bluuebunny/crossref_metadata_2025 huggingface dataset:
Untangling the brain’s neuroinflammatory and neurodegenerative transcriptional responses
Authors: Srinivasan Karpagam , Friedman Brad A. , Larson Jessica L. , Lauffer Benjamin E. , Goldstein Leonard D. , Appling Laurie L. , Borneo Jovencio , Poon Chungkee , Ho Terence , Cai Fang , Steiner Pascal , van der Brug Marcel P. , Modrusan Zora , Kaminker Joshua S. , Hansen David V.
Published: April 2016

A common approach to understanding neurodegenerative disease is comparing gene expression in diseased versus healthy tissues. We illustrate that expression profiles derived from whole tissue RNA highly reflect the degenerating tissues’ altered cellular composition, not necessarily transcriptional regulation. To accurately understand transcriptional changes that accompany neuropathology, we acutely purify neurons, astrocytes and microglia from single adult mouse brains and analyse their transcriptomes by RNA sequencing. Using peripheral endotoxemia to establish the method, we reveal highly specific transcriptional responses and altered RNA processing in each cell type, with Tnfr1 required for the astrocytic response. Extending the method to an Alzheimer’s disease model, we confirm that transcriptomic changes observed in whole tissue are driven primarily by cell type composition, not transcriptional regulation, and identify hundreds of cell type-specific changes undetected in whole tissue RNA. Applying similar methods to additional models and patient tissues will transform our understanding of aberrant gene expression in neurological disease.
Size-dependent phase transition in methylammonium lead iodide perovskite microplate crystals
Authors: Li Dehui , Wang Gongming , Cheng Hung-Chieh , Chen Chih-Yen , Wu Hao , Liu Yuan , Huang Yu , Duan Xiangfeng
Published: April 2016

Methylammonium lead iodide perovskite has attracted considerable recent interest for solution processable solar cells and other optoelectronic applications. The orthorhombic-to-tetragonal phase transition in perovskite can significantly alter its optical, electrical properties and impact the corresponding applications. Here, we report a systematic investigation of the size-dependent orthorhombic-to-tetragonal phase transition using a combined temperature-dependent optical, electrical transport and transmission electron microscopy study. Our studies of individual perovskite microplates with variable thicknesses demonstrate that the phase transition temperature decreases with reducing microplate thickness. The sudden decrease of mobility around phase transition temperature and the presence of hysteresis loops in the temperature-dependent mobility confirm that the orthorhombic-to-tetragonal phase transition is a first-order phase transition. Our findings offer significant fundamental insight on the temperature- and size-dependent structural, optical and charge transport properties of perovskite materials, and can greatly impact future exploration of novel electronic and optoelectronic devices from these materials.
Location-dependent synaptic plasticity rules by dendritic spine cooperativity
Authors: Weber Jens P. , Andrásfalvy Bertalan K. , Polito Marina , Magó Ádám , Ujfalussy Balázs B. , Makara Judit K.
Published: April 2016

Nonlinear interactions between coactive synapses enable neurons to discriminate between spatiotemporal patterns of inputs. Using patterned postsynaptic stimulation by two-photon glutamate uncaging, here we investigate the sensitivity of synaptic Ca2+ signalling and long-term plasticity in individual spines to coincident activity of nearby synapses. We find a proximodistally increasing gradient of nonlinear NMDA receptor (NMDAR)-mediated amplification of spine Ca2+ signals by a few neighbouring coactive synapses along individual perisomatic dendrites. This synaptic cooperativity does not require dendritic spikes, but is correlated with dendritic Na+ spike propagation strength. Furthermore, we show that repetitive synchronous subthreshold activation of small spine clusters produces input specific, NMDAR-dependent cooperative long-term potentiation at distal but not proximal dendritic locations. The sensitive synaptic cooperativity at distal dendritic compartments shown here may promote the formation of functional synaptic clusters, which in turn can facilitate active dendritic processing and storage of information encoded in spatiotemporal synaptic activity patterns.
Nanoscale electron transport at the surface of a topological insulator
Authors: Bauer Sebastian , Bobisch Christian A.
Published: April 2016

The use of three-dimensional topological insulators for disruptive technologies critically depends on the dissipationless transport of electrons at the surface, because of the suppression of backscattering at defects. However, in real devices, defects are unavoidable and scattering at angles other than 180° is allowed for such materials. Until now, this has been studied indirectly by bulk measurements and by the analysis of the local density of states in close vicinity to defect sites. Here, we directly measure the nanoscale voltage drop caused by the scattering at step edges, which occurs if a lateral current flows along a three-dimensional topological insulator. The experiments were performed using scanning tunnelling potentiometry for thin Bi2Se3 films. So far, the observed voltage drops are small because of large contributions of the bulk to the electronic transport. However, for the use of ideal topological insulating thin films in devices, these contributions would play a significant role.
In vitro template-change PCR to create single crossover libraries: a case study with B. thuringiensis Cry2A toxins
Authors: Shu Changlong , Zhou Jianqiao , Crickmore Neil , Li Xianchun , Song Fuping , Liang Gemei , He Kanglai , Huang Dafang , Zhang Jie
Published: April 2016

