bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and magnetic properties of multi-core nanoparticles analysed using a generalised numerical inversion method
Authors: Bender P. , Bogart L. K. , Posth O. , Szczerba W. , Rogers S. E. , Castro A. , Nilsson L. , Zeng L. J. , Sugunan A. , Sommertune J. , Fornara A. , González-Alonso D. , Barquín L. Fernández , Johansson C. 
Published: April 2017

AbstractThe structural and magnetic properties of magnetic multi-core particles were determined by numerical inversion of small angle scattering and isothermal magnetisation data. The investigated particles consist of iron oxide nanoparticle cores (9 nm) embedded in poly(styrene) spheres (160 nm). A thorough physical characterisation of the particles included transmission electron microscopy, X-ray diffraction and asymmetrical flow field-flow fractionation. Their structure was ultimately disclosed by an indirect Fourier transform of static light scattering, small angle X-ray scattering and small angle neutron scattering data of the colloidal dispersion. The extracted pair distance distribution functions clearly indicated that the cores were mostly accumulated in the outer surface layers of the poly(styrene) spheres. To investigate the magnetic properties, the isothermal magnetisation curves of the multi-core particles (immobilised and dispersed in water) were analysed. The study stands out by applying the same numerical approach to extract the apparent moment distributions of the particles as for the indirect Fourier transform. It could be shown that the main peak of the apparent moment distributions correlated to the expected intrinsic moment distribution of the cores. Additional peaks were observed which signaled deviations of the isothermal magnetisation behavior from the non-interacting case, indicating weak dipolar interactions.
English phonology and an acoustic language universal
Authors: Nakajima Yoshitaka , Ueda Kazuo , Fujimaru Shota , Motomura Hirotoshi , Ohsaka Yuki 
Published: April 2017

AbstractAcoustic analyses of eight different languages/dialects had revealed a language universal: Three spectral factors consistently appeared in analyses of power fluctuations of spoken sentences divided by critical-band filters into narrow frequency bands. Examining linguistic implications of these factors seems important to understand how speech sounds carry linguistic information. Here we show the three general categories of the English phonemes, i.e., vowels, sonorant consonants, and obstruents, to be discriminable in the Cartesian space constructed by these factors: A factor related to frequency components above 3,300 Hz was associated only with obstruents (e.g., /k/ or /z/), and another factor related to frequency components around 1,100 Hz only with vowels (e.g., /a/ or /i/) and sonorant consonants (e.g., /w/, /r/, or /m/). The latter factor highly correlated with the hypothetical concept of sonority or aperture in phonology. These factors turned out to connect the linguistic and acoustic aspects of speech sounds systematically.
Studies on the growth performance of different broiler strains at high altitude and evaluation of probiotic effect on their survivability
Authors: Kalia Sahil , K. Bharti Vijay , Gogoi Deepak , Giri Arup , Kumar Bhuvnesh 
Published: April 2017

AbstractIdentification of appropriate breeds of broilers and development of new feed additives is required for the development of poultry industry at high altitude. Therefore, this experiment was conducted first to identify the suitable broiler strain for this region. One week old chicks (150) from three broiler strains, i.e. Vencobb, RIR cross-bred, and Hubbard were randomly selected and divided equally into three groups. All the chicks were provided the same basal diet. The body weight gain and feed: gain responses were significantly (P < 0.05) improved in RIR cross-bred. Mortality was also observed lower in RIR cross-bred. Thereafter, the second trial was conducted in RIR cross-bred to evaluate the effect of probiotic supplementation (T1@ 9 gm/kg feed, T2@ 18 gm/kg feed) on their performance and mortality. No significant differences (P > 0.05) were observed in weight gain, feed intake, feed: gain, and water intake among the three groups, however, mortality from ascites and coccidiosis was reduced in probiotic treated groups. Hence, our results suggest that RIR cross-bred is suitable for rearing in high altitude regions and probiotic supplementation has no beneficial effects on production performance of broilers at high altitude. However, probiotic supplementation indicated lesser loss due to mortality of birds.
Intestinal microbiome in children with severe and complicated acute viral gastroenteritis
Authors: Chen Shih-Yen , Tsai Chi-Neu , Lee Yun-Shien , Lin Chun-Yuan , Huang Kuan-Yeh , Chao Hsun-Ching , Lai Ming-Wei , Chiu Cheng-Hsun 
Published: April 2017

