bluuebunny/crossref_metadata_2025 huggingface dataset:
Materials genomics methods for high-throughput construction of COFs and targeted synthesis
Authors: Lan Youshi , Han Xianghao , Tong Minman , Huang Hongliang , Yang Qingyuan , Liu Dahuan , Zhao Xin , Zhong Chongli
Published: December 2018

Materials genomics represents a research mode for materials development, for which reliable methods for efficient materials construction are essential. Here we present a methodology for high-throughput construction of covalent organic frameworks (COFs) based on materials genomics strategy, in which a gene partition method of genetic structural units (GSUs) with reactive sites and quasi-reactive assembly algorithms (QReaxAA) for structure generation were proposed by mimicking the natural growth processes of COFs, leading to a library of 130 GSUs and a database of ~470,000 materials containing structures with 10 unreported topologies as well as the existing COFs. As a proof-of-concept example, two generated 3D-COFs with ffc topology and two 2D-COFs with existing topologies were successfully synthesized. This work not only presents useful genomics methods for developing COFs and largely extended the COF structures, but also will stimulate the switch of materials development mode from trial-and-error to theoretical prediction-experimental validation.
Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection
Authors: Fröhlich Fabian , Reiser Anita , Fink Laura , Woschée Daniel , Ligon Thomas , Theis Fabian Joachim , Rädler Joachim Oskar , Hasenauer Jan
Published: December 2018

Single-cell time-lapse studies have advanced the quantitative understanding of cellular pathways and their inherent cell-to-cell variability. However, parameters retrieved from individual experiments are model dependent and their estimation is limited, if based on solely one kind of experiment. Hence, methods to integrate data collected under different conditions are expected to improve model validation and information content. Here we present a multi-experiment nonlinear mixed effect modeling approach for mechanistic pathway models, which allows the integration of multiple single-cell perturbation experiments. We apply this approach to the translation of green fluorescent protein after transfection using a massively parallel read-out of micropatterned single-cell arrays. We demonstrate that the integration of data from perturbation experiments allows the robust reconstruction of cell-to-cell variability, i.e., parameter densities, while each individual experiment provides insufficient information. Indeed, we show that the integration of the datasets on the population level also improves the estimates for individual cells by breaking symmetries, although each of them is only measured in one experiment. Moreover, we confirmed that the suggested approach is robust with respect to batch effects across experimental replicates and can provide mechanistic insights into the nature of batch effects. We anticipate that the proposed multi-experiment nonlinear mixed effect modeling approach will serve as a basis for the analysis of cellular heterogeneity in single-cell dynamics.
Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Authors: Francescatto Margherita , Lizio Marina , Philippens Ingrid , Pardo Luba M. , Bontrop Ronald , Sakai Mizuho , Watanabe Shoko , Itoh Masayoshi , Hasegawa Akira , Lassmann Timo , Severin Jessica , Harshbarger Jayson , Abugessaisa Imad , Kasukawa Takeya , Carninci Piero , Hayashizaki Yoshihide , Forrest Alistair R. R. , Kawaji Hideya , Rizzu Patrizia , Heutink Peter
Published: December 2018

The authors regret that Luba M. Pardo was omitted in error from the author list of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions. The authors also regret that Anemieke Rozemuller was omitted in error from the Acknowledgements of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions.
Separation of Biological Particles in a Modular Platform of Cascaded Deterministic Lateral Displacement Modules
Authors: Pariset Eloise , Parent Charlotte , Fouillet Yves , François Boizot , Verplanck Nicolas , Revol-Cavalier Frédéric , Thuaire Aurélie , Agache Vincent
Published: December 2018

Deterministic lateral displacement (DLD) has been extensively implemented in the last decade for size-based sample preparation, owing to its high separation performances for a wide range of particle dimensions. However, separating particles from 1 μm to 10 μm in one single DLD device is challenging because of the required diversity of pillar dimensions and inherent fabrication issues. This paper presents an alternative approach to achieve the extraction of E. coli bacteria from blood samples spiked with prostate cancer cells. Our approach consists in cascading individual DLD devices in a single automated platform, using flexible chambers that successively collect and inject the sample between each DLD stage without any external sample manipulation. Operating DLD separations independently enables to maximize the sorting efficiency at each step, without any disturbance from downstream stages. The proposed two-step automated protocol is applied to the separation of three types of components (bacteria, blood particles and cancer cells), with a depletion yield of 100% for cancer cells and 93% for red blood cells. This cascaded approach is presented for the first time with two DLD modules and is upscalable to improve the dynamic range of currently available DLD devices.
Vertical WS2/SnS2 van der Waals Heterostructure for Tunneling Transistors
Authors: Wang Jiaxin , Jia Rundong , Huang Qianqian , Pan Chen , Zhu Jiadi , Wang Huimin , Chen Cheng , Zhang Yawen , Yang Yuchao , Song Haisheng , Miao Feng , Huang Ru
Published: December 2018

