bluuebunny/crossref_metadata_2025 huggingface dataset:
D-β-aspartyl residue exhibiting uncommon high resistance to spontaneous peptide bond cleavage
Authors: Aki Kenzo , Okamura Emiko
Published: February 2016

Although L-amino acids were selected as main constituents of peptides and proteins during chemical evolution, D-aspartyl (Asp) residue is found in a variety of living tissues. In particular, D-β-Asp is thought to be stable than any other Asp isomers and this could be a reason for gradual accumulation in abnormal proteins and peptides to modify their structures and functions. It is predicted that D-β-Asp shows high resistance to biomolecular reactions. For instance, less reactivity of D-β-Asp is expected to bond cleavage, although such information has not been provided yet. In this work, the spontaneous peptide bond cleavage was compared between Asp isomers, by applying real-time solution-state NMR to eye lens αΑ-crystallin 51–60 fragment, S51LFRTVLD58SG60 and αΒ-crystallin 61–67 analog, F61D62TGLSG67 consisting of L-α- and D-β-Asp 58 and 62, respectively. Kinetic analysis showed how tough the uncommon D-β-Asp residue was against the peptide bond cleavage as compared to natural L-α-Asp. Differences in pKa and conformation between L-α- and D-β-Asp side chains were plausible factors to determine reactivity of Asp isomers. The present study, for the first time, provides a rationale to explain less reactivity of D-β-Asp to allow abnormal accumulation.
Cyclin-dependent kinase 2 protects podocytes from apoptosis
Authors: Saurus Pauliina , Kuusela Sara , Dumont Vincent , Lehtonen Eero , Fogarty Christopher L. , Lassenius Mariann I. , Forsblom Carol , Lehto Markku , Saleem Moin A. , Groop Per-Henrik , Lehtonen Sanna
Published: February 2016

Loss of podocytes is an early feature of diabetic nephropathy (DN) and predicts its progression. We found that treatment of podocytes with sera from normoalbuminuric type 1 diabetes patients with high lipopolysaccharide (LPS) activity, known to predict progression of DN, downregulated CDK2 (cyclin-dependent kinase 2). LPS-treatment of mice also reduced CDK2 expression. LPS-induced downregulation of CDK2 was prevented in vitro and in vivo by inhibiting the Toll-like receptor (TLR) pathway using immunomodulatory agent GIT27. We also observed that CDK2 is downregulated in the glomeruli of obese Zucker rats before the onset of proteinuria. Knockdown of CDK2, or inhibiting its activity with roscovitine in podocytes increased apoptosis. CDK2 knockdown also reduced expression of PDK1, an activator of the cell survival kinase Akt and reduced Akt phosphorylation. This suggests that CDK2 regulates the activity of the cell survival pathway via PDK1. Furthermore, PDK1 knockdown reduced the expression of CDK2 suggesting a regulatory loop between CDK2 and PDK1. Collectively, our data show that CDK2 protects podocytes from apoptosis and that reduced expression of CDK2 associates with the development of DN. Preventing downregulation of CDK2 by blocking the TLR pathway with GIT27 may provide a means to prevent podocyte apoptosis and progression of DN.
Cytomegalovirus-based vaccine expressing Ebola virus glycoprotein protects nonhuman primates from Ebola virus infection
Authors: Marzi Andrea , Murphy Aisling A. , Feldmann Friederike , Parkins Christopher J. , Haddock Elaine , Hanley Patrick W. , Emery Matthew J. , Engelmann Flora , Messaoudi Ilhem , Feldmann Heinz , Jarvis Michael A.
Published: February 2016

Ebolaviruses pose significant public health problems due to their high lethality, unpredictable emergence, and localization to the poorest areas of the world. In addition to implementation of standard public health control procedures, a number of experimental human vaccines are being explored as a further means for outbreak control. Recombinant cytomegalovirus (CMV)-based vectors are a novel vaccine platform that have been shown to induce substantial levels of durable, but primarily T-cell-biased responses against the encoded heterologous target antigen. Herein, we demonstrate the ability of rhesus CMV (RhCMV) expressing Ebola virus (EBOV) glycoprotein (GP) to provide protective immunity to rhesus macaques against lethal EBOV challenge. Surprisingly, vaccination was associated with high levels of GP-specific antibodies, but with no detectable GP-directed cellular immunity.
Effect of excessive CO2 on physiological functions in coastal diatom
Authors: Liu Feng-Jiao , Li Shun-Xing , Huang Bang-Qin , Zheng Feng-Ying , Huang Xu-Guang
Published: February 2016

Rising dissolution of anthropogenic CO2 in seawater may directly/indirectly cause ocean acidification and desalination. However, little is known about coastal physiological functions sensitivity to these processes. Here we show some links between ocean acidification/desalination and physiological functions in Thalassiosira weissflogii. Cell density (CD), protein, chlorophyll a (Chl a), malonaldehyde (MDA), superoxide dismutase (SOD), and carbonic anhydrase (CAs) were determined for the assessment of algal biomass, nutritional value, photosynthesis and respiration, lipid peroxidation, antioxidant capacity, and carbon sequestration ability. The influence of pH on the algal Chl a and MDA were extremely significant (P < 0.01). Salinity (S) on cell density and acidity (pH) on protein was significant (0.01 < P < 0.05). Additionally, a significant negative-correlation was observed between cell density and CAs. CAs and SOD had negatively correlations with CD, Chl a, protein, and MDA under pH or S influence, but positive correlation between themselves. Coastal physiological functions were affected by increasing order was acidification < acidification + desalination < desalination for Chl a and protein, desalination < acidification + desalination < acidification for SOD and CAs. Thus, the ongoing excessive CO2-driven ocean acidification and desalination should be of high attention when assessing the risks of climate change on coastal phytoplankton.
Mechanisms and consequences of ATMIN repression in hypoxic conditions: roles for p53 and HIF-1
Authors: Leszczynska Katarzyna B. , Göttgens Eva-Leonne , Biasoli Deborah , Olcina Monica M. , Ient Jonathan , Anbalagan Selvakumar , Bernhardt Stephan , Giaccia Amato J. , Hammond Ester M.
Published: February 2016