During evolution the creation of single crossover chimeras between duplicated paralogous genes is a known process for increasing diversity. Comparing the properties of homologously recombined chimeras with one or two crossovers is also an efficient strategy for analyzing relationships between sequence variation and function. However, no well-developed in vitro method has been established to create single-crossover libraries. Here we present an in vitro template-change polymerase change reaction that has been developed to enable the production of such libraries. We applied the method to two closely related toxin genes from B. thuringiensis and created chimeras with differing properties that can help us understand how these toxins are able to differentiate between insect species.
Diffraction-free beams in fractional Schrödinger equation
Authors: Zhang Yiqi , Zhong Hua , Belić Milivoj R. , Ahmed Noor , Zhang Yanpeng , Xiao Min
Published: April 2016

We investigate the propagation of one-dimensional and two-dimensional (1D, 2D) Gaussian beams in the fractional Schrödinger equation (FSE) without a potential, analytically and numerically. Without chirp, a 1D Gaussian beam splits into two nondiffracting Gaussian beams during propagation, while a 2D Gaussian beam undergoes conical diffraction. When a Gaussian beam carries linear chirp, the 1D beam deflects along the trajectories z = ±2(x − x0), which are independent of the chirp. In the case of 2D Gaussian beam, the propagation is also deflected, but the trajectories align along the diffraction cone "Equation missing" and the direction is determined by the chirp. Both 1D and 2D Gaussian beams are diffractionless and display uniform propagation. The nondiffracting property discovered in this model applies to other beams as well. Based on the nondiffracting and splitting properties, we introduce the Talbot effect of diffractionless beams in FSE.
Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet and their expression in rice
Authors: Muthamilarasan Mehanathan , Mangu Venkata R. , Zandkarimi Hana , Prasad Manoj , Baisakh Niranjan
Published: April 2016

ADP-ribosylation factors (ARFs) have been reported to function in diverse physiological and molecular activities. Recent evidences also demonstrate the involvement of ARFs in conferring tolerance to biotic and abiotic stresses in plant species. In the present study, 23 and 25 ARF proteins were identified in C3model- rice and C4model- foxtail millet, respectively. These proteins are classified into four classes (I–IV) based on phylogenetic analysis, with ARFs in classes I–III and ARF-like proteins (ARLs) in class IV. Sequence alignment and domain analysis revealed the presence of conserved and additional motifs, which may contribute to neo- and sub-functionalization of these proteins. Promoter analysis showed the presence of severalcis-regulatory elements related to stress and hormone response, indicating their role in stress regulatory network. Expression analysis of riceARFsandARLsin different tissues, stresses and abscisic acid treatment highlighted temporal and spatial diversification of gene expression. Five rice cultivars screened for allelic variations inOsARFgenes showed the presence of allelic polymorphisms in few gene loci. Altogether, the study provides insights on characteristics ofARF/ARLgenes in rice and foxtail millet, which could be deployed for further functional analysis to extrapolate their precise roles in abiotic stress responses.
HSP27 and 70 expression in thymic epithelial tumors and benign thymic alterations: diagnostic, prognostic and physiologic implications
Authors: Janik S. , Schiefer A. I. , Bekos C. , Hacker P. , Haider T. , Moser J. , Klepetko W. , Müllauer L. , Ankersmit H. J. , Moser B.
Published: April 2016

Thymic Epithelial Tumors (TETs), the most common tumors in the anterior mediastinum in adults, show a unique association with autoimmune Myasthenia Gravis (MG) and represent a multidisciplinary diagnostic and therapeutic challenge. Neither risk factors nor established biomarkers for TETs exist. Predictive and diagnostic markers are urgently needed. Heat shock proteins (HSPs) are upregulated in several malignancies promoting tumor cell survival and metastases. We performed immunohistochemical staining of HSP27 and 70 in patients with TETs (n = 101) and patients with benign thymic alterations (n = 24). Further, serum HSP27 and 70 concentrations were determined in patients with TETs (n = 46), patients with benign thymic alterations (n = 33) and volunteers (n = 49) by using ELISA. HSPs were differentially expressed in histologic types and pathological tumor stages of TETs. Weak HSP tumor expression correlated with worse freedom from recurrence. Serum HSP concentrations were elevated in TETs and MG, correlated with clinical tumor stage and histologic subtype and decreased significantly after complete tumor resection. To conclude, we found HSP expression in the vast majority of TETs, in physiologic thymus and staining intensities in patients with TETs have been associated with prognosis. However, although interesting and promising the role of HSPs in TETs as diagnostic and prognostic or even therapeutic markers need to be further evaluated.
From molecular interaction to acute promyelocytic leukemia: Calculating leukemogenesis and remission from endogenous molecular-cellular network
Authors: Yuan Ruoshi , Zhu Xiaomei , Radich Jerald P. , Ao Ping
Published: April 2016

