bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coherent transfer of electron spin correlations assisted by dephasing noise
Authors: Nakajima Takashi , Delbecq Matthieu R. , Otsuka Tomohiro , Amaha Shinichi , Yoneda Jun , Noiri Akito , Takeda Kenta , Allison Giles , Ludwig Arne , Wieck Andreas D. , Hu Xuedong , Nori Franco , Tarucha Seigo 
Published: May 2018

AbstractQuantum coherence of superposed states, especially of entangled states, is indispensable for many quantum technologies. However, it is vulnerable to environmental noises, posing a fundamental challenge in solid-state systems including spin qubits. Here we show a scheme of entanglement engineering where pure dephasing assists the generation of quantum entanglement at distant sites in a chain of electron spins confined in semiconductor quantum dots. One party of an entangled spin pair, prepared at a single site, is transferred to the next site and then adiabatically swapped with a third spin using a transition across a multi-level avoided crossing. This process is accelerated by the noise-induced dephasing through a variant of the quantum Zeno effect, without sacrificing the coherence of the entangled state. Our finding brings insight into the spin dynamics in open quantum systems coupled to noisy environments, opening an avenue to quantum state manipulation utilizing decoherence effects.
Exploring patterns enriched in a dataset with contrastive principal component analysis
Authors: Abid Abubakar , Zhang Martin J. , Bagaria Vivek K. , Zou James 
Published: May 2018

AbstractVisualization and exploration of high-dimensional data is a ubiquitous challenge across disciplines. Widely used techniques such as principal component analysis (PCA) aim to identify dominant trends in one dataset. However, in many settings we have datasets collected under different conditions, e.g., a treatment and a control experiment, and we are interested in visualizing and exploring patterns that are specific to one dataset. This paper proposes a method, contrastive principal component analysis (cPCA), which identifies low-dimensional structures that are enriched in a dataset relative to comparison data. In a wide variety of experiments, we demonstrate that cPCA with a background dataset enables us to visualize dataset-specific patterns missed by PCA and other standard methods. We further provide a geometric interpretation of cPCA and strong mathematical guarantees. An implementation of cPCA is publicly available, and can be used for exploratory data analysis in many applications where PCA is currently used.
Pressure-induced superconductivity in MoP
Authors: Chi Zhenhua , Chen Xuliang , An Chao , Yang Liuxiang , Zhao Jinggeng , Feng Zili , Zhou Yonghui , Zhou Ying , Gu Chuanchuan , Zhang Bowen , Yuan Yifang , Kenney-Benson Curtis , Yang Wenge , Wu Gang , Wan Xiangang , Shi Youguo , Yang Xiaoping , Yang Zhaorong 
Published: May 2018

AbstractTopological semimetal, a novel state of quantum matter hosting exotic emergent quantum phenomena dictated by the nontrivial band topology, has emerged as a new frontier in condensed-matter physics. Very recently, the coexistence of triply degenerate points of band crossing and Weyl points near the Fermi level was theoretically predicted and experimentally identified in MoP. Via high-pressure electrical transport measurements, we report here the emergence of pressure-induced superconductivity in MoP with a critical transition temperature Tc of ca. 2.5 K at ca. 30 GPa. No structural phase transition is observed up to ca. 60 GPa via synchrotron X-ray diffraction study. Accordingly, the topologically nontrivial band protected by the crystal structure symmetries and superconductivity are expected to coexist at pressures above 30 GPa, consistent with density functional theory calculations. Thus, the pressurized MoP represents a promising candidate of topological superconductor. Our finding is expected to stimulate further exploitation of exotic emergent quantum phenomena in novel unconventional fermion system.
The invasion of abandoned fields by a major alien tree filters understory plant traits in novel forest ecosystems
Authors: Sitzia T. , Campagnaro T. , Kotze D. J. , Nardi S. , Ertani A. 
Published: May 2018

