bluuebunny/crossref_metadata_2025 huggingface dataset:
AMAS: a fast tool for alignment manipulation and computing of summary statistics
Authors: Borowiec Marek L
Published: January 2018

The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, and creation of replicate data sets. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It performs better at concatenation and summarizing alignments than other popular tools. AMAS is a Python 3 program that relies solely on Python’s core modules. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/
Study of Gallbladder cancer in the light of proteomics
Authors: Pradhan Arpit , Saha Soham , Ghosh Shyamasree
Published: January 2018

Gallbladder carcinoma (GBC) is a chronic malignancy of the gall bladder and intrahepatic and extrahepatic common bile ducts with a high mortality rate and forms the fifth common cancer of gastrointestinal tract globally. Women remain at higher risk than men and recent studies have reported the highest rate of incidence in women from Delhi, India. GBC treatment suffers from the disadvantage of lack of suitable biomarkers for early diagnosis of the disease. Different proteomic approaches including (i) 2D gel electrophoresis (ii) Mass spectroscopic studies (iii) Isobaric tags for relative and absolute quantization (iTRAQ) -based quantitativeproteomicsstudies are being employed for detection of biomarkers in order to undertake early diagnosis of the disease. In this review we focus on (i) risk factors in GBC, (ii) diagnosis and treatment, (iii) molecular markers, and (iv) proteomic studies in GBC. The future scope of this review lies in the identifying biomarkers of GBC, and may provide directions to unraveling future implications in disease treatment.
The semantic basis of taste-shape associations
Authors: Velasco Carlos , Woods Andy T , Marks Lawrence E , Cheok Adrian David , Spence Charles
Published: January 2018

Previous research shows that people systematically match tastes with shapes. Here, we assessed the extent to which matching taste and shape stimuli share a common semantic space and whether semantically congruent versus incongruent taste/shape associations can influence the speed with which people respond to both shapes and taste words. In Experiment 1, we used semantic differentiation to assess the semantic space of both taste words and shapes. The results suggest a common semantic space containing two principal components (seemingly potency and evaluation) and two principal clusters, one including round shapes and the taste word “sweet”, and the other including angular shapes and the taste words “salty”, “sour”, and “bitter”. The former cluster appears more positively-valenced whilst less potent than the latter. In Experiment 2, two speeded classification tasks assessed whether congruent versus incongruent mappings of stimuli and responses (e.g., sweet with round versus sweet with angular) would influence participants’ speed of responding, both to shapes and to taste words. The results revealed an overall effect of congruence that was driven mostly when the participants had to classify shapes with taste words as responses. These results are consistent with previous evidence suggesting a close relation (or crossmodal correspondence) between tastes and shape curvature that may derive from common semantic coding, perhaps along the sensory-discriminative and hedonic dimensions.
Ecological Distribution of Protosteloid Amoebae in New Zealand
Authors: Zahn Geoffrey , Stevenson Stephen L. , Spiegel Frederick W.
Published: January 2018

During the period of March 2004 to December 2007, samples of aerial litter (dead but still attached plant parts) and ground litter were collected from study sites representing a wide range of latitudes (34° S to 50° S) and a variety of different types of habitats throughout New Zealand (including Stewart Island and the Auckland Islands). The objective was to survey the assemblages of protosteloid amoebae present in this region of the world. Twenty-nine described species of protosteloid amoebae were recorded, along with the heterolobesean acrasid, Acrasis rosea. Of the species recovered, Protostelium mycophaga was by far the most abundant and was found in more than half of all samples. Most species were found in fewer than 10% of the samples collected. Seven abundant or common species were found to display significant preferences for aerial litter or ground litter microhabitats. There was some evidence of a general pattern of a decrease in species richness and diversity with increasing latitude and precipitation and elevation.
Psychophysiology and high-performance cognition - a brief review of the literature
Authors: Cowley Benjamin
Published: January 2018