Acute promyelocytic leukemia (APL) remains the best example of a malignancy that can be cured clinically by differentiation therapy. We demonstrate that APL may emerge from a dynamical endogenous molecular-cellular network obtained from normal, non-cancerous molecular interactions such as signal transduction and translational regulation under physiological conditions. This unifying framework, which reproduces APL, normal progenitor, and differentiated granulocytic phenotypes as different robust states from the network dynamics, has the advantage to study transition between these states, i.e. critical drivers for leukemogenesis and targets for differentiation. The simulation results quantitatively reproduce microarray profiles of NB4 and HL60 cell lines in response to treatment and normal neutrophil differentiation, and lead to new findings such as biomarkers for APL and additional molecular targets for arsenic trioxide therapy. The modeling shows APL and normal states mutually suppress each other, both in “wiring” and in dynamical cooperation. Leukemogenesis and recovery under treatment may be a consequence of spontaneous or induced transitions between robust states, through “passes” or “dragging” by drug effects. Our approach rationalizes leukemic complexity and constructs a platform towards extending differentiation therapy by performing “dry” molecular biology experiments.
Abrupt current switching in graphene bilayer tunnel transistors enabled by van Hove singularities
Authors: Alymov Georgy , Vyurkov Vladimir , Ryzhii Victor , Svintsov Dmitry
Published: April 2016

In a continuous search for the energy-efficient electronic switches, a great attention is focused on tunnel field-effect transistors (TFETs) demonstrating an abrupt dependence of the source-drain current on the gate voltage. Among all TFETs, those based on one-dimensional (1D) semiconductors exhibit the steepest current switching due to the singular density of states near the band edges, though the current in 1D structures is pretty low. In this paper, we propose a TFET based on 2D graphene bilayer which demonstrates a record steep subthreshold slope enabled by van Hove singularities in the density of states near the edges of conduction and valence bands. Our simulations show the accessibility of 3.5 × 104 ON/OFF current ratio with 150 mV gate voltage swing and a maximum subthreshold slope of (20 μV/dec)−1 just above the threshold. The high ON-state current of 0.8 mA/μm is enabled by a narrow (~0.3 eV) extrinsic band gap, while the smallness of the leakage current is due to an all-electrical doping of the source and drain contacts which suppresses the band tailing and trap-assisted tunneling.
Liquid–liquid phase separation of N-isopropylpropionamide aqueous solutions above the lower critical solution temperature
Authors: Mochizuki Kenji , Sumi Tomonari , Koga Kenichiro
Published: April 2016

We investigate driving forces of the liquid–liquid phase separation of N-isopropylpropionamide (NiPPA) aqueous solutions above the lower critical solution temperature using molecular dynamics simulations. Spontaneous phase separations of the model aqueous solution with a modified OPLS-AA force field are observed above the experimentally determined cloud point. The destabilization toward the phase separation is confirmed by temperature dependence of the long-wavelength limit of the concentration-concentration structure factor, the dominant component of which is found to be an increasing effective attraction between NiPPA molecules. At varying temperatures, the potentials of mean force (PMFs) between a pair of NiPPA molecules at infinite dilution are obtained and decomposed into the nonpolar and Coulombic contributions. The nonpolar contribution, arising essentially from molecular volume, promotes association of NiPPA molecules with increasing temperature while the Coulombic one antagonizes the association. Thus, our analysis leads to a conclusion that the driving force of thermally induced aggregation of NiPPA molecules is the temperature dependence of the nonpolar contribution in PMF between NiPPA molecules, not the temperature dependence of the number or strength of hydrogen bonds between NiPPA and water molecules.
Joint Analysis of Radiative and Non-Radiative Electronic Relaxation Upon X-ray Irradiation of Transition Metal Aqueous Solutions
Authors: Golnak Ronny , Bokarev Sergey I. , Seidel Robert , Xiao Jie , Grell Gilbert , Atak Kaan , Unger Isaak , Thürmer Stephan , Aziz Saadullah G. , Kühn Oliver , Winter Bernd , Aziz Emad F.
Published: April 2016

L-edge soft X-ray spectroscopy has been proven to be a powerful tool to unravel the peculiarities of electronic structure of transition metal compounds in solution. However, the X-ray absorption spectrum is often probed in the total or partial fluorescence yield modes, what leads to inherent distortions with respect to the true transmission spectrum. In the present work, we combine photon- and electron-yield experimental techniques with multi-reference first principles calculations. Exemplified for the prototypical FeCl2 aqueous solution we demonstrate that the partial yield arising from the Fe3s → 2p relaxation is a more reliable probe of the absorption spectrum than the Fe3d → 2p one. For the bonding-relevant 3d → 2p channel we further provide the basis for the joint analysis of resonant photoelectron and inelastic X-ray scattering spectra. Establishing the common energy reference allows to assign both spectra using the complementary information provided through electron-out and photon-out events.
Theoretical screening of intermetallic ThMn12-type phases for new hard-magnetic compounds with low rare earth content
Authors: Körner Wolfgang , Krugel Georg , Elsässer Christian
Published: April 2016

We report on theoretical investigations of intermetallic phases derived from the ThMn12-type crystal structure. Our computational high-throughput screening (HTS) approach is extended to an estimation of the anisotropy constant K1, the anisotropy field Ha and the energy product (BH)max. The calculation of K1 is fast since it is based on the crystal field parameters and avoids expensive total-energy calculations with many k-points. Thus the HTS approach allows a very efficient search for hard-magnetic materials for which the magnetization M and the coercive field Hc connected to Ha represent the key quantities. Besides for NdFe12N which has the highest magnetization we report HTS results for several intermetallic phases based on Cerium which are interesting as alternative hard-magnetic phases because Cerium is a less ressource-critical element than Neodymium.
Regulation of aldosterone secretion by Cav1.3
Authors: Xie Catherine B. , Haris Shaikh Lalarukh , Garg Sumedha , Tanriver Gizem , Teo Ada E. D. , Zhou Junhua , Maniero Carmela , Zhao Wanfeng , Kang Soosung , Silverman Richard B. , Azizan Elena A. B. , Brown Morris J.
Published: April 2016

