bluuebunny/crossref_metadata_2025_split huggingface dataset:
Andean mountain building and magmatic arc migration driven by subduction-induced whole mantle flow
Authors: Schellart W. P. 
Published: December 2017

AbstractSubduction along the western margin of South America has been active since the Jurassic, but Andean orogeny started in the middle Cretaceous and was preceded by backarc extension in the Jurassic-Early Cretaceous. The timing and sequence of these events has remained unexplained. Here I present a four-dimensional buoyancy-driven whole-mantle subduction model implying that the ~200 Myr geological evolution can be attributed to sinking of a wide slab into a layered mantle, where upper-mantle wide-slab subduction causes backarc extension, while whole-mantle (upper+lower) wide-slab subduction drives Andean orogeny. The model reproduces the maximum shortening and crustal thickness observed in the Central Andes and their progressive northward and southward decrease. The subduction evolution coincides with a 29° decrease in slab dip angle, explaining ~200 km of Jurassic-present eastward migration of the Central Andean magmatic arc. Such arc migration negates proposed long-term subduction erosion and continental destruction, but is consistent with long-term crustal growth.
Tree co-occurrence and transcriptomic response to drought
Authors: Swenson Nathan G. , Iida Yoshiko , Howe Robert , Wolf Amy , Umaña María Natalia , Petprakob Krittika , Turner Benjamin L. , Ma Keping 
Published: December 2017

AbstractThe distribution and co-occurrence of species are partly the outcome of their interactions with environmental drivers. Drought is a key driver related to the distribution of plant species. Drought events continue to increase in frequency and severity and identifying those aspects of plant function that are related to drought is critical. Here, we perform a community-level analysis of gene expression in relation to experimental drought and relate the similarity in gene set enrichment across species to their natural co-occurrence. Species with similar gene set enrichment in response to experimental drought tend to non-randomly co-occur in a natural stand. We demonstrate that similarity in the transcriptomic response of species to drought is a significantly better indicator of natural co-occurrence than measures of functional trait similarity and phylogenetic relatedness and that transcriptomics has the capacity to greatly enhance ecological investigations of species distributions and community structure.
Serendipity and strategy in rapid innovation
Authors: Fink T. M. A. , Reeves M. , Palma R. , Farr R. S. 
Published: December 2017

AbstractInnovation is to organizations what evolution is to organisms: it is how organizations adapt to environmental change and improve. Yet despite advances in our understanding of evolution, what drives innovation remains elusive. On the one hand, organizations invest heavily in systematic strategies to accelerate innovation. On the other, historical analysis and individual experience suggest that serendipity plays a significant role. To unify these perspectives, we analysed the mathematics of innovation as a search for designs across a universe of component building blocks. We tested our insights using data from language, gastronomy and technology. By measuring the number of makeable designs as we acquire components, we observed that the relative usefulness of different components can cross over time. When these crossovers are unanticipated, they appear to be the result of serendipity. But when we can predict crossovers in advance, they offer opportunities to strategically increase the growth of the product space.
Induced unconventional superconductivity on the surface states of Bi2Te3 topological insulator
Authors: Charpentier Sophie , Galletti Luca , Kunakova Gunta , Arpaia Riccardo , Song Yuxin , Baghdadi Reza , Wang Shu Min , Kalaboukhov Alexei , Olsson Eva , Tafuri Francesco , Golubev Dmitry , Linder Jacob , Bauch Thilo , Lombardi Floriana 
Published: December 2017

