bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tools4miRs – one place to gather all the tools for miRNA analysis
Authors: Lukasik Anna , Wójcikowski Maciej , Zielenkiewicz Piotr 
Published: April 2016

Abstract
Summary: MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data.
Availability and Implementation : Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org.
Contact : piotr@ibb.waw.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
Tree inference for single-cell data
Authors: Jahn Katharina , Kuipers Jack , Beerenwinkel Niko 
Published: April 2016

AbstractUnderstanding the mutational heterogeneity within tumours is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary history of a tumour from noisy and incomplete mutation profiles of single cells. SCITE comprises a exible MCMC sampling scheme that allows the user to compute the maximum-likelihood mutation history, to sample from the posterior probability distribution, and to estimate the error rates of the underlying sequencing experiments. Evaluation on real cancer data and on simulation studies shows the scalability of SCITE to present-day single-cell sequencing data and improved reconstruction accuracy compared to existing approaches.
Formation of novel PRDM9 allele by indel events as possible trigger for tarsier-anthropoid split
Authors: Heerschop Sacha , Zischler Hans , Merker Stefan , Perwitasari-Farajallah Dyah , Driller Christine 
Published: April 2016

AbstractPRDM9is currently the sole speciation gene found in vertebrates causing hybrid sterility probably due to incompatible alleles. Its role in defining the double strand break loci during the meiotic prophase I is crucial for proper chromosome segregation. Therefore, the rapid turnover of the loci determining zinc finger array seems to be causative for incompatibilities. We here investigated the zinc finger domain-containing exon ofPRDM9in 23 tarsiers. Tarsiers, the most basal extant haplorhine primates, exhibit two frameshifting indels at the 5’-end of the array. The first mutation event interrupts the reading frame and function while the second compensates both. The fixation of this peculiar allele variant in tarsiers led to hypothesize that de‐ and reactivation of the zinc finger domain drove the speciation in early haplorhine primates. Moreover, the high allelic diversity withinTarsiuspoint to multiple effects of genetic drift reflecting their phylogeographic history since the Miocene.
Evaluation of positron emission tomography imaging to detect lymph node metastases in patients with high‐risk cutaneous squamous cell carcinoma
Authors: Fujiwara Masao , Suzuki Takahiro , Takiguchi Tetsuya , Fukamizu Hidekazu , Tokura Yoshiki 
Published: April 2016

AbstractTen to twenty percent of high‐risk cutaneous squamous cell carcinoma (cSCC) can metastasize to regional lymph nodes. Detection of nodal metastasis is mandatory to manage high‐risk cSCC. This study was aimed to evaluate the 18F‐fluorodeoxyglucose positron emission tomography (FDG‐PET) imaging to assess lymph node (LN) metastasis of high‐risk cSCC patients. Twenty‐six patients with histologically proven primary cSCC were enrolled. All patients underwent whole‐body PET prior to lymphoscintigraphy and subsequent sentinel LN biopsy. The maximum standardized uptake value (SUVmax) of more than 2.5 is generally evaluated as a positive PET finding indicative of malignancy. On the basis of the histopathological and PET findings, 30 LN from 26 patients were categorized into four groups: (i) histologically negative and PET negative (true‐negative; n = 22); (ii) histologically positive and PET negative (false‐negative; n = 0); (iii) histologically positive and PET positive (true‐positive; n = 3); and (iv) histologically negative and PET positive (false‐positive; n = 5). The mean SUVmax was significantly higher in the true‐positive cases (11.0 ± 2.8) than in the false‐positive cases (3.4 ± 0.6). In the false‐positive cases, the number of tumor‐infiltrating inflammatory cells at the primary skin site was highest among the four groups, suggesting that inflammation contributed to the false‐positive uptake of FDG. Although we cannot negate the possibility of the presence of PET‐undetectable micrometastasis, the SUVmax value may be useful for avoidance of excess performance of sentinel LN biopsy.
Cyclic AMP signaling enhances lipopolysaccharide sensitivity and interleukin‐33 production in RAW264.7 macrophages
Authors: Sato Shizuka , Yanagawa Yoshiki , Hiraide Sachiko , Iizuka Kenji 
Published: April 2016