Hypoxia-induced replication stress is one of the most physiologically relevant signals known to activate ATM in tumors. Recently, the ATM interactor (ATMIN) was identified as critical for replication stress-induced activation of ATM in response to aphidicolin and hydroxyurea. This suggests an essential role for ATMIN in ATM regulation during hypoxia, which induces replication stress. However, ATMIN also has a role in base excision repair, a process that has been demonstrated to be repressed and less efficient in hypoxic conditions. Here, we demonstrate that ATMIN is dispensable for ATM activation in hypoxia and in contrast to ATM, does not affect cell survival and radiosensitivity in hypoxia. Instead, we show that in hypoxic conditions ATMIN expression is repressed. Repression of ATMIN in hypoxia is mediated by both p53 and HIF-1α in an oxygen dependent manner. The biological consequence of ATMIN repression in hypoxia is decreased expression of the target gene, DYNLL1. An expression signature associated with p53 activity was negatively correlated with DYNLL1 expression in patient samples further supporting the p53 dependent repression of DYNLL1. Together, these data demonstrate multiple mechanisms of ATMIN repression in hypoxia with consequences including impaired BER and down regulation of the ATMIN transcriptional target, DYNLL1.
Fast Virtual Stenting with Active Contour Models in Intracranical Aneurysm
Authors: Zhong Jingru , Long Yunling , Yan Huagang , Meng Qianqian , Zhao Jing , Zhang Ying , Yang Xinjian , Li Haiyun
Published: February 2016

Intracranial stents are becoming increasingly a useful option in the treatment of intracranial aneurysms (IAs). Image simulation of the releasing stent configuration together with computational fluid dynamics (CFD) simulation prior to intervention will help surgeons optimize intervention scheme. This paper proposed a fast virtual stenting of IAs based on active contour model (ACM) which was able to virtually release stents within any patient-specific shaped vessel and aneurysm models built on real medical image data. In this method, an initial stent mesh was generated along the centerline of the parent artery without the need for registration between the stent contour and the vessel. Additionally, the diameter of the initial stent volumetric mesh was set to the maximum inscribed sphere diameter of the parent artery to improve the stenting accuracy and save computational cost. At last, a novel criterion for terminating virtual stent expanding that was based on the collision detection of the axis aligned bounding boxes was applied, making the stent expansion free of edge effect. The experiment results of the virtual stenting and the corresponding CFD simulations exhibited the efficacy and accuracy of the ACM based method, which are valuable to intervention scheme selection and therapy plan confirmation.
Quantitative analysis of iontophoretic drug delivery from micropipettes
Authors: Kirkpatrick D. C. , Walton L. R. , Edwards M. A. , Wightman R. M.
Published: February 2016

Ejection rates of microiontophoretic drug delivery were examined and can be predicted from initial pipette conditions.
Organoselenium and DMAP co-catalysis: regioselective synthesis of medium-sized halolactones and bromooxepanes from unactivated alkenes
Authors: Verma Ajay , Jana Sadhan , Durga Prasad Ch. , Yadav Abhimanyu , Kumar Sangit
Published: February 2016

A co-catalytic system has been developed for the synthesis of medium-sized halolactones and bromooxepanes possessing high transannular strain. Mechanistic studies reveal that quaternary selenium intermediate is involved in catalysis.
Reactive oxygen species formed in organic lithium–oxygen batteries
Authors: Schwager Patrick , Dongmo Saustin , Fenske Daniela , Wittstock Gunther
Published: February 2016

The generation of reactive oxygen species has been assumed to occur during the charging reaction of lithium-oxygen batteries with organic electrolytes. Here we show independently by fluorescence microscopy and scanning electrochemical microscopy that superoxide is also formed and released into the solution during the discharge reaction.
In search of metal hydrides: an X-ray absorption and emission study of [NiFe] hydrogenase model complexes
Authors: Hugenbruch Stefan , Shafaat Hannah S. , Krämer Tobias , Delgado-Jaime Mario Ulises , Weber Katharina , Neese Frank , Lubitz Wolfgang , DeBeer Serena
Published: February 2016

Insight into the factors that favor metal–hydride interactions in NiFe-hydrogenase models is obtained through X-ray spectroscopic and quantum chemical studies.
Rationale for the implementation of reference electrodes in ionic liquids
Authors: Bonnaud C. , Billard I. , Papaiconomou N. , Chainet E. , Leprêtre J. C.
Published: February 2016

A comparison between quasi-reference and reference electrodes was carried out in ionic liquid media by cyclic voltammetry. The stability and the reliability of these reference electrodes are discussed.
Heteroleptic Ru(ii)-bipyridine complexes based on hexylthioether-, hexyloxy- and hexyl-substituted thienylenevinylenes and their application in dye-sensitized solar cells
Authors: Urbani Maxence , Sánchez Carballo María , Kumar Sangeeta Amit , Vázquez Purificación , Grätzel Michael , Khaja Nazeeruddin Mohammad , Langa Fernando , Torres Tomás
Published: February 2016