AbstractThe abandonment of agricultural use is a common driver of spontaneous reforestation by alien trees. The N-fixing black locust (Robinia pseudoacacia L.) is a major alien invader of old fields in Europe. Here we show that canopy dominance by this tree may filter the frequency distribution of plant functional traits in the understory of secondary woodlands. Higher soil C/N ratio and available P are associated with black locust stands, while higher soil phenols associate with native tree stands. These environmental effects result in differences in understory flowering periods, reproduction types and life forms. Our findings emphasize the effect of a major alien tree on functional plant trait composition in the early stages of spontaneous reforestation of abandoned lands, implying the development of a novel forest ecosystem on a large geographical scale.
Convergent Pathways in Idiopathic Autism Revealed by Time Course Transcriptomic Analysis of Patient-Derived Neurons
Authors: DeRosa Brooke A. , El Hokayem Jimmy , Artimovich Elena , Garcia-Serje Catherine , Phillips Andre W. , Van Booven Derek , Nestor Jonathan E. , Wang Lily , Cuccaro Michael L. , Vance Jeffery M. , Pericak-Vance Margaret A. , Cukier Holly N. , Nestor Michael W. , Dykxhoorn Derek M. 
Published: May 2018

AbstractPotentially pathogenic alterations have been identified in individuals with autism spectrum disorders (ASDs) within a variety of key neurodevelopment genes. While this hints at a common ASD molecular etiology, gaps persist in our understanding of the neurodevelopmental mechanisms impacted by genetic variants enriched in ASD patients. Induced pluripotent stem cells (iPSCs) can model neurodevelopment in vitro, permitting the characterization of pathogenic mechanisms that manifest during corticogenesis. Taking this approach, we examined the transcriptional differences between iPSC-derived cortical neurons from patients with idiopathic ASD and unaffected controls over a 135-day course of neuronal differentiation. Our data show ASD-specific misregulation of genes involved in neuronal differentiation, axon guidance, cell migration, DNA and RNA metabolism, and neural region patterning. Furthermore, functional analysis revealed defects in neuronal migration and electrophysiological activity, providing compelling support for the transcriptome analysis data. This study reveals important and functionally validated insights into common processes altered in early neuronal development and corticogenesis and may contribute to ASD pathogenesis.
Crosstalk between Hedgehog pathway and energy pathways in human adipose-derived stem cells: A deep sequencing analysis of polysome-associated RNA
Authors: Shigunov Patrícia , Balvedi Lucas Titton , Santos Marlon Dias Mariano , Herai Roberto H. , de Aguiar Alessandra Melo , Dallagiovanna Bruno 
Published: May 2018

AbstractAdult stem cells are considered promising candidates for cellular therapies due to their capacity to differentiate and self-renew. Differentiation leads to changes in the metabolism, structure, and gene expression patterns of cells. Hedgehog is one of the pathways that is involved in the enhancement of osteogenesis and chondrogenesis in adult stem cells, but its mechanisms are poorly understood. In this study, we treated adipose tissue-derived stem cells (ADSC) with two well-characterized drugs, purmorphamine (Hedgehog pathway activator) and cyclopamine (Hedgehog pathway inhibitor), and identified mRNAs associated with polysomes in each treatment group to determine the post transcriptional genetic networks governed by the Hedgehog pathway. Activation of the Hedgehog pathway by purmorphamine results in significant upregulation of mRNAs associated with cellular communication and signal transduction. Furthermore, our experiments show that cyclopamine acts late downregulating GLI1 expression in ADSCs but promotes the upregulation of mRNAs associated with energy pathways and metabolism at early times. Through in silico analysis, we identified some miRNAs, such as miR-355, that could regulate these mRNAs association with polysomes and thereby modulate the Hedgehog pathway. Our results suggest that activation of the Hedgehog pathway by purmorphamine also results in a negative regulation of mRNAs in the protein translation machinery.
One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon
Authors: Machado Valeria N. , Collins Rupert A. , Ota Rafaela P. , Andrade Marcelo C. , Farias Izeni P. , Hrbek Tomas 
Published: May 2018