Aldosterone-producing adenomas (APAs) vary in phenotype and genotype. Zona glomerulosa (ZG)-like APAs frequently have mutations of an L-type calcium channel (LTCC) CaV1.3. Using a novel antagonist of CaV1.3, compound 8, we investigated the role of CaV1.3 on steroidogenesis in the human adrenocortical cell line, H295R and in primary human adrenal cells. This investigational drug was compared with the common antihypertensive drug nifedipine, which has 4.5-fold selectivity for the vascular LTCC, CaV1.2, over CaV1.3. In H295R cells transfected with wild-type or mutant CaV1.3 channels, the latter produced more aldosterone than wild-type, which was ameliorated by 100 μM of compound 8. In primary adrenal and non-transfected H295R cells, compound 8 decreased aldosterone production similar to high concentration of nifedipine (100 μM). Selective CaV1.3 blockade may offer a novel way of treating primary hyperaldosteronism, which avoids the vascular side effects of CaV1.2-blockade and provides targeted treatment for ZG-like APAs with mutations of CaV1.3.
Genome-wide association studies for fatty acid metabolic traits in five divergent pig populations
Authors: Zhang Wanchang , Bin Yang  , Zhang Junjie , Cui Leilei , Ma Junwu , Chen Congying , Ai Huashui , Xiao Shijun , Ren Jun , Huang Lusheng
Published: April 2016

Fatty acid composition profiles are important indicators of meat quality and tasting flavor. Metabolic indices of fatty acids are more authentic to reflect meat nutrition and public acceptance. To investigate the genetic mechanism of fatty acid metabolic indices in pork, we conducted genome-wide association studies (GWAS) for 33 fatty acid metabolic traits in five pig populations. We identified a total of 865 single nucleotide polymorphisms (SNPs), corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes. Our findings not only confirmed seven previously reported QTL with stronger association strength, but also revealed four novel population-specific loci, showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes. We proposed a list of candidate genes at the identified loci, including three novel genes (FADS2, SREBF1 and PLA2G7). Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. These findings advance our understanding of the genetic basis of fatty acid composition in pigs. The results from European hybrid commercial pigs can be immediately transited into breeding practice for beneficial fatty acid composition.
Newcastle disease virus NP and P proteins induce autophagy via the endoplasmic reticulum stress-related unfolded protein response
Authors: Cheng Jing-Hua , Sun Ying-Jie , Zhang Fan-Qing , Zhang Xiao-Rong , Qiu Xv-Sheng , Yu Li-Ping , Wu Yan-Tao , Ding Chan
Published: April 2016

Newcastle disease virus (NDV) can replicate and trigger autophagy in human tumor cells. Our previous study confirmed the critical role of autophagy in NDV infection. Here we studied the role of NDV structural proteins in the induction of autophagy through endoplasmic reticulum (ER) stress-related unfolded protein response (UPR) pathways. Ectopic expression of the NDV nucleocapsid protein (NP) or phosphoprotein (P) was sufficient to induce autophagy. NP or P expression also altered ER homeostasis. The PERK and ATF6 pathways, but not the XBP1 pathway, all of which are components of the UPR, were activated in both NDV-infected and NP or P-transfected cells. Knockdown of PERK or ATF6 inhibited NDV-induced autophagy and reduced the extent of NDV replication. Collectively, these data suggest not only roles for the NDV NP and P proteins in autophagy, but also offer new insights into the mechanisms of NDV-induced autophagy through activation of the ER stress-related UPR pathway.
CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations
Authors: Pan Changtian , Ye Lei , Qin Li , Liu Xue , He Yanjun , Wang Jie , Chen Lifei , Lu Gang
Published: April 2016

The CRISPR/Cas9 system has successfully been used in various organisms for precise targeted gene editing. Although it has been demonstrated that CRISPR/Cas9 system can induce mutation in tomato plants, the stability of heredity in later generations and mutant specificity induced by the CRISPR/Cas9 system in tomato plants have not yet been elucidated in detail. In this study, two genes, SlPDS and SlPIF4, were used for testing targeted mutagenesis in tomato plants through an Agrobacterium tumefaciens-mediated transformation method. A high mutation frequency was observed in all tested targets in the T0 transgenic tomato plants, with an average frequency of 83.56%. Clear albino phenotypes were observed for the psd mutants. High frequencies of homozygous and biallelic mutants were detected even in T0 plants. The majority of the detected mutations were 1- to 3-nucleotide deletions, followed by 1-bp insertions. The target mutations in the T0 lines were stably transmitted to the T1 and T2 generations, without new modifications or revision. Off-target activities associated with SlPDS and SlPIF4 were also evaluated by sequencing the putative off-target sites and no clear off-target events were detected. Our results demonstrate that the CRISPR/Cas9 system is an efficient tool for generating stable and heritable modifications in tomato plants.
Anti-gastric cancer activity in three-dimensional tumor spheroids of bufadienolides
Authors: Wang Jixia , Zhang Xiuli , Li Xiaolong , Zhang Yun , Hou Tao , Wei Lai , Qu Lala , Shi Liying , Liu Yanfang , Zou Lijuan , Liang Xinmiao
Published: April 2016

