bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial permeability transition pore induction is linked to formation of the complex of ATPase C-subunit, polyhydroxybutyrate and inorganic polyphosphate
Authors: Elustondo P A , Nichols M , Negoda A , Thirumaran A , Zakharian E , Robertson G S , Pavlov E V
Published: December 2016

Mitochondrial permeability transition pore (mPTP) opening allows free movement of ions and small molecules leading to mitochondrial membrane depolarization and ATP depletion that triggers cell death. A multi-protein complex of the mitochondrial ATP synthase has an essential role in mPTP. However, the molecular identity of the central 'pore' part of mPTP complex is not known. A highly purified fraction of mammalian mitochondria containing C-subunit of ATPase (C-subunit), calcium, inorganic polyphosphate (polyP) and polyhydroxybutyrate (PHB) forms ion channels with properties that resemble the native mPTP. We demonstrate here that amount of this channel-forming complex dramatically increases in intact mitochondria during mPTP activation. This increase is inhibited by both Cyclosporine A, an inhibitor of mPTP and Ruthenium Red, an inhibitor of the Mitochondrial Calcium Uniporter. Similar increases in the amount of complex formation occurs in areas of mouse brain damaged by ischemia-reperfusion injury. These findings suggest that calcium-induced mPTP is associated with de novo assembly of a channel comprising C-subunit, polyP and PHB.
Questions and controversies: the role of necroptosis in liver disease
Authors: Dara Lily , Liu Zhang-Xu , Kaplowitz Neil
Published: December 2016

Acute and chronic liver injury results in hepatocyte death and turnover. If injury becomes chronic, the continuous cell death and turnover leads to chronic inflammation, fibrosis and ultimately cirrhosis and hepatocellular carcinoma. Controlling liver cell death both in acute injury, to rescue the liver from acute liver failure, and in chronic injury, to curb secondary inflammation and fibrosis, is of paramount importance as a therapeutic strategy. Both apoptosis and necrosis occur in the liver, but the occurrence of necroptosis in the liver and its contribution to liver disease is controversial. Necroptosis is a form of regulated necrosis which occurs in certain cell types when caspases (+/−cIAPs) are inhibited through the RIPK1-RIPK3 activation of MLKL. The occurrence of necroptosis in the liver has recently been examined in multiple liver injury models with conflicting results. The aim of this review is to summarize the published data with an emphasis on the controversies and remaining questions in the field.
Interatomic Coulombic decay cascades in multiply excited neon clusters
Authors: Nagaya K. , Iablonskyi D. , Golubev N. V. , Matsunami K. , Fukuzawa H. , Motomura K. , Nishiyama T. , Sakai T. , Tachibana T. , Mondal S. , Wada S. , Prince K. C. , Callegari C. , Miron C. , Saito N. , Yabashi M. , Demekhin Ph. V. , Cederbaum L. S. , Kuleff A. I. , Yao M. , Ueda K.
Published: December 2016

In high-intensity laser light, matter can be ionized by direct multiphoton absorption even at photon energies below the ionization threshold. However on tuning the laser to the lowest resonant transition, the system becomes multiply excited, and more efficient, indirect ionization pathways become operative. These mechanisms are known as interatomic Coulombic decay (ICD), where one of the species de-excites to its ground state, transferring its energy to ionize another excited species. Here we show that on tuning to a higher resonant transition, a previously unknown type of interatomic Coulombic decay, intra-Rydberg ICD occurs. In it, de-excitation of an atom to a close-lying Rydberg state leads to electron emission from another neighbouring Rydberg atom. Moreover, systems multiply excited to higher Rydberg states will decay by a cascade of such processes, producing even more ions. The intra-Rydberg ICD and cascades are expected to be ubiquitous in weakly-bound systems exposed to high-intensity resonant radiation.
Discovery of a new type of topological Weyl fermion semimetal state in MoxW1−xTe2
Authors: Belopolski Ilya , Sanchez Daniel S. , Ishida Yukiaki , Pan Xingchen , Yu Peng , Xu Su-Yang , Chang Guoqing , Chang Tay-Rong , Zheng Hao , Alidoust Nasser , Bian Guang , Neupane Madhab , Huang Shin-Ming , Lee Chi-Cheng , Song You , Bu Haijun , Wang Guanghou , Li Shisheng , Eda Goki , Jeng Horng-Tay , Kondo Takeshi , Lin Hsin , Liu Zheng , Song Fengqi , Shin Shik , Hasan M. Zahid
Published: December 2016

The recent discovery of a Weyl semimetal in TaAs offers the first Weyl fermion observed in nature and dramatically broadens the classification of topological phases. However, in TaAs it has proven challenging to study the rich transport phenomena arising from emergent Weyl fermions. The series MoxW1−xTe2 are inversion-breaking, layered, tunable semimetals already under study as a promising platform for new electronics and recently proposed to host Type II, or strongly Lorentz-violating, Weyl fermions. Here we report the discovery of a Weyl semimetal in MoxW1−xTe2 at x=25%. We use pump-probe angle-resolved photoemission spectroscopy (pump-probe ARPES) to directly observe a topological Fermi arc above the Fermi level, demonstrating a Weyl semimetal. The excellent agreement with calculation suggests that MoxW1−xTe2 is a Type II Weyl semimetal. We also find that certain Weyl points are at the Fermi level, making MoxW1−xTe2 a promising platform for transport and optics experiments on Weyl semimetals.
SCN4B acts as a metastasis-suppressor gene preventing hyperactivation of cell migration in breast cancer
Authors: Bon Emeline , Driffort Virginie , Gradek Frédéric , Martinez-Caceres Carlos , Anchelin Monique , Pelegrin Pablo , Cayuela Maria-Luisa , Marionneau-Lambot Séverine , Oullier Thibauld , Guibon Roseline , Fromont Gaëlle , Gutierrez-Pajares Jorge L. , Domingo Isabelle , Piver Eric , Moreau Alain , Burlaud-Gaillard Julien , Frank Philippe G. , Chevalier Stéphan , Besson Pierre , Roger Sébastien
Published: December 2016

