bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Authors: Middelkamp H. H. T. , Verboven A. H. A. , De Sá Vivas A. G. , Schoenmaker C. , Klein Gunnewiek T. M. , Passier R. , Albers C. A. , ‘t Hoen P. A. C. , Nadif Kasri N. , van der Meer A. D.
Published: January 2021

In vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.
Acyl-CoA thioesterase activity of peroxisomal ABC protein ABCD1 is required for the transport of very long-chain acyl-CoA into peroxisomes
Authors: Kawaguchi Kosuke , Mukai Emi , Watanabe Shiro , Yamashita Atsushi , Morita Masashi , So Takanori , Imanaka Tsuneo
Published: January 2021

The ABCD1 protein, one of the four ATP-binding cassette (ABC) proteins in subfamily D, is located on the peroxisomal membrane and is involved in the transport of very long chain fatty acid (VLCFA)-CoA into peroxisomes. Its mutation causes X-linked adrenoleukodystophy (X-ALD): an inborn error of peroxisomal β-oxidation of VLCFA. Whether ABCD1 transports VLCFA-CoA as a CoA ester or free fatty acid is controversial. Recently, Comatose (CTS), a plant homologue of human ABCD1, has been shown to possess acyl-CoA thioesterase (ACOT) activity, and it is suggested that this activity is required for transport of acyl-CoA into peroxisomes. However, the precise transport mechanism is unknown. Here, we expressed human His-tagged ABCD1 in methylotrophic yeast, and characterized its ACOT activity and transport mechanism. The expressed ABCD1 possessed both ATPase and ACOT activities. The ACOT activity of ABCD1 was inhibited by p-chloromercuribenzoic acid (pCMB), a cysteine-reactive compound. Furthermore, we performed a transport assay with ABCD1-containing liposomes using 7-nitro-2–1,3-benzoxadiazol-4-yl (NBD)-labeled acyl-CoA as the substrate. The results showed that the fatty acid produced from VLCFA-CoA by ABCD1 is transported into liposomes and that ACOT activity is essential during this transport process. We propose a detailed mechanism of VLCFA-CoA transport by ABCD1.
Application of green tea catechins, polysaccharides, and flavonol prevent fine dust induced bronchial damage by modulating inflammation and airway cilia
Authors: Kim Juewon , Choi Hyunjung , Choi Dong-Hwa , Park Kyuhee , Kim Hyung-June , Park Miyoung
Published: January 2021

Airborne fine dust particles (FDPs) have been identified as major toxins in air pollution that threaten human respiratory health. While searching for an anti-FDP reagent, we found that green tea extract (GTE) and fractions rich in flavonol glycosides (FLGs) and crude tea polysaccharides (CTPs) had protective effects against FDP-stimulated cellular damage in the BEAS-2B airway epithelial cell line. The GTE, FLGs, and CTPs significantly increased viability and lowered oxidative stress levels in FDP-treated cells. Combined treatment with GTE, FLGs, and CTPs also exerted synergistic protective effects on cells and attenuated FDP-induced elevations in inflammatory gene expression. Moreover, the green tea components increased the proportion of ciliated cells and upregulated ciliogenesis in the airway in FDP-stimulated BEAS-2B cells. Our findings provide insights into how natural phytochemicals protect the airway and suggest that green tea could be used to reduce FDP-induced airway damage as an ingredient in pharmaceutical, nutraceutical, and also cosmeceutical products.
Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
Authors: Lee Jeong Hoon , Kweon Solbi , Park Yu Rang
Published: January 2021

Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.
Author Correction: Context-aware experience sampling reveals the scale of variation in affective experience
Authors: Hoemann Katie , Khan Zulqarnain , Feldman Mallory J. , Nielson Catie , Devlin Madeleine , Dy Jennifer , Barrett Lisa Feldman , Wormwood Jolie B. , Quigley Karen S.
Published: January 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Noble-metal nanoparticle labelling multiplex miRNAs by ICP-MS readout with internal standard isotopes of 115In and 209Bi
Authors: Zhang Fei , Yong Li , Hua Xia , You Fan , Wang Bin , Feng Yu-Liang , Mao Li
Published: January 2021

A small sized (less than 20 nm) noble-metal nanoparticle labelled ICP-MS (NP-ICP-MS) is proposed for high-throughput microRNA (miRNA) determination.
Highly selective simultaneous determination of Cu(ii), Co(ii), Ni(ii), Hg(ii), and Mn(ii) in water samples using microfluidic paper-based analytical devices
Authors: Kamnoet Pornphimon , Aeungmaitrepirom Wanlapa , Menger Ruth F. , Henry Charles S.
Published: January 2021

The process for simultaneous analysis of five metal ions with one device by using Bc, PAR, DTZ, PAR, and DMG for Cu(ii), Co(ii), Hg(ii), Mn(ii), and Ni(ii) detection, respectively.
Optimization of gold nanorod arrays for surface enhanced Raman spectroscopy (SERS) detection of atrazine
Authors: Albarghouthi Najwan , MacMillan Presley , Brosseau Christa L.
Published: January 2021

Modified gold nanorod arrays are used as SERS substrates for the detection of atrazine.
A colorimetric sensor for detecting thiourea based on inhibiting peroxidase-like activity of gold–platinum nanoparticles
Authors: Zhao Yuqi , Fu Qingjie , Cui Xiaoqian , Chi Hui , Lu Yongzhuang , Liu Xiaoli , Yu Miao , Fei Qiang , Feng Guodong , Shan Hongyan , Huan Yanfu
Published: January 2021

