bluuebunny/crossref_metadata_2025 huggingface dataset:
IGF1R as a Key Target in High Risk, Metastatic Medulloblastoma
Authors: Svalina Matthew N. , Kikuchi Ken , Abraham Jinu , Lal Sangeet , Davare Monika A. , Settelmeyer Teagan P. , Young Michael C. , Peckham Jennifer L. , Cho Yoon-Jae , Michalek Joel E. , Hernandez Brian S. , Berlow Noah E. , Jackson Melanie , Guillaume Daniel J. , Selden Nathan R. , Bigner Darell D. , Nazemi Kellie J. , Green Sarah C. , Corless Christopher L. , Gultekin Sakir , Mansoor Atiya , Rubin Brian P. , Woltjer Randall , Keller Charles
Published: June 2016

Risk or presence of metastasis in medulloblastoma causes substantial treatment-related morbidity and overall mortality. Through the comparison of cytokines and growth factors in the cerebrospinal fluid (CSF) of metastatic medulloblastoma patients with factors also in conditioned media of metastatic MYC amplified medulloblastoma or leptomeningeal cells, we were led to explore the bioactivity of IGF1 in medulloblastoma by elevated CSF levels of IGF1, IGF-sequestering IGFBP3, IGFBP3-cleaving proteases (MMP and tPA) and protease modulators (TIMP1 and PAI-1). IGF1 led not only to receptor phosphorylation but also accelerated migration/adhesion in MYC amplified medulloblastoma cells in the context of appropriate matrix or meningothelial cells. Clinical correlation suggests a peri-/sub-meningothelial source of IGF-liberating proteases that could facilitate leptomeningeal metastasis. In parallel, studies of key factors responsible for cell autonomous growth in MYC amplified medulloblastoma prioritized IGF1R inhibitors. Together, our studies identify IGF1R as a high value target for clinical trials in high risk medulloblastoma.
A 3D in vitro model to explore the inter-conversion between epithelial and mesenchymal states during EMT and its reversion
Authors: Bidarra S. J. , Oliveira P. , Rocha S. , Saraiva D. P. , Oliveira C. , Barrias C. C.
Published: June 2016

Epithelial-to-mesenchymal transitions (EMT) are strongly implicated in cancer dissemination. Intermediate states, arising from inter-conversion between epithelial (E) and mesenchymal (M) states, are characterized by phenotypic heterogeneity combining E and M features and increased plasticity. Hybrid EMT states are highly relevant in metastatic contexts, but have been largely neglected, partially due to the lack of physiologically-relevant 3D platforms to study them. Here we propose a new in vitro model, combining mammary E cells with a bioengineered 3D matrix, to explore phenotypic and functional properties of cells in transition between E and M states. Optimized alginate-based 3D matrices provided adequate 3D microenvironments, where normal epithelial morphogenesis was recapitulated, with formation of acini-like structures, similar to those found in native mammary tissue. TGFβ1-driven EMT in 3D could be successfully promoted, generating M-like cells. TGFβ1 removal resulted in phenotypic switching to an intermediate state (RE cells), a hybrid cell population expressing both E and M markers at gene/protein levels. RE cells exhibited increased proliferative/clonogenic activity, as compared to M cells, being able to form large colonies containing cells with front-back polarity, suggesting a more aggressive phenotype. Our 3D model provides a powerful tool to investigate the role of the microenvironment on metastable EMT stages.
Excessive Activation of TGFβ by Spinal Instability Causes Vertebral Endplate Sclerosis
Authors: Bian Qin , Jain Amit , Xu Xin , Kebaish Khaled , Crane Janet L. , Zhang Zhendong , Wan Mei , Ma Lei , Riley Lee H. , Sponseller Paul D. , Guo X. Edward , Lu Willian Weijia , Wang Yongjun , Cao Xu
Published: June 2016

Narrowed intervertebral disc (IVD) space is a characteristic of IVD degeneration. EP sclerosis is associated with IVD, however the pathogenesis of EP hypertrophy is poorly understood. Here, we employed two spine instability mouse models to investigate temporal and spatial EP changes associated with IVD volume, considering them as a functional unit. We found that aberrant mechanical loading leads to accelerated ossification and hypertrophy of EP, decreased IVD volume and increased activation of TGFβ. Overexpression of active TGFβ in CED mice showed a similar phenotype of spine instability model. Administration of TGFβ Receptor I inhibitor attenuates pathologic changes of EP and prevents IVD narrowing. The aberrant activation of TGFβ resulting in EPs hypertrophy-induced IVD space narrowing provides a pharmacologic target that could have therapeutic potential to delay DDD.
TIGAR contributes to ischemic tolerance induced by cerebral preconditioning through scavenging of reactive oxygen species and inhibition of apoptosis
Authors: Zhou Jun-Hao , Zhang Tong-Tong , Song Dan-Dan , Xia Yun-Fei , Qin Zheng-Hong , Sheng Rui
Published: June 2016