ABSTRACTWhile it has been suggested that IL‐33 plays pathogenic roles in various disorders, the factors that stimulate IL‐33 production are poorly characterized. In the present study, the effect of cyclic adenosine monophosphate (cAMP) signaling on IL‐33 production in RAW264.7 macrophages in response to various doses of LPS was examined. High‐dose LPS treatment induced IL‐33 and TNF protein production in RAW264.7 macrophages. In contrast, low‐dose LPS failed to induce IL‐33 production while significantly inducing TNF production. In the presence of the membrane‐permeable cAMP analog 8‐Br‐cAMP, low‐dose LPS induced vigorous IL‐33 production. This phenomenon was consistent with amounts of mRNA. Similarly, the cAMP‐increasing agent adrenaline also enhanced the sensitivity of RAW264.7 macrophages to LPS as demonstrated by IL‐33 production. The protein kinase A (PKA) inhibitor H89 blocked the effects of 8‐Br‐cAMP and adrenaline on IL‐33 production, suggesting that PKA is involved in IL‐33 induction. Taken together, cAMP‐mediated signaling pathway appears to enhance the sensitivity of RAW264.7 macrophages to LPS with respect to IL‐33 production. Our findings suggest that stress events and the subsequent secretion of adrenaline enhance macrophage production via IL‐33; this process may be associated with the pathogenesis of various disorders involving IL‐33.
Monitoring fluid substitution in rock samples from noise correlation
Authors: Barbouteau Sandra , Rasolofosaon Patrick , Dubos‐Sallée Noalwenn , Vassil Virginie , Nauroy Jean‐François 
Published: April 2016

ABSTRACTAn alternative laboratory technique to measure the elastic constants of solid samples, based on the analysis of the cross‐correlation spectra of the vibratory response of randomly excited short solid cylinders, has been recently proposed. The aim of this paper is to check the ability of the technique called passive ultrasonic interferometry to monitor fluid substitution in different rock samples. Velocity variations due to fluid substitution are easily measured if the wave attenuation in the fluid‐saturated rock is not too large (typically in rocks with few cracks or microfractures).The experimental results are in agreement with the predictions of Biot–Gassmann poroelastic theory. The effect of substituting water with a stiffer saturating fluid, such as ethylene glycol, is to increase the overall bulk modulus of the rock, without any substantial effect on shear modulus. Furthermore, the experimental results compare well with those obtained independently with conventional pulse‐transmission technique using ultrasonic transducers. However, the measured pulse‐transmission bulk moduli are slightly larger than the corresponding measured ultrasonic interferometry moduli, with the deviation increasing with increasing fluid viscosity. This can be explained by dispersion due to wave‐induced flow of the viscous fluid since pulse‐transmission experiments involve higher frequencies than ultrasonic interferometry experiments.
Regularized tomographic inversion with geological constraints
Authors: Lipari Vincenzo , Urbano Domenico , Spadavecchia Emmanuel , Panizzardi Jacopo , Bienati Nicola 
Published: April 2016

ABSTRACTReflection tomography is the industry standard tool for velocity model building, but it is also an ill‐posed inverse problem as its solution is not unique. The usual way to obtain an acceptable result is to regularize tomography by feeding the inversion with some a priori information. The simplest regularization forces the solution to be smooth, implicitly assuming that seismic velocity exhibits some degree of spatial correlation. However, velocity is a rock property; thus, the geometry and structure of rock formations should drive correlation in velocity depth models. This observation calls for constraints driven by geological models.In this work, we present a set of structural constraints that feed reflection tomography with geometrical information. These constraints impose the desired characteristics (flatness, shape, position, etc.) on imaged reflectors but act on the velocity update. Failure to respect the constraints indicates either velocity inaccuracies or wrong assumptions concerning the constraints.Reflection tomography with structural constraints is a flexible framework that can be specialized in order to achieve different goals: among others, to flatten the base of salt bodies or detachment surfaces, to recover the horizontalness of oil–water contacts, or to impose the co‐location of the same imaged horizon between PP and PS images.The straightforward application of structural constraints is that of regularizing tomography through geological information, particularly at the latest stages of the depth imaging workflow, when the depth migration structural setting reached a consistent geological interpretation. Structural constraints are also useful in minimizing the well‐to‐seismic mis‐ties. Moreover, they can be used as a tool to check the consistency of interpreters' hypothesis with seismic data. Indeed, inversion with structural constraints will preserve image focusing only if the interpreters' insights are consistent with the data.Results from synthetic and real data demonstrate the effectiveness of reflection tomography with structural constraints.
Response of migrating raptors to an increasing number of wind farms
Authors: Cabrera‐Cruz Sergio A. , Villegas‐Patraca Rafael 
Published: April 2016

