bluuebunny/crossref_metadata_2025 huggingface dataset:
The oncometabolite 2-hydroxyglutarate activates the mTOR signalling pathway
Authors: Carbonneau Mélissa , M. Gagné Laurence , Lalonde Marie-Eve , Germain Marie-Anne , Motorina Alena , Guiot Marie-Christine , Secco Blandine , Vincent Emma E. , Tumber Anthony , Hulea Laura , Bergeman Jonathan , Oppermann Udo , Jones Russell G. , Laplante Mathieu , Topisirovic Ivan , Petrecca Kevin , Huot Marc-Étienne , Mallette Frédérick A.
Published: September 2016

The identification of cancer-associated mutations in the tricarboxylic acid (TCA) cycle enzymes isocitrate dehydrogenases 1 and 2 (IDH1/2) highlights the prevailing notion that aberrant metabolic function can contribute to carcinogenesis. IDH1/2 normally catalyse the oxidative decarboxylation of isocitrate into α-ketoglutarate (αKG). In gliomas and acute myeloid leukaemias, IDH1/2 mutations confer gain-of-function leading to production of the oncometabolite R-2-hydroxyglutarate (2HG) from αKG. Here we show that generation of 2HG by mutated IDH1/2 leads to the activation of mTOR by inhibiting KDM4A, an αKG-dependent enzyme of the Jumonji family of lysine demethylases. Furthermore, KDM4A associates with the DEP domain-containing mTOR-interacting protein (DEPTOR), a negative regulator of mTORC1/2. Depletion of KDM4A decreases DEPTOR protein stability. Our results provide an additional molecular mechanism for the oncogenic activity of mutant IDH1/2 by revealing an unprecedented link between TCA cycle defects and positive modulation of mTOR function downstream of the canonical PI3K/AKT/TSC1-2 pathway.
PKA inhibits WNT signalling in adrenal cortex zonation and prevents malignant tumour development
Authors: Drelon Coralie , Berthon Annabel , Sahut-Barnola Isabelle , Mathieu Mickaël , Dumontet Typhanie , Rodriguez Stéphanie , Batisse-Lignier Marie , Tabbal Houda , Tauveron Igor , Lefrançois-Martinez Anne-Marie , Pointud Jean-Christophe , Gomez-Sanchez Celso E. , Vainio Seppo , Shan Jingdong , Sacco Sonia , Schedl Andreas , Stratakis Constantine A. , Martinez Antoine , Val Pierre
Published: September 2016

Adrenal cortex physiology relies on functional zonation, essential for production of aldosterone by outer zona glomerulosa (ZG) and glucocorticoids by inner zona fasciculata (ZF). The cortex undergoes constant cell renewal, involving recruitment of subcapsular progenitors to ZG fate and subsequent lineage conversion to ZF identity. Here we show that WNT4 is an important driver of WNT pathway activation and subsequent ZG differentiation and demonstrate that PKA activation prevents ZG differentiation through WNT4 repression and WNT pathway inhibition. This suggests that PKA activation in ZF is a key driver of WNT inhibition and lineage conversion. Furthermore, we provide evidence that constitutive PKA activation inhibits, whereas partial inactivation of PKA catalytic activity stimulates β-catenin-induced tumorigenesis. Together, both lower PKA activity and higher WNT pathway activity lead to poorer prognosis in adrenocortical carcinoma (ACC) patients. These observations suggest that PKA acts as a tumour suppressor in the adrenal cortex, through repression of WNT signalling.
The importance of copy number variation in congenital heart disease
Authors: Costain Gregory , Silversides Candice K , Bassett Anne S
Published: September 2016

Congenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD. These include de novo and inherited variants at established (chromosome 22q11.2), emerging (chromosome 1q21.1), and novel loci across the genome. Variable expression of rare CNVs provides support for the notion of a genetic spectrum of CHD that crosses traditional anatomic classification boundaries. Clinical genetic testing using genome-wide technologies (e.g., chromosomal microarray analysis) is increasingly employed in prenatal, paediatric and adult settings. CNV discoveries in CHD have translated to changes to clinical management, prognostication and genetic counselling. The convergence of findings at individual gene and at pathway levels is shedding light on the mechanisms that govern human cardiac morphogenesis. These clinical and research advances are helping to inform whole-genome sequencing, the next logical step in delineating the genetic architecture of CHD.
Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines
Authors: Wilson Stephen , Qi Jianfei , Filipp Fabian V.
Published: September 2016

Sequence motifs are short, recurring patterns in DNA that can mediate sequence-specific binding for proteins such as transcription factors or DNA modifying enzymes. The androgen response element (ARE) is a palindromic, dihexameric motif present in promoters or enhancers of genes targeted by the androgen receptor (AR). Using chromatin immunoprecipitation sequencing (ChIP-Seq) we refined AR-binding and AREs at a genome-scale in androgen-insensitive and androgen-responsive prostate cancer cell lines. Model-based searches identified more than 120,000 ChIP-Seq motifs allowing for expansion and refinement of the ARE. We classified AREs according to their degeneracy and their transcriptional involvement. Additionally, we quantified ARE utilization in response to somatic copy number amplifications, AR splice-variants, and steroid treatment. Although imperfect AREs make up 99.9% of the motifs, the degree of degeneracy correlates negatively with validated transcriptional outcome. Weaker AREs, particularly ARE half sites, benefit from neighboring motifs or cooperating transcription factors in regulating gene expression. Taken together, ARE full sites generate a reliable transcriptional outcome in AR positive cells, despite their low genome-wide abundance. In contrast, the transcriptional influence of ARE half sites can be modulated by cooperating factors.
Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view
Authors: Turroni Silvia , Fiori Jessica , Rampelli Simone , Schnorr Stephanie L. , Consolandi Clarissa , Barone Monica , Biagi Elena , Fanelli Flaminia , Mezzullo Marco , Crittenden Alyssa N. , Henry Amanda G. , Brigidi Patrizia , Candela Marco
Published: September 2016

