bluuebunny/crossref_metadata_2025 huggingface dataset:
Exogenous hormone use, reproductive factors and risk of intrahepatic cholangiocarcinoma among women: results from cohort studies in the Liver Cancer Pooling Project and the UK Biobank
Authors: Petrick Jessica L. , McMenamin Úna C. , Zhang Xuehong , Zeleniuch-Jacquotte Anne , Wactawski-Wende Jean , Simon Tracey G. , Sinha Rashmi , Sesso Howard D. , Schairer Catherine , Rosenberg Lynn , Rohan Thomas E. , Robien Kim , Purdue Mark P. , Poynter Jenny N. , Palmer Julie R. , Lu Yunxia , Linet Martha S. , Liao Linda M. , Lee I-Min , Koshiol Jill , Kitahara Cari M. , Kirsh Victoria A. , Hofmann Jonathan N. , Graubard Barry I. , Giovannucci Edward , Gaziano J. Michael , Gapstur Susan M. , Freedman Neal D. , Florio Andrea A. , Chong Dawn Q. , Chen Yu , Chan Andrew T. , Buring Julie E. , Freeman Laura E. Beane , Bea Jennifer W. , Cardwell Christopher R. , Campbell Peter T. , McGlynn Katherine A.
Published: May 2020

Background

Intrahepatic cholangiocarcinoma (ICC) arises from cholangiocytes in the intrahepatic bile duct and is the second most common type of liver cancer. Cholangiocytes express both oestrogen receptor-α and -β, and oestrogens positively modulate cholangiocyte proliferation. Studies in women and men have reported higher circulating oestradiol is associated with increased ICC risk, further supporting a hormonal aetiology. However, no observational studies have examined the associations between exogenous hormone use and reproductive factors, as proxies of endogenous hormone levels, and risk of ICC.

Methods

We harmonised data from 1,107,498 women who enroled in 12 North American-based cohort studies (in the Liver Cancer Pooling Project, LCPP) and the UK Biobank between 1980–1998 and 2006–2010, respectively. Cox proportional hazards regression models were used to generate hazard ratios (HR) and 95% confidence internals (CI). Then, meta-analytic techniques were used to combine the estimates from the LCPP (n = 180 cases) and the UK Biobank (n = 57 cases).

Results

Hysterectomy was associated with a doubling of ICC risk (HR = 1.98, 95% CI: 1.27–3.09), compared to women aged 50–54 at natural menopause. Long-term oral contraceptive use (9+ years) was associated with a 62% increased ICC risk (HR = 1.62, 95% CI: 1.03–2.55). There was no association between ICC risk and other exogenous hormone use or reproductive factors.

Conclusions

This study suggests that hysterectomy and long-term oral contraceptive use may be associated with an increased ICC risk.
Molecular profiling of stroma highlights stratifin as a novel biomarker of poor prognosis in pancreatic ductal adenocarcinoma
Authors: Robin Fabien , Angenard Gaëlle , Cano Luis , Courtin-Tanguy Laetitia , Gaignard Elodie , Khene Zine-Eddine , Bergeat Damien , Clément Bruno , Boudjema Karim , Coulouarn Cédric , Sulpice Laurent
Published: May 2020

Background

Pancreatic ductal adenocarcinoma (PDAC) is a deadly cancer worldwide, as a result of a late diagnosis and limited therapeutic options. Tumour microenvironment (or stroma) plays a key role in cancer onset and progression and constitutes an intrinsic histological hallmark of PDAC. Thus we hypothesised that relevant prognostic biomarkers and therapeutic targets can be identified in the stroma.

Methods

Laser microdissection of the stroma from freshly frozen PDAC was combined to gene expression profiling. Protein expression of candidate biomarkers was evaluated by immunohistochemistry on tissue microarrays (n = 80 tumours) and by ELISA in plasma samples (n = 51 patients).

Results

A signature made of 1256 genes that significantly discriminate the stroma from the non-tumour fibrous tissue was identified. Upregulated genes were associated with inflammation and metastasis processes and linked to NF-Kappa B and TGFβ pathways. TMA analysis validated an increased expression of SFN, ADAMTS12 and CXCL3 proteins in the stroma of PDAC. Stromal expression of SFN was further identified as an independent prognostic factor of overall (p = 0.003) and disease-free survival (DFS) (p = 0.034). SFN plasma expression was significantly associated with reduced DFS (p = 0.006).

