bluuebunny/crossref_metadata_2025_split huggingface dataset:
The antisymmetry of distortions
Authors: VanLeeuwen Brian K. , Gopalan Venkatraman 
Published: November 2015

AbstractDistortions are ubiquitous in nature. Under perturbations such as stresses, fields or other changes, a physical system reconfigures by following a path from one state to another; this path, often a collection of atomic trajectories, describes a distortion. Here we introduce an antisymmetry operation called distortion reversal that reverses a distortion pathway. The symmetry of a distortion pathway is then uniquely defined by a distortion group; it has the same form as a magnetic group that involves time reversal. Given its isomorphism to magnetic groups, distortion groups could have a commensurate impact in the study of distortions, as the magnetic groups have had in the study of magnetic structures. Distortion symmetry has important implications for a range of phenomena such as structural and electronic phase transitions, diffusion, molecular conformational changes, vibrations, reaction pathways and interface dynamics.
Ultrafast response of monolayer molybdenum disulfide photodetectors
Authors: Wang Haining , Zhang Changjian , Chan Weimin , Tiwari Sandip , Rana Farhan 
Published: November 2015

AbstractThe strong light emission and absorption exhibited by single atomic layer transitional metal dichalcogenides in the visible to near-infrared wavelength range make them attractive for optoelectronic applications. In this work, using two-pulse photovoltage correlation technique, we show that monolayer molybdenum disulfide photodetector can have intrinsic response times as short as 3 ps implying photodetection bandwidths as wide as 300 GHz. The fast photodetector response is a result of the short electron–hole and exciton lifetimes in this material. Recombination of photoexcited carriers in most two-dimensional metal dichalcogenides is dominated by nonradiative processes, most notable among which is Auger scattering. The fast response time, and the ease of fabrication of these devices, make them interesting for low-cost ultrafast optical communication links.
MicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes
Authors: Cantini Laura , Isella Claudio , Petti Consalvo , Picco Gabriele , Chiola Simone , Ficarra Elisa , Caselle Michele , Medico Enzo 
Published: November 2015

AbstractColorectal cancer (CRC) transcriptional subtypes have been recently identified by gene expression profiling. Here we describe an analytical pipeline, microRNA master regulator analysis (MMRA), developed to search for microRNAs potentially driving CRC subtypes. Starting from a microRNA–mRNA tumour expression data set, MMRA identifies candidate regulator microRNAs by assessing their subtype-specific expression, target enrichment in subtype mRNA signatures and network analysis-based contribution to subtype gene expression. When applied to a CRC data set of 450 samples, assigned to subtypes by 3 different transcriptional classifiers, MMRA identifies 24 candidate microRNAs, in most cases downregulated in the stem/serrated/mesenchymal (SSM) poor prognosis subtype. Functional validation in CRC cell lines confirms downregulation of the SSM subtype by miR-194, miR-200b, miR-203 and miR-429, which share target genes and pathways mediating this effect. These results show that, by combining statistical tests, target prediction and network analysis, MMRA effectively identifies microRNAs functionally associated to cancer subtypes.
Generation of functional hippocampal neurons from self-organizing human embryonic stem cell-derived dorsomedial telencephalic tissue
Authors: Sakaguchi Hideya , Kadoshima Taisuke , Soen Mika , Narii Nobuhiro , Ishida Yoshihito , Ohgushi Masatoshi , Takahashi Jun , Eiraku Mototsugu , Sasai Yoshiki 
Published: November 2015

AbstractThe developing dorsomedial telencephalon includes the medial pallium, which goes on to form the hippocampus. Generating a reliable source of human hippocampal tissue is an important step for cell-based research into hippocampus-related diseases. Here we show the generation of functional hippocampal granule- and pyramidal-like neurons from self-organizing dorsomedial telencephalic tissue using human embryonic stem cells (hESCs). First, we develop a hESC culture method that utilizes bone morphogenetic protein (BMP) and Wnt signalling to induce choroid plexus, the most dorsomedial portion of the telencephalon. Then, we find that titrating BMP and Wnt exposure allowed the self-organization of medial pallium tissues. Following long-term dissociation culture, these dorsomedial telencephalic tissues give rise to Zbtb20+/Prox1+ granule neurons and Zbtb20+/KA1+ pyramidal neurons, both of which were electrically functional with network formation. Thus, we have developed an in vitro model that recapitulates human hippocampus development, allowing the generation of functional hippocampal granule- and pyramidal-like neurons.
Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea
Authors: Li Meng , Baker Brett J. , Anantharaman Karthik , Jain Sunit , Breier John A. , Dick Gregory J. 
Published: November 2015

