bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of the optimal duration of behavioral observations based on an automated continuous monitoring system in tree swallows (Tachycineta bicolor): is one hour good enough?
Authors: Lendvai Adam Z , Akçay Çağlar , Ouyang Jenny Q , Dakin Roslyn , Domalik Alice D , St John Prianka S , Stanback Mark T , Moore Ignacio T , Bonier Fran
Published: January 2018

Studies of animal behavior often rely on human observation, which introduces a number of limitations on sampling. Recent developments in automated logging of behaviors make it possible to circumvent some of these problems. Once verified for efficacy and accuracy, these automated systems can be used to determine optimal sampling regimes for behavioral studies. Here, we used a radio-frequency identification (RFID) system to quantify parental effort in a bi-parental songbird species: the tree swallow (Tachycineta bicolor). We found that the accuracy of the RFID monitoring system was similar to that of video-recorded behavioral observations for quantifying parental visits. Using RFID monitoring, we also quantified the optimum duration of sampling periods for male and female parental effort by looking at the relationship between nest visit rates estimated from sampling periods with different durations and the total visit numbers for the day. The optimum sampling duration (the shortest observation time that explained the most variation in total daily visits per unit time) was 1h for both sexes. These results show that RFID and other automated technologies can be used to quantify behavior when human observation is constrained, and the information from these monitoring technologies can be useful for evaluating the efficacy of human observation methods.
A new direction for Soundscape Ecology? Toward the extraction and evaluation of ecologically-meaningful soundscape objects using sparse coding methods
Authors: Eldridge Alice C , Casey Michael , Moscoso Paola , Peck Mika
Published: January 2018

Efficient methods of biodiversity assessment and monitoring are central to ecological research and crucial in conservation management; technological advances in remote acoustic sensing inspire new approaches. In line with the emerging field of Soundscape Ecology (Pijanowski et al., 2011), the acoustic approach is based on the rationale that the ecological processes occurring within a landscape are tightly linked to and reflected in the high-level structure of the patterns of sounds emanating from those landscapes – the soundscape. Rather than attempting to recognise species-specific calls, either manually or automatically, analysis of the high-level structure of the soundscape tackles the problem of diversity assessment at the community (rather than species) level (Pijanowski et al., 2011; Farina, 2014). Preliminary work has attempted to make a case for community-level acoustic indices (e.g. Pieretti et al., 2011; Farina, 2014; Sueur et al., 2008); existing indices provide simple statistical summaries of the frequency or time domain signal. We suggest that under this approach, the opportunity to analyse spectro-temporal structural information is diminished, limiting power both as monitoring and investigative tools. In this paper we consider sparse-coding and source separation algorithms (SIPLCA-2D) as a means to access and summarise ecologically-meaningful sound objects. In doing so we highlight a possible new approach for understanding and assessing ecologically relevant interactions within the conceptual framework of Soundscape Ecology.
A New Method for Ecoacoustics? Toward the Extraction and Evaluation of Ecologically-Meaningful Sound Objects using Sparse Coding Methods
Authors: Eldridge Alice C , Casey Michael , Moscoso Paola , Peck Mika
Published: January 2018

Efficient methods of biodiversity assessment and monitoring are central to ecological research and crucial in conservation management. Technological advances in remote acoustic sensing inspire new perspectives in ecology: environmental sound monitoring is emerging as a reliable non-invasive proxy for ecological complexity (Sueur and Farina, 2015). Rather than attempting to recognise species-specific calls, either manually or automatically, we are interested in monitoring the global acoustic environment, tackling the problem of diversity assessment at the community (rather than species) level. Preliminary work has attempted to make a case for community-level acoustic indices (e.g. Pieretti et al., 2011; Farina, 2014; Sueur et al., 2008b) which provide simple statistical summaries of the frequency or time domain signal. We suggest that under this approach, the opportunity to analyse spectro-temporal structural information is diminished, limiting their power both as monitoring and investigative tools. In this paper we consider sparse-coding and source separation algorithms (specifically, shift-invariant probabilistic latent component analysis in 2D) as a means to access and summarise ecologically-meaningful sound objects. In doing so we highlight a possible new approach for understanding and assessing ecologically relevant interactions within the conceptual framework of ecoacoustics.
Intron gain by tandem genomic duplication: a novel case and a modification of the traditional model
Authors: Ma Ming-Yue , Niu Deng-Ke
Published: January 2018

Origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. Recently gained introns would be especially useful for the study of the mechanism(s) of intron gain because the evolutionary traces might have not been erased by randomly accumulated mutations. However, the mechanism(s) of intron gain remain unclear due to the presence of a few solid cases. A widely cited model of intron gain is tandem genomic duplication, in which the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. However, successful recognition and splicing of an intron require many more signals than those at the two splicing sites. We found that the second intron of the potato RNA-dependent RNA polymerase gene PGSC0003DMG402000361 is absent in the orthologous genes of other Solanaceae plants, and sequence similarity showed that the major part of the new intron is a direct duplication of the 3' side of the upstream intron. In addition to the new intron, a downstream exonic segment of 168bp has also been duplicated. Most of the splicing signals were inherited from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3' splicing site, two putative exonic splicing enhancers and the GC contents differentiated between the intron and exon. We propose a modified version of the tandem genomic duplication model, termed as the partial duplication of the preexisting intron/exon structure.
Summertime dosage-dependent hypersensitivity to an angiotensin II receptor blocker
Authors: Forsdyke Donald R
Published: January 2018

Summertime dips in blood pressure (BP), both in normotensive and hypertensive subjects, are well known. However, the dips are small and are not related to particular forms or doses of antihypertensive medication. Nevertheless it is the practice in some quarters to decrease antihypertensive medication in summer, and/or increase in winter. Large scale studies being inconclusive, there are calls for long-term examination of the relationship between environmental temperature and blood pressure in single individuals under medication. While analyzing data from a subject whose BP had been controlled for a decade with the angiotensin-II receptor blocker losartan, an extreme, dosage-dependent, summertime dip came to light. Downward dosage adjustment appeared essential and may have prevent hypotension-related pathology. The benefits of aggressive medication (the “J curve” phenomenon) being debated, the possibility of seasonal hypersensitivity, explicable in terms of differential signaling by countervailing receptors, should be taken into account when considering dosage adjustments in hypertensive subjects.
The impact of test case summaries on bug fixing performance: An empirical investigation
Authors: Panichella Sebastiano , Panichella Annibale , Beller Moritz , Zaidman Andy , Gall Harald C
Published: January 2018

Automated test generation tools have been widely investigated with the goal of reducing the cost of testing activities. However, generated tests have been shown not to help developers in detecting and finding more bugs even though they reach higher structural coverage compared to manual testing. The main reason is that generated tests are difficult to understand and maintain. Our paper proposes an approach, coined TestScribe, which automatically generates test case summaries of the portion of code exercised by each individual test, thereby improving understandability. We argue that this approach can complement the current techniques around automated unit test generation or search-based techniques designed to generate a possibly minimal set of test cases. In evaluating our approach we found that (1) developers find twice as many bugs, and (2) test case summaries significantly improve the comprehensibility of test cases, which is considered particularly useful by developers.
Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
Authors: Messiha Hanan L. , Kent Edward , Malys Naglis , Carroll Kathleen M. , Mendes Pedro , Smallbone Kieran
Published: January 2018

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.
Time-of-day effects in implicit associations are probably selection effects, not circadian rhythms
Authors: Schofield Timothy P
Published: January 2018