Conclusions

We demonstrated that gene expression changes within the stroma of PDAC correlate with tumour progression, and we identified Stratifin as a novel independent prognostic biomarker.
HDAC7 promotes the oncogenicity of nasopharyngeal carcinoma cells by miR-4465-EphA2 signaling axis
Authors: Li Qi-Guang , Xiao Ta , Zhu Wei , Yu Zheng-Zheng , Huang Xiao-Pu , Yi Hong , Lu Shan-Shan , Tang Yao-Yun , Huang Wei , Xiao Zhi-Qiang
Published: May 2020

HDAC7 plays a crucial role in cancers, and is the main drug target of several HDAC inhibitors. However, the role and mechanism of HDAC7 in nasopharyngeal carcinoma (NPC) are still unclear. In this study, we observed that HDAC7 was significantly upregulated in the NPC tissues relative to normal nasopharyngeal mucosa (NNM) tissues, HDAC7 expression levels were positively correlated with NPC progression and negatively correlated with patient prognosis, and HDAC7 knockdown dramatically inhibited the in vitro proliferation, migration, and invasion of NPC cells, and the growth of NPC xenografts in mice, indicating the HDAC7 promotes the oncogenicity of NPC. Mechanistically, HDAC7 promoted the in vitro proliferation, migration, and invasion of NPC cells by upregulating EphA2, in which miR-4465 mediated HDAC7-regulating EphA2, a direct target gene of miR-4465. We further showed that miR-4465 was significantly downregulated in the NPC tissues relative to NNM tissues, and inhibited the in vitro proliferation, migration, and invasion of NPC cells by targeting EphA2 expression. Moreover, we observed that the expressions of HDAC7, miR-4465, and EphA2 in NPC tissues were correlated. The results suggest that HDAC7 promotes the oncogenicity of NPC by downregulating miR-4465 and subsequently upregulating EphA2, highlighting HDAC7 as a potential therapeutic target for NPC.
Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis
Authors: Huang Gaoxingyu , Zhang Yanqing , Zhu Xuechen , Zeng Chao , Wang Qifan , Zhou Qiang , Tao Qinghua , Liu Minhao , Lei Jianlin , Yan Chuangye , Shi Yigong
Published: May 2020

The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5–7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.
Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium
Authors: Neuhaus Alexander , Selvaraj Muniyandi , Salzer Ralf , Langer Julian D. , Kruse Kerstin , Kirchner Lennart , Sanders Kelly , Daum Bertram , Averhoff Beate , Gold Vicki A. M.
Published: May 2020

Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus (‘wide’ and ‘narrow’), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility.
Identification of a prefrontal cortex-to-amygdala pathway for chronic stress-induced anxiety
Authors: Liu Wei-Zhu , Zhang Wen-Hua , Zheng Zhi-Heng , Zou Jia-Xin , Liu Xiao-Xuan , Huang Shou-He , You Wen-Jie , He Ye , Zhang Jun-Yu , Wang Xiao-Dong , Pan Bing-Xing
Published: May 2020

Dysregulated prefrontal control over amygdala is engaged in the pathogenesis of psychiatric diseases including depression and anxiety disorders. Here we show that, in a rodent anxiety model induced by chronic restraint stress (CRS), the dysregulation occurs in basolateral amygdala projection neurons receiving mono-directional inputs from dorsomedial prefrontal cortex (dmPFC→BLA PNs) rather than those reciprocally connected with dmPFC (dmPFC↔BLA PNs). Specifically, CRS shifts the dmPFC-driven excitatory-inhibitory balance towards excitation in the former, but not latter population. Such specificity is preferential to connections made by dmPFC, caused by enhanced presynaptic glutamate release, and highly correlated with the increased anxiety-like behavior in stressed mice. Importantly, low-frequency optogenetic stimulation of dmPFC afferents in BLA normalizes the enhanced prefrontal glutamate release onto dmPFC→BLA PNs and lastingly attenuates CRS-induced increase of anxiety-like behavior. Our findings thus reveal a target cell-based dysregulation of mPFC-to-amygdala transmission for stress-induced anxiety.
Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL
Authors: Sloan Jeremy , Hakenjos Jana P. , Gebert Michael , Ermakova Olga , Gumiero Andrea , Stier Gunter , Wild Klemens , Sinning Irmgard , Lohmann Jan U.
Published: May 2020

Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable to the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.
Solvent-mediated assembly of atom-precise gold–silver nanoclusters to semiconducting one-dimensional materials
Authors: Yuan Peng , Zhang Ruihua , Selenius Elli , Ruan Pengpeng , Yao Yangrong , Zhou Yang , Malola Sami , Häkkinen Hannu , Teo Boon K. , Cao Yang , Zheng Nanfeng
Published: May 2020

Bottom-up design of functional device components based on nanometer-sized building blocks relies on accurate control of their self-assembly behavior. Atom-precise metal nanoclusters are well-characterizable building blocks for designing tunable nanomaterials, but it has been challenging to achieve directed assembly to macroscopic functional cluster-based materials with highly anisotropic properties. Here, we discover a solvent-mediated assembly of 34-atom intermetallic gold–silver clusters protected by 20 1-ethynyladamantanes into 1D polymers with Ag–Au–Ag bonds between neighboring clusters as shown directly by the atomic structure from single-crystal X-ray diffraction analysis. Density functional theory calculations predict that the single crystals of cluster polymers have a band gap of about 1.3 eV. Field-effect transistors fabricated with single crystals of cluster polymers feature highly anisotropic p-type semiconductor properties with ≈1800-fold conductivity in the direction of the polymer as compared to cross directions, hole mobility of ≈0.02 cm2 V−1 s−1, and an ON/OFF ratio up to ≈4000. This performance holds promise for further design of functional cluster-based materials with highly anisotropic semiconducting properties.
Coherent multidimensional photoelectron spectroscopy of ultrafast quasiparticle dressing by light
Authors: Reutzel Marcel , Li Andi , Wang Zehua , Petek Hrvoje
Published: May 2020

