bluuebunny/crossref_metadata_2025 huggingface dataset:
Durable and self-hydrating tungsten carbide-based composite polymer electrolyte membrane fuel cells
Authors: Zheng Weiqing , Wang Liang , Deng Fei , Giles Stephen A. , Prasad Ajay K. , Advani Suresh G. , Yan Yushan , Vlachos Dionisios G.
Published: August 2017

Proton conductivity of the polymer electrolyte membranes in fuel cells dictates their performance and requires sufficient water management. Here, we report a simple, scalable method to produce well-dispersed transition metal carbide nanoparticles. We demonstrate that these, when added as an additive to the proton exchange Nafion membrane, provide significant enhancement in power density and durability over 100 hours, surpassing both the baseline Nafion and platinum-containing recast Nafion membranes. Focused ion beam/scanning electron microscope tomography reveals the key membrane degradation mechanism. Density functional theory exposes that OH• and H• radicals adsorb more strongly from solution and reactions producing OH• are significantly more endergonic on tungsten carbide than on platinum. Consequently, tungsten carbide may be a promising catalyst in self-hydrating crossover gases while retarding desorption of and capturing free radicals formed at the cathode, resulting in enhanced membrane durability.
Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities
Authors: Butaitė Elena , Baumgartner Michael , Wyder Stefan , Kümmerli Rolf
Published: August 2017

All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have become model organisms to study social dilemmas in laboratory systems, we know little about their relevance in natural communities. Here, we show that social interactions mediated by a single shareable compound necessary for growth (the iron-scavenging pyoverdine) have important consequences for competitive dynamics in soil and pond communities ofPseudomonasbacteria. We find that pyoverdine non- and low-producers co-occur in many natural communities. While non-producers have genes coding for multiple pyoverdine receptors and are able to exploit compatible heterologous pyoverdines from other community members, producers differ in the pyoverdine types they secrete, offering protection against exploitation from non-producers with incompatible receptors. Our findings indicate that there is both selection for cheating and cheating resistance, which could drive antagonistic co-evolution and diversification in natural bacterial communities.
Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes
Authors: Pham Hoang Long , Wong Adison , Chua Niying , Teo Wei Suong , Yew Wen Shan , Chang Matthew Wook
Published: August 2017

Environmental pH is a fundamental signal continuously directing the metabolism and behavior of living cells. Programming the precise cellular response toward environmental pH is, therefore, crucial for engineering cells for increasingly sophisticated functions. Herein, we engineer a set of riboswitch-based pH-sensing genetic devices to enable the control of gene expression according to differential environmental pH. We next develop a digital pH-sensing system to utilize the analogue-sensing behavior of these devices for high-resolution recording of host cell exposure to discrete external pH levels. The application of this digital pH-sensing system is demonstrated in a genetic program that autonomously regulated the evolutionary engineering of host cells for improved tolerance to a broad spectrum of organic acids, a valuable phenotype for metabolic engineering and bioremediation applications.
Herbivores rescue diversity in warming tundra by modulating trait-dependent species losses and gains
Authors: Kaarlejärvi Elina , Eskelinen Anu , Olofsson Johan
Published: August 2017

Climate warming is altering the diversity of plant communities but it remains unknown which species will be lost or gained under warming, especially considering interactions with other factors such as herbivory and nutrient availability. Here, we experimentally test effects of warming, mammalian herbivory and fertilization on tundra species richness and investigate how plant functional traits affect losses and gains. We show that herbivory reverses the impact of warming on diversity: in the presence of herbivores warming increases species richness through higher species gains and lower losses, while in the absence of herbivores warming causes higher species losses and thus decreases species richness. Herbivores promote gains of short-statured species under warming, while herbivore removal and fertilization increase losses of short-statured and resource-conservative species through light limitation. Our results demonstrate that both rarity and traits forecast species losses and gains, and mammalian herbivores are essential for preventing trait-dependent extinctions and mitigate diversity loss under warming and eutrophication.
Redox-active conducting polymers modulate Salmonella biofilm formation by controlling availability of electron acceptors
Authors: Gomez-Carretero Salvador , Libberton Ben , Svennersten Karl , Persson Kristin , Jager Edwin , Berggren Magnus , Rhen Mikael , Richter-Dahlfors Agneta
Published: August 2017

Biofouling is a major problem caused by bacteria colonizing abiotic surfaces, such as medical devices. Biofilms are formed as the bacterial metabolism adapts to an attached growth state. We studied whether bacterial metabolism, hence biofilm formation, can be modulated in electrochemically active surfaces using the conducting conjugated polymer poly(3,4-ethylenedioxythiophene) (PEDOT). We fabricated composites of PEDOT doped with either heparin, dodecyl benzene sulfonate or chloride, and identified the fabrication parameters so that the electrochemical redox state is the main distinct factor influencing biofilm growth. PEDOT surfaces fitted into a custom-designed culturing device allowed for redox switching in Salmonella cultures, leading to oxidized or reduced electrodes. Similarly large biofilm growth was found on the oxidized anodes and on conventional polyester. In contrast, biofilm was significantly decreased (52–58%) on the reduced cathodes. Quantification of electrochromism in unswitched conducting polymer surfaces revealed a bacteria-driven electrochemical reduction of PEDOT. As a result, unswitched PEDOT acquired an analogous electrochemical state to the externally reduced cathode, explaining the similarly decreased biofilm growth on reduced cathodes and unswitched surfaces. Collectively, our findings reveal two opposing effects affecting biofilm formation. While the oxidized PEDOT anode constitutes a renewable electron sink that promotes biofilm growth, reduction of PEDOT by a power source or by bacteria largely suppresses biofilm formation. Modulating bacterial metabolism using the redox state of electroactive surfaces constitutes an unexplored method with applications spanning from antifouling coatings and microbial fuel cells to the study of the role of bacterial respiration during infection.
Quantum generalisation of feedforward neural networks
Authors: Wan Kwok Ho , Dahlsten Oscar , Kristjánsson Hlér , Gardner Robert , Kim M. S.
Published: August 2017