The sensor is based on the peroxidase-like activity of Au@PtNPs. Thiourea can quickly be detected by the color change of the solution. The method was applied to the determination of thiourea in practical samples.
Chemical probes reveal the timing of early chlorination in vancomycin biosynthesis
Authors: Leng Daniel J. , Greule Anja , Cryle Max J. , Tosin Manuela
Published: January 2021

Chemical probes were used to intercept peptide biosynthetic intermediates in vancomycin formation in vivo.
Surface-enhanced Raman spectroscopy (SERS): a powerful technique to study the SEI layer in batteries
Authors: Piernas-Muñoz M. J. , Tornheim A. , Trask S. , Zhang Z. , Bloom I.
Published: January 2021

The solid electrolyte interphase (SEI) layer on a silicon anode is investigated by SERS.
Asymmetric syntheses of spiro[benzofuro-cyclopenta[1,2-b]indole–indoline] scaffolds via consecutive cyclization
Authors: Zhang Heng , Guan Xu-Kai , Sun Dong-Yang , Liu Guo-Feng , Gao Ji-Gang , Zhang Guang-Liang , Zhang Suo-Qin
Published: January 2021

Highly diastereo- and enantioselective spiro[benzofuro-cyclopenta[1,2-b]indole–indoline] scaffolds with five successive stereogenic centers and two spiroheterocycles were synthesized via consecutive cyclization.
Kinetics of the photocatalysed reduction of oxygen by CdS probed using photoinduced absorption spectroscopy (PIAS)
Authors: McNeill Aaron , O’Rourke Christopher , Mills Andrew
Published: January 2021

Photoinduced absorption spectroscopy and reaction rate measurements probe O2 reduction by an SED, photocatalysed by CdS.
A conjugated tetracarboxylate anode for stable and sustainable Na-ion batteries
Authors: Qin Kaiqiang , Holguin Kathryn , Mohammadiroudbari Motahareh , Luo Chao
Published: January 2021

A conjugated tetracarboxylate, Na4C10H2O8, shows low redox potentials (∼0.65 V), long cycle life (1000 cycles), and fast charging capability (up to 2 A g−1), demonstrating a promising organic anode for stable and sustainable Na-ion batteries.
Mechanical study of a copper dietary supplement, copper glycinate hydrate
Authors: Azeem Muhammad , Li Kai , Qin Yan , Dong Liyuan , Li Wei
Published: January 2021

Here, the mechanical properties of a copper-based dietary supplement were systematically investigated via a combined theoretical–experimental approach.
Two-step hydrothermal synthesis of (NH4)xWO3 hollow spherical and hierarchical structures
Authors: Ou Ping , Su Xuhong , Zeng Yang , Zhang Feifei , Liu Jiahao , Wang Chong , Yang Shuhua , Wang Hebin , Wen Yufeng , Zhao Hongjin
Published: January 2021

Two novel (NH4)xWO3 structures were prepared by a two-step hydrothermal route. Also, the possible formation mechanism of these two (NH4)xWO3 structures was proposed and discussed.
Magnetism and electronic structures of bismuth (stannum) films at the CrI3 (CrBr3) interface
Authors: Chen Li , Jiang Chuan , Yang Maoyou , Hu Tao , Meng Yan , Lei Jie , Zhang Mingjian
Published: January 2021

From first-principles calculations, the magnetism and electronic structures of bilayer bismuth (stannum) films at the monolayer CrI3 (CrBr3) interface are studied.
Understanding Fermi resonances in the complex vibrational spectra of the methyl groups in methylamines
Authors: Huang Qian-Rui , Endo Tomoya , Mishra Saurabh , Zhang Bingbing , Chen Li-Wei , Fujii Asuka , Jiang Ling , Patwari G. Naresh , Matsuda Yoshiyuki , Kuo Jer-Lai
Published: January 2021

Vibrational spectra of the methyl groups in mono-methylamine (MMA), dimethylamine (DMA), and trimethylamine (TMA) monomers and their clusters were measured to capture their spectral features as a result of bend/umbrella-stretch Fermi resonance (FR).
Effect of iodine doping on the electrical, thermal and mechanical properties of SnSe for thermoelectric applications
Authors: Das Amit , Chauhan Avnee , Trivedi Vikrant , Tiadi Minati , Kumar Ravi , Battabyal Manjusha , Satapathy Dillip K.
Published: January 2021

We report the evolution of the thermoelectric and mechanical properties of n-type SnSe obtained by iodine doping at the Se site.
Tunnelling splitting patterns in some partially deuterated water trimers
Authors: Eraković Mihael , Cvitaš Marko T.
Published: January 2021

First characterization of the tunnelling splitting pattern in mixed water trimer isotopomers via the dynamics of flips and bifurcations.
Modifying conformational distribution of chiral tetrahydro-2-furoic acid through its interaction with water: a rotational spectroscopic and theoretical investigation
Authors: Xie Fan , Mahendiran Sethupathy , Seifert Nathan A. , Xu Yunjie
Published: January 2021