Depending on the applied strength, electromagnetic fields in electronic materials can induce dipole transitions between eigenstates or distort the Coulomb potentials that define them. Between the two regimes, they can also modify the electronic properties in more subtle ways when electron motion becomes governed by time and space-periodic potentials. The optical field introduces new virtual bands through Floquet engineering that under resonant conditions interacts strongly with the preexisting bands. Under such conditions the virtual bands can become real, and real ones become virtual as the optical fields and electronic band dispersions entangle the electronic response. We reveal optical dressing of electronic bands in a metal by exciting four-photon photoemission from the Cu(111) surface involving a three-photon resonant transition from the Shockley surface band to the first image potential band. Attosecond resolved interferometric scanning between identical pump–probe pulses and its Fourier analysis reveal how the optical field modifies the electronic properties of a solid through combined action of dipole excitation and field dressing.
The NMDA receptor regulates competition of epithelial cells in the Drosophila wing
Authors: Banreti Agnes R. , Meier Pascal
Published: May 2020

Cell competition is an emerging principle that eliminates suboptimal or potentially dangerous cells. For ‘unfit’ cells to be detected, their competitive status needs to be compared to the collective fitness of cells within a tissue. Here we report that the NMDA receptor controls cell competition of epithelial cells and Myc supercompetitors in the Drosophila wing disc. While clonal depletion of the NMDA receptor subunit NR2 results in their rapid elimination via the TNF/Eiger>JNK signalling pathway, local over-expression of NR2 causes NR2 cells to acquire supercompetitor-like behaviour that enables them to overtake the tissue through clonal expansion that causes, but also relies on, the killing of surrounding cells. Consistently, NR2 is utilised by Myc clones to provide them with supercompetitor status. Mechanistically, we find that the JNK>PDK signalling axis in ‘loser’ cells reprograms their metabolism, driving them to produce and transfer lactate to winners. Preventing lactate transfer from losers to winners abrogates NMDAR-mediated cell competition. Our findings demonstrate a functional repurposing of NMDAR in the surveillance of tissue fitness.
Benthic fauna declined on a whitening Antarctic continental shelf
Authors: Pineda-Metz Santiago E. A. , Gerdes Dieter , Richter Claudio
Published: May 2020

Ice retreat in West Antarctica and Antarctic Peninsula has led to important changes in seafloor communities and gains in benthic blue carbon. In most of the Antarctic, however, sea ice increased between the 1970s and 2014, but its effects on the benthos remain largely unexplored. Here, we provide a 1988–2014 record of macro- and megafauna from the north-eastern Weddell Sea shelf, where benthic biomass decreased by two thirds and composition shifted from suspension feeders to deposit feeders. Concomitant increases in sea-ice cover suggest a reduced flux of primary production to the benthos. As benthic communities are major repositories for Antarctic biodiversity and play an important role in biogeochemical cycling, the observed changes have far-reaching consequences for the Antarctic ecosystem and its feedback to the climate system. The findings underscore the importance of long-term ecological monitoring in a region vulnerable to warming and ice-shelf collapse.
Selective NMR observation of the SEI–metal interface by dynamic nuclear polarisation from lithium metal
Authors: Hope Michael A. , Rinkel Bernardine L. D. , Gunnarsdóttir Anna B. , Märker Katharina , Menkin Svetlana , Paul Subhradip , Sergeyev Ivan V. , Grey Clare P.
Published: May 2020

While lithium metal represents the ultimate high-energy-density battery anode material, its use is limited by dendrite formation and associated safety risks, motivating studies of the solid–electrolyte interphase layer that forms on the lithium, which is key in controlling lithium metal deposition. Dynamic nuclear polarisation enhanced NMR can provide important structural information; however, typical exogenous dynamic nuclear polarisation experiments, in which organic radicals are added to the sample, require cryogenic sample cooling and are not selective for the interface between the metal and the solid–electrolyte interphase. Here we instead exploit the conduction electrons of lithium metal to achieve an order of magnitude hyperpolarisation at room temperature. We enhance the 7Li, 1H and 19F NMR spectra of solid–electrolyte interphase species selectively, revealing their chemical nature and spatial distribution. These experiments pave the way for more ambitious room temperature in situ dynamic nuclear polarisation studies of batteries and the selective enhancement of metal–solid interfaces in a wider range of systems.
Publisher Correction: Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells
Authors: Reyes Alvaro Plaza , Petrus-Reurer Sandra , Sánchez Sara Padrell , Kumar Pankaj , Douagi Iyadh , Bartuma Hammurabi , Aronsson Monica , Westman Sofie , Lardner Emma , André Helder , Falk Anna , Nandrot Emeline F. , Kvanta Anders , Lanner Fredrik
Published: May 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: The morphology, molecular development and ecological function of pseudonectaries on Nigella damascena (Ranunculaceae) petals
Authors: Liao Hong , Fu Xuehao , Zhao Huiqi , Cheng Jie , Zhang Rui , Yao Xu , Duan Xiaoshan , Shan Hongyan , Kong Hongzhi
Published: May 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Using Coherence-based spectro-spatial filters for stimulus features prediction from electro-corticographic recordings
Authors: Delgado Saa Jaime , Christen Andy , Martin Stephanie , Pasley Brian N. , Knight Robert T. , Giraud Anne-Lise
Published: May 2020

