bluuebunny/crossref_metadata_2025_split huggingface dataset:
Round-robin differential-phase-shift quantum key distribution with a passive decoy state method
Authors: Liu Li , Guo Fen-Zhuo , Qin Su-Juan , Wen Qiao-Yan 
Published: February 2017

AbstractRecently, a new type of protocol named Round-robin differential-phase-shift quantum key distribution (RRDPS QKD) was proposed, where the security can be guaranteed without monitoring conventional signal disturbances. The active decoy state method can be used in this protocol to overcome the imperfections of the source. But, it may lead to side channel attacks and break the security of QKD systems. In this paper, we apply the passive decoy state method to the RRDPS QKD protocol. Not only can the more environment disturbance be tolerated, but in addition it can overcome side channel attacks on the sources. Importantly, we derive a new key generation rate formula for our RRDPS protocol using passive decoy states and enhance the key generation rate. We also compare the performance of our RRDPS QKD to that using the active decoy state method and the original RRDPS QKD without any decoy states. From numerical simulations, the performance improvement of the RRDPS QKD by our new method can be seen.
Linking gene expression to productivity to unravel long- and short-term responses of seagrasses exposed to CO2 in volcanic vents
Authors: Olivé Irene , Silva João , Lauritano Chiara , Costa Monya M. , Ruocco Miriam , Procaccini Gabriele , Santos Rui 
Published: February 2017

AbstractOcean acidification is a major threat for marine life but seagrasses are expected to benefit from high CO2.In situ(long-term) and transplanted (short-term) plant incubations of the seagrassCymodocea nodosawere performed near and away the influence of volcanic CO2vents at Vulcano Island to test the hypothesis of beneficial effects of CO2on plant productivity. We relate, for the first time, the expression of photosynthetic, antioxidant and metal detoxification-related genes to net plant productivity (NPP). Results revealed a consistent pattern between gene expression and productivity indicating water origin as the main source of variability. However, the hypothesised beneficial effect of high CO2around vents was not supported. We observed a consistent long- and short-term pattern of gene down-regulation and 2.5-fold NPP decrease in plants incubated in water from the vents and a generalized up-regulation and NPP increase in plants from the vent site incubated with water from the Reference site. Contrastingly, NPP of specimens experimentally exposed to a CO2range significantly correlated with CO2availability. The down-regulation of metal-related genes inC. nodosaleaves exposed to water from the venting site suggests that other factors than heavy metals, may be at play at Vulcano confounding the CO2effects.
The selective flow of volatile organic compounds in conductive polymer-coated microchannels
Authors: Hossein-Babaei Faramarz , Hooshyar Zare Ali 
Published: February 2017

AbstractMany gaseous markers of critical biological, physicochemical, or industrial occurrences are masked by the cross-sensitivity of the sensors to the other active components present at higher concentrations. Here, we report the strongly selective diffusion and drift of contaminant molecules in air-filled conductive polymer-coated microfluidic channels for the first time. Monitoring the passage of different target molecules through microchannels coated with Poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) revealed that contaminants such as hexane, benzene, and CO pass through the channel unaffected by the coating while methanol, ethanol, and partly acetone are blocked. The observations are explained with reference to the selective interactions between the conductive polymer surface and target gas molecules amplified by the large wall/volume ratio in microchannels. The accumulated quantitative data point at the hydrogen bonding as the mechanism of wall adsorption; dipole-dipole interactions are relatively insignificant. The presented model facilitates a better understanding of how the conductive polymer-based chemical sensors operate.
Proteins analysed as virtual knots
Authors: Alexander Keith , Taylor Alexander J. , Dennis Mark R. 
Published: February 2017

AbstractLong, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.
HRGFish: A database of hypoxia responsive genes in fishes
Authors: Rashid Iliyas , Nagpure Naresh Sahebrao , Srivastava Prachi , Kumar Ravindra , Pathak Ajey Kumar , Singh Mahender , Kushwaha Basdeo 
Published: February 2017

