bluuebunny/crossref_metadata_2025 huggingface dataset:
circ-CBFB upregulates p66Shc to perturb mitochondrial dynamics in APAP-induced liver injury
Authors: Wang Zhecheng , Zhao Yan , Sun Ruimin , Sun Yu , Liu Deshun , Lin Musen , Chen Zhao , Zhou Junjun , Lv Li , Tian Xiaofeng , Yao Jihong
Published: November 2020

p66Shc, a master regulator of mitochondrial reactive oxygen species (mtROS), is a crucial mediator of hepatocyte oxidative stress. However, its functional contribution to acetaminophen (APAP)-induced liver injury and the mechanism by which it is modulated remain unknown. Here, we aimed to assess the effect of p66Shc on APAP-induced liver injury and to evaluate if circular RNA (circRNA) functions as a competitive endogenous RNA (ceRNA) to mediate p66Shc in APAP-induced liver injury. p66Shc-, miR-185-5p-, and circ-CBFB-silenced mice were injected with APAP. AML12 cells were transfected with p66Shc, miR-185-5p, and circ-CBFB silencing or overexpression plasmids or siRNAs prior to APAP stimulation. p66Shc was upregulated in liver tissues in response to APAP, and p66Shc silencing in vivo protected mice from APAP-induced mitochondrial dynamics perturbation and liver injury. p66Shc knockdown in vitro attenuated mitochondrial dynamics and APAP-induced hepatocyte injury. Mechanically, p66Shc perturbs mitochondrial dynamics partially by inhibiting OMA1 ubiquitination. miR-185-5p, which directly suppressed p66Shc translation, was identified by microarray and bioinformatics analyses, and its overexpression attenuated mitochondrial dynamics and hepatocyte injury in vitro. Furthermore, luciferase, pull-down and RNA immunoprecipitation assays demonstrated that circ-CBFB acts as a miRNA sponge of miR-185-5p to mediate p66Shc in APAP-induced liver injury. circ-CBFB knockdown also alleviated APAP-induced mitochondrial dynamics perturbation and hepatocyte injury. More importantly, we found that the protective effects of circ-CBFB knockdown on p66Shc, mitochondrial dynamics and liver injury were abolished by miR-185-5p inhibition both in vivo and in vitro. In conclusion, p66Shc is a key regulator of APAP-induced liver injury that acts by triggering mitochondrial dynamics perturbation. circ-CBFB functions as a ceRNA to regulate p66Shc during APAP-induced liver injury, which may provide a potential therapeutic target.
Neutrophils in liver diseases: pathogenesis and therapeutic targets
Authors: Liu Kai , Wang Fu-Sheng , Xu Ruonan
Published: November 2020

Previously, it was assumed that peripheral neutrophils are a homogeneous population that displays antimicrobial functions. However, recent data have revealed that neutrophils are heterogeneous and are additionally involved in tissue damage and immune regulation. The phenotypic and functional plasticity of neutrophils has been identified in patients with cancer, inflammatory disorders, infections, and other diseases. Currently, neutrophils, with their autocrine, paracrine, and immune modulation functions, have been shown to be involved in liver diseases, including viral hepatitis, nonalcoholic steatohepatitis, alcoholic liver disease, liver fibrosis, cirrhosis, liver failure, and liver cancer. Accordingly, this review summarizes the role of neutrophils in liver diseases.
Single-particle tracking of the formation of a pseudoequilibrium state prior to charged microgel cluster formation at interfaces
Authors: Bi Wuguo , Yeow Edwin K. L.
Published: November 2020

The correlation between micron-sized particles and their self-assembly at fluid interfaces is important in several applications, including the stabilization of Pickering emulsions and creation of colloidosomes. In this study, through real-time visualization of the diffusion of microgel particles at the air–water interface of an aqueous pendant drop, the formation of a pseudoequilibrium state is observed prior to cluster formation. It is shown here that at the microscopic level, a pendant drop surface has nonuniform principal curvatures and exhibits positive deviatoric curvature (+∆c) gradients. The +∆c gradients confer superdiffusive motion to single ionic microgel particles and are responsible for bringing particles that are initially far apart to common sites on the interface with high curvatures. Prior to two-particle cluster formation, the balance between pairwise repulsion, capillary attraction and +∆c-induced energy that pushes the pair of particles to a high curvature creates a pseudoequilibrium state where the interparticle distance remains relatively invariant for a long period of time. This observation is also noted during higher-order cluster formation. Thereafter, a sufficiently strong long-range attraction potential is activated to facilitate cluster formation. Real-time tracking of the evolution of cluster formation provides useful insights into the interplay between various interactions experienced by ionic microgels.
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
Authors: Dellicour Simon , Lequime Sebastian , Vrancken Bram , Gill Mandev S. , Bastide Paul , Gangavarapu Karthik , Matteson Nathaniel L. , Tan Yi , du Plessis Louis , Fisher Alexander A. , Nelson Martha I. , Gilbert Marius , Suchard Marc A. , Andersen Kristian G. , Grubaugh Nathan D. , Pybus Oliver G. , Lemey Philippe
Published: November 2020

Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.
LSH mediates gene repression through macroH2A deposition
Authors: Ni Kai , Ren Jianke , Xu Xiaoping , He Yafeng , Finney Richard , Braun Simon M. G. , Hathaway Nathaniel A. , Crabtree Gerald R. , Muegge Kathrin
Published: November 2020

The human Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is a severe disease with increased mortality caused by mutation in the LSH gene. Although LSH belongs to a family of chromatin remodeling proteins, it remains unknown how LSH mediates its function on chromatin in vivo. Here, we use chemical-induced proximity to rapidly recruit LSH to an engineered locus and find that LSH specifically induces macroH2A1.2 and macroH2A2 deposition in an ATP-dependent manner. Tethering of LSH induces transcriptional repression and silencing is dependent on macroH2A deposition. Loss of LSH decreases macroH2A enrichment at repeat sequences and results in transcriptional reactivation. Likewise, reduction of macroH2A by siRNA interference mimicks transcriptional reactivation. ChIP-seq analysis confirmed that LSH is a major regulator of genome-wide macroH2A distribution. Tethering of ICF4 mutations fails to induce macroH2A deposition and ICF4 patient cells display reduced macroH2A deposition and transcriptional reactivation supporting a pathogenic role for altered marcoH2A deposition. We propose that LSH is a major chromatin modulator of the histone variant macroH2A and that its ability to insert marcoH2A into chromatin and transcriptionally silence is disturbed in the ICF4 syndrome.
Establishment of Neurospora crassa as a model organism for fungal virology
Authors: Honda Shinji , Eusebio-Cope Ana , Miyashita Shuhei , Yokoyama Ayumi , Aulia Annisa , Shahi Sabitree , Kondo Hideki , Suzuki Nobuhiro
Published: November 2020

The filamentous fungusNeurospora crassais used as a model organism for genetics, developmental biology and molecular biology. Remarkably, it is not known to host or to be susceptible to infection with any viruses. Here, we identify diverse RNA viruses inN. crassaand otherNeurosporaspecies, and show thatN. crassasupports the replication of these viruses as well as some viruses from other fungi. Several encapsidated double-stranded RNA viruses and capsid-less positive-sense single-stranded RNA viruses can be experimentally introduced intoN. crassaprotoplasts or spheroplasts. This allowed us to examine viral replication and RNAi-mediated antiviral responses in this organism. We show that viral infection upregulates the transcription of RNAi components, and that Dicer proteins (DCL-1, DCL-2) and an Argonaute (QDE-2) participate in suppression of viral replication. Our study thus establishesN. crassaas a model system for the study of host-virus interactions.
A single-cell atlas and lineage analysis of the adult Drosophila ovary
Authors: Rust Katja , Byrnes Lauren E. , Yu Kevin Shengyang , Park Jason S. , Sneddon Julie B. , Tward Aaron D. , Nystul Todd G.
Published: November 2020

TheDrosophilaovary is a widely used model for germ cell and somatic tissue biology. Here we use single-cell RNA-sequencing (scRNA-seq) to build a comprehensive cell atlas of the adultDrosophilaovary that contains transcriptional profiles for every major cell type in the ovary, including the germline stem cells and their niche cells, follicle stem cells, and previously undescribed subpopulations of escort cells. In addition, we identifyGal4lines with specific expression patterns and perform lineage tracing of subpopulations of escort cells and follicle cells. We discover that a distinct subpopulation of escort cells is able to convert to follicle stem cells in response to starvation or upon genetic manipulation, including knockdown ofescargot, or overactivation of mTor or Toll signalling.
Evidence of the Berezinskii-Kosterlitz-Thouless phase in a frustrated magnet
Authors: Hu Ze , Ma Zhen , Liao Yuan-Da , Li Han , Ma Chunsheng , Cui Yi , Shangguan Yanyan , Huang Zhentao , Qi Yang , Li Wei , Meng Zi Yang , Wen Jinsheng , Yu Weiqiang
Published: November 2020

The Berezinskii-Kosterlitz-Thouless (BKT) mechanism, building upon proliferation of topological defects in 2D systems, is the first example of phase transition beyond the Landau-Ginzburg paradigm of symmetry breaking. Such a topological phase transition has long been sought yet undiscovered directly in magnetic materials. Here, we pin down two transitions that bound a BKT phase in an ideal 2D frustrated magnet TmMgGaO4, via nuclear magnetic resonance under in-plane magnetic fields, which do not disturb the low-energy electronic states and allow BKT fluctuations to be detected sensitively. Moreover, by applying out-of-plane fields, we find a critical scaling behavior of the magnetic susceptibility expected for the BKT transition. The experimental findings can be explained by quantum Monte Carlo simulations applied on an accurate triangular-lattice Ising model of the compound which hosts a BKT phase. These results provide a concrete example for the BKT phase and offer an ideal platform for future investigations on the BKT physics in magnetic materials.
How Rh surface breaks CO2 molecules under ambient pressure
Authors: Kim Jeongjin , Ha Hyunwoo , Doh Won Hui , Ueda Kohei , Mase Kazuhiko , Kondoh Hiroshi , Mun Bongjin Simon , Kim Hyun You , Park Jeong Young
Published: November 2020