AbstractThe aim of the present study was to evaluate the microbiota of children with severe or complicated acute viral gastroenteritis (AGE). To that end, next-generation sequencing (NGS) technology was used to sequence the 16S ribosomal RNA (16S rRNA) gene in 20 hospitalized pediatric patients with severe or complicated AGE and a further 20 otherwise healthy children; the fecal microbiome was then assessed. Comparative metagenomics data were analyzed by a Wilcoxon rank–sum test and hierarchical clustering analysis of bacterial reads. The statistical analyses showed a significantly decreased Shannon diversity index (entropy score) of the intestinal microbiota in patients with severe AGE compared with normal controls (P = 0.017) and patients with mild-to-moderate AGE (P = 0.011). The intestinal microbiota score of the 5 patients with rotavirus AGE was significantly lower than that of those with norovirus infection (P = 0.048). Greater richness in Campylobacteraceae (P = 0.0003), Neisseriaceae (P = 0.0115), Methylobacteriaceae (P = 0.0004), Sphingomonadaceae (P = 0.0221), and Enterobacteriaceae (P = 0.0451) was found in patients with complicated AGE compared with normal controls. The data suggest a significant reduction in intestinal microbial diversity in patients with severe AGE, particularly those with rotavirus infection.
Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice
Authors: Razzaque Samsad , Haque Taslima , Elias Sabrina M. , Rahman Md. Sazzadur , Biswas Sudip , Schwartz Scott , Ismail Abdelbagi M. , Walia Harkamal , Juenger Thomas E. , Seraj Zeba I. 
Published: April 2017

AbstractGlobal increase in salinity levels has made it imperative to identify novel sources of genetic variation for tolerance traits, especially in rice. The rice landrace Horkuch, endemic to the saline coastal area of Bangladesh, was used in this study as the source of tolerance in reciprocal crosses with the sensitive but high-yielding IR29 variety for discovering transcriptional variation associated with salt tolerance in the resulting populations. The cytoplasmic effect of the Horkuch background in leaves under stress showed functional enrichment for signal transduction, DNA-dependent regulation and transport activities. In roots the enrichment was for cell wall organization and macromolecule biosynthesis. In contrast, the cytoplasmic effect of IR29 showed upregulation of apoptosis and downregulation of phosphorylation across tissues relative to Horkuch. Differential gene expression in leaves of the sensitive population showed downregulation of GO processes like photosynthesis, ATP biosynthesis and ion transport. Roots of the tolerant plants conversely showed upregulation of GO terms like G-protein coupled receptor pathway, membrane potential and cation transport. Furthermore, genes involved in regulating membrane potentials were constitutively expressed only in the roots of tolerant individuals. Overall our work has developed genetic resources and elucidated the likely mechanisms associated with the tolerance response of the Horkuch genotype.
Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes
Authors: Wong Hon Lun , Visscher Pieter T. , White III Richard Allen , Smith Daniela-Lee , Patterson Molly M. , Burns Brendan P. 
Published: April 2017

AbstractThe role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.
Bitter Taste Receptor Agonists Mitigate Features of Allergic Asthma in Mice
Authors: Sharma Pawan , Yi Roslyn , Nayak Ajay P. , Wang Nadan , Tang Francesca , Knight Morgan J. , Pan Shi , Oliver Brian , Deshpande Deepak A. 
Published: April 2017