AbstractPiranhas and pacus (Characiformes: Serrasalmidae) are a charismatic but understudied family of Neotropical fishes. Here, we analyse a DNA barcode dataset comprising 1,122 specimens, 69 species, 16 genera, 208 localities, and 34 major river drainages in order to make an inventory of diversity and to highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using four methods of species discovery—incorporating both tree and distance based techniques—we report between 76 and 99 species-like clusters, i.e. between 20% and 33% ofa prioriidentified taxonomic species were represented by more than one mtDNA lineage. There was a high degree of congruence between clusters, with 60% supported by three or four methods. Pacus of the genusMyloplusexhibited the most intraspecific variation, with six of the 13 species sampled found to have multiple lineages. Conversely, piranhas of theSerrasalmus rhombeusgroup proved difficult to delimit with these methods due to genetic similarity and polyphyly. Overall, our results recognise substantially underestimated diversity in the serrasalmids, and emphasise the Guiana and Brazilian Shield rivers as biogeographically important areas with multiple cases of across-shield and within-shield diversifications. We additionally highlight the distinctiveness and complex phylogeographic history of rheophilic taxa in particular, and suggest multiple colonisations of these habitats by different serrasalmid lineages.
Post-stroke insomnia in community-dwelling patients with chronic motor stroke: Physiological evidence and implications for stroke care
Authors: Sterr A. , Kuhn M. , Nissen C. , Ettine D. , Funk S. , Feige B. , Umarova R. , Urbach H. , Weiller C. , Riemann D. 
Published: May 2018

AbstractQuestionnaire studies suggest that stroke patients experience sustained problems with sleep and daytime sleepiness, but physiological sleep studies focussing specifically on the chronic phase of stroke are lacking. Here we report for the first time physiological data of sleep and daytime sleepiness obtained through the two gold-standard methods, nocturnal polysomnography and the Multiple Sleep Latency Test. Data from community-dwelling patients with chronic right-hemispheric stroke (>12 months) were compared to sex- and age-matched controls. Behavioural and physiological measures suggested that stroke patients had poorer sleep with longer sleep latencies and lower sleep efficiency. Patients further spent more time awake during the night, and showed greater high-frequency power during nonREM sleep than controls. At the same time the Multiple Sleep Latency Test revealed greater wake efficiency in patients than controls. Importantly these findings were not due to group differences in sleep disordered breathing or periodic limb movements. Post-stroke insomnia is presently not adequately addressed within the care pathway for stroke. A holistic approach to rehabilitation and care provision, that includes targeted sleep interventions, is likely to enhance long-term outcome and quality of live in those living with chronic deficits after stroke.
Hetero-Multivalency of Pseudomonas aeruginosa Lectin LecA Binding to Model Membranes
Authors: Worstell Nolan C. , Singla Akshi , Saenkham Panatda , Galbadage Thushara , Sule Preeti , Lee Dongheon , Mohr Alec , Kwon Joseph Sang-Il , Cirillo Jeffrey D. , Wu Hung-Jen 
Published: May 2018

AbstractA single glycan-lectin interaction is often weak and semi-specific. Multiple binding domains in a single lectin can bind with multiple glycan molecules simultaneously, making it difficult for the classic “lock-and-key” model to explain these interactions. We demonstrated that hetero-multivalency, a homo-oligomeric protein simultaneously binding to at least two types of ligands, influences LecA (a Pseudomonas aeruginosa adhesin)-glycolipid recognition. We also observed enhanced binding between P. aeruginosa and mixed glycolipid liposomes. Interestingly, strong ligands could activate weaker binding ligands leading to higher LecA binding capacity. This hetero-multivalency is probably mediated via a simple mechanism, Reduction of Dimensionality (RD). To understand the influence of RD, we also modeled LecA’s two-step binding process with membranes using a kinetic Monte Carlo simulation. The simulation identified the frequency of low-affinity ligand encounters with bound LecA and the bound LecA’s retention of the low-affinity ligand as essential parameters for triggering hetero-multivalent binding, agreeing with experimental observations. The hetero-multivalency can alter lectin binding properties, including avidities, capacities, and kinetics, and therefore, it likely occurs in various multivalent binding systems. Using hetero-multivalency concept, we also offered a new strategy to design high-affinity drug carriers for targeted drug delivery.
Transcriptome analysis of the reef-building octocoral, Heliopora coerulea
Authors: Guzman Christine , Shinzato Chuya , Lu Tsai-Ming , Conaco Cecilia 
Published: May 2018