The recent characterization of the gut microbiome of traditional rural and foraging societies allowed us to appreciate the essential co-adaptive role of the microbiome in complementing our physiology, opening up significant questions on how the microbiota changes that have occurred in industrialized urban populations may have altered the microbiota-host co-metabolic network, contributing to the growing list of Western diseases. Here, we applied a targeted metabolomics approach to profile the fecal metabolome of the Hadza of Tanzania, one of the world’s few remaining foraging populations, and compared them to the profiles of urban living Italians, as representative of people in the post-industrialized West. Data analysis shows that during the rainy season, when the diet is primarily plant-based, Hadza are characterized by a distinctive enrichment in hexoses, glycerophospholipids, sphingolipids, and acylcarnitines, while deplete in the most common natural amino acids and derivatives. Complementary to the documented unique metagenomic features of their gut microbiome, our findings on the Hadza metabolome lend support to the notion of an alternate microbiome configuration befitting of a nomadic forager lifestyle, which helps maintain metabolic homeostasis through an overall scarcity of inflammatory factors, which are instead highly represented in the Italian metabolome.
Oscillation of mineral compositions in Core SG-1b, western Qaidam Basin, NE Tibetan Plateau
Authors: Fang Xiaomin , Li Minghui , Wang Zhengrong , Wang Jiuyi , Li Jiao , Liu Xiaoming , Zan Jinbo
Published: September 2016

Uplift of the Tibetan Plateau since the Late Miocene has greatly affected the nature of sediments deposited in the Qaidam Basin. However, due to the scarcity of continuously dated sediment records, we know little about how minerals responded to this uplift. In order to understand this response, we here present results from the high-resolution mineral profile from a borehole (7.3–1.6 Ma) in the Basin, which shows systematic oscillations of various evaporite and clay minerals that can be linked to the variation of regional climate and tectonic history. In particular, x-ray diffraction (XRD) analyses show that carbonate minerals consist mainly of calcite and aragonite, with minor ankerite and dolomite. Evaporates consist of gypsum, celesite and halite. Clay minerals are principally Fe-Mg illite, mixed layers of illite/smectite and chlorite, with minor kaolinite and smectite. Following implications can be drawn from the oscillations of these minerals phases: (a) the paleolake was brackish with high salinity after 7.3 Ma, while an abrupt change in the chemical composition of paleolake water (e.g. Mg/Ca ratio, SO42− concentration, salinity) occurred at 3.3 Ma; (b) the three changes at ~6.0 Ma, 4.5–4.1 Ma and 3.3 Ma were in response to rapid erosions/uplift of the basin; (c) pore water or fluid was Fe/Mg-rich in 7.3–6.0 Ma, Mg-rich in 6.0–4.5 Ma, and K-rich in 4.1–1.6 Ma; and (d) evaporation rates were high, but weaker than today’s.
Neuroprotective effect of docosahexaenoic acid nanoemulsion on erectile function in a rat model of bilateral cavernous nerve injury
Authors: Liao Chun-Hou , Wu Yi-No , Chen Bin-Huei , Lin Ying-Hung , Ho Hsiu-O , Chiang Han-Sun
Published: September 2016

There is an unmet need for treatment of erectile dysfunction resulting from radical prostatectomy and cavernous nerve (CN) injury. Given the neuroprotective properties of docosahexaenoic acid (DHA), we investigated its effect on penile functional and structural recovery in a rat model of bilateral cavernous nerve injury. Rats were subject to CN injury and received intraperitoneal administration of either vehicle or a DHA nanoemulsion (nano-DHA) at 10, 50, or 250 μg/kg. Functional testing and histological analyses were performed at 28 days post-injury. The maximum intracavernosal pressure (ICP) and other measures of erectile function were significantly higher in the nano-DHA groups than in the vehicle group (p < 0.05). The ratio of area of expression of neuronal nitric oxide synthase (nNOS)/β-III tubulin, numbers of axon and smooth muscle cell content were significantly higher in the 50 μg/kg nano-DHA group than in the vehicle group (p < 0.05). A qualitative increase in the smooth muscle cells/collagen ratio and decrease in apoptosis was observed in the nano-DHA groups relative to the vehicle group: however, these differences were not statistically significant. Our data demonstrate that nano-DHA, particularly the 50 μg/kg regimen, improves erectile function after bilateral CN injury in rats by neuroprotection and other anti-fibrotic and anti-apoptotic mechanisms.
Regulatory T cells control strain specific resistance to Experimental Autoimmune Prostatitis
Authors: Breser Maria L. , Lino Andreia C. , Motrich Ruben D. , Godoy Gloria J. , Demengeot Jocelyne , Rivero Virginia E.
Published: September 2016

Susceptibility to autoimmune diseases results from the encounter of a complex and long evolved genetic context with a no less complex and changing environment. Major actors in maintaining health are regulatory T cells (Treg) that primarily dampen a large subset of autoreactive lymphocytes escaping thymic negative selection. Here, we directly asked whether Treg participate in defining susceptibility and resistance to Experimental Autoimmune Prostatitis (EAP). We analyzed three common laboratory strains of mice presenting with different susceptibility to autoimmune prostatitis upon immunization with prostate proteins. The NOD, the C57BL/6 and the BALB/c mice that can be classified along a disease score ranging from severe, mild and to undetectable, respectively. Upon mild and transient depletion of Treg at the induction phase of EAP, each model showed an increment along this score, most remarkably with the BALB/c mice switching from a resistant to a susceptible phenotype. We further show that disease associates with the upregulation of CXCR3 expression on effector T cells, a process requiring IFNγ. Together with recent advances on environmental factors affecting Treg, these findings provide a likely cellular and molecular explanation to the recent rise in autoimmune diseases incidence.
Enteric neurons from Parkinson’s disease patients display ex vivo aberrations in mitochondrial structure
Authors: Baumuratov A. S. , Antony P. M. A. , Ostaszewski M. , He F. , Salamanca L. , Antunes L. , Weber J. , Longhino L. , Derkinderen P. , Koopman W. J. H. , Diederich N. J.
Published: September 2016