The traditional approach in neuroscience relies on encoding models where brain responses are related to different stimuli in order to establish dependencies. In decoding tasks, on the contrary, brain responses are used to predict the stimuli, and traditionally, the signals are assumed stationary within trials, which is rarely the case for natural stimuli. We hypothesize that a decoding model assuming each experimental trial as a realization of a random process more likely reflects the statistical properties of the undergoing process compared to the assumption of stationarity. Here, we propose a Coherence-based spectro-spatial filter that allows for reconstructing stimulus features from brain signal’s features. The proposed method extracts common patterns between features of the brain signals and the stimuli that produced them. These patterns, originating from different recording electrodes are combined, forming a spatial filter that produces a unified prediction of the presented stimulus. This approach takes into account frequency, phase, and spatial distribution of brain features, hence avoiding the need to predefine specific frequency bands of interest or phase relationships between stimulus and brain responses manually. Furthermore, the model does not require the tuning of hyper-parameters, reducing significantly the computational load attached to it. Using three different cognitive tasks (motor movements, speech perception, and speech production), we show that the proposed method consistently improves stimulus feature predictions in terms of correlation (group averages of 0.74 for motor movements, 0.84 for speech perception, and 0.74 for speech production) in comparison with other methods based on regularized multivariate regression, probabilistic graphical models and artificial neural networks. Furthermore, the model parameters revealed those anatomical regions and spectral components that were discriminant in the different cognitive tasks. This novel method does not only provide a useful tool to address fundamental neuroscience questions, but could also be applied to neuroprosthetics.
Effect of commercial vaginal products on the growth of uropathogenic and commensal vaginal bacteria
Authors: Hung Kristin J. , Hudson Patricia L. , Bergerat Agnes , Hesham Helai , Choksi Namit , Mitchell Caroline
Published: May 2020

Half of postmenopausal women experience genitourinary syndrome of menopause, for which many use lubricating vaginal products. The effect of vaginal products on uropathogenic and commensal vaginal bacteria is poorly understood. We evaluated the effect of five common vaginal products (KY Jelly, Replens Silky Smooth lubricant, coconut oil, Replens Long-Lasting moisturizer or Trimo-San) on growth and viability ofEscherichia coliandLactobacillus crispatus. Bacteria were co-cultured products alone and in the presence of both vaginal epithelial cells and selected products. Bacterial growth was compared between conditions using an unpaired t-test or ANOVA, as appropriate. All products except for coconut oil significantly inhibited growth of laboratory and clinical strains ofEscherichia coli(p < 0.02). Only two products (Replens Long-Lasting moisturizer and Trimo-San) significantly inhibited growth ofLactobacillus crispatus(p < 0.01), while the product Replens Silky Smooth stimulated growth (p < 0.01). Co-culture of selected products in the presence of vaginal epithelial cells eliminated the inhibitory effects of the products on E. coli. In conclusion,in vitroexposure to vaginal moisturizing and lubricating products inhibited growth ofEscherichia coli, though the inhibition was mitigated by the presence of vaginal epithelial cells.Lactobacillus crispatusdemonstrated less growth inhibition thanEscherichia coli.
Reconfigurable Meta-Coupler Employing Hybrid Metal-Graphene Metasurfaces
Authors: Tavakol Mohammad Reza , Khavasi Amin
Published: May 2020

Efficient excitation of surface wave (SW) remains one of the most challenging considerations in the photonics and plasmonics areas. Inspired by recent investigations of metasurfaces, we propose a hybrid metal-graphene transmitarray converting incident propagating wave (PW) to SW, as a solution for SW excitations–a meta-coupler. The structure comprises ultra-thin four-layer transparent metasurfaces in which H-shaped etched metal films together with graphene patches are employed, and also all four layers are identical. Full-wave simulations demonstrate that the suggested meta-coupler possesses an efficiency of 46% and a directivity of 19 dB, which is promising in the terahertz (THz) range. At the same time, in light of unique graphene characteristics, the proposed device is tunable and easily reconfigurable, i.e., the direction of converted SWs can be electrically switched from right to left and vice versa. We believe that this system responds to emerging applications such as THz communications and sensing, and furthermore the employed architecture introduce electrostatically tunable building blocks being able to develop graphene plasmonic components effectively.
Discovering the hidden messages within cell trajectories using a deep learning approach for in vitro evaluation of cancer drug treatments
Authors: Mencattini A. , Di Giuseppe D. , Comes M. C. , Casti P. , Corsi F. , Bertani F. R. , Ghibelli L. , Businaro L. , Di Natale C. , Parrini M. C. , Martinelli E.
Published: May 2020

