bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pigmentation pattern and developmental constraints: flight muscle attachment sites delimit the thoracic trident of Drosophila melanogaster
Authors: Gibert Jean-Michel , Mouchel-Vielh Emmanuèle , Peronnet Frédérique 
Published: March 2018

AbstractIn their seminal paper published in 1979, Gould and Lewontin argued that some traits arise as by-products of the development of other structures and not for direct utility in themselves. We show here that this applies to the trident, a pigmentation pattern observed on the thorax of Drosophila melanogaster. Using reporter constructs, we show that the expression domain of several genes encoding pigmentation enzymes follows the trident shape. This domain is complementary to the expression pattern of stripe (sr), which encodes an essential transcription factor specifying flight muscle attachment sites. We demonstrate that sr limits the expression of these pigmentation enzyme genes to the trident by repressing them in its own expression domain, i.e. at the flight muscle attachment sites. We give evidence that repression of not only yellow but also other pigmentation genes, notably tan, is involved in the trident shape. The flight muscle attachment sites and sr expression patterns are remarkably conserved in dipterans reflecting the essential role of sr. Our data suggest that the trident is a by-product of flight muscle attachment site patterning that arose when sr was co-opted for the regulation of pigmentation enzyme coding genes.
Predicting affective valence using cortical hemodynamic signals
Authors: Trambaiolli Lucas R. , Biazoli Claudinei E. , Cravo André M. , Sato João R. 
Published: March 2018

AbstractAscribing affective valence to stimuli or mental states is a fundamental property of human experiences. Recent neuroimaging meta-analyses favor the workspace hypothesis for the neural underpinning of valence, in which both positive and negative values are encoded by overlapping networks but are associated with different patterns of activity. In the present study, we further explored this framework using functional near-infrared spectroscopy (fNIRS) in conjunction with multivariate analyses. We monitored the fronto-temporal and occipital hemodynamic activity of 49 participants during the viewing of affective images (passive condition) and during the imagination of affectively loaded states (active condition). Multivariate decoding techniques were applied to determine whether affective valence is encoded in the cortical areas assessed. Prediction accuracies of 89.90 ± 13.84% and 85.41 ± 14.43% were observed for positive versus neutral comparisons, and of 91.53 ± 13.04% and 81.54 ± 16.05% for negative versus neutral comparisons (passive/active conditions, respectively). Our results are consistent with previous studies using other neuroimaging modalities that support the affective workspace hypothesis and the notion that valence is instantiated by the same network, regardless of whether the affective experience is passively or actively elicited.
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution
Authors: Blanchoud Simon , Rutherford Kim , Zondag Lisa , Gemmell Neil J. , Wilson Megan J. 
Published: March 2018

AbstractTunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.
Coherent changes of wintertime surface air temperatures over North Asia and North America
Authors: Yu Bin , Lin Hai 
Published: March 2018

AbstractThe surface temperature variance and its potential change with global warming are most prominent in winter over Northern Hemisphere mid-high latitudes. Consistent wintertime surface temperature variability has been observed over large areas in Eurasia and North America on a broad range of time scales. However, it remains a challenge to quantify where and how the coherent change of temperature anomalies occur over the two continents. Here we demonstrate the coherent change of wintertime surface temperature anomalies over North Asia and the central-eastern parts of North America for the period from 1951 to 2015. This is supported by the results from the empirical orthogonal function analysis of surface temperature and temperature trend anomalies over the Northern Hemisphere extratropical lands and the timeseries analysis of the regional averaged temperature anomalies over North Asia and the Great Plains and Great Lakes. The Asian-Bering-North American (ABNA) teleconnection provides a pathway to connect the regional temperature anomalies over the two continents. The ABNA is also responsible for the decadal variation of the temperature relationship between North Asia and North America.
Looking for variable molecular markers in the chestnut gall wasp Dryocosmus kuriphilus: first comparison across genes
Authors: Bonal Raúl , Vargas-Osuna Enrique , Mena Juan Diego , Aparicio José Miguel , Santoro María , Martín Angela 
Published: March 2018

