bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation 8.5%-efficient submodule using 5%-efficient DSSCs via three-dimensional angle array and light-trapping layer
Authors: Sim Yeon Hyang , Yun Min Ju , Cha Seung I. , Lee Dong Yoon 
Published: January 2020

AbstractExpanding the application area of photovoltaics to urban environments demands high efficiency under low-intensity lighting conditions, as well as omnidirectional light trapping. Dye-sensitized solar cells are of particular interest in this regard, owing to their superior electricity production in dim light; however, an improvement in dye-sensitized solar cells efficiency is required for successful implementation. We developed a light-trapping layer within the photoanode of dye-sensitized solar cells and configured these cells into an angled three-dimensional (3D) array creating a submodule to improve efficiency. The light-trapping layer increases the travel distance of the light within the photoanode, thus improving electron generation by the photons of the omnidirectional incident light. The 3D angled array suppresses recombination and internal resistance losses, improving the collection efficiency by increasing the relative cell surface area with respect to the light projection area. Using the proposed configuration, we achieved a dye-sensitized solar cells submodule efficiency of 8.5% using 5%-efficient dye-sensitized solar cells with a pot-shaped light-trapping layer and a 60° angled 3D array for the submodule. Considering that there is room for further improvement, our proposed photovoltaics configuration is expected to overcome the current limitations of dye-sensitized solar cells, thus providing promising photovoltaics modules for urban environments.
Monitoring spatiotemporal changes in chaperone-mediated autophagy in vivo
Authors: Dong S. , Aguirre-Hernandez C. , Scrivo A. , Eliscovich C. , Arias E. , Bravo-Cordero J. J. , Cuervo A. M. 
Published: January 2020

AbstractAutophagy malfunctioning occurs in multiple human disorders, making attractive the idea of chemically modulating it with therapeutic purposes. However, for many types of autophagy, a clear understanding of tissue-specific differences in their activity and regulation is missing because of lack of methods to monitor these processes in vivo. Chaperone-mediated autophagy (CMA) is a selective type of autophagy that until now has only been studied in vitro and not in the tissue context at single cell resolution. Here, we develop a transgenic reporter mouse that allows dynamic measurement of CMA activity in vivo using image-based procedures. We identify previously unknown spatial and temporal differences in CMA activity in multiple organs and in response to stress. We illustrate the versatility of this model for monitoring CMA in live animals, organotypic cultures and cell cultures from these mice, and provide practical examples of multiorgan response to drugs that modulate CMA.
Surface protein imputation from single cell transcriptomes by deep neural networks
Authors: Zhou Zilu , Ye Chengzhong , Wang Jingshu , Zhang Nancy R. 
Published: January 2020

AbstractWhile single cell RNA sequencing (scRNA-seq) is invaluable for studying cell populations, cell-surface proteins are often integral markers of cellular function and serve as primary targets for therapeutic intervention. Here we propose a transfer learning framework, single cell Transcriptome to Protein prediction with deep neural network (cTP-net), to impute surface protein abundances from scRNA-seq data by learning from existing single-cell multi-omic resources.
Fibrinogen induces neural stem cell differentiation into astrocytes in the subventricular zone via BMP signaling
Authors: Pous Lauriane , Deshpande Sachin S. , Nath Suvra , Mezey Szilvia , Malik Subash C. , Schildge Sebastian , Bohrer Christian , Topp Könül , Pfeifer Dietmar , Fernández-Klett Francisco , Doostkam Soroush , Galanakis Dennis K. , Taylor Verdon , Akassoglou Katerina , Schachtrup Christian 
Published: January 2020

