of geospatial data, allows the display of environmental layers and acquisition of environmental metrics relative to the positions of georeferenced individuals. Currently, CartograTree uses the Google Maps API to load environmental data. Limitations inherent to this API are driving new development with a focus on functionality to provide efficient queries of numerous environmental metrics.
Sexual reproduction in the Caribbean coral genus Isophyllia (Scleractinia: Mussidae) in Puerto Rico
Authors: Soto Derek , Weil Ernesto
Published: January 2018

The sexual pattern, reproductive mode, and timing of reproduction of Isophyllia sinuosa and Isophyllia rigida, two Caribbean Mussids, were assessed by histological analysis of specimens collected monthly during 2000-2001. Results indicate that both species are simultaneous hermaphroditic brooders, with a single annual gametogenetic cycle. Spermatocytes and oocytes of different stages were found within the same mesentery indicating sequential maturation for extended planulation. Oocytes begin development 7-8 months prior to spermaries; beginning in May in I. sinuosa and August in I. rigida. Gametes of both sexes matured simultaneously; May-June in I. rigida and March-April in I. sinuosa. Planulae were observed in I. sinuosa during April and in I. rigida from June through September. Significantly higher polyp and mesenterial fecundity were found in I. rigida compared to I. sinuosa. Significantly larger oocyte sizes were found in I. sinuosa than in I. rigida, however significantly larger planula sizes were I. rigida compared to I. sinuosa. Hermaphroditism is the exclusive sexual pattern within the Mussidae; brooding has also been documented within the related Mussid genera Mussa, Scolymia and Mycetophyllia. These results represent the first description of the sexual characteristics of I. rigida and refute the previous description for I. sinuosa.
Cytokine regulation of stem cells
Authors: Singh Gyanesh , Korkaya Hasan
Published: January 2018

Different types of stem cells are targeted by a number of cytokines that alter proliferation, differentiation, or other properties of stem cells. Stem cells are known to express various cytokine genes. As IL-12, IL-14, G-CSF, and GM-CSF expression is lost after the differentiation of MSCs, these factors might have major contribution to pluripotency. Several other cytokines that are produced by immune cells, frequently target stem cells. Modulation of stem cell functions by cytokines can be a cause of various diseases including cancer. Stem cells can show immunosuppressive properties by a number of mechanisms. MSC-induced immunosuppression is often mediated by IFN-γ, TNF-α, IL-1α, or IL-1β. In co-culture experiments, MSCs were able to control T cells IL-2 response, or, dendritic cells TNF-α and IL-10 secretion. MSCs are also known to cause decreased interferon γ (IFN-γ) and increased IL-4 production by immune cells. However, the outcome in most of the cases depends on the presence of various factors that might synergize or antagonize with each other.
AliTV-interactive visualization of whole genome comparisons
Authors: Ankenbrand Markus J. , Hohlfeld Sonja , Hackl Thomas , Förster Frank
Published: January 2018

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation of the initial results. Limitations of existing software inspired us to develop our new tool AliTV, which provides interac- tive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV.
Targeted manipulation of neuronal activity in behaving adult flies
Authors: Hampel Stefanie , Seeds Andrew Michael
Published: January 2018

The ability to control the activity of specific neurons in freely behaving animals provides an effective way to probe the contributions of neural circuits to behavior. Wide interest in studying principles of neural circuit function using the fruit fly Drosophila melanogaster has fueled the construction of an extensive transgenic toolkit for performing such neural manipulations. Here we describe approaches for using these tools to manipulate the activity of specific neurons and assess how those manipulations impact the behavior of flies. We also describe methods for examining connectivity among multiple neurons that together form a neural circuit controlling a specific behavior. This work provides a resource for researchers interested in examining how neurons and neural circuits contribute to the rich repertoire of behaviors performed by flies.
Effects of grazing intensity and the use of veterinary medical products on dung beetle biodiversity in the sub-mountainous landscape of Central Italy
Authors: Tonelli Mattia , Verdú José R. , Zunino Mario E.
Published: January 2018