AbstractTopological superconductivity is central to a variety of novel phenomena involving the interplay between topologically ordered phases and broken-symmetry states. The key ingredient is an unconventional order parameter, with an orbital component containing a chiral p
x
+ ip
y
wave term. Here we present phase-sensitive measurements, based on the quantum interference in nanoscale Josephson junctions, realized by using Bi2Te3 topological insulator. We demonstrate that the induced superconductivity is unconventional and consistent with a sign-changing order parameter, such as a chiral p
x
+ ip
y
component. The magnetic field pattern of the junctions shows a dip at zero externally applied magnetic field, which is an incontrovertible signature of the simultaneous existence of 0 and π coupling within the junction, inherent to a non trivial order parameter phase. The nano-textured morphology of the Bi2Te3 flakes, and the dramatic role played by thermal strain are the surprising key factors for the display of an unconventional induced order parameter.
Input-dependent regulation of excitability controls dendritic maturation in somatosensory thalamocortical neurons
Authors: Frangeul Laura , Kehayas Vassilis , Sanchez-Mut Jose V. , Fièvre Sabine , Krishna-K K. , Pouchelon Gabrielle , Telley Ludovic , Bellone Camilla , Holtmaat Anthony , Gräff Johannes , Macklis Jeffrey D. , Jabaudon Denis 
Published: December 2017

AbstractInput from the sensory organs is required to pattern neurons into topographical maps during development. Dendritic complexity critically determines this patterning process; yet, how signals from the periphery act to control dendritic maturation is unclear. Here, using genetic and surgical manipulations of sensory input in mouse somatosensory thalamocortical neurons, we show that membrane excitability is a critical component of dendritic development. Using a combination of genetic approaches, we find that ablation of N-methyl-d-aspartate (NMDA) receptors during postnatal development leads to epigenetic repression of Kv1.1-type potassium channels, increased excitability, and impaired dendritic maturation. Lesions to whisker input pathways had similar effects. Overexpression of Kv1.1 was sufficient to enable dendritic maturation in the absence of sensory input. Thus, Kv1.1 acts to tune neuronal excitability and maintain it within a physiological range, allowing dendritic maturation to proceed. Together, these results reveal an input-dependent control over neuronal excitability and dendritic complexity in the development and plasticity of sensory pathways.
The dynamic dimer structure of the chaperone Trigger Factor
Authors: Morgado Leonor , Burmann Björn M. , Sharpe Timothy , Mazur Adam , Hiller Sebastian 
Published: December 2017

AbstractThe chaperone Trigger Factor (TF) from Escherichia coli forms a dimer at cellular concentrations. While the monomer structure of TF is well known, the spatial arrangement of this dimeric chaperone storage form has remained unclear. Here, we determine its structure by a combination of high-resolution NMR spectroscopy and biophysical methods. TF forms a symmetric head-to-tail dimer, where the ribosome binding domain is in contact with the substrate binding domain, while the peptidyl-prolyl isomerase domain contributes only slightly to the dimer affinity. The dimer structure is highly dynamic, with the two ribosome binding domains populating a conformational ensemble in the center. These dynamics result from intermolecular in trans interactions of the TF client-binding site with the ribosome binding domain, which is conformationally frustrated in the absence of the ribosome. The avidity in the dimer structure explains how the dimeric state of TF can be monomerized also by weakly interacting clients.
Bioinspired graphene membrane with temperature tunable channels for water gating and molecular separation
Authors: Liu Jingchong , Wang Nü , Yu Li-Juan , Karton Amir , Li Wen , Zhang Weixia , Guo Fengyun , Hou Lanlan , Cheng Qunfeng , Jiang Lei , Weitz David A. , Zhao Yong 
Published: December 2017

AbstractSmart regulation of substance permeability through porous membranes is highly desirable for membrane applications. Inspired by the stomatal closure feature of plant leaves at relatively high temperature, here we report a nano-gating membrane with a negative temperature-response coefficient that is capable of tunable water gating and precise small molecule separation. The membrane is composed of poly(N-isopropylacrylamide) covalently bound to graphene oxide via free-radical polymerization. By virtue of the temperature tunable lamellar spaces of the graphene oxide nanosheets, the water permeance of the membrane could be reversibly regulated with a high gating ratio. Moreover, the space tunability endows the membrane with the capability of gradually separating multiple molecules of different sizes. This nano-gating membrane expands the scope of temperature-responsive membranes and has great potential applications in smart gating systems and molecular separation.
RAN translation at C9orf72-associated repeat expansions is selectively enhanced by the integrated stress response
Authors: Green Katelyn M. , Glineburg M. Rebecca , Kearse Michael G. , Flores Brittany N. , Linsalata Alexander E. , Fedak Stephen J. , Goldstrohm Aaron C. , Barmada Sami J. , Todd Peter K. 
Published: December 2017

