bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamics and efficiency of an autonomous on-chip Maxwell’s demon
Authors: Kutvonen Aki , Koski Jonne , Ala-Nissila Tapio 
Published: February 2016

AbstractIn his famous letter in 1870, Maxwell describes how Joule’s law can be violated “only by the intelligent action of a mere guiding agent”, later coined as Maxwell’s demon by Lord Kelvin. In this letter we study thermodynamics of information using an experimentally feasible Maxwell’s demon setup based a single electron transistor capacitively coupled to a single electron box, where both the system and the Demon can be clearly identified. Such an engineered on-chip Demon measures and performes feedback on the system, which can be observed as cooling whose efficiency can be adjusted. We present a detailed analysis of the system and the Demon, including the second law of thermodynamics for bare and coarse grained entropy production and the flow of information as well as efficiency of information production and utilization. Our results demonstrate how information thermodynamics can be used to improve functionality of modern nanoscale devices.
Photoluminescence and photocatalytic properties of rhombohedral CuGaO2 nanoplates
Authors: Shi Linlin , Wang Fei , Wang Yunpeng , Wang Dengkui , Zhao Bin , Zhang Ligong , Zhao Dongxu , Shen Dezhen 
Published: February 2016

AbstractRhombohedral phase CuGaO2 nanoplates with a diameter of about 10 μm were synthesized via low temperature hydrothermal method. Room temperature and low temperature photoluminescence of the obtained CuGaO2 nanoplates were characterized. CuGaO2 nanoplates exhibited blue emission at room temperature and free exciton emission were appeared at low temperature. The blue emission is originated from defects such as Cu vacancies, which is the possible origin of p-type conductivity. The appearance of free exciton emission can demonstrate the direct bandgap transition behavior of CuGaO2 nanoplates. The as-prepared p-type CuGaO2 nanoplates were further decorated by n-type ZnO nanoparticles via calcination method to fabricate p-n junction nanocomposites. The nanocomposites exhibited enhanced photocatalytic activity which can be ascribed to the effective separation of photogenerated carriers by the internal electrostatic field in the p-n junction region and the enhanced light absorption properties resulted from sub-bandgap absorption effect of p-n junction. This work has offered a new insight into the design of p-n junction devices using p-type CuGaO2 nanoplates.
Recurrent Spiking Networks Solve Planning Tasks
Authors: Rueckert Elmar , Kappel David , Tanneberg Daniel , Pecevski Dejan , Peters Jan 
Published: February 2016

AbstractA recurrent spiking neural network is proposed that implements planning as probabilistic inference for finite and infinite horizon tasks. The architecture splits this problem into two parts: The stochastic transient firing of the network embodies the dynamics of the planning task. With appropriate injected input this dynamics is shaped to generate high-reward state trajectories. A general class of reward-modulated plasticity rules for these afferent synapses is presented. The updates optimize the likelihood of getting a reward through a variant of an Expectation Maximization algorithm and learning is guaranteed to convergence to a local maximum. We find that the network dynamics are qualitatively similar to transient firing patterns during planning and foraging in the hippocampus of awake behaving rats. The model extends classical attractor models and provides a testable prediction on identifying modulating contextual information. In a real robot arm reaching and obstacle avoidance task the ability to represent multiple task solutions is investigated. The neural planning method with its local update rules provides the basis for future neuromorphic hardware implementations with promising potentials like large data processing abilities and early initiation of strategies to avoid dangerous situations in robot co-worker scenarios.
Rhus coriaria suppresses angiogenesis, metastasis and tumor growth of breast cancer through inhibition of STAT3, NFκB and nitric oxide pathways
Authors: El Hasasna Hussain , Saleh Alaaeldin , Samri Halima Al , Athamneh Khawlah , Attoub Samir , Arafat Kholoud , Benhalilou Nehla , Alyan Sofyan , Viallet Jean , Dhaheri Yusra Al , Eid Ali , Iratni Rabah 
Published: February 2016