Previous study showed that TIGAR (TP53-induced glycolysis and apoptosis regulator) protected ischemic brain injury via enhancing pentose phosphate pathway (PPP) flux and preserving mitochondria function. This study was aimed to study the role of TIGAR in cerebral preconditioning. The ischemic preconditioning (IPC) and isoflurane preconditioning (ISO) models were established in primary cultured cortical neurons and in mice. Both IPC and ISO increased TIGAR expression in cortical neurons. Preconditioning might upregulate TIGAR through SP1 transcription factor. Lentivirus mediated knockdown of TIGAR significantly abolished the ischemic tolerance induced by IPC and ISO. ISO also increased TIGAR in mouse cortex and hippocampus and alleviated subsequent brain ischemia-reperfusion injury, while the ischemic tolerance induced by ISO was eliminated with TIGAR knockdown in mouse brain. ISO increased the production of NADPH and glutathione (GSH) and scavenged reactive oxygen species (ROS), while TIGAR knockdown decreased GSH and NADPH production and increased the level of ROS. Supplementation of ROS scavenger NAC and PPP product NADPH effectively rescue the neuronal injury caused by TIGAR deficiency. Notably, TIGAR knockdown inhibited ISO-induced anti-apoptotic effects in cortical neurons. These results suggest that TIGAR participates in the cerebral preconditioning through reduction of ROS and subsequent cell apoptosis.
Casimir switch: steering optical transparency with vacuum forces
Authors: Liu Xi-fang , Li Yong , Jing H.
Published: June 2016

The Casimir force, originating from vacuum zero-point energy, is one of the most intriguing purely quantum effects. It has attracted renewed interests in current field of nanomechanics, due to the rapid size decrease of on-chip devices. Here we study the optomechanically-induced transparency (OMIT) with a tunable Casimir force. We find that the optical output rate can be significantly altered by the vacuum force, even terminated and then restored, indicating a highly-controlled optical switch. Our result addresses the possibility of designing exotic optical nano-devices by harnessing the power of vacuum.
Deletion of Brg1 causes abnormal hair cell planer polarity, hair cell anchorage, and scar formation in mouse cochlea
Authors: Jin Yecheng , Ren Naixia , Li Shiwei , Fu Xiaolong , Sun Xiaoyang , Men Yuqin , Xu Zhigang , Zhang Jian , Xie Yue , Xia Ming , Gao Jiangang
Published: June 2016

Hair cells (HCs) are mechanosensors that play crucial roles in perceiving sound, acceleration, and fluid motion. The precise architecture of the auditory epithelium and its repair after HC loss is indispensable to the function of organ of Corti (OC). In this study, we showed that Brg1 was highly expressed in auditory HCs. Specific deletion of Brg1 in postnatal HCs resulted in rapid HC degeneration and profound deafness in mice. Further experiments showed that cell-intrinsic polarity of HCs was abolished, docking of outer hair cells (OHCs) by Deiter’s cells (DCs) failed, and scar formation in the reticular lamina was deficient. We demonstrated that Brg1 ablation disrupted the Gαi/Insc/LGN and aPKC asymmetric distributions, without overt effects on the core planer cell polarity (PCP) pathway. We also demonstrated that Brg1-deficient HCs underwent apoptosis, and that leakage in the reticular lamina caused by deficient scar formation shifted the mode of OHC death from apoptosis to necrosis. Together, these data demonstrated a requirement for Brg1 activity in HC development and suggested a role for Brg1 in the proper cellular structure formation of HCs.
Extensive coronavirus-induced membrane rearrangements are not a determinant of pathogenicity
Authors: Maier Helena J. , Neuman Benjamin W. , Bickerton Erica , Keep Sarah M. , Alrashedi Hasan , Hall Ross , Britton Paul
Published: June 2016

Positive-strand RNA (+RNA) viruses rearrange cellular membranes during replication, possibly in order to concentrate and arrange viral replication machinery for efficient viral RNA synthesis. Our previous work showed that in addition to the conserved coronavirus double membrane vesicles (DMVs), Beau-R, an apathogenic strain of avian Gammacoronavirus infectious bronchitis virus (IBV), induces regions of ER that are zippered together and tethered open-necked double membrane spherules that resemble replication organelles induced by other +RNA viruses. Here we compared structures induced by Beau-R with the pathogenic lab strain M41 to determine whether membrane rearrangements are strain dependent. Interestingly, M41 was found to have a low spherule phenotype. We then compared a panel of pathogenic, mild and attenuated IBV strains in ex vivo tracheal organ culture (TOC). Although the low spherule phenotype of M41 was conserved in TOCs, each of the other tested IBV strains produced DMVs, zippered ER and spherules. Furthermore, there was a significant correlation for the presence of DMVs with spherules, suggesting that these structures are spatially and temporally linked. Our data indicate that virus induced membrane rearrangements are fundamentally linked to the viral replicative machinery. However, coronavirus replicative apparatus clearly has the plasticity to function in different structural contexts.
T cells expressing CD19-specific Engager Molecules for the Immunotherapy of CD19-positive Malignancies
Authors: Velasquez Mireya Paulina , Torres David , Iwahori Kota , Kakarla Sunitha , Arber Caroline , Rodriguez-Cruz Tania , Szoor Arpad , Bonifant Challice L. , Gerken Claudia , Cooper Laurence J. N. , Song Xiao-Tong , Gottschalk Stephen
Published: June 2016