Van der Waals heterostructures composed of two-dimensional (2D) transition metal dichalcogenides (TMD) materials have stimulated tremendous research interest in various device applications, especially in energy-efficient future-generation electronics. Such ultra-thin stacks as tunnel junction theoretically present unprecedented possibilities of tunable relative band alignment and pristine interfaces, which enable significant performance enhancement for steep-slope tunneling transistors. In this work, the optimal 2D-2D heterostructure for tunneling transistors is presented and elaborately engineered, taking into consideration both electric properties and material stability. The key challenges, including band alignment and metal-to-2D semiconductor contact resistances, are optimized separately for integration. By using a new dry transfer technique for the vertical stack, the selected WS2/SnS2 heterostructure-based tunneling transistor is fabricated for the first time, and exhibits superior performance with comparable on-state current and steeper subthreshold slope than conventional FET, as well as on-off current ratio over 106 which is among the highest value of 2D-2D tunneling transistors. A visible negative differential resistance feature is also observed. This work shows the great potential of 2D layered semiconductors for new heterostructure devices and can guide possible development of energy-efficient future-generation electronics.
High-efficiency freezing-induced loading of inorganic nanoparticles and proteins into micron- and submicron-sized porous particles
Authors: German Sergei V. , Novoselova Marina V. , Bratashov Daniil N. , Demina Polina A. , Atkin Vsevolod S. , Voronin Denis V. , Khlebtsov Boris N. , Parakhonskiy Bogdan V. , Sukhorukov Gleb B. , Gorin Dmitry A.
Published: December 2018

We demonstrate a novel approach to the controlled loading of inorganic nanoparticles and proteins into submicron- and micron-sized porous particles. The approach is based on freezing/thawing cycles, which lead to high loading densities. The process was tested for the inclusion of Au, magnetite nanoparticles, and bovine serum albumin in biocompatible vaterite carriers of micron and submicron sizes. The amounts of loaded nanoparticles or substances were adjusted by the number of freezing/thawing cycles. Our method afforded at least a three times higher loading of magnetite nanoparticles and a four times higher loading of protein for micron vaterite particles, in comparison with conventional methods such as adsorption and coprecipitation. The capsules loaded with magnetite nanoparticles by the freezing-induced loading method moved faster in a magnetic field gradient than did the capsules loaded by adsorption or coprecipitation. Our approach allows the preparation of multicomponent nanocomposite materials with designed properties such as remote control (e.g. via the application of an electromagnetic or acoustic field) and cargo unloading. Such materials could be used as multimodal contrast agents, drug delivery systems, and sensors.
Backscattering design for a focusing grating coupler with fully etched slots for transverse magnetic modes
Authors: Hoffmann Jahn , Schulz K. Marvin , Pitruzzello Giampaolo , Fohrmann Lena Simone , Petrov Alexander Yu. , Eich Manfred
Published: December 2018

Grating couplers are a fundamental building block of integrated optics as they allow light to be coupled from free-space to on-chip components and vice versa. A challenging task in designing any grating coupler is represented by the need for reducing back reflections at the waveguide-grating interface, which introduce additional losses and undesirable interference fringes. Here, we present a design approach for focusing TM grating couplers that minimizes these unwanted reflections by introducing a modified slot that fulfills an anti-reflection condition. We show that this antireflection condition can be met only for the Bloch mode of the grating that concentrates in the dielectric. As a consequence the light is scattered from the grating coupler with a negative angle, referred to as “backscattering design”. Our analytic model shows that the anti-reflection condition is transferrable to grating couplers on different waveguide platforms and that it applies for both TE and TM polarizations. Our experimentally realized focusing grating coupler for TM-modes on the silicon photonics platform has a coupling loss of (3.95 ± 0.15) dB at a wavelength of 1.55 µm. It has feature sizes above 200 nm and fully etched slots. The reflectivity between the grating coupler and the connected waveguide is suppressed to below 0.16%.
Regulation of phosphorus bioavailability by iron nanoparticles in a monomictic lake
Authors: Saeed H. , Hartland A. , Lehto N. J. , Baalousha M. , Sikder M. , Sandwell D. , Mucalo M. , Hamilton D. P.
Published: December 2018

Dissolved reactive phosphorous (DRP) in lake systems is conventionally considered to predominate over other dissolved P species, however, this view neglects an important set of interactions that occurs between P and reactive iron hydroxide surfaces. This study addresses the coupling of P with dispersed iron nanoparticles in lakes, an interaction that may fundamentally alter the bioavailability of P to phytoplankton. We used diffusive gradients in thin films (DGT) and ultrafiltration to study Fe-P coupling in the water column of a monomictic lake over a hydrological year. Fe and P were predominantly colloidal (particle diameters > ~5 nm < ~20 nm) in both oxic epilimnetic and anaerobic hypolimnetic waters, but they were both DGT-labile under sub-oxic conditions, consistent with diffusion and dissolution of Fe-and-P-bearing colloids within the DGT diffusive gel. During peak stratification, increases in Fe and P bioavailability were spatially and temporally coincident with Fe nanoparticle dissolution and the formation of a deep chlorophyll maximum at 5–8 m depth. These results provide a window into the coupling and decoupling of P with mobile iron colloids, with implications for our understanding of the behaviour of nutrients and their influence on phytoplankton community dynamics.
Quantification of protein mobility and associated reshuffling of cytoplasm during chemical fixation
Authors: Huebinger Jan , Spindler Jessica , Holl Kristin J. , Koos Björn
Published: December 2018

To understand cellular functionalities, it is essential to unravel spatio-temporal patterns of molecular distributions and interactions within living cells. The technological progress in fluorescence microscopy now allows in principle to measure these patterns with sufficient spatial resolution. However, high resolution imaging comes with long acquisition times and high phototoxicity. Therefore, physiological live cell imaging is often unfeasible and chemical fixation is employed. Yet, fixation methods have not been rigorously investigated, in terms of pattern preservation, at the resolution at which cells can now be imaged. A key parameter for this is the time required until fixation is complete. During this time, cells are under unphysiological conditions and patterns decay. We demonstrate here that formaldehyde fixation takes more than one hour for cytosolic proteins in cultured cells. Other small aldehydes, glyoxal and acrolein, did not perform better. Associated with this, we found a distinct displacement of proteins and lipids, including their loss from cells. Fixations using glutaraldehyde were faster than four minutes and retained most cytoplasmic proteins. Surprisingly, autofluorescence produced by glutaraldehyde was almost completely absent with supplementary addition of formaldehyde without compromising fixation speed. These findings indicate, which cellular processes can actually be reliably imaged after a certain chemical fixation.
Power laws and critical fragmentation in global forests
Authors: Saravia Leonardo A. , Doyle Santiago R. , Bond-Lamberty Ben
Published: December 2018

