bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymer translocation through nano-pores in vibrating thin membranes
Authors: Menais Timothée , Mossa Stefano , Buhot Arnaud 
Published: December 2016

AbstractPolymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer can accommodate several bases at the same time, making difficult accurate sequencing applications. More recently, the use of graphene membranes has paved the way to new sequencing capabilities, with the possibility to measure transverse currents, among other advances. The reduced thickness of these new membranes poses new questions on the effect of deformability and vibrations of the membrane on the translocation process, two features which are not taken into account in the well established theoretical frameworks. Here, we make a first step forward in this direction. We report numerical simulation work on a model system simple enough to allow gathering significant insight on the effect of these features on the average translocation time, with appropriate statistical significance. We have found that the interplay between thermal fluctuations and the deformability properties of the nano-pore play a crucial role in determining the process. We conclude by discussing new directions for further work.
Oral Cnm-positive Streptococcus Mutans Expressing Collagen Binding Activity is a Risk Factor for Cerebral Microbleeds and Cognitive Impairment
Authors: Watanabe Isao , Kuriyama Nagato , Miyatani Fumitaro , Nomura Ryota , Naka Shuhei , Nakano Kazuhiko , Ihara Masafumi , Iwai Komei , Matsui Daisuke , Ozaki Etsuko , Koyama Teruhide , Nishigaki Masaru , Yamamoto Toshiro , Tamura Aiko , Mizuno Toshiki , Akazawa Kentaro , Takada Akihiro , Takeda Kazuo , Yamada Kei , Nakagawa Masanori , Tanaka Tokutaro , Kanamura Narisato , Friedland Robert P. , Watanabe Yoshiyuki 
Published: December 2016

AbstractCerebral microbleeds (CMBs) are an important risk factor for stroke and dementia. We have shown that the collagen binding surface Cnm protein expressed on cnm-positive Streptococcus mutans is involved in the development of CMBs. However, whether the collagen binding activity of cnm-positive S. mutans is related to the nature of the CMBs or to cognitive impairment is unclear. Two-hundred seventy nine community residents (70.0 years) were examined for the presence or absence of cnm-positive S. mutans in the saliva by PCR and collagen binding activity, CMBs, and cognitive function were evaluated. Cnm-positive S. mutans was detected more often among subjects with CMBs (p < 0.01) than those without. The risk of CMBs was significantly higher (odds ratio = 14.3) in the group with S. mutans expressing collagen binding activity, as compared to the group without that finding. Deep CMBs were more frequent (67%) and cognitive function was lower among subjects with cnm-positive S. mutans expressing collagen binding activity. This work supports the role of oral health in stroke and dementia and proposes a molecular mechanism for the interaction.
Artificial high birefringence in all-dielectric gradient grating for broadband terahertz waves
Authors: Chen Meng , Fan Fei , Xu Shi-Tong , Chang Sheng-Jiang 
Published: December 2016

AbstractSubwavelength dielectric gratings are widely applied in the phase and polarization manipulation of light. However, the dispersion of the normal dielectric gratings is not flat while their birefringences are not enough in the THz regime. In this paper, we have fabricated two all-dielectric gratings with gradient grids in the THz regime, of which artificial birefringence is much larger than that of the equal-grid dielectric grating demonstrated by both experiments and simulations. The transmission and dispersion characteristics are also improved since the gradient grids break the periodicity of grating lattices as a chirp feature. From 0.6–1.4 THz, a broadband birefringence reaches 0.35 with a low dispersion and good linearity of phase shift, and the maximum phase shift is 1.4π. Furthermore, these gradient gratings are applied as half-wave plates and realize a linear polarization conversion with a conversion rate over 99%, also much higher than the equal-grid gratings. These gradient gratings show great advantages compared to the periodic gratings and provide a new way in the designing of artificial birefringence material.
Experimental evidence for chemical mate guarding in a moth
Authors: Hosseini Seyed Ali , van Wijk Michiel , Ke Gao , Goldansaz Seyed Hossein , Schal Coby , Groot Astrid T. 
Published: December 2016