AbstractRecently, we reported that Rhus coriaria exhibits anticancer activities by promoting cell cycle arrest and autophagic cell death of the metastatic triple negative MDA-MB-231 breast cancer cells. Here, we investigated the effect of Rhus coriaria on the migration, invasion, metastasis and tumor growth of TNBC cells. Our current study revealed that non-cytotoxic concentrations of Rhus coriaria significantly inhibited migration and invasion, blocked adhesion to fibronectin and downregulated MMP-9 and prostaglandin E2 (PgE2). Not only did Rhus coriaria decrease their adhesion to HUVECs and to lung microvascular endothelial (HMVEC-L) cells, but it also inhibited the transendothelial migration of MDA-MB-231 cells through TNF-α-activated HUVECs. Furthermore, we found that Rhus coriaria inhibited angiogenesis, reduced VEGF production in both MDA-MB-231 and HUVECs and downregulated the inflammatory cytokines TNF-α, IL-6 and IL-8. The underlying mechanism for Rhus coriaria effects appears to be through inhibiting NFκB, STAT3 and nitric oxide (NO) pathways. Most importantly, by using chick embryo tumor growth assay, we showed that Rhus coriaria suppressed tumor growth and metastasis in vivo. The results described in the present study identify Rhus coriaria as a promising chemopreventive and therapeutic candidate that modulate triple negative breast cancer growth and metastasis.
Effects of memory on the shapes of simple outbreak trees
Authors: Plazzotta Giacomo , Kwan Christopher , Boyd Michael , Colijn Caroline 
Published: February 2016

AbstractGenomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset.
Neuroimaging evidence of deficient axon myelination in Wolfram syndrome
Authors: Lugar Heather M. , Koller Jonathan M. , Rutlin Jerrel , Marshall Bess A. , Kanekura Kohsuke , Urano Fumihiko , Bischoff Allison N. , Shimony Joshua S. , Hershey Tamara ,   the Washington University Wolfram Syndrome Research Study Group, Austin P. , Beato B. , Bihun E. , Doty T. , Earhart G. , Eisenstein S. , Hoekel J. , Karzon R. , Licis A. , Manwaring L. , Paciorkowski A. R. , Pepino de Gruev Y. , Permutt A. , Pickett K. , Ranck S. , Reiersen A. , Tychsen L. , Viehoever A. , Wasson J. , White N. H. 
Published: February 2016

AbstractWolfram syndrome is a rare autosomal recessive genetic disease characterized by insulin dependent diabetes and vision, hearing and brain abnormalities which generally emerge in childhood. Mutations in the WFS1 gene predispose cells to endoplasmic reticulum stress-mediated apoptosis and may induce myelin degradation in neuronal cell models. However, in vivo evidence of this phenomenon in humans is lacking. White matter microstructure and regional volumes were measured using magnetic resonance imaging in children and young adults with Wolfram syndrome (n = 21) and healthy and diabetic controls (n = 50). Wolfram patients had lower fractional anisotropy and higher radial diffusivity in major white matter tracts and lower volume in the basilar (ventral) pons, cerebellar white matter and visual cortex. Correlations were found between key brain findings and overall neurological symptoms. This pattern of findings suggests that reduction in myelin is a primary neuropathological feature of Wolfram syndrome. Endoplasmic reticulum stress-related dysfunction in Wolfram syndrome may interact with the development of myelin or promote degeneration of myelin during the progression of the disease. These measures may provide objective indices of Wolfram syndrome pathophysiology that will be useful in unraveling the underlying mechanisms and in testing the impact of treatments on the brain.
Synthesis and characterization of vertically standing MoS2 nanosheets
Authors: Li Han , Wu Huaqiang , Yuan Shuoguo , Qian He 
Published: February 2016