AbstractThe blue coral, Heliopora coerulea, is a reef-building octocoral that prefers shallow water and exhibits optimal growth at a temperature close to that which causes bleaching in scleractinian corals. To better understand the molecular mechanisms underlying its biology and ecology, we generated a reference transcriptome for H. coerulea using next-generation sequencing. Metatranscriptome assembly yielded 90,817 sequences of which 71% (64,610) could be annotated by comparison to public databases. The assembly included transcript sequences from both the coral host and its symbionts, which are related to the thermotolerant C3-Gulf ITS2 type Symbiodinium. Analysis of the blue coral transcriptome revealed enrichment of genes involved in stress response, including heat-shock proteins and antioxidants, as well as genes participating in signal transduction and stimulus response. Furthermore, the blue coral possesses homologs of biomineralization genes found in other corals and may use a biomineralization strategy similar to that of scleractinians to build its massive aragonite skeleton. These findings thus offer insights into the ecology of H. coerulea and suggest gene networks that may govern its interactions with its environment.
Determination of strain relaxation in InGaN/GaN nanowalls from quantum confinement and exciton binding energy dependent photoluminescence peak
Authors: Sankaranarayanan Sandeep , Chouksey Shonal , Saha Pratim , Pendem Vikas , Udai Ankit , Aggarwal Tarni , Ganguly Swaroop , Saha Dipankar 
Published: May 2018

AbstractGaN based nanostructures are being increasingly used to improve the performance of various devices including light emitting diodes and lasers. It is important to determine the strain relaxation in these structures for device design and better prediction of device characteristics and performance. We have determined the strain relaxation in InGaN/GaN nanowalls from quantum confinement and exciton binding energy dependent photoluminescence peak. We have further determined the strain relaxation as a function of nanowall dimension. With a decrease in nanowall dimension, the lateral quantum confinement and exciton binding energy increase and the InGaN layer becomes partially strain relaxed which decreases the piezoelectric polarization field. The reduced polarization field decreases quantum confined Stark effect along the c-axis and increases electron-hole wave-function overlap which further increases the exciton binding energy. The strong dependency of the exciton binding energy on strain is used to determine the strain relaxation in these nanostructures. An analytical model based on fractional dimension for GaN/InGaN/GaN heterostructures along with self-consistent simulation of Schrodinger and Poisson equations are used to theoretically correlate them. The larger effective mass of GaN along with smaller perturbation allows the fractional dimensional model to accurately describe our system without requiring first principle calculations.
KvN mechanics approach to the time-dependent frequency harmonic oscillator
Authors: Ramos-Prieto Irán , Urzúa-Pineda Alejandro R. , Soto-Eguibar Francisco , Moya-Cessa Héctor M. 
Published: May 2018

AbstractUsing the Ermakov-Lewis invariants appearing in KvN mechanics, the time-dependent frequency harmonic oscillator is studied. The analysis builds upon the operational dynamical model, from which it is possible to infer quantum or classical dynamics; thus, the mathematical structure governing the evolution will be the same in both cases. The Liouville operator associated with the time-dependent frequency harmonic oscillator can be transformed using an Ermakov-Lewis invariant, which is also time dependent and commutes with itself at any time. Finally, because the solution of the Ermakov equation is involved in the evolution of the classical state vector, we explore some analytical and numerical solutions.
A robust ex vivo experimental platform for molecular-genetic dissection of adult human neocortical cell types and circuits
Authors: Ting Jonathan T. , Kalmbach Brian , Chong Peter , de Frates Rebecca , Keene C. Dirk , Gwinn Ryder P. , Cobbs Charles , Ko Andrew L. , Ojemann Jeffrey G. , Ellenbogen Richard G. , Koch Christof , Lein Ed 
Published: May 2018