T cells expressing chimeric antigen receptors (CARs) or the infusion of bispecific T-cell engagers (BITEs) have shown antitumor activity in humans for CD19-positive malignancies. While BITEs redirect the large reservoir of resident T cells to tumors, CAR T cells rely on significant in vivo expansion to exert antitumor activity. We have shown that it is feasible to modify T cells to secrete solid tumor antigen-specific BITEs, enabling T cells to redirect resident T cells to tumor cells. To adapt this approach to CD19-positive malignancies we now generated T cells expressing secretable, CD19-specific BITEs (CD19-ENG T cells). CD19-ENG T cells recognized tumor cells in an antigen-dependent manner as judged by cytokine production and tumor killing and redirected bystander T cells to tumor cells. Infusion of CD19-ENG T cells resulted in regression of leukemia or lymphoma in xenograft models and a survival advantage in comparison to control mice. Genetically modified T cells expressing engager molecules may present a promising addition to current CD19-targeted immunotherapies.
Distinct mechanisms regulate Cdx2 expression in the blastocyst and in trophoblast stem cells
Authors: Rayon Teresa , Menchero Sergio , Rollán Isabel , Ors Inmaculada , Helness Anne , Crespo Miguel , Nieto Andres , Azuara Véronique , Rossant Janet , Manzanares Miguel
Published: June 2016

The first intercellular differences during mammalian embryogenesis arise in the blastocyst, producing the inner cell mass and the trophectoderm. The trophectoderm is the first extraembryonic tissue and does not contribute to the embryo proper, its differentiation instead forming tissues that sustain embryonic development. Crucial roles in extraembryonic differentiation have been identified for certain transcription factors, but a comprehensive picture of the regulation of this early specification is still lacking. Here, we investigated whether the regulatory mechanisms involved in Cdx2 expression in the blastocyst are also utilized in the postimplantation embryo. We analyzed an enhancer that is regulated through Hippo and Notch in the blastocyst trophectoderm, unexpectedly finding that it is inactive in the extraembryonic structures at postimplantation stages. Further analysis identified other Cdx2 regulatory elements including a stem-cell specific regulatory sequence and an element that drives reporter expression in the trophectoderm, a subset of cells in the extraembryonic region of the postimplantation embryo and in trophoblast stem cells. The cross-comparison in this study of cis-regulatory elements employed in the blastocyst, stem cell populations and the postimplantation embryo provides new insights into early mammalian development and suggests a two-step mechanism in Cdx2 regulation.
Incident Angle- and Polarization-Insensitive Metamaterial Absorber using Circular Sectors
Authors: Lee Dongju , Hwang Jung Gyu , Lim Daecheon , Hara Tadayoshi , Lim Sungjoon
Published: June 2016

In this paper, an incident angle- and polarization-insensitive metamaterial absorber is proposed for X-band applications. A unit cell of the proposed absorber has a square patch at the centre and four circular sectors are rotated around the square patch. The vertically and horizontally symmetric structure of the unit cell enables polarization-insensitivity. The circular sector of the unit cell enables an angle-insensitivity. The performances of the proposed absorber are demonstrated with a full-wave simulation and measurements. The angular sensitivity is studied at different inner angles of the circular sector. When the inner angle of the circular sector is 90°, the simulated absorptivity is higher than 90%, and the frequency variation is less than 0.96% for incident angles up to 70°. The measured absorptivity at 10.44 GHz is close to 100% for all the polarization angles under normal incidence. When the incident angles are varied from 0°– 60°, the measured absorptivity is maintained above 90% for both the transverse electric (TE) and the transverse magnetic (TM) modes.
Flow cytometry may allow microscope-independent detection of holocentric chromosomes in plants
Authors: Zedek František , Veselý Pavel , Horová Lucie , Bureš Petr
Published: June 2016

Two chromosomal structures, known as monocentric and holocentric chromosomes, have evolved in eukaryotes. Acentric fragments of monocentric chromosomes are unequally distributed to daughter cells and/or lost, while holocentric fragments are inherited normally. In monocentric species, unequal distribution should generate chimeras of cells with different nuclear DNA content. We investigated whether such differences in monocentric species are detectable by flow cytometry (FCM) as (i) a decreased nuclear DNA content and (ii) an increased coefficient of variance (CV) of the G1 peak after gamma radiation-induced fragmentation. We compared 13 monocentric and 9 holocentric plant species. Unexpectedly, monocentrics and holocentrics did not differ with respect to parameters (i) and (ii) in their response to gamma irradiation. However, we found that the proportion of G2 nuclei was highly elevated in monocentrics after irradiation, while holocentrics were negligibly affected. Therefore, we hypothesize that DNA-damaging agents induce cell cycle arrest leading to endopolyploidy only in monocentric and not (or to much lesser extent) in holocentric plants. While current microscope-dependent methods for holocentrism detection are unreliable for small and numerous chromosomes, which are common in holocentrics, FCM can use somatic nuclei. Thus, FCM may be a rapid and reliable method of high-throughput screening for holocentric candidates across plant phylogeny.
Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly
Authors: Wragg David , Marti-Marimon Maria , Basso Benjamin , Bidanel Jean-Pierre , Labarthe Emmanuelle , Bouchez Olivier , Le Conte Yves , Vignal Alain
Published: June 2016

Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.
Insights into the role of sulfated glycans in cancer cell adhesion and migration through use of branched peptide probe
Authors: Brunetti Jlenia , Depau Lorenzo , Falciani Chiara , Gentile Mariangela , Mandarini Elisabetta , Riolo Giulia , Lupetti Pietro , Pini Alessandro , Bracci Luisa
Published: June 2016