Time-of-day effects in human psychological functioning have been known of since the 1800s. However, outside of those specifically focused on the quantification of circadian rhythms, they have largely been neglected. Moves toward online data collection now mean that psychological investigations take place around the clock, which affords researchers the ability to easily study time-of-day effects. Recent analyses have shown, for instance, that implicit attitudes have time-of-day effects. The plausibility that these effects indicate circadian rhythms rather than selection effects is considered in the current study. There was little evidence that the time-of-day effects in implicit attitudes shifted appropriately with factors known to influence circadian rhythms, and even variables that cannot logically show circadian rhythms demonstrated stronger time-of-day effects than did implicit attitudes. Taken together, these results suggest that time-of-day effects in implicit attitudes are more likely to represent selection effects rather than circadian rhythms, but do not rule out the latter possibility.
Discovery of a few photosynthesis models through red light absorbance-transmittance of the e1 leaf sectors of newly bred hybrids of maize (Zea mays L.)
Authors: Adhikari Nav Raj , Ghimire Surya Kant , Sah Shrawan Kumar , Koirala Keshab Babu
Published: January 2018

Background: Pipeline hybrids of maize must be evaluated very intensively and from several perspectives in order to extract reliability of success of the hybrids in farmers’ field before their release as cultivars and to extract some useful physiology preferably photosynthesis, source-sink relationship and tolerance of green LS (leaf sectors) under biotic and abiotic stresses as scientists’ bonus. For it, five pipeline single cross hybrids of yellow maize have been examined from the standpoint of photosynthetic potentiality of central leaf and nutrient mobilization from it to ear for grain fill. Materials and methods: Just above ear (e1) leaf have been minutely examined through ratio of absorbance to transmittance of red light of 650 nm (RAT) measure, chl and N concentration (conc). From correlation coefficients (r) computed between frequency of LS of varying RAT SPAD (Soil Plant Analysis and Development) measures, chl and N conc; few photosynthetic models have been proposed to explain leaf physiologies and its effects on grain yields. Results and discussions: Through analysis of frequency distribution of RAT measures and r between frequency of LS of varying RAT SPAD measure and grain yield, RATA Makai model has been proposed to explain for a variety of efficiency of antennae to harvest light energy especially red photons and transfer the energy to reaction centers (RCs). It includes two types of classification of antenna. Next is diversity model to explain existence of four types leaf sector such as narrow, medium, wide diversity with least bad LS in central leaf of the maize based on photosynthetic efficiency of variety of the photosynthetic e1 LS that they are differentially contributing to grain yields. This sort of LS diversity study helps classify character of LS based on RAT and or chl and N conc. A few more models proposed in it are NARC (Nitrogen Concentration in Antenna and Reaction Centers) and PAY (Protein Amounts and its effects on Yield) based on r between grain yield and leaf N and protein amounts. In addition; strong positive r has been found between grain yields and the frequencies of the LS of 46-52 RAT SPAD; 46-56 µg cm-2 of chl conc and 2-2.3% N of dry weight; This way, we proposed about threshold and upper limit of the RAT SPAD, chl and N conc in maize leaves. It implies that cells in these ranges are genotype based multiplicative and physiologically active and competent to make their identity in the e1 leaf of the hybrids for GY contribution. In addition, next model of ‘green car’ with the four kinds of proportion of green and carotenoid (car) conc: high green-high car to produce high grain yield and remaining proportion such as high green-low car, low green-high car and low green-low car on maize leaves to cause low grain yield has been proposed. Concept of high green-low car conc in maize leaf gives extended model of no car-no food.
Cockroaches join the fight against infection: an improved insect host system for Francisella tularensis
Authors: Eklund Bridget E , Gilson Tricia Nathan , Mahdi Osama , Huntley Jason F , Horzempa Joseph , Fisher Nathan A
Published: January 2018