AbstractRepeat-associated non-AUG (RAN) translation allows for unconventional initiation at disease-causing repeat expansions. As RAN translation contributes to pathogenesis in multiple neurodegenerative disorders, determining its mechanistic underpinnings may inform therapeutic development. Here we analyze RAN translation at G4C2 repeat expansions that cause C9orf72-associated amyotrophic lateral sclerosis and frontotemporal dementia (C9RAN) and at CGG repeats that cause fragile X-associated tremor/ataxia syndrome. We find that C9RAN translation initiates through a cap- and eIF4A-dependent mechanism that utilizes a CUG start codon. C9RAN and CGG RAN are both selectively enhanced by integrated stress response (ISR) activation. ISR-enhanced RAN translation requires an eIF2α phosphorylation-dependent alteration in start codon fidelity. In parallel, both CGG and G4C2 repeats trigger phosphorylated-eIF2α-dependent stress granule formation and global translational suppression. These findings support a model whereby repeat expansions elicit cellular stress conditions that favor RAN translation of toxic proteins, creating a potential feed-forward loop that contributes to neurodegeneration.
Tuning the interactions between chiral plasmonic films and living cells
Authors: Zhao Xueli , Xu Liguang , Sun Maozhong , Ma Wei , Wu Xiaoling , Xu Chuanlai , Kuang Hua 
Published: December 2017

AbstractDesigning chiral materials to manipulate the biological activities of cells has been an important area not only in chemistry and material science, but also in cell biology and biomedicine. Here, we introduce monolayer plasmonic chiral Au nanoparticle (NP) films modified withl- ord-penicillamine (Pen) to be developed for cell growth, differentiation, and retrieval. The monolayer films display high chiroptical activity, with circular dichroism values of 3.5 mdeg at 550 nm and 26.8 mdeg at 775 nm. Thel-Pen-NP films accelerate cell proliferation, whereas thed-Pen-NP films have the opposite effect. Remote irradiation with light is chosen to noninvasively collect the cells. The results demonstrate that left circularly polarized light improves the efficiency of cell detachment up to 91.2% forl-Pen-NP films. These findings will facilitate the development of cell culture in biomedical application and help to understand natural homochirality.
Scaling of Yu-Shiba-Rusinov energies in the weak-coupling Kondo regime
Authors: Hatter Nino , Heinrich Benjamin W. , Rolf Daniela , Franke Katharina J. 
Published: December 2017

AbstractThe competition of the free-spin state of a paramagnetic impurity on a superconductor with its screened counterpart is characterized by the energy scale of Kondo screening compared to the superconducting pairing energy Δ. When the experimental temperature suppresses Kondo screening, but preserves superconductivity, i.e., when Δ/kB > T > TK (kB is Boltzmann’s constant and TK the Kondo temperature), this description fails. Here, we explore this temperature range in a set of manganese phthalocyanine molecules decorated with ammonia on Pb(111). We show that these molecules suffice the required energy conditions by exhibiting weak-coupling Kondo resonances. We correlate the Yu-Shiba-Rusinov bound states energy inside the superconducting gap with the intensity of the Kondo resonance. The observed correlation follows the expectations for a classical spin on a superconductor. This finding is important in view of many theoretical predictions using a classical spin model, in particular for the description of Majorana bound states in magnetic nanostructures on superconducting substrates.
A control analysis perspective on Katz centrality
Authors: Sharkey Kieran J. 
Published: December 2017