We propose a quantum generalisation of a classical neural network. The classical neurons are firstly rendered reversible by adding ancillary bits. Then they are generalised to being quantum reversible, i.e., unitary (the classical networks we generalise are called feedforward, and have step-function activation functions). The quantum network can be trained efficiently using gradient descent on a cost function to perform quantum generalisations of classical tasks. We demonstrate numerically that it can: (i) compress quantum states onto a minimal number of qubits, creating a quantum autoencoder, and (ii) discover quantum communication protocols such as teleportation. Our general recipe is theoretical and implementation-independent. The quantum neuron module can naturally be implemented photonically.
Rapid LC-MS Based High-Throughput Screening Method, Affording No False Positives or False Negatives, Identifies a New Inhibitor for Carbonic Anhydrase
Authors: Imaduwage Kasun P. , Lakbub Jude , Go Eden P. , Desaire Heather
Published: August 2017

Developing effective high-throughput screening (HTS) methods is of paramount importance in the early stage of drug discovery. While rugged and robust assays may be easily developed for certain enzymes, HTS assays designed to identify ligands that block protein binding are much more challenging to develop; attenuating the number of false positives and false negatives under high-throughput screening conditions is particularly difficult. We describe an MS-based HTS workflow that addresses these challenges. The assay mitigates false positives by selectively identifying positive hits exclusively when a ligand at the binding site of interest is displaced; it mitigates false negatives by detecting a reporter compound that ionizes well, not by detecting the ligand binder, which may not ionize. The method was validated by detecting known binders of three proteins, pepsin, maltose binding protein (MBP), and carbonic anhydrase (CA) in the presence of hundreds of non-binders. We also identified a novel CA binder, pifithrin-µ, which could not have been identified by any other MS-based assay because of its poor ionization efficiency. This new method addresses many of the challenges that are currently encountered during high-throughput screening.
Angiotensin II affects inflammation mechanisms via AMPK-related signalling pathways in HL-1 atrial myocytes
Authors: Kim Nami , Jung Youngae , Nam Miso , Sun Kang Mi , Lee Min Kyung , Cho Youngjin , Choi Eue-Keun , Hwang Geum-Sook , Soo Kim Hyeon
Published: August 2017

Inflammation is a common cause of cardiac arrhythmia. Angiotensin ІІ (Ang ІІ) is a major contributing factor in the pathogenesis of cardiac inflammation; however, its underlying molecular mechanism remains unclear. Here, we explored the effect of Ang ІІ on inflammatory mechanisms and oxidative stress using HL-1 atrial myocytes. We showed that Ang ІІ activated c-Jun N-terminal kinase (JNK) phosphorylation and other inflammatory markers, such as transforming growth factor-β1 (TGF-β1) and tumor necrosis factor-α (TNF-α). Ang ІІ decreased oxygen consumption rate, which resulted in reactive oxygen species (ROS) generation and inhibition of ROS blocked Ang II-mediated JNK phosphorylation and TGF-β1 induction. Ang ІІ induced the expression of its specific receptor, AT1R. Ang II-induced intracellular calcium production associated with Ang ІІ-mediated signalling pathways. In addition, the generated ROS and calcium stimulated AMPK phosphorylation. Inhibiting AMPK blocked Ang II-mediated JNK and TGF-β signalling pathways. Ang ІІ concentration, along with TGF-β1 and tumor necrosis factor-α levels, was slightly increased in plasma of patients with atrial fibrillation. Taken together, these results suggest that Ang ІІ induces inflammation mechanisms through an AMPK-related signalling pathway. Our results provide new molecular targets for the development of therapeutics for inflammation-related conditions, such as atrial fibrillation.
Hub-driven remote synchronization in brain networks
Authors: Vlasov Vladimir , Bifone Angelo
Published: August 2017

The phenomenon of “remote synchronization” (RS), first observed in a star network of oscillators, involves synchronization of unconnected peripheral nodes through a hub that maintains independent dynamics. In the RS regime the central hub was thought to serve as a passive gate for information transfer between nodes. Here, we investigate the physical origin of this phenomenon. Surprisingly, we find that a hub node can drive remote synchronization of peripheral oscillators even in the presence of a repulsive mean field, thus actively governing network dynamics while remaining asynchronous. We study this novel phenomenon in complex networks endowed with multiple hub-nodes, a ubiquitous feature of many real-world systems, including brain connectivity networks. We show that a change in the natural frequency of a single hub can alone reshape synchronization patterns across the entire network, and switch from direct to remote synchronization, or to hub-driven desynchronization. Hub-driven RS may provide a mechanism to account for the role of structural hubs in the organization of brain functional connectivity networks.
An LC-MS Approach to Quantitative Measurement of Ammonia Isotopologues
Authors: Spinelli Jessica B. , Kelley Liam P. , Haigis Marcia C.
Published: August 2017