AbstractMolybdenum disulfide (MoS2) has been attracting much attentions due to its excellent electrical and optical properties. We report here the synthesis of large-scale and uniform MoS2 nanosheets with vertically standing morphology using chemical vapor deposition method. TEM observations clearly reveal the growth mechanism of these vertical structures. It is suggested that the vertical structures are caused by the compression and extrusion between MoS2 islands. More importantly, the vertical morphology of two dimensional (2D) materials hold many promising potential applications. We demonstrate here the as-synthesized vertically standing MoS2 nanosheets could be used for hydrogen evolution reaction, where the exchange current density is about 70 times of bulk MoS2. The field emission performance of vertically standing MoS2 were also improved due to the abundantly exposed edges.
Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II
Authors: Mulholland Sam , Turpin Eleanor R. , Bonev Boyan B. , Hirst Jonathan D. 
Published: February 2016

AbstractLanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin-lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. An Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wild-type. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N-terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2inserts into the membrane and we propose this as the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.
Large pinning forces and matching effects in YBa2Cu3O7-δ thin films with Ba2Y(Nb/Ta)O6 nano-precipitates
Authors: Opherden Lars , Sieger Max , Pahlke Patrick , Hühne Ruben , Schultz Ludwig , Meledin Alexander , Van Tendeloo Gustaaf , Nast Rainer , Holzapfel Bernhard , Bianchetti Marco , MacManus-Driscoll Judith L. , Hänisch Jens 
Published: February 2016

AbstractThe addition of mixed double perovskite Ba2Y(Nb/Ta)O6(BYNTO) to YBa2Cu3O7−δ(YBCO) thin films leads to a large improvement of the in-field current carrying capability. For low deposition rates, BYNTO grows as well-oriented, densely distributed nanocolumns. We achieved a pinning force density of 25 GN/m3at 77 K at a matching field of 2.3 T, which is among the highest values reported for YBCO. The anisotropy of the critical current density shows a complex behavior whereby additional maxima are developed at field dependent angles. This is caused by a matching effect of the magnetic fieldsc-axis component. The exponentNof the current-voltage characteristics (inversely proportional to the creep rateS) allows the depinning mechanism to be determined. It changes from a double-kink excitation below the matching field to pinning-potential-determined creep above it.
Conserved miR-26b enhances ovarian granulosa cell apoptosis through HAS2-HA-CD44-Caspase-3 pathway by targeting HAS2
Authors: Liu Jiying , Tu Fei , Yao Wang , Li Xinyu , Xie Zhuang , Liu Honglin , Li Qifa , Pan Zengxiang 
Published: February 2016

AbstractThe hyaluronan synthase 2 (HAS2)-hyaluronic acid (HA)-CD44-Caspase-3 pathway is involved in ovarian granulosa cell (GC) functions in mammals. HAS2 is a key enzyme required for HA synthesis and is the key factor in this pathway. However, the regulation of HAS2 and the HAS2-mediated pathway by microRNAs in GCs is poorly understood. Here, we report that miR-26b regulates porcine GC (pGC) apoptosis through the HAS2-HA-CD44-Caspase-3 pathway by binding directly to the 3′- untranslated region of HAS2 mRNA. Knockdown of miR-26b reduced pGC apoptosis. Luciferase reporter assays demonstrated that HAS2 is a direct target of miR-26b in pGCs. Knockdown and overexpression of miR-26b increased and decreased, respectively, HA content and HAS2 and CD44 expression in pGCs. At the same time, inhibition and overexpression of miR-26b decreased and increased the expression of Caspase-3, a downstream factor in the HAS2-HA-CD44 pathway. Moreover, knockdown of HAS2 enhanced pGC apoptosis, reduced the inhibitory effects of a miR-26b inhibitor on pGC apoptosis, repressed HA content and CD44 expression and promoted Caspase-3 expression. In addition, overexpression of HAS2 has a opposite effect. Collectively, miR-26b positively regulates pGC apoptosis via a novel HAS2-HA-CD44-Caspase-3 pathway by targeting the HAS2 gene.
Giant absorption of light by molecular vibrations on a chip
Authors: Karabchevsky A. , Kavokin A. V. 
Published: February 2016