The preferred conformations and conformational cooling paths of tetrahydro-2-furoic acid–water are established and the “lubrification” effects of water revealed.
Asymmetric organocatalysis: an enabling technology for medicinal chemistry
Authors: Han Bo , He Xiang-Hong , Liu Yan-Qing , He Gu , Peng Cheng , Li Jun-Long
Published: January 2021

This review provides a comprehensive overview of the recent applications of organocatalytic strategies in pharmaceutical synthesis, with a focus on the preparation of antiviral, anticancer, neuroprotective, cardiovascular, antibacterial and antiparasitic agents.
Synthesis, structure, electrochemistry and magnetism of cobalt-, nickel- and zinc-containing [M4(OH)3(H2O)2(α-SiW10O36.5)2]13− (M = Co2+, Ni2+, and Zn2+)
Authors: Haider Ali , Bassil Bassem S. , Lin Zhengguo , Ma Xiang , Haferl Peter J. , Bindra Jasleen K. , Kinyon Jared , Zhang Guangjin , Keita Bineta , Dalal Naresh S. , Kortz Ulrich
Published: January 2021

Three novel heteropolytungstates, [MII4(OH)3(H2O)2(α-SiW10O36.5)2]13− (M = Co, Ni, and Zn), were synthesized and structurally characterized, and magnetic and electrochemical studies are presented.
Recent advances in metal–organic frameworks as adsorbent materials for hazardous dye molecules
Authors: Parmar Bhavesh , Bisht Kamal Kumar , Rajput Gunjan , Suresh Eringathodi
Published: January 2021

Recent studies on metal–organic framework (MOF)-based adsorbents for the removal of carcinogenic organic dye pollutants have been summarized with a handful of recent examples.
Elucidating the paramagnetic interactions of an inorganic–organic hybrid radical-functionalized Mn-Anderson cluster
Authors: Lin Chang-Gen , Hutin Marie , Busche Christoph , Bell Nicola L. , Long De-Liang , Cronin Leroy
Published: January 2021

A family of polyoxometalate-based magnetic compounds were synthesized by anchoring N-oxide type TEMPO radicals onto an Anderson type polyoxometalate cluster.
Controllable synthesis of Cu–Ni–M (M = S, P and Se) hybrid nanoarrays for efficient water splitting reaction
Authors: Chen Nannan , Wang Yanhong , Du Xiaoqiang , Zhang Xiaoshuang
Published: January 2021

The results demonstrate that Cu–Ni–S/NF//Cu–Ni–P/NF pairs show superior water splitting performance with only requiring a cell voltage of 1.50 V to achieve a current density of 20 mA cm−2.
Recent advances in the biomedical applications of black phosphorus quantum dots
Authors: Miao Yuhang , Wang Xiaojing , Sun Jie , Yan Zhong
Published: January 2021

Zero-dimensional (0D) black phosphorus quantum dots (BPQDs), the new derivatives of black phosphorus (BP) nanomaterials, have attracted considerable attention since they were first prepared in 2015.
Electrochemical coupling halobenzene into biphenyl on a reusable Pd nanoparticle-coated carbon-paper electrode at ambient conditions
Authors: Wang Chao-Nan , Lu Yong-Heng , Liu Yue , Liu Jun , Yang Yao-Yue , Zhao Zhi-Gang
Published: January 2021

Electrochemical homo-coupling halobenzene into biphenyl compounds on the Pd/C surface.
One-step bulk fabrication of a CaO/carbon heterogeneous catalyst from calcium citrate for rapid synthesis of dimethyl carbonate (DMC) by transesterification of ethylene carbonate (EC)
Authors: Wei Qiang , Zhang Gang , Yao Jie , Chen Xuejun , Wang Gongying , Yang Xiangui
Published: January 2021

Providing a simpler, more economical and more innovative method for rapid preparation of carbon-based inorganic nanoparticles.
A simple method to construct a low-cost immunosensor based on a dithiol-functionalized polydopamine platform
Authors: Liu Bo , Yang Luanying , Wang Gang , He Sha , Wang Xiaobo , Ye Ling
Published: January 2021

A simple and low-cost electrochemical CEA immunosensor was investigated via the self-polymerization of dopamine and a dithiol compound spacer for the covalent immobilization of antibodies. The designed CEA immunosensor exhibited a linear response and a low detection limit.
Photothermal behaviour of titanium nitride nanoparticles evaluated by transient X-ray diffraction
Authors: Diroll Benjamin T. , Brumberg Alexandra , Leonard Ariel A. , Panuganti Shobhana , Watkins Nicolas E. , Cuthriell Shelby A. , Harvey Samantha M. , Kinigstein Eli D. , Yu Jin , Zhang Xiaoyi , Kanatzidis Mercouri G. , Wasielewski Michael R. , Chen Lin X. , Schaller Richard D.
Published: January 2021

Metal nitrides are a promising non-toxic, inexpensive, and durable material for photothermal applications. The photothermal properties of titanium nitride are measured using time-resolved X-ray diffraction following optical excitation.
Synthesis of C3-sulfone substituted naphthols via rhodium(iii)-catalyzed annulation of sulfoxonium ylides with alkynylsulfones
Authors: Xie Wucheng , Jian Xinyi , Zhang Liyang , Jin Kexin , Shi Junjun , Zhu Feng
Published: January 2021