The replacement of forest areas with human-dominated landscapes usually leads to fragmentation, altering the structure and function of the forest. Here we studied the dynamics of forest patch sizes at a global level, examining signals of a critical transition from an unfragmented to a fragmented state, using the MODIS vegetation continuous field. We defined wide regions of connected forest across continents and big islands, and combined five criteria, including the distribution of patch sizes and the fluctuations of the largest patch over the last sixteen years, to evaluate the closeness of each region to a fragmentation threshold. Regions with the highest deforestation rates–South America, Southeast Asia, Africa–all met these criteria and may thus be near a critical fragmentation threshold. This implies that if current forest loss rates are maintained, wide continental areas could suddenly fragment, triggering extensive species loss and degradation of ecosystems services.
Publisher Correction: A Pilot Study on Tocilizumab for Treating Refractory Adult-Onset Still’s Disease
Authors: Li Ting , Gu Liyang , Wang Xiaodong , Guo Li , Shi Hui , Yang Chengde , Chen Sheng
Published: December 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Transcriptome-wide analysis of a baculovirus using nanopore sequencing
Authors: Boldogkői Zsolt , Moldován Norbert , Szűcs Attila , Tombácz Dóra
Published: December 2018

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a prototypic baculovirus infecting specific insects. AcMNPV contains a large double-stranded DNA genome encoding a complex transcriptome. This virus has a widespread application as a vector for the expression of heterologous proteins. Here, we present a dataset, derived from Oxford Nanopore Technologies (ONT) long-read sequencing platform. We used both cDNA and direct RNA sequencing techniques. The dataset contains 520,310 AcMNPV and 1,309,481 host cell reads using the regular cDNA-sequencing method of ONT technique, whereas altogether 6,456 reads were produced by using direct RNA-sequencing. We also used a Cap-selection protocol for certain ONT samples, and obtained 2,568,669 reads by using this method. The raw reads were aligned to the AcMNPV reference genome (KM667940.1). Here, we openly released the ‘static’ and the dynamic transcript catalogue of AcMNPV. This dataset can be used for deep analyses of the transcriptomic and epitranscriptomic patterns of the AcMNPV and the host cell. The data can be also useful for the validation of different bioinformatics software packages and analysis tools.
Genome analysis of Mycobacterium avium subspecies hominissuis strain 109
Authors: Matern William M. , Bader Joel S. , Karakousis Petros C.
Published: December 2018

Infection with Mycobacterium avium is a significant cause of morbidity and its treatment requires the use of multiple antibiotics for more than 12 months. In the current work, we provide the genome sequence, gene annotations, gene ontology annotations, and protein homology data for M. avium strain 109 (MAC109), which has been used extensively in preclinical studies. The de novo assembled genome consists of a circular chromosome of length 5,188,883 bp and two circular plasmids of sizes 147,100 bp and 16,516 bp. We have named the plasmids pMAC109a and pMAC109b, respectively. Based on its genome, we confirm that MAC109 should be classified as Mycobacterium avium subsp. hominissuis. Using genome annotation software, we identified 4,841 coding sequences and annotated these with Gene Ontology (GO) terms. Additionally, we wrote software to generate a database of homologous proteins among MAC109 and eight other commonly used mycobacterial laboratory strains. The resulting database may be useful for translating genetic data between various strains of mycobacteria, and the software may be applied readily to other organisms.
A linked open data representation of patents registered in the US from 2005–2017
Authors: Hassan Mofeed M. , Zaveri Amrapali , Lehmann Jens
Published: December 2018

Patents are widely used to protect intellectual property and a measure of innovation output. Each year, the USPTO grants over

150
,
000

patents to individuals and companies all over the world. In fact, there were more than

280
,
000

patent grants issued in the US in

2015

. However, accessing, searching and analyzing those patents is often still cumbersome and inefficient. To overcome those problems, Google indexes patents and converts them to Extensible Markup Language (XML) files using Optical Character Recognition (OCR) techniques. In this article, we take this idea one step further and provide semantically rich, machine-readable patents using the Linked Data principles. We have converted the data spanning

12

years

−

i.e.

2005

−

2017

from XML to Resource Description Framework (RDF) format, conforming to the Linked Data principles and made them publicly available for re-use. This data can be integrated with other data sources in order to further simplify use cases such as trend analysis, structured patent search & exploration and societal progress measurements. We describe the conversion, publishing, interlinking process along with several use cases for the USPTO Linked Patent data.
Dual-template molecularly imprinted polymers for dispersive solid-phase extraction of fluoroquinolones in water samples coupled with high performance liquid chromatography
Authors: Lu Wenhui , Liu Jie , Li Jinhua , Wang Xiaoyan , Lv Min , Cui Rong , Chen Lingxin
Published: December 2018

Dual-template molecularly imprinted polymers were synthesized using norfloxacin and enrofloxacin as templates by precipitation polymerization with a multi-template imprinting strategy.
A dual signal amplification nanosensor based on SERS technology for detection of tumor-related DNA
Authors: Lin Duo , Gong Tianxun , Qiu Sufang , Wu Qiong , Tseng Ching-Yu , Kong Kien Voon , Chen Guannan , Chen Rong
Published: December 2018