SummaryFlying birds have been documented to respond in different ways to the presence of wind farms. Such responses are species‐ and site‐specific, with wind farm design playing an important role. Between 2009 and 2014, the length of rows of wind turbines within our study area increased from 3·4 km to ∼7·5 km, and the total area occupied by wind farms increased from 6·47 km2to 14·21 km2. This area is located on an important migratory corridor in southern Mexico.We used marine radar and hawk‐watch monitoring stations to collect data during six consecutive autumn seasons from a single wind farm. We analysed the response of migrating raptors to the presence of two new wind farms by comparing the mean bearing of flight trajectories and the number of intersections km−1of trajectories with wind farm areas between 2009–2011 and 2012–2014, representing the pre‐ and post‐construction stages of the new wind farms.Mean raptor count was >600 000 individuals for the six seasons. The most abundant species were Turkey VultureCathartes aura, Swainson's HawkButeo swainsoniand Broad‐winged hawkButeo platypterus. Between 79% and 97% of migration occurred in October. Radar monitoring overlapped with the peak migratory activity each season.We observed significant differences between periods, involving more scattering in flight bearings and less intersections km−1of trajectory in the post‐ than in the pre‐construction period, implying an avoidance of the new wind farms.Synthesis and applications. We show that migrating raptors adjusted their flight trajectories to avoid new wind farms, but also discuss the extent and limitations of our findings. Our results from our hawk‐watch monitoring station, which represent the first published account about the seasonality and intensity of raptor migration in the area, could be used by decision‐makers for careful planning of future wind energy developments in the area. Our results might aid in the conservation of those species of raptors that migrate through the Isthmus of Tehuantepec.
Latitudinal variation in herbivory: hemispheric asymmetries and the role of climatic drivers
Authors: Zhang Shuang , Zhang Yuxin , Ma Keming 
Published: April 2016

Summary

In the past, it was widely accepted that herbivory decreased with latitude. However, several empirical studies have failed to support this hypothesis, leading to strong debate. In addition to providing a quantitative assessment of the latitudinal gradient in herbivory, our study aims to provide new information about the role of climatic factors in shaping the latitudinal gradient in herbivory.

Through the collection and analysis of published data on herbivory, we tested the latitudinal herbivory hypothesis (LH hypothesis) and the relationship of temperature and precipitation to herbivory.

Based on 1890 data points distributed world‐wide from more than 1000 plant species, our results show that herbivory decreased with latitude and increased with temperature only in the Northern Hemisphere. In contrast, in the Southern Hemisphere, herbivory did not have a relationship with latitude and tended to decrease with temperature.

Synthesis. This study shows the LH hypothesis is supported only in the Northern Hemisphere and highlights the importance of temperature in explaining the pattern of herbivory at the global scale. These possible hemispheric asymmetries in herbivory should not be overlooked in future studies.
Genetic and functional characterization of a novel meta‐pathway for degradation of naringenin in Herbaspirillum seropedicae SmR1
Authors: Maria Marin Anelis , de la Torre Jésus , Ricardo Marques Oliveira Alfredo , Barison Andersson , Satie Chubatsu Leda , Adele Monteiro Rose , de Oliveira Pedrosa Fabio , Maltempi de Souza Emanuel , Wassem Roseli , Duque Estrella , Ramos Juan‐Luis 
Published: April 2016