Multicellular spheroids of cancer cells have been increasingly used to screen anti-tumor compounds, owing to their in vivo like microenvironment and structure as well as compatibility to high-throughput/high-content screening. Here we report the potency and efficacy of a family of bufadienolides to inhibit the growth of gastric cancer cell line HGC-27 in three-dimensional (3D) spheroidal models. Examining the morphological and growth patterns of several cell lines in round-bottomed ultra-low attachment microplate suggested that HGC-27 cells formed reproducibly multicellular spheroidal structures. Profiling of 15 natural bufadienolides isolated from toad skin indicated that 8 14-hydroxy bufadienolides displayed inhibitory activity of the growth of HGC-27 spheroids in a dose-dependent manner. Notably, compared to clinical drugs taxol and epirubicin, active bufadienolides were found to penetrate more effectively into the HGC-27 spheroids, but with a narrower effective concentration range and a shorter lasting inhibitory effect. Furthermore, compared to two-dimensional (2D) cell monolayer assays, active bufadienolides exhibited weaker efficacy and different potency in 3D spheroid model, demonstrating the great potential of 3D multicellular cell spheroid models in anti-cancer drug discovery and development.
KIAA1522 is a novel prognostic biomarker in patients with non-small cell lung cancer
Authors: Liu Yi-Zhen , Yang Hai , Cao Jian , Jiang Yan-Yi , Hao Jia-Jie , Xu Xin , Cai Yan , Wang Ming-Rong
Published: April 2016

Nowadays, no robust biomarkers have been applied to clinical practice to provide prognostic evaluation of non-small cell lung cancer (NSCLC). This study aims to identify new potential prognostic biomarkers for NSCLC. In the present work, KIAA1522 is screened out from two independent GEO datasets as aberrantly up-regulated gene in NSCLC tissues. We evaluate KIAA1522 expression immunohistochemically in 583 NSCLC tissue samples and paired non-tumor tissues. KIAA1522 displays stronger staining in NSCLC cases than in adjacent normal lung tissues. Importantly, patients with KIAA1522 overexpression had a significantly shorter overall survival compared to those with low expression (P < 0.00001). Multivariate Cox regression analyses show that KIAA1522 is an independent prognostic indicator, even for early-stage NSCLCs (P = 0.00025, HR = 2.317, 95%CI: 1.477–3.635). We also found that high expression of KIAA1522 is a significant risk factor for decreased overall survival of the patients who received platinum-based chemotherapy. Gene set enrichment analysis (GSEA) and functional studies reveal that KIAA1522 is associated with oncogenic KRAS pathways. Taken together, high expression of KIAA1522 can be used as an independent biomarker for predication of poor survival and platinum-resistance of NSCLC patients and aberrant KIAA1522 might be a new target for the therapy of the disease.
Role of an Oxidant Mixture as Surface Modifier of Porous Silicon Microstructures Evaluated by Spectroscopic Ellipsometry
Authors: Montiel-González Zeuz , Escobar Salvador , Nava Rocío , del Río J. Antonio , Tagüeña-Martínez Julia
Published: April 2016

Current research on porous silicon includes the construction of complex structures with luminescent and/or photonic properties. However, their preparation with both characteristics is still challenging. Recently, our group reported a possible method to achieve that by adding an oxidant mixture to the electrolyte used to produce porous silicon. This mixture can chemically modify their microstructure by changing the thickness and surface passivation of the pore walls. In this work, we prepared a series of samples (with and without oxidant mixture) and we evaluated the structural differences through their scanning electron micrographs and their optical properties determined by spectroscopic ellipsometry. The results showed that ellipsometry is sensitive to slight variations in the porous silicon structure, caused by changes in their preparation. The fitting process, based on models constructed from the features observed in the micrographs, allowed us to see that the mayor effect of the oxidant mixture is on samples of high porosity, where the surface oxidation strongly contributes to the skeleton thinning during the electrochemical etching. This suggests the existence of a porosity threshold for the action of the oxidant mixture. These results could have a significant impact on the design of complex porous silicon structures for different optoelectronic applications.
Physiological responses to daily light exposure
Authors: Yang Yefeng , Yu Yonghua , Yang Bo , Zhou Hong , Pan Jinming
Published: April 2016

