bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the stability of homologous gene duplications in a plant RNA virus
Authors: Willemsen Anouk , Zwart Mark P. , Higueras Pablo , Sardanyés Josep , Elena Santiago F. 
Published: June 2016

AbstractOne of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The low prevalence of gene duplication in RNA viruses most likely reflects the strong selective constraints against increasing genome size. Here we investigated the stability of genetically redundant sequences and how adaptive evolution proceeds to remove them. We generated plant RNA viruses with potentially beneficial gene duplications, measured their fitness and performed experimental evolution, hereby exploring their genomic stability and evolutionary potential. We found that all gene duplication events resulted in a loss of viability or significant reductions in fitness. Moreover, upon evolving the viable viruses and analyzing their genomes, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration, the size of the gene and the position for duplication. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that the fitness of viruses with duplications is not enough information to predict genomic stability as a recombination rate dependent on the genetic context – the duplicated gene and its position – is also required. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses, and we identify factors that constrain the maintenance of duplicated genes.
Coevolutionary Dynamics of Costly Bonding Ritual and Altruism
Authors: Frost Karl 
Published: June 2016

AbstractWhile altruistic behavior and bonding in altruistic pairs or groups of cooperators is observed throughout the animal kingdom, the genetic evolution of such is on an ongoing source of debate, curiosity, and conflict in the behavioral sciences. Many such bonded groups and pairs are observed to take part in costly ritualized movement behavior that is hypothesized to trigger or maintain altruistic sentiments amongst the participants. Such costly ritualized practices could have evolved if they engaged pre-existing behavioral instincts that manifest as altruism in the new context of ritual bonding. While this seems at first to be a ‘Green Beard’ hypothesis (‘marker (ie., ‘green beard’) as honest signal of altruistic intent', an hypothesis well-known to be problematic), it is distinct in two important ways. First, the ritual as marker is costly, and second the ritual engages a pre-existing behavioral potential caused by genes which, importantly, have some other benefit. This paper models the genetic coevolutionary dynamics both analytically and through simulation. It finds that such coevolution can lead to fixation of altruism in a population or to cycling of altruism in the population, depending on the balance of costs and benefits. Where cycling occurs, even though altruism is consistently present in the population, population mean fitness declines with the introduction of these bonding rituals.
16SpeB: Towards defining bacterial species boundaries by intra-species gene sequence identity
Authors: Wong Adam Chun-Nin , Ng Patrick , Douglas Angela E. 
Published: June 2016

ABSTRACTSummary16SpeB (16S rRNA-basedSpeciesBoundary) is a package of Perl programs that evaluates total sequence variation of a bacterial species at the levels of the whole 16S rRNA sequences or single hypervariable (V) regions, using publicly-available sequences. The 16SpeB pipelines filter sequences from duplicated strains and of low quality, extracts a V region of interest using general primer sequences, and calculates sequence percentage identity (%ID) through all possible pairwise alignments.ResultsThe minimum %ID of 16S rRNA gene sequences for 15 clinically-important bacterial species, as determined by 16SpeB, ranged from 82.6% to 99.8%. The relationship between minimum %ID of V2/V6 regions and full-gene sequences varied among species, indicating that %ID species limits should be resolved independently for each region of the 16S rRNA gene and bacterial species.Availability16SpeB and user manual are freely available for download from:https://github.com/pnpnpn/16SpeB. A video tutorial is available at:https://youtu.be/Vd6YmMhyBiAContactcw442@cornell.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Differential stimulation of the retina with glutamate toward a neurotransmitter-based retinal prosthesis
Authors: Rountree Corey M. , Inayat Samsoon , Troy John B. , Saggere Laxman 
Published: June 2016

ABSTRACTSubretinal stimulation of the retina with neurotransmitters, the normal means of conveying visual information, is a potentially better alternative to electrical stimulation widely used in current retinal prostheses for treating blindness from photoreceptor degenerative diseases. Yet, no retinal stimulation study exploiting the inner retinal pathways exists. Here, we demonstrate the feasibility of differentially stimulating retinal ganglion cells (RGCs) through the inner nuclear layer of the retina with glutamate, a primary neurotransmitter chemical, in a biomimetic way. We show that controlled pulsatile delivery of glutamate into the subsurface of explanted wild-type rat retinas elicits highly localized simultaneous inhibitory and excitatory spike rate responses in OFF and ON RGCs. We also present the spatiotemporal characteristics of RGC responses to subretinally injected glutamate and the therapeutic stimulation parameters. Our findings could pave the way for future development of a neurotransmitter-based subretinal prosthesis offering more naturalistic vision and better visual acuity than electrical prostheses.
Employee ownership and firm performance: a meta‐analysis
Authors: O'Boyle Ernest H. , Patel Pankaj C. , Gonzalez‐Mulé Erik 
Published: June 2016