The psychophysiological method can be used to detect some simple cognitive states such as arousal, attentiveness, or mental workload. This approach can be especially interesting when cognition has some productive purpose, as in knowledge work, and tends to be related to human-computer interaction (HCI). However more interesting for applied purposes are acts of coordinated high-level cognition. High- level (or higher-order) cognition (HLC) is typically associated with decision making, problem solving, and executive control of cognition and action. Further, an intuitive approach for assessing whether someone is engaged in HLC is to measure their performance of a known task. Given this, it is reasonable to define high-performance cognition (HPC) as HLC under some performance restriction, such as real-time pressure or expert skill level. Such states are also interesting for HCI in work, and their detection represents an ambitious aim for using the psychophysiological method. We report a brief review of the literature on the topic.
Odd versus even? An investigation on the impact of number of food items on plating preferences
Authors: Woods Andy T , Michel Charles , Spence Charles
Published: January 2018

We report on the results of a series of large-scale computer-based preference tests (conducted at The Science Museum in London and online) that evaluated for the first time the widely-held belief in kitchens that food should be plated in odd rather than even numbers of elements on the plate in order to maximize the eye appeal of a dish. Participants were presented with pairs of plates of food showing odd versus even number of seared scallops (3 vs. 4), arranged in a line or as a polygon, on either a round or square white plate. No consistent evidence for a preference for 3 or 4 number of food items was found. The implications of these results are discussed.
DNA methylation within intron 2 of the Stat1 gene is reduced in colon tissue from interleukin-10 gene-deficient mice compared with healthy control mice
Authors: Barnett Matthew PG , Russ Anna E , McNabb Warren C , Roy Nicole C
Published: January 2018

Background. Epigenetic influences have been implicated in the development of autoimmunity. While such mechanisms have been linked to mouse models of intestinal inflammation, and to human inflammatory bowel disease (IBD), the involvement of epigenetic mechanisms in the pathogenesis of intestinal inflammation in the interleukin-10 gene-deficient (Il10 –/– ) mouse model of IBD has not yet been reported. This study investigated the hypothesis that changes observed in the expression of Stat1 and Ppara in colon tissue of Il10 –/– mice are associated with differential methylation of CpG sites within key regulatory regions of these genes. Methods. Colon tissue was collected from Il10 –/– and C57BL/6JArc mice at 6 (pre-inflammation) or 12 (established inflammation) weeks of age. Methylation levels of CpG sites within selected regions of the Stat1 and Ppara genes were assessed using MALDI-TOF mass spectrometry in DNA extracted from mouse colon tissue. Results. Methylation of specific CpG sites within intron 2, but not the proximal promoter, of the Stat1 gene was reduced in colon tissue from Il10 –/– mice at 12 weeks of age compared with colon tissue C57BL/6JArc mice at 12 weeks of age. Discussion. These data provide preliminary evidence that DNA methylation is altered in the Il10 –/– mouse model of IBD, and this may be linked with changes in the expression levels of genes that play a key role in inflammation. Further studies are required to confirm these observations, and to establish a causative link between methylation at specific sites (such as intron 2 of Stat1) and gene expression.
Two continents and two names for a Neotropical colletid bee species (Hymenoptera: Colletidae: Neopasiphaeinae): Hoplocolletes ventralis (Friese, 1924)
Authors: Almeida Eduardo A B , Quinteiro Fábio B
Published: January 2018

Neopasiphaeinae bees (Apoidea: Colletidae) are well known for their Amphinotic distribution in the Australian and Neotropical regions. Affinities between colletid taxa in Australia and South America have been speculated for decades, and have been confirmed by recent phylogenetic hypotheses that indicate a biogeographic scenario compatible with a trans-Antarctic biotic connection during the Paleogene. Despite this proximity, no species occurs on both sides of the Pacific Ocean, but the Neotropical species Hoplocolletes ventralis (Friese, 1924), which was described as an Australian taxon due to an error in the specimen labels. This mistake was recognized by C.D.Michener 50 years ago. We herein report that the same labeling problem also happened with Dasycolletes chalceus Friese, 1924, which remained as a tentatively placed species in the Australian genus Leioproctus until now. Moreover, Dasycolletes chalceus is interpreted as a synonym of Dasycolletes ventralis. We also provide a revised diagnosis for Hoplocolletes, describe the male of H. ventralis in detail for the first time, including a comparative study of its genitalia and associated sterna.
Genome-wide identification of hypoxia-induced enhancer regions
Authors: Kamps-Hughes Nick , Preston Jessica L , Randel Melissa A , Johnson Eric A
Published: January 2018