AbstractThe quick spread of the chestnut gall wasp Dryocosmus kuriphilus in Europe constitutes an outstanding example of recent human-aided biological invasion with dramatic economic losses. We screened for the first time a set of five nuclear and mitochondrial genes from D. kuriphilus collected in the Iberian Peninsula, and compared the sequences with those available from the native and invasive range of the species. We found no genetic variability in Iberia in none of the five genes, moreover, the three genes compared with other European samples showed no variability either. We recorded four cytochrome b haplotypes in Europe; one was genuine mitochondrial DNA and the rest nuclear copies of mitDNA (numts), what stresses the need of careful in silico analyses. The numts formed a separate cluster in the gene tree and at least two of them might be orthologous, what suggests that the invasion might have started with more than one individual. Our results point at a low initial population size in Europe followed by a quick population growth. Future studies assessing the expansion of this pest should include a large number of sampling sites and use powerful nuclear markers (e. g. Single Nucleotide Polymorphisms) to detect genetic variability.
Apolipoprotein A-II induces acute-phase response associated AA amyloidosis in mice through conformational changes of plasma lipoprotein structure
Authors: Yang Mu , Liu Yingye , Dai Jian , Li Lin , Ding Xin , Xu Zhe , Mori Masayuki , Miyahara Hiroki , Sawashita Jinko , Higuchi Keiichi 
Published: March 2018

AbstractDuring acute-phase response (APR), there is a dramatic increase in serum amyloid A (SAA) in plasma high density lipoproteins (HDL). Elevated SAA leads to reactive AA amyloidosis in animals and humans. Herein, we employed apolipoprotein A-II (ApoA-II) deficient (Apoa2
−/−
) and transgenic (Apoa2Tg) mice to investigate the potential roles of ApoA-II in lipoprotein particle formation and progression of AA amyloidosis during APR. AA amyloid deposition was suppressed in Apoa2
−/−
mice compared with wild type (WT) mice. During APR, Apoa2
−/−
mice exhibited significant suppression of serum SAA levels and hepatic Saa1 and Saa2 mRNA levels. Pathological investigation showed Apoa2
−/−
mice had less tissue damage and less inflammatory cell infiltration during APR. Total lipoproteins were markedly decreased in Apoa2
−/−
mice, while the ratio of HDL to low density lipoprotein (LDL) was also decreased. Both WT and Apoa2
−/−
mice showed increases in LDL and very large HDL during APR. SAA was distributed more widely in lipoprotein particles ranging from chylomicrons to very small HDL in Apoa2
−/−
mice. Our observations uncovered the critical roles of ApoA-II in inflammation, serum lipoprotein stability and AA amyloidosis morbidity, and prompt consideration of therapies for AA and other amyloidoses, whose precursor proteins are associated with circulating HDL particles.
Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses
Authors: Khan Abid , Li Ru-Jian , Sun Jian-Tian , Ma Fang , Zhang Huai-Xia , Jin Jing-Hao , Ali Muhammad , Haq Saeed ul , Wang Jun-E , Gong Zhen-Hui 
Published: March 2018

AbstractThe dirigent (DIR and DIR-like) proteins involved in lignification, play a pivotal role against biotic and abiotic stresses in plants. However, no information is available about DIR gene family in pepper (Capsicum annuum L.). In this study, 24 putative dirigent genes (CaDIRs) were identified, their gene structure, genome location, gene duplication and phylogenetic relationship were elucidated. Tissue-specific expression analysis displayed the highest transcription levels in flower, stem and leaf. Some CaDIRs were up-regulated by virulent (CaDIR2, 3, 6, 7, 11, 14, 16, 22 and 23) and avirulent (CaDIR3, 5, 7, 16, 20, 22, 23 and 24) Phytophthora capsici strains, as well as by Methyl jasmonate, salicylic acid, NaCl and mannitol stresses. Acid-soluble lignin content increased (103.21%) after P. capsici inoculation (48-hour). Silencing of CaDIR7 weakened plant defense by reducing (~50%) root activity and made plants more susceptible (35.7%) to P. capsici and NaCl (300 mM). Leaf discs of the CaDIR7:silenced plants exposed to NaCl and mannitol (300 mM each), exhibited a significant decrease (56.25% and 48% respectively) in the chlorophyll content. These results suggested that CaDIR7 is involved in pepper defense response against pathogen and abiotic stresses and the study will provide basic insights for future research regarding CaDIRs.
Real-time distribution of pelagic fish: combining hydroacoustics, GIS and spatial modelling at a fine spatial scale
Authors: Muška Milan , Tušer Michal , Frouzová Jaroslava , Mrkvička Tomáš , Ricard Daniel , Seďa Jaromír , Morelli Federico , Kubečka Jan 
Published: March 2018

