bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeated evolution of camouflage in speciose desert rodents
Authors: Boratyński Zbyszek , Brito José C. , Campos João C. , Cunha José L. , Granjon Laurent , Mappes Tapio , Ndiaye Arame , Rzebik-Kowalska Barbara , Serén Nina 
Published: June 2017

AbstractThere are two main factors explaining variation among species and the evolution of characters along phylogeny: adaptive change, including phenotypic and genetic responses to selective pressures, and phylogenetic inertia, or the resemblance between species due to shared phylogenetic history. Phenotype-habitat colour match, a classic Darwinian example of the evolution of camouflage (crypsis), offers the opportunity to test the importance of historical versus ecological mechanisms in shaping phenotypes among phylogenetically closely related taxa. To assess it, we investigated fur (phenotypic data) and habitat (remote sensing data) colourations, along with phylogenetic information, in the species-rich Gerbillus genus. Overall, we found a strong phenotype-habitat match, once the phylogenetic signal is taken into account. We found that camouflage has been acquired and lost repeatedly in the course of the evolutionary history of Gerbillus. Our results suggest that fur colouration and its covariation with habitat is a relatively labile character in mammals, potentially responding quickly to selection. Relatively unconstrained and substantial genetic basis, as well as structural and functional independence from other fitness traits of mammalian colouration might be responsible for that observation.
Excess reciprocity distorts reputation in online social networks
Authors: Livan Giacomo , Caccioli Fabio , Aste Tomaso 
Published: June 2017

AbstractThe peer-to-peer (P2P) economy relies on establishing trust in distributed networked systems, where the reliability of a user is assessed through digital peer-review processes that aggregate ratings into reputation scores. Here we present evidence of a network effect which biases digital reputation, revealing that P2P networks display exceedingly high levels of reciprocity. In fact, these are much higher than those compatible with a null assumption that preserves the empirically observed level of agreement between all pairs of nodes, and rather close to the highest levels structurally compatible with the networks’ reputation landscape. This indicates that the crowdsourcing process underpinning digital reputation can be significantly distorted by the attempt of users to mutually boost reputation, or to retaliate, through the exchange of ratings. We uncover that the least active users are predominantly responsible for such reciprocity-induced bias, and that this fact can be exploited to obtain more reliable reputation estimates. Our findings are robust across different P2P platforms, including both cases where ratings are used to vote on the content produced by users and to vote on user profiles.
Family aggression in a social lizard
Authors: Botterill-James Thomas , Halliwell Ben , McKeown Simon , Sillince Jacinta , Uller Tobias , Wapstra Erik , While Geoffrey M. 
Published: June 2017

AbstractThe evolution of family living is underpinned by conflict and cooperation between family members. While family groups can be maintained by reducing conflict between parents and offspring, interactions between siblings may play an equally important role. Here, we compared the level of aggressive interactions between siblings to that between parents and their offspring in the family living skinkLiopholis whitii. Aggressive interactions occurred much more frequently between siblings and between fathers and offspring than between mothers and their offspring. These results suggest that ecological and social conditions that reduce conflict between siblings and between males and offspring will be fundamental in the evolutionary maintenance and diversification of family living in these lizards.
Transcriptome profiling of Cucumis metuliferus infected by Meloidogyne incognita provides new insights into putative defense regulatory network in Cucurbitaceae
Authors: Ling Jian , Mao Zhenchuan , Zhai Mingjuan , Zeng Feng , Yang Yuhong , Xie Bingyan 
Published: June 2017