Here we present a genome-wide method for de novo identification of enhancer regions and apply it to find enhancers that have increased activity after hypoxia. The method links fragmented genomic DNA to the transcription of randomer molecule identifiers and measures the functional enhancer activity of the library by massively parallel sequencing. We transfected a Drosophila melanogaster library into S2 cells in normoxia and hypoxia, and assayed 4,599,881 genomic DNA fragments in parallel. The locations of the enhancer regions strongly correlate with genes up-regulated after hypoxia and previously described enhancers. Novel enhancer regions were identified and integrated with RNAseq data and transcription factor motifs to describe the hypoxic response on a genome-wide basis as a complex regulatory network involving multiple stress-response pathways. This work provides a novel method for high-throughput assay of enhancer activity and the genome-scale identification of hypoxia-activated enhancers in Drosophila.
An explicit solution for calculating optimum spawning stock size from Ricker's stock recruitment curve
Authors: Scheuerell Mark D.
Published: January 2018

Ricker’s stock recruitment model is widely used to describe the spawner-offspring relationship for fishes. After model fitting, the spawning stock size that produces the maximum sustainable yield (SMSY), and the harvest corresponding to it (UMSY), are two of the most common biological reference points of interest to fisheries managers. However, to date there has been no explicit solution for either reference point because of the transcendental nature of the equation needed to solve for them. Therefore, numerical or statistical approximations have been used for more than 30 years. Here I provide explicit formulae for calculating both SMSY and UMSY in terms of the productivity and density-dependent parameters from Ricker’s model.
Impact of restricted forward greedy feature selection technique on bug prediction
Authors: Kasinathan Muthukumaran , Neti Lalita Bhanu Murthy
Published: January 2018

Several change metrics and source code metrics have been introduced and proved to be effective in bug prediction. Researchers performed comparative studies of bug prediction models built using the individual metrics as well as combination of these metrics. In this paper, we investigate the impact of feature selection in bug prediction models by analyzing the misclassification rates of these models with and without feature selection in place. We conduct our experiments on five open source projects by considering numerous change metrics and source code metrics. And this study aims to figure out the reliable subset of metrics that are common amongst all projects.
Functional consequences of prey acclimation to ocean acidification for the prey and its predator
Authors: Dupont Sam T , Mercurio Matteo , Giacoletti Antonio , Rinaldi Alessandro , Mirto Simone , D'Acquisto Leonardo , Sabatino Maria Antonietta , Sara Gianluca
Published: January 2018

Ocean acidification is the suite of chemical changes to the carbonate system of seawater as a consequence of anthropogenic carbon dioxide (CO2) emissions. Despite a growing body of evidences demonstrating the negative effects of ocean acidification on marine species, the consequences at the ecosystem level are still unclear. One factor limiting our ability to upscale from species to ecosystem is the poor mechanistic understanding of the functional consequences of the observed effects on organisms. This is particularly true in the context of species interactions. The aim of this work was to investigate the functional consequence of the exposure of a prey (the mussel Brachidontes pharaonis) to ocean acidification for both the prey and its predator (the crab Eriphia verrucosa). Mussels exposed to pH 7.5 for >4 weeks showed significant decreases in condition index and in mechanical properties (65% decrease in maximum breaking load) as compared with mussels acclimated to pH 8.0. This translated into negative consequences for the mussel in presence of the predator crab. The crab feeding efficiency increased through a significant 27% decrease in prey handling time when offered mussels acclimated to the lowest pH. The predator was also negatively impacted by the acclimation of the prey, probably as a consequence of a decreased food quality. When fed with prey acclimated under decreased pH for 3 months, crab assimilation efficiency significantly decreased by 30% and its growth rate was 5 times slower as compared with crab fed with mussels acclimated under high pH. Our results highlight the important to consider physiological endpoints in the context of species interactions.
Towards a standard model for research in agent-based modeling and simulation
Authors: Fachada Nuno , Lopes Vitor V , Martins Rui C , Rosa Agostinho C
Published: January 2018