Based on autopsy material mitochondrial dysfunction has been proposed being part of the pathophysiological cascade of Parkinson’s disease (PD). However, in living patients, evidence for such dysfunction is scarce. As the disease presumably starts at the enteric level, we studied ganglionic and mitochondrial morphometrics of enteric neurons. We compared 65 ganglia from 11 PD patients without intestinal symptoms and 41 ganglia from 4 age-matched control subjects. We found that colon ganglia from PD patients had smaller volume, contained significantly more mitochondria per ganglion volume, and displayed a higher total mitochondrial mass relative to controls. This suggests involvement of mitochondrial dysfunction in PD at the enteric level. Moreover, in PD patients the mean mitochondrial volume declined in parallel with motor performance. Ganglionic shrinking was evident in the right but not in the left colon. In contrast, mitochondrial changes prevailed in the left colon suggesting that a compensatory increase in mitochondrial mass might counterbalance mitochondrial dysfunction in the left colon but not in the right colon. Reduction in ganglia volume and combined mitochondrial morphometrics had both predictive power to discriminate between PD patients and control subjects, suggesting that both parameters could be used for early discrimination between PD patients and healthy individuals.
Isogyres – Manifestation of Spin-orbit interaction in uniaxial crystal: A closed-fringe Fourier analysis of conoscopic interference
Authors: Samlan C. T. , Naik Dinesh N. , Viswanathan Nirmal K.
Published: September 2016

Discovered in 1813, the conoscopic interference pattern observed due to light propagating through a crystal, kept between crossed polarizers, shows isochromates and isogyres, respectively containing information about the dynamic and geometric phase acquired by the beam. We propose and demonstrate a closed-fringe Fourier analysis method to disentangle the isogyres from the isochromates, leading us to the azimuthally varying geometric phase and its manifestation as isogyres. This azimuthally varying geometric phase is shown to be the underlying mechanism for the spin-to-orbital angular momentum conversion observed in a diverging optical field propagating through a z-cut uniaxial crystal. We extend the formalism to study the optical activity mediated uniaxial-to-biaxial transformation due to a weak transverse electric field applied across the crystal. Closely associated with the phase and polarization singularities of the optical field, the formalism enables us to understand crystal optics in a new way, paving the way to anticipate several emerging phenomena.
Light-tunable Fano resonance in metal-dielectric multilayer structures
Authors: Hayashi S. , Nesterenko D. V. , Rahmouni A. , Ishitobi H. , Inouye Y. , Kawata S. , Sekkat Z.
Published: September 2016

High-Q optical Fano resonances realized in a variety of plasmonic nanostructures and metamaterials are very much promising for the development of new potent photonic devices, such as optical sensors and switches. One of the key issues in the development is to establish ways to effectively modulate the Fano resonance by external perturbations. Dynamic tuning of the Fano resonance applying the mechanical stress and electric fields has already been demonstrated. Here, we demonstrate another way of tuning, i.e., photo-tuning of the Fano resonance. We use a simple metal-dielectric multilayer structure that exhibits a sharp Fano resonance originating from coupling between a surface plasmon polariton mode and a planar waveguide mode. Using a dielectric waveguide doped with azo dye molecules that undergo photoisomerization, we succeeded in shifting the Fano resonance thorough photo-modulation of the propagation constant of the waveguide mode. The present work demonstrates the feasibility of photo-tuning of the Fano resonance and opens a new avenue towards potential applications of the Fano resonance.
Bexarotene targets autophagy and is protective against thromboembolic stroke in aged mice with tauopathy
Authors: Huuskonen Mikko T. , Loppi Sanna , Dhungana Hiramani , Keksa-Goldsteine Velta , Lemarchant Sighild , Korhonen Paula , Wojciechowski Sara , Pollari Eveliina , Valonen Piia , Koponen Juho , Takashima Akihiko , Landreth Gary , Goldsteins Gundars , Malm Tarja , Koistinaho Jari , Kanninen Katja M.
Published: September 2016

Stroke is a highly debilitating, often fatal disorder for which current therapies are suitable for only a minor fraction of patients. Discovery of novel, effective therapies is hampered by the fact that advanced age, primary age-related tauopathy or comorbidities typical to several types of dementing diseases are usually not taken into account in preclinical studies, which predominantly use young, healthy rodents. Here we investigated for the first time the neuroprotective potential of bexarotene, an FDA-approved agent, in a co-morbidity model of stroke that combines high age and tauopathy with thromboembolic cerebral ischemia. Following thromboembolic stroke bexarotene enhanced autophagy in the ischemic brain concomitantly with a reduction in lesion volume and amelioration of behavioral deficits in aged transgenic mice expressing the human P301L-Tau mutation. Inin vitrostudies bexarotene increased the expression of autophagy markers and reduced autophagic flux in neuronal cells expressing P301L-Tau. Bexarotene also restored mitochondrial respiration deficits in P301L-Tau neurons. These newly described actions of bexarotene add to the growing amount of compelling data showing that bexarotene is a potent neuroprotective agent, and identify a novel autophagy-modulating effect of bexarotene.
Comparative analysis of linker histone H1, MeCP2, and HMGD1 on nucleosome stability and target site accessibility
Authors: Riedmann Caitlyn , Fondufe-Mittendorf Yvonne N.
Published: September 2016