The development of metastases largely relies on the capacity of cancer cells to invade extracellular matrices (ECM) using two invasion modes termed ‘mesenchymal’ and ‘amoeboid’, with possible transitions between these modes. Here we show that the SCN4B gene, encoding for the β4 protein, initially characterized as an auxiliary subunit of voltage-gated sodium channels (NaV) in excitable tissues, is expressed in normal epithelial cells and that reduced β4 protein levels in breast cancer biopsies correlate with high-grade primary and metastatic tumours. In cancer cells, reducing β4 expression increases RhoA activity, potentiates cell migration and invasiveness, primary tumour growth and metastatic spreading, by promoting the acquisition of an amoeboid–mesenchymal hybrid phenotype. This hyperactivated migration is independent of NaV and is prevented by overexpression of the intracellular C-terminus of β4. Conversely, SCN4B overexpression reduces cancer cell invasiveness and tumour progression, indicating that SCN4B/β4 represents a metastasis-suppressor gene.
Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences
Authors: Boehm Volker , Gerbracht Jennifer V. , Marx Marie-Charlotte , Gehring Niels H.
Published: December 2016

The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5′–3′ mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3′ UTRs of cytokine mRNAs reveals the contribution of 5′–3′ decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.
Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction
Authors: Hanebuth Marie A. , Kityk Roman , Fries Sandra J. , Jain Alok , Kriel Allison , Albanese Veronique , Frickey Tancred , Peter Christine , Mayer Matthias P. , Frydman Judith , Deuerling Elke
Published: December 2016

Hsp70 chaperones assist de novo folding of newly synthesized proteins in all cells. In yeast, the specialized Hsp70 Ssb directly binds to ribosomes. The structural basis and functional mode of recruitment of Ssb to ribosomes is not understood. Here, we present the molecular details underlying ribosome binding of Ssb in Saccharomyces cerevisiae. This interaction is multifaceted, involving the co-chaperone RAC and two specific regions within Ssb characterized by positive charges. The C-terminus of Ssb mediates the key contact and a second attachment point is provided by a KRR-motif in the substrate binding domain. Strikingly, ribosome binding of Ssb is not essential. Autonomous ribosome attachment becomes necessary if RAC is absent, suggesting a dual mode of Ssb recruitment to nascent chains. We propose, that the multilayered ribosomal interaction allows positioning of Ssb in an optimal orientation to the tunnel exit guaranteeing an efficient nascent polypeptide interaction.
Revealing region-specific biofilm viscoelastic properties by means of a micro-rheological approach
Authors: Cao Huayu , Habimana Olivier , Safari Ashkan , Heffernan Rory , Dai Yihong , Casey Eoin
Published: December 2016

Particle-tracking microrheology is an in situ technique that allows quantification of biofilm material properties. It overcomes the limitations of alternative techniques such as bulk rheology or force spectroscopy by providing data on region specific material properties at any required biofilm location and can be combined with confocal microscopy and associated structural analysis. This article describes single particle tracking microrheology combined with confocal laser scanning microscopy to resolve the biofilm structure in 3 dimensions and calculate the creep compliances locally. Samples were analysed from Pseudomonas fluorescens biofilms that were cultivated over two timescales (24 h and 48 h) and alternate ionic conditions (with and without calcium chloride supplementation). The region-based creep compliance analysis showed that the creep compliance of biofilm void zones is the primary contributor to biofilm mechanical properties, contributing to the overall viscoelastic character.
Spatial and temporal analysis of extreme sea level and storm surge events around the coastline of the UK
Authors: Haigh Ivan D. , Wadey Matthew P. , Wahl Thomas , Ozsoy Ozgun , Nicholls Robert J. , Brown Jennifer M. , Horsburgh Kevin , Gouldby Ben
Published: December 2016

In this paper we analyse the spatial footprint and temporal clustering of extreme sea level and skew surge events around the UK coast over the last 100 years (1915–2014). The vast majority of the extreme sea level events are generated by moderate, rather than extreme skew surges, combined with spring astronomical high tides. We distinguish four broad categories of spatial footprints of events and the distinct storm tracks that generated them. There have been rare events when extreme levels have occurred along two unconnected coastal regions during the same storm. The events that occur in closest succession (<4 days) typically impact different stretches of coastline. The spring/neap tidal cycle prevents successive extreme sea level events from happening within 4–8 days. Finally, the 2013/14 season was highly unusual in the context of the last 100 years from an extreme sea level perspective.
Dataset of eye disease-related proteins analyzed using the unfolding mutation screen
Authors: McCafferty Caitlyn L. , Sergeev Yuri V.
Published: December 2016