Agent-based modeling (ABM) is a bottom-up modeling approach, where each entity of the system being modeled is uniquely represented as an independent decision-making agent. ABMs are very sensitive to implementation details. Thus, it is very easy to inadvertently introduce changes which modify model dynamics. Such problems usually arise due to the lack of transparency in model descriptions, which constrains how models are assessed, implemented and replicated. In this paper, we present PPHPC, a model which aims to serve as a standard in agent based modeling research, namely, but not limited to, conceptual model specification, statistical analysis of simulation output, model comparison and parallelization studies. This paper focuses on the first two aspects (conceptual model specification and statistical analysis of simulation output), also providing a canonical implementation of PPHPC. The paper serves as a complete reference to the presented model, and can be used as a tutorial for simulation practitioners who wish to improve the way they communicate their ABMs.
Ten simple rules for digital data storage
Authors: Hart Edmund , Barmby Pauline , LeBauer David , Michonneau François , Mount Sarah , Mulrooney Patrick , Poisot Timothée , Woo Kara H , Zimmerman Naupaka , Hollister Jeffrey W
Published: January 2018

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.
Structure and stability of recombinant bovine odorant-binding protein: II. Unfolding of the monomeric forms
Authors: Stepanenko Olga V , Roginskii Denis O , Stepanenko Olesya V , Kuznetsova Irina M , Uversky Vladimir N , Turoverov Konstantin K
Published: January 2018

In a family of monomeric odorant-binding proteins (OBPs), bovine OBP (bOBP), that lacks conserved disulfide bond found in other OBPs, occupies unique niche because of its ability to form domain-swapped dimers. In this study, we analyzed conformational stabilities of the recombinant bOBP and its monomeric variants, the bOBP-Gly121+ mutant containing an additional glycine residue after the residue 121 of the bOBP, and the GCC-bOBP mutant obtained from the bOBP-Gly121+ form by introduction of the Trp64Cys/His155Cys double mutation to restore the canonical disulfide bond. We also analyzed the effect of the natural ligand binding on the conformational stabilities of these bOBP variants. Our data are consistent with the conclusion that the unfolding-refolding pathways of the recombinant bOBP and its mutant monomeric forms bOBP-Gly121+ and GCC-bOBP are similar and do not depend on the oligomeric status of the protein. This clearly shows that the information on the unfolding-refolding mechanism is encoded in the structure of the bOBP monomers. However, the process of the bOBP unfolding is significantly complicated by the formation of the domain-swapped dimer, and the rates of the unfolding-refolding reactions essentially depend on the conditions in which the protein is located.
Effects of 16S rDNA sampling on estimates of endosymbiont lineages in sucking lice
Authors: Allen Julie M , Burleigh J Gordon , Light Jessica E , Reed David L
Published: January 2018

Co-evolution between insects and their endosymbiotic bacteria can be detected by constructing and comparing their phylogenetic trees. Even though taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships and estimates of the number of endosymbiont lineages within a host group have used only a small percentage of available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. We found that sampling of 16S rDNA sequences affected the estimates of endosymbiont diversity in sucking lice until we reached a threshold of genetic diversity. Sampling by maximizing the diversity of 16S rDNA sequences was more efficient than simply randomly sampling available 16S rDNA sequences. Although simulation results support the finding of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that there is still uncertainty in estimates of the number of endosymbiont origins inferred from 16S rDNA alone.
Is there an association between elongation factor 1-α overdominance in the seastar Pisaster ochraceus and “seastar wasting disease”?
Authors: Wares John , Schiebelhut Lauren
Published: January 2018

In recent years, a massive plague has killed millions of seastars, of many different species, along the Pacific coast of North America. This disease, known as 'seastar wasting disease' (SSWD), is thought to be caused by viral infection. In the affected seastar Pisaster ochraceus, previous work had identified that the elongation factor 1-α locus harbored an intronic insertion allele that is lethal when homozygous yet appears to be maintained at moderate frequency in populations through increased fitness for heterozygotes. The environmental conditions supporting this increased fitness are unknown, but overdominance is often associated with disease. Here, we evaluate seastars from 3 regional populations of P. ochraceus to identify the relationship between SSWD and genotype. Although our data suggest that there may be decreased infection or mortality rates in individuals that are heterozygous at this locus, the effect is small and not statistically significant.
MetaR: simple, high-level languages for data analysis with the R ecosystem
Authors: Campagne Fabien , Digan William ER , Simi Manuele
Published: January 2018

Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast, we applied language workbench technology (LWT) to create a data analysis language, called MetaR, tailored for biologists with no programming experience, as well as expert bioinformaticians and statisticians. A key novelty of this approach is its ability to blend user interface with scripting in such a way that beginners and experts alike can analyze data productively in the same analysis platform. While presenting MetaR, we explain how a judicious use of LWT eliminates problems that have historically contributed to data analysis bottlenecks. These results show that language design with LWT can be a compelling approach for developing intelligent data analysis tools.
Frequency components with negative resistance for intellectual measurement systems
Authors: Krynochkin Roman V
Published: January 2018

The aim of the given paper is a critical analysis of the prospects of further development of the frequency components with negative resistance. The possible and most promising areas of the development of new and improvement of existing frequency components in various technical fields, such as measurement of non-electrical and electrical parameters, the creation of computer systems and components of radio circuits, are shown.The most promising components, the development of which probably has a substantial interest for further improvement of technical and economic parameters of the engineering equipment, is given in a separate group.
Pest suppression by ant biodiversity is modified by pest biodiversity
Authors: Gonthier David J , Kuesel Ryan , Perfecto Ivette
Published: January 2018

Agroecosystems are often complex ecosystems with diverse food webs. Changes in food web complexity may have important context-dependent consequences for pest control strategies. The success of predator introductions to suppress pests may depend on the diversity of pests. For crops with diverse pest assemblages, it is hypothesized that diverse predator communities are needed to suppress diverse pest assemblages below damaging levels. In this study, we compare the ability of ant predator monocultures and polycultures to suppress single- and diverse- (three species) pest assemblages in a coffee foodweb. We use a factorial experiment that compared treatments of predator and pest diversity to understand the impact of pest diversity on multiple predator effects. We show that predator polycultures enhanced pest risk relative to predator monocultures significantly more in the diverse-pest treatment relative to in the single-pest treatments for two of three pest species. Further, we show that pest diversity significantly reduced pest risk in all predator treatments except for the predator polyculture treatment. These results suggest that pest diversity may reduce the efficiency of single predator species at suppressing pest damage, but do not limit multiple predator species. This in turn leads to stronger effects of predator diversity with greater pest diversity. These results highlight the need to consider foodweb complexity, such as pest diversity, when designing and implementing biology control programs.
Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring
Authors: Mártinez-Marqués Adrián , Carleos Carlos Enrique , García-Vazquez Eva , Borrell Pichs Yaisel J.
Published: January 2018

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.
Habitat-of-origin predicts degree of adaptation in urban tolerant birds
Authors: Conole Lawrence E
Published: January 2018

Urban exploiters and adapters are often coalesced under a term of convenience as ‘urban tolerant’. This useful but simplistic characterisation masks a more nuanced interplay between and within assemblages of birds that are more or less well adapted to a range of urban habitats. Furthermore, cues are generally sought in behavioural ecology and physiology for the degree to which particular bird species are predisposed to urban living. The data in this paper are focused on two assemblages characterised as urban exploiters and suburban adapters from Melbourne, Australia. This study departs from the approach taken in many others of similar kind in that urban bird assemblages that form the basis of the work were identified at the landscape scale and from direct data analyses rather than indirect inference. Further, this paper employs a paired, partitioned analysis of exploiter and adapter preferences for points along the urban-rural gradient that seeks to decompose the overall trend into diagnosable parts for each assemblage. In the present paper I test the hypotheses that the distinct urban exploiter and suburban adapter assemblages within the broad urban tolerant grouping in Melbourne vary in their responses within the larger group to predictor variables, and that the most explanatory predictor variables vary between the two assemblages. In the end, habitat-of-origin better predicts degree of adaptation amongst urban tolerant birds.
When charity is outrage: The benefits and pitfalls of incentivized peer review
Authors: Chatterjee Pranab , Seth Bhavna , Price Amy , Steel Graham , Biswas Rakesh
Published: January 2018