AbstractIn polyandrous species, males seek to maximize their reproductive output by monopolizing their mate. Often the male transfers substances to the female that suppress her sexual receptivity or antagonize the behavior of competing males; both are usually transferred in seminal fluids and represent forms of chemical mate guarding. In moths, more long-range female sex pheromones have been identified than in any other animal group, and males often display with close-range sex pheromones, yet odor-based post-copulatory mate guarding has not been described in moths so far. We tested the hypothesis that the male sex pheromone in the noctuid moth Heliothis virescens perfumes the female and functions as an anti-aphrodisiac. Indeed, virgin females perfumed with male pheromone extract, or with its main component, mated significantly less than control virgin females, and this effect persisted for two successive nights. This chemical mate guarding strategy was disadvantageous for H. virescens females, because the reproductive output of twice-mated females was significantly higher than that of once-mated females. Since the female and male sex pheromones are biosynthetically related in this and other moth species, chemical mate guarding may also impose selection pressure on the long-range female sex pheromone channel and consequently affect the evolution of sexual communication.
Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development
Authors: Wen Zhuo , Chen Geng , Zhu Sibo , Zhu Jinhang , Li Bin , Song Yunjie , Li Suqing , Shi Leming , Zheng Yuanting , Li Menglong 
Published: December 2016

AbstractAccumulating evidence suggests that noncoding RNAs (ncRNAs) have important regulatory functions. However, lacking of functional annotations for ncRNAs hampered us from carrying out the subsequent functional or predictive research. Here we dissected the expression profiles of 3,458 rat noncoding genes using rat bodymap RNA-sequencing data consisting of 11 solid organs over four developmental stages (juvenile, adolescent, adult and aged) from both sexes, and conducted a comprehensive analysis of differentially expressed noncoding genes (DEnGs) between various conditions. We then constructed a co-expression network between protein-coding and noncoding genes to infer biological functions of noncoding genes. Modules of interest were linked to online databases including DAVID for functional annotation and pathway analysis. Our results indicated that noncoding genes are functionally enriched through pathways similar to those of protein-coding genes. Terms about development of the immune system were enriched with genes from age-related modules, whereas terms about sexual reproduction were enriched with genes in sex-related modules. We also built connection networks on some significant modules to visualize the interactions and regulatory relationship between protein-coding and noncoding genes. Our study could improve our understanding and facilitate a deeper investigation on organ/age/sex-related regulatory events of noncoding genes, which may lead to a superior preclinical model for drug development and translational medicine.
Gram positive and Gram negative bacteria differ in their sensitivity to cold plasma
Authors: Mai-Prochnow Anne , Clauson Maryse , Hong Jungmi , Murphy Anthony B. 
Published: December 2016

AbstractCold atmospheric-pressure plasma (CAP) is a relatively new method being investigated for antimicrobial activity. However, the exact mode of action is still being explored. Here we report that CAP efficacy is directly correlated to bacterial cell wall thickness in several species. Biofilms of Gram positive Bacillus subtilis, possessing a 55.4 nm cell wall, showed the highest resistance to CAP, with less than one log10 reduction after 10 min treatment. In contrast, biofilms of Gram negative Pseudomonas aeruginosa, possessing only a 2.4 nm cell wall, were almost completely eradicated using the same treatment conditions. Planktonic cultures of Gram negative Pseudomonas libanensis also had a higher log10 reduction than Gram positive Staphylococcus epidermidis. Mixed species biofilms of P. aeruginosa and S. epidermidis showed a similar trend of Gram positive bacteria being more resistant to CAP treatment. However, when grown in co-culture, Gram negative P. aeruginosa was more resistant to CAP overall than as a mono-species biofilm. Emission spectra indicated OH and O, capable of structural cell wall bond breakage, were present in the plasma. This study indicates that cell wall thickness correlates with CAP inactivation times of bacteria, but cell membranes and biofilm matrix are also likely to play a role.
Foxa1 is essential for development and functional integrity of the subthalamic nucleus
Authors: Gasser Emanuel , Johannssen Helge C. , Rülicke Thomas , Zeilhofer Hanns Ulrich , Stoffel Markus 
Published: December 2016

