bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome of the Cauliflower mosaic virus, a plant pararetrovirus, is highly methylated in the nucleus
Authors: Omae Natsuki , Suzuki Masashi , Ugaki Masashi 
Published: June 2020

Cytosine methylation is an important defense against invasive DNAs. Here, cytosine methylation profiles of a plant pararetrovirus, Cauliflower mosaic virus (CaMV), were investigated. Nuclear CaMV DNA is highly methylated throughout the genome including at transcription regulatory regions, but the virion DNA is unmethylated. In vitro CG methylation of the viral 35S promoter reduces transcription from the downstream gene. Although nuclear CaMV DNA is highly methylated, its transcripts are accumulated in the nucleus. The data suggest that a small population of unmethylated viral genomes produced through reverse transcription are constantly delivered back to the nucleus. Small RNA profiles suggest that methylation of the CaMV DNA may be due to de novo methylation through 21‐, 22‐, and 24‐nt small RNAs with adenines at their 5' terminus.
Canonic‐Like HER Activity of Cr1–xMoxB2 Solid Solution: Overpowering Pt/C at High Current Density
Authors: Park Hyounmyung , Lee Eunsoo , Lei Ming , Joo Hyunkeun , Coh Sinisa , Fokwa Boniface P. T. 
Published: June 2020

AbstractAbundant transition metal borides are emerging as substitute electrochemical hydrogen evolution reaction (HER) catalysts for noble metals. Herein, an unusual canonic‐like behavior of the c lattice parameter in the AlB2‐type solid solution Cr1–xMoxB2 (x = 0, 0.25, 0.4, 0.5, 0.6, 0.75, 1) and its direct correlation to the HER activity in 0.5 M H2SO4 solution are reported. The activity increases with increasing x, reaching its maximum at x = 0.6 before decreasing again. At high current densities, Cr0.4Mo0.6B2 outperforms Pt/C, as it needs 180 mV less overpotential to drive an 800 mA cm−2 current density. Cr0.4Mo0.6B2 has excellent long‐term stability and durability showing no significant activity loss after 5000 cycles and 25 h of operation in acid. First‐principles calculations have correctly reproduced the nonlinear dependence of the c lattice parameter and have shown that the mixed metal/B layers, such as (110), promote hydrogen evolution more efficiently for x = 0.6, supporting the experimental results.
A Tumor‐Microenvironment‐Responsive Lanthanide–Cyanine FRET Sensor for NIR‐II Luminescence‐Lifetime In Situ Imaging of Hepatocellular Carcinoma
Authors: Zhao Mengyao , Li Benhao , Wu Yifan , He Haisheng , Zhu Xinyan , Zhang Hongxin , Dou Chaoran , Feng Lishuai , Fan Yong , Zhang Fan 
Published: June 2020

AbstractDeep tissue imaging in the second near‐infrared (NIR‐II) window holds great promise for widespread fundamental research. However, inhomogeneous signal attenuation due to tissue absorption and scattering hampers its application for accurate in vivo biosensing. Here, lifetime‐based in situ hepatocellular carcinoma (HCC) detection in NIR‐II region is presented using a tumor‐microenvironment (peroxynitrite, ONOO−)‐responsive lanthanide–cyanine Förster resonance energy transfer (FRET) nanosensor. A specially designed ONOO−‐responsive NIR‐II dye, MY‐1057, is synthesized as the FRET acceptor. Robust lifetime sensing is demonstrated to be independent of tissue penetration depth. Tumor lesions are accurately distinguished from normal tissue due to the recovery lifetime. Magnetic resonance imaging and liver dissection results illustrate the reliability of lifetime‐based detection in single and multiple HCC models. Moreover, the ONOO− amount can be calculated according to the standard curve.
Designing Champion Nanostructures of Tungsten Dichalcogenides for Electrocatalytic Hydrogen Evolution
Authors: Han Wenqian , Liu Zihan , Pan Yanbo , Guo Guannan , Zou Jinxiang , Xia Yan , Peng Zhenmeng , Li Wei , Dong Angang 
Published: June 2020