AbstractMethods for efficiently controlling dynamics propagated on networks are usually based on identifying the most influential nodes. Knowledge of these nodes can be used for the targeted control of dynamics such as epidemics, or for modifying biochemical pathways relating to diseases. Similarly they are valuable for identifying points of failure to increase network resilience in, for example, social support networks and logistics networks. Many measures, often termed ‘centrality’, have been constructed to achieve these aims. Here we consider Katz centrality and provide a new interpretation as a steady-state solution to continuous-time dynamics. This enables us to implement a sensitivity analysis which is similar to metabolic control analysis used in the analysis of biochemical pathways. The results yield a centrality which quantifies, for each node, the net impact of its absence from the network. It also has the desirable property of requiring a node with a high centrality to play a central role in propagating the dynamics of the system by having the capacity to both receive flux from others and then to pass it on. This new perspective on Katz centrality is important for a more comprehensive analysis of directed networks.
Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families
Authors: Moretti Ana I. S. , Pavanelli Jessyca C. , Nolasco Patrícia , Leisegang Matthias S. , Tanaka Leonardo Y. , Fernandes Carolina G. , Wosniak João , Kajihara Daniela , Dias Matheus H. , Fernandes Denise C. , Jo Hanjoong , Tran Ngoc-Vinh , Ebersberger Ingo , Brandes Ralf P. , Bonatto Diego , Laurindo Francisco R. M. 
Published: December 2017

AbstractProtein disulfide isomerases (PDIs) support endoplasmic reticulum redox protein folding and cell-surface thiol-redox control of thrombosis and vascular remodeling. The family prototype PDIA1 regulates NADPH oxidase signaling and cytoskeleton organization, however the related underlying mechanisms are unclear. Here we show that genes encoding human PDIA1 and its two paralogs PDIA8 and PDIA2 are each flanked by genes encoding Rho guanine-dissociation inhibitors (GDI), known regulators of RhoGTPases/cytoskeleton. Evolutionary histories of these three microsyntenic regions reveal their emergence by two successive duplication events of a primordial gene pair in the last common vertebrate ancestor. The arrangement, however, is substantially older, detectable in echinoderms, nematodes, and cnidarians. Thus, PDI/RhoGDI pairing in the same transcription orientation emerged early in animal evolution and has been largely maintained. PDI/RhoGDI pairs are embedded into conserved genomic regions displaying common cis-regulatory elements. Analysis of gene expression datasets supports evidence for PDI/RhoGDI coexpression in developmental/inflammatory contexts. PDIA1/RhoGDIα were co-induced in endothelial cells upon CRISP-R-promoted transcription activation of each pair component, and also in mouse arterial intima during flow-induced remodeling. We provide evidence for physical interaction between both proteins. These data support strong functional links between PDI and RhoGDI families, which likely maintained PDI/RhoGDI microsynteny along > 800-million years of evolution.
Ground-state cooling of a mechanical oscillator in a hybrid optomechanical system including an atomic ensemble
Authors: Zeng Wei , Nie Wenjie , Li Ling , Chen Aixi 
Published: December 2017

AbstractWe investigate dynamical properties and the ground-state cooling of a mechanical oscillator in an optomechanical system coupling with an atomic ensemble. In this hybrid optomechanical system, an atomic ensemble which consists of two-level atoms couples with the cavity field. Here we consider the case where the atomic ensemble is in higher excitation. Studies show that the atom-field coupling strength can obviously influence the cooling process, and we can achieve the ground-state cooling of the mechanical oscillator by choosing the appropriate physical parameters of the system. Our cooling mechanism has potential applications in quantum information processing and procession measurement.
Utilization of blood by-products: An in silico and experimental combined study for BSA usage
Authors: Arrutia Fátima , Fernández Rebeca , Menéndez Carlos , González Ulises A. , Riera Francisco A. 
Published: December 2017