AbstractMicrobial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.
Fennoscandian freshwater control on Greenland hydroclimate shifts at the onset of the Younger Dryas
Authors: Muschitiello Francesco , Pausata Francesco S. R. , Watson Jenny E. , Smittenberg Rienk H. , Salih Abubakr A. M. , Brooks Stephen J. , Whitehouse Nicola J. , Karlatou-Charalampopoulou Artemis , Wohlfarth Barbara 
Published: November 2015

AbstractSources and timing of freshwater forcing relative to hydroclimate shifts recorded in Greenland ice cores at the onset of Younger Dryas, ∼12,800 years ago, remain speculative. Here we show that progressive Fennoscandian Ice Sheet (FIS) melting 13,100–12,880 years ago generates a hydroclimate dipole with drier–colder conditions in Northern Europe and wetter–warmer conditions in Greenland. FIS melting culminates 12,880 years ago synchronously with the start of Greenland Stadial 1 and a large-scale hydroclimate transition lasting ∼180 years. Transient climate model simulations forced with FIS freshwater reproduce the initial hydroclimate dipole through sea-ice feedbacks in the Nordic Seas. The transition is attributed to the export of excess sea ice to the subpolar North Atlantic and a subsequent southward shift of the westerly winds. We suggest that North Atlantic hydroclimate sensitivity to FIS freshwater can explain the pace and sign of shifts recorded in Greenland at the climate transition into the Younger Dryas.
Paracingulate sulcus morphology is associated with hallucinations in the human brain
Authors: Garrison Jane R. , Fernyhough Charles , McCarthy-Jones Simon , Haggard Mark ,   The Australian Schizophrenia Research Bank, Carr Vaughan , Schall Ulrich , Scott Rodney , Jablensky Assen , Mowry Bryan , Michie Patricia , Catts Stanley , Henskens Frans , Pantelis Christos , Loughland Carmel , Simons Jon S. 
Published: November 2015

AbstractHallucinations are common in psychiatric disorders, and are also experienced by many individuals who are not mentally ill. Here, in 153 participants, we investigate brain structural markers that predict the occurrence of hallucinations by comparing patients with schizophrenia who have experienced hallucinations against patients who have not, matched on a number of demographic and clinical variables. Using both newly validated visual classification techniques and automated, data-driven methods, hallucinations were associated with specific brain morphology differences in the paracingulate sulcus, a fold in the medial prefrontal cortex, with a 1 cm reduction in sulcal length increasing the likelihood of hallucinations by 19.9%, regardless of the sensory modality in which they were experienced. The findings suggest a specific morphological basis for a pervasive feature of typical and atypical human experience.
Directional nanotopographic gradients: a high-throughput screening platform for cell contact guidance
Authors: Zhou Qihui , Kühn Philipp T. , Huisman Thirsa , Nieboer Elsje , van Zwol Charlotte , van Kooten Theo G. , van Rijn Patrick 
Published: November 2015

AbstractA novel approach was developed using PDMS-substrates with surface-aligned nanotopography gradients, varying unidirectional in amplitude and wavelength, for studying cell behavior with regard to adhesion and alignment. The gradients target more surface feature parameters simultaneously and provide more information with fewer experiments and are therefore vastly superior with respect to individual topography substrates. Cellular adhesion experiments on non-gradient aligned nanowrinkled surfaces displayed a linear relationship of osteoblast cell adhesion with respect to topography aspect ratio. Additionally, an aspect ratio of 0.25 was found to be most efficient for cell alignment. Modification of the surface preparation method allowed us to develop an approach for creating surface nanotopography gradients which innovatively provided a superior data collection with fewer experiments showing that 1) low amplitude with small wavenumber is best for osteoblast cell adhesion 2) indeed higher aspect ratios are favorable for alignment however only with features between 80–180 nm in amplitude and 450–750 nm in wavelength with a clear transition between adhesion and alignment efficiency and 3) disproved a linear relationship of cell adhesion towards aspect ratio as was found for single feature substrate analysis.
Graphene oxide and H2 production from bioelectrochemical graphite oxidation
Authors: Lu Lu , Zeng Cuiping , Wang Luda , Yin Xiaobo , Jin Song , Lu Anhuai , Jason Ren Zhiyong 
Published: November 2015

AbstractGraphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2 and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost and it may stimulate a new area of research in MES.
Producing human ceramide-NS by metabolic engineering using yeast Saccharomyces cerevisiae
Authors: Murakami Suguru , Shimamoto Toshi , Nagano Hideaki , Tsuruno Masahiro , Okuhara Hiroaki , Hatanaka Haruyo , Tojo Hiromasa , Kodama Yukiko , Funato Kouichi 
Published: November 2015