A series of eight Ru(II) sensitizers incorporating thienylenevinylene-functionalised bipyridines as ancillary ligand is reported.
Structural characterization, phase transition and switchable dielectric behaviors in a new zigzag chain organic–inorganic hybrid compound: [C3H7NH3]2SbI5
Authors: Mao Chen-Yu , Liao Wei-Qiang , Wang Zhong-Xia , Li Peng-Fei , Lv Xing-Hui , Ye Heng-Yun , Zhang Yi
Published: February 2016

A new zigzag chain organic–inorganic hybrid compound with the general formula R2MI5, [n-C3H7NH3]2[SbI5], exhibits a switchable dielectric character.
Inorganic sulfur–nitrogen compounds: from gunpowder chemistry to the forefront of biological signaling
Authors: Cortese-Krott Miriam M. , Butler Anthony R. , Woollins J. Derek , Feelisch Martin
Published: February 2016

History, chemical properties and emerging biology of HSNO/SNO−, SSNO−and [ONN(O)-SO3]2−and their role in the sulfide/nitric oxide cross talk.
Stable neutral radicals of planar N2O2-type dipyrrin platinum complexes: hybrid radicals of the delocalized organic π-orbital and platinum d-orbital
Authors: Yamamura M. , Takizawa H. , Gobo Y. , Nabeshima T.
Published: February 2016

Stable neutral radicals of the N2O2-dipyrrin platinum complexes exhibit a delocalized radical character with a contribution by the platinum d-orbital.
Dietary fiber and blood pressure control
Authors: Aleixandre A. , Miguel M.
Published: February 2016

In the past few years, new strategies as dietary fiber to control blood pressure levels are emerging by developing new bioactive components of foods. The implicated mechanisms are under research.
Bioactivity, proximate, mineral and volatile profiles along the flowering stages of Opuntia microdasys (Lehm.): defining potential applications
Authors: Chahdoura Hassiba , Barreira João C. M. , Fernández-Ruiz Virginia , Morales Patricia , Calhelha Ricardo C. , Flamini Guido , Soković Marina , Ferreira Isabel C. F. R. , Achour Lotfi
Published: February 2016

Opuntia spp. flowers have been traditionally used for medical purposes, mostly because of their diversity in bioactive molecules with health promoting properties.
Investigation of the self-absorption effect using spatially resolved laser-induced breakdown spectroscopy
Authors: Yi Rongxing , Guo Lianbo , Li Changmao , Yang Xinyan , Li Jiaming , Li Xiangyou , Zeng Xiaoyan , Lu Yongfeng
Published: February 2016

This study discovered the distributional difference of self-absorption effect in laser-induced breakdown spectroscopy, and investigated the method to reduce the self-absorption effect.
Solution processed reduced graphene oxide electrodes for organic photovoltaics
Authors: Petridis Constantinos , Konios Dimitrios , Stylianakis Minas M. , Kakavelakis George , Sygletou Maria , Savva Kyriaki , Tzourmpakis Pavlos , Krassas Miron , Vaenas Naoum , Stratakis Emmanuel , Kymakis Emmanuel
Published: February 2016

Since the isolation of free standing graphene in 2004, graphene research has experienced a phenomenal growth.
Red lead degradation: monitoring of color change over time
Authors: Zhao Yang , Tang Yun , Tong Tong , Sun Zhijun , Yu Zongren , Zhu Yixuan , Tong Hua
Published: February 2016

Time and color functions indicated the mechanism and process of red lead discoloration.
Preparation and self-assembly of amphiphilic polylysine dendrons
Authors: Mirsharghi Sahar , Knudsen Kenneth D. , Bagherifam Shahla , Nyström Bo , Boas Ulrik
Published: February 2016

Polylysine dendrons with lipid tails prepared by divergent solid-phase synthesis showed self-assembling properties in aqueous solutions.
Crosslinking of comb-shaped polymer anion exchange membranes via thiol–ene click chemistry
Authors: Zhu Liang , Zimudzi Tawanda J. , Li Nanwen , Pan Jing , Lin Bencai , Hickner Michael A.
Published: February 2016

To produce anion conductive and durable polymer electrolytes for alkaline fuel cell applications, a series of cross-linked quaternary ammonium functionalized poly(2,6-dimethyl-1,4-phenylene oxide)s with mass-based ion exchange capacities (IEC) ranging from 1.80 to 2.55 mmol g−1were synthesizedviathiol–ene click chemistry.
Multi-functionalized graphene oxide complex as a plasmid delivery system for targeting hepatocellular carcinoma therapy
Authors: Wang Chunyang , Wang Xiaoqin , Lu Tong , Liu Fangshi , Guo Baofeng , Wen Naiyan , Du Yanwei , Lin Hang , Tang Jun , Zhang Ling
Published: February 2016

A novel and efficient graphene-based gene delivery vector was prepared, the effect of changing the PEI content on the size, stability and transfection efficiency were investigated.
Nitrogen and sulfur co-doped graphene aerogels as an efficient metal-free catalyst for oxygen reduction reaction in an alkaline solution
Authors: Wu Mei , Dou Zhiyu , Chang Jingjing , Cui Lili
Published: February 2016