Peer review remains the standard method to vet scholarly work and to assess their suitability for publication in academic journals. As the debate about the effectiveness of peer review has taken center stage, it has pushed the peer reviewers out of the limelight. In this article, the authors take a look at the various endeavors undertaken to incentivize the process of peer review. This gives rise to another debate, whether peer review should be incentivized at all, and if it is, then what is the most appropriate method. This article mentions the emerging trends of “pay for peer review” and the moral and ethical implications of this method. The authors also provide possible processes in which a journal, supported by an academic or professional body, may undertake the issue of incentivizing the largely anonymous and un‑credited work of peer reviewers who remain the sentinels of the world of published evidence.
Charity is welcome: The international benefits and pitfalls of peer Review
Authors: Steel Graham , Price Amy , Seth Bhavna , Biswas Rakesh , Chatterjee Pranab
Published: January 2018

Peer review is the traditional method for validating academic work and this process is not without complications. Debates about the way peer reviewing is accomplished, the hazy but sensational world of retractions and the costs of publishing for authors are taking center stage. In no other field do people conceive and build the work, pay for it, inspect it, distribute it and buy it back again for their continued survival. Still after all this investment they can struggle for rights of access. In order to stem the tide of discontent, incentives for peer reviewers were introduced. The authors investigate the many faceted approaches to incentivize the process of peer review and consider what value they add, if any. The authors explore other avenues to benefit the largely anonymous and uncredited work of peer reviewers who remain the sentinels of the world of published evidence.
Multi-token code suggestions using statistical language models
Authors: Santos Eddie A , Hindle Abram
Published: January 2018

We present an application of the naturalness of software to provide multi-token code suggestions in GitHub’s Atom text editor. We extended the results of a simple n-gram prediction model using the "mean surprise" metric—the arithmetic mean of the surprisal of several successive single-token predictions. After an error-fraught evaluation, there is not enough evidence to conclude that Gamboge significantly improves programmer productivity. We conclude by discussing several directions for future research in code suggestion and more using naturalness.
Transcranial direct current stimulation in mild cognitive impairment: methodology for a randomized controlled trial
Authors: Alencastro Aline S , Pereira Danilo A , Brasil-Neto Joaquim P
Published: January 2018

Background: Transcranial direct current stimulation (tDCS) is a non-invasive neuromodulatory technique that has shown encouraging results regarding performance improvement of normal subjects in tests of executive functions. Moreover, when applied repeatedly in daily sessions, tDCS has shown therapeutic potential in various neuropsychiatric disorders. However, there is a need for double-blind, placebo-controlled studies to determine the true therapeutic potential of this portable, low-cost and non-invasive treatment. Mild cognitive impairment (MCI) of the amnestic subtype may evolve into Alzheimer’s dementia (AD) and pharmacological approaches have not been successful in ameliorating symptoms or halting progression to AD. Here we propose a protocol for studying a possible role for tDCS on improvement of MCI symptoms in older patients. Methods/Design: This will be a double-blind, placebo-controlled study of the effects of anodal tDCS over the left dorsolateral prefrontal cortex of patients with MCI. Patients aged 60-90 years will be randomly assigned to either real tDCS or sham stimulation. Twenty-minute real or sham tDCS sessions, 5 days a week, will be performed over the course of two weeks. The Rivermead Behavioural Memory Test (RBMT), California Verbal Learning Test, Rey Verbal Auditory Learning Test (RVALT) and Digit Span (WAIS-IV) will be assessed at baseline, after the first and second weeks of treatment, as well as one and three months after the last tDCS session. The primary outcome will be change in test scores over time. Secondary outcomes will be self-reported memory improvement and possible side effects of tDCS. Discussion: This study will evaluate possible therapeutic applications of tDCS for treatment of MCI. tDCS is a portable and low-cost neuromodulatory technique that has been found to increase performance of both normal subjects and patients in many cognitive tasks. It will also examine the tolerability, program adherence and possible side effects of this novel technique in this age group. The information obtained in this study should be useful in planning further studies in which tDCS could be combined with other treatment modalities, such as cognitive training.
Plastome data reveal multiple geographic origins of Quercus Group Ilex
Authors: Simeone Marco Cosimo , Grimm Guido W , Papini Alessio , Vessella Federico , Cardoni Simone , Tordoni Enrico , Piredda Roberta , Franc Alain , Denk Thomas
Published: January 2018