The tetra-branched peptide NT4 selectively binds to different human cancer cells and tissues. NT4 specifically binds to sulfated glycosaminoglycans on cancer cell membranes. Since sulfated glycosaminoglycans are involved in cancer cell interaction with the extracellular matrix, we evaluated the effect of NT4 on cancer cell adhesion and migration. We demonstrated here that the branched peptide NT4 binds sulfated glycosaminoglycans with high affinity and with preferential binding to heparan sulfate. NT4 inhibits cancer cell adhesion and migration on different proteins, without modifying cancer cell morphology or their ability to produce protrusions, but dramatically affecting the directionality and polarity of cell movement. Results obtained by taking advantage of the selective targeting of glycosaminoglycans chains by NT4, provide insights into the role of heparan sulfate proteoglycans in cancer cell adhesion and migration and suggest a determinant role of sulfated glycosaminoglycans in the control of cancer cell directional migration.
A novel recombinant 6Aβ15-THc-C chimeric vaccine (rCV02) mitigates Alzheimer’s disease-like pathology, cognitive decline and synaptic loss in aged 3 × Tg-AD mice
Authors: Yu Yun-Zhou , Liu Si , Wang Hai-Chao , Shi Dan-Yang , Xu Qing , Zhou Xiao-Wei , Sun Zhi-Wei , Huang Pei-Tang
Published: June 2016

Alzheimer’s disease (AD) is a neurodegenerative disorder that impairs memory and cognition. Targeting amyloid-β (Aβ) may be currently the most promising immunotherapeutic strategy for AD. In this study, a recombinant chimeric 6Aβ15-THc-C immunogen was formulated with alum adjuvant as a novel Aβ B-cell epitope candidate vaccine (rCV02) for AD. We examined its efficacy in preventing the cognitive deficit and synaptic impairment in 3 × Tg-AD mice. Using a toxin-derived carrier protein, the rCV02 vaccine elicited robust Aβ-specific antibodies that markedly reduced AD-like pathology and improved behavioral performance in 3 × Tg-AD mice. Along with the behavioral improvement in aged 3 × Tg-AD mice, rCV02 significantly decreased calpain activation concurrent with reduced soluble Aβ or oligomeric forms of Aβ, probably by preventing dynamin 1 and PSD-95 degradation. Our data support the hypothesis that reducing Aβ levels in rCV02-immunized AD mice increases the levels of presynaptic dynamin 1 and postsynaptic PSD-95 allowing functional recovery of cognition. In conclusion, this novel and highly immunogenic rCV02 shows promise as a new candidate prophylactic vaccine for AD and may be useful for generating rapid and strong Aβ-specific antibodies in AD patients with pre-existing memory Th cells generated after immunization with conventional tetanus toxoid vaccine.
Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities
Authors: Zhou Yanjun , He Liu , Zhang Wenwen , Hu Jingjing , Shi Zhengshuang
Published: June 2016

Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for unfolded proteins. The α-helices are the dominant structures in many proteins. For these proteins, how could the α-structures occur from the least in unfolded to the most in folded states? Populations of the minor α-conformation in model peptides provide vital information. Reliable determination of populations of the α-conformers in these peptides that exist in multiple equilibriums of different conformations remains a challenge. Combined analyses on data from AcGXPNH2 and AcGXGNH2 peptides allow us to derive the populations of PII, β and α in AcGXGNH2. Our results show that on average residue X in AcGXGNH2 adopt PII, β, and α 44.7%, 44.5% and 10.8% of time, respectively. The contents of α-conformations for different amino acids define an α-helix nucleation propensity scale. With derived PII, β and α-contents, we can construct a free energy-conformation diagram on each AcGXGNH2 in aqueous solution for the three major backbone conformations. Our results would have broad implications on early-stage events of protein folding.
Heritability and Reversibility of DNA Methylation Induced by in vitro Grafting between Brassica juncea and B. oleracea
Authors: Cao Liwen , Yu Ningning , Li Junxing , Qi Zhenyu , Wang Dan , Chen Liping
Published: June 2016

Grafting between tuber mustard and red cabbage produced a chimeric shoot apical meristem (SAM) of TTC, consisting of Layers I and II from Tuber mustard and Layer III from red Cabbage. Phenotypic variations, which mainly showed in leaf shape and SAM, were observed in selfed progenies GSn (GS = grafting-selfing, n = generations) of TTC. Here the heritability of phenotypic variation and its association with DNA methylation changes in GSn were investigated. Variation in leaf shape was found to be stably inherited to GS5, but SAM variation reverted over generations. Subsequent measurement of DNA methylation in GS1 revealed 5.29–6.59% methylation changes compared with tuber mustard (TTT), and 31.58% of these changes were stably transmitted to GS5, but the remainder reverted to the original status over generations, suggesting grafting-induced DNA methylation changes could be both heritable and reversible. Sequence analysis of differentially methylated fragments (DMFs) revealed methylation mainly changed within transposons and exon regions, which further affected the expression of genes, including flowering time- and gibberellin response-related genes. Interestingly, DMFs could match differentially expressed siRNA of GS1, GS3 and GS5, indicating that grafting-induced DNA methylation could be directed by siRNA changes. These results suggest grafting-induced DNA methylation may contribute to phenotypic variations induced by grafting.
An autism-associated mutation in CaV1.3 channels has opposing effects on voltage- and Ca2+-dependent regulation
Authors: Limpitikul Worawan B. , Dick Ivy E. , Ben-Johny Manu , Yue David T.
Published: June 2016