A dual signal amplification array based on SERS is developed by photo-triggered release of probes for reliable and sensitive DNA detection.
Persistent generation of hydroxyl radicals in Tris–Co(ii) complex–H2O2 systems for long-lasting multicolored chemical lights
Authors: Li Zhe , Wang Lianying , Yuan Zhiqin , Lu Chao
Published: December 2018

Aqueous luminol tablet–Tris–Co(ii)–PVP–H2O2 chemical light systems through the continuous generation of ˙OH and sustained luminol and H2O2 release are presented.
Building two-dimensional metal–organic networks with tin
Authors: Rodríguez L. M. , Fuhr J. D. , Machaín P. , Ascolani H. , Lingenfelder M. , Gayone J. E.
Published: December 2018

We report the first example of a surface-supported 2D metal–organic network with Sn atoms as coordination centres.
A symbiotic supramolecular approach to the design of novel amphiphiles with antibacterial properties against MSRA
Authors: Tyuleva Stilyana N. , Allen Nyasha , White Lisa J. , Pépés Antigoni , Shepherd Helena J. , Saines Paul J. , Ellaby Rebecca J. , Mulvihill Daniel P. , Hiscock Jennifer R.
Published: December 2018

The co-formulation of supramolecular self-associating amphiphiles (SSAs) enhances solution state physicochemical properties and increases efficacy against methicillin-resistant Staphylococcus aureus.
Synthesis and nitric oxide releasing properties of novel fluoroS-nitrosothiols
Authors: Zhou Yang , Tan Jinyi , Dai Yuping , Yu Yanmin , Zhang Qi , Meyerhoff Mark E.
Published: December 2018

A novel family fluoroS-nitrosothiols is developed as NO donors, to stoichiometrically release NO with the clean formation of corresponding disulfides.
Boosting oxygen reduction activity with low-temperature derived high-loading atomic cobalt on nitrogen-doped graphene for efficient Zn–air batteries
Authors: Li Jiantao , Liu Haoyun , Wang Manman , Lin Chao , Yang Wei , Meng Jiashen , Xu Yanan , Owusu Kwadwo Asare , Jiang Benli , Chen Chuanxi , Fan Danian , Zhou Liang , Mai Liqiang
Published: December 2018

High-loading atomic cobalt (12.8 wt%) dispersed on nitrogen-doped graphene was successfully synthesized via considerably low temperature pyrolysis.
Unlocking the catalytic potential of tris(3,4,5-trifluorophenyl)borane with microwave irradiation
Authors: Carden Jamie L. , Gierlichs Lukas J. , Wass Duncan F. , Browne Duncan L. , Melen Rebecca L.
Published: December 2018

The catalytic activity of tris(3,4,5-trifluorophenyl)borane has been explored in the 1,2-hydroboration reactions of unsaturated substrates.
Recognition of the π-hole donor ability of iodopentafluorobenzene – a conventional σ-hole donor for crystal engineering involving halogen bonding
Authors: Eliseeva Anastasiya A. , Ivanov Daniil M. , Novikov Alexander S. , Kukushkin Vadim Yu.
Published: December 2018

This study is the first recognition of iodopentafluorobenzene's π-hole donor ability.
Preparation, optimization and evolution of the kinetic mechanism of an Fe-MIL-88A metal–organic framework
Authors: Bagherzadeh Elham , Zebarjad Seyed Mojtaba , Madaah Hosseini Hamid Reza , Chagnon Pierre
Published: December 2018

Investigating the kinetics of crystallization, growth behavior and morphological changes through statistical studies of Fe-MIL-88A suggested an autocatalytic nucleation mechanism.
Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature
Authors: Dubey Vikas , Daschakraborty Snehasis
Published: December 2018

Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.
In situ growth of triazine–heptazine based carbon nitride film for efficient (photo)electrochemical performance
Authors: Jia Qiaohui , Zhang Sufen , Gao Ziwei , Yang Peng , Gu Quan
Published: December 2018

Carbon nitride polymer film with a triazine–heptazine network on FTO as a bifunctional electrode shows boosted (photo)electrochemical performance for water splitting.
Selective production of para-xylene and light olefins from methanol over the mesostructured Zn–Mg–P/ZSM-5 catalyst
Authors: Zhang Jiaoyu , Zhu Xiaolin , Zhang Shanhe , Cheng Ming , Yu Mingxuan , Wang Guowei , Li Chunyi
Published: December 2018

The mesostructured Zn–Mg–P/ZSM-5 catalyst is efficient in converting methanol to p-xylene and light olefins, with the additional mesoporosity compensating for the activity loss during modification.
Engineering of lysine cyclodeaminase conformational dynamics for relieving substrate and product inhibitions in the biosynthesis of l-pipecolic acid
Authors: Ying Hanxiao , Wang Jing , Shi Ting , Zhao Yilei , Ouyang Pingkai , Chen Kequan
Published: December 2018

Efficient biocatalytic process construction by relieving substrate and product inhibitions via identification and engineering of enzyme conformational dynamics.
Asymmetric ring opening of racemic epoxides for enantioselective synthesis of (S)-β-amino alcohols by a cofactor self-sufficient cascade biocatalysis system
Authors: Zhang Jian-Dong , Yang Xiao-Xiao , Jia Qiao , Zhao Jian-Wei , Gao Li-Li , Gao When-Chao , Chang Hong-Hong , Wei Wen-Long , Xu Jian-He
Published: December 2018