AbstractSeveral studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.
Rapid differentiation of human pluripotent stem cells into functional neurons by mRNAs encoding transcription factors
Authors: Goparaju Sravan Kumar , Kohda Kazuhisa , Ibata Keiji , Soma Atsumi , Nakatake Yukhi , Akiyama Tomohiko , Wakabayashi Shunichi , Matsushita Misako , Sakota Miki , Kimura Hiromi , Yuzaki Michisuke , Ko Shigeru B. H. , Ko Minoru S. H. 
Published: February 2017

AbstractEfficient differentiation of human pluripotent stem cells (hPSCs) into neurons is paramount for disease modeling, drug screening, and cell transplantation therapy in regenerative medicine. In this manuscript, we report the capability of five transcription factors (TFs) toward this aim: NEUROG1, NEUROG2, NEUROG3, NEUROD1, and NEUROD2. In contrast to previous methods that have shortcomings in their speed and efficiency, a cocktail of these TFs as synthetic mRNAs can differentiate hPSCs into neurons in 7 days, judged by calcium imaging and electrophysiology. They exhibit motor neuron phenotypes based on immunostaining. These results indicate the establishment of a novel method for rapid, efficient, and footprint-free differentiation of functional neurons from hPSCs.
System-wide detection of protein-small molecule complexes suggests extensive metabolite regulation in plants
Authors: Veyel Daniel , Kierszniowska Sylwia , Kosmacz Monika , Sokolowska Ewelina Maria , Michaelis Aenne , Luzarowski Marcin , Szlachetko Jagoda , Willmitzer Lothar , Skirycz Aleksandra 
Published: February 2017

AbstractProtein small molecule interactions are at the core of cell regulation controlling metabolism and development. We reasoned that due to the lack of system wide approaches only a minority of those regulatory molecules are known. In order to see whether or not this assumption is true we developed an effective approach for the identification of small molecules having potential regulatory role that obviates the need of protein or small molecule baits. At the core of this approach is a simple biochemical co-fractionation taking advantage of size differences between proteins and small molecules. Metabolomics based analysis of small molecules co-fractionating with proteins identified a multitude of small molecules in Arabidopsis suggesting the existence of numerous, small molecules/metabolites bound to proteins representing potential regulatory molecules. The approach presented here uses Arabidopsis cell cultures, but is generic and hence applicable to all biological systems.
Testicular activin and follistatin levels are elevated during the course of experimental autoimmune epididymo–orchitis in mice
Authors: Nicolas Nour , Michel Vera , Bhushan Sudhanshu , Wahle Eva , Hayward Susan , Ludlow Helen , de Kretser David M. , Loveland Kate L. , Schuppe Hans-Christian , Meinhardt Andreas , Hedger Mark P. , Fijak Monika 
Published: February 2017

AbstractExperimental autoimmune epididymo-orchitis (EAEO) is a model of chronic inflammation, induced by immunisation with testicular antigens, which reproduces the pathology of some types of human infertility. Activins A and B regulate spermatogenesis and steroidogenesis, but are also pro-inflammatory, pro-fibrotic cytokines. Expression of the activins and their endogenous antagonists, inhibin and follistatin, was examined in murine EAEO. Adult untreated and adjuvant-treated control mice showed no pathology. All mice immunised with testis antigens developed EAEO by 50 days, characterised by loss of germ cells, immune cell infiltration and fibrosis in the testis, similar to biopsies from human inflamed testis. An increase of total CD45+ leukocytes, comprising CD3+ T cells, CD4 + CD8− and CD4 + CD25+ T cells, and a novel population of CD4 + CD8+ double positive T cells was also detected in EAEO testes. This was accompanied by increased expression of TNF, MCP-1 and IL-10. Activin A and B and follistatin protein levels were elevated in EAEO testes, with peak activin expression during the active phase of the disease, whereas mRNA expression of the inhibin B subunits (InhaandInhbb) and activin receptor subunits (Acvr1bandAcvr2b) were downregulated. These data suggest that activin–follistatin regulation may play a role during the development of EAEO.
Interleukin-33 produced by M2 macrophages and other immune cells contributes to Th2 immune reaction of IgG4-related disease
Authors: Furukawa Sachiko , Moriyama Masafumi , Miyake Kensuke , Nakashima Hitoshi , Tanaka Akihiko , Maehara Takashi , Iizuka-Koga Mana , Tsuboi Hiroto , Hayashida Jun-Nosuke , Ishiguro Noriko , Yamauchi Masaki , Sumida Takayuki , Nakamura Seiji 
Published: February 2017