CaV1.3 channels are a major class of L-type Ca2+ channels which contribute to the rhythmicity of the heart and brain. In the brain, these channels are vital for excitation-transcription coupling, synaptic plasticity, and neuronal firing. Moreover, disruption of CaV1.3 function has been associated with several neurological disorders. Here, we focus on the de novo missense mutation A760G which has been linked to autism spectrum disorder (ASD). To explore the role of this mutation in ASD pathogenesis, we examined the effects of A760G on CaV1.3 channel gating and regulation. Introduction of the mutation severely diminished the Ca2+-dependent inactivation (CDI) of CaV1.3 channels, an important feedback system required for Ca2+ homeostasis. This reduction in CDI was observed in two major channel splice variants, though to different extents. Using an allosteric model of channel gating, we found that the underlying mechanism of CDI reduction is likely due to enhanced channel opening within the Ca2+-inactivated mode. Remarkably, the A760G mutation also caused an opposite increase in voltage-dependent inactivation (VDI), resulting in a multifaceted mechanism underlying ASD. When combined, these regulatory deficits appear to increase the intracellular Ca2+ concentration, thus potentially disrupting neuronal development and synapse formation, ultimately leading to ASD.
Discovery of Novel Splice Variants and Regulatory Mechanisms for Microsomal Triglyceride Transfer Protein in Human Tissues
Authors: Suzuki Takashi , Swift Larry L.
Published: June 2016

Microsomal triglyceride transfer protein (MTP) is a unique lipid transfer protein essential for the assembly of triglyceride-rich lipoproteins by the liver and intestine. Previous studies in mice identified a splice variant of MTP with an alternate first exon. Splice variants of human MTP have not been reported. Using PCR approaches we have identified two splice variants in human tissues, which we have named MTP-B and MTP-C. MTP-B has a unique first exon (Ex1B) located 10.5 kb upstream of the first exon (Ex1A) for canonical MTP (MTP-A); MTP-C contains both first exons for MTP-A and MTP-B. MTP-B was found in a number of tissues, whereas MTP-C was prominent in brain and testis. MTP-B does not encode a protein; MTP-C encodes the same protein encoded by MTP-A, although MTP-C translation is strongly inhibited by regulatory elements within its 5′-UTR. Using luciferase assays, we demonstrate that the promoter region upstream of exon 1B is quite adequate to drive expression of MTP. We conclude that alternate splicing plays a key role in regulating cellular MTP levels by introducing distinct promoter regions and unique 5′-UTRs, which contain elements that alter translation efficiency, enabling the cell to optimize MTP activity.
Effects of bioirrigation of non-biting midges (Diptera: Chironomidae) on lake sediment respiration
Authors: Baranov Viktor , Lewandowski Jörg , Romeijn Paul , Singer Gabriel , Krause Stefan
Published: June 2016

Bioirrigation or the transport of fluids into the sediment matrix due to the activities of organisms such as bloodworms (larvae of Diptera, Chironomidae), has substantial impacts on sediment respiration in lakes. However, previous quantifications of bioirrigation impacts of Chironomidae have been limited by technical challenges such as the difficulty to separate faunal and bacterial respiration. This paper describes a novel method based on the bioreactive tracer resazurin for measuring respiration in-situ in non-sealed systems with constant oxygen supply. Applying this new method in microcosm experiments revealed that bioirrigation enhanced sediment respiration by up to 2.5 times. The new method is yielding lower oxygen consumption than previously reported, as it is only sensitive to aerobic heterotrophous respiration and not to other processes causing oxygen decrease. Hence it decouples the quantification of respiration of animals and inorganic oxygen consumption from microbe respiration in sediment.
Discovery of a rhamnose utilization pathway and rhamnose-inducible promoters in Pichia pastoris
Authors: Liu Bo , Zhang Yuwei , Zhang Xue , Yan Chengliang , Zhang Yuhong , Xu Xinxin , Zhang Wei
Published: June 2016

The rhamnose utilization pathway in Pichia pastoris has not been clarified although this strain can grow well on rhamnose as a sole carbon source. In this study, four genes, PAS_chr4_0338, PAS_chr4_0339, PAS_chr4_0340 and PAS_chr4_0341, were, for the first time, predicted to be involved in rhamnose metabolism along with the previously identified gene PAS_chr1_4-0075. Moreover, expression of these genes, especially PAS_chr4_0341 and PAS_chr1_4-0075 designated as LRA4 and LRA3, was confirmed to significantly increase and clearly decrease in the presences of rhamnose and glucose, respectively. LRA4 encoding a putative L-2-keto-3-deoxyrhamnonate aldolase, was further confirmed via gene disruption and gene complementation to participate in rhamnose metabolism. Using β-galactosidase and green fluorescent protein as reporters, the promoters of LRA4 and LRA3 performed well in driving efficient production of heterologous proteins. By using food grade rhamnose instead of the toxic compound methanol as the inducer, the two promoters would be excellent candidates for driving the production of food-grade and therapeutically important recombinant proteins.
Preparation of an aptamer based organic–inorganic hybrid monolithic column with gold nanoparticles as an intermediary for the enrichment of proteins
Authors: Zhao Jin-cheng , Zhu Qing-yun , Zhao Ling-yu , Lian Hong-zhen , Chen Hong-yuan
Published: June 2016

Gold nanoparticles are used as an intermediary in a sandwich structure for the preparation of an aptamer-based organic–inorganic hybrid affinity monolithic column.
Can saliva testing replace blood measurements for health monitoring? Insights from a correlation study of salivary and whole blood glutathione in humans
Authors: Ngamchuea Kamonwad , Batchelor-McAuley Christopher , Cowen Philip J. , Williams Clare , Gonçalves Luís Moreira , Compton Richard G.
Published: June 2016