Ammonia is a fundamental aspect of metabolism spanning all of phylogeny. Metabolomics, including metabolic tracing studies, are an integral part of elucidating the role of ammonia in these systems. However, current methods for measurement of ammonia are spectrophotometric, and cannot distinguish isotopologues of ammonia, significantly limiting metabolic tracing studies. Here, we describe a novel LC-MS-based method that quantitatively assesses both 14N-and 15N-isotopologues of ammonia in polar metabolite extracts. This assay (1) quantitatively measures the concentration of ammonia in polar metabolite isolates used for metabolomic studies, and (2) accurately determines the percent isotope abundance of 15N-ammonia in a cell lysate for 15N-isotope tracing studies. We apply this assay to quantitatively measure glutamine-derived ammonia in lung cancer cell lines with differential expression of glutaminase.
Mott Transition and Magnetism in Rare Earth Nickelates and its Fingerprint on the X-ray Scattering
Authors: Haule Kristjan , Pascut Gheorghe L.
Published: August 2017

The metal-insulator transition (MIT) remains among the most thoroughly studied phenomena in solid state physics, but the complexity of the phenomena, which usually involves cooperation of many degrees of freedom including orbitals, fluctuating local moments, magnetism, and the crystal structure, have resisted predictive ab-initio treatment. Here we develop ab-initio theoretical method for correlated electron materials, based on Dynamical Mean Field Theory, which can predict the change of the crystal structure across the MIT at finite temperature. This allows us to study the coupling between electronic, magnetic and orbital degrees of freedom with the crystal structure across the MIT in rare-earth nickelates. We predict the electronic free energy profile of the competing states, and the theoretical magnetic ground state configuration, which is in agreement with neutron scattering data, but is different from the magnetic models proposed before. The resonant elastic X-ray response at the K-edge, which was argued to be a probe of the charge order, is theoretically modelled within the Dynamical Mean Field Theory, including the core-hole interaction. We show that the line-shape of the measured resonant elastic X-ray response can be explained with the “site-selective” Mott scenario without real charge order on Ni sites.
Controlling Directed Protein Interaction Networks in Cancer
Authors: Kanhaiya Krishna , Czeizler Eugen , Gratie Cristian , Petre Ion
Published: August 2017

Control theory is a well-established approach in network science, with applications in bio-medicine and cancer research. We build on recent results for structural controllability of directed networks, which identifies a set of driver nodes able to control an a-priori defined part of the network. We develop a novel and efficient approach for the (targeted) structural controllability of cancer networks and demonstrate it for the analysis of breast, pancreatic, and ovarian cancer. We build in each case a protein-protein interaction network and focus on the survivability-essential proteins specific to each cancer type. We show that these essential proteins are efficiently controllable from a relatively small computable set of driver nodes. Moreover, we adjust the method to find the driver nodes among FDA-approved drug-target nodes. We find that, while many of the drugs acting on the driver nodes are part of known cancer therapies, some of them are not used for the cancer types analyzed here; some drug-target driver nodes identified by our algorithms are not known to be used in any cancer therapy. Overall we show that a better understanding of the control dynamics of cancer through computational modelling can pave the way for new efficient therapeutic approaches and personalized medicine.
Increased incidence of cytomegalovirus coinfection in HCV-infected patients with late liver fibrosis is associated with dysregulation of JAK-STAT pathway
Authors: Ibrahim Marwa K. , Khedr Ahmed , Bader El Din Noha G. , Khairy Ahmed , El Awady Mostafa K.
Published: August 2017

Herein, we examined the association between cytomegalovirus (CMV) coinfection and the progression of liver fibrosis in hepatitis C virus (HCV) infection, and investigated the effect of CMV coinfection on JAK-STAT pathway. CMV DNAemia was detected by PCR in DNA from controls (n = 120), and HCV patients with early (F0-F1, n = 131) and late (F2-F4, n = 179) liver fibrosis. By quantitative real time PCR (qRT-PCR), we examined the profile of 8 JAK-STAT transcripts in PBMCs RNA from 90 HCV patients (39 CMV positive and 51 CMV negative), 4 CMV mono-infected patients, and 15 controls. Our results demonstrated higher incidence of CMV in F2-F4 group than in control (OR 5.479, 95% CI 3.033–9.895, p < 0.0001) or F0-F1 groups (OR 2, 95% CI 1.238–3.181, p = 0.005). qRT-PCR showed downregulation of STAT2 (p = 0.006) and IRF7 (p = 0.02) in CMV positive group compared to CMV negative one. The downregulation of STAT2 and IRF7 was mainly in CMV positive patients with late fibrosis compared to CMV negative patients (p = 0.0007 for IRF7 and p = 0.01 for STAT2). Our results are the first to report that CMV coinfection is a possible risk factor for the progression of HCV-induced liver fibrosis, and thereby CMV screening and treatment are important for HCV patients.
HMGB1/Advanced Glycation End Products (RAGE) does not aggravate inflammation but promote endogenous neural stem cells differentiation in spinal cord injury
Authors: Wang Hongyu , Mei Xifan , Cao Yang , Liu Chang , Zhao Ziming , Guo Zhanpeng , Bi Yunlong , Shen Zhaoliang , Yuan Yajiang , Guo Yue , Song Cangwei , Bai Liangjie , Wang Yansong , Yu Deshui
Published: August 2017