Asymmetric ring opening of racemic epoxides to enantiopure β-amino alcohols via a cascade biocatalysis system.
The nature of active centers catalyzing oxygen electro-reduction at platinum surfaces in alkaline media
Authors: Liang Yunchang , McLaughlin David , Csoklich Christoph , Schneider Oliver , Bandarenka Aliaksandr S.
Published: December 2018

The recently introduced electrochemical scanning tunneling microscopy noise measurements were applied to directly identify active centers for oxygen electro-reduction at Pt-based surfaces in three alkaline electrolytes under reaction conditions.
Simultaneous extraction and enrichment of polyphenol and lutein from marigold (Tagetes erecta L.) flower by an enzyme-assisted ethanol/ammonium sulfate system
Authors: Fu Xiao-Qian , Zhang Gen-Lin , Deng Long , Dang Yan-Yan
Published: December 2018

Enzyme-assisted aqueous two-phase extraction was investigated for simultaneous extraction and enrichment of polyphenol and lutein.
An integrated high-throughput strategy enables the discovery of multifunctional ionic liquids for sustainable chemical processes
Authors: Zhu Anlian , Li Lingjun , Zhang Chi , Shen Yutan , Tang Mingjie , Bai Lili , Du Chunyan , Zhang Suojiang , Wang Jianji
Published: December 2018

An integrated high-throughput strategy was developed to facilitate the fast identifications of multifunctional ionic liquids for sustainable chemical processes.
Optimization of analytical conditions for precise and accurate isotope analyses of Li, Mg, Fe, Cu, and Zn by MC-ICPMS
Authors: Hu Yan , Teng Fang-Zhen
Published: December 2018

This work presents optimized analytical protocols for the accurate and precise measurements of a selection of stable metal isotopes on Nu Plasma II MC-ICPMS to facilitate their applications in earth and planetary sciences.
Sample temperature effect on laser ablation and analytical capabilities of laser induced breakdown spectroscopy
Authors: Lednev V. N. , Grishin M. Ya. , Sdvizhenskii P. A. , Asyutin R. D. , Tretyakov R. S. , Stavertiy A. Ya. , Pershin S. M.
Published: December 2018

The influence of sample temperature on the laser ablation process and analytical capabilities of laser induced breakdown spectroscopy (LIBS) was studied systematically.
Correction: Synthesis and anticonvulsant activity of phenoxyacetyl derivatives of amines, including aminoalkanols and amino acids
Authors: Pańczyk Katarzyna , Żelaszczyk Dorota , Koczurkiewicz Paulina , Słoczyńska Karolina , Pękala Elżbieta , Żesławska Ewa , Nitek Wojciech , Żmudzki Paweł , Marona Henryk , Waszkielewicz Anna
Published: December 2018

Correction for ‘Synthesis and anticonvulsant activity of phenoxyacetyl derivatives of amines, including aminoalkanols and amino acids’ by Katarzyna Pańczyk et al., MedChemComm, 2018, DOI: 10.1039/c8md00430g.
Mouse metallothionein-1 and metallothionein-2 are not biologically interchangeable in an animal model of multiple sclerosis, EAE
Authors: Comes Gemma , Fernandez-Gayol Olaya , Molinero Amalia , Giralt Mercedes , Capdevila Mercè , Atrian Silvia , Hidalgo Juan
Published: December 2018

Mice treated daily with MT2 (but not MT1) showed a significant amelioration of the clinical course of experimental autoimmune encephalomyelitis (EAE).
Environmentally benign and cost-effective synthesis of water soluble red light emissive gold nanoclusters: selective and ultra-sensitive detection of mercuric ions
Authors: Kundu Aniruddha , Park Byeongho , Ray Chaiti , Oh Juyeong , Jun Seong Chan
Published: December 2018

A green approach to synthesize red emissive gold nanoclusters for nano-molar detection of mercuric ions.
Coumarin-substituted 1,2,4-triazole-derived silver(i) and gold(i) complexes: synthesis, characterization and anticancer studies
Authors: Achar Gautam , C. R. Shahini , Patil Siddappa A. , Małecki Jan Grzegorz , Budagumpi Srinivasa
Published: December 2018

A series of coumarin-substituted 1,2,4-triazolium salts and their respective silver– and gold– N-heterocyclic carbene complexes have been reported. The complexes displayed promising anticancer activity with GI50 values of up to 0.354 μM and 8.5983 μM against MCF 7 and HT-29 cell lines, respectively.
Phthalazine-trione as a blue-green light-emitting moiety: crystal structures, photoluminescence and theoretical calculations
Authors: Martins Felipe Terra , Maia Lauro June Queiroz , Gasparotto Gisane , Valdo Ana Karoline Silva Medanha , Nascimento Neto José Antônio , Ribeiro Leandro , de Freitas Rego Yuri , da Silva Cleiton Moreira , de Fátima Ângelo
Published: December 2018

Phthalazine-trione was found to be a new robust blue-green light-emitting fluorophore, regardless of the substitution pattern.
Synthesis, structural, biological andin silicostudies of new 5-arylidene-4-thiazolidinone derivatives as possible anticancer, antimicrobial and antitubercular agents
Authors: Sunil Kumar A. , Kudva Jyothi , Bharath B. R. , Ananda K. , Sadashiva Rajitha , Madan Kumar S. , Revanasiddappa B. C. , Kumar Vasantha , Rekha P. D. , Naral Damodara
Published: December 2018

Thiazolidinone–sulfonamide hybrids emerged as promising anticancer and antitubercular agents, and their anticancer activity was confirmed by docking studies.
Enzymeless electrochemical determination of hydrogen peroxide at a heteropolyanion-based composite film electrode
Authors: Zhu Di , Zuo Jingwei , Tan Lichao , Pang Haijun , Ma Huiyuan
Published: December 2018