Grazing extensification and intensification are among the main problems affecting European grasslands. We analyze the impact of grazing intensity (low and moderate) and the use of veterinary medical products (VMPs) on the dung beetle community in the province of Pesaro-Urbino (Italy). Grazing intensity is a key factor in explaining the diversity of dung beetles. In the case of the alpha diversity component, sites with a low level of grazing activity – related in a previous step to the subsequent abandonment of traditional farming – is characterized by a loss of species richness (q = 0) and a reduction in alpha diversity at the levels q = 1 and q = 2. In the case of beta diversity, sites with a different grazing intensity show remarkable differences in terms of the composition of their species assemblages. The use of VMPs is another important factor in explaining changes in dung beetle diversity. In sites with a traditional use of VMPs, a significant loss of species richness and biomass is observed, as is a notable effect on beta diversity. In addition, the absence of indicator species in sites with a historical use of VMPs corroborates the hypothesis that these substances have a ubiquitous effect on dung beetles. However, the interaction between grazing activity and VMPs when it comes to explaining changes in dung beetle diversity is less significant (or is not significant) than the main effects (each factor separately) for alpha diversity, biomass and species composition. This may be explained if we consider that both factors affect the various species differently. In other words, the reduction in dung availability affects several larger species more than it does very small species, although this does not imply that the former are more susceptible to injury caused by the ingestion of dung contaminated with VMPs. Finally, in order to prevent negative consequences for dung beetle diversity, we propose the maintenance of a moderate grazing intensity and the rational use of VMPs. It is our view that organic management can prevent excessive extensification while providing an economic stimulus to the sector. Simultaneously, it can also prevent the abuse of VMPs.
Angling for data: Recreational anglers’ records of conger eel (Conger conger) landings from the English Channel between 1990-1991
Authors: Johnson Magnus L , Wheeler Philip
Published: January 2018

Declines in commercial fish stocks have been well documented through government records of catches. Here we demonstrate that records from anglers, if appropriately interpreted, can be used to provide detailed retrospective data on population trends in fish species. We highlight this with reference to records of conger eel from the British Conger Club that show a decline in size and abundance of conger through the 1990s, during which time the commercial extraction of the species increased markedly. Anglers’ records are a potentially important source of quantitative data on population trends of a number of poorly studied species.
Supply-side barriers to maternal health care utilization at health sub-centres in India
Authors: Singh Aditya
Published: January 2018

Introduction: There exist several barriers to maternal health service utilization in developing countries. Most of the previous studies conducted in India have focused on demand-side barriers, while only a few have touched upon supply-side barriers. None of the previous studies in India have investigated the factors that affect maternal health care utilization at Health Sub-Centers (HSC) in India, despite the fact that these institutions, as the nearest available public healthcare facilities in rural areas, play a significant role in providing affordable maternal health care. Therefore, this study aims to examine the supply-side determinants of maternal service utilization at HSCs in rural India.

Data and Methods: This study uses health facility data from the nationally representative District-Level Household Survey, which was collected in 2007–2008 to examine the effect of supply-side variables on the utilization of maternal healthcare services across HSCs in rural India. Since the dependent variables (the number of antenatal registrations, in-facility deliveries, and postnatal care services) are count variables with considerable dispersion, the data has been analyzed using negative binomial regression instead of Poisson regression.

Results: The results show that those HSCs run by a contractual auxiliary nurse midwife (ANM) are likely to offer a lower volume of services when compared to those run by a permanent ANM. The availability of obstetric drugs, weighing scale, blood pressure equipment is associated with the increased utilization of antenatal and postnatal services. The unavailability of labor/examination table and bed screen is associated with a reduction in the number of safe deliveries and postnatal services. The utilization of services is expected to increase if essential facilities, such as water, telephone, toilet, and electricity, are available at HSCs. Monitoring of an ANM’s work by the Village Health and Sanitation Committee (VHSC) and the in-service training of ANMs appear to have a positive impact on the utilization of services. The distance of an ANM’s actual residence from the sub-center village where she works is negatively associated with the utilization of delivery and postnatal services. These findings are robust to the inclusion of several demand-side factors.