Francisella tularensis is a zoonotic bacterial pathogen that causes severe disease in a wide range of host animals, including humans. Well-developed murine models of F. tularensis pathogenesis are available, but they do not meet the needs of all investigators. Instead, researchers are increasingly turning to insect host systems to: (1) allow high-throughput that is cost-prohibitive or ethically-questionable in mammals; (2) enable studies of host-pathogen interactions when mammalian facilities are unavailable; and (3) provide valuable information about environmental persistence and transmission. However, the utility of previously-described insect hosts is limited because of temperature restriction, short lifespans, and concerns about the immunological status of insects mass-produced for other purposes. Here, we present a novel host species, the orange spotted (OS) cockroach (Blaptica dubia), that overcomes these limitations and is readily infected by F. tularensis. Intrahemocoel inoculation was accomplished using standard laboratory equipment and lethality was directly proportional to the number of bacteria injected. Disease progression differed in insects housed at low and high temperatures, a pattern indicative of a switch between virulence and transmission phenotypes. As in mammalian hosts, F. tularensis mutants lacking key virulence components were attenuated in OS cockroaches. Finally, antibiotics were delivered to infected OS cockroaches by systemic injection and controlled feeding; in the latter case, protection correlated with oral bioavailability in mammals. Collectively, these results demonstrate that this new host system should facilitate discovery of factors that control F. tularensis virulence, immune evasion, and transmission while also providing a platform for early stage drug discovery and development.
Direct numerical simulation of transitional pulsatile stenotic flow using Lattice Boltzmann Method
Authors: Jain Kartik
Published: January 2018

In the present work, I perform direct numerical simulations of pulsatile flow through a 75% eccentric stenosis using the Lattice Boltzmann Method. The stenosis was studied by Varghese et al. (2007b) in a benchmark computation and the goal of this work is to validate the LBM solver Musubi for transitional flows in anatomically realistic geometries. Whereas most of the study reproduces and compares simulation results from Musubi against the benchmark, the latter part quantifies the Kolmogorov micro-scales and discusses the role of space and time resolutions for the simulation of a transitional flow. The LBM results show an excellent agreement with the previously published results thereby increasing confidence on our Musubi solver for the simulation of transitional flows. The aim of this study is not to compare the computational efficiency of the code or the method but only the physics of the flow.
FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models
Authors: Christensen Anders Steen , Hamelryck Thomas , Jensen Jan H
Published: January 2018

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.
The predictability of mixture toxicity of demethylase inhibiting fungicides to Daphnia magna depends on life-cycle parameters
Authors: Hassold Enken , Backhaus Thomas
Published: January 2018

A variety of different fungicides is found simultaneously in surface waters, among which demethylase inhibitors (DMIs) are a major group. The joint toxicity of four DMIs from different chemical classes (Fenarimol, Prochloraz, Triadimefon and Pyrifenox) was investigated in the reproduction test with Daphnia magna, following an extended protocol according to ISO 10706. We assessed the toxicity of the DMI mixtures across different endpoints and effect levels and evaluated the predictability of their joint action using Concentration Addition (CA) and Independent Action (IA). The mixture reduced fecundity, delayed molting and caused characteristic malformations in offspring in a concentration-dependend manner which is possibly due to an anti-ecdysteroid action, as previously described for individual DMIs. However, also mixture-specific effects were observed: exposed daphnids reached sexual maturity already after the third juvenile molt, and thus significantly earlier than unexposed daphnids, which needed four juvenile molts to reach maturity. This effect is not caused by any of the DMIs alone. Additionally, the percentage of aborted broods was synergistically higher than expected by either CA or IA. IA underestimates the mixture toxicity for all parameters. The predictive quality of CA differed between life history responses, but was always within a factor of two to the observed toxicity. The parameter “fecundity reduction, counting only normally developed offspring” was the most sensitive endpoint, while the parameter “fecundity reduction, counting all living offspring” was slightly less sensitive. The mixture caused a 90% reduction in fecundity at individual concentrations that only provoke 7% effect or less, which calls for a mixture-specific toxicity assessment of DMI fungicides.
Morphometric variation of extant platyrrhine molars: taxonomic implications for fossil platyrrhines
Authors: Nova Delgado Mónica , Galbany Jordi , Pérez-Pérez Alejandro
Published: January 2018