We describe a novel method to achieve a universal, massive, and fully automated analysis of cell motility behaviours, starting from time-lapse microscopy images. The approach was inspired by the recent successes in application of machine learning for style recognition in paintings and artistic style transfer. The originality of the method relies i) on the generation of atlas from the collection of single-cell trajectories in order to visually encode the multiple descriptors of cell motility, and ii) on the application of pre-trained Deep Learning Convolutional Neural Network architecture in order to extract relevant features to be used for classification tasks from this visual atlas. Validation tests were conducted on two different cell motility scenarios: 1) a 3D biomimetic gels of immune cells, co-cultured with breast cancer cells in organ-on-chip devices, upon treatment with an immunotherapy drug; 2) Petri dishes of clustered prostate cancer cells, upon treatment with a chemotherapy drug. For each scenario, single-cell trajectories are very accurately classified according to the presence or not of the drugs. This original approach demonstrates the existence of universal features in cell motility (a so called “motility style”) which are identified by the DL approach in the rationale of discovering the unknown message in cell trajectories.
Algebraic Study of diatomic Molecules: homonuclear molecules H2 and N2
Authors: Amiri N. , Ghapanvari M. , Jafarizadeh M. A.
Published: May 2020

It is the aim of this study to discuss for two-body systems like homonuclear molecules in which eigenvalues and eigenfunctions are obtained by exact solutions of the solvable models based on SU(1, 1) Lie algebras. Exact solutions of the solvable Hamiltonian regarding the relative motion in a two-body system on Lie algebras were obtained. The U(1) ↔ O(2), U(3) ↔ O(4) and Uq(3) ↔ Oq(4) transitional Hamiltonians are employed to described for H2 and N2 molecules. Applications to the rotation-vibration spectrum for the diatomic molecule indicate that complicated Hamiltonian can be easily determined via the exactly solvable method. The results confirm the mixing of both vibrating and rotating structures in H2 and N2 molecules.
The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies
Authors: Vanderzande Stijn , Zheng Ping , Cai Lichun , Barac Goran , Gasic Ksenija , Main Dorrie , Iezzoni Amy , Peace Cameron
Published: May 2020

Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, thefruticosasubgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and theaviumand thefruticosasubgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.
Enhanced stability of quantum Hall skyrmions under radio-frequency radiations
Authors: Pan W. , Reno J. L. , Reyes A. P.
Published: May 2020

We present in this paper the results from a recent study on the stability of the quantum Hall skyrmions state at a Landau level filling factor (ν) close to ν = 1 in a narrow GaAs quantum well. Consistent with previous work, a resonant behavior is observed in the resistively detected NMR measurements. In the subsequent current-voltage (I-V) measurements to examine its breakdown behavior under radio frequency radiations, we observe that the critical current assumes the largest value right at the 75As nuclear resonant frequency. We discuss possible origin for this unexpectedly enhanced stability.
Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories
Authors: Demongeot Jacques , Seligmann Hervé
Published: May 2020

Ribosomal RNAs are complex structures that presumably evolved by tRNA accretions. Statistical properties of tRNA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RNA secondary structures resemble those of tRNAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RNA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome’s core is most ancient and peripheral elements most recent. Comparisons between (a) and (b) accretions orders with RNA ring secondary structure scales show that recent rRNA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. Theoretical minimal RNA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study.
The role of reagent adding sequence in the NH4+-N recovery by MAP method
Authors: He Caiqing , Chen Yunnen , Liu Chen , Jiang Yang , Yin Ruoyu , Qiu Tingsheng
Published: May 2020

Ammonium-nitrogen (NH4+-N) recovery from high concentration of NH4+-N-containing wastewater by struvite (MgNH4PO4·6H2O, MAP) precipitation method has been realized, but whether NH4+-N recovery under different reagent adding sequence of NaOH, solid Mg salt and P salt can generate different effects, remains ambiguous. In view of the problem, four modes to add reagents were investigated in detail on the formation of struvite. The results show that the Mode IV (M-IV, i.e. using 50% NH4+-N wastewater to dissolve completely the Mg salt and the P salt, respectively and then simultaneously poured into a beaker to mix the solution evenly and adjust the pH to 9.5.) has the highest NH4+-N recovery efficiency (90.80%) and the maximum mass of precipitates (896 mg) because of the more amount of alkali and initial seed formation. From the morphology of the obtained precipitates, it can be seen that sample M-IV is more loose and porous than the others. XRD patterns show that the four products under the different modes basically agree with the standard MAP.
Detection of Tuberculosis by The Analysis of Exhaled Breath Particles with High-resolution Mass Spectrometry
Authors: Chen Dapeng , Bryden Wayne A. , Wood Robin
Published: May 2020