Conclusion: To improve maternal healthcare utilization at sub-centers, the government should ensure the availability of basic infrastructure, drugs, and equipment at all sub-centers. Monitoring of ANMs’ work by VHSCs could play an important role in improving healthcare utilization at the HSCs; therefore, it is important to establish VHSCs in each sub-center village. The issue of the relatively low utilization of maternity services in the HSCs that are run solely by contractual ANMs needs to be investigated further.
From computer operating systems to biodiversity: co-emergence of ecological and evolutionary patterns
Authors: Keil Petr , Bennett Joanne M , Burgeois Bérenger , García-Peña Gabriel E , MacDonald Andrew M , Meyer Carsten , Ramirez Kelly S , Yguel Benjamin
Published: January 2018

Comparisons between biodiversity and other complex systems can facilitate cross-disciplinary exchange of theories and the identification of key system processes and constraints. For example, due to qualitative structural and functional analogies to biological systems, coupled with good data accessibility, computer operating systems offer opportunities for comparison with biodiversity. However, it remains largely untested if the two systems also share quantitative patterns. Here, we employ analogies between GNU/Linux operating systems (distros) and biological species, and look for a number of well-established ecological and evolutionary patterns in the Linux universe. We demonstrate that patterns of the Linux universe match the macroecological patterns: Linux distro commonness and rarity (popularity of a distro) follow a lognormal distribution, power law mean-variance scaling of temporal fluctuation, and there is a significant relationship between niche breadth (number of software packages) and commonness. The diversity in the Linux universe also follows general macroevolutionary patterns: The number of phylogenetic lineages increases linearly through time, with clear per-species diversification and extinction slowdowns, something that is unobservable in biology. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. Our study provides foundations for using Linux as a model system for eco-evolutionary studies, as well as insights into patterns and dynamics of computer operating systems, which may be used to inform their future development and maintenance. The co-emergence of patterns across systems suggests that some patterns might be produced by system-level properties, independently of system identity, which offers an empirical argument for non-biological explanations of fundamental biodiversity patterns.
Quantitative analysis of rat adipose tissue cell recovery, and non-fat cell volume, in primary cell cultures
Authors: Rotondo Floriana , Romero María del Mar , Ho-Palma Ana Cecilia , Remesar Xavier , Fernández-López José Antonio , Alemany Marià
Published: January 2018

Background. White adipose tissue (WAT) is a complex, disperse, multifunctional organ which contains adipocytes, and a large proportion of fat, but also other cell types, active in defence, regeneration and signalling functions. Studies with adipocytes often require their isolation from WAT breaking up the matrix collagen fibres, but primary cultures of these cells could not be easily correlated to intact WAT, since often recovery and viability are unknown. Experimental design. Epididymal WAT of 4-6 young adult rats was used to isolate adipocytes with collagenase. Careful recording of lipid content of tissue, and all fraction volumes and weights, allowed us to trace the amount of initial WAT fat remaining in the cell preparation. Functionality was estimated by incubation with glucose and measurement of lactate production. Non-adipocyte cells were also recovered and their sizes (and those of adipocytes) were also measured. The presence of non-nucleated cells (erythrocytes) was also estimated. Results. Cell numbers and sizes were correlated from all fractions to intact WAT. Tracing the lipid content, the recovery of adipocytes in the final, metabolically active, preparation was in the range of 70-75%. Adipocytes were 7%, erythrocytes 68% and other stromal (nucleated cells) 24% of total WAT cells. However, their overall volumes were, 91%, 0.05%, and 0.2% of WAT. Non-fat volume of adipocytes was 2.5% of WAT. Conclusions. The methodology presented here allows for a direct quantitative reference to the original tissue of studies using isolated cells. We have found, also, that the "live cell mass" of adipose tissue is very small (about 25 µL/g for adipocytes and 2 µL/g stromal, plus about 1 µL/g blood). This fact, translates into an extremely high (with respect to the actual "live cytoplasm" size) metabolic activity, which make WAT an even more significant agent in the control of energy metabolism.
Correlation between predictability index and the error performance of customer baseline load (CBL) calculation
Authors: Mohajeryami Saeed , Cecchi Valentina
Published: January 2018