AbstractIgG4-related disease (IgG4-RD) is characterized by elevated serum IgG4 and marked infiltration of IgG4-positive cells in multiple organs. Interleukin-33 (IL-33) is a recently described cytokine that is secreted by damaged epithelial cells, macrophages, and dendritic cells, and potently activates helper T type 2 (Th2) immune responses, which have been suggested to play a major role in IgG4 production of IgG4-RD. Here, we assessed the expression of IL-33 and related molecules in the salivary glands (SGs) of patients with IgG4-RD versus that in patients with Sjögren’s syndrome (SS) and controls. Expression of IL-33 and its receptor (ST2) was strongly detected around ectopic germinal centers (GCs) in the SGs from patients with IgG4-RD, whereas IL-33 was expressed only in epithelial cells in patients with SS and controls. Moreover, IL-33 and CD68+/CD163+ macrophages were mainly distributed around ectopic GCs in patients with IgG4-RD. Double immunofluorescence staining showed that IL-33 expression co-localized with CD68+/CD163+ macrophages. Finally, mRNA expression levels of IL-33 showed a positive correlation to those of Th2 cytokines (IL-4 and IL-13) in patients with IgG4-RD. Our data suggest that IL-33 produced by M2 macrophages might contribute to the pathogenesis of IgG4-RD via aberrant activation of Th2 immune responses.
Antifouling potential of Nature-inspired sulfated compounds
Authors: Almeida Joana R. , Correia-da-Silva Marta , Sousa Emília , Antunes Jorge , Pinto Madalena , Vasconcelos Vitor , Cunha Isabel 
Published: February 2017

AbstractNatural products with a sulfated scaffold have emerged as antifouling agents with low or nontoxic effects to the environment. In this study 13 sulfated polyphenols were synthesized and tested for antifouling potential using the anti-settlement activity of mussel (Mytilus galloprovincialis) plantigrade post-larvae and bacterial growth inhibition towards four biofilm-forming bacterial strains. Results show that some of these Nature-inspired compounds were bioactive, particularly rutin persulfate (2), 3,6-bis(β-D-glucopyranosyl) xanthone persulfate (6), and gallic acid persulfate (12) against the settlement of plantigrades. The chemical precursors of sulfated compounds 2 and 12 were also tested for anti-settlement activity and it was possible to conclude that bioactivity is associated with sulfation. While compound 12 showed the most promising anti-settlement activity (EC50 = 8.95 μg.mL−1), compound 2 also caused the higher level of growth inhibition in bacteria Vibrio harveyi (EC20 = 12.5 μg.mL−1). All the three bioactive compounds 2, 6, and 12 were also found to be nontoxic to the non target species Artemia salina (<10% mortality at 250 μM) and Vibrio fischeri (LC50 > 1000 μg.mL−1). This study put forward the relevance of synthesizing non-natural sulfated small molecules to generate new nontoxic antifouling agents.
Flavichalasines A–M, cytochalasan alkaloids from Aspergillus flavipes
Authors: Wei Guangzheng , Tan Dongdong , Chen Chunmei , Tong Qingyi , Li Xiao-Nian , Huang Jinfeng , Liu Junjun , Xue Yongbo , Wang Jianping , Luo Zengwei , Zhu Hucheng , Zhang Yonghui 
Published: February 2017