A number of genetic diseases are a result of missense mutations in protein structure. These mutations can lead to severe protein destabilization and misfolding. The unfolding mutation screen (UMS) is a computational method that calculates unfolding propensities for every possible missense mutation in a protein structure. The UMS validation demonstrated a good agreement with experimental and phenotypical data. 15 protein structures (a combination of homology models and crystal structures) were analyzed using UMS. The standard and clustered heat maps, and patterned protein structure from the analysis were stored in a UMS library. The library is currently composed of 15 protein structures from 14 inherited eye diseases including retina degenerations, glaucoma, and cataracts, and contains data for 181,110 mutations. The UMS protein library introduces 13 new human models of eye disease related proteins and is the first collection of the consistently calculated unfolding propensities, which could be used as a tool for the express analysis of novel mutations in clinical practice, next generation sequencing, and genotype-to-phenotype relationships in inherited eye disease.
Colonic luminal microbiota and bacterial metabolite composition in pregnant Huanjiang mini-pigs: effects of food composition at different times of pregnancy
Authors: Kong Xiang-feng , Ji Yu-jiao , Li Hua-wei , Zhu Qian , Blachier F. , Geng Mei-mei , Chen Wen , Yin Yu-long
Published: December 2016

The gut harbours diverse and complex microbiota, which influence body health including nutrient metabolism, immune development, and protection from pathogens. Pregnancy is associated with immune and metabolic changes that might be related to microbiota compositional dynamics. We therefore investigated the colonic luminal bacteria community in Huanjiang mini-pigs fed diets with different nutrient levels from the first to third trimester of pregnancy. The concentrations of intestinal metabolites including short-chain fat acids, NH3-N, indole, skatole, and bioamines were also determined. We found that the colonic bacteria species richness estimators (Chao1 and ACE) decreased with increased gestational age. The dominant phyla identified were Firmicutes and Bacteroidetes; the dominant genera were Lactobacillus, Treponema, Ruminococcus, Clostridium, and Prevotella. In addition, microbiota displayed spatial and temporal heterogeneity in composition, diversity, and species abundance in different colonic segments from the first to third trimester of pregnancy. Furthermore, the bacterial metabolites also changed according to the diet used and the pregnancy stage. These findings suggest that colonic bacteria richness decreased as gestational age increased, and that the higher nutrient level diet increased the production of metabolites related to nitrogen metabolism. However, although the higher nutrient diet was associated with pregnancy syndrome, causal links remain to be determined.
Submillimetre Network Formation by Light-induced Hybridization of Zeptomole-level DNA
Authors: Iida Takuya , Nishimura Yushi , Tamura Mamoru , Nishida Keisuke , Ito Syoji , Tokonami Shiho
Published: December 2016

Macroscopic unique self-assembled structures are produced via double-stranded DNA formation (hybridization) as a specific binding essential in biological systems. However, a large amount of complementary DNA molecules are usually required to form an optically observable structure via natural hybridization, and the detection of small amounts of DNA less than femtomole requires complex and time-consuming procedures. Here, we demonstrate the laser-induced acceleration of hybridization between zeptomole-level DNA and DNA-modified nanoparticles (NPs), resulting in the assembly of a submillimetre network-like structure at the desired position with a dramatic spectral modulation within several minutes. The gradual enhancement of light-induced force and convection facilitated the two-dimensional network growth near the air-liquid interface with optical and fluidic symmetry breakdown. The simultaneous microscope observation and local spectroscopy revealed that the assembling process and spectral change are sensitive to the DNA sequence. Our findings establish innovative guiding principles for facile bottom-up production via various biomolecular recognition events.
Purslane (Portulaca oleracea) Seed Consumption And Aerobic Training Improves Biomarkers Associated with Atherosclerosis in Women with Type 2 Diabetes (T2D)
Authors: Dehghan Firouzeh , Soori Rahman , Gholami Khadijeh , Abolmaesoomi Mitra , Yusof Ashril , Muniandy Sekaran , Heidarzadeh Sara , Farzanegi Parvin , Ali azarbayjani Mohammad
Published: December 2016

The aim of this study was to investigate the responses of atherosclerosis plaque biomarkers to purslane seed consumption and aerobic training in women with T2D. 196 women with T2D were assigned into; (1) placebo (PL), (2) aerobic training+placebo (AT + PL), 3) purslane seeds (PS), aerobic training+purslane seeds (AT + PS). The training program and purslane seeds consumption (2.5 g lunch and 5 g dinner) were carried out for 16 weeks. The components of purslane seed were identified and quantified by GC–MS. Blood samples were withdrawn via venipuncture to examine blood glucose, low-density lipoprotein (LDL), high-density lipoprotein (HDL), cholesterol, triglycerides (TG), creatinine, urea, uric acid, NF-κB, GLP1, GLP1R, TIMP-1, MMP2, MMP9, CRP, CST3, and CTSS expressions. Blood glucose, LDL, cholesterol, TG, creatinine, urea, and uric acid levels in the (P), (AT), and (AT + PS) groups were significantly decreased compared to the pre-experimental levels or the placebo group, while HDL, significantly increased. Furthermore, the protein and mRNA levels of NF-κB, TIMP-1, MMP2 &9, CRP, CST3, and CTSS in the (P), (AT), (AT + PS) significantly decreased compared to pre-experimental or the placebo group, while level of GLP1 and GLP1-R increased drastically. Findings suggest that purslane seed consumption alongside exercising could improve atherosclerosis plaque biomarkers through synergistically mechanisms in T2D.
Dynamical tuning between nearly perfect reflection, absorption, and transmission of light via graphene/dielectric structures
Authors: Linder Jacob , Halterman Klaus
Published: December 2016