This paper attempts to explore the correlation between the content of high frequency component of customers' historical consumption data (measured by a proposed index called predictability index) and the accuracy of Customer Baseline Load (CBL) calculation methods. In this paper, the customer's consumption signal is transformed from time-domain to frequency domain to separate the high and low frequency components of the consumption signal. Then, after reconstructing the time-domain equivalent of both of these signals, the predictability index for all customers are calculated. The data employed by this study belong to Australian Energy Market Operation (AEMO), and is the hourly consumption of 189 customers for the time span of a year (2012). This index is proposed to be used for the purpose of clustering the customers into different bins by K-means clustering algorithm. Then the CBL for customers of each bin is calculated by two methods of CAISO and Randomized Controlled Trial (RCT), and then the average error in each bin is computed. Afterwards, the correlation between the average P_index of each bin, and its normalized average error is calculated. It is found that there is a strong correlation between the P_index and the error performance of the CBL calculation methods.
SLIMM: Species level identification of microorganisms from metagenomes
Authors: Dadi Temesgen Hailemariam , Renard Bernhard , Wieler Lothar H. , Semmler Torsten , Reinert Knut
Published: January 2018

Identification and quantification of microorganisms is an important step in studying the alpha and beta diversities within and between microbial communities respectively. Both, identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than using 16S-rRNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins. The existing microbial community profiling tools commonly deal with this problem by either preparing signature-based unique references or assigning an ambiguous read to its least common ancestor in a taxonomic tree. The former method is limited to making use of the reads which can be mapped to the curated regions, while the later suffer from the lack of uniquely-mapping reads at higher (more specific) taxonomic ranks. Moreover, even if the tools exhibited generally good performance in calling the organisms present in a sample, there is room for improvement in calling the correct relative abundance of the organisms. We present a new method Species Level Identification of Microorganisms from Metagenomes (SLIMM) which addresses the above issues by using coverage information of reference genomes to remove unlikely genomes from the analysis and subsequently gain more uniquely-mapping reads to assign at higher ranks of a taxonomic tree. SLIMM is based on a few, seemingly easy steps which lead to a tool that outperforms state-of-the-art tools in run-time and/or memory usage while being on par or better in computing quantitative and qualitative information at the species level.
PaPrBaG: A random forest approach for the detection of novel pathogens from NGS data
Authors: Deneke Carlus , Rentzsch Robert , Renard Bernhard Y
Published: January 2018

The reliable detection of novel bacterial pathogens from next generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from reference database used. Here, we present the random forest based approach PaPrBaG (Pathogenicity Prediction for Bacterial Genomes). PaPrBaG overcomes genetic divergence by training on a wide set of species with known pathogenicity phenotype. To that end we generated a novel label source of pathogenic and non-pathogenic bacterial strains, using a rule-based protocol to annotate pathogenicity based on genome metadata. A detailed comparative study reveals that PaPrBaG has several advantages over sequence similarity approaches. Most importantly, it always provides a prediction whereas other approaches discard a large number of sequencing reads that are far away from currently known reference genomes. Furthermore, PaPrBaG remains reliable even at very low genomic coverages. Combining PaPrBaG with existing approaches further improves prediction results.
The influence of age and anthropometric variables on winning and losing in professional mixed martial arts
Authors: Kirk Christopher
Published: January 2018

