bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary morphology of the lizard chemosensory system
Authors: Baeckens Simon , Herrel Anthony , Broeckhoven Chris , Vasilopoulou-Kampitsi Menelia , Huyghe Katleen , Goyens Jana , Van Damme Raoul 
Published: August 2017

AbstractForaging mode plays a pivotal role in traditional reconstructions of squamate evolution. Transitions between modes are said to spark concerted changes in the morphology, physiology, behaviour, and life history of lizards. With respect to their sensory systems, species that adopt a sit-and-wait strategy are thought to rely on visual cues primarily, while actively hunting species would predominantly use chemical information. The morphology of the tongue and the vomeronasal-organs is believed to mirror this dichotomy. Still, support for this idea of concerted evolution of the morphology of the lizard sensory system merely originates from studies comparing only a few, distantly related taxa that differ in many aspects of their biology besides foraging mode. Hence, we compared vomeronasal-lingual morphology among closely related lizard species (Lacertidae). Our findings show considerable interspecific variation indicating that the chemosensory system of lacertids has undergone substantial change over a short evolutionary time. Although our results imply independent evolution of tongue and vomeronasal-organ form, we find evidence for co-variation between sampler and sensor, hinting towards an ‘optimization’ for efficient chemoreception. Furthermore, our findings suggest species’ degree of investment in chemical signalling, and not foraging behaviour, as a leading factor driving the diversity in vomeronasal-lingual morphology among lacertid species.
Prognostic performance of three lymph node staging schemes for patients with Siewert type II adenocarcinoma of esophagogastric junction
Authors: Xu Jinming , Cao Jinlin , Wang Luming , Wang Zhitian , Wang Yiqing , Wu Yihua , Lv Wang , Hu Jian 
Published: August 2017

AbstractThe prognostic performance of different lymph node staging schemes for adenocarcinoma of esophagogastric junction (AEG) remains controversial. The objective of the present study was to compare the prognostic efficacy of the number of lymph node metastases (LNMs), the positive lymph node ratio (LNR) and the log odds of positive lymph nodes (LODDS). Patients diagnosed with Siewert type II AEG were included from the Surveillance, Epidemiology, and End Results database. Harrell’s C-index statistic, Schemper’s proportion of explained variation (PEV), the Akaike information criterion (AIC) and restricted cubic spine analyses were adopted to assess the predictive accuracy of LNM, LNR and LODDS. A total of 1302 patients with post-surgery Siewert type II AEG were included. LNM, LNR and LODDS all showed significant prognostic value in the multivariate Cox regression analyses. LODDS performed higher predictive accuracy than LNM and LNR, with relatively higher C-index, higher Schemper’s PEV value and lower AIC value. For patients with no nodes involved, LODDS still performed significantly discriminatory utility. LODDS showed more accurate prognostic performance than LNM and LNR for post-surgery Siewert type II AEG, and it could help to detect survival heterogeneity for patients with no positive lymph nodes involved.
Distinct clinical features between acute and chronic progressive parenchymal neuro-Behçet disease: meta-analysis
Authors: Ishido Mizuho , Horita Nobuyuki , Takeuchi Masaki , Shibuya Etsuko , Yamane Takahiro , Kawagoe Tatsukata , Ishido Takehito , Minegishi Kaoru , Yoshimi Ryusuke , Kirino Yohei , Hirohata Shunsei , Ishigatsubo Yoshiaki , Takeno Mitsuhiro , Kaneko Takeshi , Mizuki Nobuhisa 
Published: August 2017