AbstractNeural stem/progenitor cells (NSPCs) originating from the subventricular zone (SVZ) contribute to brain repair during CNS disease. The microenvironment within the SVZ stem cell niche controls NSPC fate. However, extracellular factors within the niche that trigger astrogliogenesis over neurogenesis during CNS disease are unclear. Here, we show that blood-derived fibrinogen is enriched in the SVZ niche following distant cortical brain injury in mice. Fibrinogen inhibited neuronal differentiation in SVZ and hippocampal NSPCs while promoting astrogenesis via activation of the BMP receptor signaling pathway. Genetic and pharmacologic depletion of fibrinogen reduced astrocyte formation within the SVZ after cortical injury, reducing the contribution of SVZ-derived reactive astrocytes to lesion scar formation. We propose that fibrinogen is a regulator of NSPC-derived astrogenesis from the SVZ niche via BMP receptor signaling pathway following injury.
Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering
Authors: Kunnus Kristjan , Vacher Morgane , Harlang Tobias C. B. , Kjær Kasper S. , Haldrup Kristoffer , Biasin Elisa , van Driel Tim B. , Pápai Mátyás , Chabera Pavel , Liu Yizhu , Tatsuno Hideyuki , Timm Cornelia , Källman Erik , Delcey Mickaël , Hartsock Robert W. , Reinhard Marco E. , Koroidov Sergey , Laursen Mads G. , Hansen Frederik B. , Vester Peter , Christensen Morten , Sandberg Lise , Németh Zoltán , Szemes Dorottya Sárosiné , Bajnóczi Éva , Alonso-Mori Roberto , Glownia James M. , Nelson Silke , Sikorski Marcin , Sokaras Dimosthenis , Lemke Henrik T. , Canton Sophie E. , Møller Klaus B. , Nielsen Martin M. , Vankó György , Wärnmark Kenneth , Sundström Villy , Persson Petter , Lundberg Marcus , Uhlig Jens , Gaffney Kelly J. 
Published: January 2020

AbstractThe non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip)2]2+ photosensitizer, where bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kα and Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278 fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered (3MC) excited state surface. This 3MC state is populated with a 110 fs time constant by 40% of the excited molecules while the rest relax to a 3MLCT excited state. The sensitivity of the Kα XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1 s and 2p core-ionized states surfaces.
High-harmonic generation from spin-polarised defects in solids
Authors: Mrudul M. S. , Tancogne-Dejean Nicolas , Rubio Angel , Dixit Gopal 
Published: January 2020

AbstractThe generation of high-order harmonics in gases enabled to probe the attosecond electron dynamics in atoms and molecules with unprecedented resolution. Extending these techniques to solids, which were originally developed for atomic and molecular gases, requires a fundamental understanding of the physics that has been partially addressed theoretically. Here, we employ time-dependent density-functional theory to investigate how the electron dynamics resulting in high-harmonic emission in monolayer hexagonal boron nitride is affected by the presence of vacancies. We show how these realistic spin-polarised defects modify the harmonic emission and demonstrate that important differences exist between harmonics from a pristine solid and a defected solid. In particular, we found that the different spin channels are affected differently by the presence of the spin-polarised point defect. Moreover, the localisation of the wavefunction, the geometry of the defect, and the electron–electron interaction are all crucial ingredients to describe high-harmonic generation in defected solids.
Evidence for an ancient BRCA1 pathogenic variant in inherited breast cancer patients from Senegal
Authors: Ndiaye Rokhaya , Diop Jean Pascal Demba , Bourdon-Huguenin Violaine , Dem Ahmadou , Diouf Doudou , Dieng Mamadou Moustapha , Diop Pape Saloum , Kane Gueye Serigne Modou , Ba Seydi Abdoul , Dia Yacouba , Ka Sidy , Mbengue Babacar , Thiam Alassane , Sylla Niang Maguette , Gueye Papa Madieye , Faye Oumar , Lopez Sall Philomene , Cisse Aynina , Diop Papa Amadou , Sobol Hagay , Dieye Alioune 
Published: January 2020

AbstractBRCA1 and BRCA2 are the most incriminated genes in inherited breast/ovarian cancers. Several pathogenic variants of these genes conferring genetic predisposition have been described in different populations but rarely in sub-Saharan Africa. The objectives of this study were to identify pathogenic variants of the BRCA genes involved in hereditary breast cancer in Senegal and to search for a founder effect. We recruited after free informed consent, 27 unrelated index cases diagnosed with breast cancer and each having a family history. Mutation screening of the genes identified a duplication of ten nucleotides c.815_824dupAGCCATGTGG, (p.Thr276Alafs) (NM_007294.3) located in exon 11 of BRCA1 gene, in 15 index cases (allelic frequency 27.7%). The pathogenic variant has been previously reported in African Americans as a founder mutation of West African origin. Haplotypes analysis of seven microsatellites surrounding the BRCA1 gene highlights a shared haplotype encompassing ~400 kb between D17S855 and D17S1325. This haplotype was not detected in none of 15 healthy controls. Estimation of the age of the pathogenic variant suggested that it occurred ~1400 years ago. Our study identified a founder pathogenic variant of BRCA1 predisposing to breast cancer and enabled the establishment of an affordable genetic test as a mean of prevention for Senegalese women at risk.
Quantum teleportation using highly coherent emission from telecom C-band quantum dots
Authors: Anderson M. , Müller T. , Huwer J. , Skiba-Szymanska J. , Krysa A. B. , Stevenson R. M. , Heffernan J. , Ritchie D. A. , Shields A. J. 
Published: January 2020