Utilization of carbon dioxide (CO2) molecules leads to increased interest in the sustainable synthesis of methane (CH4) or methanol (CH3OH). The representative reaction intermediate consisting of a carbonyl or formate group determines yields of the fuel source during catalytic reactions. However, their selective initial surface reaction processes have been assumed without a fundamental understanding at the molecular level. Here, we report direct observations of spontaneous CO2 dissociation over the model rhodium (Rh) catalyst at 0.1 mbar CO2. The linear geometry of CO2 gas molecules turns into a chemically active bent-structure at the interface, which allows non-uniform charge transfers between chemisorbed CO2 and surface Rh atoms. By combining scanning tunneling microscopy, X-ray photoelectron spectroscopy at near-ambient pressure, and computational calculations, we reveal strong evidence for chemical bond cleavage of O‒CO* with ordered intermediates structure formation of (2 × 2)-CO on an atomically flat Rh(111) surface at room temperature.
A highly-active, stable and low-cost platinum-free anode catalyst based on RuNi for hydroxide exchange membrane fuel cells
Authors: Xue Yanrong , Shi Lin , Liu Xuerui , Fang Jinjie , Wang Xingdong , Setzler Brian P. , Zhu Wei , Yan Yushan , Zhuang Zhongbin
Published: November 2020

The development of cost-effective hydroxide exchange membrane fuel cells is limited by the lack of high-performance and low-cost anode hydrogen oxidation reaction catalysts. Here we report a Pt-free catalyst Ru7Ni3/C, which exhibits excellent hydrogen oxidation reaction activity in both rotating disk electrode and membrane electrode assembly measurements. The hydrogen oxidation reaction mass activity and specific activity of Ru7Ni3/C, as measured in rotating disk experiments, is about 21 and 25 times that of Pt/C, and 3 and 5 times that of PtRu/C, respectively. The hydroxide exchange membrane fuel cell with Ru7Ni3/C anode can deliver a high peak power density of 2.03 W cm−2 in H2/O2 and 1.23 W cm−2 in H2/air (CO2-free) at 95 °C, surpassing that using PtRu/C anode catalyst, and good durability with less than 5% voltage loss over 100 h of operation. The weakened hydrogen binding of Ru by alloying with Ni and enhanced water adsorption by the presence of surface Ni oxides lead to the high hydrogen oxidation reaction activity of Ru7Ni3/C. By using the Ru7Ni3/C catalyst, the anode cost can be reduced by 85% of the current state-of-the-art PtRu/C, making it highly promising in economical hydroxide exchange membrane fuel cells.
Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements
Authors: Pinilla-Redondo Rafael , Shehreen Saadlee , Marino Nicole D. , Fagerlund Robert D. , Brown Chris M. , Sørensen Søren J. , Fineran Peter C. , Bondy-Denomy Joseph
Published: November 2020

Many prokaryotes employ CRISPR–Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I–F (Pseudomonas, Pectobacterium, and Serratia), I–E (Pseudomonas and Serratia), and I–C (Pseudomonas). We uncover 11 type I–F and/or I–E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.
Injury triggers fascia fibroblast collective cell migration to drive scar formation through N-cadherin
Authors: Jiang Dongsheng , Christ Simon , Correa-Gallegos Donovan , Ramesh Pushkar , Kalgudde Gopal Shruthi , Wannemacher Juliane , Mayr Christoph H. , Lupperger Valerio , Yu Qing , Ye Haifeng , Mück-Häusl Martin , Rajendran Vijayanand , Wan Li , Liu Juan , Mirastschijski Ursula , Volz Thomas , Marr Carsten , Schiller Herbert B. , Rinkevich Yuval
Published: November 2020

Scars are more severe when the subcutaneous fascia beneath the dermis is injured upon surgical or traumatic wounding. Here, we present a detailed analysis of fascia cell mobilisation by using deep tissue intravital live imaging of acute surgical wounds, fibroblast lineage-specific transgenic mice, and skin-fascia explants (scar-like tissue in a dish – SCAD). We observe that injury triggers a swarming-like collective cell migration of fascia fibroblasts that progressively contracts the skin and form scars. Swarming is exclusive to fascia fibroblasts, and requires the upregulation of N-cadherin. Both swarming and N-cadherin expression are absent from fibroblasts in the upper skin layers and the oral mucosa, tissues that repair wounds with minimal scar. Impeding N-cadherin binding inhibits swarming and skin contraction, and leads to reduced scarring in SCADs and in animals. Fibroblast swarming and N-cadherin thus provide therapeutic avenues to curtail fascia mobilisation and pathological fibrotic responses across a range of medical settings.
Sub-nanoliter metabolomics via mass spectrometry to characterize volume-limited samples
Authors: Li Yafeng , Bouza Marcos , Wu Changsheng , Guo Hengyu , Huang Danning , Doron Gilad , Temenoff Johnna S. , Stecenko Arlene A. , Wang Zhong Lin , Fernández Facundo M.
Published: November 2020