AbstractNeuro-Behçet’s disease (NBD) is subcategorized into parenchymal-NBD (P-NBD) and non-parenchymal-NBD types. Recently, P-NBD has been further subdivided into acute P-NBD (A-P-NBD) and chronic progressive P-NBD (CP-P-NBD). Although an increasing number of studies have reported the various clinical features of A-P-NBD and CP-P-NBD over the last two decades, there was a considerable inconsistency. Two investigators systematically searched four electrical databases to detect studies that provided sufficient data to assess the specific characteristics of A-P-NBD and CP-P-NBD. All meta-analysis was carried out by employing the random-model generic inverse variance method. We included 11 reports consisted of 184 A-P-NBD patients and 114 CP-P-NBD patients. While fever (42% for A-P-NBD, 5% for CP-P-NBD, p < 0.001, I2 = 93%) was more frequently observed in A-P-NBD cases; sphincter disturbances (9%, 34%, P = 0.005, I2 = 87%), ataxia (16%, 57%, P < 0.001, I2 = 92%), dementia (7%, 61%, P < 0.001, I2 = 97%), confusion (5%, 18%, P = 0.04, I2 = 76%), brain stem atrophy on MRI (4%, 75%, P < 0.001, I2 = 98%), and abnormal MRI findings in cerebellum (7%, 54%, P = 0.02, I2 = 81%) were more common in CP-P-NBD. Cerebrospinal fluid cell count (94/mm3, 11/mm3, P = 0.009, I2 = 85%) was higher in A-P-NBD cases. We demonstrated that A-P-NBD and CP-P-NBD had clearly different clinical features and believe that these data will help future studies investigating P-NBD.
Odorant-odorant metabolic interaction, a novel actor in olfactory perception and behavioral responsiveness
Authors: Hanser Hassan-Ismail , Faure Philippe , Robert-Hazotte Aline , Artur Yves , Duchamp-Viret Patricia , Coureaud Gérard , Heydel Jean-Marie 
Published: August 2017

AbstractIn the nasal olfactory epithelium, olfactory metabolic enzymes ensure odorant clearance from the olfactory receptor environment. This biotransformation of odorants into deactivated polar metabolites is critical to maintaining peripheral sensitivity and perception. Olfactory stimuli consist of complex mixtures of odorants, so binding interactions likely occur at the enzyme level and may impact odor processing. Here, we used the well-described model of mammary pheromone-induced sucking-related behavior in rabbit neonates. It allowed to demonstrate how the presence of different aldehydic odorants efficiently affects the olfactory metabolism of this pheromone (an aldehyde too: 2-methylbut-2-enal). Indeed, according to in vitro and ex vivo measures, this metabolic interaction enhances the pheromone availability in the epithelium. Furthermore, in vivo presentation of the mammary pheromone at subthreshold concentrations efficiently triggers behavioral responsiveness in neonates when the pheromone is in mixture with a metabolic challenger odorant. These findings reveal that the periphery of the olfactory system is the place of metabolic interaction between odorants that may lead, in the context of odor mixture processing, to pertinent signal detection and corresponding behavioral effect.
Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus
Authors: Chen Juan , Zeng Xu , Yang Yan Long , Xing Yong Mei , Zhang Qi , Li Jia Mei , Ma Ke , Liu Hong Wei , Guo Shun Xing 
Published: August 2017

AbstractThe lion’s mane mushroomHericium erinaceusis a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungusH. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome ofH.erinaceusreveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroomAmanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites fromH. erinaceusand provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.
Small molecule-based lineage switch of human adipose-derived stem cells into neural stem cells and functional GABAergic neurons
Authors: Park Jihye , Lee Nayeon , Lee Jaekwang , Choe Eun Kyung , Kim Min Kyung , Lee Jeonghoon , Byun Min Soo , Chon Myong-Wuk , Kim Seong Who , Lee C. Justin , Kim Ju Han , Kwon Jun Soo , Chang Mi-Sook 
Published: August 2017