Chromatin architectural proteins (CAPs) bind the entry/exit DNA of nucleosomes and linker DNA to form higher order chromatin structures with distinct transcriptional outcomes. How CAPs mediate nucleosome dynamics is not well understood. We hypothesize that CAPs regulate DNA target site accessibility through alteration of the rate of spontaneous dissociation of DNA from nucleosomes. We investigated the effects of histone H1, high mobility group D1 (HMGD1), and methyl CpG binding protein 2 (MeCP2), on the biophysical properties of nucleosomes and chromatin. We show that MeCP2, like the repressive histone H1, traps the nucleosome in a more compact mononucleosome structure. Furthermore, histone H1 and MeCP2 hinder model transcription factor Gal4 from binding to its cognate DNA site within the nucleosomal DNA. These results demonstrate that MeCP2 behaves like a repressor even in the absence of methylation. Additionally, MeCP2 behaves similarly to histone H1 and HMGD1 in creating a higher-order chromatin structure, which is susceptible to chromatin remodeling by ISWI. Overall, we show that CAP binding results in unique changes to nucleosome structure and dynamics.
Genetically Low Vitamin D Levels, Bone Mineral Density, and Bone Metabolism Markers: a Mendelian Randomisation Study
Authors: Li Shan-Shan , Gao Li-Hong , Zhang Xiao-Ya , He Jin-We , Fu Wen-Zhen , Liu Yu-Juan , Hu Yun-Qiu , Zhang Zhen-Lin
Published: September 2016

Low serum 25-hydroxyvitamin D (25OHD) is associated with osteoporosis and osteoporotic fracture, but it remains uncertain whether these associations are causal. We conducted a Mendelian randomization (MR) study of 1,824 postmenopausal Chinese women to examine whether the detected associations between serum 25OHD and bone mineral density (BMD) and bone metabolism markers were causal. In observational analyses, total serum 25OHD was positively associated with BMD at lumbar spine (P = 0.003), femoral neck (P = 0.006) and total hip (P = 0.005), and was inversely associated with intact parathyroid hormone (PTH) (P = 8.18E-09) and procollagen type 1 N-terminal propeptide (P1NP) (P = 0.020). By contract, the associations of bioavailable and free 25OHD with all tested outcomes were negligible (allP > 0.05). The use of four single nucleotide polymorphisms, GC-rs2282679, NADSYN1-rs12785878, CYP2R1-rs10741657 and CYP24A1-rs6013897, as candidate instrumental variables in MR analyses showed that none of the two stage least squares models provided evidence for associations between serum 25OHD and either BMD or bone metabolism markers (all P > 0.05). We suggest that after controlling for unidentified confounding factors in MR analyses, the associations between genetically low serum 25OHD and BMD and bone metabolism markers are unlikely to be causal.
Fungal Aflatoxins Reduce Respiratory Mucosal Ciliary Function
Authors: Lee Robert J. , Workman Alan D. , Carey Ryan M. , Chen Bei , Rosen Phillip L. , Doghramji Laurel , Adappa Nithin D. , Palmer James N. , Kennedy David W. , Cohen Noam A.
Published: September 2016

Aflatoxins are mycotoxins secreted byAspergillus flavus, which can colonize the respiratory tract and cause fungal rhinosinusitis or bronchopulmonary aspergillosis.A. flavusis the second leading cause of invasive aspergillosis worldwide. Because many respiratory pathogens secrete toxins to impair mucociliary immunity, we examined the effects of acute exposure to aflatoxins on airway cell physiology. Using air-liquid interface cultures of primary human sinonasal and bronchial cells, we imaged ciliary beat frequency (CBF), intracellular calcium, and nitric oxide (NO). Exposure to aflatoxins (0.1 to 10 μM; 5 to 10 minutes) reduced baseline (~6–12%) and agonist-stimulated CBF. Conditioned media (CM) fromA. fumigatus,A. niger, andA. flavuscultures also reduced CBF by ~10% after 60 min exposure, but effects were blocked by an anti-aflatoxin antibody only withA. flavusCM. CBF reduction required protein kinase C but was not associated with changes in calcium or NO. However, AFB2reduced NO production by ~50% during stimulation of the ciliary-localized T2R38 receptor. Using a fluorescent reporter construct expressed in A549 cells, we directly observed activation of PKC activity by AFB2. Aflatoxins secreted by respiratoryA. flavusmay impair motile and chemosensory functions of airway cilia, contributing to pathogenesis of fungal airway diseases.
Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
Authors: Feng Chenchen , Zhang Jian , Li Xuecang , Ai Bo , Han Junwei , Wang Qiuyu , Wei Taiming , Xu Yong , Li Meng , Li Shang , Song Chao , Li Chunquan
Published: September 2016

Metabolic pathway analysis is a popular strategy for comprehensively researching metabolites and genes of interest associated with specific diseases. However, the traditional pathway identification methods do not accurately consider the combined effect of these interesting molecules and neglects expression correlations or topological features embedded in the pathways. In this study, we propose a powerful method, Subpathway-CorSP, for identifying metabolic subpathway regions. This method improved on original pathway identification methods by using a subpathway identification strategy and emphasizing expression correlations between metabolites and genes of interest based on topological features within the metabolic pathways. We analyzed a prostate cancer data set and its metastatic sub-group data set with detailed comparison of Subpathway-CorSP with four traditional pathway identification methods. Subpathway-CorSP was able to identify multiple subpathway regions whose entire corresponding pathways were not detected by traditional pathway identification methods. Further evidences indicated that Subpathway-CorSP provided a robust and efficient way of reliably recalling cancer-related subpathways and locating novel subpathways by the combined effect of metabolites and genes. This was a novel subpathway strategy based on systematically considering expression correlations and topological features between metabolites and genes of interest within given pathways.
Rational engineering of a virulence gene from Mycobacterium tuberculosis facilitates proteomic analysis of a natural protein N-terminus
Authors: Reyna Cristal , Mba Medie Felix , Champion Matthew M. , Champion Patricia A.
Published: September 2016