The feasibility of using saliva samples as diagnostic for health status is assessed.
Determination of residual automotive lubricant oil and residual solvent used in a dry wash as adulterants in Brazilian S-10 diesel (B7) using mid-infrared spectroscopy data and chemometric methods
Authors: Mazivila Sarmento Júnior , Maria de Souza Letícia , Abubakar Ibrahim Muhammad , Mavulula Elisa Langa , Neto Waldomiro Borges
Published: June 2016

This paper presents methodologies for quantification of adulterants and discrimination between adulterated and unadulterated samples of Brazilian S-10 diesel using MIR spectroscopy and PLS-DA, PLS.
Visible-light-induced photocatalytic azotrifluoromethylation of alkenes with aryldiazonium salts and sodium triflinate
Authors: Yu Xing-Long , Chen Jia-Rong , Chen Dong-Zhen , Xiao Wen-Jing
Published: June 2016

Visible light photocatalytic azotrifluoromethylation of alkenes with aryldiazonium salts and sodium triflinate is described, which gave the trifluoromethylated azo compounds in good yields.
Energetic aminated-azole assemblies from intramolecular and intermolecular N–H⋯O and N–H⋯N hydrogen bonds
Authors: He Chunlin , Yin Ping , Mitchell Lauren A. , Parrish Damon A. , Shreeve Jean'ne M.
Published: June 2016

Extensive H-bond interactions in four aminated azoles give them comprehensive properties, such as high density, good thermal stability and reasonable sensitivity as well as high detonation performance.
Design and synthesis of luminescent porous coordination polymers for chromaticity modulation, sensing of nitrobenzene and iodine encapsulation
Authors: Wang Haijun , Cheng Fujun , Zou Changchang , Li Qianqian , Hua Yinying , Duan Jingui , Jin Wanqin
Published: June 2016

A family of porous coordination polymers constructed from C2v symmetry ligands with increased conjugation moieties was systematically designed and prepared, which is highly promising for chromaticity modulation, sensing of nitrobenzene, and I2 encapsulation.
Mechanism of X-ray excited optical luminescence (XEOL) in europium doped BaAl2O4 phosphor
Authors: Rezende Marcos V. dos S. , Montes Paulo J. R. , Andrade Adriano B. , Macedo Zelia S. , Valerio Mário E. G.
Published: June 2016

This paper reports a luminescence mechanism in Eu-doped BaAl2O4 excited with monochromatic X-rays (also known as X-ray excited optical luminescence – XEOL) from synchrotron radiation.
Defect induced tunable near infrared emission of Er–CeO2 by heterovalent co-dopants
Authors: Florea Mihaela , Avram Daniel , Cojocaru Bogdan , Tiseanu Ion , Parvulescu Vasile , Tiseanu Carmen
Published: June 2016

We investigate the effects of heterovalent co-dopants on the structural and emission properties of 1% Er–CeO2 nanoparticles.
Flexibility of short DNA helices under mechanical stretching
Authors: Zoli Marco
Published: June 2016

The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair.
Synergy between experimental and computational approaches to homogeneous photoredox catalysis
Authors: Demissie Taye B. , Hansen Jørn H.
Published: June 2016

In this Frontiers article, we highlight how state-of-the-art density functional theory calculations can contribute to the field of homogeneous photoredox catalysis.
Correction: Microencapsulation of probiotics in hydrogel particles: enhancing Lactococcus lactis subsp. cremoris LM0230 viability using calcium alginate beads
Authors: Yeung Timothy W. , Arroyo-Maya Izlia J. , McClements David J. , Sela David A.
Published: June 2016

Correction for ‘Microencapsulation of probiotics in hydrogel particles: enhancing Lactococcus lactis subsp. cremoris LM0230 viability using calcium alginate beads’ by Timothy W. Yeung et al., Food Funct., 2016, 7, 1797–1804.
Heterojunction Cr2O3/CuO:Ni photocathodes for enhanced photoelectrochemical performance
Authors: Mohd Nasir Siti Nur Farhana , Yahya Mohd Khairul Najib , Mohamad Sapian Norfaizzatul Wahidah , Ahmad Ludin Norasikin , Ibrahim Mohd Adib , Sopian Kamaruzzaman , Mat Teridi Mohd Asri
Published: June 2016

Heterojunction p-type photoelectrodes consisting of chromium oxide (Cr2O3) and copper oxide (CuO)-doped nickel (Ni) were prepared using aerosol-assisted chemical vapour deposition (AACVD) and spin-coating.
Reply to the ‘Comment on “Graphene oxide regulates the bacterial community and exhibits property changes in soil”’ by C. Forstner, P. Wang, P. M. Kopittke and P. G. Dennis, RSC Adv., 2016, 6, DOI: 10.1039/C5RA26329H
Authors: Du Junjie , Hu Xiangang , Zhou Qixing
Published: June 2016

Graphene oxide regulates the bacterial community.
An efficient and controlled synthesis of persulfonylated G1 dendrimers via click reaction
Authors: Khanam Shaziya , Rai Sunil K. , Verma Deepshikha , Khanna Ranjana S. , Tewari Ashish K.
Published: June 2016