The human metabolome provides a window into the mechanisms and biomarkers of various diseases. However, because of limited availability, many sample types are still difficult to study by metabolomic analyses. Here, we present a mass spectrometry (MS)-based metabolomics strategy that only consumes sub-nanoliter sample volumes. The approach consists of combining a customized metabolomics workflow with a pulsed MS ion generation method, known as triboelectric nanogenerator inductive nanoelectrospray ionization (TENGi nanoESI) MS. Samples tested with this approach include exhaled breath condensate collected from cystic fibrosis patients as well as in vitro-cultured human mesenchymal stromal cells. Both test samples are only available in minimum amounts. Experiments show that picoliter-volume spray pulses suffice to generate high-quality spectral fingerprints, which increase the information density produced per unit sample volume. This TENGi nanoESI strategy has the potential to fill in the gap in metabolomics where liquid chromatography-MS-based analyses cannot be applied. Our method opens up avenues for future investigations into understanding metabolic changes caused by diseases or external stimuli.
Designing accurate emulators for scientific processes using calibration-driven deep models
Authors: Thiagarajan Jayaraman J. , Venkatesh Bindya , Anirudh Rushil , Bremer Peer-Timo , Gaffney Jim , Anderson Gemma , Spears Brian
Published: November 2020

Predictive models that accurately emulate complex scientific processes can achieve speed-ups over numerical simulators or experiments and at the same time provide surrogates for improving the subsequent analysis. Consequently, there is a recent surge in utilizing modern machine learning methods to build data-driven emulators. In this work, we study an often overlooked, yet important, problem of choosing loss functions while designing such emulators. Popular choices such as the mean squared error or the mean absolute error are based on a symmetric noise assumption and can be unsuitable for heterogeneous data or asymmetric noise distributions. We propose Learn-by-Calibrating, a novel deep learning approach based on interval calibration for designing emulators that can effectively recover the inherent noise structure without any explicit priors. Using a large suite of use-cases, we demonstrate the efficacy of our approach in providing high-quality emulators, when compared to widely-adopted loss function choices, even in small-data regimes.
Deep learning-enabled multi-organ segmentation in whole-body mouse scans
Authors: Schoppe Oliver , Pan Chenchen , Coronel Javier , Mai Hongcheng , Rong Zhouyi , Todorov Mihail Ivilinov , Müskes Annemarie , Navarro Fernando , Li Hongwei , Ertürk Ali , Menze Bjoern H.
Published: November 2020

Whole-body imaging of mice is a key source of information for research. Organ segmentation is a prerequisite for quantitative analysis but is a tedious and error-prone task if done manually. Here, we present a deep learning solution called AIMOS that automatically segments major organs (brain, lungs, heart, liver, kidneys, spleen, bladder, stomach, intestine) and the skeleton in less than a second, orders of magnitude faster than prior algorithms. AIMOS matches or exceeds the segmentation quality of state-of-the-art approaches and of human experts. We exemplify direct applicability for biomedical research for localizing cancer metastases. Furthermore, we show that expert annotations are subject to human error and bias. As a consequence, we show that at least two independently created annotations are needed to assess model performance. Importantly, AIMOS addresses the issue of human bias by identifying the regions where humans are most likely to disagree, and thereby localizes and quantifies this uncertainty for improved downstream analysis. In summary, AIMOS is a powerful open-source tool to increase scalability, reduce bias, and foster reproducibility in many areas of biomedical research.
Climate reverses directionality in the richness–abundance relationship across the World’s main forest biomes
Authors: Madrigal-González Jaime , Calatayud Joaquín , Ballesteros-Cánovas Juan A. , Escudero Adrián , Cayuela Luis , Rueda Marta , Ruiz-Benito Paloma , Herrero Asier , Aponte Cristina , Sagardia Rodrigo , Plumptre Andrew J. , Dupire Sylvain , Espinosa Carlos I. , Tutubalina Olga , Myint Moe , Pataro Luciano , López-Sáez Jerome , Macía Manuel J. , Abegg Meinrad , Zavala Miguel A. , Quesada-Román Adolfo , Vega-Araya Mauricio , Golubeva Elena , Timokhina Yuliya , Stoffel Markus
Published: November 2020

More tree species can increase the carbon storage capacity of forests (here referred to as the more species hypothesis) through increased tree productivity and tree abundance resulting from complementarity, but they can also be the consequence of increased tree abundance through increased available energy (more individuals hypothesis). To test these two contrasting hypotheses, we analyse the most plausible pathways in the richness-abundance relationship and its stability along global climatic gradients. We show that positive effect of species richness on tree abundance only prevails in eight of the twenty-three forest regions considered in this study. In the other forest regions, any benefit from having more species is just as likely (9 regions) or even less likely (6 regions) than the effects of having more individuals. We demonstrate that diversity effects prevail in the most productive environments, and abundance effects become dominant towards the most limiting conditions. These findings can contribute to refining cost-effective mitigation strategies based on fostering carbon storage through increased tree diversity. Specifically, in less productive environments, mitigation measures should promote abundance of locally adapted and stress tolerant tree species instead of increasing species richness.
Skeletal reorganization divergence of N-sulfonyl ynamides
Authors: Zeng Linwei , Lin Yuxin , Li Jiaming , Sajiki Hironao , Xie Hujun , Cui Sunliang
Published: November 2020