N–S-GAs 900 exhibit an interconnected porous 3D network with random orientation, crumpled sheets in SEM. The onset potential and limiting current density of N–S-GAs 900 are more positive and larger than other catalysts.
Synthesis of SiO2coated zero-valent iron/palladium bimetallic nanoparticles and their application in a nano-biological combined system for 2,2′,4,4′-tetrabromodiphenyl ether degradation
Authors: Lv Yuancai , Niu Zhuyu , Chen Yuancai , Hu Yongyou
Published: February 2016

Polybrominated diphenyl ethers (PBDEs) are emerging persistent organic pollutants and the degradation of PBDEs is still a significant challenge owing to their extreme persistence and toxicity.
First-principles investigation of the effects of Ni and Y co-doped on destabilized MgH2
Authors: Sun Gaili , Li Yuanyuan , Zhao Xinxin , Wu Jianbao , Wang Lili , Mi Yiming
Published: February 2016

The Ni and Y co-doping effect on the structural stabilities and dehydrogenation properties of destabilized MgH2 was studied by first-principles calculations.
An ultrafast hydrogel photocrosslinking method for direct laser bioprinting
Authors: Wang Zongjie , Jin Xian , Dai Ru , Holzman Jonathan F. , Kim Keekyoung
Published: February 2016

We developed an ultrafast photocrosslinking method using a low-cost blue laser diode. Cell-laden hydrogels can be crosslinked within 10 seconds with over 90% cell viability. A microtube was fabricated using the system for bioprinting applications.
Metabolite identification and pharmacokinetic study of Lamiophlomis rotata in rats
Authors: Zhang Feng , La Mingping , Gong Xiaobin , Gao Shouhong , Wu Zhijun , Sun Lianna , Tao Xia , Chen Wansheng
Published: February 2016

An ultra-high performance liquid chromatography coupled with time-of-flight mass spectrometry technique and a subsequent LC-MS/MS method were developed for metabolite profile study of Lamiophlomis rotata extract after its oral administration.
Hydrothermal self-assembly of graphene foams with controllable pore size
Authors: Deng Wei , Fang Qile , Zhou Xufeng , Cao Hailiang , Liu Zhaoping
Published: February 2016

Graphene foams with controllable pore size are fabricated by facile one-step hydrothermal self-assembly by altering the sheet sizes of GO, and uniform pore sizes as small as ∼500 nm can be successfully realized.
Cell-laden alginate/polyacrylamide beads as carriers for stem cell delivery: preparation and characterization
Authors: Rana Deepti , Tabasum Aleya , Ramalingam Murugan
Published: February 2016

The rationale behind present investigation was to enhance the encapsulation efficacy of stem cells within the polymeric gel system and retain their 3D morphology as in the native microenvironment.
Recovery of tyrosol from aqueous streams using hydrophobic ionic liquids: a first step towards developing sustainable processes for olive mill wastewater (OMW) management
Authors: Larriba Marcos , Omar Salama , Navarro Pablo , García Julián , Rodríguez Francisco , Gonzalez-Miquel Maria
Published: February 2016

Hydrophobic ILs have been proposed as VOCs replacements for tyrosol recovery from aqueous solutions, revealing promising extraction efficiency and regeneration capacity. This will help developing sustainable processes for olive mill waste management.
Enhancing coulombic efficiency and rate capability of high capacity lithium excess layered oxide cathode material by electrocatalysis of nanogold
Authors: Ma Quanxin , Mu Deying , Liu Yuanlong , Yin Shibo , Dai Changsong
Published: February 2016

A lithium-rich cathode material Li1.2Mn0.56Ni0.16Co0.08O2 modified with nanogold (Au@LMNCO) for lithium-ion (Li-ion) batteries was prepared using co-precipitation, solid-state reaction and surface treatment techniques.
Microwave-assisted ultrafast and facile synthesis of fluorescent carbon nanoparticles from a single precursor: preparation, characterization and their application for the highly selective detection of explosive picric acid
Authors: Sun Xiangcheng , He Junkai , Meng Yongtao , Zhang Lichun , Zhang Sichen , Ma Xiaoyu , Dey Swayandipta , Zhao Jing , Lei Yu
Published: February 2016

Fluorescent carbon nanoparticles were synthesized from a single precursor and applied for explosives detection.
MMP-responsive theranostic nanoplatform based on mesoporous silica nanoparticles for tumor imaging and targeted drug delivery
Authors: Hu Jing-Jing , Liu Li-Han , Li Ze-Yong , Zhuo Ren-Xi , Zhang Xian-Zheng
Published: February 2016

A novel mesoporous silica-based multifunctional theranostic nanoplatform was reported, which can not only achieve MMP-2-activated fluorescence imaging, but also realize tumor targeted drug delivery and drug release indicating.
Influence of phase structure and morphology on the photocatalytic activity of bismuth molybdates
Authors: Chen Daimei , Hao Qiang , Wang Zhihong , Ding Hao , Zhu Yongfa
Published: February 2016

Bismuth molybdate photocatalysts with different phase structures and morphologies were controllably synthesized via a refluxing method by adjusting the pH in the reaction system.
Quantum chemical clarification of the alkyl chain length threshold of nonionic surfactants for monolayer formation at the air/water interface
Authors: Vysotsky Yu. B. , Kartashynska E. S. , Belyaeva E. A. , Vollhardt D. , Fainerman V. B. , Miller R.
Published: February 2016

A theoretical basis is introduced for the experimental fact that for various surfactant classes the alkyl chain length threshold varies for the formation of condensed monolayers.
No need for external orthogonality in subsystem density-functional theory
Authors: Unsleber Jan P. , Neugebauer Johannes , Jacob Christoph R.
Published: February 2016