Long daylength artificial light exposure associates with disorders and a potential physiological mechanism has been proposed. However, previous studies have examined no more than three artificial light treatments and limited metabolic parameters, which have been insufficient to demonstrate mechanical responses. Here, comprehensive physiological response curves were established and the physiological mechanism was strengthened. Chicks were illuminated for 12, 14, 16, 18, 20, or 22 h periods each day. A quadratic relationship between abdominal adipose weight (AAW) and light period suggested that long-term or short-term light exposure could decrease the amount of AAW. Quantitative relationships between physiological parameters and daily light period were also established in this study. The relationships between triglycerides (TG), cholesterol (TC), glucose (GLU), phosphorus (P) levels and daily light period could be described by quadratic regression models. TG levels, AAW and BW positively correlated with each other, suggesting long-term light exposure significantly increased AAW by increasing TG thus resulting in greater BW. A positive correlation between blood triiodothyronine (T3) levels and BW suggested that daily long-term light exposure increased BW by thyroid hormone secretion. Though the molecular pathway remains unknown, these results suggest a comprehensive physiological mechanism through which light exposure affects growth.
Use of handheld X-ray fluorescence as a non-invasive method to distinguish between Asian and African elephant tusks
Authors: Buddhachat Kittisak , Thitaram Chatchote , Brown Janine L. , Klinhom Sarisa , Bansiddhi Pakkanut , Penchart Kitichaya , Ouitavon Kanita , Sriaksorn Khanittha , Pa-in Chalermpol , Kanchanasaka Budsabong , Somgird Chaleamchat , Nganvongpanit Korakot
Published: April 2016

We describe the use of handheld X-ray fluorescence, for elephant tusk species identification. Asian (n = 72) and African (n = 85) elephant tusks were scanned and we utilized the species differences in elemental composition to develop a functional model differentiating between species with high precision. Spatially, the majority of measured elements (n = 26) exhibited a homogeneous distribution in cross-section, but a more heterologous pattern in the longitudinal direction. Twenty-one of twenty four elements differed between Asian and African samples. Data were subjected to hierarchical cluster analysis followed by a stepwise discriminant analysis, which identified elements for the functional equation. The best equation consisted of ratios of Si, S, Cl, Ti, Mn, Ag, Sb and W, with Zr as the denominator. Next, Bayesian binary regression model analysis was conducted to predict the probability that a tusk would be of African origin. A cut-off value was established to improve discrimination. This Bayesian hybrid classification model was then validated by scanning an additional 30 Asian and 41 African tusks, which showed high accuracy (94%) and precision (95%) rates. We conclude that handheld XRF is an accurate, non-invasive method to discriminate origin of elephant tusks provides rapid results applicable to use in the field.
1700 nm dispersion managed mode-locked bismuth fiber laser
Authors: Noronen Teppo , Firstov Sergei , Dianov Evgeny , Okhotnikov Oleg G.
Published: April 2016

We demonstrate the first 1.7 μm bismuth-doped fiber laser generating ultrashort pulses via passive mode-locking. Pulse operation has been achieved for both anomalous and normal dispersion of the laser cavity owing to broadband characteristics of carbon nanotube saturable absorber. The laser delivered 1.65 ps pulses in net anomalous dispersion regime. In normal dispersion regime, the laser delivered 14 ps pulses which could be compressed to 1.2 ps using external fiber compressor.
Time-dependent quantum simulation of coronene photoemission spectra
Authors: Acocella Angela , de Simone Monica , Evangelista Fabrizio , Coreno Marcello , Rudolf Petra , Zerbetto Francesco
Published: April 2016

Explicit quantum dynamics simulations on an ensemble of thermally equilibrated molecules accurately assign and interpret the photoelectron spectra of coronene.
Self-assembly of a “double dynamic covalent” amphiphile featuring a glucose-responsive imine bond
Authors: Wu Xin , Chen Xuan-Xuan , Zhang Miao , Li Zhao , Gale Philip A. , Jiang Yun-Bao
Published: April 2016

Glucose recognitionvia in situformation of supramolecular vesicular aggregates that involve two dynamic covalent bonds.
Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions
Authors: Wen Jin , Li Wei , Chen Shuang , Ma Jing
Published: April 2016

Simulations using QM and MM methods guide the rational design of functionalized SAMs on surfaces.
Non-targeted metabolomics identified a common metabolic signature of lethal ventricular tachyarrhythmia (LVTA) in two rat models
Authors: Wang Xingxing , Wang Dian , Yu Xiaojun , Zhang Guohong , Wu Jiayan , Zhu Guanghui , Su Ruibing , Lv Junyao
Published: April 2016

Lethal ventricular tachyarrhythmia (LVTA) is the predominant underlying mechanism of sudden cardiac death (SCD).
2,4 and 2,5-bis(benzooxazol-2′-yl)hydroquinone (DHBO) and their borate complexes: synthesis and optical properties
Authors: Benelhadj Karima , Massue Julien , Ulrich Gilles
Published: April 2016

2,4 and 2,5-bis(benzooxazol-2′-yl)hydroquinone (DHBO) scaffolds show fluorescence stemming from an ESIPT process but also act as chelates toward boron fragments.
Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA
Authors: Bag Subhendu Sekhar , Talukdar Sangita , Das Suman Kalyan , Pradhan Manoj Kumar , Mukherjee Soumen
Published: April 2016

We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.
Correction: Oxidative ring-opening of ferrocenylcyclopropylamines to N-ferrocenylmethyl β-hydroxyamides
Authors: Gee Yi Sing , Goertz Niels J. M. , Gardiner Michael G. , Hyland Christopher J. T.
Published: April 2016

Correction for ‘Oxidative ring-opening of ferrocenylcyclopropylamines to N-ferrocenylmethyl β-hydroxyamides’ by Yi Sing Gee et al., Org. Biomol. Chem., 2016, 14, 2498–2503.
Synthesis and mesomorphic properties of side-chain polynorbornenes containing mono-, di- and tri-calamitic mesogenic pendant groups
Authors: Ma Shenhao , Cai Yongchen , Tu Yuanyang , Guan Yan , Chen Xiaofang
Published: April 2016