AbstractRoot-knot nematodes (RKN) represent extensive challenges to Cucurbitaceae crops. However,Cucumis metuliferus(Cm) is known to be resistant toMeloidogyne incognita(Mi) infections. Thus, analysis of differentially expressed genes may lead to a comprehensive gene expression profiling of the incompatibleCm-Miinteraction. In this study, the time-course transcriptome ofCmagainstMiinfection was monitored using RNA-Seq. More than 170000 transcripts were examined inCmroots, and 2430 genes were subsequently identified as differentially expressed in response toMiinfection. Based on function annotation and orthologs finding, the potential mechanism of transcriptional factor, cytoskeleton, pathogen-related genes and plant hormone were assessed at the transcription level. A comparison of gene expression levels betweenMi-infectedCmand cucumber plants revealed that cytoskeleton-related genes are key regulators ofCmresistance toMi. We herein discuss the dual nature of cytoskeleton-related genes in the susceptibility and resistance of plant hosts toMi. Our observations provide novel insights into the responses ofCmtoMiat the transcriptome level. The data generated in this study may be useful for elucidating the mechanism underlying resistance to RKNs in cucurbitaceous crops.
Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations
Authors: Cella Eleonora , Ciccozzi Massimo , Lo Presti Alessandra , Fogolari Marta , Azarian Taj , Prosperi Mattia , Salemi Marco , Equestre Michele , Antonelli Francesca , Conti Alessia , Cesaris Marina De , Spoto Silvia , Incalzi Raffaele Antonelli , Coppola Roberto , Dicuonzo Giordano , Angeletti Silvia 
Published: June 2017

AbstractCarbapenems resistantEnterobacteriaceaeinfections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistantK.pneumoniaestrains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion ofK.pneumoniaein support of hospital infection control. The epidemic curve of incidentK.pneumoniaecases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested thatK.pneumoniaestrains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.
Development of a computer-aided design and finite-element analysis combined method for customized Nuss bar in pectus excavatum surgery
Authors: Xie Longhan , Cai Siqi , Xie Liang , Chen Gang , Zhou Haiyu 
Published: June 2017

AbstractPectus excavatum (PEX) is the most common chest deformity in children, which is usually corrected by using the minimally invasive Nuss method. The orthopedic effect of the Nuss operation is mainly evaluated by both the Haller index and the appearance of the chest wall configuration, which is dependent on the operator’s clinical experience to a great extent. To improve the orthopedic effect, we proposed a novel method to individually design and optimize the shape of the Nuss bar and to advise its location as well as the incisions. By using the CT imaging data, the three-dimensional model of the PEX thoracic structure is reconstructed, which is further employed in finite element analysis to determine the operation plan. By referring to a healthy person who has similar chest dimensions to the PEX patient, the Nuss bar shape is designed, and according to the finding that the healthy chest wall boundary is almost convex with positive curvature, the Nuss bar shape is tuned to be a convex curve to ensure the orthopedic effect. Finite element analysis is employed to analyze the orthopedic effect and to determine the incision position of the Nuss bar. Experiments were carried out to verify the orthopedic effect of the customized Nuss bar, which showed that this method is more accurate and individualized, compared to conventional methods.
Cognitive and Metacognitive Mechanisms of Change in Metacognitive Training for Depression
Authors: Jelinek Lena , Van Quaquebeke Niels , Moritz Steffen 
Published: June 2017

AbstractMetacognitive Training for Depression (D-MCT), a low-threshold group intervention, has been shown to improve depressive symptoms. It aims at the reduction of depression by changing dysfunctional cognitive as well as metacognitive beliefs. The purpose of the present study was to investigate whether the mechanisms of change in D-MCT are cognitive (and thus primarily concern the content of cognition) or metacognitive in nature. Eighty-four outpatients with depression were included in a randomized controlled trial comparing D-MCT to an active control intervention. Level of depression, dysfunctional cognitive beliefs (DAS), and metacognitive beliefs (MCQ subscales: Positive Beliefs, Negative Beliefs, Need for Control) were assessed before (t0) and after treatment (t1). Severity of depression was also assessed 6 months later (t2). Linear regression analyses were used to determine whether change in depression from t0 to t2 was mediated by change in cognitive vs. metacognitive beliefs from t0 to t1. D-MCT’s effect on change in depression was mediated by a decrease in dysfunctional metacognitive beliefs, particularly ‘need for control’. Our findings underline that one of the key mechanisms of improvement in D-MCT is the change in metacognitive beliefs. The current study provides further support for the importance of metacognition in the treatment of depression.
Channel branching and zigzagging in negative cloud-to-ground lightning
Authors: Jiang Rubin , Qie Xiushu , Zhang Hongbo , Liu Mingyuan , Sun Zhuling , Lu Gaopeng , Wang Zhichao , Wang Yu 
Published: June 2017