AbstractIn order to exploit industrial discards, protein enzymatic hydrolysis is a currently popular methodology for obtaining bioactive peptides. However, once released, most promising peptides have to be selected from the mixture. In this work, the suitability of pepsin (EC 3.4.23.1) to hydrolyse serum albumin in order to obtain bioactive peptides was assessed. Then, a suitable process to obtain best separation of bioactive peptides was evaluated, using polyethersulfone membranes at different pH values. Serum albumin was easily hydrolysed by pepsin, reaching a DH value of the 65.64 ± 1.57% of the maximum possible. A 23.25% of the identified peptides possessed high bioactivity scores (greater than 0.5), and one of them had reported bioactivity (LLL). Charge mechanisms always predominated over the sieve effect, and best transmission was accomplished at pH values close to the peptides isoelectric points. Basic and neutral peptides with the highest scores were always the most transmitted. Membrane material had greater influence than NMWCO in determining peptide transmission. In order to obtain purified fractions rich in peptides with high bioactivity scores from serum albumin, polyethersulfone membranes (applicable to industrial scale) of 5 kDa MWCO should be used at basic pH values after pepsin digestion.
The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland
Authors: Gilbert Edmund , O’Reilly Seamus , Merrigan Michael , McGettigan Darren , Molloy Anne M. , Brody Lawrence C. , Bodmer Walter , Hutnik Katarzyna , Ennis Sean , Lawson Daniel J. , Wilson James F. , Cavalleri Gianpiero L. 
Published: December 2017

AbstractThe extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the ‘Irish DNA Atlas’, a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of ‘Gaelic’ Irish ancestry, and three of shared Irish-British ancestry. In addition we observe a major genetic barrier to the north of Ireland in Ulster. Using a reference of 6,760 European individuals and two ancient Irish genomes, we demonstrate high levels of North-West French-like and West Norwegian-like ancestry within Ireland. We show that that our ‘Gaelic’ Irish clusters present homogenous levels of ancient Irish ancestries. We additionally detect admixture events that provide evidence of Norse-Viking gene flow into Ireland, and reflect the Ulster Plantations. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry.
A highly printable and biocompatible hydrogel composite for direct printing of soft and perfusable vasculature-like structures
Authors: Suntornnond Ratima , Tan Edgar Yong Sheng , An Jia , Chua Chee Kai 
Published: November 2017

AbstractVascularization is one major obstacle in bioprinting and tissue engineering. In order to create thick tissues or organs that can function like original body parts, the presence of a perfusable vascular system is essential. However, it is challenging to bioprint a hydrogel-based three-dimensional vasculature-like structure in a single step. In this paper, we report a new hydrogel-based composite that offers impressive printability, shape integrity, and biocompatibility for 3D bioprinting of a perfusable complex vasculature-like structure. The hydrogel composite can be used on a non-liquid platform and is printable at human body temperature. Moreover, the hydrogel composite supports both cell proliferation and cell differentiation. Our results represent a potentially new vascularization strategy for 3D bioprinting and tissue engineering.
Impact of model calibration on cost-effectiveness analysis of cervical cancer prevention
Authors: Moriña David , de Sanjosé Silvia , Diaz Mireia 
Published: December 2017

AbstractMarkov chain models are commonly used to simulate the natural history of human papillomavirus infection and subsequent cervical lesions with the aim of predicting future benefits of health interventions. Developing and calibrating these models entails making a number of critical decisions that will influence the ability of the model to reflect real conditions and predict future situations. Accuracy of selected inputs and calibration procedures are two of the crucial aspects for model performance and understanding their influence is essential, especially when involves policy decisions. The aim of this work is to assess the health and economic impact on cervical cancer prevention strategies currently under discussion according to the most common methods of model calibration combined with different accuracy degree of initial inputs. Model results show large differences on the goodness of fit and cost-effectiveness outcomes depending on the calibration approach used, and these variations may affect health policy decisions. Our findings strengthen the importance of obtaining good calibrated probability matrices to get reliable health and cost outcomes, and are directly generalizable to any cost-effectiveness analysis based on Markov chain models.