Tuberculosis remains a global health threat killing over 1 million people per year. Current sputum-based diagnostics are specific but lack sensitivity resulting in treatment of many sputum negative cases. In this proof-of-concept study, we used high-resolution mass spectrometry to identify specific lipids in peripheral lung fluid samples of TB patients and controls, captured using a novel non-invasive sampling system. Exhaled respiratory particles were collected in liquid and after concentration and lipid extraction directly infused into a high-resolution mass spectrometer. High-resolution mass spectrometric data collection was conducted in a dual ion mode and chemical compositions were constructed using accurate mass measurement. Over 400 features with high segregating capacity were extracted and optimized using feature selection algorithm and machine learning, from which the accuracy of detection of positive tuberculosis patients was estimated. This current strategy provides sensitivity offered by high-resolution mass spectrometry and can be readily susceptible for developing a novel clinical assay exploring peripheral lung fluid for the detection of active TB cases.
Accuracy of ancestral state reconstruction for non-neutral traits
Authors: Holland Barbara R. , Ketelaar-Jones Saan , O’Mara Aidan R. , Woodhams Michael D. , Jordan Gregory J.
Published: May 2020

The assumptions underpinning ancestral state reconstruction are violated in many evolutionary systems, especially for traits under directional selection. However, the accuracy of ancestral state reconstruction for non-neutral traits is poorly understood. To investigate the accuracy of ancestral state reconstruction methods, trees and binary characters were simulated under the BiSSE (Binary State Speciation and Extinction) model using a wide range of character-state-dependent rates of speciation, extinction and character-state transition. We used maximum parsimony (MP), BiSSE and two-state Markov (Mk2) models to reconstruct ancestral states. Under each method, error rates increased with node depth, true number of state transitions, and rates of state transition and extinction; exceeding 30% for the deepest 10% of nodes and highest rates of extinction and character-state transition. Where rates of character-state transition were asymmetrical, error rates were greater when the rate away from the ancestral state was largest. Preferential extinction of species with the ancestral character state also led to higher error rates. BiSSE outperformed Mk2 in all scenarios where either speciation or extinction was state dependent and outperformed MP under most conditions. MP outperformed Mk2 in most scenarios except when the rates of character-state transition and/or extinction were highly asymmetrical and the ancestral state was unfavoured.
A Penicillium rubens platform strain for secondary metabolite production
Authors: Pohl Carsten , Polli Fabiola , Schütze Tabea , Viggiano Annarita , Mózsik László , Jung Sascha , de Vries Maaike , Bovenberg Roel A. L. , Meyer Vera , Driessen Arnold J. M.
Published: May 2020

We present a Penicillium rubens strain with an industrial background in which the four highly expressed biosynthetic gene clusters (BGC) required to produce penicillin, roquefortine, chrysogine and fungisporin were removed. This resulted in a minimal secondary metabolite background. Amino acid pools under steady-state growth conditions showed reduced levels of methionine and increased intracellular aromatic amino acids. Expression profiling of remaining BGC core genes and untargeted mass spectrometry did not identify products from uncharacterized BGCs. This platform strain was repurposed for expression of the recently identified polyketide calbistrin gene cluster and achieved high yields of decumbenone A, B and C. The penicillin BGC could be restored through in vivo assembly with eight DNA segments with short overlaps. Our study paves the way for fast combinatorial assembly and expression of biosynthetic pathways in a fungal strain with low endogenous secondary metabolite burden.
Revealing the complexity of ionic liquid–protein interactions through a multi-technique investigation
Authors: Bui-Le Liem , Clarke Coby J. , Bröhl Andreas , Brogan Alex P. S. , Arpino James A. J. , Polizzi Karen M. , Hallett Jason P.
Published: May 2020

Ionic liquids offer exciting possibilities for biocatalysis as solvent properties provide rare opportunities for customizable, energy-efficient bioprocessing. Unfortunately, proteins and enzymes are generally unstable in ionic liquids and several attempts have been made to explain why; however, a comprehensive understanding of the ionic liquid–protein interactions remains elusive. Here, we present an analytical framework (circular dichroism (CD), fluorescence, ultraviolet-visible (UV/Vis) and nuclear magnetic resonance (NMR) spectroscopies, and small-angle X-ray scattering (SAXS)) to probe the interactions, structure, and stability of a model protein (green fluorescent protein (GFP)) in a range (acetate, chloride, triflate) of pyrrolidinium and imidazolium salts. We demonstrate that measuring protein stability requires a similar holistic analytical framework, as opposed to single-technique assessments that provide misleading conclusions. We reveal information on site-specific ionic liquid–protein interactions, revealing that triflate (the least interacting anion) induces a contraction in the protein size that reduces the barrier to unfolding. Robust frameworks such as this are critical to advancing non-aqueous biocatalysis and avoiding pitfalls associated with single-technique investigations.
A paper-supported sandwich immunosensor based on upconversion luminescence resonance energy transfer for the visual and quantitative determination of a cancer biomarker in human serum
Authors: He Mengyuan , Shang Ning , Shen Lin , Liu Zhihong
Published: May 2020

A portable and sensitive paper-supported sandwich immunosensor based on UC-FRET was developed for the visual and quantitative determination of CEA.
A novel nanosensor for detecting tetracycline based on fluorescent palladium nanoclusters
Authors: Du Xiaoyan , Dong Wenxia , Li Zhongping , Wen Guangming , Liu Meng , Fan Xiujun
Published: May 2020