A sulfoxonium ylide directed C–H activation/alkynylsulfone annulation approach for the step-economical assembly of C3-sulfone substituted naphthols with high regioselectivity.
Organocatalytic enantioselective [2 + 4]-annulation of γ-substituted allenoates withN-acyldiazenes for the synthesis of optically active 1,3,4-oxadiazines
Authors: Guo Xing , Chen Xuling , Cheng Yuyu , Chang Xiaoyong , Li Xuechen , Li Pengfei
Published: January 2021

An enantioselective [2 + 4]-annulation of γ-substituted allenoates withN-acyldiazenes has been developed for the first time.
Xanthanoltrimer A–C: three xanthanolide sesquiterpene trimers from the fruits of Xanthium italicum Moretti isolated by HPLC-MS-SPE-NMR
Authors: Fu Jiang , Wang Ya-Nan , Ma Shuang-Gang , Li Li , Wang Xiao-Jing , Li Yong , Liu Yun-Bao , Qu Jing , Yu Shi-Shan
Published: January 2021

Xanthanoltrimer A–C, first three xanthanolide sesquiterpene trimers from the fruits of Xanthium italicum Moretti, were isolated by HPLC-MS-SPE-NMR. Xanthanoltrimer A–C had an unprecedented 5/7/6/5/7/6/5/7 polycyclic scaffold.
A cyclopenta-fused dibenzo[b,d]thiophene-co-phenanthrene macrocyclic tetraradicaloid
Authors: Lu Xuefeng , An Dongyue , Han Yi , Zou Ya , Qiao Yanjun , Zhang Ning , Chang Dongdong , Wu Jishan , Liu Yunqi
Published: January 2021

The first member of sulfur-heterocycloarene neutral tetraradicaloids, MC4-S, was synthesized in crystalline form, which displays strong global anti-aromaticity and unique properties.
Domain growth in ferronematics: slaved coarsening, emergent morphologies and growth laws
Authors: Vats Aditya , Banerjee Varsha , Puri Sanjay
Published: January 2021

Ferronematics (FNs) are suspensions of magnetic nanoparticles in nematic liquid crystals (NLCs).
Critical conditions for organic thread cutting under electric fields
Authors: Yin Shuai , Huang Yi , Wong Teck Neng
Published: January 2021

Critical conditions with electric capillary number are investigated for triggering the on-demand cutting of an organic thread in a microchannel under electric fields.
Defective Fe3GeTe2 monolayer as a promising electrocatalyst for spontaneous nitrogen reduction reaction
Authors: Ma Zuju , Xiao Chengwei , Cui Zhitao , Du Wei , Li Qiaohong , Sa Rongjian , Sun Chenghua
Published: January 2021

Defective Fe3GeTe2 exhibits high catalytic activity for the NRR involving six exothermic hydrogenation steps.
An in situ bifacial passivation strategy for flexible perovskite solar module with mechanical robustness by roll-to-roll fabrication
Authors: Wang Hongyu , Huang Zengqi , Xiao Shuqin , Meng Xiangchuan , Xing Zhi , Rao Li , Gong Chenxiang , Wu Runsheng , Hu Ting , Tan Licheng , Hu Xiaotian , Zhang Shaohua , Chen Yiwang
Published: January 2021

An in situ bifacial passivation strategy is developed to improve the performance of flexible perovskite solar module during roll-to-roll printing.
High energy density aqueous zinc–benzoquinone batteries enabled by carbon cloth with multiple anchoring effects
Authors: Luo Zhiqiang , Zheng Silin , Zhao Shuo , Jiao Xin , Gong Zongshuai , Cai Fengshi , Duan Yueqin , Li Fujun , Yuan Zhihao
Published: January 2021

Benzoquinone with high theoretical capacity is anchored on N-plasma engraved porous carbon as a desirable cathode for rechargeable aqueous Zn-ion batteries. Such batteries display tremendous potential in large-scale energy storage applications.
Quantifying the reaction mechanisms of a high-capacity CuP2/C composite anode for potassium ion batteries
Authors: Zhao Chen , Chen Huixin , Liu Haodong , Yin Liang , Zhang Qiaobao , Yu Sicen , Liu Ping , Zhong Guiming , Lu Can-Zhong , Yang Yong
Published: January 2021

The evolution process of various K–P alloys in a prepared CuP2/C composite for potassium ion batteries is illustrated, revealing that POx components in the composite are reversible.
Transparent, ultraflexible, and superinsulating nanofibrous biocomposite aerogels via ambient pressure drying
Authors: Zu Guoqing , Zeng Sheng , Yang Ben , Huang Jia
Published: January 2021

We report transparent, flexible, and superinsulating biocomposite aerogels with a homogeneous, highly porous, and nanofibrous structure based on oxidized starch and polyorganosiloxane via facile ambient pressure drying for the first time.
An MnO2 nanosheet@nitrogen-doped graphene aerogel enables high specific energy and high specific power for supercapacitors and Zn–air batteries
Authors: Zhao Hui , Jiang Rijuan , Zhang Yong , Xie Beibei , Fu Jiali , Yuan Xiaona , Yang Wenxin , Wu Yan , Zhang Renjie
Published: January 2021

Ultrathin MnO2 nanosheets (MNSs) with calculated high ratio of exposed surface unit cells on conductive nitrogen-doped graphene assure the assembled aerogel high specific energy and high specific power in supercapacitors and Zn–air batteries.
Evidence of protein coronas around soft nanoparticles regardless of the chemical nature of the outer surface: structural features and biological consequences
Authors: de Castro Carlos E. , Panico Karine , Stangherlin Lucas M. , Albuquerque Lindomar J. C. , A. S. Ribeiro Caroline , da Silva Maria C. C. , Jäger Eliézer , Giacomelli Fernando C.
Published: January 2021