AbstractThe powerful suite of available genetic tools is driving tremendous progress in understanding mouse brain cell types and circuits. However, the degree of conservation in human remains largely unknown in large part due to the lack of such tools and healthy tissue preparations. To close this gap, we describe a robust and stable adult human neurosurgically-derived ex vivo acute and cultured neocortical brain slice system optimized for rapid molecular-genetic manipulation. Surprisingly, acute human brain slices exhibited exceptional viability, and neuronal intrinsic membrane properties could be assayed for at least three days. Maintaining adult human slices in culture under sterile conditions further enabled the application of viral tools to drive rapid expression of exogenous transgenes. Widespread neuron-specific labeling was achieved as early as two days post infection with HSV-1 vectors, with virally-transduced neurons exhibiting membrane properties largely comparable to uninfected neurons over this short timeframe. Finally, we demonstrate the suitability of this culture paradigm for optical manipulation and monitoring of neuronal activity using genetically encoded probes, opening a path for applying modern molecular-genetic tools to study human brain circuit function.
Combinatorial Drug Testing in 3D Microtumors Derived from GBM Patient-Derived Xenografts Reveals Cytotoxic Synergy in Pharmacokinomics-informed Pathway Interactions
Authors: Gilbert Ashley N. , Anderson Joshua C. , Duarte Christine W. , Shevin Rachael S. , Langford Catherine P. , Singh Raj , Gillespie G. Yancey , Willey Christopher D. 
Published: May 2018

AbstractGlioblastoma multiforme (GBM), the most common form of primary malignant brain cancer in adults, is a devastating disease for which effective treatment has remained elusive for over 75 years. One reason for the minimal progress during this time is the lack of accurate preclinical models to represent the patient’s tumor’s in vivo environment, causing a disconnect in drug therapy effectiveness between the laboratory and clinic. While patient-derived xenografts (PDX’s or xenolines) are excellent human tumor representations, they are not amenable to high throughput testing. Therefore, we developed a miniaturized xenoline system (microtumors) for drug testing. Nineteen GBM xenolines were profiled for global kinase (kinomic) activity revealing actionable kinase targets associated with intracranial tumor growth rate. Kinase inhibitors for these targets (WP1066, selumetinib, crizotinib, and cediranib) were selected for single and combination therapy using a fully human-derived three-dimensional (3D) microtumor model of GBM xenoline cells embedded in HuBiogel for subsequent molecular and phenotype assays. GBM microtumors closely resembled orthotopically-implanted tumors based on immunohistochemical analysis and displayed kinomic and morphological diversity. Drug response testing could be reproducibly performed in a 96-well format identifying several synergistic combinations. Our findings indicate that 3D microtumors can provide a suitable high-throughput model for combination drug testing.
Eliminate the transmission feedthrough of thermal‐piezoresistive I2 ‐BAR MEMS resonators based on reverse‐biased PN junction
Authors: Xiong Zhuang , Zhang Zhaoyun , Zhang Li , Yang He 
Published: May 2018

The thermally driving and piezo‐resistive sensing I2 ‐BAR resonators have attracted substantial attentions due to its promising features which could be widely applied for radio frequency) applications. However, one major drawback of the I2 ‐BAR resonators is that the thermal driving and the piezoresistive sensing signals are highly coupled which results in an excessive transmission feedthrough floor, masking thus the real resonance behaviours. In this work, a simple and effective approach to eliminate the feedthrough effect using reverse‐biased PN junction is presented. The device was fabricated on a p‐type silicon‐on‐insulator wafer with locally doped n‐type regions. With proper bias voltages, the thermal driving current and the output piezoresistive current were confined inside the p‐type layer and the n‐type layer, respectively. With such design concept, an improvement of 50 dB feedthrough reduction was observed comparing with the conventional measurement. The resonance behaviour can thus be physically obtained without further post data processing. This research also shows that such measurement methods can be transferred to other domains where integrated thermal driving and piezoresistive sensing transductions are required.