A controlled synthesis for persulfonylated G1 dendrimers has been standardized at room temperature through click reaction using Cu(PPh3)3Br complex in the presence of tridentate chelating ligands.
Roles of oxygen and nitrogen in control of nonlinear resistive behaviors via filamentary and homogeneous switching in an oxynitride thin film memristor
Authors: Shih Yu-Chuan , Wang Tsang-Hsuan , Huang Jian-Shiou , Lai Chih-Chung , Hong Ying-Jhan , Chueh Yu-Lun
Published: June 2016

A TiOxNy thin film, which contains controllable concentrations of oxygen and nitrogen by a single-step reactive sputtering process, exhibiting non-linear I–V behavior, was proposed and demonstrated.
Trials of a Contralateral Hearing Aid After Long-Term Unilateral Cochlear Implant Use in Early-Onset Deafness
Authors: Gottermeier Linda , De Filippo Carol , Clark Catherine
Published: June 2016

Purpose

The purpose of this study was to evaluate the practicability of binaural hearing by adding a contralateral hearing aid (HA) after long-term cochlear implant (CI) use in prelingually deaf adults.

Method

Five individuals with 1 CI volunteered for a 3-week bimodal (CI + HA) trial. HA gain was set low until sound was tolerable, then increased as listeners acclimated. Participants logged their daily listening experiences and were closely monitored by the audiologist. Measures included pre- and posttrial consonant-nucleus-consonant (CNC) word and phoneme scores and self-reports of satisfaction and listening ability in difficult situations.

Results

Acoustic stimulation was initially unpleasant, but approached comfort at target gain within the 3-week period. Benefit was demonstrated in continued voluntary HA use and higher bimodal phoneme scores compared to CI alone (8%–31% increases) for 4 of the participants.

Conclusions

When a second CI is not a consideration, a contralateral HA should be pursued as the standard of care for prelingually deaf adults despite substantial auditory deprivation in the previously unaided ear, unpleasant sensations at initial HA fit, or lack of dramatic objective test gains. Frequent audiologist contact, repeated HA adjustments, and client journals are valuable in promoting favorable outcomes with bimodal hearing (adaptation, acceptance, and benefit) for this population.
Changing availability of TV white space in the UK
Authors: Holland O. , Kokkinen H. , Wong S. , Friderikos V. , Raman A. , Dohler M. , Lema M.
Published: June 2016

The UK regulator Ofcom has held a Pilot of TV white space (TVWS) technology in the UK. On the basis of the results of this Pilot, Ofcom has varied its calculations of allowed white space device equivalent isotropically radiated powers (EIRP). Further, the World Radiocommunication Conference (WRC) 2015 has assigned 694‐790 MHz to mobile broadband on a co‐primary basis, in International Telecommunication Union (ITU) Region 1 (which includes the UK/EU). Fundamental observations on the effects of these changes on TVWS availability in the UK are provided.
Thermal behaviour analyses of gas‐insulated switchgear compartment using thermal network method
Authors: Stosur Mariusz , Szewczyk Marcin , Sowa Kacper , Dawidowski Pawel , Balcerek Przemyslaw
Published: June 2016

In development of electric power products, aspects related to thermal phenomena are becoming very important due to the fact that they guarantee the correct operation of product. The temperature limits specified by the standards cannot be exceeded which makes the knowledge of the temperature behaviour an important factor in order to predict reliability and performance of the product component in its working environment. In this study, thermal network method (TNM) is used for modelling of temperature conditions in typical geographical information system (GIS) compartment arrangements. Models implemented in ATP–EMTP software were validated with OrCAD Capture simulation environment and with high‐current measurement results. On the bases of the TNM presented as the network approach composed of heat sources, thermal resistances and capacitances which can be easily represented and calculated by means of ATP–EMTP simulation software and also with the OrCAD Capture environment. This study addresses the thermal behaviour of a standard ELK‐3 GIS compartment. Modelling in application to design rating calculations of the typical GIS compartment arrangements are presented and analysed. These analyses can serve as a base for development of more advanced ATP–EMTP models using the TNM approach.
Adaptive method for harmonic contribution assessment based on hierarchical K‐means clustering and Bayesian partial least squares regression
Authors: Zang Tianlei , He Zhengyou , Fu Ling , Wang Yan , Qian Qingquan
Published: June 2016

The accuracy of harmonic contribution assessment is severely affected by the fluctuation of utility harmonic. This study proposes an adaptive method for harmonic contribution assessment of the distribution system with multiple harmonic loads based on hierarchical clustering and regression analysis. First, the utility harmonic impedance is determined by the dominant fluctuation filtering. Then, the utility harmonic voltage data are automatically clustered into different segments based on the hierarchical K‐means clustering, which does not require a given clustering number of harmonic data. Subsequently, the harmonic contribution of each data segment is calculated with the Bayesian partial least squares regression, hence providing an adaptive estimation of the optimal principal components. Finally, the total harmonic contribution of the concerned period is obtained by weighted summation according to the length of each harmonic data segment. Simulations are carried out on the IEEE 13‐bus and 69‐bus systems. The results confirm that the approach can adapt to the fluctuation of utility harmonic and produce assessment outcomes more accurately compared with some other methods.
Probabilistic power flow calculation using the Johnson system and Sobol's quasi‐random numbers
Authors: Zhang Libo , Cheng Haozhong , Zhang Shenxi , Zeng Pingliang , Yao Liangzhong
Published: June 2016