Anthropometry and chronological age has been demonstrated to have an effect on individual performance in competitive sport, with the relationship between stature and wingspan being found to be selective criteria in many sports, although evidence for this in MMA is negligible. In this study, n = 278 professional MMA bouts were analysed with the winners and losers being compared in terms of chronological age, stature, wingspan, stature-to-wingspan ratio (S:W) and method of win/loss using paired samples t tests, Wilcoxon signed-rank tests, one way ANOVAs, Kruskal-Wallis tests (all ≤ .05) and Bayes Factor (BF 10). The results showed that for the most part anthropometric differences have no effect on who wins the bout, but taller bout losers are most likely to lose via strikes. The exception to this is at welterweight where taller participants were most likely to win, but with an anecdotal BF 10. Also at welterweight, participants with greater wingspans were most likely to lose via submission. Across the full cohort and several competitive divisions, it was found that older participants are significantly more likely to lose, and are also significantly more likely to lose via strikes. Participants who won via decision were found to be significantly older than those who won via strikes or submission.
Bioinformatics support for the Tubiom community gut microbiome project
Authors: Beier Sina , Gorska Anna , Grupp Patrick , Harbig Theresa Anisja , Flade Isabell , Huson Daniel H
Published: January 2018

The Tübiom project is a community-based project aimed at constructing a large, representative reference database of human gut microbiome profiles. The goal is to collect 10 000 profiles, along with detailed metadata on each participants health and lifestyle. All samples will be processed using identical sequencing and analysis protocols to ensure comparability. The project has four technical components: sequencing, sequence analysis, data storage and visualisation.

The project website http://www.tuebiom.de allows interested people to learn about the project, order a sampling kit and fill-in the metadata questionnaire. Once a sample as been submitted and processed, a participant can explore the taxonomic profile of their gut microbiome and compare it to the typical profile of different comparison groups.This community-based project also hopes to engage participants in science-propagation, spread knowledge about the gut microbiome and the importance of this area of research.

Here we provide a brief introduction to the Tübiom project and describe the bioinformatics framework that we have developed for it.
Songbird perception and production in anthropogenic noise
Authors: Proppe Darren S
Published: January 2018

Urban habitats are characterized by a number of unique environmental variables, including modified vegetative structure, fragmentation, small patch size, invasive species, and higher levels of anthropogenic noise. Many songbird species are found less frequently in these types of habitats, but this pattern is far from universal. This has led many to ask whether common urban species are more adaptable in novel environments, or whether this subset of species has been pre-adapted for urban survival. Much of my own research has been geared towards understanding the effects of anthropogenic noise on songbirds and determining which, if any, song traits facilitate higher urban persistence. However, perception of bird sounds is only a small piece of the soundscape a songbird must navigate. Other sounds, such as predator calls, may also be hampered by anthropogenic noise. Yet, less is known about how noise effects communication networks beyond the sender-receiver relationship. I will present results from a series of experiments designed to examine whether pitch and temporal plasticity can be utilized by songbirds to adapt to high levels of noise, then turn my attention towards perception, examining whether urban songbirds can perceive an aerial predator in the midst of increased noise. Finally, I ask whether we can manipulated natural behavior patterns to increase songbird diversity despite the apparent disparity in some traits between species which inhabit urban areas and those that do not.
Reef fish communities of Praia do Tofo, Mozambique, and the need for best practice management
Authors: Fordyce Alexander John
Published: January 2018

The coral reefs around Praia do Tofo, southern Mozambique, are known for their aggregations of marine megafauna but as yet few studies have comprehensively examined their broader biodiversity. This study is the first to assess the ichthyofaunal diversity of this economically important area. Methodology involved SCUBA and snorkel underwater visual censuses conducted between February and May, 2016, and the use of photographic records from 2015 to capture rare species. A total of 324 species, representing 79 families, were recorded from 16 reefs in the region. The area shows comparable species diversity and notably high family diversity in relation to other areas of the Western Indian Ocean. The trophic structure of the reefs, similar to that recorded in the wider region, suggests the reefs are in good health and fairly resilient to disturbance. This study highlights the area’s high biological value beyond its megafauna and lends support to greater management of these ecosystems for the benefit of the associated human population.
Getting off the impact factor: an antidote
Authors: Belikov Aleksey V
Published: January 2018