Exerting well-defined control over the reflection (R), absorption (A), and transmission (T) of electromagnetic waves is a key objective in quantum optics. To this end, one often utilizes hybrid structures comprised of elements with different optical properties in order to achieve features such as high R or high A for incident light. A desirable goal would be the possibility to tune between all three regimes of nearly perfect reflection, absorption, and transmission within the same device, thus swapping between the cases R → 1, A → 1, and T → 1 dynamically. We here show that a dielectric interfaced with a graphene layer on each side allows for precisely this: by tuning only the Fermi level of graphene, all three regimes can be reached in the THz regime and below. Moreover, we show that the inclusion of cylindrical defects in the system offers a different type of control of the scattering of electromagnetic waves by means of the graphene layers.
Soluble Amyloid-beta Aggregates from Human Alzheimer’s Disease Brains
Authors: Esparza Thomas J. , Wildburger Norelle C. , Jiang Hao , Gangolli Mihika , Cairns Nigel J. , Bateman Randall J. , Brody David L.
Published: December 2016

Soluble amyloid-beta (Aβ) aggregates likely contribute substantially to the dementia that characterizes Alzheimer’s disease. However, despite intensive study of in vitro preparations and animal models, little is known about the characteristics of soluble Aβ aggregates in the human Alzheimer’s disease brain. Here we present a new method for extracting soluble Aβ aggregates from human brains, separating them from insoluble aggregates and Aβ monomers using differential ultracentrifugation, and purifying them >6000 fold by dual antibody immunoprecipitation. The method resulted in <40% loss of starting material, no detectible ex vivo aggregation of monomeric Aβ, and no apparent ex vivo alterations in soluble aggregate sizes. By immunoelectron microscopy, soluble Aβ aggregates typically appear as clusters of 10–20 nanometer diameter ovoid structures with 2-3 amino-terminal Aβ antibody binding sites, distinct from previously characterized structures. This approach may facilitate investigation into the characteristics of native soluble Aβ aggregates, and deepen our understanding of Alzheimer’s dementia.
Self-cleaning of Surfaces: the Role of Surface Wettability and Dust Types
Authors: Quan Yun-Yun , Zhang Li-Zhi , Qi Rong-Hui , Cai Rong-Rong
Published: December 2016

The self-cleaning property is usually connected to superhydrophobic surfaces (SHSs) where the dust particles can be easily removed by the rolling motion of droplets. It seems that superhydrophobicity (its durability is questionable nowadays) is a necessity. However here, it is disclosed that self-cleaning can also be realized on an ordinary surface by droplet impinging. The effects of surface wettability and the types of dust particles are considered. The self-cleaning is realized by two steps: (1) the pickup of particles by the water-air interface of an impinging droplet, (2) the release of the impinging droplets from the surface. It can be observed that only the trailing edges of the droplets can pick up particles when the droplets recoil from the inclined surfaces. The hydrophilic surface can also achieve self-cleaning under some conditions. This interesting finding may be helpful for the successful implementation of self-cleaning with common surfaces.
Apparent Negative Reflection with the Gradient Acoustic Metasurface by Integrating Supercell Periodicity into the Generalized Law of Reflection
Authors: Liu Bingyi , Zhao Wenyu , Jiang Yongyuan
Published: December 2016

As the two dimensional version of the functional wavefront manipulation metamaterial, metasurface has become a research hot spot for engineering the wavefront at will with a subwavelength thickness. The wave scattered by the gradient metasurface, which is composed by the periodic supercells, is governed by the generalized Snell’s law. However, the critical angle that derived from the generalized Snell’s law circles the domain of the incident angles that allow the occurrence of the anomalous reflection and refraction, and no free space scattering waves could exist when the incident angle is beyond the critical angle. Here we theoretically demonstrate that apparent negative reflection can be realized by a gradient acoustic metasurface when the incident angle is beyond the critical angle. The underlying mechanism of the apparent negative reflection is understood as the higher order diffraction arising from the interaction between the local phase modulation and the non-local effects introduced by the supercell periodicity. The apparent negative reflection phenomena has been perfectly verified by the calculated scattered acoustic waves of the reflected gradient acoustic metasurface. This work may provide new freedom in designing functional acoustic signal modulation devices, such as acoustic isolator and acoustic illusion device.
Catalytic Conversion of Lipophilic Substrates by Phase constrained Enzymes in the Aqueous or in the Membrane Phase
Authors: Cebula Marcus , Turan Ilke Simsek , Sjödin Birgitta , Thulasingam Madhuranayaki , Brock Joseph , Chmyrov Volodymyr , Widengren Jerker , Abe Hiroshi , Mannervik Bengt , Haeggström Jesper Z. , Rinaldo-Matthis Agnes , Akkaya Engin U. , Morgenstern Ralf
Published: December 2016

Both soluble and membrane-bound enzymes can catalyze the conversion of lipophilic substrates. The precise substrate access path, with regard to phase, has however, until now relied on conjecture from enzyme structural data only (certainly giving credible and valuable hypotheses). Alternative methods have been missing. To obtain the first experimental evidence directly determining the access paths (of lipophilic substrates) to phase constrained enzymes we here describe the application of a BODIPY-derived substrate (PS1). Using this tool, which is not accessible to cytosolic enzymes in the presence of detergent and, by contrast, not accessible to membrane embedded enzymes in the absence of detergent, we demonstrate that cytosolic and microsomal glutathione transferases (GSTs), both catalyzing the activation of PS1, do so only within their respective phases. This approach can serve as a guideline to experimentally validate substrate access paths, a fundamental property of phase restricted enzymes. Examples of other enzyme classes with members in both phases are xenobiotic-metabolizing sulphotransferases/UDP-glucuronosyl transferases or epoxide hydrolases. Since specific GSTs have been suggested to contribute to tumor drug resistance, PS1 can also be utilized as a tool to discriminate between phase constrained members of these enzymes by analyzing samples in the absence and presence of Triton X-100.
Physically Transient Memory on a Rapidly Dissoluble Paper for Security Application
Authors: Bae Hagyoul , Lee Byung-Hyun , Lee Dongil , Seol Myeong-Lok , Kim Daewon , Han Jin-Woo , Kim Choong-Ki , Jeon Seung-Bae , Ahn Daechul , Park Sang-Jae , Park Jun-Young , Choi Yang-Kyu
Published: December 2016