AbstractCellular reprogramming using small molecules (SMs) without genetic modification provides a promising strategy for generating target cells for cell-based therapy. Human adipose-derived stem cells (hADSCs) are a desirable cell source for clinical application due to their self-renewal capacity, easy obtainability and the lack of safety concerns, such as tumor formation. However, methods to convert hADSCs into neural cells, such as neural stem cells (NSCs), are inefficient, and few if any studies have achieved efficient reprogramming of hADSCs into functional neurons. Here, we developed highly efficient induction protocols to generate NSC-like cells (iNSCs), neuron-like cells (iNs) and GABAergic neuron-like cells (iGNs) from hADSCs via SM-mediated inhibition of SMAD signaling without genetic manipulation. All induced cells adopted morphological, molecular and functional features of their bona fide counterparts. Electrophysiological data demonstrated that iNs and iGNs exhibited electrophysiological properties of neurons and formed neural networks in vitro. Microarray analysis further confirmed that iNSCs and iGNs underwent lineage switch toward a neural fate. Together, these studies provide rapid, reproducible and robust protocols for efficient generation of functional iNSCs, iNs and iGNs from hADSCs, which have utility for modeling disease pathophysiology and providing cell-therapy sources of neurological disorders.
Detecting PM2.5’s Correlations between Neighboring Cities Using a Time-Lagged Cross-Correlation Coefficient
Authors: Wang Fang , Wang Lin , Chen Yuming 
Published: August 2017

AbstractIn order to investigate the time-dependent cross-correlations of fine particulate (PM2.5) series among neighboring cities in Northern China, in this paper, we propose a new cross-correlation coefficient, the time-lagged q-L dependent height crosscorrelation coefficient (denoted by p
q
(τ, L)), which incorporates the time-lag factor and the fluctuation amplitude information into the analogous height cross-correlation analysis coefficient. Numerical tests are performed to illustrate that the newly proposed coefficient ρ
q
(τ, L) can be used to detect cross-correlations between two series with time lags and to identify different range of fluctuations at which two series possess cross-correlations. Applying the new coefficient to analyze the time-dependent cross-correlations of PM2.5 series between Beijing and the three neighboring cities of Tianjin, Zhangjiakou, and Baoding, we find that time lags between the PM2.5 series with larger fluctuations are longer than those between PM2.5 series withsmaller fluctuations. Our analysis also shows that cross-correlations between the PM2.5 series of two neighboring cities are significant and the time lags between two PM2.5 series of neighboring cities are significantly non-zero. These findings providenew scientific support on the view that air pollution in neighboring cities can affect one another not simultaneously but with a time lag.
Control of Early Flame Kernel Growth by Multi-Wavelength Laser Pulses for Enhanced Ignition
Authors: Dumitrache Ciprian , VanOsdol Rachel , Limbach Christopher M. , Yalin Azer P. 
Published: August 2017

AbstractThe present contribution examines the impact of plasma dynamics and plasma-driven fluid dynamics on the flame growth of laser ignited mixtures and shows that a new dual-pulse scheme can be used to control the kernel formation process in ways that extend the lean ignition limit. We perform a comparative study between (conventional) single-pulse laser ignition (λ = 1064 nm) and a novel dual-pulse method based on combining an ultraviolet (UV) pre-ionization pulse (λ = 266 nm) with an overlapped near-infrared (NIR) energy addition pulse (λ = 1064 nm). We employ OH* chemiluminescence to visualize the evolution of the early flame kernel. For single-pulse laser ignition at lean conditions, the flame kernel separates through third lobe detachment, corresponding to high strain rates that extinguish the flame. In this work, we investigate the capabilities of the dual-pulse to control the plasma-driven fluid dynamics by adjusting the axial offset of the two focal points. In particular, we find there exists a beam waist offset whereby the resulting vorticity suppresses formation of the third lobe, consequently reducing flame stretch. With this approach, we demonstrate that the dual-pulse method enables reduced flame speeds (at early times), an extended lean limit, increased combustion efficiency, and decreased laser energy requirements.
Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes
Authors: Bhat M. , Pasini E. , Copeland J. , Angeli M. , Husain S. , Kumar D. , Renner E. , Teterina A. , Allard J. , Guttman D. S. , Humar A. 
Published: August 2017