AbstractA fundamental question in lightning flash concerns why the discharge channel propagates in a zig-zag manner and produces extensive branches. Here we report the optical observation of two negative cloud-to-ground lightning discharges with very high temporal resolution of 180,000 frames per second, which shows in detail the dependence of channel branching and tortuous behavior on the stepping process of the leader development. It is found that the clustered space leaders formed in parallel ahead of the channel tip during an individual step process. The leader branching is due to the multiple connection of the clustered space leaders with the same root channel tip, which occur almost simultaneously, or successively as some space leaders/stems resurrect after interruption. Meanwhile, the irregularity of angles between the clustered space leaders and the advancing direction of leader tip is the origin of channel tortuosity. The statistical analysis on 96 steps shows a geometric-mean value of 4.4 m for the step length, ranging between 1.3 and 8.6 m, while the distance from the center of space leader to the channel is 3.6 m, ranging between 2.1 and 6.9 m. More than 50% steps occurred within an angle range of ±30° from the advancing direction of the leader.
Tunable transport property of oxygen ion in metal oxide thin film: Impact of electrolyte orientation on conductivity
Authors: Arunkumar P. , Ramaseshan R. , Dash S. , Babu K. Suresh 
Published: June 2017

AbstractQuest for efficient ion conducting electrolyte thin film operating at intermediate temperature (~600 °C) holds promise for the real-world utilization of solid oxide fuel cells. Here, we report the correlation between mixed as well as preferentially oriented samarium doped cerium oxide electrolyte films fabricated by varying the substrate temperatures (100, 300 and 500 °C) over anode/ quartz by electron beam physical vapor deposition. Pole figure analysis of films deposited at 300 °C demonstrated a preferential (111) orientation in out-off plane direction, while a mixed orientation was observed at 100 and 500 °C. As per extended structural zone model, the growth mechanism of film differs with surface mobility of adatom. Preferential orientation resulted in higher ionic conductivity than the films with mixed orientation, demonstrating the role of growth on electrochemical properties. The superior ionic conductivity upon preferential orientation arises from the effective reduction of anisotropic nature and grain boundary density in highly oriented thin films in out-of-plane direction, which facilitates the hopping of oxygen ion at a lower activation energy. This unique feature of growing an oriented electrolyte over the anode material opens a new approach to solving the grain boundary limitation and makes it as a promising solution for efficient power generation.
Invisible noise obscures visible signal in insect motion detection
Authors: Tarawneh Ghaith , Nityananda Vivek , Rosner Ronny , Errington Steven , Herbert William , Cumming Bruce G. , Read Jenny C. A. , Serrano-Pedraza Ignacio 
Published: June 2017

AbstractThe motion energy model is the standard account of motion detection in animals from beetles to humans. Despite this common basis, we show here that a difference in the early stages of visual processing between mammals and insects leads this model to make radically different behavioural predictions. In insects, early filtering is spatially lowpass, which makes the surprising prediction that motion detection can be impaired by “invisible” noise, i.e. noise at a spatial frequency that elicits no response when presented on its own as a signal. We confirm this prediction using the optomotor response of praying mantis Sphodromantis lineola. This does not occur in mammals, where spatially bandpass early filtering means that linear systems techniques, such as deriving channel sensitivity from masking functions, remain approximately valid. Counter-intuitive effects such as masking by invisible noise may occur in neural circuits wherever a nonlinearity is followed by a difference operation.
Serotyping dengue virus with isothermal amplification and a portable sequencer
Authors: Yamagishi Junya , Runtuwene Lucky R. , Hayashida Kyoko , Mongan Arthur E. , Thi Lan Anh Nguyen , Thuy Linh Nguyen , Nhat Cam Nguyen , Limkittikul Kriengsak , Sirivichayakul Chukiat , Sathirapongsasuti Nuankanya , Frith Martin , Makalowski Wojciech , Eshita Yuki , Sugano Sumio , Suzuki Yutaka 
Published: June 2017