The presence of thick protein coronas has been found around pH-responsive polymeric assemblies. They reduce the levels of cellular uptake, nevertheless with positive outputs with regard to cytotoxic effects.
Length-independent multifunctional device based on penta-tetra-pentagonal molecule: a first-principles study
Authors: Chen Tong , Ding Wence , Li Huili , Zhou Guanghui
Published: January 2021

A length-independent, stable and perfect spin-filtering, and the coexistence of dual spin-filtering and -rectifying with a high ratio, are demonstrated in designed devices.
Upconverted blue electrochemiluminescence of 9,10-diphenylanthracene with ultrafast response on photo-electro functional DNA/Ru(bpy)32+ hybrid electrode
Authors: Ozawa Ryuki , Minami Haruki , Nakamura Kazuki , Kobayashi Norihisa
Published: January 2021

Ultrafast-respondent, electrochemically triggered upconverted blue luminescence from 9,10-diphenylanthracene was obtained from DNA/Ru(bpy)32+ hybrid electrode.
Correction: Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor
Authors: Suzuki Kaho , Takaoka Yousuke , Ueda Minoru
Published: January 2021

Correction for ‘Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor’ by Kaho Suzuki et al., RSC Chem. Biol., 2021, DOI: 10.1039/d0cb00204f.
Retraction: MicroRNA-451 blockade promotes osteoblastic differentiation and skeletal anabolic effects by promoting YWHAZ-mediated RUNX2 protein stabilization
Authors: Lim Katie
Published: January 2021

Retraction of ‘MicroRNA-451 blockade promotes osteoblastic differentiation and skeletal anabolic effects by promoting YWHAZ-mediated RUNX2 protein stabilization’ by Jieen Pan et al., Med. Chem. Commun., 2018, 9, 1359–1368, DOI: 10.1039/C8MD00187A.
Sulfur and nitrogen-doped graphene quantum dots/PANI nanocomposites for supercapacitors
Authors: Kuzhandaivel Hemalatha , Manickam Sornalatha , Balasingam Suresh Kannan , Franklin Manik Clinton , Kim Hee-Je , Nallathambi Karthick Sivalingam
Published: January 2021

Sulfur and nitrogen-doped graphene quantum dots/polyaniline nanocomposites were synthesized and their electrochemical charge storage properties were tested for supercapacitor applications.
Retraction: Aclarubicin regulates glioma cell growth and DNA damage through the SIRT1/PI3K/AKT signaling pathway
Authors: Fisher Laura
Published: January 2021

Retraction of ‘Aclarubicin regulates glioma cell growth and DNA damage through the SIRT1/PI3K/AKT signaling pathway’ by Jun-Feng Huo et al., RSC Adv., 2019, 9, 28775–28782, DOI: 10.1039/C9RA05572J.
Retraction: MiR-132 enhances proliferation and migration of HaCaT cells by targeting TIMP3
Authors: Fisher Laura
Published: January 2021

Retraction of ‘MiR-132 enhances proliferation and migration of HaCaT cells by targeting TIMP3’ by Lina Jiang et al., RSC Adv., 2019, 9, 21125–21133, DOI: 10.1039/C8RA10552A.
To improve the key properties of nonlinear optical crystals assembled with tetrahedral functional building units
Authors: Bai Zhiyong , Liu Lehui , Wang Dongmei , Hu Chun-Li , Lin Zhoubin
Published: January 2021

We report a new nonlinear optical crystal assembled exclusively with tetrahedral functional building units in which enhanced birefringence (Δn) and second-harmonic generation (deff) were observed.
A-769662 inhibits adipocyte glucose uptake in an AMPK-independent manner
Authors: Kopietz Franziska , Alshuweishi Yazeed , Bijland Silvia , Alghamdi Fatmah , Degerman Eva , Sakamoto Kei , Salt Ian P. , Göransson Olga
Published: January 2021

Activation of AMP-activated protein kinase (AMPK) is considered a valid strategy for the treatment of type 2 diabetes. However, despite the importance of adipose tissue for whole-body energy homeostasis, the effect of AMPK activation in adipocytes has only been studied to a limited extent and mainly with the AMP-mimetic 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR), which has limited specificity. The aim of this study was to evaluate the effect of the allosteric AMPK activators A-769662 and 991 on glucose uptake in adipocytes. For this purpose, primary rat or human adipocytes, and cultured 3T3-L1 adipocytes, were treated with either of the allosteric activators, or AICAR, and basal and insulin-stimulated glucose uptake was assessed. Additionally, the effect of AMPK activators on insulin-stimulated phosphorylation of Akt and Akt substrate of 160 kDa was assessed. Furthermore, primary adipocytes from ADaM site binding drug-resistant AMPKβ1 S108A knock-in mice were employed to investigate the specificity of the drugs for the observed effects. Our results show that insulin-stimulated adipocyte glucose uptake was significantly reduced by A-769662 but not 991, yet neither activator had any clear effects on basal or insulin-stimulated Akt/AS160 signaling. The use of AMPKβ1 S108A mutant-expressing adipocytes revealed that the observed inhibition of glucose uptake by A-769662 is most likely AMPK-independent, a finding which is supported by the rapid inhibitory effect A-769662 exerts on glucose uptake in 3T3-L1 adipocytes. These data suggest that AMPK activation per se does not inhibit glucose uptake in adipocytes and that the effects of AICAR and A-769662 are AMPK-independent.
Identification of sulforaphane regulatory network in hepatocytes by microarray data analysis based on GEO database
Authors: Gao Lei , Wang Jinshen , Zhao Yuhua , Liu Junhua , Cai Da , Zhang Xiao , Wang Yutao , Zhang Shuqiu
Published: January 2021