AbstractFine‐tuning strain and vacancies in 2H‐phase transition‐metal dichalcogenides, although extremely challenging, is crucial for activating the inert basal plane for boosting the hydrogen evolution reaction (HER). Here, atomically curved 2H‐WS2 nanosheets with precisely tunable strain and sulfur vacancies (S‐vacancies) along with rich edge sites are synthesized via a one‐step approach by harnessing geometric constraints. The approach is based on the confined epitaxy growth of WS2 in ordered mesoporous graphene derived from nanocrystal superlattices. The spherical curvature imposed by the graphitic mesopores enables the generation of uniform strain and S‐vacancies in the as‐grown WS2 nanosheets, and simultaneous manipulation of these two key parameters can be realized by simply adjusting the pore size. In addition, the formation of unique mesoporous WS2@graphene van der Waals heterostructures ensures the ready access of active sites. Fine‐tuning the WS2 layer number, strain, and S‐vacancies enables arguably the best‐performing HER 2H‐WS2 electrocatalysts ever reported. Density functional theory calculations indicate that compared with strain, S‐vacancies play a more critical role in enhancing the HER activity.
Non‐Bonding Electron Pair versus π‐Electrons in Solution Phase Halogen Bond Catalysis: Povarov Reaction of 2‐Vinylindoles and Imines
Authors: Suzuki Takumi , Kuwano Satoru , Arai Takayoshi 
Published: June 2020

AbstractThe non‐bonding electron pair (n‐pair) of heteroatoms and π‐electrons are both efficient halogen bond (XB) acceptors. In solid and gas phase studies, n‐pairs generally prevail over π‐bonding orbitals as XB acceptors, whereas few studies have been conducted regarding the preference in solution phase. Herein, the Povarov reaction via the C−I⋅⋅⋅N XB interaction and [4+2] cycloaddition via the C−I⋅⋅⋅π XB interaction were evaluated, revealing that the n‐pair was more dominant in the XB catalysis system in solution. The XB donor‐catalyzed Povarov reaction gave diverse indolyl‐tetrahydroquinoline derivatives in good yields. Synthesis of indolyl‐quinolines was also developed.magnified image
Tribute to John B. Goodenough: From Magnetism to Rechargeable Batteries
Authors: Mauger Alain , Julien Christian M. , Armand Michel , Zaghib Karim 
Published: June 2020

AbstractIn macroeconomics, the rate of economic growth in the world is a historical phenomenon, which will mark the 20th century. It was made possible by an increasing consumption of fossil fuel. However, not only are these resources limited and unrenewable, but combustion has dramatic side effects such as emission of greenhouse gases responsible for global warming and change of climate. As a consequence, major efforts have been taken to move away from fossil fuels and switch to renewable energy including solar and wind energy. These energy sources, however, are intermittent and can be integrated into the electrical network only after regulation. Electrochemical storage is a key solution to regulate these intermittent sources of energy into smart grids. Although governments have only recently become aware of this problem, some scientists have been focusing their attention on rechargeable batteries since the 1970s, and it took until 2019 for the Nobel committee to award the Nobel prize to those who paved the path to their development. John B. Goodenough is one of the three winners of this Nobel prize, for his pioneering research on lithium‐ion batteries (LIBs). The impact of LIBs includes the development of rechargeable hybrid and electric vehicles at the expense of gasoline cars. Before the 1970s, however, John B. Goodenough had already made major contributions to materials science as a solid state physicist, including the investigation of the interplay between the magnetic and transport properties of perovskites. It is the purpose of the present work to report a brief review of the scientific works of John B. Goodenough, through selected works that demonstrate his mastery of chemistry and physics.
Long‐term rotation diversity and nitrogen effects on soil organic carbon and nitrogen stocks
Authors: Schmer Marty R. , Jin Virginia L. , Wienhold Brian J. , Becker Sophia M. , Varvel Gary E. 
Published: June 2020