For the first time, a sensitive and efficient composite film of [PB/WV–Pt@Pd]6was constructed for H2O2detection.
Dehydrogenation of formic acid catalysed by M-embedded nitrogen-doped graphene (M = Fe, Ru, Os): a DFT study
Authors: Christopher Jeyakumar Thayalaraj , Sivasankar Chinnappan
Published: December 2018

The dehydrogenation of formic acid to produce H2 and CO2 was studied theoretically by employing group VIII metal-embedded NDG.
Co3Sn2/SnO2 nanocomposite loaded on Cu foam as high-performance three-dimensional anode for lithium-ion batteries
Authors: Zhang Duo , Bi Chaoqi , Wu Qingliu , Hou Guangya , Zheng Guoqu , Wen Ming , Tang Yiping
Published: December 2018

It is a challenge to commercialize tin dioxide-based anodes for lithium-ion batteries due to their low rate capability and poor cycling performance of the electrodes.
An l-cysteine-mediated iodide-catalyzed reaction for the detection of I−
Authors: He Kaili , Chen Hongyu , Wu Cuiyan , Liu Meiling , Zhang Youyu
Published: December 2018

In this study, a highly selective and eco-friendly fluorescent sensor consisting of upconversion (UCNPs) and gold nanoparticles (AuNPs) was developed for the detection of iodide (I−).
A convenient and reproducible method for the synthesis of astatinated 4-[211At]astato-l-phenylalanineviaelectrophilic desilylation
Authors: Watanabe Shigeki , Azim Mohammad Anwar-Ul , Nishinaka Ichiro , Sasaki Ichiro , Ohshima Yasuhiro , Yamada Keiichi , Ishioka Noriko S.
Published: December 2018

Electrophilic desilylation allows for convenient and reproducible synthesis of the aromatic amino acid derivative 4-[211At]astato-l-phenylalanine.
Fluorogenic probes for super-resolution microscopy
Authors: Kozma Eszter , Kele Péter
Published: December 2018

Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
Anchoring nickel nanoparticles on three-dimensionally macro-/mesoporous titanium dioxide with a carbon layer from polydopamine using polymethylmethacrylate microspheres as sacrificial templates
Authors: Zheng Jing , Zhang Min , Miao Teng , Yang Jingxia , Xu Jingli , Alharbi Njud S. , Wakeel Muhammad
Published: December 2018

Herein, three dimensional (3D) macro-/mesoporous TiO2@C–Ni composites have been successfully fabricated, which endowed the composites with enhanced performance in catalysis and protein adsorption.
Investigation of the metabolic stability of olmutinib by validated LC-MS/MS: quantification in human plasma
Authors: Attwa Mohamed W. , Kadi Adnan A. , Darwish Hany W. , Abdelhameed Ali S.
Published: December 2018

Olmutinib (OTB, Olita™) is an orally available third-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR TKI).
Negative area compressibility of a hydrogen-bonded two-dimensional material
Authors: Feng Guoqiang , Zhang Wei-Xiong , Dong Liyuan , Li Wei , Cai Weizhao , Wei Wenjuan , Ji Lijun , Lin Zheshuai , Lu Peixiang
Published: December 2018

Very few materials expand two-dimensionally under pressure, and this extremely rare phenomenon, namely negative area compressibility (NAC), is highly desirable for technological applications in pressure sensors and actuators.
Emergence of high ORR activity through controlling local density-of-states by alloying immiscible Au and Ir
Authors: Kusada Kohei , Wu Dongshuang , Yamamoto Tomokazu , Toriyama Takaaki , Matsumura Syo , Xie Wei , Koyama Michihisa , Kawaguchi Shogo , Kubota Yoshiki , Kitagawa Hiroshi
Published: December 2018

Although Ir or Au is not active for ORR, we first demonstrate highly active Au0.5Ir0.5 alloy by emulating Pt LDOS profile.
An enzyme-free molecular catalytic device: dynamically self-assembled DNA dendrimers for in situ imaging of microRNAs in live cells
Authors: Yue Shuzhen , Song Xinyue , Song Weiling , Bi Sai
Published: December 2018

Branched catalytic hairpin assembly is proposed for dynamic self-assembly of DNA dendrimers for signal amplification and in situ imaging of microRNAs in live cells with high sensitivity and selectivity.
Phase-change switching in 2D via soft interactions
Authors: Díaz-Méndez Rogelio , Pupillo Guido , Mezzacapo Fabio , Wallin Mats , Lidmar Jack , Babaev Egor
Published: December 2018

We present a new type of phase-change behavior relevant for information storage applications, that can be observed in 2D systems with cluster-forming ability.
Effect of anisotropic diffusion on spinodal decomposition
Authors: Vuijk Hidde Derk , Brader Joseph Michael , Sharma Abhinav
Published: December 2018

Phase transition dynamics of a fluid system are very sensitive to the diffusion tensor.
In situnitridated porous nanosheet networked Co3O4–Co4N heteronanostructures supported on hydrophilic carbon cloth for highly efficient electrochemical hydrogen evolution
Authors: Liu Bin , Cheng Junye , Peng Hui-Qing , Chen Da , Cui Xiao , Shen Dong , Zhang Kui , Jiao Tianpeng , Li Minfei , Lee Chun-Sing , Zhang Wenjun
Published: December 2018