Skeletal reorganization is a type of intriguing processes because of their interesting mechanism, high atom-economy and synthetic versatility. Herein, we describe an unusual, divergent skeletal reorganization of N-sulfonyl ynamides. Upon treatment with lithium diisopropylamine (LDA), N-sulfonyl ynamides undergo a skeletal reorganization to deliver thiete sulfones, while the additional use of 1,3-dimethyl-tetrahydropyrimidin-2(1H)-one (DMPU) shifts the process to furnish propargyl sulfonamides. This skeletal reorganization divergence features broad substrate scope and scalability. Mechanistically, experimental and computational studies reveal that these processes may initiate from a lithiation/4-exo-dig cyclization cascade, and the following ligand-dependent 1,3-sulfonyl migration or β-elimination would control the chemodivergence. This protocol additionally provides a facile access to a variety of privileged molecules from easily accessible ynamides.
The nuclear pore primes recombination-dependent DNA synthesis at arrested forks by promoting SUMO removal
Authors: Kramarz Karol , Schirmeisen Kamila , Boucherit Virginie , Ait Saada Anissia , Lovo Claire , Palancade Benoit , Freudenreich Catherine , Lambert Sarah A. E.
Published: November 2020

Nuclear Pore complexes (NPCs) act as docking sites to anchor particular DNA lesions facilitating DNA repair by elusive mechanisms. Using replication fork barriers in fission yeast, we report that relocation of arrested forks to NPCs occurred after Rad51 loading and its enzymatic activity. The E3 SUMO ligase Pli1 acts at arrested forks to safeguard integrity of nascent strands and generates poly-SUMOylation which promote relocation to NPCs but impede the resumption of DNA synthesis by homologous recombination (HR). Anchorage to NPCs allows SUMO removal by the SENP SUMO protease Ulp1 and the proteasome, promoting timely resumption of DNA synthesis. Preventing Pli1-mediated SUMO chains was sufficient to bypass the need for anchorage to NPCs and the inhibitory effect of poly-SUMOylation on HR-mediated DNA synthesis. Our work establishes a novel spatial control of Recombination-Dependent Replication (RDR) at a unique sequence that is distinct from mechanisms engaged at collapsed-forks and breaks within repeated sequences.
Publisher Correction: The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
Authors: van der Weegen Yana , Golan-Berman Hadar , Mevissen Tycho E. T. , Apelt Katja , González-Prieto Román , Goedhart Joachim , Heilbrun Elisheva E. , Vertegaal Alfred C. O. , van den Heuvel Diana , Walter Johannes C. , Adar Sheera , Luijsterburg Martijn S.
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Social attraction in Drosophila is regulated by the mushroom body and serotonergic system
Authors: Sun Yuanjie , Qiu Rong , Li Xiaonan , Cheng Yaxin , Gao Shan , Kong Fanchen , Liu Li , Zhu Yan
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Persistent and reversible solid iodine electrodeposition in nanoporous carbons
Authors: Prehal Christian , Fitzek Harald , Kothleitner Gerald , Presser Volker , Gollas Bernhard , Freunberger Stefan A. , Abbas Qamar
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Machine learning property prediction for organic photovoltaic devices
Authors: Meftahi Nastaran , Klymenko Mykhailo , Christofferson Andrew J. , Bach Udo , Winkler David A. , Russo Salvy P.
Published: November 2020

Organic photovoltaic (OPV) materials are promising candidates for cheap, printable solar cells. However, there are a very large number of potential donors and acceptors, making selection of the best materials difficult. Here, we show that machine-learning approaches can leverage computationally expensive DFT calculations to estimate important OPV materials properties quickly and accurately. We generate quantitative relationships between simple and interpretable chemical signature and one-hot descriptors and OPV power conversion efficiency (PCE), open circuit potential (Voc), short circuit density (Jsc), highest occupied molecular orbital (HOMO) energy, lowest unoccupied molecular orbital (LUMO) energy, and the HOMO–LUMO gap. The most robust and predictive models could predict PCE (computed by DFT) with a standard error of ±0.5 for percentage PCE for both the training and test set. This model is useful for pre-screening potential donor and acceptor materials for OPV applications, accelerating design of these devices for green energy applications.
Predominance of non-adiabatic effects in zero-point renormalization of the electronic band gap
Authors: Miglio Anna , Brousseau-Couture Véronique , Godbout Emile , Antonius Gabriel , Chan Yang-Hao , Louie Steven G. , Côté Michel , Giantomassi Matteo , Gonze Xavier
Published: November 2020

Electronic and optical properties of materials are affected by atomic motion through the electron–phonon interaction: not only band gaps change with temperature, but even at absolute zero temperature, zero-point motion causes band-gap renormalization. We present a large-scale first-principles evaluation of the zero-point renormalization of band edges beyond the adiabatic approximation. For materials with light elements, the band gap renormalization is often larger than 0.3 eV, and up to 0.7 eV. This effect cannot be ignored if accurate band gaps are sought. For infrared-active materials, global agreement with available experimental data is obtained only when non-adiabatic effects are taken into account. They even dominate zero-point renormalization for many materials, as shown by a generalized Fröhlich model that includes multiple phonon branches, anisotropic and degenerate electronic extrema, whose range of validity is established by comparison with first-principles results.
ClimActor, harmonized transnational data on climate network participation by city and regional governments
Authors: Hsu Angel , Yeo Zhi Yi , Rauber Ross , Sun James , Kim Yunsoo , Raghavan Sowmya , Chin Nicholas , Namdeo Vasu , Weinfurter Amy
Published: November 2020