AbstractUnderstanding the impacts of long‐term fertilizer management and rotation diversity on soil C and N is needed under a changing climate. The objective of this study was to evaluate the effects of N fertilizer level and crop rotation diversity on soil organic carbon (SOC) and soil N stocks from a 34‐yr study located in eastern Nebraska. Seven crop rotations (three continuous cropping systems; two 2‐yr crop rotations; and two 4‐yr crop rotations) and three N levels were compared. Soil samples were taken to a depth of 150 cm. Differences in SOC stocks were largely confined to the 0‐ to 7.5‐cm depth, with greater SOC (P = .0002) in rotations than continuous cropping systems and greater SOC (P = .0004) in 4‐yr vs. 2‐yr rotations. Total soil N was greater with increased crop rotation diversity for the 0‐ to 30‐cm soil profile. Greater SOC levels occurred with N fertilization for the 0‐ to 7.5‐cm depth. At the 0‐ to 150‐cm soil depth, SOC stocks were similar between N levels and greater for the 4‐yr vs. 2‐yr crop rotations (P = .0492). Trends in total N stocks were similar to those of SOC stocks. Overall, crop rotation had a larger effect on SOC and N stocks than N fertilizer.
Porous‐fiber module increases infiltration and reduces runoff
Authors: Lv Zhenyu , Qin Tianling , Liu Shanshan , Nie Hanjiang , Liu Fang , Wang Jianwei 
Published: June 2020

AbstractThe porous‐fiber module (PFM) is an advanced product used for rainfall regulation and storage. Most studies focus on the characteristics of its constituent material while ignoring the impacts of PFM application on infiltration and runoff. In this study, several factors were comprehensively considered in the field control simulated rainfall experiments conducted on bare land, including two types of rainfall intensities, four PFM volumes, and two arrangements of the PFM, to evaluate the impacts. The experiments consisted of measuring soil water content variation, surface runoff of each treatment plot, and the cumulative infiltration obtained by water balance. The results demonstrated that the effect of PFM volume on infiltration and runoff was much greater than that of the PFM arrangement. The addition of PFM could improve the water‐holding capacity of soil; this effect initially strengthened and subsequently weakened with the increase in the PFM volume. The PFM embedding increased the cumulative infiltration of the experimental plots by 5.1–79.2%, delayed the runoff start time by 0–20 min, weakened the peak by 13.6–51.1%, and reduced the runoff‐yielding amount by 11.23–62.53%, compared with those of the control plot. These effects were enhanced as PFM volume increased. An empirical formula, presented as the theoretical influence of PFM volume on the product of the cumulative infiltration multiplied by the Philip model derived by the control plot, was further established for simulating the infiltration process with various PFM volumes.
Free Radical Chemistry of Phosphasilenes
Authors: Samedov Kerim , Heider Yannic , Cai Yuanjing , Willmes Philipp , Mühlhausen Daniel , Huch Volker , West Robert , Scheschkewitz David , Percival Paul W. 
Published: June 2020

AbstractUnderstanding the characteristics of radicals formed from silicon‐containing heavy analogues of alkenes is of great importance for their application in radical polymerization. Steric and electronic substituent effects in compounds such as phosphasilenes not only stabilize the Si=P double bond, but also influence the structure and species of the formed radicals. Herein we report our first investigations of radicals derived from phosphasilenes with Mes, Tip, Dur, and NMe2 substituents on the P atom, using muon spin spectroscopy and DFT calculations. Adding muonium (a light isotope of hydrogen) to phosphasilenes reveals that: a) the electron‐donor NMe2 and the bulkiest Tip‐substituted phosphasilenes form several muoniated radicals with different rotamer conformations; b) bulky Dur‐substituted phosphasilene forms two radicals (Si‐ and P‐centred); and c) Mes‐substituted phosphasilene mainly forms one species of radical, at the P centre. These significant differences result from intramolecular substituent effects.
Fabrication of microfluidic chips using controlled dissolution of3Dprinted scaffolds
Authors: Alkayyali Tartela , Ahmadi Ali 
Published: June 2020