AbstractThe recent development of a nanopore-type portable DNA sequencer has changed the way we think about DNA sequencing. We can perform sequencing directly in the field, where we collect the samples. Here, we report the development of a novel method to detect and genotype tropical disease pathogens, using dengue fever as a model. By combining the sequencer with isothermal amplification that only requires a water bath, we were able to amplify and sequence target viral genomes with ease. Starting from a serum sample, the entire procedure could be finished in a single day. The analysis of blood samples collected from 141 Indonesian patients demonstrated that this method enables the clinical identification and serotyping of the dengue virus with high sensitivity and specificity. The overall successful detection rate was 79%, and a total of 58 SNVs were detected. Similar analyses were conducted on 80 Vietnamese and 12 Thai samples with similar performance. Based on the obtained sequence information, we demonstrated that this approach is able to produce indispensable information for etiologically analyzing annual or regional diversifications of the pathogens.
Trilocular phenotype in Brassica juncea L. resulted from interruption of CLAVATA1 gene homologue (BjMc1) transcription
Authors: Xu Ping , Cao Shiqin , Hu Kaining , Wang Xiaohua , Huang Wei , Wang Gang , Lv Zewen , Liu Zhongsong , Wen Jing , Yi Bin , Ma Chaozhi , Tu Jinxing , Fu Tingdong , Shen Jinxiong 
Published: June 2017

AbstractAs a desirable agricultural trait, multilocular trait of rapeseed (Brassica rapa; Brassica napus; Brassica juncea), always represents higher yield per plant compared with bilocular plants. We previously isolated a trilocular gene locus, Bjmc1, and identified a set of molecular markers linked to the trilocular gene. With a map-based cloning, we identified that the BjMc1 was located in B genome of Brassica juncea, and it was a CLAVATA1 (CLV1) gene homologue. The insertion of a copia-LTR retrotransposable element 1 (RTE1) into the coding region of BjMc1 interrupted its transcription in rapeseed, leading to the trilocular phenotype. Phylogenetic analysis showed that Mc1 genes were conserved and widespread in land plants. Two amino acid sites had undergone positive selection in the ancestor of Mc1 genes, and then purifying selection was the dominant force after the divergence of dicots and monocots from their common ancestor in the evolutionary process, indicating that Mc1 genes are conserved in modern land plants. Our results provided new insights in molecular regulatory mechanism of multilocularity in rapeseed, and better understanding of molecular mechanism in crop yield improvement.
Microfluidic co-cultures of retinal pigment epithelial cells and vascular endothelial cells to investigate choroidal angiogenesis
Authors: Chen Li-Jiun , Ito Shuntaro , Kai Hiroyuki , Nagamine Kuniaki , Nagai Nobuhiro , Nishizawa Matsuhiko , Abe Toshiaki , Kaji Hirokazu 
Published: June 2017

AbstractAngiogenesis plays a critical role in many diseases, including macular degeneration. At present, the pathological mechanisms remain unclear while appropriate models dissecting regulation of angiogenic processes are lacking. We propose an in vitro angiogenesis process and test it by examining the co-culture of human retinal pigmental epithelial cells (ARPE-19) and human umbilical vein endothelial cells (HUVEC) inside a microfluidic device. From characterisation of the APRE-19 monoculture, the tight junction protein (ZO-1) was found on the cells cultured in the microfluidic device but changes in the medium conditions did not affect the integrity of monolayers found in the permeability tests. Vascular endothelial growth factor (VEGF) secretion was elevated under low glucose and hypoxia conditions compared to the control. After confirming the angiogenic ability of HUVEC, the cell-cell interactions were analyzed under lowered glucose medium and chemical hypoxia by exposing ARPE-19 cells to cobalt (II) chloride (CoCl2). Heterotypic interactions between ARPE-19 and HUVEC were observed, but proliferation of HUVEC was hindered once the monolayer of ARPE-19 started breaking down. The above characterisations showed that alterations in glucose concentration and/or oxygen level as induced by chemical hypoxia causes elevations in VEGF produced in ARPE-19 which in turn affected directional growth of HUVEC.
Cathepsin D regulates lipid metabolism in murine steatohepatitis
Authors: Houben Tom , Oligschlaeger Yvonne , Hendrikx Tim , Bitorina Albert V. , Walenbergh Sofie M. A. , van Gorp Patrick J. , Gijbels Marion J. J. , Friedrichs Silvia , Plat Jogchum , Schaap Frank G. , Lütjohann Dieter , Hofker Marten H. , Shiri-Sverdlov Ronit 
Published: June 2017