The phylogenetic position of many fossil platyrrhines with respect to extant ones is not yet clear. Two main hypotheses have been proposed: the layered or successive radiations hypothesis suggests that Patagonian fossils are Middle Miocene stem platyrrhines lacking modern descendants, whereas the long lineage hypothesis argues for an evolutionary continuity of all fossil platyrrhines with the extant ones. Our geometric morphometric analysis of a 15 landmark-based configuration of platyrrhines' first and second lower molars suggest that morphological stasis, may explain the reduced molar shape variation observed. Platyrrhine lower molar shape might be a primitive retention of the ancestral state affected by strong ecological constraints thoughout the radiation the main platyrrhine families. The Patagonian fossil specimens showed two distinct morphological patterns of lower molars, Callicebus -like and Saguinus -like, which might be the precursors of the extant forms, whereas the Middle Miocene specimens, though showing morphological resemblances with the Patagonian fossils, also displayed new, derived molar patternss, Alouatta- like and Pitheciinae -like, thereby suggesting that despite the overall morphological stasis of molars, phenotypic diversification of molar shape was already settled during the Middle Miocene.
A simple, sufficient, and consistent method to score the status of threats and demography of imperiled species
Authors: Malcom Jacob W , Webber Whitney M , Li Ya-Wei
Published: January 2018

Managers of large wildlife conservation programs need information on the conservation status of each of many species to strategically allocate limited resources. Oversimplified status data, however, runs the risk of missing information essential to strategic allocation. Conservation status consists of two components, the status of threats a species faces and the species’ demographic status. Neither component alone is sufficient to characterize conservation status. Here we present a simple key for scoring threat and demographic changes for species using detailed information provided in free-form textual descriptions of conservation status. Importantly, this key applies equally to any taxon and can be used where quantitative trend data for threats or demography is sparse. We scored the threat and demographic status of 37 species recently recommended for reclassification under the Endangered Species Act by the U.S. Fish and Wildlife Service (FWS) and 15 control (not recommended for reclassification) species. We then compared the threat and demographic status scores to two metrics that FWS uses for their decision-making and reports to Congress: the reclassification recommendation and the recovery priority numbers (RPNs). While the metrics reported by FWS are often consistent with our scores for 52 species analyzed, our analyses highlight two problems with the oversimplified metrics. First, we show that both metrics can mask underlying demographic declines or threat increases; for example, ~40% of species not recommended for reclassification had changes in threats or demography. Second, we show that neither metric is consistent with either threats or demography alone, but conflates the two. We propose that large conservation programs, such as FWS’s Endangered Species program, adopt our simple scoring system for threats and demography. By doing so, program administrators will have better information to monitor program effectiveness and guide their decisions.
Animal-oriented Virtual Environments: illusion, dilation, and discovery
Authors: Alicea Bradly
Published: January 2018

As a research tool, virtual environments hold immense promise for brain scientists. Yet to fully realize this potential in non-human systems, theoretical and conceptual perspectives must be developed. When selectively coupled to nervous systems, virtual environments can help us better understand the functional architecture of animals’ brains during naturalistic behaviors. While this will no doubt allow us to further our understanding of the neural basis of behavior, there is also an opportunity to uncover the diversity inherent in brain activity and behavior. This is due to two properties of virtual environments: the ability to create sensory illusions, and the ability to dilate space and/or time. These and other potential manipulations will be characterized as the effects of virtuality. These effects and their usefulness for brain science will be understood in the context of three types of neurobehavioral phenomena: sensorimotor integration, spatial navigation, and interactivity. For each of these behaviors, a combination of illusory and time dilation examples will be reviewed. Once these examples are presented, the implications for improving upon virtual models for more directly inducing the mental phenomena of illusion and time dilation will be considered. To conclude, future directions for integrating this research area into broader biological inquiry will be presented.
Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
Authors: Davis Edward W , Weisberg Alexandra J , Tabima Javier F , Grunwald Niklaus J. , Chang Jeff
Published: January 2018

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, are important for disease management. Developments in molecular methods have contributed to increasing the resolution for accurate pathogen identification but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
Intrabasin Floral Differences in the Sonoran Desert; a case study from the Casa Grande Valley
Authors: Gay Robert J , Garcia Gabriela , Gabriele Sarah , Cowgill Benjamin , Rodriguez Xavier
Published: January 2018

