bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transparency reduces predator detection in chemically protected clearwing butterflies
Authors: Arias Mónica , Mappes Johanna , Desbois Charlotte , Gordon Swanne , McClure Melanie , Elias Marianne , Nokelainen Ossi , Gomez Doris 
Published: September 2018

Abstract1. Predation is an important selective pressure and some prey have evolved warning colour signals advertising unpalatability (i.e. aposematism) as an antipredator strategy. Unexpectedly, some butterfly species from the unpalatable tribe Ithomiini possess transparent wings, an adaptation rare on land but common in water where it helps avoiding predator detection.2. We tested if transparency of butterfly wings was associated with decreased detectability by predators, by comparing four butterfly species exhibiting different degrees of transparency, ranging from fully opaque to largely transparent. We tested our prediction using using both wild birds and humans in behavioural experiments. Vision modelling predicted detectability to be similar for these two predator types.3. In concordance with predictions, more transparent species were almost never the first detected items and were detected less often than the opaque species by both birds and humans, suggesting that transparency enhances crypsis. However, humans could learn to better detect the most transparent species over time. Our study demonstrates for the first time that transparency on land likely decreases detectability by visual predators.
Bayesian Hypothesis Testing And Experimental Design For Two-Photon Imaging Data
Authors: Rogerson Luke E. , Zhao Zhijian , Franke Katrin , Berens Philipp , Euler Thomas 
Published: September 2018

AbstractVariability, stochastic or otherwise, is a central feature of neural circuits. Yet the means by which variation and uncertainty are derived from noisy observations of neural activity is often unprincipled, with too much weight placed on numerical convenience at the cost of statistical rigour. For two-photon imaging data, composed of fundamentally probabilistic streams of photon detections, the problem is particularly acute. Here, we present a complete statistical pipeline for the inference and analysis of neural activity using Gaussian Process Regression, applied to two-photon recordings of light-driven activity inex vivomouse retina. We demonstrate the flexibility and extensibility of these models, considering cases with non-stationary statistics, driven by complex parametric stimuli, in signal discrimination, hierarchical clustering and inference tasks. Sparse approximation methods allow these models to be fitted rapidly, permitting them to actively guiding the design of light stimulation in the midst of ongoing two-photon experiments.
Single-cell transcriptomics of the mouse gonadal soma reveals the establishment of sexual dimorphism in distinct cell lineages
Authors: Stévant Isabelle , Kühne Françoise , Greenfield Andy , Chaboissier Marie-Christine , Dermitzakis Emmanouil T. , Nef Serge 
Published: September 2018

SummarySex determination is a unique process that allows the study of multipotent progenitors and their acquisition of sex-specific fates during differentiation of the gonad into a testis or an ovary. Using time-series single-cell RNA sequencing (scRNA-seq) on ovarian Nr5a1-GFP+ somatic cells during sex determination, we identified a single population of early progenitors giving rise to both pre-granulosa cells and potential steroidogenic precursor cells. By comparing time-series scRNA-seq of XX and XY somatic cells, we demonstrate that the supporting cells emerge from the early progenitors with a non-sex-specific transcriptomic program, before pre-granulosa and Sertoli cells acquire their sex-specific identity. In XX and XY steroidogenic precursors similar transcriptomic profiles underlie the acquisition of cell fate, but with a delay in XX cells. Our data provide a novel framework, at single-cell resolution, for further interrogation of the molecular and cellular basis of mammalian sex determination.
How will changes in local climate affect hawksbill hatchling production in Brazil?
Authors: Montero Natalie , Marcovaldi Maria A.G. dei , Lopez–Mendilaharsu Milagros , Santos Alexsandro S. , Santos Armando J. B. , Fuentes Mariana M.P.B. 
Published: September 2018

AbstractLocal climatic conditions can influence sea turtle embryonic development and hatchling viability. Therefore, it is crucial to understand these influences as well as potential ramifications to population stability under future climate change. Here, we examined the influences of five climatic variables (air temperature, accumulated and average precipitation, humidity, solar radiation, and wind speed) at different temporal scales on hawksbill sea turtle (Eretmochelys imbricata) hatchling production at ten nesting beaches within two regions of Brazil (five nesting beaches in Rio Grande do Norte and five in Bahia). Air temperature and accumulated precipitation were the main climatic drivers of hawksbill hatching success across Brazil and in Rio Grande do Norte, while air temperature and average precipitation were the main climatic drivers of hatching success at Bahia. Solar radiation was the main climatic driver of emergence rate at both regions. Conservative and extreme climate scenarios show air temperatures are projected to increase, while precipitation projections vary between scenarios and regions throughout the 21st century. We predicted hatching success of undisturbed nests (no recorded depredation or storm-related impacts) will decrease in Brazil by 2100. This study shows the determining effects of different climate variables and their combinations on an important and critically endangered marine species.
Differences in functional connectivity along the anterior-posterior axis of human hippocampal subfields
Authors: Dalton Marshall A. , McCormick Cornelia , Maguire Eleanor A. 
Published: September 2018