AbstractUnderstanding spatial distribution of organisms in heterogeneous environment remains one of the chief issues in ecology. Spatial organization of freshwater fish was investigated predominantly on large-scale, neglecting important local conditions and ecological processes. However, small-scale processes are of an essential importance for individual habitat preferences and hence structuring trophic cascades and species coexistence. In this work, we analysed the real-time spatial distribution of pelagic freshwater fish in the Římov Reservoir (Czechia) observed by hydroacoustics in relation to important environmental predictors during 48 hours at 3-h interval. Effect of diurnal cycle was revealed of highest significance in all spatial models with inverse trends between fish distribution and predictors in day and night in general. Our findings highlighted daytime pelagic fish distribution as highly aggregated, with general fish preferences for central, deep and highly illuminated areas, whereas nighttime distribution was more disperse and fish preferred nearshore steep sloped areas with higher depth. This turnover suggests prominent movements of significant part of fish assemblage between pelagic and nearshore areas on a diel basis. In conclusion, hydroacoustics, GIS and spatial modelling proved as valuable tool for predicting local fish distribution and elucidate its drivers, which has far reaching implications for understanding freshwater ecosystem functioning.
Virtual screening, Docking, ADMET and System Pharmacology studies on Garcinia caged Xanthone derivatives for Anticancer activity
Authors: Alam Sarfaraz , Khan Feroz 
Published: March 2018

AbstractCaged xanthones are bioactive compounds mainly derived from the Garcinia genus. In this study, a structure-activity relationship (SAR) of caged xanthones and their derivatives for anticancer activity against different cancer cell lines such as A549, HepG2 and U251 were developed through quantitative (Q)-SAR modeling approach. The regression coefficient (r2), internal cross-validation regression coefficient (q2) and external cross-validation regression coefficient (pred_r2) of derived QSAR models were 0.87, 0.81 and 0.82, for A549, whereas, 0.87, 0.84 and 0.90, for HepG2, and 0.86, 0.83 and 0.83, for U251 respectively. These models were used to design and screened the potential caged xanthone derivatives. Further, the compounds were filtered through the rule of five, ADMET-risk and synthetic accessibility. Filtered compounds were then docked to identify the possible target binding pocket, to obtain a set of aligned ligand poses and to prioritize the predicted active compounds. The scrutinized compounds, as well as their metabolites, were evaluated for different pharmacokinetics parameters such as absorption, distribution, metabolism, excretion, and toxicity. Finally, the top hit compound 1G was analyzed by system pharmacology approaches such as gene ontology, metabolic networks, process networks, drug target network, signaling pathway maps as well as identification of off-target proteins that may cause adverse reactions.
Age is reflected in the Fractal Dimensionality of MRI Diffusion Based Tractography
Authors: Reishofer Gernot , Studencnik Fritz , Koschutnig Karl , Deutschmann Hannes , Ahammer Helmut , Wood Guilherme 
Published: March 2018