Tetracycline (TC) is considered one of the most widely used antibiotic medicines, and ranks the second highest in global production and usage among all antibiotics.
Effect of graphene sheet incorporation on the physicochemical properties of nano-alumina
Authors: Trusova Elena A. , Titov Dmitriy D. , Kirichenko Alexey N. , Zorin Michael Y.
Published: May 2020

The colloidal processing method was suggested for obtaining chemically homogeneous composite powder based on graphene and nano-alumina.
Pristine graphene induces innate immune training
Authors: Lebre Filipa , Boland John B. , Gouveia Pedro , Gorman Aoife L. , Lundahl Mimmi L. E. , I Lynch Roisin , O'Brien Fergal J. , Coleman Jonathan , Lavelle Ed C.
Published: May 2020

Endotoxin-free pristine graphene is capable of inducing innate training and that this effect can be modulated by incorporation in a matrix.
A Co3O4/MnCO3 heterojunction on three-dimensional nickel foam for an enhanced oxygen evolution reaction
Authors: Yang Guijin , Zhu Botao , Gao Daqiang , Fu Yujun , Zhao Jing , Li Jinyun
Published: May 2020

A Co3O4/MnCO3 heterojunction on NF with a unique architecture exhibits prominent OER activity and stability that is superior to most Co3O4-based catalysts.
Chirality and stereoisomerism of organic multicomponent crystals in the CSD
Authors: Grothe Eline , Meekes Hugo , de Gelder René
Published: May 2020

Multicomponent crystals in the CSD are classified into 49 subclasses based on chirality and residue type.
N–H⋯O hydrogen bonding to the alkoxy oxygen of a carboxylic ester group: crystal structures of methyl 2,6-diaminobenzoate and its derivatives
Authors: Yang Songjie , Garner A. Christopher , Wallis John D.
Published: May 2020

Molecules with hydrogen bonds from amino groups to both oxygens of a carboxylic ester are described, and other examples of hydrogen bonding to an ester's alkoxy oxygen atom are highlighted.
Microstructural dependent oxygen reduction reaction in a Ruddlesden–Popper perovskite (SmSr)NiO4−δ
Authors: Chauhan Manisha , Jha Pardeep K. , Bangwal Ajay S. , Jha Priyanka A. , Singh Prabhakar
Published: May 2020

Alteration in conduction pathways through Microstructural difference:Microstructural designing for Ruddlesen–Popper structured layered perovskite, (SmSr)NiO4−δ.
C–H oxidation enhancement on a gold nanoisland by atomic-undercoordination induced polarization
Authors: Lin Zezhou , Hirao Hajime , Sun Changqing , Zhang Xi
Published: May 2020

The valence band polarization of an under-coordinated corner atom enhances the electron-donation ability and enables the C–H oxidation of an Au nanoisland.
X-ray photoelectron spectroscopy of piperidinium ionic liquids: a comparison to the charge delocalised pyridinium analogues
Authors: Men Shuang , Licence Peter , Do-Thanh Chi-Linh , Luo Huimin , Dai Sheng
Published: May 2020

X-ray photoelectron spectroscopy is used to probe the impact of charge delocalisation on the electronic environment of the cation and the anion.
Computer-aided design of high-efficiency GeTe-based thermoelectric devices
Authors: Hong Min , Zheng Kun , Lyv Wanyu , Li Meng , Qu Xianlin , Sun Qiang , Xu Shengduo , Zou Jin , Chen Zhi-Gang
Published: May 2020

Enhanced thermoelectric performance by band convergence and superlattice precipitates combined with geometry optimization by computer-aided design produced a segmented thermoelectric device with a record-high conversion efficiency.
Reporting the unreported: the reliability and comparability of the literature on organic solvent nanofiltration
Authors: Le Phuong Hai Anh , Blanford Christopher F. , Szekely Gyorgy
Published: May 2020

The way forward to improve and standardize membrane reports, and to bridge the gap between academic efforts and industrial requirements.
A high-throughput system combining microfluidic hydrogel droplets with deep learning for screening the antisolvent-crystallization conditions of active pharmaceutical ingredients
Authors: Su Zhenning , He Jinxu , Zhou Peipei , Huang Lu , Zhou Jianhua
Published: May 2020

A microfluidic hydrogel droplet platform was combined with deep learning for high-throughput screening of the antisolvent-crystallization conditions of active pharmaceutical ingredients.
Template-free construction of hollow ZnFe2O4 nanotubes coated with a nano-carbon layer as a competitive anode for Li-ion batteries
Authors: Xu Senyang , Qin Li , Zaman Fakhr uz , Zhang Jinyang , Hou Linrui , Yuan Changzhou
Published: May 2020