AbstractInactivation of transcription factor Foxa1 in mice results in neonatal mortality of unknown cause. Here, we report that ablation of Foxa1 causes impaired development and loss of the subthalamic nucleus (STN). Functional deficits in the STN have been implicated in the etiology of Huntington’s and Parkinson’s disease. We show that neuronal ablation by Synapsin1-Cre-mediated Foxa1 deletion is sufficient to induce hyperlocomotion in mice. Transcriptome profiling of STN neurons in conditional Foxa1 knockout mice revealed changes in gene expression reminiscent of those in neurodegenerative diseases. We identified Ppargc1a, a transcriptional co-activator that is implicated in neurodegeneration, as a Foxa1 target. These findings were substantiated by the observation of Foxa1-dependent demise of STN neurons in conditional models of Foxa1 mutant mice. Finally, we show that the spontaneous firing activity of Foxa1-deficient STN neurons is profoundly impaired. Our data reveal so far elusive roles of Foxa1 in the development and maintenance of STN function.
Plasmonic efficiencies of nanoparticles made of metal nitrides (TiN, ZrN) compared with gold
Authors: Lalisse Adrien , Tessier Gilles , Plain Jérome , Baffou Guillaume 
Published: December 2016

AbstractMetal nitrides have been proposed to replace noble metals in plasmonics for some specific applications. In particular, while titanium nitride (TiN) and zirconium nitride (ZrN) possess localized plasmon resonances very similar to gold in magnitude and wavelength, they benefit from a much higher sustainability to temperature. For this reason, they are foreseen as ideal candidates for applications in nanoplasmonics that require high material temperature under operation, such as heat assisted magnetic recording (HAMR) or thermophotovoltaics. This article presents a detailed investigation of the plasmonic properties of TiN and ZrN nanoparticles in comparison with gold nanoparticles, as a function of the nanoparticle morphology. As a main result, metal nitrides are shown to be poor near-field enhancers compared to gold, no matter the nanoparticle morphology and wavelength. The best efficiencies of metal nitrides as compared to gold in term of near-field enhancement are obtained for small and spherical nanoparticles, and they do not exceed 60%. Nanoparticle enlargements or asymmetries are detrimental. These results mitigate the utility of metal nitrides for high-temperature applications such as HAMR, despite their high temperature sustainability. Nevertheless, at resonance, metal nitrides behave as efficient nanosources of heat and could be relevant for applications in thermoplasmonics, where heat generation is not detrimental but desired.
Surface Characteristics of Silicon Nanowires/Nanowalls Subjected to Octadecyltrichlorosilane Deposition and n-octadecane Coating
Authors: Yilbas Bekir Sami , Salhi Billel , Yousaf Muhammad Rizwan , Al-Sulaiman Fahad , Ali Haider , Al-Aqeeli Nasser 
Published: December 2016

AbstractIn this study, nanowires/nanowalls were generated on a silicon wafer through a chemical etching method. Octadecyltrichlorosilane (OTS) was deposited onto the nanowire/nanowall surfaces to alter their hydrophobicity. The hydrophobic characteristics of the surfaces were further modified via a 1.5-μm-thick layer of n-octadecane coating on the OTS-deposited surface. The hydrophobic characteristics of the resulting surfaces were assessed using the sessile water droplet method. Scratch and ultraviolet (UV)-visible reflectivity tests were conducted to measure the friction coefficient and reflectivity of the surfaces. The nanowires formed were normal to the surface and uniformly extended 10.5 μm to the wafer surface. The OTS coating enhanced the hydrophobic state of the surface, and the water contact angle increased from 27° to 165°. The n-octadecane coating formed on the OTS-deposited nanowires/nanowalls altered the hydrophobic state of the surface. This study provides the first demonstration that the surface wetting characteristics change from hydrophobic to hydrophilic after melting of the n-octadecane coating. In addition, this change is reversible; i.e., the hydrophilic surface becomes hydrophobic after the n-octadecane coating solidifies at the surface, and the process again occurs in the opposite direction after the n-octadecane coating melts.
Giant magnetoresistance, three-dimensional Fermi surface and origin of resistivity plateau in YSb semimetal
Authors: Pavlosiuk Orest , Swatek Przemysław , Wiśniewski Piotr 
Published: December 2016