Background: The purpose of this study was to determine what floral differences exist in North Mountain Park and Casa Grande Mountain Park which are both located on opposite sides of the Casa Grande Valley, Pinal County, Arizona and to attempt to explain any measured differences. Previous authors have proposed several explanations for floral variation within the Sonoran Desert including elevation, soil pH, and mineral content. This study explicitly tests several of these proposed mechanisms for determining community composition. Methods: The floral composition was measured in both North Mountain Park and Casa Grande Mountain Park through a series of transects which were sampled by multiple times in 2012 and 2013. Elevation data soil pH were also sampled. Results: The data recovered from North Mountain Park differed from the expected values in Casa Grande Mountain Park by 22%. This indicates a significant difference in the flora between these two localities that was not predicted by earlier studies. Elevation and soil pH differences between sampled localities were not significant. This suggests that mineral composition of the soil may play an important role within this basin in determining community composition. Discussion: Many factors that have been proposed in prior studies do not appear to play a significant role within the Casa Grande Valley in determining community composition. This indicates that the composition of a community is influenced by different factors in different locations within the Sonoran Desert. This makes determining overall controlling factors across an ecosystem difficult.
Preliminary evidence of a new microbial species capable of sustainable intracellular survival and transfer in mammalian cell lines
Authors: Barkwan Salwa , Rasheed Haroon , Spoloso Oladimejii
Published: January 2018

The minimisation of exposure of mammalian cell lines to potential microbial contaminants is handled by routine adherence to quality laboratory procedures. Mycoplasma, are capable of sustainable intracellular existence, are not v isible in light microscopy and must be tested for using dedicated methods. Bacterial contamination is usually detectable by relatively simple optical, spectroscopy and pH methodology. Symbiont occupation assumes an evolved mutually beneficial relationship and does occur with many eukaryote-prokaryotes, but rarely mammals. Other, purely intracellular low density, low energy and relatively stable and non-visible bacterial occupation of mammalian cytoplasm, assumes the existence of new intra-genus relationships and associated mechanisms. In this study, preliminary microscopy and sequence data has been collated implying the presence of low density Cocci in the cytoplasm of hepatocyte lines with negligible impact on cell function and behaviour.
A novel rapid assay for evaluating the efficacy of biocides to inhibit the development of marine photoautotrophic biofilms
Authors: Arrhenius Åsa , Backhaus Thomas , Hilvarsson Annelie , Wendt Ida , Zgrundo Aleksandra , Blanck Hans
Published: January 2018

In this paper a novel settlement and growth assay is presented that uses field-collected marine photoautotrophic biofilms as inoculum. The multitude of indigenous species that are the potential foulers aretherefore included in the assay, which overcomes the limitation of testing only those species that can be cultivated in the laboratory. The assay was evaluated using eight antifouling biocides. The methodological considerations are discussed thoroughly and full concentration response curves are presented for all testedbiocides. The efficacy ranking based on EC 98 values from the most to the least efficacious compound is as follows: copper pyrithione > TPBP > DCOIT > tolylfluanid > zinc pyrithione > medetomidine > copper (Cu 2+ ). The algaecide irgarol did not cause a full inhibition of settlement and growth but the inhibition leveled out at 95% already at 30 nmol l -1 , at a concentration that is clearly lower than for any other of the tested biocides.
Adeno-associated virus Type 2 Rep proteins mediate integration of lentiviral vectors
Authors: McAlister Victor J , Craig Anthony T , Owens Roland A
Published: January 2018