AbstractFractal analysis is a widely used tool to analyze the geometrical complexity of biological structures. The geometry of natural objects such as plants, clouds, cellular structures, blood vessel, and many others cannot be described sufficiently with Euclidian geometric properties, but can be represented by a parameter called the fractal dimension. Here we show that a specific estimate of fractal dimension, the correlation dimension, is able to describe changes in the structural complexity of the human brain, based on data from magnetic resonance diffusion imaging. White matter nerve fiber bundles, represented by tractograms, were analyzed with regards to geometrical complexity, using fractal geometry. The well-known age-related change of white matter tissue was used to verify changes by means of fractal dimension. Structural changes in the brain were successfully be observed and quantified by fractal dimension and compared with changes in fractional anisotropy.
The secretome from bovine mammosphere-derived cells (MDC) promotes angiogenesis, epithelial cell migration, and contains factors associated with defense and immunity
Authors: Ledet Melissa M. , Vasquez Amy K. , Rauner Gat , Bichoupan Allison A. , Moroni Paolo , Nydam Daryl V. , Van de Walle Gerlinde R. 
Published: March 2018

AbstractTreatment of bovine mastitis with intramammary antibiotics is common, yet several concerns exist including failed efficacy for individual hosts or pathogens and the inability of approved drugs to revert mastitis-induced tissue damage to healthy tissue capable of returning to full milk production. These issues, in addition to aspects of public health such as accidental antibiotic residues in saleable milk and the potential for antimicrobial resistance, support the need to find alternative therapies for this costly disease. This study shows that the secretome, or collective factors, produced by mammosphere-derived cells (MDC) promotes angiogenesis, epithelial cell migration, and contains proteins associated with immunity and defense; all of which are necessary for healing damaged mammary gland tissue. Furthermore, we found that the MDC secretome remains effective after freezing and thawing, enhancing its therapeutic potential. Our results provide a foundation for further characterization of the individual secreted factors and the rationale for using the MDC secretome as a complementary treatment for bovine mastitis.
Using bivalve chronologies for quantifying environmental drivers in a semi-enclosed temperate sea
Authors: Peharda M. , Vilibić I. , Black B. A. , Markulin K. , Dunić N. , Džoić T. , Mihanović H. , Gačić M. , Puljas S. , Waldman R. 
Published: March 2018

AbstractAnnual growth increments formed in bivalve shells are increasingly used as proxies of environmental variability and change in marine ecosystems, especially at higher latitudes. Here, we document that well-replicated and exactly dated chronologies can also be developed to capture oceanographic processes in temperate and semi-enclosed seas, such as the Mediterranean. A chronology is constructed for Glycymeris pilosa from a shallow embayment of the northern Adriatic and extends from 1979 to 2016. The chronology significantly (p < 0.05) and positively correlates to winter sea surface temperatures, but negatively correlates to summer temperatures, which suggests that extreme winter lows and extreme summer highs may be limiting to growth. However, the strongest and most consistent relationships are negative correlations with an index of the Adriatic-Ionian Bimodal Oscillating System (BiOS) for which positive values indicate the inflow of the ultraoligotrophic Eastern Mediterranean waters to the Adriatic. In contrast, the substantial freshwater flows that discharge into the Adriatic do not correlate to the bivalve chronology, emphasizing the importance of remote oceanographic processes to growth at this highly coastal site. Overall, this study underscores the potential of bivalve chronologies to capture biologically relevant, local- to regional-scale patterns of ocean circulation in mid-latitude, temperate systems.
Global Proteomics Deciphered Novel-Function of Osthole Against Pulmonary Arterial Hypertension
Authors: Yao Li , Yang Yuxia , He Guanhong , Ou Chunqing , Wang Lan , Liu Kaixuan 
Published: March 2018

AbstractPulmonary arterial hypertension (PAH) is a progressive cardiovascular-disease with high mortality lacking high-efficiency drug. Our efforts attempted to delineate therapeutic action of osthole produced by Angelica Pubescens Maxim, which has the capacity to treat PAH by exploiting an iTRAQ-based proteomic method. Excitingly, osthole was observed to significantly restore 98 of 315 differential proteins significantly modified by PAH progression. They were primarily annotated into 24 signaling pathways. Four mostly affected proteins (RPL15, Cathepsin S, Histone H3.3 and HMGB1) were experimentially validated which belonged to ribosome pathway, oxidative phosphorylation pathway, systemic lupus erythematosus pathway, complement and coagulation cascades pathway, whose modifications and modulations mostly accounted for therapeutic capacity of this compound against PAH. Altogether, our findings demonstrated that global proteomics is a promising systems-biology approach for deciphering therapeutic actions and associated mechanisms of natural products derived from traditional Chinese medicine. Importantly, osthole is supposed to be a candidate compound for new drug development to treat PAH.
Blocking interleukin-4 enhances efficacy of vaccines for treatment of opioid abuse and prevention of opioid overdose
Authors: Laudenbach Megan , Baruffaldi Federico , Robinson Christine , Carter Philipp , Seelig Davis , Baehr Carly , Pravetoni Marco 
Published: March 2018