We report the transient memory device by means of a water soluble SSG (solid sodium with glycerine) paper. This material has a hydroscopic property hence it can be soluble in water. In terms of physical security of memory devices, prompt abrogation of a memory device which stored a large number of data is crucial when it is stolen because all of things have identified information in the memory device. By utilizing the SSG paper as a substrate, we fabricated a disposable resistive random access memory (RRAM) which has good data retention of longer than 106 seconds and cycling endurance of 300 cycles. This memory device is dissolved within 10 seconds thus it can never be recovered or replicated. By employing direct printing but not lithography technology to aim low cost and disposable applications, the memory capacity tends to be limited less than kilo-bits. However, unlike high memory capacity demand for consumer electronics, the proposed device is targeting for security applications. With this regards, the sub-kilobit memory capacity should find the applications such as one-time usable personal identification, authentication code storage, cryptography key, and smart delivery tag. This aspect is attractive for security and protection system against unauthorized accessibility.
A closer look into the α-helix basin
Authors: Haimov Boris , Srebnik Simcha
Published: December 2016

α-Helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. Representation of α-helical structures with the common (φ, ψ) dihedrals, as in Ramachandran maps, does not provide informative details regarding the helical structure apart for the abstract geometric meaning of the dihedrals. We present an alternative coordinate system that describes helical conformations in terms of residues per turn (ρ) and angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ, ψ and ρ, ϑ). In this way, valuable information on the helical structure becomes directly available. Analysis of α-helical conformations acquired from the Protein Data Bank (PDB) demonstrates that a conformational energy function of the α-helix backbone can be harmonically approximated on the (ρ, ϑ) space, which is not applicable to the (φ, ψ) space due to the diagonal distribution of the conformations. The observed trends of helical conformations obtained from the PDB are captured by four conceptual simulations that theoretically examine the effects of residue bulkiness, external electric field, and externally applied mechanical forces. Flory’s isolated pair hypothesis is shown to be partially correct for α-helical conformations.
NIPTRIC: an online tool for clinical interpretation of non-invasive prenatal testing (NIPT) results
Authors: Sikkema-Raddatz Birgit , Johansson Lennart F. , de Boer Eddy N. , Boon Elles M. J. , Suijkerbuijk Ron F. , Bouman Katelijne , Bilardo Catia M. , Swertz Morris A. , Dijkstra Martijn , van Langen Irene M. , Sinke Richard J. , te Meerman Gerard J.
Published: December 2016

To properly interpret the result of a pregnant woman’s non-invasive prenatal test (NIPT), her a priori risk must be taken into account in order to obtain her personalised a posteriori risk (PPR), which more accurately expresses her true likelihood of carrying a foetus with trisomy. Our aim was to develop a tool for laboratories and clinicians to calculate easily the PPR for genome-wide NIPT results, using diploid samples as a control group. The tool takes the a priori risk and Z-score into account. Foetal DNA percentage and coefficient of variation can be given default settings, but actual values should be used if known. We tested the tool on 209 samples from pregnant women undergoing NIPT. For Z-scores < 5, the PPR is considerably higher at a high a priori risk than at a low a priori risk, for NIPT results with the same Z-score, foetal DNA percentage and coefficient of variation. However, the PPR is effectively independent under all conditions for Z-scores above 6. A high PPR for low a priori risks can only be reached at Z-scores > 5. Our online tool can assist clinicians in understanding NIPT results and conveying their true clinical implication to pregnant women, because the PPR is crucial for individual counselling and decision-making.
Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line
Authors: Chen Maoshan , Xu Rong , Ji Hong , Greening David W. , Rai Alin , Izumikawa Keiichi , Ishikawa Hideaki , Takahashi Nobuhiro , Simpson Richard J.
Published: December 2016

Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes – two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) – with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i.e., are enriched in) LIM1863 EVs, relative to the parent cell. An Ensembl/UniProtKB analysis revealed 1,937 mRNAs encode canonical proteins, 348 isoforms (including splice-variant proteins), and 119 ‘missing proteins’ (i.e., annotated in Ensembl but not UniProtKB). Further dissection of our protein/RNA data revealed that 6/151 observed RNA binding proteins have the potential to interact with ~75% of EV-enriched RNAs. Intriguingly, the co-existence of U1 and U2 ribonucleoproteins and their cognate snRNAs in LIM1863 EVs suggests a possible association of CRC EVs with recipient cell splicing events. Our data reveal several potential lncRNA CRC biomarkers and novel splicing/fusion genes that, collectively, will advance our understanding of EV biology in CRC and accelerate the development of EV-based diagnostics and therapeutics.
Intravenous hMSCs Ameliorate Acute Pancreatitis in Mice via Secretion of Tumor Necrosis Factor-α Stimulated Gene/Protein 6
Authors: He Zhigang , Hua Jie , Qian Daohai , Gong Jian , Lin Shengping , Xu Chenglei , Wei Ge , Meng Hongbo , Yang Tingsong , Zhou Bo , Song Zhenshun
Published: December 2016