Receptor for advanced glycation end products (RAGE) signaling is involved in a series of cell functions after spinal cord injury (SCI). Our study aimed to elucidate the effects of RAGE signaling on the neuronal recovery after SCI. In vivo, rats were subjected to SCI with or without anti-RAGE antibodies micro-injected into the lesion epicenter. We detected Nestin/RAGE, SOX-2/RAGE and Nestin/MAP-2 after SCI by Western blot or immunofluorescence (IF). We found that neural stem cells (NSCs) co-expressed with RAGE were significantly activated after SCI, while stem cell markers Nestin and SOX-2 were reduced by RAGE blockade. We found that RAGE inhibition reduced nestin-positive NSCs expressing MAP-2, a mature neuron marker. RAGE blockade does not improve neurobehavior Basso, Beattie and Bresnahan (BBB) scores; however, it damaged survival of ventral neurons via Nissl staining. Through in vitro study, we found that recombinant HMGB1 administration does not lead to increased cytokines of TNF-α and IL-1β, while anti-RAGE treatment reduced cytokines of TNF-α and IL-1β induced by LPS via ELISA. Meanwhile, HMGB1 increased MAP-2 expression, which was blocked after anti-RAGE treatment. Hence, HMGB1/RAGE does not exacerbate neuronal inflammation but plays a role in promoting NSCs differentiating into mature neurons in the pathological process of SCI.
Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide
Authors: Lv Qiming , Huang Zhiyuan , Xu Xiao , Tang Li , Liu Hai , Wang Chunchao , Zhou Zhuangzhi , Xin Yeyun , Xing Junjie , Peng Zhirong , Li Xiaobing , Zheng Tianqing , Zhu Lihuang
Published: August 2017

In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.
Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
Authors: Shukron Ofir , Hauer Michael , Holcman David
Published: August 2017

Stochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci, and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages. Finally, we construct a polymer model, that accounts for the local chromatin organization before and after a double-stranded DNA break (DSB), to estimate the level of chromatin decompaction. This novel passage time statistics method allows extracting transient dynamic at scales varying from one to few hundreds of nanometers, it predicts the local changes in the number of binding molecules following DSB and can be used to characterize the local dynamic of the chromatin.
Simultaneous multi-band valley-protected topological edge states of shear vertical wave in two-dimensional phononic crystals with veins
Authors: Huo Shao-yong , Chen Jiu-jiu , Huang Hong-bo , Huang Guo-liang
Published: August 2017

The introduction of the concept of valley pseudospin to phononic crystals has made a remarkable topologically protected interface transport of sound, which opens a novel research area referred to as valley Hall topological insulators. Here, we demonstrate the simultaneous multi-band edge states of shear vertical waves in two-dimensional phononic crystals with veins. The multi-band edge states are topologically valley-protected and are obtained by simultaneously gapping multiple Dirac points at K (or K′) under the inversion symmetry breaking. As the relative radius of the two adjacent steel columns varies, the band diagram undergoes a topological transition which can be characterized by topological charge distributions and opposite valley Chern numbers. Subsequently, the vortex chirality of the bulk valley modes is unveiled. With numerical simulations, simultaneous multi-band valley dependent edge states and the associated valley-protected backscattering suppression around the curved waveguide are further demonstrated. Our work could become a promising platform for applications of multi-functional topological acoustic devices.
Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease
Authors: Minter Myles R. , Hinterleitner Reinhard , Meisel Marlies , Zhang Can , Leone Vanessa , Zhang Xiaoqiong , Oyler-Castrillo Paul , Zhang Xulun , Musch Mark W. , Shen Xunuo , Jabri Bana , Chang Eugene B. , Tanzi Rudolph E. , Sisodia Sangram S.
Published: August 2017

Recent evidence suggests the commensal microbiome regulates host immunity and influences brain function; findings that have ramifications for neurodegenerative diseases. In the context of Alzheimer’s disease (AD), we previously reported that perturbations in microbial diversity induced by life-long combinatorial antibiotic (ABX) selection pressure in the APPSWE/PS1ΔE9 mouse model of amyloidosis is commensurate with reductions in amyloid-β (Aβ) plaque pathology and plaque-localised gliosis. Considering microbiota-host interactions, specifically during early post-natal development, are critical for immune- and neuro-development we now examine the impact of microbial community perturbations induced by acute ABX exposure exclusively during this period in APPSWE/PS1ΔE9 mice. We show that early post-natal (P) ABX treatment (P14-P21) results in long-term alterations of gut microbial genera (predominantly Lachnospiraceae and S24-7) and reduction in brain Aβ deposition in aged APPSWE/PS1ΔE9 mice. These mice exhibit elevated levels of blood- and brain-resident Foxp3+ T-regulatory cells and display an alteration in the inflammatory milieu of the serum and cerebrospinal fluid. Finally, we confirm that plaque-localised microglia and astrocytes are reduced in ABX-exposed mice. These findings suggest that ABX-induced microbial diversity perturbations during post-natal stages of development coincide with altered host immunity mechanisms and amyloidosis in a murine model of AD.
Tumor-infiltrating CD45RO+ Memory T Lymphocytes Predict Favorable Clinical Outcome in Solid Tumors
Authors: Hu Guoming , Wang Shimin
Published: August 2017