AbstractVibrational overtone spectroscopy of molecules is a powerful tool for drawing information on molecular structure and dynamics. It relies on absorption of near infrared radiation (NIR) by molecular vibrations. Here we show the experimental evidence of giant enhancement of the absorption of light in solutions of organic molecules due to the switch from ballistic to diffusive propagation of light through a channel silicate glass waveguide. We also experimentally address a dynamics of absorption as a function of time of adsorption of the organic molecules on a waveguide. The observed enhancement in diffusion regime is by a factor of 300 in N-Methylaniline and by factor of 80 in Aniline compared to the expected values in the case of ballistic propagation of light in a waveguide. Our results underscore the importance of a guide surface modification and the disordered molecular nano-layer in enhancement of absorption by amines on engineered integrated system.
BDNF-induced LTP is associated with rapid Arc/Arg3.1-dependent enhancement in adult hippocampal neurogenesis
Authors: Kuipers Sjoukje D. , Trentani Andrea , Tiron Adrian , Mao Xiaosong , Kuhl Dietmar , Bramham Clive R. 
Published: February 2016

AbstractAdult neurogenesis in the hippocampus is a remarkable phenomenon involved in various aspects of learning and memory as well as disease pathophysiology. Brain-derived neurotrophic factor (BDNF) represents a major player in the regulation of this unique form of neuroplasticity, yet the mechanisms underlying its pro-neurogenic actions remain unclear. Here, we examined the effects associated with brief (25 min), unilateral infusion of BDNF in the rat dentate gyrus. Acute BDNF infusion induced long-term potentiation (LTP) of medial perforant path-evoked synaptic transmission and, concomitantly, enhanced hippocampal neurogenesis bilaterally, reflected by increased dentate gyrus BrdU + cell numbers. Importantly, inhibition of activity-regulated cytoskeleton-associated protein (Arc/Arg3.1) translation through local, unilateral infusion of anti-sense oligodeoxynucleotides (ArcAS) prior to BDNF infusion blocked both BDNF-LTP induction and the associated pro-neurogenic effects. Notably, basal rates of proliferation and newborn cell survival were unaltered in homozygous Arc/Arg3.1 knockout mice. Taken together these findings link the pro-neurogenic effects of acute BDNF infusion to induction of Arc/Arg3.1-dependent LTP in the adult rodent dentate gyrus.
Inhibition of preS1-hepatocyte interaction by an array of recombinant human antibodies from naturally recovered individuals
Authors: Sankhyan Anurag , Sharma Chandresh , Dutta Durgashree , Sharma Tarang , Chosdol Kunzang , Wakita Takaji , Watashi Koichi , Awasthi Amit , Acharya Subrat K. , Khanna Navin , Tiwari Ashutosh , Sinha Subrata 
Published: February 2016

AbstractNeutralizing monoclonal antibodies are being found to be increasingly useful in viral infections. In hepatitis B infection, antibodies are proven to be useful for passive prophylaxis. The preS1 region (21–47a.a.) of HBV contains the viral hepatocyte-binding domain crucial for its attachment and infection of hepatocytes. Antibodies against this region are neutralizing and are best suited for immune-based neutralization of HBV, especially in view of their not recognizing decoy particles. Anti-preS1 (21–47a.a.) antibodies are present in serum of spontaneously recovered individuals. We generated a phage-displayed scFv library using circulating lymphocytes from these individuals and selected four preS1-peptide specific scFvs with markedly distinct sequences from this library. All the antibodies recognized the blood-derived and recombinant preS1 containing antigens. Each scFv showed a discrete binding signature, interacting with different amino acids within the preS1-peptide region. Ability to prevent binding of the preS1 protein (N-terminus 60a.a.) to HepG2 cells stably expressing hNTCP (HepG2-hNTCP-C4 cells), the HBV receptor on human hepatocytes was taken as a surrogate marker for neutralizing capacity. These antibodies inhibited preS1-hepatocyte interaction individually and even better in combination. Such a combination of potentially neutralizing recombinant antibodies with defined specificities could be used for preventing/managing HBV infections, including those by possible escape mutants.
G6PDH activity highlights the operation of the cyclic electron flow around PSI in Physcomitrella patens during salt stress
Authors: Gao Shan , Zheng Zhenbing , Huan Li , Wang Guangce 
Published: February 2016