AbstractSolid organ transplantation (SOT) outcomes have continued to improve, although long-term use of immunosuppressants can lead to complications such as diabetes, compromising post-transplant outcomes. In this study, we have characterized the intestinal microbiome (IM) composition at the metagenomic level in the context of hyperglycemia induced by immunosuppressants. Sprague-Dawley rats were subjected to doses of tacrolimus and sirolimus that reliably induce hyperglycemia and an insulin-resistant state. Subsequent exposure to probiotics resulted in reversal of hyperglycemia. 16S rRNA and metagenomic sequencing of stool were done to identify the bacterial genes and pathways enriched in immunosuppression. Bacterial diversity was significantly decreased in sirolimus-treated rats, with 9 taxa significantly less present in both immunosuppression groups: Roseburia, Oscillospira, Mollicutes, Rothia, Micrococcaceae, Actinomycetales and Staphylococcus. Following probiotics, these changes were reversed to baseline. At the metagenomic level, the balance of metabolism was shifted towards the catabolic side with an increase of genes involved in sucrose degradation, similar to diabetes. Conversely, the control rats had greater abundance of anabolic processes and genes involved in starch degradation. Immunosuppression leads to a more catabolic microbial profile, which may influence development of diabetes after SOT. Modulation of the microbiome with probiotics may help in minimizing adverse long-term effects of immunosuppression.
Relationship between fraction of exhaled nitric oxide and airway morphology assessed by three-dimensional CT analysis in asthma
Authors: Nishimoto Koji , Karayama Masato , Inui Naoki , Mori Kazutaka , Kono Masato , Hozumi Hironao , Suzuki Yuzo , Furuhashi Kazuki , Enomoto Noriyuki , Fujisawa Tomoyuki , Nakamura Yutaro , Watanabe Hiroshi , Suda Takafumi 
Published: August 2017

AbstractFraction of exhaled nitric oxide (FeNO) provides information about chronic inflammation in asthma. However, its relationship with structural changes in the airways is unknown. We aimed to evaluate the correlation between computer-based airway changes and FeNO in patients with asthma. The wall area (WA) and airway inner luminal area (Ai) of the third- to sixth-generation bronchi were measured using three-dimensional computed tomography in asthmatic patients. Each value was corrected by body surface area (BSA). Relationships between FeNO and WA/BSA and Ai/BSA were evaluated. Forty-one clinically stable patients with asthma were evaluated. FeNO was significantly correlated with WA/BSA of the third-, fourth-, fifth- and sixth-generation bronchi (Spearman correlation coefficient (ρ) = 0.326,p = 0.041;ρ = 0.356,p = 0.025;ρ = 0.496,p = 0.002; andρ = 0.529,p < 0.001, respectively). The correlation with sixth-generation bronchi was significantly greater than with the third-generation bronchi (p = 0.047). Partial rank correlation analysis indicated FeNO was significantly correlated with WA/BSA of the sixth-generation bronchi, independent from confounding factors of Ai/BSA, age, duration of asthma, dose of inhaled corticosteroid, blood eosinophil percentage, and blood IgE (ρ = 0.360,p = 0.034). In contrast, there was no correlation between FeNO and Ai/BSA. FeNO correlates with bronchial wall thickening in asthma patients. Measurement of FeNO may be useful to detect airway remodeling in asthma.
Optical absorbing origin of chiroptical activity in planar plasmonic metasurfaces
Authors: Najafabadi Atefeh Fazel , Pakizeh Tavakol 
Published: August 2017

AbstractAs a significant characteristic of many biomolecules, chemical substances, and artificial nanostructures, chirality conduce different types of optical interactions with the spin angular momentum of the impinging light field. Although, chiral arrangement and spatial phase retardation are the key factors for obtaining chirality in three-dimensional (3D) structures, the origin of chirality in the feasible planar structures has not been thoroughly addressed. Here using an intuitive and simple analytical approach, called cross-hybridization model, the essence and properties of the optical chirality of individual planar nanostructures are unveiled. In order to fundamentally address this chirality in terms of circular dichroism (CD), the chiroptical response of a simple dimer composed of the lossy nanoblocks in L-shape arrangement are investigated based on the provided optical interaction and loss effects. The theoretical findings, adequately supported by the numerical calculations, reveal that chiroptical activity occurs predominantly due to handedness-dependent absorption or heating loss in a nanostructured metasurface.
The global view of mRNA-related ceRNA cross-talks across cardiovascular diseases
Authors: Song Chao , Zhang Jian , Qi Hanping , Feng Chenchen , Chen Yunping , Cao Yonggang , Ba Lina , Ai Bo , Wang Qiuyu , Huang Wei , Li Chunquan , Sun Hongli 
Published: August 2017