Contrary to previous claims, there is no formal need for enforcing external orthogonality in subsystem density-functional theory.
Two-dimensional copper thio- and seleno-cyanates
Authors: Tsetseris Leonidas
Published: February 2016

Based on density-functional theory calculations we identify two-dimensional (2D) forms of copper thio-cyanate (CuSCN) and copper seleno-cyanate (CuSeCN).
The effect of a Ta oxygen scavenger layer on HfO2-based resistive switching behavior: thermodynamic stability, electronic structure, and low-bias transport
Authors: Zhong Xiaoliang , Rungger Ivan , Zapol Peter , Nakamura Hisao , Asai Yoshihiro , Heinonen Olle
Published: February 2016

First-principles modeling shows how resistive switching in oxide heterostructures is improved by inserting an “oxygen scavenger” layer.
Correction: Graphene-catalyzed photoreduction of dye molecules revealed by graphene enhanced Raman spectroscopy
Authors: Lee Bora , Kang Jin Hyoun , Jo Insu , Shin Dongha , Hong Byung Hee
Published: February 2016

Correction for ‘Graphene-catalyzed photoreduction of dye molecules revealed by graphene enhanced Raman spectroscopy’ by Bora Lee et al., Phys. Chem. Chem. Phys., 2016, 18, 3413–3415.
Electromagnetic susceptibility anisotropy and its importance for paramagnetic NMR and optical spectroscopy in lanthanide coordination chemistry
Authors: Blackburn Octavia A. , Edkins Robert M. , Faulkner Stephen , Kenwright Alan M. , Parker David , Rogers Nicola J. , Shuvaev Sergey
Published: February 2016

Electromagnetic susceptibility anisotropy can explain the spectroscopy and magnetism of lanthanide containing systems, but current theories have limitations.
Postprandial dietary fatty acids exert divergent inflammatory responses in retinal-pigmented epithelium cells
Authors: Montserrat-de la Paz Sergio , Naranjo M. Carmen , Bermudez Beatriz , Lopez Sergio , Moreda Wenceslao , Abia Rocio , Muriana Francisco J. G.
Published: February 2016

Postprandial triglyceride-rich lipoproteins (TRLs) lead to a complex series of events that are potentially oxidative and inflammatory.
A surface acoustic wave (SAW)-enhanced grating-coupling phase-interrogation surface plasmon resonance (SPR) microfluidic biosensor
Authors: Sonato A. , Agostini M. , Ruffato G. , Gazzola E. , Liuni D. , Greco G. , Travagliati M. , Cecchini M. , Romanato F.
Published: February 2016

A novel, surface plasmon resonance phase-interrogation based microfluidic biosensor in which surface acoustic wave-driven mixing accelerates molecule binding kinetics up to 84% of the reaction time is presented.
Alkoxide-intercalated NiFe-layered double hydroxides magnetic nanosheets as efficient water oxidation electrocatalysts
Authors: Carrasco Jose A. , Romero Jorge , Varela María , Hauke Frank , Abellán Gonzalo , Hirsch Andreas , Coronado Eugenio
Published: February 2016

Alkoxide-intercalated NiFe-layered double hydroxides were synthesizedviathe nonaqueous methanolic route. These magnetic nanosheets can be exfoliated in water and exhibit an outstanding behaviour as OER electrocatalysts.
Spectrofluorimetric determination of Hg2+ and Pb2+ using acetylcholinesterase (AChE)-based formation of silver nanoparticles
Authors: Kumar D. Nanda , Roy Jaydeep , Alex S. A. , Chandrasekaran N. , Mukherjee A.
Published: February 2016

A novel fluorimetric detection method for Hg2+ and Pb2+ based on in situ formation of AgNPs, where thiocholine (TCh), a product obtained by the hydrolysis of acetylcholine (ACh) by acetylcholinesterase (AChE), can act as a stabilizing agent.
Magnetite nanoparticles enable a rapid conversion of volatile fatty acids to methane
Authors: Yang Zhiman , Guo Rongbo , Shi Xiaoshuang , Wang Chuanshui , Wang Lin , Dai Meng
Published: February 2016

Evaluation of whether paddy soil enrichments obtained in the presence of magnetite and propionate can accelerate methane production from mixed volatile fatty acids.
Morphology-controlled synthesis of SrTiO3/TiO2 heterostructures and their photocatalytic performance for water splitting
Authors: Ha Minh Ngoc , Zhu Feng , Liu Zhifu , Wang Lichao , Liu Linyan , Lu Guanzhong , Zhao Zhe
Published: February 2016

Different morphologies of SrTiO3/TiO2 heterostructures like nanocubes, nanoparticles, nanospheres, and nanofibers were synthesized via a facile hydrothermal process, using TiO2 as both a template and precursor in Sr(OH)2 solution.
Low-cost instant CO generation at room temperature using formic acid, mesyl chloride and triethylamine
Authors: Veryser Cedrick , Van Mileghem Seger , Egle Brecht , Gilles Philippe , De Borggraeve Wim M.
Published: February 2016

A simple and robust method for instant carbon monoxide generation at room temperature using easily accessible standard lab chemicals: formic acid, mesyl chloride and triethylamine.
A light responsive two-component supramolecular hydrogel: a sensitive platform for the fabrication of humidity sensors
Authors: Samai Suman , Sapsanis Christos , Patil Sachin P. , Ezzeddine Alaa , Moosa Basem A. , Omran Hesham , Emwas Abdul-Hamid , Salama Khaled N. , Khashab Niveen M.
Published: February 2016