Employee ownership has been an area of significant practitioner and academic interest for the past four decades. Yet, empirical results on the relationship between employee ownership and firm performance remain mixed. To aggregate findings and provide potential direction for future theoretical development, we conducted a meta‐analysis of 102 samples representing 56,984 firms. Employee ownership has a small, but positive and statistically significant relation to firm performance (
= 0.04). The effect is generally positive for studies with different sampling designs (samples assessing change in performance pre‐employee–post‐employee ownership adoption or samples on firms with employee ownership), different performance operationalisation (efficiency or growth) and firm type (publicly held or privately held). Suggesting benefits of employee ownership in a variety of contexts, we found no differences in effects on performance in publicly held versus privately held firms, stock or stock option‐based ownership plans or differences in effects across different firm sizes (i.e. number of employees). We do find that the effect of employee ownership on performance has increased in studies over time and that studies with samples from outside the USA report stronger effects than those within. We also find little to no evidence of publication bias.
Adolescent Women Induce Lower Blood Alcohol Levels Than Men in a Laboratory Alcohol Self‐Administration Experiment
Authors: Jünger Elisabeth , Gan Gabriela , Mick Inge , Seipt Christian , Markovic Alexandra , Sommer Christian , Plawecki Martin H. , O'Connor Sean , Smolka Michael N. , Zimmermann Ulrich S. 
Published: June 2016

BackgroundAdolescence is a critical period for the development of alcohol use disorders; drinking habits are rather unstable and genetic influences, such as male sex and a positive family history of alcoholism (FH), are often masked by environmental factors such as peer pressure.MethodsWe investigated how sex and FH modulate alcohol use in a sample of 18‐ to 19‐year‐olds from the Dresden Longitudinal Study on Alcohol use in Young Adults. Adolescents reported their real‐life drinking in a TimeLine Follow‐Back interview. They subsequently completed a training and an experimental session of free‐access intravenous alcohol self‐administration (i.v. ASA) using the computer‐assisted alcohol infusion system to control for environmental cues as well as for biological differences in alcohol pharmacokinetics. During i.v. ASA, we assessed subjective alcohol effects at 8 time points.ResultsWomen reported significantly less real‐life drinking than men and achieved significantly lower mean arterial blood alcohol concentrations (aBACs) in the laboratory. At the same time, women reported greater sedation relative to men and rated negative effects as high as did men. A positive FH was associated with lower real‐life drinking in men but not in women. In the laboratory, FH was not linked to i.v. ASA. Greater real‐life drinking was significantly positively associated with higher mean aBACs in the laboratory, and all i.v. ASA indices were highly correlated across the 2 sessions.ConclusionsWe conclude that adolescent women chose lower aBACs because they experienced adverse alcohol effects, namely sedation and negative effects, at lower aBACs than men. A positive FH was not apparent as risk factor for drinking in our young sample. The i.v. ASA method demonstrated good external validity as well as test–retest reliability, the latter indicating that a separate training session is not required when employing the i.v. ASA paradigm.
An Archaeomagnetic Study of a Roman Bath in Southern France
Authors: Hammond M. L. , Lanos PH. , Hill M. J. , Colleoni F. 
Published: June 2016

AbstractAbsolute Thellier–Thellier archaeointensity determinations were conducted on 137 tiles and sedimentary blocks from five different structures from the ‘Site de la Molère’, southern France, to constrain the archaeological interpretation of a relative age difference between structures and add new data to the French secular variation database. We present 89 new archaeointensity and 20 new directional results, with averages of 57 (±8) μT in the second century ad and 68 (±7) μT in the third century ad. The overall data trend is consistent with the limited available data, indicating rapidly increasing field intensity from the second to the third century ad.
Multiple drivers of Holocene lake level changes at a lowland lake in northeastern Germany
Authors: Dietze Elisabeth , Słowiński Michał , Zawiska Izabela , Veh Georg , Brauer Achim 
Published: June 2016