Aims: Adeno-associated virus type 2 (AAV2) is a naturally defective human parvovirus that is being developed as a gene therapy vector. In dividing cells, AAV2 DNA persists by integration into the host chromosomes. AAV2 is unique among mammalian viruses in its ability to integrate preferentially into a particular locus within human chromosome 19, designated AAVS1(also known as Mbs 85). The AAV2 Rep68 and Rep78 proteins mediate this integration. Recent data suggest that Rep68 and Rep78 can mediate integration of non-AAV2 DNA with free ends. To test this hypothesis, we targeted insertion of different lentiviral vectors to AAVS1. Methods: Cells were co-infected with wild-type AAV2, and integrase-proficient or integrase-deficient lentivirus vectors. A highly specific PCR-based assay was used to detect lentivirus integration at AAVS1. Similar experiments were performed using lentiviral vectors containing the AAV2 rep gene. Results: All lentiviral vectors tested integrated at AAVS1, if the rep gene was present either within the lentiviral vector or supplied in trans. All that was required for integration at AAVS1 was the amino acid sequence shared between Rep68 and Rep78. The results were similar with integrase-proficient or integrase-deficient lentiviral vectors. Conclusions. The inclusion of the rep gene with lentiviral vectors may produce more predictable integration patterns.
Effect of mutualist partner identity and fidelity on plant demography
Authors: Bruna Emilio M , Izzo Thiago J , Inouye Brian D , Vasconcelos Heraldo L
Published: January 2018

Mutualisms play a central role in the origin and maintenance of biodiversity. Because many mutualisms have strong demographic effects, interspecific variation in partner quality could have important consequences for population dynamics. Nevertheless, few studies have quantified how a mutualist partner influences population growth rates; still fewer have compared the demographic impacts of multiple partner species. We used integral projection models parameterized with multi-year census data to compare the demographic effects of two ant species – Crematogaster laevis and Pheidole minutula – on the Amazonian ant-plant Maieta guianensis. Estimated population growth rates were positive (i.e., λ>1) for all ant-plant combinations. However, populations with only Pheidole minutula had the highest asymptotic growth rate (λ=1.23), followed by those colonized by Crematogaster laevis (λ=1.16), and in which the partner ant alternated between C. laevis and P. minutula at least once during our study (λ=1.15). Our results indicate that the short-term superiority of a particular mutualist partner can translate into long-term demographic benefits, and that there is a demographic cost to switching between alternative mutualist partners. Our results underscore the importance of expanding the study of mutualisms beyond the study of pair-wise interactions to consider the demographic costs and benefits of interacting with different potential partners.
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Authors: Warden Charles D , Adamson Aaron W , Neuhausen Susan L , Wu Xiwei
Published: January 2018

The Genome Analysis Toolkit (GATK) is often considered to be the “gold standard” for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but we felt that an adequate comparison against VarScan may have not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (>97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also accessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in accessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Authors: Warden Charles D , Adamson Aaron W , Neuhausen Susan L , Wu Xiwei
Published: January 2018

The Genome Analysis Toolkit (GATK) is often considered to be the “gold standard” for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an adequate comparison against VarScan may have not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (>97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also accessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in accessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.
Allogenic stem cell transplant in a patient with classical Kaposi's sarcoma
Authors: Barchas Richard
Published: January 2018

A 68 year old male with a history of classical Kaposi's sarcoma (KS) and precursor T-cell acute lymphoblastic leukemia (ALL) received an allogenic stem cell transplant from an unrelated donor to treat his ALL. He developed acute graft-vs.-host-disease (GVHD) which was treated by increasing immunosuppressants. KS, which had been in remission for years, then recurred aggressively. Tapering immunosuppressants to treat the KS was not possible because of GVHD. Chemotherapy could not be used because of its adverse effect on the bone marrow so soon after transplant. The only option was to use antiviral therapy (cidofovir) to lower the level of HHV-8, the virus that is a causal factor in KS. Although HHV-8 levels were significantly reduced, new KS lesions continued to appear. The patient developed acute kidney injury after the third cidofovir infusion and died from renal and respiratory failure soon afterward. Post-mortem revealed extensive internal KS lesions involving multiple organs. Based on the experience with this patient, allogenic transplant using an unrelated donor has been found to be a questionable treatment modality for classical KS patients requiring treatment for another condition such as leukemias and lymphomas. Post-transplant immunosuppression is required to prevent GVHD, and if it occurs, immunosuppression may have to be increased. Aggressive KS developed in this patient under these conditions, and could not be controlled by tapering immunosuppressants. Although the risk of GVHD is lower for an allogenic transplant using a matched sibling instead of an unrelated donor, the risk of both GVHD and aggressive KS both developing may still be unacceptably high.Alternative treatment modalities for these patients might include continuing with chemotherapy and autologous transplant. These avoid GVHD and lower the need for long term immunosuppression, but have a much higher risk of relapse of the underlying malignancy. Still, they could be preferable to an allogenic transplant for such cases.
Language workbench user interfaces for data analysis
Authors: Benson Victoria M , Campagne Fabien
Published: January 2018