For the past several years, more and more attention has been paid to the exploration of traditional medicinal plants. Further studies have shown that more dietary consumption of cruciferous vegetables can prevent the occurrence of tumor, indicating the potential applications in the chemoprevention of cancer. Sulforaphane (SFN) has been identified by the National Cancer Institute as a candidate for chemopreventive research; it is one of several compounds selected by the National Cancer Institute’s Rapid Access to Preventive Intervention Development Program and is currently in use. In the present study, based on the data of Gene Expression Omnibus database (GEO), the gene expression profile of hepatocytes that were treated with SFN was analyzed. The ANOVA and Limma packets in R were used to analyze the differentially expressed genes (DEGs). On this basis, gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment were further analyzed. The core gene HSP90-α (cytosolic), class A member 1 (HSP90AA1) was screened by protein–protein interaction (PPI) network established by STRING and Cytoscape software for further study. Finally, miRNAs targeted HSP90AA1 were predicted by miRanda. All in all, based on the data of GSE20479 chip, the molecular mechanism of SFN on hepatocytes was studied by a series of bioinformatics analysis methods, and it indicated that SFN might effect on the hepatocyte by regulating HSP90AA1.
Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer
Authors: Yu Jie , Zhang QianYun , Wang MengChuan , Liang SiJia , Huang HongYun , Xie Lang , Cui ChunHui , Yu JinLong
Published: January 2021

Tumor mutation burden (TMB) was a promising marker for immunotherapy. We aimed to investigate the prognostic role of TMB and its relationship with immune cells infiltration in gastric cancer (GC). We analyzed the mutation landscape of all GC cases and TMB of each GC patient was calculated and patients were divided into TMB-high and TMB-low group. Differentially expressed genes (DEGs) between the two groups were identified and pathway analysis was performed. The immune cells infiltration in each GC patient was evaluated and Kaplan–Meier analysis was performed to investigate the prognostic role of immune cells infiltration. At last, hub immune genes were identified and a TMB prognostic risk score (TMBPRS) was constructed to predict the survival outcome of GC patients. The relationships between mutants of hub immune genes and immune infiltration level in GC was investigated. We found higher TMB was correlated with better survival outcome and female patients, patients with T1-2 and N0 had higher TMB score. Altogether 816 DEGs were harvested and pathway analysis demonstrated that patients in TMB-high group were associated with neuroactive ligand–receptor interaction, cAMP signaling pathway, calcium signaling pathway. The infiltration of activated CD4+ memory T cells, follicular helper T cells, resting NK cells, M0 and M1 macrophages and neutrophils in TMB-high group were higher compared than that in TMB-low group and high macrophage infiltration was correlated with inferior survival outcome of GC patients. Lastly, the TMBPRS was constructed and GC patients with high TMBPRS had poor prognosis.
Mechanistic insights into KDM4A driven genomic instability
Authors: Young Nicolas L. , Dere Ruhee
Published: January 2021

Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase that belongs to the Fe-II dependent dioxygenase family that uses α-ketoglutarate and molecular oxygen as cofactors, is overexpressed in several cancers and is associated with an overall poor prognosis. KDM4A demethylates lysine 9 (H3K9me2/3) and lysine 36 (H3K36me3) methyl marks on histone H3. Given the complexity that exists with these marks on chromatin and their effects on transcription and proliferation, it naturally follows that demethylation serves an equally important role in these cellular processes. In this review, we highlight the role of KDM4A in transcriptional modulation, either dependent or independent of its enzymatic activity, arising from the amplification of this demethylase in cancer. KDM4A modulates re-replication of distinct genomic loci, activates cell cycle inducers, and represses proteins involved in checkpoint control giving rise to proliferative damage, mitotic disturbances and chromosomal breaks, ultimately resulting in genomic instability. In parallel, emerging evidence of non-nuclear substrates of epigenetic modulators emphasize the need to investigate the role of KDM4A in regulating non-nuclear substrates and evaluate their contribution to genomic instability in this context. The existence of promising KDM-specific inhibitors makes these demethylases an attractive target for therapeutic intervention in cancers.
Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT)
Authors: Craig Jonathan M. , Laszlo Andrew H. , Nova Ian C. , Gundlach Jens H.
Published: January 2021

Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT’s spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT’s ability to discern an enzyme’s nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
The JADE code: Coupling secular exoplanetary dynamics and photo-evaporation
Authors: Attia M. , Bourrier V. , Eggenberger P. , Mordasini C. , Beust H. , Ehrenreich D.
Published: January 2021