The prognostic role of tumor-infiltrating CD45RO+ memory T lymphocytes (CD45RO+ T cells) in human solid tumors remains controversial. Herein, we conducted a meta-analysis including 25 published studies with 4720 patients identified from PubMed and EBSCO to assess the prognostic impact of tumor-infiltrating CD45RO+ T cells in human solid tumors. We found that CD45RO+ T cell infiltration was significantly associated with improved overall survival (OS) and disease-free survival (DFS) in all types of solid tumors. In stratified analyses, CD45RO+ T cell infiltration significantly improved 1-year, 3-year and 5-year OS in colorectal, gastric and esophageal cancer, but only 5-year OS in hepatocellular carcinoma. And these cells were positively associated with 1-year, 3-year and 5-year DFS in hepatocellular, colorectal and esophageal cancer. In addition, high density of intratumoral CD45RO+ T cells inversely correlated with TNM stage of solid tumor. In conclusion, CD45RO+ memory T lymphocyte infiltration leads to a favorable clinical outcome in solid tumors, implicating that it is a valuable biomarker for prognostic prediction for human solid malignances.
Erratum: Combinatorial treatment with natural compounds in prostate cancer inhibits prostate tumor growth and leads to key modulations of cancer cell metabolism
Authors: Lodi Alessia , Saha Achinto , Lu Xiyuan , Wang Bo , Sentandreu Enrique , Collins Meghan , Kolonin Mikhail G. , DiGiovanni John , Tiziani Stefano
Published: August 2017

A correction to this article has been published and is linked from the HTML version of this article.
Identification and targeting of an FGFR fusion in a pediatric thalamic “central oligodendroglioma”
Authors: Linzey Joseph R. , Marini Bernard , McFadden Kathryn , Lorenzana Adonis , Mody Rajen , Robertson Patricia L. , Koschmann Carl
Published: August 2017

Approximately 1–5% of pediatric intracranial tumors originate in the thalamus. While great strides have been made to identify consistent molecular markers in adult oligodendrogliomas, such as the 1p/19q co-deletion, it is widely recognized that pediatric oligodendrogliomas have a vastly different molecular make-up. While pediatric thalamic or “central oligodendrogliomas” are histologically similar to peripheral pediatric oligodendrogliomas, they are behaviorally distinct and likely represent a cohesive, but entirely different entity. We describe a case of a 10-year-old girl who was diagnosed with an anaplastic glioma with features consistent with the aggressive entity often diagnosed as central or thalamic oligodendroglioma. We performed whole-exome (paired tumor and germline DNA) and transcriptome (tumor RNA) sequencing, which demonstrated an FGFR3-PHGDH fusion. We describe this fusion and our rationale for pursuing personalized, targeted therapy for the patient’s tumor that may potentially play a role in the treatment of similar cases.
Erratum: Triplet p-wave pairing correlation in low-doped zigzag graphene nanoribbons
Authors: Ma Tianxing , Yang Fan , Huang Zhongbing , Lin Hai-Qing
Published: August 2017

Scientific Reports 7: Article number: 42262; published online: 10 February 2017; updated: 29 August 2017. This article was published twice in error during a change in production systems. The publisher apologizes to the authors and readers for the error. When citing this work, please refer to the original version.
Accelerated DNA methylation age in adolescent girls: associations with elevated diurnal cortisol and reduced hippocampal volume
Authors: Davis E G , Humphreys K L , McEwen L M , Sacchet M D , Camacho M C , MacIsaac J L , Lin D T S , Kobor M S , Gotlib I H
Published: August 2017

Numerous studies have linked exposure to stress to adverse health outcomes through the effects of cortisol, a product of the stress response system, on cellular aging processes. Accelerated DNA methylation age is a promising epigenetic marker associated with stress and disease risk that may constitute a link from stress response to changes in neural structures. Specifically, elevated glucocorticoid signaling likely contributes to accelerating DNA methylation age, which may signify a maladaptive stress-related cascade that leads to hippocampal atrophy. We examined the relations among diurnal cortisol levels, DNA methylation age and hippocampal volume in a longitudinal study of 46 adolescent girls. We computed area under the curve from two daily cortisol collection periods, and calculated DNA methylation age using previously established methods based on a set of CpG sites associated with chronological age. We computed a residual score by partialling out chronological age; higher discrepancies reflect relatively accelerated DNA methylation age. We assessed hippocampal volume via T1-weighted images and automated volumetric segmentation. We found that greater diurnal cortisol production was associated with accelerated DNA methylation age, which in turn was associated with reduced left hippocampal volume. Finally, accelerated DNA methylation age significantly mediated the association between diurnal cortisol and left hippocampal volume. Thus, accelerated DNA methylation age may be an epigenetic marker linking hypothalamic–pituitary–adrenal axis dysregulation with neural structure. If these findings are replicated, the current study provides a method for advancing our understanding of mechanisms by which glucocorticoid signaling is associated with cellular aging and brain development.
Single-molecule conductance of DNA gated and ungated by DNA-binding molecules
Authors: Harashima Takanori , Kojima Chie , Fujii Shintaro , Kiguchi Manabu , Nishino Tomoaki
Published: August 2017

Single-molecule conductance can be controllably modulated by DNA-binding molecules.
Rhodium(iii)-catalyzed regio- and stereoselective benzylic α-fluoroalkenylation with gem-difluorostyrenes
Authors: Kong Lingheng , Liu Bingxian , Zhou Xukai , Wang Fen , Li Xingwei
Published: August 2017