Polynorbornenes containing mesogenic side groups with a controlled number and substituted position were synthesized and their mesomorphic properties were systematically investigated.
Modulation of singlet oxygen generation in halogenated BODIPY dyes by substitution at their meso position: towards a solvent-independent standard in the vis region
Authors: Epelde-Elezcano Nerea , Martínez-Martínez Virginia , Peña-Cabrera Eduardo , Gómez-Durán César F. A. , Arbeloa Iñigo López , Lacombe Sylvie
Published: April 2016

Halogenated BODIPY with different substitutions patterns at their meso position are deeply analyzed. One of them is proposed as a suitable reference with high singlet oxygen quantum yield, practically solvent-independent in a broad polarity range.
Alkylated histidine based short cationic antifungal peptides: synthesis, biological evaluation and mechanistic investigations
Authors: Mittal Sherry , Kaur Sarabjit , Swami Anuradha , Maurya Indresh K. , Jain Rahul , Wangoo Nishima , Sharma Rohit K.
Published: April 2016

Novel antifungal peptides are described with some peptides exhibiting selective activity againstC. neoformans. Cytotoxicity and mechanistic studies reveal their applicability as effective antimicrobials with less susceptibility to drug resistance.
Tailoring in vitro biological and mechanical properties of polyvinyl alcohol reinforced with threshold carbon nanotube concentration for improved cellular response
Authors: Kaur Tejinder , Thirugnanam Arunachalam
Published: April 2016

The development of living bone tissue constructs with structural, mechanical and functional similarities to natural bone are the major challenges in bone tissue engineering.
Correction: Functional modulation and directed assembly of an enzyme through designed non-natural post-translation modification
Authors: Hartley Andrew M. , Zaki Athraa J. , McGarrity Adam R. , Robert-Ansart Cecile , Moskalenko Andriy V. , Jones Gareth F. , Craciun Monica F. , Russo Saverio , Elliott Martin , Macdonald J. Emyr , Jones D. Dafydd
Published: April 2016

Correction for ‘Functional modulation and directed assembly of an enzyme through designed non-natural post-translation modification’ by Andrew M. Hartley et al., Chem. Sci., 2015, 6, 3712–3717.
Water oxidation catalysis by using nano-manganese ferrite supported 1D-(tunnelled), 2D-(layered) and 3D-(spinel) manganese oxides
Authors: Elmacı Gökhan , Frey Carolin E. , Kurz Philipp , Zümreoğlu-Karan Birgül
Published: April 2016

A first comparative study on 1D-, 2D- and 3D-manganese oxides supported by iron oxide nanoparticles for use as water oxidation catalysts is presented.
Chemically functionalized 3D graphene hydrogel for high performance gas sensing
Authors: Wu Jin , Tao Kai , Zhang Jing , Guo Yuanyuan , Miao Jianmin , Norford Leslie K.
Published: April 2016

A one-step synthesized and chemically functionalized 3D graphene hydrogel is exploited for highly selective and sensitive NO2 and CO2 sensing.
Achieving high efficiency and improved stability in large-area ITO-free perovskite solar cells with thiol-functionalized self-assembled monolayers
Authors: Chang Chih-Yu , Chang Yu-Chia , Huang Wen-Kuan , Liao Wen-Chi , Wang Hung , Yeh Chieh , Tsai Bo-Chou , Huang Yu-Ching , Tsao Cheng-Si
Published: April 2016

A promising approach towards highly efficient and stable large-area ITO-free perovskite solar cells is demonstrated by employing thiol-functionalized self-assembled monolayers as interfacial modification layers.
Shape-controlled cobalt phosphide nanoparticles as volatile organic solvent sensor
Authors: Pradhan Bapi , Kumar Gundam Sandeep , Dalui Amit , Khan Ali Hossain , Satpati Biswarup , Ji Qingmin , Shrestha Lok Kumar , Ariga Katsuhiko , Acharya Somobrata
Published: April 2016

Shape-controlled cobalt phosphide nanostructures have been synthesized using a one-pot reaction strategy for sensing volatile organic solvent molecules.
Perovskite ferroelectrics and relaxor-ferroelectric solid solutions with large intrinsic electrocaloric response over broad temperature ranges
Authors: Khassaf H. , Mantese J. V. , Bassiri-Gharb N. , Kutnjak Z. , Alpay S. P.
Published: April 2016

Electrocaloric materials have emerged as a viable technology for solid state heating/cooling and waste heat recovery applications. We provide a general methodology for theoretical analysis to both assess and guide the way in discovering new high performance electrocalorics.
Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2
Authors: Hornyak Peter , Askwith Trevor , Walker Sarah , Komulainen Emilia , Paradowski Michael , Pennicott Lewis E. , Bartlett Edward J. , Brissett Nigel C. , Raoof Ali , Watson Mandy , Jordan Allan M. , Ogilvie Donald J. , Ward Simon E. , Atack John R. , Pearl Laurence H. , Caldecott Keith W. , Oliver Antony W.
Published: April 2016

Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5′-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II (TOP2). TDP2 facilitates therapeutic resistance to topoisomerase poisons, which are widely used in the treatment of a range of cancer types. Consequently, TDP2 is an interesting target for the development of small molecule inhibitors that could restore sensitivity to topoisomerase-directed therapies. Previous studies identified a class of deazaflavin-based molecules that showed inhibitory activity against TDP2 at therapeutically useful concentrations, but their mode of action was uncertain. We have confirmed that the deazaflavin series inhibits TDP2 enzyme activity in a fluorescence-based assay, suitable for high-throughput screen (HTS)-screening. We have gone on to determine crystal structures of these compounds bound to a ‘humanized’ form of murine TDP2. The structures reveal their novel mode of action as competitive ligands for the binding site of an incoming DNA substrate, and point the way to generating novel and potent inhibitors of TDP2.
Large Sublingual Dermoid Cyst: A Case of Mandibular Prognathism
Authors: Berbel Pablo , Ostrosky Alejandro , Tosti Franco
Published: April 2016

Dermoid cysts are unusual neoplasms and can occur in every part of the human body. They represent only 6.9% of all dermoid cysts in the head and neck region; in the oral cavity, the incidence is low, approximately 1.6% of all dermoid cysts. Our aim is to present an unusual case of a large sublingual dermoid cyst with mandibular prognathism caused by cyst growth. We reported a case of a large sublingual dermoid cyst in an 8-year-old female patient. A bibliographic research from 1937 to 2013 is reviewed and we found only three cases of mandibular deformity, of which only one was a dermoid cyst of the floor of the mouth. Removal of dermoid cysts of the floor of the mouth should be completed as early as detected, especially in newborns and infants when osseous growth abnormalities could result if removal is delayed.
Multi-shell model of ion-induced nucleic acid condensation
Authors: Tolokh Igor S. , Drozdetski Aleksander V. , Pollack Lois , Baker Nathan A. , Onufriev Alexey V.
Published: April 2016

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.”
High performance mini-gas chromatography-flame ionization detector system based on micro gas chromatography column
Authors: Zhu Xiaofeng , Sun Jianhai , Ning Zhanwu , Zhang Yanni , Liu Jinhua
Published: April 2016

Monitoring Volatile organic compounds (VOCs) was a very important measure for preventing environmental pollution, therefore, a mini gas chromatography (GC) flame ionization detector (FID) system integrated with a mini H2 generator and a micro GC column was developed for environmental VOC monitoring. In addition, the mini H2 generator was able to make the system explode from far away due to the abandoned use of a high pressure H2 source. The experimental result indicates that the fabricated mini GC FID system demonstrated high repeatability and very good linear response, and was able to rapidly monitor complicated environmental VOC samples.
Phospho-silicate glass gated 4H-SiC metal-oxide-semiconductor devices: Phosphorus concentration dependence
Authors: Jiao C. , Ahyi A. C. , Xu C. , Morisette D. , Feldman L. C. , Dhar S.
Published: April 2016

The correlation between phosphorus concentration in phospho-silicate glass (PSG) gate dielectrics and electrical properties of 4H-SiC MOS devices has been investigated. Varying P uptake in PSG is achieved by changing the POCl3 post-oxidation annealing temperature. The density of interface traps (Dit) at the PSG/4H-SiC interface decreases as the amount of interfacial P increases. Most significantly, the MOSFET channel mobility does not correlate with Dit for all samples, which is highly unusual for SiC MOSFETs. Further analysis reveals two types of field-effect mobility (μfe) behavior, depending on the annealing temperature. Annealing at 1000 °C improves the channel mobility most effectively, with a peak value ∼105 cm2 V−1 s−1, and results in a surface phonon scattering limited mobility at high oxide field. On the other hand, PSG annealed at other temperatures results in a surface roughness scattering limited mobility at similar field.
Generalized model screening potentials for Fermi-Dirac plasmas
Authors: Akbari-Moghanjoughi M.
Published: April 2016

In this paper, some properties of relativistically degenerate quantum plasmas, such as static ion screening, structure factor, and Thomson scattering cross-section, are studied in the framework of linearized quantum hydrodynamic theory with the newly proposed kinetic γ-correction to Bohm term in low frequency limit. It is found that the correction has a significant effect on the properties of quantum plasmas in all density regimes, ranging from solid-density up to that of white dwarf stars. It is also found that Shukla-Eliasson attractive force exists up to a few times the density of metals, and the ionic correlations are seemingly apparent in the radial distribution function signature. Simplified statically screened attractive and repulsive potentials are presented for zero-temperature Fermi-Dirac plasmas, valid for a wide range of quantum plasma number-density and atomic number values. Moreover, it is observed that crystallization of white dwarfs beyond a critical core number-density persists with this new kinetic correction, but it is shifted to a much higher number-density value of n0 ≃ 1.94 × 1037 cm−3 (1.77 × 1010 gr cm−3), which is nearly four orders of magnitude less than the nuclear density. It is found that the maximal Thomson scattering with the γ-corrected structure factor is a remarkable property of white dwarf stars. However, with the new γ-correction, the maximal scattering shifts to the spectrum region between hard X-ray and low-energy gamma-rays. White dwarfs composed of higher atomic-number ions are observed to maximally Thomson-scatter at slightly higher wavelengths, i.e., they maximally scatter slightly low-energy photons in the presence of correction.