The administration of mesenchymal stem cells/multipotent mesenchymal stromal cells (MSCs) to enhance tissue repair is currently undergoing clinical trials. Some studies, including our previous work, have also revealed the beneficial effect of MSCs in severe acute pancreatitis (SAP); however, their mechanisms or mode of action remain controversial. In this study, we demonstrated that intravenously (i.v.)-administered human MSCs (hMSCs) remarkably promoted recovery from experimental SAP without significant engraftment of hMSCs in the damaged pancreas. Interestingly, we found that i.v.-administered hMSCs with knockdown of TSG-6 expression lost most of their anti-inflammatory effects and thus could not significantly ameliorate SAP. As expected, the effects of hMSCs were also duplicated by i.v. infusion of recombinant TSG-6. Furthermore, our results showed that the increase of oxidative stress, activation of the NLRP3 inflammasome and NF-κB signaling in SAP was substantially inhibited following administration of hMSCs or TSG-6, which was dependent on the presence of CD-44 receptors in acinar cells. In conclusion, our study, for the first time, revealed that novel mechanisms are responsible for the immunomodulatory effect of i.v. hMSCs.
High-quality and Large-size Topological Insulator Bi2Te3-Gold Saturable Absorber Mirror for Mode-Locking Fiber Laser
Authors: Chen Hou-Ren , Tsai Chih-Ya , Cheng Hsin-Ming , Lin Kuei-Huei , Yen Po-Hsiu , Chen Chyong-Hua , Hsieh Wen-Feng
Published: December 2016

A novel high-quality, large-size, reflection-type topological insulator Bi2Te3-Gold (BG) film-based nonlinear optical modulator has been successfully fabricated as a two-dimensional saturable absorber mirror (SAM) by pulsed laser deposition (PLD). This BG-SAM possesses saturation fluence of 108.3 μJ/cm2, modulation depth (ΔR) of 6.5%, non-saturable loss of 38.4%, high damage threshold above 1.354 mJ/cm2 and excellent uniformity providing for the generation of passive mode-locked (ML) pulses for erbium-doped fiber lasers (EDFLs) on a large sample area. Under 124 mW 976 nm pumping, We obtained 452-fs continuous-wave ML pulses with pulse energy of 91 pJ and full width at half-maximum (FWHM) of 6.72-nm from this EDFL. The results clearly evidence that the PLD is an efficient method for fabricating BG-SAM that is suitable for a compact ultrafast ML fiber laser system.
Direct synthesis of hydrogen peroxide from plasma-water interactions
Authors: Liu Jiandi , He Bangbang , Chen Qiang , Li Junshuai , Xiong Qing , Yue Guanghui , Zhang Xianhui , Yang Size , Liu Hai , Liu Qing Huo
Published: December 2016

Hydrogen peroxide (H2O2) is usually considered to be an important reagent in green chemistry since water is the only by-product in H2O2involved oxidation reactions. Early studies show that direct synthesis of H2O2by plasma-water interactions is possible, while the factors affecting the H2O2production in this method remain unclear. Herein, we present a study on the H2O2synthesis by atmospheric pressure plasma-water interactions. The results indicate that the most important factors for the H2O2production are the processes taking place at the plasma-water interface, including sputtering, electric field induced hydrated ion emission, and evaporation. The H2O2production rate reaches ~1200 μmol/h when the liquid cathode is purified water or an aqueous solution of NaCl with an initial conductivity of 10500 μS cm−1.
Association between peripheral arterial occlusive disease and cardiothoracic ratio in patients on chronic hemodialysis
Authors: Liou Kang-Yi , Liou Hung-Hsiang , Fang Yu-Wei , Leu Jyh-Gang , Tsai Ming-Hsien
Published: December 2016

The cardiothoracic ratio (CTR) and peripheral arterial occlusive disease (PAOD) are related to mortality in hemodialysis patients. However, data on the association between PAOD and CTR are limited. In this study, we aim to elucidate this relationship in patients on chronic hemodialysis. Using a retrospective cross-sectional study of 622 Taiwanese patients, we investigated the association of PAOD and CTR. PAOD was significantly associated with CTR in the crude analysis. The odds ratio (OR) for CTR >0.5 was 1.77 [95% confidence interval (CI), 1.32–2.37], and the odds ratio for CTR >0.6 was 2.18 [95% CI, 1.44–3.30]. After adjusting for confounding variables, this difference continued to exhibit significant predictive power for CTR >0.6 (OR, 1.88; 95% CI, 1.14–3.11), but the predictive power for CTR >0.5 was attenuated (OR, 1.41; 95% CI, 0.98–2.03). In the subgroup analysis, PAOD was an independent factor for CTR >0.6, particularly in elderly and female patients or patients with hemoglobin >10 mg/dl and with no history of cardiovascular disease. In this research, we showed that the detection of PAOD was independently associated with CTR >0.6 in patients on chronic hemodialysis.
Revealing extraordinary tensile plasticity in layered Ti-Al metal composite
Authors: Huang M. , Fan G. H. , Geng L. , Cao G. J. , Du Y. , Wu H. , Zhang T. T. , Kang H. J. , Wang T. M. , Du G. H. , Xie H. L.
Published: December 2016

Layered Ti-Al metal composite (LMC) fabricated by hot-pressing and hot-rolling process displays higher ductility than that of both components. In this paper, a combination of digital image correlation (DIC) and X-ray tomography revealed that strain delocalization and constrained crack distribution are the origin of extraordinary tensile ductility. Strain delocalization was derived from the transfer of strain partitioning between Ti and Al layer, which relieved effectively the strain localization of LMC. Furthermore, the extensive cracks of LMC were restricted in the interface due to constraint effect. Layered architecture constrained the distribution of cracks and significantly relieved the strain localization. Meanwhile, the transfer of strain partitioning and constrained crack distribution were believed to inhibit the strain localization of Ti and change the deformation mechanisms of Ti. Our finding enriches current understanding about simultaneously improving the strength and ductility by structural design.
Clonal spread of mcr-1 in PMQR-carrying ST34 Salmonella isolates from animals in China
Authors: Li Xing-Ping , Fang Liang-Xing , Song Jia-Qi , Xia Jing , Huo Wei , Fang Jin-Tao , Liao Xiao-Ping , Liu Ya-Hong , Feng Youjun , Sun Jian
Published: December 2016