AbstractMicrofluidic chips are commonly fabricated using soft lithography, which often requires a clean room and micropatterning equipment. Recently, microfluidic chips are increasingly fabricated using 3D printing, but this technology is still limited in smallest channel printability, transparency, supports residue, and biocompatibility. In this work, a simple, fast, and inexpensive step is introduced to fabricate polydimethylsiloxane (PDMS) microfluidic chips using enhanced internal scaffold removal (eISR). It is found that final channel dimension decreases by 0.22 ± 0.02 μm/revolution with a 7% error using eISR. Surface topology is inspected after dissolution using scanning electron microscopy. A T‐junction device, bifurcation channels, and curved channels are fabricated to demonstrate the usability of eISR in multiple applications. Compared to previous methods, eISR provides acrylonitrile–butadiene–styrene dissolution before PDMS casting to achieve thinner and smoother channels produced using a commercial 3D printer.
Gravitational potential formulae between two bodies with finite dimensions
Authors: Ansari Abdullah A. , Abouelmagd Elbaz I. 
Published: June 2020

AbstractThe aim of this paper is to analyze and shed light on the potential relations between two bodies of finite dimensions and different shapes. After explaining the properties of different shaped bodies, we analyze the gravitational potential between an irregular body and a point mass, followed by the potential relation between two irregular bodies with discussion of its different properties. We also explore the potential relation between two solid cylinders, which can be degraded to 16 potential relations; one of these relations is the potential relation between two finite straight segments. With a new development for the potential relation, we evaluate the gravitational potential between a heterogeneous irregular body and a point mass followed by the potential between two heterogeneous irregular bodies with N−layers, which also can be reduced to the potential between two oblate or prolate heterogeneous bodies. We demonstrate that this relation can be degraded to many potential relations between two bodies, because it depends on the moments of inertia of the body's shape. Finally, we emphasize that this relation is considered a golden relation, which can be developed to generate the potential relation between different shaped bodies, either natural celestial bodies or between celestial and artificial bodies.
DNAMethylation Associated with Mitochondrial Dysfunction in a South African Autism Spectrum Disorder Cohort
Authors: Stathopoulos Sofia , Gaujoux Renaud , Lindeque Zander , Mahony Caitlyn , Van Der Colff Rachelle , Van Der Westhuizen Francois , O'Ryan Colleen 
Published: June 2020

AbstractAutism spectrum disorder (ASD) is characterized by phenotypic heterogeneity and a complex genetic architecture which includes distinctive epigenetic patterns. We report differential DNA methylation patterns associated with ASD in South African children. An exploratory whole‐epigenome methylation screen using the Illumina 450 K MethylationArray identified differentially methylated CpG sites between ASD and controls that mapped to 898 genes (P≤ 0.05) which were enriched for nine canonical pathways converging on mitochondrial metabolism and protein ubiquitination. Targeted Next Generation Bisulfite Sequencing of 27 genes confirmed differential methylation between ASD and control in our cohort. DNA pyrosequencing of two of these genes, the mitochondrial enzyme Propionyl‐CoA Carboxylase subunit Beta (PCCB) and Protocadherin Alpha 12 (PCDHA12), revealed a wide range of methylation levels (9–49% and 0–54%, respectively) in both ASD and controls. Three CpG loci were differentially methylated inPCCB(P≤ 0.05), whilePCDHA12, previously linked to ASD, had two significantly different CpG sites (P≤ 0.001) between ASD and control. Differentially methylated CpGs were hypomethylated in ASD. Metabolomic analysis of urinary organic acids revealed that three metabolites, 3‐hydroxy‐3‐methylglutaric acid (P= 0.008), 3‐methyglutaconic acid (P= 0.018), and ethylmalonic acid (P= 0.043) were significantly elevated in individuals with ASD. These metabolites are directly linked to mitochondrial respiratory chain disorders, with a putative link toPCCB, consistent with impaired mitochondrial function. Our data support an association between DNA methylation and mitochondrial dysfunction in the etiology of ASD.Autism Res2020, 13: 1079‐1093. © 2020 The Authors.Autism Research published by International Society for Autism Researchpublished by Wiley Periodicals, Inc.Lay SummaryEpigenetic changes are chemical modifications of DNA which can change gene function. DNA methylation, a type of epigenetic modification, is linked to autism. We examined DNA methylation in South African children with autism and identified mitochondrial genes associated with autism. Mitochondria are power‐suppliers in cells and mitochondrial genes are essential to metabolism and energy production, which are important for brain cells during development. Our findings suggest that some individuals with ASD also have mitochondrial dysfunction.
Specialized RSC: Substrate Specificities for a Conserved Chromatin Remodeler
Authors: Hainer Sarah J. , Kaplan Craig D. 
Published: June 2020