Articles published in high Impact factor (IF) journals receive higher visibility and attached prestige, regardless of their actual scientific merit. This results in unfair gain in subsequent number of citations to these articles, which also further increases the journals’ IFs. While there is a gradual move in assessment of researchers from IFs towards individual performance metrics, such as the h-index, those metrics are calculated on the basis of citation counts, and hence are still affected by the described phenomena. Naturally, this leads to increased submission and rejection rates in high IF journals, considerably delaying publication of manuscripts and wasting researchers’ time. Additionally, an article’s visibility increases with time, as it accumulates citations, thus severely disadvantaging new articles and early-career researchers. Here I propose a simple method for evaluation of individual articles and researchers that compensates for the effects of the journal IF and article age. In essence, the number of citations to an article is divided by the median number of citations to the articles published in the same journal in the same year. This ratio indicates the performance of an article relative to its closest competitors, is free from journal and age bias, and thus reflects an article’s scientific merit. An author’s (or institution’s) index is calculated as the sum of these article scores. Widespread adoption of this index, especially by decision-making authorities, will refocus scientists from besieging elitist journals to actually doing research.
In-silico prediction and modeling of the Entamoeba histolytica proteins: Serine-rich Entamoeba histolytica protein and peroxiredoxin
Authors: Manochitra Kumar , Parija Subhash Chandra
Published: January 2018

Background: Amoebiasis is the third most common parasitic cause of morbidity and mortality particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence arises a necessity for a better diagnostic approach. Serine-rich Entamoeba histolytica protein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal in E. histolytica virulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential which are not available till date. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using relevant in-silico methods.

Methods:The amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.

Results: The protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be a extracellular protein, peroxiredoxin was a peripheral membrane protein, while Gal/GalAc was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All three proteins exhibited similarity in their structures and were mostly composed of loops.

Discussion:The structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of three sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.
Pests, diseases and crop protection practices in the smallholder sweetpotato production system of the highlands of Papua New Guinea
Authors: Gurr Geoff M , Liu Jian , Johnson Anne C , Woruba Deane N , Kirchhof Gunnar , Fujinuma Ryosuke , Sirabis William , Jeffery Yapo , Akkinapally Ramakrishna
Published: January 2018

Sweetpotato (Ipomea batatans) is a food crop of global significance. The storage roots and foliage of crop are attacked by a wide range of pests and diseases. Whilst these are generally well controlled in developed countries using approaches such as clean planting material and monitoring with pheromone traps to guide insecticide use, research into methods suitable for developing countries has lagged. In Papua New Guinea (PNG), sweetpotato is grown extensively as a subsistence crop and commercial production as a cash crop is developing. We report results from a survey of 33 smallholder producers located in the Highlands of PNG where the crop is of particular importance. Surveys of interviewees’ crops showed high levels of pest and disease impact to foliage, stems and storage roots, especially in crops that were several years old. Weevils (Curculionidae) were reportedly the most damaging pests and scab (caused by the fungus Elisnoe batatus) the most damaging disease. Most producers reported root damage from the former and foliar damage from the latter but the general level of knowledge of pest and disease types was low. Despite the apparency of pest and disease signs and symptoms and recognition of their importance by farmers, a large majority of producers reported practiced no active pest or disease management. This was despite low numbers of farmers reporting use of traditional cultural practices including phytosanitary measures and insecticidal plants that had the scope for far wider use. Only one respondent reported use of insecticide though pesticides were available in nearby cities. This low level of pest and disease management in most cases, likely due to paucity in biological and technical knowledge among growers, hampers efforts to establish food security and constrains the development of sweetpotato as a cash crop.
A computer simulation model for Strongyloides infection
Authors: Levenhagen Marcelo A , Ferreira Gustavo A , Pereira Getúlio M , Santos Anderson R
Published: January 2018