AbstractCeramide is one of the most important intercellular components responsible for the barrier and moisture retention functions of the skin. Because of the risks involved with using products of animal origin and the low productivity of plants, the availability of ceramides is currently limited. In this study, we successfully developed a system that produces sphingosine-containing human ceramide-NS in the yeast Saccharomyces cerevisiae by eliminating the genes for yeast sphingolipid hydroxylases (encoded by SUR2 and SCS7) and introducing the gene for a human sphingolipid desaturase (encoded by DES1). The inactivation of the ceramidase gene YDC1, overexpression of the inositol phosphosphingolipid phospholipase C gene ISC1 and endoplasmic reticulum localization of the DES1 gene product resulted in enhanced production of ceramide-NS. The engineered yeast strains can serve as hosts not only for providing a sustainable source of ceramide-NS but also for developing further systems to produce sphingosine-containing sphingolipids.
Hardy exotics species in temperate zone: can “warm water” crayfish invaders establish regardless of low temperatures?
Authors: Veselý Lukáš , Buřič Miloš , Kouba Antonín 
Published: November 2015

AbstractThe spreading of new crayfish species poses a serious risk for freshwater ecosystems; because they are omnivores they influence more than one level in the trophic chain and they represent a significant part of the benthic biomass. Both the environmental change through global warming and the expansion of the pet trade increase the possibilities of their spreading. We investigated the potential of four “warm water” highly invasive crayfish species to overwinter in the temperate zone, so as to predict whether these species pose a risk for European freshwaters. We used 15 specimens of each of the following species: the red swamp crayfish (Procambarus clarkii), the marbled crayfish (Procambarus fallax f. virginalis), the yabby (Cherax destructor) and the redclaw (Cherax quadricarinatus). Specimens were acclimatized and kept for 6.5 months at temperatures simulating the winter temperature regime of European temperate zone lentic ecosystems. We conclude that the red swamp crayfish, marbled crayfish and yabby have the ability to withstand low winter temperatures relevant for lentic habitats in the European temperate zone, making them a serious invasive threat to freshwater ecosystems.
Highly-accurate metabolomic detection of early-stage ovarian cancer
Authors: Gaul David A. , Mezencev Roman , Long Tran Q. , Jones Christina M. , Benigno Benedict B. , Gray Alexander , Fernández Facundo M. , McDonald John F. 
Published: November 2015

AbstractHigh performance mass spectrometry was employed to interrogate the serum metabolome of early-stage ovarian cancer (OC) patients and age-matched control women. The resulting spectral features were used to establish a linear support vector machine (SVM) model of sixteen diagnostic metabolites that are able to identify early-stage OC with 100% accuracy in our patient cohort. The results provide evidence for the importance of lipid and fatty acid metabolism in OC and serve as the foundation of a clinically significant diagnostic test.
Size-Dependent Melting Behavior of Colloidal In, Sn and Bi Nanocrystals
Authors: Liu Minglu , Wang Robert Y. 
Published: November 2015

AbstractColloidal nanocrystals are a technologically important class of nanostructures whose phase change properties have been largely unexplored. Here we report on the melting behavior of In, Sn and Bi nanocrystals dispersed in a polymer matrix. This polymer matrix prevents the nanocrystals from coalescing with one another and enables previously unaccessed observations on the melting behavior of colloidal nanocrystals. We measure the melting temperature, melting enthalpy and melting entropy of colloidal nanocrystals with diameters of approximately 10 to 20 nm. All of these properties decrease as nanocrystal size decreases, although the depression rate for melting temperature is comparatively slower than that of melting enthalpy and melting entropy. We also observe an elevated melting temperature during the initial melt-freeze cycle that we attribute to surface stabilization from the organic ligands on the nanocrystal surface. Broad endothermic melting valleys and very large supercoolings in our calorimetry data suggest that colloidal nanocrystals exhibit a significant amount of surface pre-melting and low heterogeneous nucleation probabilities during freezing.
Accurate label-free reaction kinetics determination using initial rate heat measurements
Authors: Honarmand Ebrahimi Kourosh , Hagedoorn Peter-Leon , Jacobs Denise , Hagen Wilfred R. 
Published: November 2015