Close-in planets evolve under extreme conditions, which raises questions about their origins and current nature. Two evolutionary mechanisms thought to play a predominant role are orbital migration, which brings them close to their star, and atmospheric escape under the resulting increased irradiation. Yet their relative roles remain poorly understood, in part because we lack numerical models that couple the two mechanisms with high precision and on secular timescales. To address this need, we developed the Joining Atmosphere and Dynamics for Exoplanets (JADE) code, which simulates the secular atmospheric and dynamical evolution of a specific planet around its star, and can include the perturbation induced by a distant third body. On the dynamical side, the three dimensional evolution of the orbit is modeled under stellar and planetary tidal forces, a relativistic correction, and the action of the distant perturber. On the atmospheric side, the vertical structure of the atmosphere is integrated over time based on its thermodynamical properties, inner heating, and the evolving stellar irradiation, which results, in particular, in extreme ultraviolet induced photo-evaporation. The JADE code is benchmarked on GJ436 b, which is a prototype of the evaporating giants on eccentric, misaligned orbits at the edge of the hot Neptunes desert. We confirm previous results that the orbital architecture of GJ436 b is well explained by Kozai migration and bring to light a strong interplay between its atmospheric and orbital evolution. During the resonance phase, the atmosphere pulsates in tune with the Kozai cycles, which leads to stronger tides and an earlier migration. This triggers a strong atmospheric evaporation several billion years after the planet formed, refining the paradigm that mass loss is dominant in the early age of close-in planets. These results suggest that the edge of the desert could be formed of warm Neptunes whose evaporation was delayed by Kozai migration. They strengthen the importance of coupling atmospheric and dynamical evolution over secular timescales, which the JADE code will allow for one to simulate for a wide range of systems.
Characterisation of the hydrospheres of TRAPPIST-1 planets
Authors: Acuña Lorena , Deleuil Magali , Mousis Olivier , Marcq Emmanuel , Levesque Maëva , Aguichine Artyom
Published: January 2021

Context. Planetary mass and radius data suggest that low-mass exoplanets show a wide variety of densities. This includes sub-Neptunes, whose low densities can be explained with the presence of a volatile-rich layer. Water is one of the most abundant volatiles, which can be in the form of different phases depending on the planetary surface conditions. To constrain their composition and interior structure, models must be developed that accurately calculate the properties of water at its different phases.

Aims. We present an interior structure model that includes a multiphase water layer with steam, supercritical, and condensed phases. We derive the constraints for planetary compositional parameters and their uncertainties, focusing on the multi-planetary system TRAPPIST-1, which presents both warm and temperate planets.

Methods. We use a 1D steam atmosphere in radiative-convective equilibrium with an interior whose water layer is in supercritical phase self-consistently. For temperate surface conditions, we implement liquid and ice Ih to ice VII phases in the hydrosphere. We adopt a Markov chain Monte Carlo inversion scheme to derive the probability distributions of core and water compositional parameters.

Results. We refine the composition of all planets and derive atmospheric parameters for planets ‘b’ and ‘c’. The latter would be in a post-runaway greenhouse state and could be extended enough to be probed by space missions such as JWST. Planets ‘d’ to ‘h’ present condensed ice phases, with maximum water mass fractions below 20%.

Conclusions. The derived amounts of water for TRAPPIST-1 planets show a general increase with semi-major axis, with the exception of planet d. This deviation from the trend could be due to formation mechanisms, such as migration and an enrichment of water in the region where planet d formed, or an extended CO2-rich atmosphere.
Modeling of child labour exploitation status in Indonesia using multilevel binary logistic regression
Authors: Sari Liza Kurnia , Wardana Lissa Octavia
Published: January 2021

The Indonesian constitution recognizes guarantees the right of the child to rest and leisure, to engage in play, and recreational activities appropriate to the age of the child so that they should not be working. Employers are also prohibited to employ children. However, many children come to work because of poverty, even though child labour is close to exploitation. Theoretically, individual and contextual factors affect the exploitation status of child labour. This study aims to analyze the variables that influence the exploitation of child labour in Indonesia based on data from the National Socio-Economic Survey (Susenas) in 2018. The random effect test shows that there are differences between regency/municipality so that multilevel binary logistic regression performs better than one level binary logistic regression. More than 80 percent of child labourers are exploited in terms of education and working hours. Variables that significantly influence the exploitation status of child labour at the individual level are gender, the occupation sector of child labour, and the occupation sector of the household head. Meanwhile, poverty rates and mean years of schooling significantly influence the exploitation status of child labour at the regional level.
Statistical modelling of bus travel time with Burr distribution
Authors: Low Victor Jian Ming , Khoo Hooi Ling , Khoo Wooi Chen
Published: January 2021

A better understanding of the travel time distribution shape or pattern could improve the decision made by the transport operator to estimate the travel time required for the vehicle to travel from one place to another. Finding the most appropriate distribution to represent the day-to-day travel time variation of an individual link of a bus route is the main purpose of this study. Klang Valley, Malaysia is the study area for the research. A consecutive of 7 months ten bus routes automatic vehicle location (AVL) data are used to examine the distribution performance. The leading distribution proposed for the research is the Burr distribution. Both symmetrical and asymmetrical distributions that have been proposed in existing studies are also used for comparison purposes. Maximum likelihood estimation is applied for parameter estimation while loglikelihood value, Akaike information criterion (AIC) and Bayesian information criterion (BIC) are applied for performance assessment of the distributions. Promising results are obtained by the leading model in all different kinds of operating environment and could be treated as the preliminary preparation for further reliability analysis.
Rank 2 preservers on symmetric matrices with zero trace
Authors: Kok Wai Keong
Published: January 2021