AbstractPhotosynthetic performances and glucose-6-phosphate dehydrogenase (G6PDH) activity inPhyscomitrella patenschanged greatly during salt stress and recovery. InP. patens, the cyclic electron flow around photosystem (PS) I was much more tolerant to high salt stress than PSII. After high salt stress, the PSII activity recovered much more slowly than that of PSI, which was rapidly restored to pretreatment levels even as PSII was almost inactivate. This result suggested that after salt stress the recovery of the cyclic electron flow around PSI was independent of PSII activity. In addition, G6PDH activity and NADPH content increased under high salt stress. When G6PDH activity was inhibited by glucosamine (Glucm, a G6PDH inhibitor), the cyclic electron flow around PSI and the NADPH content decreased significantly. Additionally, after recovery in liquid medium containing Glucm, the PSI activity was much lower than in liquid medium without Glucm. These results suggested the PSI activity was affected significantly by G6PDH activity and the NADPH content. Based on the above results, we propose that G6PDH inP. patenshas a close relationship with the photosynthetic process, possibly providing NADPH for the operation of the cyclic electron flow around PSI during salt stress and promoting the restoration of PSI.
Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases
Authors: Yang Diane , Scavuzzo Marissa A , Chmielowiec Jolanta , Sharp Robert , Bajic Aleksandar , Borowiak Malgorzata 
Published: February 2016

AbstractEfficient gene editing is essential to fully utilize human pluripotent stem cells (hPSCs) in regenerative medicine. Custom endonuclease-based gene targeting involves two mechanisms of DNA repair: homology directed repair (HDR) and non-homologous end joining (NHEJ). HDR is the preferred mechanism for common applications such knock-in, knock-out or precise mutagenesis, but remains inefficient in hPSCs. Here, we demonstrate that synchronizing synchronizing hPSCs in G2/M with ABT phase increases on-target gene editing, defined as correct targeting cassette integration, 3 to 6 fold. We observed improved efficiency using ZFNs, TALENs, two CRISPR/Cas9, and CRISPR/Cas9 nickase to target five genes in three hPSC lines: three human embryonic stem cell lines, neural progenitors and diabetic iPSCs. neural progenitors and diabetic iPSCs. Reversible synchronization has no effect on pluripotency or differentiation. The increase in on-target gene editing is locus-independent and specific to the cell cycle phase as G2/M phase enriched cells show a 6-fold increase in targeting efficiency compared to cells in G1 phase. Concurrently inhibiting NHEJ with SCR7 does not increase HDR or improve gene targeting efficiency further, indicating that HR is the major DNA repair mechanism after G2/M phase arrest. The approach outlined here makes gene editing in hPSCs a more viable tool for disease modeling, regenerative medicine and cell-based therapies.
Collective chemotaxis and segregation of active bacterial colonies
Authors: Amar M. Ben 
Published: February 2016

AbstractStill recently, bacterial fluid suspensions have motivated a lot of works, both experimental and theoretical, with the objective to understand their collective dynamics from universal and simple rules. Since some species are active, most of these works concern the strong interactions that these bacteria exert on a forced flow leading to instabilities, chaos and turbulence. Here, we investigate the self-organization of expanding bacterial colonies under chemotaxis, proliferation and eventually active-reaction. We propose a simple model to understand and quantify the physical properties of these living organisms which either give cohesion or on the contrary dispersion to the colony. Taking into account the diffusion and capture of morphogens complicates the model since it induces a bacterial density gradient coupled to bacterial density fluctuations and dynamics. Nevertheless under some specific conditions, it is possible to investigate the pattern formation as a usual viscous fingering instability. This explains the similarity and differences of patterns according to the physical bacterial suspension properties and explain the factors which favor compactness or branching.