SummaryIn this study, a random mutant library of Herbaspirillum seropedicae SmR1 was constructed by Tn5 insertion and a mutant incapable of utilizing naringenin as a carbon source was isolated. The Tn5 transposon was found to be inserted in the fdeE gene (Hsero_1007), which encodes a monooxygenase. Two other mutant strains in fdeC (Hsero_1005) and fdeG (Hsero_1009) genes coding for a dioxygenase and a putative cyclase, respectively, were obtained by site‐directed mutagenesis and then characterized. Liquid Chromatography coupled to mass spectrometry (LC‐MS)/MS analyses of culture supernatant from the fdeE mutant strain revealed that naringenin remained unaltered, suggesting that the FdeE protein is involved in the initial step of naringenin degradation. LC‐MS/MS analyses of culture supernatants from the wild‐type (SmR1) and FdeC deficient mutant suggested that in H. seropedicae SmR1 naringenin is first mono‐oxygenated by the FdeE protein, to produce 5,7,8‐trihydroxy‐2‐(4‐hydroxyphenyl)−2,3‐dihydro‐4H‐chromen‐4‐one, that is subsequently dioxygenated and cleaved at the A‐ring by the FdeC dioxygenase, since the latter compound accumulated in the fdeC strain. After meta‐cleavage of the A‐ring, the subsequent metabolic steps generate oxaloacetic acid that is metabolized via the tricarboxylic acid cycle. This bacterium can also modify naringenin by attaching a glycosyl group to the B‐ring or a methoxy group to the A‐ring, leading to the generation of dead‐end products.
Thioredoxins are involved in the activation of the PMK1 MAP kinase pathway during appressorium penetration and invasive growth in Magnaporthe oryzae
Authors: Zhang Shijie , Jiang Cong , Zhang Qiang , Qi Linlu , Li Chaohui , Xu Jin‐Rong 
Published: April 2016

SummaryIn Magnaporthe oryzae, the Mst11‐Mst7‐Pmk1 MAP kinase pathway is essential for appressorium formation and invasive growth. To determine their roles in Pmk1 activation and plant infection, we characterized the two thioredoxin genes, TRX1 and TRX2, in M. oryzae. Whereas the Δtrx1 mutants had no detectable phenotypes, deletion of TRX2 caused pleiotropic defects in growth, conidiation, light sensing, responses to stresses and plant infection progresses. The Δtrx1 Δtrx2 double mutant had more severe defects than the Δtrx2 mutant and was non‐pathogenic in infection assays. The Δtrx2 and Δtrx1 Δtrx2 mutant rarely formed appressoria on hyphal tips and were defective in invasive growth after penetration. Pmk1 phosphorylation was barely detectable in the Δtrx2 and Δtrx1 Δtrx2 mutants. Deletion of TRX2 affected proper folding or intra‐/inter‐molecular interaction of Mst7 and expression of the dominant active MST7 allele partially rescued the defects of the Δtrx1 Δtrx2 mutant. Furthermore, Cys305 is important for Mst7 function and Trx2 directly interacts with Mst7 in co‐IP assays. Our data indicated that thioredoxins play important roles in intra‐cellular ROS signalling and pathogenesis in M. oryzae. As the predominant thioredoxin gene, TRX2 may regulate the activation of Pmk1 MAPK via its effects on Mst7.
Impact of an intense water column mixing (0–1500 m) on prokaryotic diversity and activities during an open‐ocean convection event in the NW Mediterranean Sea
Authors: Severin Tatiana , Sauret Caroline , Boutrif Mehdi , Duhaut Thomas , Kessouri Fayçal , Oriol Louise , Caparros Jocelyne , Pujo‐Pay Mireille , Durrieu de Madron Xavier , Garel Marc , Tamburini Christian , Conan Pascal , Ghiglione Jean‐François 
Published: April 2016