This study puts forward a probabilistic power flow calculation method based on the Johnson system and Sobol's quasi‐random numbers. The Johnson system is utilised to simulate the distribution function of one dimensional variable and model the correlation of multiple uncertainties with historical data of the uncertainties. The improved Sobol's quasi‐random number generator is adopted to produce the low‐discrepancy samples in Monte Carlo simulation. The accuracy of the Johnson system is compared with other modelling methods of uncertainties and the comparison of Sobol's quasi‐random numbers and other techniques, such as Latin hypercube sampling and simple random sampling are presented for the cases of IEEE 30‐bus system and IEEE 118‐bus system.
Fundamental frequency switching strategy for grid‐connected cascaded H‐bridge multilevel inverter to mitigate voltage harmonics at the point of common coupling
Authors: Hajizadeh Mehdi , Fathi Seyed Hamid
Published: June 2016

Cascaded H‐bridge multilevel inverter with isolated dc sources is a suitable choice as an interface between grid and distributed generation (DG) sources. The main duty of the interface inverter is to adapt voltage of the grid and DG source while active and reactive power exchange is also controlled by it. Conventional fundamental frequency switching methods have been studied so far only for quality improvement of the inverter output voltage. However, for the grid‐connected applications, voltage quality at the point of common coupling (PCC) is more important than the inverter output voltage. This study presents a modified harmonic mitigation fundamental frequency switching method for the grid‐connected cascaded H‐bridge multilevel inverters. The goal is to calculate optimum switching angles of the inverter which satisfy the standard limits for the total harmonic distortion and harmonic contents of the voltage waveform at PCC considering specifications of the grid. This is also to be achieved with minimum required amount of the coupling impedance. Genetic algorithm optimisation program based on the modified switching method is employed for a sample system including a three‐phase cascaded H‐bridge seven‐level inverter connected to a harmonic polluted grid. Computer simulation using Simulink/MATLAB is performed, the results of which confirm effectiveness of the proposed method.
Study on characteristics of magnetic memory testing signal based on the stress concentration field
Authors: Liu Bin , He Yao Y. , Zhang Hai , Fernandes Henrique , Fu Ying , Maldague Xavier
Published: June 2016

Metal magnetic memory testing technology has been effectively used in stress concentration areas and micro‐cracks detection of ferromagnetic metal components. However, due to the lack of profound theoretical basis and effective experimental research, the magnetic memory signal characteristics and magnetism quantitative relationship has not yet been determined. In this study, the full electronic potential magneto‐mechanical model is established which is using the norm conserving pseudo‐potential algorithm based on the first‐principle. The quantitative relationship is then calculated between the stress concentration and the magnetic memory signal. The calculation results show that the changes of the wave function, which result from the stress concentration in the solid band, are the fundamental cause of the magnetic memory phenomenon, and atomic magnetic moment, lattice constant and the magnetic flux leakage signal strength linearly changes as a function of stress trend. As the stress concentration reached the critical stress point, the lattice structure was damaged, and the magnetic memory signal had undergone mutation. In this study, the experimental results are consistent with the theoretical calculation results.
High-quality Thermodynamic Data on the Stability Changes of Proteins Upon Single-site Mutations
Authors: Pucci Fabrizio , Bourgeas Raphaël , Rooman Marianne
Published: June 2016

We have set up and manually curated a dataset containing experimental information on the impact of amino acid substitutions in a protein on its thermal stability. It consists of a repository of experimentally measured melting temperatures (Tm) and their changes upon point mutations (ΔTm) for proteins having a well-resolved x-ray structure. This high-quality dataset is designed for being used for the training or benchmarking of in silico thermal stability prediction methods. It also reports other experimentally measured thermodynamic quantities when available, i.e., the folding enthalpy (ΔH) and heat capacity (ΔCP) of the wild type proteins and their changes upon mutations (ΔΔH and ΔΔCP), as well as the change in folding free energy (ΔΔG) at a reference temperature. These data are analyzed in view of improving our insights into the correlation between thermal and thermodynamic stabilities, the asymmetry between the number of stabilizing and destabilizing mutations, and the difference in stabilization potential of thermostable versus mesostable proteins.
Superlattice periodicity and magnetic properties of Ba2FeMoO6/Ba0.5Sr0.5TiO3 system
Authors: Kim Kyeong-Won , Ghosh Siddhartha , Buvaev Sanal , Hebard Arthur F. , Norton David P.
Published: June 2016

Superlattice (SL) structures of Ba2FeMoO6/Ba0.5Sr0.5TiO3 were grown via pulsed laser deposition on high quality ultra-smooth SrTiO3 substrates. N number of ferroelectric Ba0.5Sr0.5TiO3 layers were grown on five layers of ferromagnetic Ba2FeMoO6 and their structural, magnetic, transport, and magneto-transport properties were examined, focusing on the effects of superlattice periodicity of Ba0.5Sr0.5TiO3 layers. XRD analysis of SLs proved their layered superlattice structure. Magnetic study of the SLs showed increment of saturation magnetization and decrease of Curie temperature when compared to magnetization of pure Ba2FeMoO6 thin film. Magneto-transport measurement showed the presence of negative magneto-resistance in all superlattice samples, similar to magneto-transport behavior of pure Ba2FeMoO6 thin film. Hall measurement and transport study showed a consistent increment of anomalous Hall effect and temperature dependent conductivity, respectively, with the number of Ba0.5Sr0.5TiO3 layers.