The supramolecular self-assembly of a two-component hydrogel afforded a stimuli responsive hydrogel at room temperature.
Effects of nanocrystalline hydroxyapatites on macrophage polarization
Authors: Linares J. , Fernández A. B. , Feito M. J. , Matesanz M. C. , Sánchez-Salcedo S. , Arcos D. , Vallet-Regí M. , Rojo J. M. , Portolés M. T.
Published: February 2016

Nanocrystalline hydroxyapatites favour the macrophage polarization towards a M2 reparative phenotype, ensuring an appropriate response in the implantation site.
External consensus in multi‐agent systems with large consecutive data loss under unreliable networks
Authors: Adilla Mohd Subha Nurul , Liu Guo‐Ping
Published: February 2016

This study discusses the external consensus problem for non‐identical networked multi‐agent systems with network data loss, considering both uniform and random consecutive data losses induced by long periods of transmission failure. A novel approach using a combination of prediction strategy and constant control gain based on gain error ratio (GER) is proposed for solving the problem. The main contribution of this study is a simple and practical way of selecting control gain using GER to help overcome prediction inaccuracies caused by the prediction process during a long period of consecutive data loss. The feasibility and performance of the proposed consensus protocol is demonstrated through simulation and practical experiment.
Deadlock and blockage control for manufacturing systems with failure‐prone workstations
Authors: Yue Hao , Xing Keyi , Hu Hesuan , Wu Weimin , Su Hongye
Published: February 2016

It is essential to avoid deadlock and blockage in the operation of an automated manufacturing system (AMS) since they cripple a part of the system, if not the whole, and then deteriorate system performance. Though a large number of approaches are developed to resolve this issue, few of them are directly applicable to AMSs with failure‐prone resources. This study focuses on the supervision for deadlock avoidance and blockage control in a class of AMSs with multiple unreliable resources, where each resource is a workstation. The authors hope that the system, under the control of a supervisor, can at all time automatically continue producing parts whose processing routes do not contain any of the currently failed workstations. Inspired by the widely known Banker's algorithm and a resource order policy, this study presents a robust supervisory controller that satisfies the above desired requirement. All the evidence shows that authors' policy performs better than the original one in terms of permissiveness. Furthermore, an example AMS from existing literature is used to illustrate the effectiveness of authors' proposed method.
Stability and exact observability of discrete stochastic singular systems based on generalised Lyapunov equations
Authors: Xing Shuangyun , Zhang Qingling
Published: February 2016

The stability and exact observability problems of discrete stochastic singular systems based on generalised Lyapunov equations are investigated in this study. First, some new conditions for the existence and uniqueness of the solutions to discrete stochastic singular systems are given, and then, a new type generalised Lyapunov equation is proposed. Based on these results, a sufficient condition for stochastic stability of the systems is derived via the solution of the proposed generalised Lyapunov equation. Moreover, the relationship between the solution of the generalised Lyapunov equation and structure properties of discrete stochastic singular systems is discussed as well. Especially, the relationship between the solution of the generalised Lyapunov equation and the stochastic stability of discrete stochastic singular systems with non‐causal behaviour is studied for the first time. Second, another new type generalised Lyapunov equation for exactly observable discrete stochastic singular systems is proposed. Meanwhile, the relationships among the stochastic stability of the systems, exact observability and the solution of the proposed generalised Lyapunov equation are investigated. Finally, simulation examples are worked out to validate the effectiveness of the obtained theoretical results.
Estimation of low‐frequency modes in power system using robust modified Prony
Authors: Rai Shekha , Lalani Dhaval , Nayak Sisir Kumar , Jacob Tony , Tripathy Praveen
Published: February 2016

This study proposes to modify improved Prony method by suggesting to use robust covariance matrix for the identification of low frequency power system modes utilising the real time data obtained from phasor measurement unit. The methods reported in the current literature are many based on l2‐norm minimisation, the estimated modes from these methods are severely affected in the presence of an outlier or bad measurements. Hence, there is a need to develop the method which can provide a good estimate of the modes even in the presence of outliers in the measurements. In order to mitigate the effect of such bad data, this study proposes a robust Prony estimator for estimating the low frequency modes of power systems. The method is based on minimum covariance determinant technique to find the robust covariance followed by improved Prony to estimate the modes. In this study the proposed method is compared with other methods such as improved Prony, etc. on synthetic test signal at different signal‐to‐noise ratio in the presence of outliers. Furthermore, the effectiveness of the proposed method is also shown on two area system and real time probing data of the Western Electricity Coordinating Council network.
Field programmable gate array implementation of a single‐input fuzzy proportional–integral–derivative controller for DC–DC buck converters
Authors: Chang Changyuan , Yuan Yubo , Jiang Tianlin , Zhou Zhongjie
Published: February 2016

The design and field programmable gate array implementation of a single‐input fuzzy (SIF) proportional–integral–derivative (PID) control scheme applied to DC–DC buck converters are presented. The SIF logic reduces the number of fuzzy rules and therefore the hardware resource occupancy without control property degradation compared with the double‐input fuzzy (DIF) controller, which is realised by transforming the two‐dimension rule tables into one‐dimension rule vectors using signed distance method and genetic algorithm. The adopted signed distance method requires the two‐dimension rule tables to be of Toeplitz structure, which is realised by establishing the inference rules through analysing the system response curve. The fuzzy logic regulates the PID parameters based on the conditions of the power converters. As a result, the SIF‐PID controller is superior to the conventional PID controller and is similar to DIF‐PID controller in terms of the control performance. The proposed controller has been validated with simulation and experimental results.
β-Substituting alanine synthases: roles in cysteine metabolism and abiotic and biotic stress signalling in plants
Authors: Tahir Jibran , Dijkwel Paul
Published: February 2016