Mass spectrometry (MS) for the detection of proteins is an indispensable tool for evaluating the biological processes of the proteome. Proteomics frequently requires proteolysis of proteins into peptide fragments. Proteins can be refractory to ideal proteolysis at the sequence level rendering them difficult to analyze by routine proteomics methods. EsxA (ESAT-6, Early Secreted Antigen, 6kDa) is a major virulence determinant of Mycobacterium tuberculosis, the cause of human tuberculosis. EsxA is routinely used to evaluate mycobacterial virulence in the laboratory and as a biomarker for tuberculosis in humans. The sequence of EsxA hinders deeper MS analysis beyond routine detection. Here we engineer the sequence of EsxA to add desirable tryptic properties aimed at improving complex MS analysis. We demonstrate that EsxA variants are amenable to MS analysis and remain functional in established in vitro and ex vivo assays of Esx-1-function. We provide the first demonstration of molecular engineering to specifically improve MS analysis of individual microbial proteins.
Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples
Authors: Zhu Jing , Deane Natasha G. , Lewis Keeli B. , Padmanabhan Chandrasekhar , Washington M. Kay , Ciombor Kristen K. , Timmers Cynthia , Goldberg Richard M. , Beauchamp R. Daniel , Chen Xi
Published: September 2016

Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter®and Affymetrix GeneChip®Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.
Optical thermometry based on level anticrossing in silicon carbide
Authors: Anisimov A. N. , Simin D. , Soltamov V. A. , Lebedev S. P. , Baranov P. G. , Astakhov G. V. , Dyakonov V.
Published: September 2016

We report a giant thermal shift of 2.1 MHz/K related to the excited-state zero-field splitting in the silicon vacancy centers in 4H silicon carbide. It is obtained from the indirect observation of the optically detected magnetic resonance in the excited state using the ground state as an ancilla. Alternatively, relative variations of the zero-field splitting for small temperature differences can be detected without application of radiofrequency fields, by simply monitoring the photoluminescence intensity in the vicinity of the level anticrossing. This effect results in an all-optical thermometry technique with temperature sensitivity of 100 mK/Hz1/2 for a detection volume of approximately 10−6 mm3. In contrast, the zero-field splitting in the ground state does not reveal detectable temperature shift. Using these properties, an integrated magnetic field and temperature sensor can be implemented on the same center.
Surface and stratigraphic elemental analysis of an ancient Egyptian cartonnage using Laser-Induced Breakdown Spectroscopy (LIBS)
Authors: Nassef O. Aied , Ahmed Harby E. , Harith M. A.
Published: September 2016

An archeological Egyptian cartonnage dating back to the Greco-Roman period around the third century BC was elementally analyzedviathe sample-friendly technique, Laser Induced Breakdown Spectroscopy (LIBS).
Light-induced spatial separation of charges toward different crystal facets of square-like WO3
Authors: Gong Huihua , Ma Ruirui , Mao Fang , Liu Kewei , Cao Hongmei , Yan Hongjian
Published: September 2016

Light-induced preferential migration of electrons and holes to the minor (200) and (020) facets and the dominant (002) facets of square-like WO3, respectively, resulted in the square-like WO3nanoplates with Pt loaded mainly on dominant (002) facets shows higher photocatalytic activity than that Pt loaded on the minor facets.
Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation
Authors: Yu H. , Qiu X. , Behzad A. R. , Musteata V. , Smilgies D.-M. , Nunes S. P. , Peinemann K.-V.
Published: September 2016

Membranes with a hierarchical porous structure and an isoporous skin could be manufactured from a block copolymer blend by pure solvent evaporation (drying induced phase separation).
Attachment of composite porous supra-particles to air–water and oil–water interfaces: theory and experiment
Authors: Paunov Vesselin N. , Al-Shehri Hamza , Horozov Tommy S.
Published: September 2016

We developed and tested a theoretical model connecting the wettabilities of fluid-infused porous supra-particles and their smaller particle building blocks at a fluid–liquid interface.
Two-dimensional exciton properties in monolayer semiconducting phosphorus allotropes
Authors: Villegas Cesar E. P. , Rodin A. S. , Carvalho Alexandra , Rocha A. R.
Published: September 2016

Ab initiomany-body perturbation theory calculations for the excitonic properties of two-dimensional blue and black phosphorus allotropes are performed and validated with hydrogenic effective models.
Insights into the mechanism for ring-opening polymerization of lactide catalyzed by Zn(C6F5)2/organic superbase Lewis pairs
Authors: Li Xiao-Qing , Wang Bin , Ji He-Yuan , Li Yue-Sheng
Published: September 2016

A plausible mechanism for ring-opening polymerization of lactide catalyzed by Zn(C6F5)2-based Lewis pairs was proposed based on in situ NMR and MALDI-TOF MS analyses. Several experimental results show very good consistency with the proposed mechanism.
Dehydrogenation of benzyl alcohol with N2O as the hydrogen acceptor catalyzed by the rhodium(i) carbene complex: insights from quantum chemistry calculations
Authors: Xie Hujun , Li Yang , Huang Lvtao , Nong Fangli , Ren Gerui , Fan Ting , Lei Qunfang , Fang Wenjun
Published: September 2016