Since initial identification in China, the widespread geographical occurrence of plasmid-mediated colistin resistance gene mcr-1 in Enterobacteriaceae has been of great concern. In this study, a total of 22 Salmonella enterica were resistant to colistin, while only five isolates which belonged to ST34 Salmonella enterica serovar Typhimurium (S. Typhimurium) were mcr-1 positive. Four of them shared nearly identical PFGE type, although they were from different host species and diverse geographical locations. All the mcr-1-positive S. Typhimurium exhibited multi-resistant phenotypes including ampicillin, streptomycin, gentamicin, florfenicol, nalidixic acid, tetracycline, trimethoprim-sulfamethox, in addition to colistin. The oqxAB and aac(6′)-Ib-cr genes were present alone or in combination in four (80.0%) and five (100%) isolates, respectively. The mcr-1 gene was located on a transferable IncI2 plasmid in the four genetically related strains. In the other one strain, mcr-1 was located on an approximately 190 kb IncHI2 plasmid. In conclusion, we report five mcr-1-positive S. Typhimurium/ST34 isolates. Both clonal expansion and horizontal transmission of IncI2-type plasmids were involved in the spread of the mcr-1 gene in Salmonella enterica from food-producing animals in China. There is a great need to monitor the potential dissemination of the mcr-1 gene.
Turning Diamagnetic Microbes into Multinary Micro-Magnets: Magnetophoresis and Spatio-Temporal Manipulation of Individual Living Cells
Authors: Lee Hojae , Hong Daewha , Cho Hyeoncheol , Kim Ji Yup , Park Ji Hun , Lee Sang Hee , Kim Ho Min , Fakhrullin Rawil F. , Choi Insung S.
Published: December 2016

Inspired by the biogenic magnetism found in certain organisms, such as magnetotactic bacteria, magnetic nanomaterials have been integrated into living cells for bioorthogonal, magnetic manipulation of the cells. However, magnetized cells have so far been reported to be only binary system (on/off) without any control of magnetization degree, limiting their applications typically to the simple accumulation or separation of cells as a whole. In this work, the magnetization degree is tightly controlled, leading to the generation of multiple subgroups of the magnetized cells, and each subgroup is manipulated independently from the other subgroups in the pool of heterogeneous cell-mixtures. This work will provide a strategic approach to tailor-made fabrication of magnetically functionalized living cells as micro-magnets, and open new vistas in biotechnological and biomedical applications, which highly demand the spatio-temporal manipulation of living cells.
RCANs regulate the convergent roles of NFATc1 in bone homeostasis
Authors: Kim Jung Ha , Kim Kabsun , Kim Inyoung , Seong Semun , Jeong Byung-chul , Nam Kwang-Il , Kim Kyung Keun , Molkentin Jeffery D. , Kim Nacksung
Published: December 2016

Activation of calcineurin-dependent nuclear factor of activated T cells c1 (NFATc1) is convergent for normal bone homeostasis. NFATc1 regulates both osteoclastogenesis and osteoblastogenesis. Here we investigated the roles of regulator of calcineurin (RCAN) genes in bone homeostasis. RCANs function as potent physiological inhibitors of calcineurin. Overexpression of RCANs in osteoclast precursor cells attenuated osteoclast differentiation, while their overexpression in osteoblasts enhanced osteoblast differentiation and function. Intriguingly, opposing effects of RCANs in both cell types were shown by blocking activation of the calcineurin-NFATc1 pathway. Moreover, the disruption of RCAN1 or RCAN2 in mice resulted in reduced bone mass, which is associated with strongly increased osteoclast function and mildly reduced osteoblast function. Taken together, RCANs play critical roles in bone homeostasis by regulating both osteoclastogenesis and osteoblastogenesis, and they serve as inhibitors for calcineurin-NFATc1 signaling both in vivo and in vitro.
Adsorption of perfluorocarboxylic acids at the silica surface
Authors: Shafique Umer , Dorn Vivien , Paschke Albrecht , Schüürmann Gerrit
Published: December 2016

Experimental findings suggest a molecular mechanism for the adsorption of perfluorocarboxylic acids (anionic surfactants) at the negatively charged silica surface.
Cationic gemini surfactant as a dual linker for a cholic acid-modified polysaccharide in aqueous solution: thermodynamics of interaction and phase behavior
Authors: Bai Guangyue , Wu Hui , Lou Pengxiao , Wang Yujie , Nichifor Marieta , Zhuo Kelei , Wang Jianji , Bastos Margarida
Published: December 2016

The cross-linking effect of gemini surfactant at only a small mole fraction can tune the aggregate structure of cholic acid-modified polysaccharide.
Water oxidation mediated by ruthenium oxide nanoparticles supported on siliceous mesocellular foam
Authors: Gustafson Karl P. J. , Shatskiy Andrey , Verho Oscar , Kärkäs Markus D. , Schluschass Bastian , Tai Cheuk-Wai , Åkermark Björn , Bäckvall Jan-Erling , Johnston Eric V.
Published: December 2016