Cities and regions have become increasingly engaged in global climate change governance. They are pledging their own climate mitigation targets and participating in membership networks that typically are transnational in nature and engage thousands of subnational governments. Researching these growing trends in participation has been difficult due to the disparate and inconsistent nature of this self-reported data. To facilitate future analyses of these actors, we introduce ClimActor, the largest harmonized global dataset of more than 10,000 city and regional governments participating in networks like the Global Covenant of Mayors for Climate and Energy, C40 Cities for Climate Leadership, ICLEI Local Leaders for Sustainability, among others. We include key contextual information on each actor’s population, geographic location, and administrative jurisdiction to facilitate disambiguation of potential overlaps in actions or emissions. We also provide a series of cleaning functions based on phonetic and fuzzy string matching algorithms within an open-source R package to make it easy for anyone to immediately use the ClimActor dataset with other relevant data.
Improved classification of rheumatoid arthritis with a score including anti-acetylated ornithine antibodies
Authors: Rodriguez-Martínez Lorena , Bang Holger , Regueiro Cristina , Nuño Laura , Triguero-Martinez Ana , Peiteado Diana , Ortiz Ana M. , Villalba Alejandro , Martinez-Feito Ana , Balsa Alejandro , Gonzalez-Alvaro Isidoro , Gonzalez Antonio
Published: November 2020

The presence of rheumatoid factor (RF) or anti-cyclic citrullinated peptide (anti-CCP) autoantibodies contributes to the current rheumatoid arthritis (RA) classification criteria. These criteria involve stratification on antibody levels, which limits reproducibility, and underperform in the RA patients without RF and anti-CCP. Here, we have explored if two anti-acetylated peptide antibodies (AAPA), anti-acetylated lysine (AcLys) and anti-acetylated ornithine (AcOrn), could improve the performance of the current criteria. The analysis was done in 1062 prospectively-followed early arthritis (EA) patients. The anti-AcOrn were more informative than the anti-AcLys, the conventional RA antibodies and the anti-carbamylated protein antibodies. The anti-AcOrn produced a classification that did not require antibody levels and showed improved specificity (77.6% vs. 72.6%, p = 0.003) and accuracy (79.0% vs. 75.8%, p = 0.002) over the current criteria. These improvements were obtained with a scoring system that values concordance between anti-AcOrn, RF and anti-CCP. No significant gain was obtained in sensitivity (80.2% vs. 78.8%, p = 0.25) or in improving the classification of the RA patients lacking RF and anti-CCP, although the anti-AcOrn ranked first among the analysed new antibodies. Therefore, the anti-AcOrn antibodies could contribute to the improvement of RA classification criteria by exploiting antibody concordance.
Determinants of length of stay after cesarean sections in the Friuli Venezia Giulia Region (North-Eastern Italy), 2005–2015
Authors: Cegolon L. , Mastrangelo G. , Maso G. , Pozzo G. Dal , Heymann W. C. , Ronfani L. , Barbone F.
Published: November 2020

Since Italy has the highest cesarean section (CS) rate (38.1%) among all European countries, the containment of health care costs associated with CS is needed, along with control of length of hospital stay (LOS) following CS. This population based cross-sectional study aims to investigate LoS post CS (overall CS, OCS; planned CS, PCS; urgent/emergency CS, UCS), in Friuli Venezia Giulia (a region of North-Eastern Italy) during 2005–2015, adjusting for a considerable number factors, including various obstetric conditions/complications. Maternal and newborn characteristics (health care setting and timeframe; maternal health factors; child’s size factors; child’s fragility factors; socio-demographic background; obstetric history; obstetric conditions) were used as independent variables. LoS (post OCS, PCS, UCS) was the outcome measure. The statistical analysis was conducted with multivariable linear (LoS expressed as adjusted mean, in days) as well as logistic (adjusted proportion of LoS > 4 days vs. LoS ≤ 4 days, using a 4 day cutoff for early discharge, ED) regression. An important decreasing trend over time in mean LoS and LoS > ED was observed for both PCS and UCS. LoS post CS was shorter with parity and history of CS, whereas it was longer among non-EU mothers. Several obstetric conditions/complications were associated with extended LoS. Whilst eclampsia/pre-eclampsia and preterm gestations (33–36 weeks) were predominantly associated with longer LoS post UCS, for PCS LoS was significantly longer with birthweight 2.0–2.5 kg, multiple birth and increasing maternal age. Strong significant inter-hospital variation remained after adjustment for the major clinical conditions. This study shows that routinely collected administrative data provide useful information for health planning and monitoring, identifying inter-hospital differences that could be targeted by policy interventions aimed at improving the efficiency of obstetric care. The important decreasing trend over time of LoS post CS, coupled with the impact of some socio-demographic and obstetric history factors on LoS, seemingly suggests a positive approach of health care providers of FVG in decision making on hospitalization length post CS. However, the significant role of several obstetric conditions did not influence hospital variation. Inter-hospital variations of LoS could depend on a number of factors, including the capacity to discharge patients into the surrounding non-acute facilities. Further studies are warranted to ascertain whether LoS can be attributed to hospital efficiency rather than the characteristics of the hospital catchment area.
Activation of toll like receptor 4 (TLR4) promotes cardiomyocyte apoptosis through SIRT2 dependent p53 deacetylation
Authors: Katare Parmeshwar Bajirao , Nizami Hina Lateef , Paramesha Bugga , Dinda Amit K. , Banerjee Sanjay K.
Published: November 2020