AbstractTwo new tetracyclic cytochalasans, flavichalasines A and B (1 and 2), three new pentacyclic cytochalasans, flavichalasines C–E (3–5), and eight new tricyclic cytochalasans, flavichalasines F–M (6–13), together with eight known analogues (14–21), were isolated from the solid culture of Aspergillus flavipes. Structures of these new compounds were elucidated on the basis of extensive spectroscopic analyses including 1D, 2D NMR and HRESIMS data. Their absolute configurations were determined by comparison of their experimental ECD with either computed ECD or experimental ECD spectrum of known compound. The structure and absolute configuration of 2 were further determined by X-ray crystallographic diffraction. Flavichalasine A (1) represents the first example of cytochalasan with a terminal double bond at the macrocyclic ring and flavichalasine E (5) is the only cytochalasan with an α-oriented oxygen-bridge in D ring. These new compounds were evaluated for their cytotoxic activities against seven human cancer cell lines, of which, 6 and 14 displayed moderate inhibitory activities against tested cell lines. In addition, compounds 6 and 14 induced apoptosis of HL60 cells by activation of caspase-3 and degradation of PARP.
Accelerated biodegradation of silk sutures through matrix metalloproteinase activation by incorporating 4-hexylresorcinol
Authors: Jo You-Young , Kweon HaeYong , Kim Dae-Won , Kim Min-Keun , Kim Seong-Gon , Kim Jwa-Young , Chae Weon-Sik , Hong Sam-Pyo , Park Young-Hwan , Lee Si Young , Choi Je-Yong 
Published: February 2017

AbstractSilk suture material is primarily composed of silk fibroin and regarded as a non-resorbable material. It is slowly degraded by proteolysis when it is implanted into the body. 4-Hexylresorcinol (4HR) is a well-known antiseptic. In this study, the biodegradability of 4HR-incorporated silk sutures were compared to that of untreated silk sutures and polyglactin 910 sutures, a commercially available resorbable suture. 4HR-incorporated silk sutures exhibited anti-microbial properties. Matrix metalloproteinase (MMP) can digest a wide spectrum of proteins. 4HR increased MMP-2, -3, and -9 expression in RAW264.7 cells. MMP-2, -3, and -9 were able to digest not only silk fibroin but also silk sutures. Consequently, 59.5% of the 4HR-incorporated silk suture material remained at 11 weeks after grafting, which was similar to that of polyglactin 910 degradation (56.4% remained). The residual amount of bare silk suture material at 11 weeks after grafting was 91.5%. The expression levels of MMP-2, -3 and -9 were high in the 4HR-incorporated silk suture-implanted site 12 weeks after implantation. In conclusion, 4HR-treated silk sutures exhibited anti-microbial properties and a similar level of bio-degradation to polyglactin 910 sutures and induced higher expression of MMP-2, -3, and -9 in macrophages.
Profound seasonal shrinking and regrowth of the ossified braincase in phylogenetically distant mammals with similar life histories
Authors: Dechmann Dina K. N. , LaPoint Scott , Dullin Christian , Hertel Moritz , Taylor Jan R. E. , Zub Karol , Wikelski Martin 
Published: February 2017

AbstractOntogenetic changes in skull shape and size are ubiquitous in altricial vertebrates, but typically unidirectional and minimal in full-grown animals. Red-toothed shrews exhibit a rare exception, where the shape, mass and size of the skull, brain, and several major organs, show significant bidirectional seasonal changes. We now show a similar but male-biased shrinking (16%) and regrowth (8%) in the standardized braincase depth of least weasels (Mustela nivalis). Juvenile weasels also exhibit a growth overshoot, followed by a shrinkage period lasting until the end of their first winter. Only male weasels then regrow during their second summer. High-resolution CT scans suggest areas of the skull are affected differently during shrinking and regrowth in both species. This suggests multiple evolutionary drivers: while the shrinking likely facilitates survival during seasonal low resource availability in these high-metabolic mammals with year-round activity, the regrowth may be most strongly influenced by high investment into reproduction and territories, which is male-biased in the weasels. Our data provide evidence for convergent evolution of skull and thus brain shrinkage and regrowth, with important implications for understanding adaptations to changing environments and for applied research on the correlated changes in bone structure, brain size and the many other affected organs.
Boosting laser-ion acceleration with multi-picosecond pulses
Authors: Yogo A. , Mima K. , Iwata N. , Tosaki S. , Morace A. , Arikawa Y. , Fujioka S. , Johzaki T. , Sentoku Y. , Nishimura H. , Sagisaka A. , Matsuo K. , Kamitsukasa N. , Kojima S. , Nagatomo H. , Nakai M. , Shiraga H. , Murakami M. , Tokita S. , Kawanaka J. , Miyanaga N. , Yamanoi K. , Norimatsu T. , Sakagami H. , Bulanov S. V. , Kondo K. , Azechi H. 
Published: February 2017