Three cycles were considered for the formation of benzaldehyde, benzyl benzoate and benzoic acid.
Synthesis of three series of ruthenium tris-diimine complexes containing acridine-based π-extended ligands using an efficient “chemistry on the complex” approach
Authors: Lefebvre Jean-François , Saadallah Dounia , Traber Philipp , Kupfer Stephan , Gräfe Stefanie , Dietzek Benjamin , Baussanne Isabelle , De Winter Julien , Gerbaux Pascal , Moucheron Cécile , Chavarot-Kerlidou Murielle , Demeunynck Martine
Published: September 2016

Novel multi-step chemistry on the complex strategy.
Gold nanoparticles supported by imidazolium-based porous organic polymers for nitroarene reduction
Authors: Su Yanqing , Li Xiaoju , Wang Yangxin , Zhong Hong , Wang Ruihu
Published: September 2016

Gold nanoparticles supported by imidazolium-based porous organic polymers exhibit higher catalytic activity, selectivity and recyclability than those supported by a non-ionic analogue.
Aerosol synthesis of phase-controlled iron–graphene nanohybrids through FeOOH nanorod intermediates
Authors: Lv X. S. , Qiu Y. , Wang Z. Y. , Jiang G. M. , Chen Y. T. , Xu X. H. , Hurt R. H.
Published: September 2016

We present a continuous method for hybridizing Fe-based nanoparticles with carbon in the form of graphene-encapsulated Fe-based particles with core–shell symmetry that allows control of iron particle size, shape, phase, and stability.
A kinetic mechanism of repair of DNA containing α-anomeric deoxyadenosine by human apurinic/apyrimidinic endonuclease 1
Authors: Timofeyeva N. A. , Fedorova O. S.
Published: September 2016

The structure of αdA promotes its recognition by APE1 but dramatically impedes formation of a catalytically competent complex.
Processable 2D materials beyond graphene: MoS2liquid crystals and fibres
Authors: Jalili Rouhollah , Aminorroaya-Yamini Sima , Benedetti Tania M. , Aboutalebi Seyed Hamed , Chao Yunfeng , Wallace Gordon G. , Officer David L.
Published: September 2016

Engineered molybdenum disulfide (MoS2) crystals with preferred orientation can readily exfoliate into ultra-large MoS2sheets that form liquid crystalline dispersions in water.
Traceless reductive ligation at a tryptophan site: a facile access to β-hydroxytryptophan appended peptides
Authors: Bajaj Kiran , Sakhuja Rajeev , Pillai Girinath G.
Published: September 2016

One-pot methodology (reduction & O to N migration); synthesis of β-hydroxytryptophan appended native peptides; computational support for the mechanism.
Screening of Neu5Acα(2–6)gal isomer preferences of siglecs with a sialic acid microarray
Authors: Yadav Rohan , Leviatan Ben-Arye Shani , Subramani Balamurugan , Padler-Karavani Vered , Kikkeri Raghavendra
Published: September 2016

The synthesis of Neu5Acα(2–6)Gal structural analogs showed distinct binding patterns with conserved siglecs (hCD22 and mCD22) compared to rapid evolving siglecs (Siglecs -3 & -10).
An Ni–PyBisulidine complex for the asymmetric hydrophosphonylation of aldehydes
Authors: Zeng Youmao , Deng Ping , Zhang Shixiong , Yan Hong , Liang Guojuan , Xiong Yan , Zhou Hui
Published: September 2016

A novel Ni–PyBisulidine complex has been developed for the asymmetric hydrophosphonylation of aldehydes.
Structurally defined nanographene-containing conjugated polymers for high quality dispersions and optoelectronic applications
Authors: Wang Po-I. , Pisula Wojciech , Müllen Klaus , Liaw Der-Jang
Published: September 2016

A new conjugated polymer with nanographenes shows excellent dispersibility in N-cyclohexyl-2-pyrrolidone and remarkable emission from exfoliated nanographenes.
Facile synthesis of annulated heterocyclic benzo[kl]acridine derivatives via one-pot N–H/C–H coupling
Authors: Zagranyarski Yulian , Skabeev Artem , Ma Yingjie , Müllen Klaus , Li Chen
Published: September 2016

A facile and efficient synthesis of benzo[kl]acridines was developed based on a domino reaction via a combinatorial catalyst approach.
Tailoring the electronic properties among oxoarsine, arsinoyl and arsine oxide isomers: the simplest molecular systems with an arsenic–oxygen bond
Authors: Viana Rommel B.
Published: September 2016

The main goal of this investigation is to understand the reaction pathways and the electronic and spectroscopy properties of AsOHn radicals (n = 0–3), which are some of the simplest compound models with an arsenic–oxygen bond.
Mn2+ oxidation, playing counteractive role in electro-oxidation of ammonia, hinders the generation of free chlorine
Authors: Ma Xiaoxia , Tang Jinjing , Yuan Yunan , Liu Zuohua , Tao Changyuan
Published: September 2016

The influence of coexisting metal ions on NH3 removal and the concentration changes of intermediate products was explored. The removal rate of NH3 reached 93.57% by removing Mn2+ which seriously affected NH3 removal.
The synthesis of iminothiophenone-fused quinolines and evaluation of their serendipitous reactions
Authors: Shiri Morteza , Faghihi Zeinab , Oskouei Hossein A. , Heravi Majid M. , Fazelzadeh Shima , Notash Behrouz
Published: September 2016

The novel synthesis of tricyclic 2-(cyclohexylimino)thieno[2,3-b]quinolin-3(2H)-ones from the reaction of 2-mercaptoquinoline-3-carbaldehydes and isocyanides in methanol without the use of any additive is described.
Magnetic combined cross-linked enzyme aggregates of horseradish peroxidase and glucose oxidase: an efficient biocatalyst for dye decolourization
Authors: Zhou Liya , Tang Wei , Jiang Yanjun , Ma Li , He Ying , Gao Jing
Published: September 2016