AbstractThere is a paucity of information about how human hippocampal subfields are functionally connected to each other and to neighbouring extra-hippocampal cortices. In particular, little is known about whether patterns of functional connectivity (FC) differ down the anterior-posterior axis of each subfield. Here, using high resolution structural MRI we delineated the hippocampal subfields in healthy young adults. This included the CA fields, separating DG/CA4 from CA3, separating the pre/parasubiculum from the subiculum, and also segmenting the uncus. We then used high resolution resting state functional MRI to interrogate FC. We first analysed the FC of each hippocampal subfield in its entirety, in terms of FC with other subfields and with the neighbouring regions, namely entorhinal, perirhinal, posterior parahippocampal and retrosplenial cortices. Next, we analysed FC for different portions of each hippocampal subfield along its anterior-posterior axis, in terms of FC between different parts of a subfield, FC with other subfield portions, and FC of each subfield portion with the neighbouring cortical regions of interest. We found that intrinsic functional connectivity between the subfields aligned generally with the tri-synaptic circuit but also extended beyond it. Our findings also revealed that patterns of functional connectivity between the subfields and neighbouring cortical areas differed markedly along the anterior-posterior axis of each hippocampal subfield. Overall, these results contribute to ongoing efforts to characterise human hippocampal subfield connectivity, with implications for understanding hippocampal function.HighlightsHigh resolution resting state functional MRI scans were collectedWe investigated functional connectivity (FC) of human hippocampal subfieldsWe specifically examined FC along the anterior-posterior axis of subfieldsFC between subfields extended beyond the canonical tri-synaptic circuitDifferent portions of subfields showed different patterns of FC with neocortex
Temperate grass allergy season defined by spatio-temporal shifts in airborne pollen communities
Authors: Brennan Georgina L. , Potter Caitlin , Vere Natasha de , Griffith Gareth W. , Skjøth Carsten A. , Osborne Nicholas J. , Wheeler Benedict W. , McInnes Rachel N. , Clewlow Yolanda , Barber Adam , Hanlon Helen M. , Hegarty Matthew , Jones Laura , Kurganskiy Alexander , Rowney Francis M. , Armitage Charlotte , Adams-Groom Beverley , Ford Col R. , Petch Geoff M. ,   The PollerGEN Consortium, Creer Simon 
Published: September 2018

AbstractGrass pollen is the world’s most harmful outdoor aeroallergen and sensitivity varies between species. Different species of grass flower at different times, but it is not known how airborne communities of grass pollen change in time and space. Persistence and high mobility of grass pollen could result in increasingly diverse seasonal pollen communities. Conversely, if grass pollen does not persist for an extended time in the air, shifting pollen communities would be predicted throughout the summer months. Here, using targeted high throughput sequencing, we tracked the seasonal progression of airborne Poaceae pollen biodiversity across Britain, throughout the grass allergy season. All grass genera displayed discrete, temporally restricted peaks of pollen incidence which varied with latitude, revealing that the taxonomic composition of grass pollen exposure changes substantially across the allergy season. By developing more refined aeroallergen profiling, we predict that our findings will facilitate the exploration of links between taxon-specific exposure of harmful grass pollen and disease, with concomitant socio-economic benefits.
hsegHMM: Hidden Markov Model-based Allele-specific Copy Number Alteration Analysis Accounting for Hypersegmentation
Authors: Choo-Wosoba Hyoyoung , Albert Paul S , Zhu Bin 
Published: September 2018

AbstractBackground:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next generation sequencing platforms produce abundant read counts at the base-pair resolution across the exome or whole genome which is susceptible to hypersegmentation, a phenomenon where numerous regions with very short length are falsely identified as SCNA.Results:We propose hsegHMM, a hidden Markov model approach that accounts for hypersegmentation for allele-specific SCNA analysis. hsegHMM provides statistical inference of copy number profiles by using an effcient E-M algorithm procedure. Through simulation and application studies, we found that hsegHMM handles hypersegmentation effectively with a t-distribution as a part of the emission probability distribution structure and a carefully defined state space. We also compared hsegHMM with FACETS which is a current method for allele-specific SCNA analysis. For the application, we use a renal cell carcinoma sample from The Cancer Genome Atlas (TCGA) study.Conclusions:We demonstrate the robustness of hsegHMM to hypersegmentation. Furthermore, hsegHMM provides the quantification of uncertainty in identifying allele-specific SCNAs over the entire chromosomes. hsegHMM performs better than FACETS when read depth (coverage) is uneven across the genome.
Gene-specific transcriptional memory in mammalian cell lineages
Authors: Phillips Nicholas E. , Mandic Aleksandra , Omidi Saeed , Naef Felix , Suter David M. 
Published: September 2018

AbstractPhenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combined live-cell imaging of short- lived transcriptional reporters in mouse embryonic stem cells with mathematical modelling to quantify the propagation of transcriptional activity over time and across cell generations. In sister cells we found mean transcriptional activity to be strongly correlated and transcriptional dynamics tended to be synchronous; both features control how quickly sister cells diverge in a gene-specific manner. Mean transcriptional activity was also highly correlated between mother and daughter cells, leading to multi-generational transcriptional memory whose duration scaled with the spread of transcriptional activities in the population. The resulting family-specific transcriptional levels suggest a potential role of transcriptional memory in patterning tissue gene expression.
Genome-wide identification and expression specificity analysis of the DNA methyltransferase gene family under adversity stresses in cotton
Authors: Yang Xiaomin , Lu Xuke , Chen Xiugui , Wang Delong , Wang Junjuan , Wang Shuai , Guo Lixue , Chen Chao , Wang Xiaoge , Zhang Binglei , Han Mingge , Ye Wuwei 
Published: September 2018

AbstractDNA methylation is an important epigenetic mode of genomic DNA modification that is an important part of maintaining epigenetic content and regulating gene expression. DNA methyltransferases (MTases) are the key enzymes in the process of DNA methylation. Thus far, there has been no systematic analysis the DNA MTases found in cotton. In this study, the whole genome of cotton C5-Mtase coding genes was identified and analyzed using a bioinformatics method based on information from the cotton genome. In this study, 51 DNA MTase genes were identified, of which 8 belonged toG. raimondii(group D), 9 belonged toG. arboretumL. (group A), 16 belonged toG. hirsutumL. (group AD1) and 18 belonged toG. barbadebseL. (group AD2). Systematic evolutionary analysis divided the 51 genes into four subfamilies, including 7 MET homologous proteins, 25 CMT homologous proteins, 14 DRM homologous proteins and 5 DNMT2 homologous proteins. Further studies showed that the DNA MTases in cotton were more phylogenetically conserved. The comparison of their protein domains showed that the C-terminal functional domain of the 51 proteins had six conserved motifs involved in methylation modification, indicating that the protein has a basic catalytic methylation function and the difference in the N-terminal regulatory domains of the 51 proteins divided the proteins into four classes, MET, CMT, DRM and DNMT2, in which DNMT2 lacks an N-terminal regulatory domain. Gene expression in cotton is not the same under different stress treatments. Different expression patterns of DNA MTases show the functional diversity of the cotton DNA methyltransferase gene family. VIGS silenced Gossypium hirsutum l. in the cotton seedling of DNMT2 family geneGhDMT6, after stress treatment the growth condition was better than the control. The distribution of DNA MTases varies among cotton species. Different DNA MTase family members have different genetic structures, and the expression level changes with different stresses, showing tissue specificity. Under salt and drought stress,G. hirsutumL. TM-1 increased the number of genes more thanG. raimondiiandG. arboreumL.Shixiya1. The resistance of Gossypium hirsutum L.TM-1 to cold, drought and salt stress was increased after the plants were silenced withGhDMT6gene.
Every cloud has a silver lining: Moderate plant water stress positively impacts development, immunity, and gut microbiota of a specialist herbivore
Authors: Rosa E , Minard G , Lindholm J , Saastamoinen M 
Published: September 2018

AbstractThe ongoing global temperature rise has led to increasing frequency of drought events, negatively impacting vegetation and the living organisms relying on it. Extreme drought killing host plants can clearly reduce herbivore fitness, but the impact of moderate host plant water stress on insect herbivores can vary, and may even be beneficial. The Finnish Glanville fritillary butterfly (Melitaea cinxia) has faced reduced precipitation in recent years, which has impacted population dynamics. However, whether the negative effects depend on extreme desiccation killing the host plant or moderate drought impacting plant quality remains unclear. We assessed the performance of larvae fed on moderately water-stressedPlantago lanceolatain terms of growth, gut microbial composition and immune response. We found that larvae fed on water-stressed plants had better growth, a more heterogeneous bacterial community and a shifted fungal community in the gut, and up-regulated the expression of one candidate immune gene (pelle), whereas survival remained unaffected. Most of the measured traits showed considerable variation due to family structure. Our data suggest that in temperate regions moderate host plant water stress can positively shape resource acquisition of this specialized insect herbivore, potentially by increasing nutrient accessibility or concentration. Potentially, the better larval performance may be mediated by a shift of the microbiota on water-stressed plants, calling for further research especially on the understudied gut fungal community.
Risky home with easy food: Denning of a generalistic and widely distributed carnivore red fox
Authors: Reshamwala Hussain S. , Mahar Neeraj , Dirzo Rodolfo , Habib Bilal 
Published: September 2018