AbstractUsing one of the world most powerful laser facility, we demonstrate for the first time that high-contrast multi-picosecond pulses are advantageous for proton acceleration. By extending the pulse duration from 1.5 to 6 ps with fixed laser intensity of 1018 W cm−2, the maximum proton energy is improved more than twice (from 13 to 33 MeV). At the same time, laser-energy conversion efficiency into the MeV protons is enhanced with an order of magnitude, achieving 5% for protons above 6 MeV with the 6 ps pulse duration. The proton energies observed are discussed using a plasma expansion model newly developed that takes the electron temperature evolution beyond the ponderomotive energy in the over picoseconds interaction into account. The present results are quite encouraging for realizing ion-driven fast ignition and novel ion beamlines.
The inflammatory state provokes sexual dimorphism in left ventricular and electrocardiographic effects of chronic cyclosporine in rats
Authors: El-Bassossy Hany M. , Banjar Zainy M. , El-Mas Mahmoud M. 
Published: February 2017

AbstractAlthough cardiotoxicity has been recognized as an adverse effect of cyclosporine A (CSA), no information exists regarding sex specificity of CSA cardiotoxicity. We tested the hypothesis that left ventricular (LV) and electrocardiographic (ECG) effects of CSA and related inflammatory/histopathological derangements are sex related. CSA reduced the LV slope of end-systolic pressure volume relationship and increased isovolumic relaxation constant. These effects were more pronounced in male compared to female rats, suggesting LV systolic and diastolic dysfunction. ECG recordings showed elevated ST segments and increased QTc and T peak trend intervals in CSA-treated male rats, markers of LV ischemia and arrhythmogenesis. In female rats, CSA delayed AV conduction, as reflected by prolonged PR interval. Other sex-related effects for CSA included (i) increased blood cholesterol, and reduced rates of rise and fall in LV pressure and nuclear factor kappa B and angiotensin receptors type 1 expressions in male rats, and (ii) increased LV adiponectin in females. Histopatholgically, CSA caused vascular congestion, blood extravasation, and pyknotic or even absent nuclei in both sexes. In conclusion, rats exhibit sex-independent susceptibility to negative LV and histopathological influences of CSA. These effects become more intensified in male rats, perhaps on account of aggravated ischemic and inflammatory milieus.
Activating Killer Immunoglobulin Receptors and HLA-C: a successful combination providing HIV-1 control
Authors: Malnati Mauro S. , Ugolotti Elisabetta , Monti Maria Cristina , Battista Davide De , Vanni Irene , Bordo Domenico , Sironi Francesca , Larghero Patrizia , Marco Eddi Di , Biswas Priscilla , Poli Guido , Vicenzi Elisa , Riva Agostino , Tarkowski Maciej , Tambussi Giuseppe , Nozza Silvia , Tripodi Gino , Marras Francesco , De Maria Andrea , Pistorio Angela , Biassoni Roberto 
Published: February 2017

AbstractSeveral studies demonstrated a relevant role of polymorphisms located within the HLA-B and -C loci and the Killer Immunoglobulin Receptors (KIRs) 3DL1 and 3DS1 in controlling HIV-1 replication. KIRs are regulatory receptors expressed at the surface of NK and CD8+ T-cells that specifically bind HLA-A and -B alleles belonging to the Bw4 supratype and all the -C alleles expressing the C1 or C2 supratype. We here disclose a novel signature associated with the Elite Controller but not with the long-term nonprogressor status concerning 2DS activating KIRs and HLA-C2 alleles insensitive to miRNA148a regulation. Overall, our findings support a crucial role of NK cells in the control of HIV-1 viremia.