AbstractAccurate label-free methods or assays to obtain the initial reaction rates have significant importance in fundamental studies of enzymes and in application-oriented high throughput screening of enzyme activity. Here we introduce a label-free approach for obtaining initial rates of enzyme activity from heat measurements, which we name initial rate calorimetry (IrCal). This approach is based on our new finding that the data recorded by isothermal titration calorimetry for the early stages of a reaction, which have been widely ignored, are correlated to the initial rates. Application of the IrCal approach to various enzymes led to accurate enzyme kinetics parameters as compared to spectroscopic methods and enabled enzyme kinetic studies with natural substrate, e.g. proteases with protein substrates. Because heat is a label-free property of almost all reactions, the IrCal approach holds promise in fundamental studies of various enzymes and in use of calorimetry for high throughput screening of enzyme activity.
Intravoxel Incoherent Motion Diffusion-weighted Magnetic Resonance Imaging for Monitoring the Early Response to ZD6474 from Nasopharyngeal Carcinoma in Nude Mouse
Authors: Cui Yanfen , Zhang Caiyuan , Li Xiaoming , Liu Huanhuan , Yin Bing , Xu Tianyong , Zhang Yong , Wang Dengbin 
Published: November 2015

AbstractEarly therapeutic effects of anti-angiogenic agent ZD6474 upon nasopharyngeal carcinoma (NPC) in nude mouse were monitored by using intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI). Mice bearing NPC underwent IVIM DWI at baseline and after 1, 3 and 7 days of treatment with ZD6474 or vehicle (n = 12 per group). Parameters of apparent diffusion coefficient (ADC), true diffusion coefficient (D), perfusion fraction (f) and blood pseudodiffusion coefficient (D*) at different time points were compared between the two groups or within the treated group. In the treated group, the perfusion-related parameters f and D* of the tumors decreased significantly on day 1 while the diffusion-related parameters ADC and D were significantly higher beginning on day 3 compared with the control group. The decreases in f on day 1 and D* on day 3 were moderately correlated with the smaller tumor size change on day 7. Moderate correlations were established between MVD and f and D* as well as between increased TUNEL or decreased Ki-67 index and ADC and D. This study supports that IVIM DWI is sensitive to detect the ZD6474-induced changes in NPC in nude mouse and the f parameter could predict early response to anti-angiogenic treatment.
Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging
Authors: Dukic Maja , Adams Jonathan D. , Fantner Georg E. 
Published: November 2015

AbstractOptical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.
Screening and transport in 2D semiconductor systems at low temperatures
Authors: Das Sarma S. , Hwang E. H. 
Published: November 2015

AbstractLow temperature carrier transport properties in 2D semiconductor systems can be theoretically well-understood within RPA-Boltzmann theory as being limited by scattering from screened Coulomb disorder arising from random quenched charged impurities in the environment. In this work, we derive a number of analytical formula, supported by realistic numerical calculations, for the relevant density, mobility and temperature range where 2D transport should manifest strong intrinsic (i.e., arising purely from electronic effects) metallic temperature dependence in different semiconductor materials arising entirely from the 2D screening properties, thus providing an explanation for why the strong temperature dependence of the 2D resistivity can only be observed in high-quality and low-disorder 2D samples and also why some high-quality 2D materials manifest much weaker metallicity than other materials. We also discuss effects of interaction and disorder on the 2D screening properties in this context as well as compare 2D and 3D screening functions to comment why such a strong intrinsic temperature dependence arising from screening cannot occur in 3D metallic carrier transport. Experimentally verifiable predictions are made about the quantitative magnitude of the maximum possible low-temperature metallicity in 2D systems and the scaling behavior of the temperature scale controlling the quantum to classical crossover.
Novel, Synergistic Antifungal Combinations that Target Translation Fidelity
Authors: Moreno-Martinez Elena , Vallieres Cindy , Holland Sara L. , Avery Simon V. 
Published: November 2015

AbstractThere is an unmet need for new antifungal or fungicide treatments, as resistance to existing treatments grows. Combination treatments help to combat resistance. Here we develop a novel, effective target for combination antifungal therapy. Different aminoglycoside antibiotics combined with different sulphate-transport inhibitors produced strong, synergistic growth-inhibition of several fungi. Combinations decreased the respective MICs by ≥8-fold. Synergy was suppressed in yeast mutants resistant to effects of sulphate-mimetics (like chromate or molybdate) on sulphate transport. By different mechanisms, aminoglycosides and inhibition of sulphate transport cause errors in mRNA translation. The mistranslation rate was stimulated up to 10-fold when the agents were used in combination, consistent with this being the mode of synergistic action. A range of undesirable fungi were susceptible to synergistic inhibition by the combinations, including the human pathogens Candida albicans, C. glabrata and Cryptococcus neoformans, the food spoilage organism Zygosaccharomyces bailii and the phytopathogens Rhizoctonia solani and Zymoseptoria tritici. There was some specificity as certain fungi were unaffected. There was no synergy against bacterial or mammalian cells. The results indicate that translation fidelity is a promising new target for combinatorial treatment of undesirable fungi, the combinations requiring substantially decreased doses of active components compared to each agent alone.