Novel Co3O4–Co4N porous nanosheet networks were controllably synthesized on hydrophilic carbon cloth throughin situnitridation using nitrogen plasma.
Achievable highVocof carbon based all-inorganic CsPbIBr2perovskite solar cells through interface engineering
Authors: Guo Zhanglin , Teo Siowhwa , Xu Zhenhua , Zhang Chu , Kamata Yusuke , Hayase Shuzi , Ma Tingli
Published: December 2018

TheVocof carbon based CsPbIBr2PSCs can be highly boosted through the surface passivation of SnO2films.
Ultralight CoNi/rGO aerogels toward excellent microwave absorption at ultrathin thickness
Authors: Zhao Hai-Bo , Cheng Jin-Bo , Zhu Jia-Yi , Wang Yu-Zhong
Published: December 2018

Ultralight CoNi/rGO aerogels exhibit excellent microwave absorption performances at an ultrathin thickness of 0.8 mm.
From nanofibers to ordered ZnO/NiO heterojunction arrays for self-powered and transparent UV photodetectors
Authors: Zhang Zhiming , Ning Yi , Fang Xiaosheng
Published: December 2018

Ordered ZnO/NiO heterojunction arrays prepared via electrospinning using three-assisted-electrodes were achieved for high-performance self-powered ultraviolet photodetectors.
LncRNAs, MALAT1 and lnc-DC as potential biomarkers for multiple sclerosis diagnosis
Authors: Shaker Olfat G. , Mahmoud Rania H. , Abdelaleem Omayma O. , Ibrahem Enas G. , Mohamed Abdelrahmaan A. , Zaki Othman M. , Abdelghaffar Noha K. , Ahmed Tarek I. , Hemeda Nada F. , Ahmed Naglaa A. , Mansour Dina F.
Published: December 2018

Long non-coding RNAs (lncRNAs) play an important role in gene regulation and show greater tissue specificity and complexity of biological functions. There is on-going research in their contribution in autoimmune diseases like multiple sclerosis (MS). Our study aimed at the evaluation of serum levels of lncRNAs, MALAT1 and lnc-DC in MS patients and the investigation of the association between these lncRNAs and the disease activity. Serum from 45 MS patients and 45 healthy controls was separated. MALAT1 and lnc-DC expression levels were assayed by qRT-PCR. MALAT1 and lnc-DC were significantly increased in MS patients (P=0.004 and P=0.006, respectively) in comparison with controls. There was a significant increase in expression of MALAT1 in secondary progressive MS (SPMS) subgroup compared with controls (P<0.0001); however, significant elevation of lnc-DC was demonstrated in relapsing remitting MS (RRMS) subtype (P=0.003) compared with normal controls. A positive association between the expression levels of MALAT1 and lnc-DC (r = 0.513, P < 0.0001) in MS patients was detected. Moreover, positive correlation was observed between MALAT1and lnc-DC in RRMS (r = 0.569, P = 0.001). Serum levels of MALAT1 and lnc-DC may serve as potential novel molecular biomarkers for MS diagnosis and may provide a new direction for its treatment.
AMPK: a therapeutic target of heart failure—not only metabolism regulation
Authors: Li Xuan , Liu Jia , Lu Qingguo , Ren Di , Sun Xiaodong , Rousselle Thomas , Tan Yi , Li Ji
Published: December 2018

Heart failure (HF) is a serious disease with high mortality. The incidence of this disease has continued to increase over the past decade. All cardiovascular diseases causing dysfunction of various physiological processes can result in HF. AMP-activated protein kinase (AMPK), an energy sensor, has pleiotropic cardioprotective effects and plays a critical role in the progression of HF. In this review, we highlight that AMPK can not only improve the energy supply in the failing heart by promoting ATP production, but can also regulate several important physiological processes to restore heart function. In addition, we discuss some aspects of some potential clinical drugs which have effects on AMPK activation and may have value in treating HF. More studies, especially clinical trials, should be done to evaluate manipulation of AMPK activation as a potential means of treating HF.
Substrate polyspecificity and conformational relevance in ABC transporters: new insights from structural studies
Authors: Wright Jack , Muench Stephen P. , Goldman Adrian , Baker Alison
Published: December 2018

Transport of molecules and ions across biological membranes is an essential process in all organisms. It is carried out by a range of evolutionarily conserved primary and secondary transporters. A significant portion of the primary transporters belong to the ATP-binding cassette (ABC) superfamily, which utilise the free-energy from ATP hydrolysis to shuttle many different substrates across various biological membranes, and consequently, are involved in both normal and abnormal physiology. In humans, ABC transporter-associated pathologies are perhaps best exemplified by multidrug-resistance transporters that efflux many xenobiotic compounds due to their remarkable substrate polyspecificity. Accordingly, understanding the transport mechanism(s) is of great significance, and indeed, much progress has been made in recent years, particularly from structural studies on ABC exporters. Consequently, the general mechanism of ‘alternate access’ has been modified to describe individual transporter nuances, though some aspects of the transport process remain unclear. Moreover, as new information has emerged, the physiological relevance of the ‘open-apo’ conformation of MsbA (a bacterial exporter) has been questioned and, by extension, its contribution to mechanistic models. We present here a comprehensive overview of the most recently solved structures of ABC exporters, focusing on new insights regarding the nature of substrate polyspecificity and the physiological relevance of the ‘open-apo’ conformation. This review evaluates the claim that the latter may be an artefact of detergent solubilisation, and we hypothesise that the biophysical properties of the membrane play a key role in the function of ABC exporters allowing them to behave like a ‘spring-hinge’ during their transport cycle.
Phage-based biocontrol strategies and their application in agriculture and aquaculture
Authors: Dy Ron L. , Rigano Luciano A. , Fineran Peter C.
Published: December 2018