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK-matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. Main plastid haplotypes shared by distinct oak lineages from the same geographic region and high plastid diversity in members of Group Ilex are indicative for a polyphyletic origin of their plastomes. The results suggest that incomplete lineage sorting and repeated phases of unidirectional introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
Western scrub-jays do not appear to attend to functionality in Aesop’s Fable experiments
Authors: Logan Corina J , Harvey Brigit D , Schlinger Barney A , Rensel Michelle
Published: January 2018

Western scrub-jays are known for their highly discriminatory and flexible behaviors in a caching (food storing) context. However, it is unknown whether their cognitive abilities are restricted to a caching context. To explore this question, we tested scrub-jays in a non-caching context using the Aesop’s Fable paradigm, where a partially filled tube of water contains a floating food reward and objects must be inserted to displace the water and bring the food within reach. We found that scrub-jays did not attend to the functional properties of objects or tubes, and were not motivated to participate in these experiments, suggesting that either this paradigm was ecologically irrelevant or perhaps their flexibility is restricted to a caching context.
Trophic diversity of seagrass detritus copepods: A consequence of species-specific specialization or a random diet?
Authors: Mascart Thibaud , De Troch Marleen , Remy François , Michel Loïc , Lepoint Gilles
Published: January 2018

One of the major ecological research questions is understanding how biodiversity influences ecosystem functioning. Unravelling interspecific feeding preferences of organisms with overlapping trophic niches will give part of the answer. Subsequently, the present study displays the trophic diversity of a benthic copepod community in a North-Western Corsican Posidonia oceanica seagrass ecosystem. These seagrass meadows are often interrupted by bare sand patches serving as deposition area for loose detritus. The accumulated macrophytodetritus, mainly derived from senescent macrophytes, harbour a diverse community of Harpacticoida (Crustacea, Copepoda). The most abundant copepods (i.e. three harpacticoids and one calanoid, belonging to different eco-morphological types) and their potential food sources (i.e. macrophytodetritus, epiphytic biofilm and suspended organic matter) were analysed for stable isotope ratios (δ13C, δ15N) and total lipids content. The results revealed a harpacticoid copepod feeding preference towards the epiphytic biofilm, while calanoid copepods preferred suspended organic matter. Additionally, a species-specific composition variation revealed finer partitioning of food resources (e.g. different micro-organisms present in the biofilm like bacteria, diatoms, fungi) over time.In conclusion, results showed species-specific food preferences, resulting in trophic niche and resource partitioning. Every eco-morphological type seems to cope in different ways with temporal fluctuations of food sources to comply with their nutritional needs. This illustrates the high resilience of the copepod community present in macrophytodetritus accumulations. Moreover, our results underlined the importance of multiple biomarker species-specific analysis in trophic ecology studies, especially in complex and dynamic environments offering numerous food items to consumers.
Convergent synthesis and biological evaluation of vitamin D analogues as potential anticancer agents
Authors: Kutner Andrzej
Published: January 2018