Many German lakes experienced significant water level declines in recent decades that are not fully understood due to the short observation period. At a typical northeastern German groundwater‐fed lake with a complex basin morphology, an acoustic sub‐bottom profile was analysed together with a transect of five sediment cores, which were correlated using multiple proxies (sediment facies, μ‐XRF, macrofossils, subfossil Cladocera). Shifts in the boundary between sand and mud deposition were controlled by lake level changes, and hence, allowed the quantification of an absolute lake level amplitude of ~8 m for the Holocene. This clearly exceeded observed modern fluctuations of 1.3 m (AD 1973–2010). Past lake level changes were traced continuously using the calcium‐record. During high lake levels, massive organic muds were deposited in the deepest lake basin, whereas lower lake levels isolated the sub‐basins and allowed carbonate deposition. During the beginning of the Holocene (>9700 cal. a BP), lake levels were high, probably due to final melting of permafrost and dead‐ice remains. The establishment of water‐use intensive Pinus forests caused generally low (3–4 m below modern) but fluctuating lake levels (9700–6400 cal. a BP). Afterwards, the lake showed an increasing trend and reached a short‐term highstand at c. 5000 cal. a BP (4 m above modern). At the transition towards a cooler and wetter late Holocene, forests dominated by Quercus and Fagus and initial human impact probably contributed more positively to groundwater recharge. Lake levels remained high between 3800 and 800 cal. a BP, but the lake system was not sensitive enough to record short‐term fluctuations during this period. Lake level changes were recorded again when humans profoundly affected the drainage system, land cover and lake trophy. Hence, local Holocene water level changes reflect feedbacks between catchment and vegetation characteristics and human impact superimposed by climate change at multiple temporal scales.
Is dipyridamole useful in improving left ventricular systolic and diastolic function in patients with coronary slow flow?
Authors: Suner Arif , Cetin Mustafa 
Published: June 2016

BackgroundCoronary slow flow (CSF) is an angiographic finding characterized by delayed opacification of epicardial coronary arteries without obstructive coronary disease. Previous studies have shown greater impairment of left ventricular (LV) systolic and diastolic function in patients with CSF. We aimed to examine the effect of dipyridamole on these functions.MethodsOur study included 40 patients with CSF and 40 subjects with normal coronary arteries. Conventional echocardiography Doppler imaging (CDI) and tissue Doppler echocardiography imaging (TDI) were used to evaluate LV systolic and diastolic function before and 2 months after treatment with dipyridamole.ResultsUsing CDI, we observed that early diastolic velocity (E) was significantly lower in patients with CSF, while late diastolic velocity (A), E/A ratio, isovolumic relaxation time, and myocardial performance index (MPI) were significantly higher in CSF patients compared with controls. Similarly, while early myocardial velocity (Em) was significantly lower, late myocardial velocity (Am), Em/Am ratio, isovolumic relaxation time (IRT), and MPI were significantly higher in CSF patients according to TDI measurements. Although there was no significant improvement in conventional Doppler parameters, there was significant normalization in tissue Doppler parameters after treatment with dipyridamole.ConclusionLeft ventricular systolic and diastolic function may be negatively affected by CSF. Dipyridamole may improve these functions, especially at the tissue level.
Avoidance of an aposematically coloured butterfly by wild birds in a tropical forest
Authors: DELL'AGLIO DENISE D. , STEVENS MARTIN , JIGGINS CHRIS D. 
Published: June 2016

1. Birds are considered to be the primary selective agents for warning colouration in butterflies, and select for aposematic mimicry by learning to avoid brightly coloured prey after unpleasant experiences. It has long been thought that bright colouration plays an important role in promoting the avoidance of distasteful prey by birds.2. The hypothesis that warning colouration facilitates memorability and promotes predator avoidance was tested by means of a field experiment using distasteful model butterflies. Artificial butterflies with a Heliconius colour pattern unknown to local birds were generated using bird vision models, either coloured or achromatic, and hung in tree branches in a tropical forest. Two sequential trials were conducted at each site to test avoidance by naïve and experienced predators.3. There was a significant reduction in predation in the second trial. Also, coloured models were attacked less than achromatic models. Specifically, coloured butterflies were attacked significantly less in the second trial, but there was no significant decrease in predation on achromatic models.4. The present results imply an important role for colour in enhancing aversion of aposematic butterflies. It has also been demonstrated that previous experience of distasteful prey can lead to enhanced avoidance in subsequent trials, supporting mimicry theory.
Modeling Population Growth and Response to Harvest for River Otters in Illinois
Authors: Nielsen Clayton K. 
Published: June 2016

AbstractPopulation modeling is an invaluable tool for predicting wildlife population dynamics and the effects of management. I created a state‐space population model for unharvested river otters in the Illinois, Kaskaskia, and Wabash river basins in Illinois, and modeled future harvest at 5%, 10%, and 20% levels. River otter populations increased in the absence of harvest during 2000 – 2009 to 8,408 ± 1,934 individuals (λ = 1.11 ± 0.09). Harvest at 0%, 5%, 10%, and 20% levels resulted in continued population growth over time, with annual harvest numbers ranging from 446 – 1,786 in 2010 to 884 – 2,614 in 2014, depending on harvest scenario. I concluded that river otter populations in Illinois were thriving and capable of withstanding a regulated harvest.
Impacts of Pollutants on Beavers and Otters with Implications for Ecosystem Ramifications
Authors: Peterson Elizabeth K. , Schulte Bruce A. 
Published: June 2016