Rh(iii)-Catalyzed fluoroalkenylation of a benzylic C–H bond has been realized under mild conditions with high regio- and stereoselectivity.
Palladium-catalyzed oxidative amination of homoallylic alcohols: sequentially installing carbonyl and amino groups along an alkyl chain
Authors: Ouyang Lu , Huang Jiuzhong , Li Jianxiao , Qi Chaorong , Wu Wanqing , Jiang Huanfeng
Published: August 2017

A novel Pd-catalyzed intermolecular oxidative amination of homoallylic alcohols affording valuable β-amino acetones under mild conditions has been developed.
ZORRO: zirconium oxide resonators for all-in-one Raman and whispering-gallery-mode optical sensing
Authors: Bontempi N. , Vassalini I. , Danesi S. , Alessandri I.
Published: August 2017

We report the observation of whispering-gallery modes in 2 μm-sized SiO2/ZrO2 core/shell beads utilized as all-dielectric Raman enhancers.
A family of microscale 2 × 2 × 2 Pocket Cubes
Authors: Aldossary Minahi S. , Zhu Jian , Porob Rakesh R. , Deng Da
Published: August 2017

A family of Pocket Cubes with different chemical compositions but with the same overall mesoscale microstructures was prepared for potential applications in energy storage and water treatment.
Fragmentation of KrN+ clusters after electron impact ionization II. Long-time dynamics simulations of Kr7+ evolution and the role of initial electronic excitation
Authors: Janeček Ivan , Stachoň Martin , Gadea Florent Xavier , Kalus René
Published: August 2017

Long time simulations, up to 100 ns, have been performed for the fragmentation of Kr7+ clusters after electron impact ionization, and have been compared with experiment.
Excited state dynamics of symmetric and asymmetric Cr3(dpa)4Cl2 measured using femtosecond transient absorption spectroscopy
Authors: Cheng Chao-Han , Wang Wen-Zhen , Peng Shie-Ming , Chen I-Chia
Published: August 2017

Relaxation pathway of excited states in extended metal atom chain complex Cr3(dpa)4Cl2.
Analysis of Warburg's impedance and its equivalent electric circuits
Authors: Barbero G. , Lelidis I.
Published: August 2017

The analogy between a transmission line and an electrolytic cell is not physically grounded.
Separate mechanisms of ion oligomerization tune the physicochemical properties of n-butylammonium acetate: cation-base clusters vs. anion-acid dimers
Authors: Berton Paula , Kelley Steven P. , Wang Hui , Myerson Allan S. , Rogers Robin D.
Published: August 2017

Ions comprising protic ionic liquids strongly interact with their neutral acid and base forms as exemplified by n-butylammonium acetate in the presence of excess n-butylamine or acetic acid.
Enantioselective synthesis of sulfoxide using an SBA-15 supported vanadia catalyst: a computational elucidation using a QM/MM approach
Authors: Kaur Navjot , Gupta Shuchi , Goel Neetu
Published: August 2017

Metal catalyzed asymmetric oxidation of prochiral sulfides is one of the prevailing strategies to produce enantiopure sulfoxides.
Supramolecular catalysis and dynamic assemblies for medicine
Authors: Feng Zhaoqianqi , Zhang Tengfei , Wang Huaimin , Xu Bing
Published: August 2017

This review provides new insights into supramolecular catalysis and dynamic regulation of molecular assemblies for biomedical applications.
Retraction: Catalytic decomposition of ammonium dinitramide (ADN) as high energetic material over CuO-based catalysts
Authors: Simpson Anna
Published: August 2017

Retraction of ‘Catalytic decomposition of ammonium dinitramide (ADN) as high energetic material over CuO-based catalysts’ by Rachid Amrousse et al., Catalysis Science and Technology, 2013, 3, 2614–2619.
Photocatalytic fixation of nitrogen to ammonia: state-of-the-art advancements and future prospects
Authors: Chen Xingzhu , Li Neng , Kong Zhouzhou , Ong Wee-Jun , Zhao Xiujian
Published: August 2017

The state-of-the-art developments in the photocatalytic reduction of N2 to NH3 are presented by classifying the photocatalysts based on chemical composition. Additionally, the correlation between the modification of catalysts and their photocatalytic activity is highlighted.
Supramolecular helical nanofibers formed by an achiral monopyrrolotetrathiafulvalene derivative: water-triggered gelation and chiral evolution
Authors: Liu Yucun , Jia Yu , Zhu Enwei , Liu Lihui , Qiao Yu , Che Guangbo , Yin Bingzhu
Published: August 2017

An achiral MPTTF-based gelator could form left- and right-handed supramolecular assemblies in pure DMF, whereas it turned into an opaque gel with right-handed nanofibers after adding small amounts of water.
Nanostructured BN–TiO2 composite with ultra-high photocatalytic activity
Authors: Singh Bikramjeet , kaur Gurpreet , Singh Paviter , Singh Kulwinder , Sharma Jeewan , Kumar Manjeet , Bala Rajni , Meena Ramovatar , Sharma Saurabh Kumar , Kumar Akshay
Published: August 2017

Boron nitride and titanium oxide composite (BN–TiO2) photocatalyst endowed with high specific surface area and large pore size was synthesized by ice bath method.
Responsive photonic barcodes for sensitive multiplex bioassay
Authors: Luan Chengxin , Xu Yueshuang , Fu Fanfan , Wang Huan , Xu Qionghua , Chen Baoan , Zhao Yuanjin
Published: August 2017