Cysteine is required for the synthesis of proteins and metabolites, and is therefore an indispensable compound for growth and development. The β-substituting alanine synthase (BSAS) gene family encodes enzymes known as O-acetylserine thiol lyases (OASTLs), which carry out cysteine biosynthesis in plants. The functions of the BSAS isoforms have been reported to be crucial in assimilation of S and cysteine biosynthesis, and homeostasis in plants. In this review we explore the functional variation in this classic pyridoxal-phosphate-dependent enzyme family of BSAS isoforms. We discuss how specialisation and divergence in BSAS catalytic activities makes a more dynamic set of biological routers that integrate cysteine metabolism and abiotic and biotic stress signalling in Arabidopsis thaliana (L.) Heynh. and also other species. Our review presents a universal scenario in which enzymes modulating cysteine metabolism promote survival and fitness of the species by counteracting internal and external stress factors.
Obesity causes weight increases in prepubertal and pubertal male offspring and is related to changes in spermatogenesis and sperm production in rats
Authors: Navya Harish , Yajurvedi Hanumant Narasinhacharya
Published: February 2016

The effect of obesity on testicular activity in prepubertal and pubertal rats was investigated in the present study. Obesity was induced in adult females by feeding a high-calorie diet (HCD). These females were mated with normal males and were fed an HCD during pregnancy and lactation. The male offspring born to obese mothers and fed an HCD after weaning were found to be obese. Seminiferous tubules of offspring from control mothers (OCM) and offspring from HCD-fed mothers (OHCDM) had the same set of germ cells at different age intervals, namely spermatogonia, leptotene spermatocytes, zygotene spermatocytes, pachytene spermatocytes and round and elongated spermatids on postnatal days (PND) 7, 13, 17, 24 and 36, and on the day of preputial separation, respectively. However, there was a significant decrease in round and elongated spermatids and the epididymal sperm count, coupled with a significant decrease in testosterone and an increase in leptin serum concentrations in OHCDM compared with OCM. These results show that obesity in prepubertal rats does not affect the age-dependent appearance of germ cells according to developmental hierarchy, but it does interfere with spermatid formation, resulting in a reduced sperm count, which may be due to a deficiency of testosterone mediated by hyperleptinaemia.
Phylogeography of north-eastern Australia’s Cyrtodactylus radiation: a habitat switch highlights adaptive capacity at a generic level
Authors: Wilmer Jessica Worthington , Couper Patrick
Published: February 2016

The genus Cyrtodactylus is the most diverse and widely distributed group of geckos in the world. Throughout their extensive range, species exploit a diverse range of habitats and are able to partition niches locally. Recent work has shown that Cyrtodactylus geckos in Queensland, Australia, have radiated in situ after colonisation by an arboreal Papuan ancestor and have undergone a habitat switch to rock dwelling during their evolutionary history. Using mitochondrial data we conducted a phylogeographic and molecular dating analysis to investigate the historical biogeography of Cyrtodactylus species in north Queensland. Our analyses show that after the arrival of a Papuan rainforest-dwelling ancestor, Cyrtodactylus diverged into two major lineages: one more restricted in northern Cape York and the other more widespread. Discordance in the timing of the speciation events and phylogeographic distribution within the two lineages likely reflect regional differences in the continuity of mesic rock habitats and climatic variability over the last 15 million years. Reconstructing the history of habitat use on a pre-existing global phylogeny reveals that switches between major habitat ecologies, rock and forest, have occurred multiple times in this genus. The ability to transition between different habitat types may have contributed to the global diversification of these geckos.
Zamenhof and the liberal-communitarian debate
Authors: Schor Esther
Published: February 2016

This paper proposes to analyze the early thinking of Ludwig Lazarus Zamenhof (1859–1917) in light of the so-called liberal/communitarian debate. In the early 1980s, the debate was launched: On the liberal side were proponents of a liberal self bearing rights, irrespective of identity (John Rawls) and on the communitarian side, champions of communities with prerogatives and purposes (Michael Sandel). But this debate has become in recent years a dialogue, each side challenging the other to assimilate its claims, be they ontological, political, or ethical. This paper argues that, a century earlier, Zamenhof was involved in a similar dialogue between liberalism and communitarianism, inventing a movement that could potentially balance human rights with notions of the good espoused by different communities. The political potential of Esperanto, however, was undermined (though not collapsed) by the Declaration of Boulogne, which eschewed deliberative debate and abjected religious and ethical ideals.
Key Workers: Toward an Occupational History of the Private Music Teacher in England and Wales, c.1861–c.1921
Authors: Russell Dave
Published: February 2016

Making particular use of material drawn from the Census of England and Wales, this article confirms that music teaching was above all an urban activity, increasingly dominated by women, albeit with some local variation, and that the highest provision of teaching was invariably in middle-class areas. Seaside resorts and suburbia were especially prominent market locations by the early twentieth century, with the south-east particularly favoured. The often-derided part-time teacher is shown to have been a key figure in working-class communities. While teachers showed little interest in formal professionalization, it is argued that they were probably better paid than has been assumed and were able at least to maintain a social position within the lower-middle and skilled working classes that most were born into. Although women's careers were frequently short, for a growing minority, music teaching was a serious career option. It is suggested that teachers met contemporary needs rather more effectively than some have claimed.
Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry
Authors: Temu Tikira , Mann Matthias , Räschle Markus , Cox Jürgen
Published: February 2016