AbstractAsthma is characterized by airway inflammation, mucus secretion, remodeling and hyperresponsiveness (AHR). Recent research has established the bronchodilatory effect of bitter taste receptor (TAS2R) agonists in various models. Comprehensive pre-clinical studies aimed at establishing effectiveness of TAS2R agonists in disease models are lacking. Here we aimed to determine the effect of TAS2R agonists on features of asthma. Further, we elucidated a mechanism by which TAS2R agonists mitigate features of asthma. Asthma was induced in mice using intranasal house dust mite or aerosol ova-albumin challenge, and chloroquine or quinine were tested in both prophylactic and treatment models. Allergen challenge resulted in airway inflammation as evidenced by increased immune cells infiltration and release of cytokines and chemokines in the lungs, which were significantly attenuated in TAS2R agonists treated mice. TAS2R agonists attenuated features of airway remodeling including smooth muscle mass, extracellular matrix deposition and pro-fibrotic signaling, and also prevented mucus accumulation and development of AHR in mice. Mechanistic studies using human neutrophils demonstrated that inhibition of immune cell chemotaxis is a key mechanism by which TAS2R agonists blocked allergic airway inflammation and exerted anti-asthma effects. Our comprehensive studies establish the effectiveness of TAS2R agonists in mitigating multiple features of allergic asthma.
Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin
Authors: Phillips-Jones Mary K. , Channell Guy , Kelsall Claire J. , Hughes Charlotte S. , Ashcroft Alison E. , Patching Simon G. , Dinu Vlad , Gillis Richard B. , Adams Gary G. , Harding Stephen E. 
Published: April 2017

AbstractVanA-type resistance to glycopeptide antibiotics in clinical enterococci is regulated by the VanSARAtwo-component signal transduction system. The nature of the molecular ligand that is recognised by the VanSAsensory component has not hitherto been identified. Here we employ purified, intact and active VanSAmembrane protein (henceforth referred to as VanS) in analytical ultracentrifugation experiments to study VanS oligomeric state and conformation in the absence and presence of vancomycin. A combination of sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge (SEDFIT, SEDFIT-MSTAR and MULTISIG analysis) showed that VanS in the absence of the ligand is almost entirely monomeric (molar massM = 45.7 kDa) in dilute aqueous solution with a trace amount of high molar mass material (M ~ 200 kDa). The sedimentation coefficientssuggests the monomer adopts an extended conformation in aqueous solution with an equivalent aspect ratio of ~(12 ± 2). In the presence of vancomycin over a 33% increase in the sedimentation coefficient is observed with the appearance of additional higherscomponents, demonstrating an interaction, an observation consistent with our circular dichroism measurements. The two possible causes of this increase ins– either a ligand induced dimerization and/or compaction of the monomer are considered.
Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species
Authors: Zhang Yanjie , Sun Jin , Chen Chong , Watanabe Hiromi K. , Feng Dong , Zhang Yu , Chiu Jill M.Y. , Qian Pei-Yuan , Qiu Jian-Wen 
Published: April 2017

AbstractPolynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.).
An optimized transit peptide for effective targeting of diverse foreign proteins into chloroplasts in rice
Authors: Shen Bo-Ran , Zhu Cheng-Hua , Yao Zhen , Cui Li-Li , Zhang Jian-Jun , Yang Cheng-Wei , He Zheng-Hui , Peng Xin-Xiang 
Published: April 2017

AbstractVarious chloroplast transit peptides (CTP) have been used to successfully target some foreign proteins into chloroplasts, but for other proteins these same CTPs have reduced localization efficiencies or fail completely. The underlying cause of the failures remains an open question, and more effective CTPs are needed. In this study, we initially observed that two E.coli enzymes, EcTSR and EcGCL, failed to be targeted into rice chloroplasts by the commonly-used rice rbcS transit peptide (rCTP) and were subsequently degraded. Further analyses revealed that the N-terminal unfolded region of cargo proteins is critical for their localization capability, and that a length of about 20 amino acids is required to attain the maximum localization efficiency. We considered that the unfolded region may alleviate the steric hindrance produced by the cargo protein, by functioning as a spacer to which cytosolic translocators can bind. Based on this inference, an optimized CTP, named RC2, was constructed. Analyses showed that RC2 can more effectively target diverse proteins, including EcTSR and EcGCL, into rice chloroplasts. Collectively, our results provide further insight into the mechanism of CTP-mediated chloroplastic localization, and more importantly, RC2 can be widely applied in future chloroplastic metabolic engineering, particularly for crop plants.
Over-expression of microRNA-1 causes arrhythmia by disturbing intracellular trafficking system
Authors: Su Xiaomin , Liang Haihai , Wang He , Chen Guizhi , Jiang Hua , Wu Qiuxia , Liu Tianyi , Liu Qiushuang , Yu Tong , Gu Yunyan , Yang Baofeng , Shan Hongli 
Published: April 2017