AbstractVery strong magnetoresistance and a resistivity plateau impeding low temperature divergence due to insulating bulk are hallmarks of topological insulators and are also present in topological semimetals where the plateau is induced by magnetic field, when time-reversal symmetry (protecting surface states in topological insulators) is broken. Similar features were observed in a simple rock-salt-structure LaSb, leading to a suggestion of the possible non-trivial topology of 2D states in this compound. We show that its sister compound YSb is also characterized by giant magnetoresistance exceeding one thousand percent and low-temperature plateau of resistivity. We thus performed in-depth analysis of YSb Fermi surface by band calculations, magnetoresistance, and Shubnikov–de Haas effect measurements, which reveals only three-dimensional Fermi sheets. Kohler scaling applied to magnetoresistance data accounts very well for its low-temperature upturn behavior. The field-angle-dependent magnetoresistance demonstrates a 3D-scaling yielding effective mass anisotropy perfectly agreeing with electronic structure and quantum oscillations analysis, thus providing further support for 3D-Fermi surface scenario of magnetotransport, without necessity of invoking topologically non-trivial 2D states. We discuss data implying that analogous field-induced properties of LaSb can also be well understood in the framework of 3D multiband model.
Functional human induced hepatocytes (hiHeps) with bile acid synthesis and transport capacities: A novel in vitro cholestatic model
Authors: Ni Xuan , Gao Yimeng , Wu Zhitao , Ma Leilei , Chen Chen , Wang Le , Lin Yunfei , Hui Lijian , Pan Guoyu 
Published: December 2016

AbstractDrug-induced cholestasis is a leading cause of drug withdrawal. However, the use of primary human hepatocytes (PHHs), the gold standard for predicting cholestasis in vitro, is limited by their high cost and batch-to-batch variability. Mature hepatocyte characteristics have been observed in human induced hepatocytes (hiHeps) derived from human fibroblast transdifferentiation. Here, we evaluated whether hiHeps could biosynthesize and excrete bile acids (BAs) and their potential as PHH alternatives for cholestasis investigations. Quantitative real-time PCR (qRT-PCR) and western blotting indicated that hiHeps highly expressed BA synthases and functional transporters. Liquid chromatography tandem mass spectrometry (LC-MS/MS) showed that hiHeps produced normal intercellular unconjugated BAs but fewer conjugated BAs than human hepatocytes. When incubated with representative cholestatic agents, hiHeps exhibited sensitive drug-induced bile salt export pump (BSEP) dysfunction, and their response to cholestatic agent-mediated cytotoxicity correlated well with that of PHHs (r2 = 0.8032). Deoxycholic acid (DCA)-induced hepatotoxicity in hiHeps was verified by elevated aspartate aminotransferase (AST) and γ-glutamyl-transferase (γ-GT) levels. Mitochondrial damage and cell death suggested DCA-induced toxicity in hiHeps, which were attenuated by hepatoprotective drugs, as in PHHs. For the first time, hiHeps were reported to biosynthesize and excrete BAs, which could facilitate predicting cholestatic hepatotoxicity and screening potential therapeutic drugs against cholestasis.
Biological marks of early-life socioeconomic experience is detected in the adult inflammatory transcriptome
Authors: Castagné Raphaële , Kelly-Irving Michelle , Campanella Gianluca , Guida Florence , Krogh Vittorio , Palli Domenico , Panico Salvatore , Sacerdote Carlotta , Tumino Rosario , Kleinjans Jos , de Kok Theo , Kyrtopoulos Soterios A. , Lang Thierry , Stringhini Silvia , Vermeulen Roel , Vineis Paolo , Delpierre Cyrille , Chadeau-Hyam Marc 
Published: December 2016

AbstractConsistent evidence is accumulating to link lower socioeconomic position (SEP) and poorer health, and the inflammatory system stands out as a potential pathway through which socioeconomic environment is biologically embedded. Using bloodderived genome-wide transcriptional profiles from 268 Italian participants of the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, we evaluated the association between early life, young and later adulthood SEP and the expression of 845 genes involved in human inflammatory responses. These were examined individually and jointly using several inflammatory scores. Our results consistently show that participants whose father had a manual (as compared to nonmanual) occupation exhibit, later in life, a higher inflammatory score, hence indicating an overall increased level of expression for the selected inflammatory-related genes. Adopting a life course approach, these associations remained statistically significant upon adjustment for later-in-life socioeconomic experiences. Sensitivity analyses indicated that our findings were not affected by the way the inflammatory score was calculated, and were replicated in an independent study. Our study provides additional evidence that childhood SEP is associated with a sustainable upregulation of the inflammatory transcriptome, independently of subsequent socioeconomic experiences. Our results support the hypothesis that early social inequalities impacts adult physiology.
Role and mechanism of the AMPK pathway in waterborne Zn exposure influencing the hepatic energy metabolism of Synechogobius hasta
Authors: Wu Kun , Huang Chao , Shi Xi , Chen Feng , Xu Yi-Huan , Pan Ya-Xiong , Luo Zhi , Liu Xu 
Published: December 2016