AbstractThe remodel the structure of chromatin (RSC) nucleosome remodeling complex is a conserved chromatin regulator with roles in chromatin organization, especially over nucleosome depleted regions therefore functioning in gene expression. Recent reports in Saccharomyces cerevisiae have identified specificities in RSC activity toward certain types of nucleosomes. RSC has now been shown to preferentially evict nucleosomes containing the histone variant H2A.Z in vitro. Furthermore, biochemical activities of distinct RSC complexes has been found to differ when their nucleosome substrate is partially unraveled. Mammalian BAF complexes, the homologs of yeast RSC and SWI/SNF complexes, are also linked to nucleosomes with H2A.Z, but this relationship may be complex and extent of conservation remains to be determined. The interplay of remodelers with specific nucleosome substrates and regulation of remodeler outcomes by nucleosome composition are tantalizing questions given the wave of structural data emerging for RSC and other SWI/SNF family remodelers.
Development of a highly sensitive microplate luminometer using ATP bioluminescence
Authors: Kawabe Shunsuke , Uchiho Yuichi 
Published: June 2020

AbstractAnalytical techniques using ATP bioluminescence, which has a high quantum yield and substrate specificity, are widely used in various assays, such as luciferase reporter assays, in the biological sciences. Although most microplate luminometers can be used to measure ATP luminescence with 96‐well or 384‐well microplates, their ATP detection limits are typically several tens of amol, which is not sufficient for evaluating cell activities and variability within small samples, such as those containing only a few cells. To analyze cell activities at low ATP concentrations, a more sensitive microplate luminometer is required. Therefore, in this study, we developed an automated highly sensitive microplate luminometer that could perform reagent dispensing and bioluminescence measurement with a 96‐well microplate within 10 min. ATP bioluminescence was detected by pressing a photomultiplier tube (PMT) against a microplate surface to seal the measured well with the light‐receiving surface of the PMT. This enabled a high light collection efficiency and low luminescence crosstalk, defined as the intensity of stray light from an adjacent well. As a result, the ATP detection limit was 0.97 amol, and the luminescence crosstalk was 4.4 × 10−6. Both values were one order of magnitude better than that of a typical microplate luminometer. In addition, the same gradient linearity of luminescence intensity against the ATP concentration was confirmed for both high and low ATP concentrations, and the dynamic range of our microplate luminometer was 106. Overall, our findings demonstrated that our novel microplate luminometer may have wide application in biological sciences research.
Axillary nodal metastatic burden in patients with breast cancer with clinically positive axillary nodes
Authors: Niinikoski L , Hukkinen K , Leidenius M H K , Heikkilä P , Mattson J , Meretoja T J 
Published: June 2020

Abstract

Background
The aim of this study was to determine preoperative factors and tumour characteristics related to a high nodal tumour burden in patients with clinically node-positive breast cancer. These findings were used to construct a predictive tool to evaluate the patient-specific risk of having more than two axillary lymph node metastases.

Methods
Altogether, 507 consecutive patients with breast cancer and axillary lymph node metastasis diagnosed by preoperative ultrasound-guided needle biopsy were reviewed. These patients underwent breast surgery and axillary lymph node dissection at Helsinki University Hospital between 2010 and 2014. Patients were grouped into those with one or two, and those with more than two lymph node metastases.

Results
There were 153 patients (30·2 per cent) with one or two lymph node metastases and 354 (69·8 per cent) with more than two metastases. Five-year disease-free survival was poorer for the latter group (P = 0·032). Five-year overall survival estimates for patients with one or two and those with more than two lymph node metastases were 87·0 and 81·4 per cent respectively (P = 0·215). In multivariable analysis, factors significantly associated with more than two lymph node metastases were: age, tumour size, lymphovascular invasion in the primary tumour, extracapsular extension of metastasis in lymph nodes, and morphology of lymph nodes. These factors were included in a multivariable predictive model, which had an area under the curve of 0·828 (95 per cent c.i. 0·787 to 0·869).

Conclusion
The present study provides a patient-specific prediction model for evaluating nodal tumour burden in patients with clinically node-positive breast cancer.