Cardiomyocyte inflammation followed by apoptosis and fibrosis is an important mediator for development and progression of heart failure. Activation of toll-like receptor 4 (TLR4), an important regulator of inflammation, causes the progression of cardiac hypertrophy and injury. However, the precise mechanism of TLR4-mediated adverse cardiac outcomes is still elusive. The present study was designed to find the role of TLR4 in cardiac fibrosis and apoptosis, and molecular mechanism thereof. Rats were treated with TLR4 agonist (LPS 12.5 μg/kg/day) through osmotic pump for 14 days. To simulate the condition in vitro, H9c2 cells were treated with LPS (1 μg/ml). Similarly, H9c2 cells were transfected with TLR4 and SIRT2 c-DNA clone for overexpression. Myocardial oxidative stress, inflammation, fibrosis and mitochondrial parameters were evaluated both in vitro and in vivo. Cardiac inflammation after LPS treatment was confirmed by increased TNF-α and IL-6 expression in rat heart. There was a marked increase in oxidative stress as observed by increased TBARS and decreased endogenous antioxidants (GSH and catalase), along with mitochondrial dysfunction as measured by mitochondrial complex activity in LPS-treated rat hearts. Histopathological examination showed the presence of cardiac fibrosis after LPS treatment. Protein expression of nuclear p53 and cleaved caspase-7/caspase-9 was significantly increased in LPS treated heart. Similar to in vivo study, nuclear translocation of p53, mitochondrial dysfunction and cellular apoptosis were observed in H9c2 cells treated with LPS. Our data also indicate that decreased expression of SIRT2 was associated with increased acetylation of p53 after LPS treatment. In conclusion, TLR4 activation in rats promotes cardiac inflammation, mitochondrial dysfunction, apoptosis and fibrosis. p53 and caspase 7/caspase 9 were found to play an important role in TLR4-mediated apoptosis. Our data suggest that, reducing TLR4 mediated fibrosis and apoptosis could be a novel approach in the treatment of heart failure, keeping in the view the major role played by TLR4 in cardiac inflammation.
MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks
Authors: da Silva David Attuy Vey , Brendebach Holger , Grützke Josephine , Dieckmann Ralf , Soares Rodrigo Martins , de Lima Julia Teresa Ribeiro , Keid Lara Borges , Hofreuter Dirk , Al Dahouk Sascha
Published: November 2020

Brucellosis is one of the most common bacterial zoonoses worldwide affecting not only livestock and wildlife but also pets. Canine brucellosis is characterized by reproductive failure in dogs. Human Brucella canis infections are rarely reported but probably underestimated due to insufficient diagnostic surveillance. To improve diagnostics, we investigated dogs in a breeding kennel that showed clinical manifestations of brucellosis and revealed positive blood cultures. As an alternative to the time-consuming and hazardous classical identification procedures, a newly developed species-specific intact-cell matrix-assisted laser desorption/ionization–time of flight mass spectrometry analysis was applied, which allowed for rapid identification of B. canis and differentiation from closely related B. suis biovar 1. High-throughput sequencing and comparative genomics using single nucleotide polymorphism analysis clustered our isolates together with canine and human strains from various Central and South American countries in a distinct sub-lineage. Hence, molecular epidemiology clearly defined the outbreak cluster and demonstrated the endemic situation in South America. Our study illustrates that MALDI-TOF MS analysis using a validated in-house reference database facilitates rapid B. canis identification at species level. Additional whole genome sequencing provides more detailed outbreak information and leads to a deeper understanding of the epidemiology of canine brucellosis.
Designing profitable, resource use efficient and environmentally sound cereal based systems for the Western Indo-Gangetic plains
Authors: Jat Hanuman S. , Kumar Virender , Datta Ashim , Choudhary Madhu , Yadvinder-Singh  , Kakraliya Suresh K. , Poonia Tanuja , McDonald Andrew J. , Jat Mangi L. , Sharma Parbodh C.
Published: November 2020

In the western Indo-Gangetic plains, issues of deterioration in soil, water, and environment quality coupled with low profitability jeopardize the sustainability of the dominant rice–wheat (RW) system. To address these issues, crop diversification and conservation agriculture (CA)-based management hold considerable promise but the adoption of both approaches has been low, and additional evidence generation from a multi-criteria productivity and sustainability perspective is likely required to help drive the change. Compared to prevailing farmers’ practice (FP), results suggest that CA-based rice management increased profitability by 13% and energy use efficiency (EUE) by 21% while reducing irrigation by 19% and global warming potential (GWP) by 28%. By substituting CA-based maize for rice, similar mean profitability gains were realized (16%) but transformative improvements in irrigation (− 84%), EUE (+ 231%), and GWP (− 95%) were observed compared to FP. Inclusion of mungbean in the rotation (i.e. maize-wheat-mungbean) with CA-based management increased the system productivity, profitability, and EUE by 11, 25 and 103%, respectively while decreasing irrigation water use by 64% and GWP by 106% compared to FP. Despite considerable benefits from the CA-based maize-wheat system, adoption of maize is not widespread due to uneven market demand and assured price guarantees for rice.
Hybrid perfect metamaterial absorber for microwave spin rectification applications
Authors: Qian Jie , Gou Peng , Pan Hong , Zhu Liping , Gui Y. S. , Hu C.-M. , An Zhenghua
Published: November 2020