SummaryOpen‐ocean convection is a fundamental process for thermohaline circulation and biogeochemical cycles that causes spectacular mixing of the water column. Here, we tested how much the depth‐stratified prokaryotic communities were influenced by such an event, and also by the following re‐stratification. The deep convection event (0–1500 m) that occurred in winter 2010–2011 in the NW Mediterranean Sea resulted in a homogenization of the prokaryotic communities over the entire convective cell, resulting in the predominance of typical surface Bacteria, such as Oceanospirillale and Flavobacteriales. Statistical analysis together with numerical simulation of vertical homogenization evidenced that physical turbulence only was not enough to explain the new distribution of the communities, but acted in synergy with other parameters such as exported particulate and dissolved organic matters. The convection also stimulated prokaryotic abundance (+21%) and heterotrophic production (+43%) over the 0–1500 m convective cell, and resulted in a decline of cell‐specific extracellular enzymatic activities (−67%), thus suggesting an intensification of the labile organic matter turnover during the event. The rapid re‐stratification of the prokaryotic diversity and activities in the intermediate layer 5 days after the intense mixing indicated a marked resilience of the communities, apart from the residual deep mixed water patch.
Effect of Lactobacillus plantarum LS5 on oxidative stability and lipid modifications of Doogh
Authors: Hashemi Seyed Mohammad Bagher , Shahidi Fakhri , Mortazavi Seyed Ali , Milani Elnaz , Eshaghi Zarrin 
Published: April 2016

The oxidative stability and lipid modifications of Doogh prepared with Lactobacillus plantarum LS5 and control Doogh were compared during storage for 22 days. In vitro scavenging activity against 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) free radicals showed that L. plantarum LS5 had radical scavenging activities (49.6%). Peroxide value, conjugated diene value and anisidine value measurements in Doogh lipid samples in combination with Fourier transform infrared spectroscopy demonstrated that Doogh prepared with L. plantarum LS5 was more stable than the control against formation of primary and secondary oxidation products. Furthermore, higher concentrations of short‐chain fatty acids (butyric and caproic) and unsaturated fatty acids were found in Doogh treated with L. plantarum LS5. Changes in the thermograms of all samples were also observed. Results of differential scanning calorimetry indicated that melting points of lipids from treated Doogh were lower than for the control. It was concluded that L. plantarum LS5 could be used as a natural preservative in functional dairy products and could beneficially affect the consumer by providing dietary sources of antioxidants.
Farmer Participation, Entry and Exit Decisions in the Italian Crop Insurance Programme
Authors: Santeramo F. G. , Goodwin B. K. , Adinolfi F. , Capitanio F. 
Published: April 2016

AbstractThe factors affecting the demand for agricultural insurance in theUSAhave been extensively studied over the last two decades. However, the determinants of a farm's entry and exit decisions in the insurance market have received relatively little attention. Turnover in the insurance book of business is an important issue in most private and public crop insurance plans. Moreover, insurance markets in theEUare still largely under‐investigated. We investigate empirically the determinants of crop insurance participation in Italy. We show that the participation rate is high for large firms and that it is negatively correlated with crop diversification, which is itself a form of insurance. High premiums tend to inhibit both entry and exit from the insurance market. Larger and wealthier farms are more likely to adopt insurance and renew coverage over time. We discuss implications of our results for public intervention and the private industry. In particular, we demonstrate that the decision to drop coverage by an insured grower may differ significantly from the corresponding decision to enroll in an insurance programme by an uninsured farmer. To the extent that policymakers want to encourage participation in subsidized crop insurance programmes, education and outreach efforts toward uninsured farmers may differ substantially from those directed toward keeping insured farmers enrolled in the programme. We investigate these differences.
Measuring House Price Bubbles
Authors: Bourassa Steven C. , Hoesli Martin , Oikarinen Elias 
Published: April 2016

AbstractUsing data for six metropolitan housing markets in three countries, this article provides a comparison of methods used to measure house price bubbles. We use an asset pricing approach to identify bubble periods retrospectively and then compare those results with results produced by six other methods. We also apply the various methods recursively to assess their ability to identify bubbles as they form. In view of the complexity of the asset pricing approach, we conclude that a simple price–rent ratio measure is a reliable method both ex post and in real time. Our results have important policy implications because a reliable signal that a bubble is forming could be used to avoid further house price increases.