Meeting global food demands for a growing human population with finite natural resources is a major challenge. Aquaculture and agriculture are critical to satisfy food requirements, yet suffer significant losses from bacterial diseases. Therefore, there is an urgent need to develop novel antimicrobial strategies, which is heightened by increasing antibiotic resistance. Bacteriophages (phages) are viruses that specifically infect bacteria, and phage-derived therapies are promising treatments in the fight against bacterial diseases. Here, we describe multiple ways that phages and phage-based technologies can be used as antimicrobials. Antimicrobial activity can be achieved through lysis of targeted bacteria by virulent phages or lytic enzymes. Alternatively, phages can be engineered for the delivery of lethal genes and other cargoes to kill bacteria and to manipulate the bacterial response to conventional antibiotics. We also briefly highlight research exploring phages as potential biocontrol agents with examples from agriculture and aquaculture.
Characterisation of sensor kinase by CD spectroscopy: golden rules and tips
Authors: Siligardi Giuliano , Hughes Charlotte S. , Hussain Rohanah
Published: December 2018

This is a review that describes the golden rules and tips on how to characterise the molecular interactions of membrane sensor kinase proteins with ligands using mainly circular dichroism (CD) spectroscopy. CD spectroscopy is essential for this task as any conformational change observed in the far-UV (secondary structures (α-helix, β-strands, poly-proline of type II, β-turns, irregular and folding) and near-UV regions [local environment of the aromatic side-chains of amino acid residues (Phe, Tyr and Trp) and ligands (drugs) and prosthetic groups (porphyrins, cofactors and coenzymes (FMN, FAD, NAD))] upon ligand addition to the protein can be used to determine qualitatively and quantitatively ligand-binding interactions. Advantages of using CD versus other techniques will be discussed. The difference CD spectra of the protein–ligand mixtures calculated subtracting the spectra of the ligand at various molar ratios can be used to determine the type of conformational changes induced by the ligand in terms of the estimated content of the various elements of protein secondary structure. The highly collimated microbeam and high photon flux of Diamond Light Source B23 beamline for synchrotron radiation circular dichroism (SRCD) enable the use of minimal amount of membrane proteins (7.5 µg for a 0.5 mg/ml solution) for high-throughput screening. Several examples of CD titrations of membrane proteins with a variety of ligands are described herein including the protocol tips that would guide the choice of the appropriate parameters to conduct these titrations by CD/SRCD in the best possible way.
A tough row to hoe: when replication forks encounter DNA damage
Authors: Patel Darshil R. , Weiss Robert S.
Published: December 2018

Eukaryotic cells continuously experience DNA damage that can perturb key molecular processes like DNA replication. DNA replication forks that encounter DNA lesions typically slow and may stall, which can lead to highly detrimental fork collapse if appropriate protective measures are not executed. Stabilization and protection of stalled replication forks ensures the possibility of effective fork restart and prevents genomic instability. Recent efforts from multiple laboratories have highlighted several proteins involved in replication fork remodeling and DNA damage response pathways as key regulators of fork stability. Homologous recombination factors such as RAD51, BRCA1, and BRCA2, along with components of the Fanconi Anemia pathway, are now known to be crucial for stabilizing stalled replication forks and preventing nascent strand degradation. Several checkpoint proteins have additionally been implicated in fork protection. Ongoing work in this area continues to shed light on a sophisticated molecular pathway that balances the action of DNA resection and fork protection to maintain genomic integrity, with important implications for the fate of both normal and malignant cells following replication stress.
The precise molecular signals that control endothelial cell–cell adhesion within the vessel wall
Authors: Schimmel Lilian , Gordon Emma
Published: December 2018

Endothelial cell–cell adhesion within the wall of the vasculature controls a range of physiological processes, such as growth, integrity and barrier function. The adhesive properties of endothelial cells are tightly controlled by a complex cascade of signals transmitted from the surrounding environment or from within the cells themselves, with the dynamic nature of cellular adhesion and the regulating signalling networks now beginning to be appreciated. Here, we summarise the current knowledge of the mechanisms controlling endothelial cell–cell adhesion in the developing and mature blood vasculature.
Functional and behavioral consequences of Parkinson's disease-associated LRRK2-G2019S mutation
Authors: Benson Deanna L. , Matikainen-Ankney Bridget A. , Hussein Ayan , Huntley George W.
Published: December 2018

LRRK2 mutation is the most common inherited, autosomal dominant cause of Parkinson's disease (PD) and has also been observed in sporadic cases. Most mutations result in increased LRRK2 kinase activity. LRRK2 is highly expressed in brain regions that receive dense, convergent innervation by dopaminergic and glutamatergic axons, and its levels rise developmentally coincident with glutamatergic synapse formation. The onset and timing of expression suggests strongly that LRRK2 regulates the development, maturation and function of synapses. Several lines of data in mice show that LRRK2-G2019S, the most common LRRK2 mutation, produces an abnormal gain of pathological function that affects synaptic activity, spine morphology, persistent forms of synapse plasticity and behavioral responses to social stress. Effects of the mutation can be detected as early as the second week of postnatal development and can last or have consequences that extend into adulthood and occur in the absence of dopamine loss. These data suggest that the generation of neural circuits that support complex behaviors is modified by LRRK2-G2019S. Whether such alterations impart vulnerability to neurons directly or indirectly, they bring to the forefront the idea that neural circuits within which dopamine neurons eventually degenerate are assembled and utilized in ways that are distinct from circuits that lack this mutation and may contribute to non-motor symptoms observed in humans with PD.