Metamaterials provide compelling capabilities to manipulate electromagnetic waves beyond the natural materials and can dramatically enhance both their electric and magnetic fields. The enhanced magnetic fields, however, are far less utilized than the electric counterparts, despite their great potential in spintronics. In this work, we propose and experimentally demonstrate a hybrid perfect metamaterial absorbers which combine the artificial metal/insulator/metal (MIM) metamaterial with the natural ferromagnetic material permalloy (Py) and realize remarkably larger spin rectification effect. Magnetic hot spot of the MIM metamaterial improves considerably electromagnetic coupling with spins in the embedded Py stripes. With the whole hybridized structure being optimized based on coupled-mode theory, perfect absorption condition is approached and an approximately 190-fold enhancement of spin-rectifying photovoltage is experimentally demonstrated at the ferromagnetic resonance at 7.1 GHz. Our work provides an innovative solution to harvest microwave energy for spintronic applications, and opens the door to hybridized magnetism from artificial and natural magnetic materials for emergent applications such as efficient optospintronics, magnonic metamaterials and wireless energy transfer.
Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum
Authors: Lira Bruno Silvestre , Oliveira Maria José , Shiose Lumi , Wu Raquel Tsu Ay , Rosado Daniele , Lupi Alessandra Cavalcanti Duarte , Freschi Luciano , Rossi Magdalena
Published: November 2020

Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.
Carotid sinus nerve stimulation attenuates alveolar bone loss and inflammation in experimental periodontitis
Authors: Ribeiro Aline Barbosa , Brognara Fernanda , da Silva Josiane Fernandes , Castania Jaci Airton , Fernandes Patrícia Garani , Tostes Rita C. , Salgado Helio Cesar
Published: November 2020

Baroreceptor and chemoreceptor reflexes modulate inflammatory responses. However, whether these reflexes attenuate periodontal diseases has been poorly examined. Thus, the present study determined the effects of electrical activation of the carotid sinus nerve (CSN) in rats with periodontitis. We hypothesized that activation of the baro and chemoreflexes attenuates alveolar bone loss and the associated inflammatory processes. Electrodes were implanted around the CSN, and bilateral ligation of the first mandibular molar was performed to, respectively, stimulate the CNS and induce periodontitis. The CSN was stimulated daily for 10 min, during nine days, in unanesthetized animals. On the eighth day, a catheter was inserted into the left femoral artery and, in the next day, the arterial pressure was recorded. Effectiveness of the CNS electrical stimulation was confirmed by hypotensive responses, which was followed by the collection of a blood sample, gingival tissue, and jaw. Long-term (9 days) electrical stimulation of the CSN attenuated bone loss and the histological damage around the first molar. In addition, the CSN stimulation also reduced the gingival and plasma pro-inflammatory cytokines induced by periodontitis. Thus, CSN stimulation has a protective effect on the development of periodontal disease mitigating alveolar bone loss and inflammatory processes.
A local difference in blood–brain barrier permeability in the caudate putamen and thalamus of a rat brain induced by focused ultrasound
Authors: Huh Hyungkyu , Park Tae Young , Seo Hyeon , Han Mun , Jung Byeongjin , Choi Hyo Jin , Lee Eun-Hee , Pahk Ki Joo , Kim Hyungmin , Park Juyoung
Published: November 2020

A blood–brain barrier (BBB) opening induced by focused ultrasound (FUS) has been widely studied as an effective way of treating brain diseases. We investigate the effect of ultrasound’s incidence angle at caudate putamen (Cp) and thalamus (Th) of the rat brain by inducing the same power of focused ultrasound that corresponds to the acoustic pressure of 0.65 MPa in free field. The BBB permeability (Ktrans) was quantitatively evaluated with dynamic contrast-enhanced magnetic resonance imaging. The group averaged (n = 11) maximum Ktrans at Cp (0.021 ± 0.012 min−1) was 1.39 times smaller than the Ktrans of Th (0.029 ± 0.01 min−1) with p = 0.00343. The group averaged (n = 6) ultrasound’s incidence angles measured using the computed tomography image of rat skulls were compared with the maximum Ktrans and showed a negatively linear relation R2 = 0.7972). The maximum acoustic pressure computed from the acoustic simulation showed higher average acoustic pressures at Th (0.37 ± 0.02 MPa) compared to pressures at Cp (0.32 ± 0.01 MPa) with p = 0.138 × 10−11. More red blood cell were observed at the Th region compared to the Cp region in the tissue staining. These results indicate that localized characteristics of the sonication target within the subject should be considered for safer and more efficient BBB disruption induced by FUS.