Despite high success rate in treating human Strongyloides infection with ivermectin, there is no consensus about the treatment of hyperinfection by helminths of the genus Strongyloides in immunocompromised people. Chances of survival of patients suffering from strongyloidiasis hyperinfection near 50%, with the toxicity of ivermectin in nervous system aggravating the puzzle. Creation of computer models capable of faithfully reproduce established knowledge about Strongyloides infection may be useful to understand the dynamics of infection and possible treatment. A computer model was developed in COPASI using ordinary differential equations representing dynamics of helminth life cycle in a hyperinfection. A combination of Boolean variables representing an ’immunosuppressed’ host and ’treated’ with four doses of ivermectin (200 μkg −1 ) raises four scenarios for time course simulations. Humoral and cellular immune responses were modeled using previous experiments whose data were approximated by ordinary functions. Three experiments, associated to strongyloidiasis hyperinfection, were successfully reproduced. A fourth scenario (immunosuppressed ∧ treated) yielded similar results compared to literature: four doses of ivermectin (200 μkg −1 ) were sufficient to restrain an infection, without a need for prolonged treatment. However, the smallest dosage does not suffice. A computational model for Strongyloides infection is available in SBML file format. The computational model here proposed for simulation of a hyperinfection by Strongyloides achieved similar results to previous experiments with hosts. It could allow us an in silico understanding of several aspects of infections caused by parasites of the genus Strongyloides.
The man-machine integration era
Authors: Bilar Daniel
Published: January 2018

Through sensor ubiquity, the man-machine integration era is upon us. This integration is taking place in distributed, continuously changing, optimizing/learning, finite precision feedback systems. Security challenges of such systems abound, also due to constantly co-evolving threat actors and changing environments. Are we adequately preparing to defend such systems, and more importantly: how do we ensure they are worth defending?

This position paper posits we are ill-prepared, due to perverse incentives affecting methodology, results and foundational corpuses. With respect to the first question, we will corroborate this ill-preparedness in the context of a basic requirement – situational awareness – for so-called Moving Target Defenses. We’ll argue that the second question hinges on a deceptively straightforward permanence invariant: The ability to robustly encode the infinite value of a human being in finite precision systems. Here too, we are failing to develop needed toolsets and skills.

Successfully tackling both questions may determine the future winning model of the man-machine integration era; whether we’ll lose the Republic of the People to the People’s Republic.
VSEARCH: a versatile open source tool for metagenomics
Authors: Rognes Torbjørn , Flouri Tomáš , Nichols Ben , Quince Christopher , Mahé Frédéric
Published: January 2018

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.

Methods. When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.

Results. VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e. format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0.

Discussion. VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
Detecting communicative intent in a computerised test of joint attention
Authors: Caruana Nathan , McArthur Genevieve , Woolgar Alexandra , Brock Jon
Published: January 2018

The successful navigation of social interactions depends on a range of cognitive faculties – including the ability to achieve joint attention with others to share information and experiences. We investigated the influence that intention monitoring processes have on gaze-following response times during joint attention. We employed a virtual reality task in which 16 healthy adults engaged in a collaborative game with a virtual partner to locate a target in a visual array. In the Search task, the virtual partner was programmed to engage in non-communicative gaze shifts in search of the target, establish eye contact, and then display a communicative gaze shift to guide the participant to the target. In the NoSearch task, the virtual partner simply established eye contact and then made a single communicative gaze shift towards the target (i.e., there were no non-communicative gaze shifts in search of the target). Thus, only the Search task required participants to monitor their partner’s communicative intent before responding to joint attention bids. We found that gaze following was significantly slower in the Search task than the NoSearch task. However, the same effect on response times was not observed when participants completed non-social control versions of the Search and NoSearch tasks, in which the avatar’s gaze was replaced by arrow cues. These data demonstrate that the intention monitoring processes involved in differentiating communicative and non-communicative gaze shifts during the Search task had a measureable influence on subsequent joint attention behaviour. The empirical and methodological implications of these findings for the fields of autism and social neuroscience will be discussed.