AbstractDue to the obesity epidemic, non-alcoholic steatohepatitis (NASH) is a prevalent liver disease, characterized by fat accumulation and inflammation of the liver. However, due to a lack of mechanistic insight, diagnostic and therapeutic options for NASH are poor. Recent evidence has indicated cathepsin D (CTSD), a lysosomal enzyme, as a marker for NASH. Here, we investigated the function of CTSD in NASH by using an in vivo and in vitro model. In addition to diminished hepatic inflammation, inhibition of CTSD activity dramatically improved lipid metabolism, as demonstrated by decreased plasma and liver levels of both cholesterol and triglycerides. Mechanistically, CTSD inhibition resulted in an increased conversion of cholesterol into bile acids and an elevated excretion of bile acids via the feces, indicating that CTSD influences lipid metabolism. Consistent with these findings, treating Wt BMDMs with PepA in vitro showed a similar decrease in inflammation and an analogous effect on cholesterol metabolism. Conclusion: CTSD is a key player in the development of hepatic inflammation and dyslipidemia. Therefore, aiming at the inhibition of the activity of CTSD may lead to novel treatments to combat NASH.
Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum
Authors: Payton Laura , Perrigault Mickael , Hoede Claire , Massabuau Jean-Charles , Sow Mohamedou , Huvet Arnaud , Boullot Floriane , Fabioux Caroline , Hegaret Hélène , Tran Damien 
Published: June 2017

AbstractAs a marine organism, the oyster Crassostrea gigas inhabits a complex biotope governed by interactions between the moon and the sun cycles. We used next-generation sequencing to investigate temporal regulation of oysters under light/dark entrainment and the impact of harmful algal exposure. We found that ≈6% of the gills’ transcriptome exhibits circadian expression, characterized by a nocturnal and bimodal pattern. Surprisingly, a higher number of ultradian transcripts were also detected under solely circadian entrainment. The results showed that a bloom of Alexandrium minutum generated a remodeling of the bivalve’s temporal structure, characterized by a loss of oscillations, a genesis of de novo oscillating transcripts, and a switch in the period of oscillations. These findings provide unprecedented insights into the diurnal landscape of the oyster’s transcriptome and pleiotropic remodeling due to toxic algae exposure, revealing the intrinsic plasticity of the cycling transcriptome in oysters.
Bone morphogenetic protein 4 promotes the survival and preserves the structure of flow-sorted Bhlhb5+ cochlear spiral ganglion neurons in vitro
Authors: Waqas Muhammad , Sun Shan , Xuan Chuanyin , Fang Qiaojun , Zhang Xiaoli , Islam Irum-us , Qi Jieyu , Zhang Shasha , Gao Xia , Tang Mingliang , Shi Haibo , Li Huawei , Chai Renjie 
Published: June 2017

AbstractSGNs are the primary auditory neurons, and damage or loss of SGNs leads to sensorineural hearing loss. BMP4 is a growth factor that belongs to the TGF-β superfamily and has been shown to play a key role during development, but little is known about its effect on postnatal cochlear SGNs in mice. In this study, we used the P3 Bhlhb5-cre/tdTomato transgenic mouse model and FACS to isolate a pure population of Bhlhb5+ SGNs. We found that BMP4 significantly promoted SGN survival after 7 days of culture. We observed fewer apoptotic cells and decreased expression of pro-apoptotic marker genes after BMP4 treatment. We also found that BMP4 promoted monopolar neurite outgrowth of isolated SGNs, and high concentrations of BMP4 preserved the number and the length of neurites in the explant culture of the modiolus harboring the SGNs. We showed that high concentration of BMP4 enhanced neurite growth as determined by the higher average number of filopodia and the larger area of the growth cone. Finally, we found that high concentrations of BMP4 significantly elevated the synapse density of SGNs in explant culture. Thus, our findings suggest that BMP4 has the potential to promote the survival and preserve the structure of SGNs.