Synthetic analogs of 1alpha,25-dihydroxycholecalciferol [1alpha,25-(OH)2D3] and 1alpha,25-dihydroxyergocalciferol [1alpha,25-(OH)2D2] have long been considered as key regulators of calcium and phosphate homeostasis. These analogs have been recently investigated as potential therapeutics against a number of pathological states, including metabolic, dermatological, immune and hyperproliferative diseases. Analogues of 1alpha,25-(OH)2D3 and 1alpha,25-(OH)2D2, modified in the cyclohexane A-ring and in the aliphatic side-chain, potentiated the efficiency of cytostatics and/or cooperated efficiently with polyphenol in human myeloid leukemia cells (HL60, U937 and MOLM-13) and in several animal models of leukemias and solid tumours. The therapeutic effect resulted from the thorough combination of several key factors, including the selection of vitamin D-sensitive cancer model, type of cytostatic, the right scheme and route of administration of both therapeutics, correlation with vitamin D receptor level and managing of the hypercalcemic side effect of vitamin D. In this work our synthesis and biological evaluation is outlined of a novel generation of vitamin D analogs as well as our investigation of their anticancer profile in vitro and in vivo. Our convergent synthesis started from vitamin D-like advanced intermediates and separately prepared side-chain fragments. This way, in an over twenty-step syntheses, a series of analogs were obtained containing, compared to the parent vitamin D hormones, 1alpha,25-(OH)2D3 and 1alpha,25-(OH)2D2, an additional chiral center or conjugated diene system in the side-chain and/or modified 5,6-trans or 19-nor A-ring. Some of the new analogs, pre-selected in a number of in vitro models, showed, in the combined treatment with cytostatics, the beneficial activity profile in both, murine colon cancer MC38 and in human colon cancer HT-29 cells. Our analogues also modulated expression of genes related to stem-like phenotype in vitamin D receptor (VDR) positive colon cancer cells, HT-29 and HCT-116, at different differentiation states, undergoing renewal after the treatment with 5-FU. The analogs induced differentiation of VDR positive A375 and VDR negative SK-MEL 188b human melanoma cells. Some of our analogs also displayed moderate cytotoxic and pro-apoptotic activity in diffuse large B-cell lymphoma (DLBCL) and concentration and time-dependent antiproliferative action upon stimulated B-cells from healthy donors. Data available from the protein data bank were used for the rational design of the next generation of analogs by minimizing the electrostatic interaction energies, after the reconstruction of a charge densities using pseudoatom databank. Due to a low calcemic activity and anticancer profile in vivo, selected new analogues might be considered as promising candidates for further preclinical evaluation as potential anticancer agents.
Urban park size, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City
Authors: Munshi-South Jason , Nagy Christopher
Published: January 2018

Severe fragmentation is a typical fate of native remnant habitats in cities, and urban wildlife with limited dispersal ability are predicted to lose genetic variation in isolated urban patches. However, little information exists on the extent of habitat required in urban green spaces to conserve genetic variation. In this study, we examine whether isolation in New York City (NYC) parks results in genetic bottlenecks in white-footed mice (Peromyscus leucopus), and test the hypothesis that park size is associated with genetic variability using nonlinear regression and information-theoretic model selection. White-footed mice have previously been documented to exhibit male-biased dispersal, which may create disparities in genetic variation between males and females in urban parks. We use genotypes of 18 neutral microsatellite data and four different statistical tests to assess this prediction. Given that sex-biased dispersal may create disparities between population genetic patterns inferred from bi- vs. uni-parentally inherited markers, we also sequenced a 324 bp segment of the mitochondrial D-loop for independent inferences of historical demography variation in urban P. leucopus. We report that isolation in urban parks does not necessarily result in genetic bottlenecks; only three out of 14 populations in NYC parks exhibited a signature of a recent bottleneck at 18 neutral microsatellite loci. Mouse populations in larger urban parks also do not generally contain greater genetic variation than populations in smaller parks. These results should be encouraging to conservation biologists working in human-dominated landscapes, as even small networks of green spaces may be sufficient to maintain self-sustaining populations and evolutionary potential of native species. We also found that isolation in urban parks results in weak to nonexistent sex-biased dispersal in a species known to exhibit male-biased dispersal in less fragmented environments. In contrast to nuclear loci, mitochondrial D-loop haplotypes exhibited a mutational pattern of demographic expansion after a recent bottleneck or selective sweep. Estimates of the timing of this expansion indicate that it occurred concurrent with urbanization of NYC over the last few dozens to hundreds of years. Given the general non-neutrality of mtDNA in many systems and evidence of selection on related coding sequences in urban P. leucopus, we argue that the P. leucopus mitochondrial genome experienced recent negative selection against haplotypes not favored in isolated urban parks. In general, rapid adaptive evolution driven by urbanization, global climate change, and other human-caused factors is underappreciated by evolutionary biologists, but many more cases will likely be documented in the near future.