AbstractCompeting endogenous RNA (ceRNA) have received wide attention because they are a novel way to regulate genes through sharing microRNAs (miRNAs) that are crucial for complex processes in many diseases. However, no systematic analysis of ceRNA mechanism in cardiovascular disease (CVD) is known. To gain insights into the global properties of ceRNAs in multi-CVDs, we constructed the global view of mRNA-related ceRNA cross-talk in eight major CVDs from ~2,800 samples. We found common features that could be used to uncover similarities among different CVDs and highlighted a common core ceRNA network across CVDs. Comparative analysis of hub ceRNAs in each network revealed three types of hubs, which might play key roles in diverse biological processes. Importantly, by combining CVD-related pathway genes with ceRNA-ceRNA interactions, common modules that might exert functions in specific mechanisms were identified. In addition, our study investigated a potential mechanistic linkage between pathway cross-talk and ceRNA cross-talk. In summary, this study uncovered and systematically characterized global properties of mRNA-related ceRNA cross-talks across CVDs, which may provide a new layer for exploring biological mechanisms and shed new light on cardiology.
Transcriptome and proteome analysis reveal new insight into proximal and distal responses of wheat to foliar infection by Xanthomonas translucens
Authors: Garcia-Seco D. , Chiapello M. , Bracale M. , Pesce C. , Bagnaresi P. , Dubois E. , Moulin L. , Vannini C. , Koebnik R. 
Published: August 2017

AbstractThe molecular details of local plant response against Xanthomonas translucens infection is largely unknown. Moreover, there is no knowledge about effects of the pathogen on the root’s transcriptome and proteome. Therefore, we investigated the global gene and protein expression changes both in leaves and roots of wheat (Triticum aestivum) 24 h post leaf infection of X. translucens. This simultaneous analysis allowed us to obtain insight into possible metabolic rearrangements in above- and belowground tissues and to identify common responses as well as specific alterations. At the site of infection, we observed the implication of various components of the recognition, signaling, and amplification mechanisms in plant response to the pathogen. Moreover, data indicate a massive down-regulation of photosynthesis and confirm the chloroplast as crucial signaling hub during pathogen attack. Notably, roots responded as well to foliar attack and their response significantly differed from that locally triggered in infected leaves. Data indicate that roots as a site of energy production and synthesis of various secondary metabolites may actively influence the composition and colonisation level of root-associated microbes. Finally, our results emphasize the accumulation of jasmonic acid, pipecolic acid and/or the downstream mediator of hydrogen peroxide as long distal signals from infected leaves to roots.
Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing
Authors: Du Yushen , Chi Xiumei , Wang Chong , Jiang Jing , Kong Fei , Yan Hongqing , Wang Xiaomei , Li Jie , Wu Nicholas C. , Dai Lei , Zhang Tian-Hao , Shu Sara , Zhou Jian , Yoshizawa Janice M. , Li Xinmin , Bhattacharya Debika , Wu Ting-ting , Niu Junqi , Sun Ren 
Published: August 2017

AbstractDespite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2–5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations. The detection limit of minor viral haplotypes reached 0.1% for individual patient sample. Dominance of “a determinant” polymorphisms were observed in two children, which pre-existed as minor quasispecies in maternal samples. In all four pairs of MTCT samples, we consistently observed a significant overlap of viral haplotypes shared between mother and child. We also demonstrate that the data can be potentially useful to estimate the bottleneck effect during HBV MTCT, which provides information to optimize treatment for reducing the frequency of MTCT.