1D hollow ZnFe2O4 nanotubes coated with an ultrathin nano-carbon layer are delicately constructed via an efficient template-free strategy and exhibited superior rate behaviors and a long lifespan as a competitive anode for Li-ion batteries.
Complexes of BiCl3 with hydrazone derived ligands: a Möbius-like discrete metal chelate versus a salt-like porous polymeric structure
Authors: Akbari Afkhami Farhad , Mahmoudi Ghodrat , Miroslaw Barbara , Qu Fengrui , Gupta Arunava , Frontera Antonio , Zubkov Fedor I. , Zangrando Ennio , Safin Damir A.
Published: May 2020

Reaction of BiCl3 with hydrazone derived ligands yielded a new Möbius-like discrete metal chelate [Bi(LI)Cl3] and a salt-like porous polymeric structure ([H2LII]2[BiCl5]·EtOH)n.
Proton exchange membrane with plasmon-active surface for enhancement of fuel cell effectivity
Authors: Elashnikov R. , Zahorjanova K. , Miliutina E. , Kolska Z. , Cieslar M. , Svorcik V. , Lyutakov O.
Published: May 2020

The design and implementation of an advanced active fuel cell on the basis of plasmon-assisted chemical redox transformations is proposed.
Dual-sensitized upconversion-assisted, triple-band absorbing luminescent solar concentrators
Authors: Nam Seong Kyung , Kim Kiwon , Kang Ji-Hwan , Moon Jun Hyuk
Published: May 2020

Luminescent solar concentrator-photovoltaic systems (LSC-PV) harvest solar light by using transparent photoluminescent plates, which is expected to be particularly useful for building-integrated PV applications.
Plasma-assisted filling electron beam lithography for high throughput patterning of large area closed polygon nanostructures
Authors: Tan You Sin , Liu Hailong , Ruan Qifeng , Wang Hao , Yang Joel K. W.
Published: May 2020

The PFEBL process allows enhancement of electron beam writing efficiency for patterning of closed polygon structures using a post-exposure plasma treatment.
A super stable assembled P nanowire with variant structural and magnetic/electronic properties via transition metal adsorption
Authors: Wang Shukai , Gu Jinxing , Dong Yinan , Sai Linwei , Li Fengyu
Published: May 2020

By means of first-principles calculations, a super stable one-dimensional P nanowire was assembled by P8 and P2 clusters, and sandwich chains with diverse magnetic and electronic properties can be reached upon transition metal adsorption.
Spin-coated fluorinated PbS QD superlattice thin film with high hole mobility
Authors: Xia Pan , Davies Daniel W. , Patel Bijal B. , Qin Maotong , Liang Zhiming , Graham Kenneth R. , Diao Ying , Tang Ming Lee
Published: May 2020

Thin films of PbS quantum dots with short fully fluorinated trifluoromethylthiolate ligands (⊖SCF3) were spin-coated. TEM and GISAXS indicated a cubic superlattice. Thin film transistor hole mobilities as high as 0.085 cm2 V−1 s−1 were obtained.
Correction: Anomalous polarization dependence of Raman scattering and crystallographic orientation of black phosphorus
Authors: Kim Jungcheol , Lee Jae-Ung , Lee Jinhwan , Park Hyo Ju , Lee Zonghoon , Lee Changgu , Cheong Hyeonsik
Published: May 2020

Correction for ‘Anomalous polarization dependence of Raman scattering and crystallographic orientation of black phosphorus’ by Jungcheol Kim et al., Nanoscale, 2015, 7, 18708–18715, DOI: 10.1039/C5NR04349B.
Influence of the polymer matrix on the viscoelastic behaviour of vitrimers
Authors: Spiesschaert Yann , Taplan Christian , Stricker Lucas , Guerre Marc , Winne Johan M. , Du Prez Filip E.
Published: May 2020

Vitrimers, an emerging field of research, in which still many fundamental aspects of material design remain to be explored. Here, we systematically explore the effect of the choice of the matrix on a dynamic exchange reaction in a polymer network.
Synthesis of unstrained Criegee intermediates: inverse α-effect and other protective stereoelectronic forces can stop Baeyer–Villiger rearrangement of γ-hydroperoxy-γ-peroxylactones
Authors: Vil' Vera A. , Barsegyan Yana A. , Kuhn Leah , Ekimova Maria V. , Semenov Egor A. , Korlyukov Alexander A. , Terent'ev Alexander O. , Alabugin Igor V.
Published: May 2020

Protecting stereoelectronic effects prevent Baeyer–Villiger rearrangement and stabilize γ-OX-γ-peroxylactones (X = H, OH), the previously elusive non-strained Criegee intermediates.
Correction: Enantioselective synthesis of isochromans and tetrahydroisoquinolines by C–H insertion of donor/donor carbenes
Authors: Nickerson Leslie A. , Bergstrom Benjamin D. , Gao Mingchun , Shiue Yuan-Shin , Laconsay Croix J. , Culberson Matthew R. , Knauss Walker A. , Fettinger James C. , Tantillo Dean J. , Shaw Jared T.
Published: May 2020

Correction for ‘Enantioselective synthesis of isochromans and tetrahydroisoquinolines by C–H insertion of donor/donor carbenes’ by Leslie A. Nickerson et al., Chem. Sci., 2020, 11, 494–498, DOI: 10.1039/C9SC05111B.