AbstractDens are crucial for the survival of all canids, however, for a meso-carnivore like red fox, denning is of greater importance as they utilize dens all throughout the year for protection, resting and breeding. The red fox known for its generalist and opportunistic behavior and extremely good adaptability to the dynamic anthropogenic changes is the most widespread and successful wild land carnivore. With an ever-growing human population the choice of space for wild animals is limited and such adaptability is important for species survival. In this study we examined the denning preferences and den characteristics of red fox. Intensive surveys were conducted across two study sites Chiktan and Changthang. Foxes preferred to den on mountain slopes (43.70 ± 3.38 SE) where human disturbances were minimal. The red fox chose den sites closer to human settlements, water and road as compared to random points (Pillai’s trace = .487, F= 31.014 and P = 3.497e-14), which are risky and may expose the pups to humans but also provide the advantage of procuring anthropogenic food subsidies. In Changthang, foxes preferred to den at a greater distance (936 ± 223 meters) from human settlements as compared to Chiktan (403 ± 50 meters). The present research is of broad significance, given the increasing presence of human settlements within original animal ranges, even in remote harsh environments like the Trans-Himalaya.
Patterns in international ICT entrepreneurship: Mexico’s case
Authors: Larios Hernandez Guillermo Jesus 
Published: September 2018

Purpose
The purpose of this paper is to understand the antecedents of small and medium-sized enterprises (SME) internationalization for a small set of Mexican ICT entrepreneurial firms, connected with subsectoral positions in a smile-shaped curve. Such antecedents constitute exploratory patterns related to simplified internationalization characteristics in terms of market choice, founder background and aspatial affiliations, providing a complementary technique to identify elements that shape SME internationalization in Latin America.

Design/methodology/approach
A value-added “smiling” curve is sketched according to North American Industry Classification System (NAICS) industry classification, mapping a non-probabilistic purposive sample of Mexican SMEs. The csQCA has been applied to the sample based on secondary data. Mexico’s ICT export behavior is also analyzed.

Findings
Internationalized SMEs in the sample tend to group in patterns that approach higher value-added positions in the “smiling” curve, exemplifying a type of non-geographic clustering. Particular groups seem to precede market selection (North America vs Latin America). The founder’s background does not determine internationalization choices. The sample included counterexamples (new entrants, limited cases involving research and development activities), which when analyzed suggest relevant literature validations.

Originality/value
This research contextualizes sectoral SME internationalization from a Latin American perspective, identifying simple patterns around particular ICT subsectors. It focuses on a type of international entrepreneurship that becomes exceptional in developing regions: technology-oriented. csQCA is presented as a preliminary (exploratory) technique to draw alternative theoretical frameworks for SME internationalization, specifically, market selection and aspatial cluster behavior around value-added chains, leading to new theoretical perspectives in SME internationalization.
Development of a script-based versatile three-dimensional body measurement system
Authors: Kim Minsuk , Kim Sungmin 
Published: September 2018

Purpose
The purpose of this paper is to develop a versatile and extensible three-dimensional (3D) body measurement system.

Design/methodology/approach
An integrated development environment and a script language compiler were designed for easy definition of measurement process.

Findings
Researchers can do every kind of anthropometric research with respect to gender, age or race simply by writing appropriate scripts.

Research limitations/implications
System does not support the management of 3D data itself. The possible flaws of data should be removed by other hardware specific software.

Practical implications
Researchers without comprehensive knowledge of computer programming can conduct complex anthropometric research by simply learning the concise script language.

Social implications
This system will facilitate many anthropometric research works and will help to provide valuable information to many industries.

Originality/value
This is the first script language based body data analysis system. The script language consists of about 60 simple commands. Researchers will be able to concentrate more on the research topic itself than on the painstaking computer programming.
Drawing a gastronomy landscape from food markets’ produce
Authors: Fusté-Forné Francesc 
Published: September 2018

Purpose
Food markets represent a pathway to explore the authenticity and identity of a territory. Markets are a crucial example among food tourism practices in urban contexts. This paper aims to analyze the products that build the particular food landscape of Costa Daurada, Catalonia, Spain.

Design/methodology/approach
To achieve it, the research was based on the study of foods offered in three regional markets.

Findings
Results show how Costa Daurada is gastronomically characterized and what products convey the diversity and singularity of the region.

Originality/value
The originality of this paper lies on the building of a regional gastronomy landscape on the basis of the iconic products delivered at local food markets, regarded as shared spaces between locals and tourists.