In this study, the magnetic combined cross-linked enzyme aggregates (combi-CLEAs) of glucose oxidase (GOD) and horseradish peroxidase (HRP) were designed and prepared successfully.
Low-temperature gas–solid carbonation of magnesia and magnesium hydroxide promoted by non-immersive contact with water
Authors: Highfield James , Chen Jason , Haghighatlari Mojtaba , Åbacka Jacob , Zevenhoven Ron
Published: September 2016

From high-pressure gas–solid thermogravimetry, the presence of water at high relative humidity (>25% RH) caused a drastic acceleration in the rate of CO2 absorption into MgO and Mg(OH)2 producing magnesite and hydrocarbonate precursors below 200 °C.
Carriers for nano zerovalent iron (nZVI): synthesis, application and efficiency
Authors: Adusei-Gyamfi Junias , Acha Victor
Published: September 2016

An in-depth study accessing all possible carriers used for the synthesis of nZVI and their effect on pollution remediation.
MOF nanoparticles of MIL-68(Al), MIL-101(Cr) and ZIF-11 for thin film nanocomposite organic solvent nanofiltration membranes
Authors: Echaide-Górriz Carlos , Sorribas Sara , Téllez Carlos , Coronas Joaquín
Published: September 2016

MOF nanoparticles of MIL-68(Al), MIL-101(Cr) and ZIF-11 for thin film nanocomposite organic solvent nanofiltration.
Fabrication and corrosion resistance properties of super-hydrophobic coatings on iron and steel substrates by creating micro-/nano-structures and modifying rough surfaces
Authors: Lv Dandan , Shao Hongfei , Gao Xiang , Lu Ke , Lu Haifeng , Ma Houyi
Published: September 2016

Super-hydrophobic surfaces are usually prepared by manipulating the surface roughness and surface chemistry of various materials.
Chitosan functionalized thermosponge nano-carriers for prolonged retention and local delivery of chymopapain at the nucleus pulposus in porcine discs ex vivo
Authors: Choi Won Il , Sahu Abhishek , Vilos Cristian , Lee Jong Hyun , Kim Sunghyun , Hong Young Ki , Sul Donggeun , Hwang Sun Wook , Lee Sang Heon , Tae Giyoong
Published: September 2016

Chitosan functionalized nano-carriers could function as an efficient delivery carrier for local administration of chymopapain to reduce the side effect associated with chemonucleolysis.
Zinc-based deep eutectic solvent-mediated hydroxylation and demethoxylation of lignin for the production of wood adhesive
Authors: Hong Shu , Lian Hailan , Sun Xiang , Pan Dong , Carranza Arturo , Pojman John A. , Mota-Morales Josué D.
Published: September 2016

Choline chloride–ZnCl2 deep-eutectic solvent (ChCl–ZnCl2 DES), mole ratio 1 : 2, was used to improve the chemical reactivity of wheat straw alkali lignin under different temperatures and times of pretreatment.
Superhydrophilic cubic boron nitride films
Authors: Teii Kungen , Kawakami Shinji , Matsumoto Seiichiro
Published: September 2016

Preparation of superhydrophilic cubic boron nitride (cBN) films with contact angles of polar and apolar liquids of almost zero degree.
Bio-inspired synthesis of hybrid tube-like structures based on CaCO3 and type I-collagen
Authors: Tovani C. B. , Zancanela D. C. , Faria A. N. , Ciancaglini P. , Ramos A. P.
Published: September 2016

Tube-like hybrid particles based on calcium carbonate, a biocompatible mineral, and collagen, enhance osteoblasts viability.
Facile synthesis of a nickel vanadate/Ni composite and its electrochemical performance as an anode for lithium ion batteries
Authors: Li Yang , Kong Ling-Bin , Liu Mao-Cheng , Kang Long
Published: September 2016

Ni3V2O8/Ni composites are synthesized by a simple hydrothermal route, and show high-rate capability and outstanding long-life cycling stability as a new anode material for Li-ion batteries.
Improvement of corrosion resistance and magnetic properties for sintered NdFeB by alumina sol-containing conversion film
Authors: Cao Rui , Zhu Liqun , Liu Huicong , Yang Xin , Nan Haiyang , Li Weiping
Published: September 2016

Formation of alumina sol conversion film by using the chemical activity of NdFeB magnets.
Multiple functionalization of tungsten disulfide inorganic nanotubes by covalently grafted conductive polythiophenes
Authors: Ben Ishay Rivka , Harel Yifat , Lavi Ronit , Lellouche Jean-Paul
Published: September 2016

Covalently grafted nanometric polythiophene adlayers have been generated towards morphologically well-defined core–shell WS2 INTs/polymer composites achieving high charge conductivity.
Pd(0) supported on N-doped graphene quantum dot modified cellulose as an efficient catalyst for the green reduction of nitroaromatics
Authors: Keshipour Sajjad , Adak Kamran
Published: September 2016

A new efficient catalyst was introduced for the green reduction of nitroaromatics.
Enhanced visible light induced photocatalytic activity on the degradation of organic pollutants by SnO nanoparticle decorated hierarchical ZnO nanostructures
Authors: Harish S. , Archana J. , Navaneethan M. , Silambarasan A. , Nisha K. D. , Ponnusamy S. , Muthamizhchelvan C. , Ikeda H. , Aswal D. K. , Hayakawa Y.
Published: September 2016

One (1D) and two-dimensional (2D) nanostructures of zinc oxide and tin oxide (ZnO/SnO) nanocomposites were synthesized by a hydrothermal method using ethylenediamine (EDA) as a capping ligand.
Preparation of a liquefied banana pseudo-stem based PVAc-nanosilica hybrid membrane and its modification by octadecyltrichlorosilane
Authors: Fan-rong Meng , Yu-cang Zhang , Ji-hui Li , Wen-xing Fu , Jie Zhang
Published: September 2016