AbstractDysregulation of intracellular trafficking system plays a fundamental role in the progression of cardiovascular disease. Up-regulation of miR-1 contributes to arrhythmia, we sought to elucidate whether intracellular trafficking contributes to miR-1-driven arrhythmia. By performing microarray analyses of the transcriptome in the cardiomyocytes-specific over-expression of microRNA-1 (miR-1 Tg) mice and the WT mice, we found that these differentially expressed genes in miR-1 Tg mice were significantly enrichment with the trafficking-related biological processes, such as regulation of calcium ion transport. Also, the qRT-PCR and western blot results validated that Stx6, Braf, Ube3a, Mapk8ip3, Ap1s1, Ccz1 and Gja1, which are the trafficking-related genes, were significantly down-regulated in the miR-1 Tg mice. Moreover, we found that Stx6 was decreased in the heart of mice after myocardial infarction and in the hypoxic cardiomyocytes, and further confirmed that Stx6 is a target of miR-1. Meanwhile, knockdown of Stx6 in cardiomyocytes resulted in the impairments of PLM and L-type calcium channel, which leads to the increased resting ([Ca2+]i). On the contrary, overexpression of Stx6 attenuated the impairments of miR-1 or hypoxia on PLM and L-type calcium channel. Thus, our studies reveals that trafficking-related gene Stx6 may regulate intracellular calcium and is involved in the occurrence of cardiac arrhythmia, which provides new insights in that miR-1 participates in arrhythmia by regulating the trafficking-related genes and pathway.
Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors
Authors: Lagorce David , Douguet Dominique , Miteva Maria A. , Villoutreix Bruno O. 
Published: April 2017

AbstractThe modulation of PPIs by low molecular weight chemical compounds, particularly by orally bioavailable molecules, would be very valuable in numerous disease indications. However, it is known that PPI inhibitors (iPPIs) tend to have properties that are linked to poor Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and in some cases to poor clinical outcomes. Previously reported in silico analyses of iPPIs have essentially focused on physicochemical properties but several other ADMET parameters would be important to assess. In order to gain new insights into the ADMET properties of iPPIs, computations were carried out on eight datasets collected from several databases. These datasets involve compounds targeting enzymes, GPCRs, ion channels, nuclear receptors, allosteric modulators, oral marketed drugs, oral natural product-derived marketed drugs and iPPIs. Several trends are reported that should assist the design and optimization of future PPI inhibitors, either for drug discovery endeavors or for chemical biology projects.
SnoN Stabilizes the SMAD3/SMAD4 Protein Complex
Authors: Walldén Karin , Nyman Tomas , Hällberg B. Martin 
Published: April 2017

AbstractTGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling.
The CACNA1C risk allele rs1006737 is associated with age-related prefrontal cortical thinning in bipolar I disorder
Authors: Soeiro-de-Souza M G , Lafer B , Moreno R A , Nery F G , Chile T , Chaim K , da Costa Leite C , Machado-Vieira R , Otaduy M C G , Vallada H 
Published: April 2017

AbstractCalcium channels control the inflow of calcium ions into cells and are involved in diverse cellular functions. The CACNA1C gene polymorphism rs1006737 A allele has been strongly associated with increased risk for bipolar disorder (BD) and with modulation of brain morphology. The medial prefrontal cortex (mPFC) has been widely associated with mood regulation in BD, but the role of this CACNA1C polymorphism in mPFC morphology and brain aging has yet to be elucidated. One hundred seventeen euthymic BD type I subjects were genotyped for CACNA1C rs1006737 and underwent 3 T three-dimensional structural magnetic resonance imaging scans to determine cortical thickness of mPFC components (superior frontal cortex (sFC), medial orbitofrontal cortex (mOFC), caudal anterior cingulate cortex (cACC) and rostral anterior cingulate cortex (rACC)). Carriers of the CACNA1C allele A exhibited greater left mOFC thickness compared to non-carriers. Moreover, CACNA1C A carriers showed age-related cortical thinning of the left cACC, whereas among A non-carriers there was not an effect of age on left cACC cortical thinning. In the sFC, mOFC and rACC (left or right), a negative correlation was observed between age and cortical thickness, regardless of CACNA1C rs1006737 A status. Further studies investigating the direct link between cortical thickness, calcium channel function, apoptosis mechanism and their underlying relationship with aging-associated cognitive decline in BD are warranted.