An efficient catalyst for chemical and photochemical water oxidation was developed by immobilization of RuO2 nanoparticles on pyridine-functionalized mesoporous silica.
Designing ordered mesoporous aluminosilicates under acidic conditions via an intrinsic hydrolysis method
Authors: Krishna Nunna V. , Selvam Parasuraman
Published: December 2016

A novel intrinsic hydrolysis method was employed for the synthesis of well-ordered mesoporous aluminosilicates, viz., H-AlSBA-15 and H-AlIITM-56, with trivalent aluminium, exclusively, in a tetrahedral framework structure.
Ag2S nanoparticle-decorated MoS2 for enhanced electrocatalytic and photoelectrocatalytic activity in water splitting
Authors: Wang Min , Ju Peng , Li Wen , Zhao Yun , Han Xiuxun
Published: December 2016

Tight nanojunctions between Ag2S and MoS2 were constructed, which facilitates the separation of photogenerated charge carriers.
Influence of double (w1/o/w2) emulsion composition on lubrication properties
Authors: Oppermann A. K. L. , Verkaaik L. C. , Stieger M. , Scholten E.
Published: December 2016

This article focusses on the influence of composition (level of fat reduction, mechanical properties of w1 droplets) on lubrication properties of double (w1/o/w2) emulsions.
Highly chemoselective reduction of nitroarenes over non-noble metal nickel-molybdenum oxide catalysts
Authors: Huang Haigen , Wang Xueguang , Li Xu , Chen Chenju , Zou Xiujing , Ding Weizhong , Lu Xionggang
Published: December 2016

A non-noble Ni-MoO3/CN@SBA-15 catalyst exhibits unprecedented catalytic activity and chemoselectivity for the reduction of nitroarenes to anilines in ethanol with hydrazine hydrate.
Computational model of inductively coupled plasma sources in comparison to experimental data for different torch designs and plasma conditions. Part I: experimental study
Authors: Voronov M. , Hoffmann V. , Engelhard C. , Buscher W.
Published: December 2016

Fundamental diagnostics of ICP in a low-argon-flow and standard Fassel-type torches including optical, electrical and infrared measurements.
Investigation of the oxidative transformation of roxarsone by electrochemistry coupled to hydrophilic interaction liquid chromatography/mass spectrometry
Authors: Frensemeier Lisa M. , Büter Lars , Vogel Martin , Karst Uwe
Published: December 2016

The oxidative transformation of the animal feed additive roxarsone was investigated using electrochemistry (EC) coupled to hydrophilic interaction liquid chromatography (HILIC) and mass spectrometry.
Real-time observation of protein aggregates in pharmaceutical formulations using liquid cell electron microscopy
Authors: DiMemmo Lynn M. , Cameron Varano A. , Haulenbeek Jonathan , Liang Yanping , Patel Kaya , Dukes Madeline J. , Zheng Songyan , Hubert Mario , Piccoli Steven P. , Kelly Deborah F.
Published: December 2016

Understanding the properties of protein-based therapeutics is a common goal of biologists and physicians.
Synthesis, characterization, solubilization, cytotoxicity and antioxidant activity of aminomethylated dihydroquercetin
Authors: Li Jianxia , Dong Jieqiong , Ouyang Jie , Cui Jie , Chen Yuan , Wang Fengjun , Wang Jianzhong
Published: December 2016

We successfully synthesised an efficient, water-soluble, nontoxic, and high antioxidant activity dihydroquercetin derivative (DHQA) by aminomethylation reaction.
An all-solid-state asymmetric device based on a polyaniline hydrogel for a high energy flexible supercapacitor
Authors: Heydari Hamid , Gholivand Mohammad B.
Published: December 2016

3D porous PANI hydrogel and a gel electrolyte were used to fabricate a high performance, all-solid-state, flexible asymmetric supercapacitor with an energy density of up to 6.16 mW h cm−3.
Chemoprotective activity of mixed valence polyoxovanadates against diethylsulphate in E. coli cultures: insights from solution speciation studies
Authors: Postal K. , Maluf D. F. , Valdameri G. , Rüdiger A. L. , Hughes D. L. , de Sá E. L. , Ribeiro R. R. , de Souza E. M. , Soares J. F. , Nunes G. G.
Published: December 2016

Cell survival after treatment with dimethylsulphate in the presence of polyoxovanadates.
Pro-oxidant effects of nano-TiO2on Chlamydomonas reinhardtii during short-term exposure
Authors: von Moos Nadia , Koman Volodymyr B. , Santschi Christian , Martin Olivier J. F. , Maurizi Lionel , Jayaprakash Amarnath , Bowen Paul , Slaveykova Vera I.
Published: December 2016

This is the first continuous quantification of abiotic and biotic nano-TiO2– stimulated H2O2revealing that measured extracellular and intracellular pro-oxidant endpoints inC. reinhardtiican differ significantly.
Optoelectrical, morphological and mechanical features of nitrophenyl supported poly(1,3,4-oxadiazole)s and their nanocomposites with TiO2
Authors: Kaippamangalath Nimisha , Gopalakrishnapanicker Unnikrishnan , Shiju E. , Chandrasekharan K.
Published: December 2016

Charge transfer phenomenon and redox behaviour, of PPNO/PNPPO nanocomposites, triggered by TiO2 nanoparticles.
High work function with reduced phase separation of PSS in metal oxide modified PEDOT:PSS interlayers for organic photovoltaics
Authors: Kanwat Anil , Jang Jin
Published: December 2016

(a) Formation of insulating PSS on the surface of thin films, (b) dark J–V characteristics of the regular geometry OPVs with neat PEDOT:PSS and metal oxide doped PEDOT:PSS interlayers.