A hydrophobic LBP–PVAc nanocomposite membrane with enhanced mechanical properties was prepared by adding silica sol and treating with OTS.
Up/down-converted green luminescence of Er3+–Yb3+ doped paramagnetic gadolinium molybdate: a highly sensitive thermographic phosphor for multifunctional applications
Authors: Sinha Shriya , Mahata Manoj Kumar , Kumar Kaushal
Published: September 2016

Optical temperature sensing and nano-heating behavior of Er3+–Yb3+ doped multifunctional gadolinium molybdate phosphor.
Potentially antibreast cancer enamidines via azide–alkyne–amine coupling and their molecular docking studies
Authors: Bansode Prakash , Jadhav Jagannath , Kurane Rajanikant , Choudhari Prafulla , Bhatia Manish , Khanapure Sharanabasappa , Salunkhe Rajashri , Rashinkar Gajanan
Published: September 2016

Potentially antibreast cancer enamidines were synthesized and evaluated against human breast cancer cell line MCF7 displaying GI50values lower than doxorubicin.
Effective synthesis of highly fluorescent nitrogen doped carbon nanoparticles for selective sensing of Hg2+ in food and cosmetics samples
Authors: Liu Juanjuan , Chen Yonglei , Wang Weifeng , Feng Jie , Peng Shoujiao , Ma Sudai , Chen Hongli , Chen Xingguo
Published: September 2016

The as prepared N-doped CNPs could serve as an effective fluorescent sensing probe for Hg2+ detection.
Determination of residual chloride content in ionic liquids using LA-ICP-MS
Authors: Bonta Maximilian , Anderl Thomas , Cognigni Alice , Hejazifar Mahtab , Bica Katharina , Limbeck Andreas
Published: September 2016

Residual chloride in ionic liquids is analyzed using LA-ICP-MS in a sustainable and easy-to-handle approach.
Preservation of osteoblasts and BM-MSCs biological properties after consecutive passages with the thermal-liftoff method
Authors: Zhuang Meiling , Liu Tianqing , Ge Dan , Song Kedong , Guan Shui
Published: September 2016

Thermo-responsive surfaces based on PNIPAAm provide a novel way to harvest cells with temperature reduction.
Protecting microRNAs from RNase degradation with steric DNA nanostructures
Authors: Qian H. , Tay C. Y. , Setyawati M. I. , Chia S. L. , Lee D. S. , Leong D. T.
Published: September 2016

A DNA nanostructure bearing a “Shuriken” shape is designed to deliver, protect and activate microRNA-145 functionality in human colorectal cancer cells. This novel DNA nanostructure enabled therapeutic platform greatly suppresses cancer cell proliferation and tumor growth.
Cross-linked cationic diblock copolymer worms are superflocculants for micrometer-sized silica particles
Authors: Penfold Nicholas J. W. , Ning Yin , Verstraete Pierre , Smets Johan , Armes Steven P.
Published: September 2016

Cationic diblock copolymer worms can be used as flocculants for micrometer-sized silica particles provided that they are covalently stabilized via core cross-linking.
Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid
Authors: Hughes Zak E. , Walsh Tiffany R.
Published: September 2016

Molecular dynamics simulations predict that a combination of sodium dodecylbenzene sulphonate surfactant molecules and nanodiamonds are able to induce a lowering of the phase transition temperatures of tristearin bilayers.
Black rutile (Sn, Ti)O2 initializing electrochemically reversible Sn nanodots embedded in amorphous lithiated titania matrix for efficient lithium storage
Authors: Xu Jijian , Dong Wujie , Song Changsheng , Tang Yufeng , Zhao Wenli , Hong Zhanglian , Huang Fuqiang
Published: September 2016

New black rutile (Sn, Ti)O2 initializing electrochemically reversible Sn nanodots embedded in an amorphous lithiated titania matrix is designed to simultaneously harvest the large reversible capacity, high rate performance and superior cycling stability.
A highly active and durable CuPdPt/C electrocatalyst for an efficient hydrogen evolution reaction
Authors: Ding Tao , Wang Zhengyun , Zhang Li , Wang Chunde , Sun Yuan , Yang Qing
Published: September 2016

A highly dispersive CuPdPt/C catalyst for an efficient hydrogen evolution reaction with excellent activity and stability.
Stabilizing nickel-rich layered cathode materials by a high-charge cation doping strategy: zirconium-doped LiNi0.6Co0.2Mn0.2O2
Authors: Schipper Florian , Dixit Mudit , Kovacheva Daniela , Talianker Michael , Haik Ortal , Grinblat Judith , Erickson Evan M. , Ghanty Chandan , Major Dan T. , Markovsky Boris , Aurbach Doron
Published: September 2016

The high charge-state dopant Zr4+ improves the structural stability and electrochemical behavior of the lithiated transition metal oxide LiNi0.6Co0.2Mn0.2O2.
Engineering of modular organic photovoltaic devices with dye sensitized architecture
Authors: Chal Pousali , Shit Arnab , Nandi Arun K.
Published: September 2016

Dye sensitized organic solar cells based on citric acid doped PANI–perylenetetracarboxyldiimide exhibit a moderate efficiency of 4.32%.
Photon energy storage materials with high energy densities based on diacetylene–azobenzene derivatives
Authors: Han Ggoch Ddeul , Park Sarah S. , Liu Yun , Zhitomirsky David , Cho Eugene , Dincă Mircea , Grossman Jeffrey C.
Published: September 2016

Photocontrolled self-assembly of molecules can be utilized to significantly improve the photon energy storage in photoswitching materials.