Summary: To enable mass spectrometry (MS)-based proteomic studies with poorly characterized organisms, we developed a computational workflow for the homology-driven assembly of a non-redundant reference sequence dataset. In the automated pipeline, translated DNA sequences (e.g. ESTs, RNA deep-sequencing data) are aligned to those of a closely related and fully sequenced organism. Representative sequences are derived from each cluster and joined, resulting in a non-redundant reference set representing the maximal available amino acid sequence information for each protein. We here applied NOmESS to assemble a reference database for the widely used model organism Xenopus laevis and demonstrate its use in proteomic applications.

Availability and implementation: NOmESS is written in C#. The source code as well as the executables can be downloaded from http://www.biochem.mpg.de/cox. Execution of NOmESS requires BLASTp and cd-hit in addition.

Contact:  cox@biochem.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad
Authors: Sanchez-Pulido Luis , Ponting Chris P.
Published: February 2016

Summary: Vasohibin-1 and Vasohibin-2 regulate angiogenesis, tumour growth and metastasis. Their molecular functions, however, were previously unknown, in large part owing to their perceived lack of homology to proteins of known structure and function. To identify their functional amino acids and domains, their molecular activity and their evolutionary history, we undertook an in-depth analysis of Vasohibin sequences. We find that Vasohibin proteins are previously undetected members of the transglutaminase-like cysteine protease superfamily, and all possess a non-canonical Cys-His-Ser catalytic triad. We further propose a calcium-dependent activation mechanism for Vasohibin proteins. These findings can now be used to design constructs for protein structure determination and to develop enzyme inhibitors as angiogenic regulators to treat metastasis and tumour growth.

Contact:  luis.sanchezpulido@dpag.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data
Authors: Burkett Kelly M. , McNeney Brad , Graham Jinko
Published: February 2016

Summary: The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

Availability and implementation: sampletrees is implemented in C ++. The source code, documentation and test files are available at http://stat.sfu.ca/statgen/research/sampletrees.html. The R package Rsampletrees is available on CRAN http://cran.r-project.org/web/packages/Rsampletrees/index.html.

Contact: kburkett@uottawa.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Multi-omics enrichment analysis using the GeneTrail2 web service
Authors: Stöckel Daniel , Kehl Tim , Trampert Patrick , Schneider Lara , Backes Christina , Ludwig Nicole , Gerasch Andreas , Kaufmann Michael , Gessler Manfred , Graf Norbert , Meese Eckart , Keller Andreas , Lenhof Hans-Peter
Published: February 2016

Motivation: Gene set analysis has revolutionized the interpretation of high-throughput transcriptomic data. Nowadays, with comprehensive studies that measure multiple -omics from the same sample, powerful tools for the integrative analysis of multi-omics datasets are required.

Results: Here, we present GeneTrail2, a web service allowing the integrated analysis of transcriptomic, miRNomic, genomic and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results. We used GeneTrail2 to explore pathogenic mechanisms of Wilms tumors. We not only succeeded in revealing signaling cascades that may contribute to the malignancy of blastemal subtype tumors but also identified potential biomarkers for nephroblastoma with adverse prognosis. The presented use-case demonstrates that GeneTrail2 is well equipped for the integrative analysis of comprehensive -omics data and may help to shed light on complex pathogenic mechanisms in cancer and other diseases.

Availability and implementation: GeneTrail2 can be freely accessed under https://genetrail2.bioinf.uni-sb.de.

Contact: dstoeckel@bioinf.uni-sb.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins
Authors: Stražar Martin , Žitnik Marinka , Zupan Blaž , Ule Jernej , Curk Tomaž
Published: February 2016

Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control of gene expression, including splicing, transport, polyadenylation and RNA stability. To model protein–RNA interactions by considering all available sources of information, it is necessary to integrate the rapidly growing RBP experimental data with the latest genome annotation, gene function, RNA sequence and structure. Such integration is possible by matrix factorization, where current approaches have an undesired tendency to identify only a small number of the strongest patterns with overlapping features. Because protein–RNA interactions are orchestrated by multiple factors, methods that identify discriminative patterns of varying strengths are needed.

Results: We have developed an integrative orthogonality-regularized nonnegative matrix factorization (iONMF) to integrate multiple data sources and discover non-overlapping, class-specific RNA binding patterns of varying strengths. The orthogonality constraint halves the effective size of the factor model and outperforms other NMF models in predicting RBP interaction sites on RNA. We have integrated the largest data compendium to date, which includes 31 CLIP experiments on 19 RBPs involved in splicing (such as hnRNPs, U2AF2, ELAVL1, TDP-43 and FUS) and processing of 3’UTR (Ago, IGF2BP). We show that the integration of multiple data sources improves the predictive accuracy of retrieval of RNA binding sites. In our study the key predictive factors of protein–RNA interactions were the position of RNA structure and sequence motifs, RBP co-binding and gene region type. We report on a number of protein-specific patterns, many of which are consistent with experimentally determined properties of RBPs.

Availability and implementation: The iONMF implementation and example datasets are available at https://github.com/mstrazar/ionmf.

Contact: tomaz.curk@fri.uni-lj.si

Supplementary information:  Supplementary data are available at Bioinformatics online.