Biological data analysis software is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Dataflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with the dataflow abstraction, and that do not require specialized user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that cannot be directly expressed with the dataflow model. In contrast, we show here that Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/).
Models of knot and stem development in black spruce trees indicate a shift in allocation priority to branches when growth is limited
Authors: Duchateau Emmanuel , Auty David , Mothe Frédéric , Longuetaud Fleur , Ung Chhun Huor , Achim Alexis
Published: January 2018

The branch autonomy principle, which states that the growth of individual branches can be predicted from their morphology and position in the forest canopy irrespective of the characteristics of the tree, has been used to simplify models of branch growth in trees. However, observed changes in allocation priority within trees towards branches growing in light-favoured conditions, referred to as ‘Milton’s Law of resource availability and allocation’, have raised questions about the applicability of the branch autonomy principle. We present models linking knot ontogeny to the secondary growth of the main stem in black spruce (Picea mariana (Mill.) B.S.P.), which were used to assess the patterns of assimilate allocation over time, both within and between trees. Data describing the annual radial growth of 445 stem rings and the three-dimensional shape of 5377 knots were extracted from optical scans and X-ray computed tomography images taken along the stems of 10 trees. Total knot to stem area increment ratios (KSR) were calculated for each year of growth, and statistical models were developed to describe the annual development of knot diameter and curvature as a function of stem radial increment, total tree height, stem diameter, and the position of knots along an annual growth unit. KSR varied as a function of tree age and of the height to diameter ratio of the stem, a variable indicative of the competitive status of the tree. Simulations of the development of an individual knot showed that an increase in the stem radial growth rate was associated with an increase in the initial growth of the knot, but also with a shorter lifespan. Our results provide support for ‘Milton’s Law’, since they indicate that allocation priority is given to locations where the potential return is the highest. The developed models provided realistic simulations of knot morphology within trees, which could be integrated into a functional-structural model of tree growth and above-ground resource partitioning.
Self-generated morphology in lagoon reefs
Authors: Blakeway David , Hamblin Michael G
Published: January 2018

The shapes and forms of coral reefs are generally attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. A spectrum of realistic reef forms can be generated by varying a single parameter representing this characteristic. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. Inherent reef growth forms are best expressed in sheltered lagoons. The purest forms arise where a single type of reef builder prevails, as in the cellular reefs of the Abrolhos. In these cases reef morphology can be considered a phenotype of the predominant reef building organism.
A Research data Sharing Game
Authors: Pronk Tessa E , Wiersma Paulien H , van Weerden Anne
Published: January 2018

While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. For individuals, it is less obvious that the benefits of sharing data outweigh the associated costs, i.e. time and money. In this sense the problem of data sharing resembles a typical game in interactive decision theory, more commonly known as game theory. Within this framework we analyse in this paper how different measures to promote sharing and reuse of research data affect sharing and not sharing individuals. We find that the scientific community can benefit from top-down policies to enhance sharing data even when the act of sharing itself implies a cost. Namely, if (almost) everyone shares, many individuals can gain a higher efficiency as datasets can be reused. Additionally, measures to ensure better data retrieval and quality can compensate for sharing costs by enabling reuse. Nevertheless, an individual researcher who decides not to share omits the costs of sharing. Assuming that the natural tendency will be to use a strategy that will lead to maximisation of individual efficiency it is seen that, as more individuals decide not to share, there is a point at which average efficiency for both sharing and non-sharing researchers becomes lower than was originally the case and scientific community efficiency steadily drops. With this in mind, we conclude that the key to motivate the researcher to share data lies in reducing the costs associated with sharing, or even better, turning it into a benefit.