Let F be a field, V1 and V2 be vector spaces of matrices over F and let ρ be the rank function. If T :V1 → V2 is a linear map, and k a fixed positive integer, we say that T is a rank k preserver if for any matrix Aϵ, V1 ρ(A) = k implies ρ(T( A))= k . In this paper, we characterize those rank 2 preservers on symmetric matrices with zero trace under certain conditions.
Some properties of various types of matrix factorization
Authors: Ng Wei Shean , Tan Wei Wen
Published: January 2021

Matrix factorizations or matrix decompositions are methods that represent a matrix as a product of two or more matrices. There are various types of matrix factorizations such as LU factorization, Cholesky factorization, singular value decomposition etc. Matrix factorization is widely used in pattern recognition, image denoising, data clustering etc. Motivated by these applications, some properties and applications of various types of matrix factorizations are studied. One of the purposes of matrix factorization is to ease the computation. Thus, comparisons in term of computation time of various matrix factorizations in different areas are carried out.
Performance of a new integrated computer-assisted system (CADe/CADx) for detection and characterization of colorectal neoplasia
Authors: Weigt Jochen , Repici Alessandro , Antonelli Giulio , Afifi Ahmed , Kliegis Leon , Correale Loredana , Hassan Cesare , Neumann Helmut
Published: January 2021

Background Use of artificial intelligence may increase detection of colorectal neoplasia at colonoscopy by improving lesion recognition (CADe) and reduce pathology costs by improving optical diagnosis (CADx).

Methods A multicenter library of ≥ 200 000 images from 1572 polyps was used to train a combined CADe/CADx system. System testing was performed on two independent image sets (CADe: 446 with polyps, 234 without; CADx: 267) from 234 polyps, which were also evaluated by six endoscopists (three experts, three non-experts).

Results CADe showed sensitivity, specificity, and accuracy of 92.9 %, 90.6 %, and 91.7 %, respectively. Experts showed significantly higher accuracy and specificity, and similar sensitivity, while non-experts + CADe showed comparable sensitivity but lower specificity and accuracy than CADe and experts. CADx showed sensitivity, specificity, and accuracy of 85.0 %, 79.4 %, and 83.6 %, respectively. Experts showed comparable performance, whereas non-experts + CADx showed comparable accuracy but lower specificity than CADx and experts.

Conclusions The high accuracy shown by CADe and CADx was similar to that of experts, supporting further evaluation in a clinical setting. When using CAD, non-experts achieved a similar performance to experts, with suboptimal specificity.
Palladium(II)-Catalyzed C(sp)–C(sp2) Coupling: A Direct Approach to Multi-Substituted Pyrrolo[1,2-a]pyrazines
Authors: Zhang Guolin , Yu Yongping , He Chang , Wang Zijuan , Chen Yitong
Published: January 2021

A direct synthesis of multi-substituted pyrrolo[1,2-a]pyrazines via palladium(II)-catalyzed C(sp)–C(sp2) cascade coupling and intramolecular cyclization in the presence of ligand was developed. This reaction originates from phenylboronic acids and readily synthesized 2-carbonyl- or 2-formylpyrroloacetonitriles, and affords products in good to excellent yields for a diversity of substrates. Additionally, a possible mechanism for the transformation is proposed.
Controlled Ring-Opening Polymerization of O-Carboxyanhydrides to Synthesize Functionalized Poly(α-Hydroxy Acids)
Authors: Wang Xiaoqian , Chin Ai Lin , Tong Rong
Published: January 2021

Poly(α-hydroxy acids), as a family of biodegradable polyesters, are valuable materials due to their broad applications in packaging, agriculture, and biomedical engineering. Herein we highlight and explore recent advances of catalysts in controlled ring-opening polymerization of O-carboxyanhydrides towards functionalized poly(α-hydroxy acids), especially metal catalyst-mediated controlled polymerization. Limitations of current polymerization strategies of O-carboxyanhydrides are discussed.
Resonant impurity level of Ni in the valence band of Pb1−xSnxTe alloys
Authors: Skipetrov E. P. , Konstantinov N. S. , Bogdanov E. V. , Knotko A. V. , Slynko V. E.
Published: January 2021

The phase and elemental compositions and galvanomagnetic properties (4.2 K ≤ T ≤ 300 K, B ≤ 0.07 T) of samples from a single-crystal Pb1−x−ySnxNiyTe ingot (x = 0.08, y = 0.01) synthesized by the Bridgman–Stockbarger method were studied. Microscopic inclusions enriched in nickel were found. It is shown that in the main phase, the tin concentration increases exponentially along the ingot (x = 0.06–0.165), while the concentration of nickel impurity does not exceed 0.4 mol %. A significant increase in the concentration of holes along the ingot and an abnormal increase in the Hall coefficient with increasing temperature were found; both are due to the pinning of the Fermi level by the resonant nickel level located in the valence band. The dependences of the hole concentration and of the Fermi energy at T = 4.2 K on the tin concentration in alloys are calculated using the two-band Kane dispersion law. A qualitative model of electronic structure rearrangement is proposed. The model takes into account the movement of the nickel level into the depth of the valence band with an increase in tin concentration and the redistribution of electrons between the valence band and the level. The energy position of the nickel level and the speed of its movement relative to the top of the valence band with an increase in the tin content in Pb1−xSnxTe alloys are estimated.