AbstractPrevious studies have investigated the physiological responses in the liver ofSynechogobius hastaexposed to waterborne zinc (Zn). However, at present, very little is known about the underlying molecular mechanisms of these responses. In this study, RNA sequencing (RNA-seq) was performed to analyse the differences in the hepatic transcriptomes between control and Zn-exposedS.hasta. A total of 36,339 unigenes and 1,615 bp of unigene N50 were detected. These genes were further annotated to the Nonredundant protein (NR), Nonredundant nucleotide (Nt), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG) and Gene Ontology (GO) databases. After 60 days of Zn exposure, 708 and 237 genes were significantly up- and down-regulated, respectively. Many differentially expressed genes (DEGs) involved in energy metabolic pathways were identified, and their expression profiles suggested increased catabolic processes and reduced biosynthetic processes. These changes indicated that waterborne Zn exposure increased the energy production and requirement, which was related to the activation of the AMPK signalling pathway. Furthermore, using the primary hepatocytes ofS.hasta, we identified the role of the AMPK signalling pathway in Zn-influenced energy metabolism.
Defective Acetylcholine Receptor Subunit Switch Precedes Atrophy of Slow-Twitch Skeletal Muscle Fibers Lacking ERK1/2 Kinases in Soleus Muscle
Authors: Wang Shuo , Seaberg Bonnie , Paez-Colasante Ximena , Rimer Mendell 
Published: December 2016

AbstractTo test the role of extracellular-signal regulated kinases 1 and 2 (ERK1/2) in slow-twitch, type 1 skeletal muscle fibers, we studied the soleus muscle in mice genetically deficient for myofiber ERK1/2. Young adult mutant soleus was drastically wasted, with highly atrophied type 1 fibers, denervation at most synaptic sites, induction of “fetal” acetylcholine receptor gamma subunit (AChRγ), reduction of “adult” AChRε, and impaired mitochondrial biogenesis and function. In weanlings, fiber morphology and mitochondrial markers were mostly normal, yet AChRγ upregulation and AChRε downregulation were observed. Synaptic sites with fetal AChRs in weanling muscle were ~3% in control and ~40% in mutants, with most of the latter on type 1 fibers. These results suggest that: (1) ERK1/2 are critical for slow-twitch fiber growth; (2) a defective γ/ε-AChR subunit switch, preferentially at synapses on slow fibers, precedes wasting of mutant soleus; (3) denervation is likely to drive this wasting, and (4) the neuromuscular synapse is a primary subcellular target for muscle ERK1/2 function in vivo.
HOPX functions as a tumour suppressor in head and neck cancer
Authors: Yap Lee Fah , Lai Sook Ling , Patmanathan Sathya Narayanan , Gokulan Ravindran , Robinson C. Max , White Joe B. , Chai San Jiun , Rajadurai Pathmanathan , Prepageran Narayanan , Liew Yew Toong , Lopes Victor , Wei Wenbin , Hollows Robert J. , Murray Paul G. , Lambert Daniel W. , Hunter Keith D. , Paterson Ian C. 
Published: December 2016

AbstractHead and neck squamous cell carcinoma (HNSCC) is generalized term that encompasses a diverse group of cancers that includes tumours of the oral cavity (OSCC), oropharynx (OPSCC) and nasopharynx (NPC). Genetic alterations that are common to all HNSCC types are likely to be important for squamous carcinogenesis. In this study, we have investigated the role of the homeodomain-only homeobox gene, HOPX, in the pathogenesis of HNSCC. We show that HOPX mRNA levels are reduced in OSCC and NPC cell lines and tissues and there is a general reduction of HOPX protein expression in these tumours and OPSCCs. HOPX promoter methylation was observed in a subset of HNSCCs and was associated with a worse overall survival in HPV negative tumours. RNAseq analysis of OSCC cells transfected with HOPX revealed a widespread deregulation of the transcription of genes related to epithelial homeostasis and ectopic over-expression of HOPX in OSCC and NPC cells inhibited cell proliferation, plating efficiency and migration, and enhanced sensitivity to UVA-induced apoptosis. Our results demonstrate that HOPX functions as a tumour suppressor in HNSCC and suggest a central role for HOPX in suppressing epithelial carcinogenesis.