A novel responsive photonic barcode was developed for sensitive multiplex bioassay with fluorescent signal self-amplification.
Correction: Nanocrystalline Fe–Fe2O3 particle-deposited N-doped graphene as an activity-modulated Pt-free electrocatalyst for oxygen reduction reaction
Authors: Dhavale Vishal M. , Singh Santosh K. , Nadeema Ayasha , Gaikwad Sachin S. , Kurungot Sreekumar
Published: August 2017

Correction for ‘Nanocrystalline Fe–Fe2O3 particle-deposited N-doped graphene as an activity-modulated Pt-free electrocatalyst for oxygen reduction reaction’ by Vishal M. Dhavale et al., Nanoscale, 2015, 7, 20117–20125.
Progress towards the broad use of non-peptide synthetic macrocycles in drug discovery
Authors: Whitty Adrian , Viarengo Lauren A. , Zhong Mengqi
Published: August 2017

The broad use of non-peptide synthetic macrocycles in drug discovery is benefitting from recent advances in our understanding of what molecular properties define a useful macrocyclic screening hit.
Base-mediated diastereoselective [4 + 3] annulation of in situ generated ortho-quinone methides with C,N-cyclic azomethine imines
Authors: Xu Jianfeng , Yuan Shiru , Peng Jingyi , Miao Maozhong , Chen Zhengkai , Ren Hongjun
Published: August 2017

An efficient base-mediated [4 + 3] annulation reaction of ortho-quinone methides with C,N-cyclic azomethine imines is disclosed.
Recent advances in transition-metal-catalyzed reactions of alkynes with isoxazoles
Authors: Li Long , Tan Tong-De , Zhang Ying-Qi , Liu Xin , Ye Long-Wu
Published: August 2017

In this review, recent progress in the transition-metal-catalyzed formal annulations of alkynes with isoxazoles for the efficient synthesis of N-heterocycles is discussed.
Origins of high catalyst loading in copper(i)-catalysed Ullmann–Goldberg C–N coupling reactions
Authors: Sherborne Grant J. , Adomeit Sven , Menzel Robert , Rabeah Jabor , Brückner Angelika , Fielding Mark R. , Willans Charlotte E. , Nguyen Bao N.
Published: August 2017

A mechanistic investigation of Ullmann–Goldberg reactions using common bases led to the identification of pathways for catalyst deactivation. The solid form of the inorganic phase was found to have critical influence on the mechanism of the reaction.
Molecular design of upconversion nanoparticles for gene delivery
Authors: Lai Wing-Fu , Rogach Andrey L. , Wong Wing-Tak
Published: August 2017

Upconversion nanoparticles (UCNPs) represent an important topic in nanotechnology, and have extended possibilities in gene delivery beyond the reach of many existing technologies.
Designing transition metal and nitrogen-codoped SrTiO3(001) perovskite surfaces as efficient photocatalysts for water splitting
Authors: Yang Yang , Zheng Weijie , Cheng Daojian , Cao Dapeng
Published: August 2017

Development of an efficient photocatalyst with both strong visible light absorption and high charge mobility is highly desirable but still remains a great challenge.
Performance evaluation of gasoline alternatives using a thermodynamic spark-ignition engine model
Authors: Gschwend Dominik , Soltic Patrik , Edinger Philip , Wokaun Alexander , Vogel Frédéric
Published: August 2017

In light of climate change and the fact that surface transportation heavily relies on internal combustion engines, many different alternatives to gasoline have been proposed.
Emergence of epithelial cell density waves
Authors: Yabunaka Shunsuke , Marcq Philippe
Published: August 2017

Epithelial cell monolayers exhibit traveling mechanical waves. We rationalize this observation by studying bifurcations in a hydrodynamic model that takes into account the spatio-temporal variations of the cell density field.
Responsive, switchable wormlike micelles for CO2/N2 and redox dual stimuli based on selenium-containing surfactants
Authors: Jiang Jianzhong , Zhang Duyan , Yin JinChao , Cui Zhenggang
Published: August 2017

A dual-stimuli responsive, wormlike micelle system was developed using a switchable selenium-containing surfactant, dihendecylcarboxylic acid sodium selenide (C11-Se-C11), and a commercially available surfactant, cetyltrimethyl ammonium bromide (CTAB).
Self-assembly behaviour of hetero-nuclear Janus dumbbells
Authors: O'Toole Patrick , Munaò Gianmarco , Giacometti Achille , Hudson Toby S.
Published: August 2017

We investigate the fluid structure and self-assembly of a system of Janus dumbbells by means of aggregation-volume-bias Monte Carlo simulations and Simulated Annealing techniques.
Structural behavior of competitive temperature and pH-responsive tethered polymer layers
Authors: Morochnik Simona , Nap Rikkert J. , Ameer Guillermo A. , Szleifer Igal
Published: August 2017

Herein, we develop a molecular theory to examine a class of pH and temperature-responsive tethered polymer layers.
Vascular induction and cell infiltration into peptide-modified bioactive silk fibroin hydrogels
Authors: Kambe Yusuke , Murakoshi Akie , Urakawa Hiroshi , Kimura Yoshiharu , Yamaoka Tetsuji
Published: August 2017