AbstractVaccines offer an option to treat heroin and prescription opioid abuse and prevent fatal overdoses. Opioid vaccines elicit antibodies that block opioid distribution to the brain and reduce opioid-induced behavioral effects and toxicity. The major limitation to the translation of addiction vaccines is that efficacy is observed only in subjects achieving optimal drug-specific serum antibody levels. This study tested whether efficacy of a vaccine against oxycodone is increased by immunomodulators targeting key cytokine signaling pathways involved in B and T cell lymphocyte activation. Blockage of IL-4 signaling increased vaccine efficacy in blocking oxycodone distribution to the brain and protection against opioid-induced behavior and toxicity in mice. This strategy generalized to a peptide-protein conjugate immunogen, and a tetanus-diphtheria-pertussis vaccine. These data demonstrate that cytokine-based immunomodulators increase efficacy of vaccines against small molecules, peptides and proteins, and identify IL-4 as a pharmacological target for improving efficacy of next-generation vaccines.
Fathers’ eye colour sways daughters’ choice of both long- and short-term partners
Authors: Bressan Paola , Damian Valeria 
Published: March 2018

AbstractIn several species, mate choice is influenced by parental features through sexual imprinting, but in humans evidence is scarce and open to alternative explanations. We examined whether daughters’ preference for mates with light vs dark eyes is affected by the eye colour of parents. In an online study, over one thousand women rated the attractiveness of men as potential partners for either a long- or a short-term relationship. Each male face was shown twice, with light (blue or green) and with dark (brown or dark brown) eyes. Having a light-eyed father increased the preference for light-eyed men in both relationship contexts. Having light eyes increased this preference too, but only when men were regarded as potential long-term companions. Asymmetrically, in real life, father’s eye colour was the only predictor of partner’s eye colour; own colour was irrelevant. Mother’s eye colour never mattered, affecting neither preferences nor real-life choices. The effect of paternal eye colour was modulated by the quality of the relationship between father and daughter, suggesting (flexible) sexual imprinting rather than a simple inheritance of maternal preferences. Our data provide evidence that in humans, as in birds and sheep, visual experience of parental features shapes later sexual preferences.
In Vivo 3D Histomorphometry Quantifies Bone Apposition and Skeletal Progenitor Cell Differentiation
Authors: Yeh Shu-Chi A. , Wilk Katarzyna , Lin Charles P. , Intini Giuseppe 
Published: March 2018

AbstractHistomorphometry and Micro-CT are commonly used to assess bone remodeling and bone microarchitecture. These approaches typically require separate cohorts of animals to analyze 3D morphological changes and involve time-consuming immunohistochemistry preparation. Intravital Microscopy (IVM) in combination with mouse genetics may represent an attractive option to obtain bone architectural measurements while performing longitudinal monitoring of dynamic cellular processesin vivo. In this study we utilized two-photon, multicolor fluorescence IVM together with a lineage tracing reporter mouse model to image skeletal stem cells (SSCs) in their calvarial suture niche and analyze their differentiation fate after stimulation with an agonist of the canonical Wnt pathway (recombinant Wnt3a). Ourin vivohistomorphometry analyses of bone formation, suture volume, and cellular dynamics showed that recombinant Wnt3a induces new bone formation, differentiation and incorporation of SSCs progeny into newly forming bone. IVM technology can therefore provide additional dynamic 3D information to the traditional static 2D histomorphometry.