AbstractAnthropogenic pollution has impacted ecosystems and organisms globally. Aquatic freshwater systems are of particular concern because of their importance to human health and livelihoods. Sentinel species can serve as indicators for both individual and population‐level health risks to both wildlife and humans, and therefore facilitate the mitigation and prevention of such contamination. When such species are also keystone species and/or ecological engineers in aquatic ecosystems, understanding the influence of pollutants on their physiology and behavior acquires added importance. Given that river otters (Lontra canadensisandLutra lutra) and beavers (Castor canadensisandC. fiber) serve such roles and are susceptible to a wide‐range of anthropogenic pollution, this makes them prime candidates as indicators or sentinels of aquatic ecosystem health. We review published evidence on the toxicological impacts of pollutants in beavers and river otters and discuss the implications of exposure to their behavioral systems, conservation, and surrounding ecosystem.
New Evidence of the Semi‐Aquatic Nimba Otter Shrew (Micropotamogale lamottei) at Mount Nimba and in the Putu Range of Liberia – Uncertain Future for an Evolutionary Distinct and Globally Endangered (EDGE) Species in the Face of Recent Industrial Developments
Authors: Decher J. , Gray C.R. , Garteh J.C. , Kilpatrick C.W. , Kuhn H.J. , Phalan B. , Monadjem A. , Kadjo B. , Jacquet F. , Denys C. 
Published: June 2016

AbstractNew records of the endemic semi‐aquatic Nimba Otter Shrew Micropotamogale lamottei (Tenrecidae, Potamogalinae) were obtained during recent Environmental Impact Assessments (EIAs) in Liberia. We discuss the future of this Evolutionary Distinct and Globally Endangered (EDGE) species in the face of large‐scale landscape transformations. In an attempt to assess genetic diversity and genetic differentiation of M. lamottei throughout its distributional range, we examined two mitochondrial loci (cytochrome b and 12S rRNA) from five samples of Nimba Otter Shrews at three localities in Liberia and compared the 12S sequences with a GenBank sequence from Côte d'Ivoire. While all six individuals examined had unique mitochondrial haplotypes, the sequence divergence among these haplotypes was less than 1 %. However, the FST values indicated substantial differences between East Nimba and the other two populations. Recognizing that the genetic results are based on very small samples, the data suggest that the three populations experienced sufficient gene flow in the past, preventing sequence divergence, but currently there is substantially reduced gene flow with the East Nimba population. More targeted surveys in the Upper Guinea Region are recommended for this elusive species using aquatic traps in combination with an environmental DNA (eDNA) approach.
Climate predicts the proportion of divaricate plant species in New Zealand arborescent assemblages
Authors: Lusk Christopher H. , McGlone Matthew S. , Overton Jacob McC. 
Published: June 2016

AbstractAimPuzzling features of plants are sometimes explained as legacies of co‐evolution with extinct herbivores. One example is the convergent evolution of a small‐leaved, twiggy ‘divaricate’ form in > 50 woody species in New Zealand. This growth form was first interpreted as a response to the Plio‐Pleistocene onset of frosty, droughty environments, but opinion now favours the hypothesis that it arose as a defence against large herbivorous birds (moa). It has been argued that the extinction of moa during the last millennium has left divaricate plants at risk of being out‐competed by faster growing broadleaved competitors, yet their current abundance in some habitats suggests this growth form might confer other advantages besides protection against avian browsing. We aimed to clarify the adaptive significance of the divaricate growth form by identifying environmental correlates of its geographic distribution in New Zealand.LocationThe main islands of the New Zealand archipelago, spanning latitude c. 34.5–47° S.MethodsWe used generalized additive models to examine the environmental correlates of the proportion of local tree and shrub assemblages contributed by divaricate species, on 1152 0.04 ha plots distributed across a wide range of climate and landforms.ResultsA model with four climatic variables explained 37% of the observed variation. Mean minimum temperature of the coldest month was the single best predictor of the proportion of divaricate species in arborescent assemblages, with annual solar radiation, vapour pressure deficit and annual water deficit also contributing to the final model. Divaricates made their largest contributions to assemblages in the rain shadow of the Southern Alps, on sites with cold winters, low solar radiation and significant vapour pressure deficits, where potential evapotranspiration exceeds precipitation by > 130 mm. No physiographic variables (e.g. slope) contributed to the final model.Main conclusionsThe distribution of divaricate plants suggests they cope with frosty, droughty environments better than most other elements of New Zealand's arborescent flora. This may reflect selection for both (1) physiological resistance to frost and drought and (2) deterrence of herbivores, as climatic constraints on plant growth rates probably leave seedlings exposed for longer to ground‐dwelling browsers. However, the widespread persistence of divaricate plants during the c. 450‐year hiatus between the extinction of moa and the onset of widespread browsing by introduced ungulates suggests that even in the absence of large herbivores, divaricates are well adapted to frosty, droughty environments.