A vascular-inducing peptide was produced recombinantly to stimulate the replacement of silk fibroin hydrogels by vascularized tissuesin vivo.
miR-494 up-regulates the PI3K/Akt pathway via targetting PTEN and attenuates hepatic ischemia/reperfusion injury in a rat model
Authors: Su Song , Luo De , Liu Xiangdong , Liu Jiang , Peng Fangyi , Fang Cheng , Li Bo
Published: August 2017

A rat HIRI model was constructed and treated with an intraperitoneal injection of agomir-miR-494 or agomir-NC (negative control) for 7 days after the surgery. The pathophysiological changes in sham-operated rats, HIRI, HIRI + agomir-miR-494, and HIRI + agomir-NC were compared. The effect of miR-494 was also assessed in an H2O2-induced apoptosis model. Hepatic AML12 cells were transfected with mimics NC or miR-494 mimics, followed by 6-h H2O2 treatment. Cell proliferation and apoptosis were detected by CCK8 assay and flow cytometry, respectively. Further, the miR-494 target gene was identified by luciferase reporter assay, and verified both in vitro and in vivo experiments. The activity of AKT pathway was further analyzed in vivo by Western blot. HIRI + agomir-miR-494 rats exhibited significantly higher miR-494 expression, lower serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), and glutamate dehydrogenase (GLDH) level, lower hepatic MDA, TOA, and OSI, alleviated hepatic necrosis, reduced hepatocyte apoptosis, and decreased expression of apoptosis-related proteins, when compared with HIRI + agomir-NC rats (P<0.05 or 0.01). After H2O2 treatment, AML-12 cells transfected with miR-494 mimics had significantly higher proliferation and lower apoptosis rate compared with mimics NC group (P<0.01). PTEN was identified as an miR-494 target gene. PTEN expression was significantly down-regulated in AML12 cells transfected with miR-494 mimics, and was up-regulated by treatment of miR-494 inhibitor (P<0.01). Moreover, HIRI + agomir-miR-494 rats exhibited significantly lower PTEN expression, and higher p-AKT, p-mTOR, and p-p70S6K levels compared with HIRI + agomir-NC rats. Therefore, miR-494 protected rats against hepatic ischemia/reperfusion (I/R) injury through down-regulating its downstream target gene PTEN, leading to the activation of PI3K/AKT signaling pathway.
Predictive role of galectin-1 and integrin α5β1 in cisplatin-based neoadjuvant chemotherapy of bulky squamous cervical cancer
Authors: Zhu Haiyan , Chen Aixue , Li Saisai , Tao Xuejiao , Sheng Bo , Chetry Mandika , Zhu Xueqiong
Published: August 2017

Although galectin-1 and integrin α5β1 confer chemoresistance to certain types of cancer, whether their expression predicts the response to cisplatin-based neoadjuvant chemotherapy (NACT) in squamous cervical cancer remains unclear. Paired tumor samples (pre- and post-chemotherapy) were obtained from 35 bulky squamous cervical cancer patients treated with cisplatin-based NACT and radical hysterectomy at our hospital between January 2007 and August 2014. The expression of galectin-1 and integrin α5β1 in tumor cells and stromal cells was analyzed by immunohistochemistry. The correlation between galectin-1/integrin α5β1 and apoptosis-associated markers was investigated by using the The Cancer Genome Atlas (TCGA) RNA-sequencing data. Seventeen patients were identified as chemotherapy responders and 18 as non-responders. Galectin-1 and integrin α5β1-positive immunostaining was more frequently observed in stromal cells than its in tumor cells. The expression of galectin-1 and integrin α5β1 in stromal and tumor cells was significantly down-regulated in postchemotherapy cervical cancer tissues. High levels of galectin-1 and integrin α5β1 in stromal were associated with a negative chemotherapy response in squamous cervical cancer patients treated with cisplatin-based NACT. Additionally, the expression of galectin-1 and integrin α5 correlated negatively with caspase 3/caspase 8 by using the TCGA RNA-sequencing data. Galectin-1 and integrin α5β1 expression in stromal may serve as a prediction of the responses to cisplatin-based NACT for patients with bulky squamous cervical cancer. Galectin-1 and integrin α5β1 may be implicated in the development of chemoresistance in cervical cancer via suppressing apoptosis.
Pilot contamination mitigation strategies in massive MIMO systems
Authors: Gong Zijun , Li Cheng , Jiang Fan
Published: August 2017

Compared with the traditional multi‐user MIMO (multiple‐input and multiple‐output), massive MIMO aims to serve tens of users with hundreds of antennas on each base station. All users can use the same time–frequency resources through space division multiple access, leading to vast improvement on spectral efficiency. However, to achieve the benefits, channel state information is usually required, and the acquisition is difficult in massive MIMO systems. Theoretically, each user should be assigned with orthogonal pilot sequences to avoid interference; however, due to the huge number of users (much more than available orthogonal pilot sequences) in service, pilot reuse in adjacent cells is inevitable, causing inter‐cell interference. This phenomenon is often referred to as pilot contamination (PC) and is believed to be the fundamental limit on system capacity of massive MIMO systems. To solve this problem, many methods have been proposed since 2010, when the concept of massive MIMO was first proposed. In this study, the authors reviewed these methods, categorised them into four groups and compared their advantages and limitations. Although a survey on PC has been conducted by Elijah et al., where they tried to cover various aspects of the PC issue, their work focuses on the analysis of rationale and limitations of different contamination mitigation methods. Besides, performance evaluations are conducted and presented.