AbstractA practical way to link separate nodes in quantum networks is to send photons over the standard telecom fibre network. This requires sub-Poissonian photon sources in the wavelength band around 1550 nm, with photon coherence times sufficient to enable the many interference-based technologies at the heart of quantum networks. Here, we show that droplet epitaxy InAs/InP quantum dots emitting in the telecom C-band can provide photons with coherence times exceeding 1 ns under low power non-resonant excitation, and demonstrate that these coherence times enable near-optimal interference with a C-band polarisation-encoded laser qubit, with visibilities only limited by the quantum dot multiphoton emission. Using entangled photons, we further show teleportation of such qubits in six different bases with average postselected fidelity reaching 88.3 ± 4.0%. Beyond direct applications in long-distance quantum communication, the high degree of coherence in these quantum dots is promising for future spin-based telecom quantum network applications.
Role of Adhesion Stress in Controlling Transition between Plastic, Grinding and Breakaway Regimes of Adhesive Wear
Authors: Dimaki Andrey V. , Shilko Evgeny V. , Dudkin Ivan V. , Psakhie Sergey G. , Popov Valentin L. 
Published: January 2020

AbstractA discrete-element based model of elastic-plastic materials with non-ideal plasticity and with an account of both cohesive and adhesive interactions inside the material is developed and verified. Based on this model, a detailed study of factors controlling the modes of adhesive wear is performed. Depending on the material and loading parameters, we observed three main modes of wear: slipping, plastic grinding, cleavage, and breakaway. We find that occurrence of a particular mode is determined by the combination of two dimensionless material parameters: (1) the ratio of the adhesive stress to the pure shear strength of the material, and (2) sensitivity parameter of material shear strength to local pressure. The case study map of asperity wear modes in the space of these parameters has been constructed. Results of this study further develop the findings of the widely discussed studies by the groups of J.-F. Molinari and L. Pastewka.
Early pregnancy ultrasound measurements and prediction of first trimester pregnancy loss: A logistic model
Authors: Detti Laura , Francillon Ludwig , Christiansen Mary E. , Peregrin-Alvarez Irene , Goedecke Patricia J. , Bursac Zoran , Roman Robert A. 
Published: January 2020

AbstractOur objective was to prospectively validate the use of gestational sac (GS), yolk sac (YS) diameter, crown-rump length (CRL), and embryonal heart rate (HR) dimensions to identify early pregnancy loss. This was a prospective cohort study of first trimester pregnancies. GS and YS diameter, CRL, and HR measurements were serially obtained in singleton and twin pregnancies from 6 through 10 weeks’ gestation. Non-parametric tests and logistic regression models were used for comparisons of distributions and testing of associations. A total of 252 patients were included, of which 199 were singleton pregnancies, 51 were twins, and 2 were triplets (304 total fetuses). Fifty-two patients had 61 losses. We built nomograms with the changes of the parameters evaluated in ongoing, as well as in pregnancy loss. In the pregnancies which failed, all the parameters showed significant changes, with different temporal onsets: GS and YS were the first to become abnormal, deviating from normality as early as 6 weeks’ gestation (OR 0.01, 95% CI 0.0–0.09, and OR 3.36, 95% CI 1.53–7.34, respectively), followed by changes in HR, and CRL, which became evident at 7 and 8 weeks (OR 0.96, 95% CI 0.92–1.0, and OR 0.59, 95% CI 0.48–0.73, respectively). Our observations showed that, after 5 complete weeks’ gestation, a small GS and a large YS reliably predicted pregnancy loss. The YS reliably identified the occurrence of a miscarriage at least 7 days prior its occurrence. CRL and HR became abnormal at a later time in pregnancy and closer to the event. These findings have important implications for patient counseling and care planning, as well as a potential bearing on cost effectiveness within early pregnancy care.
A bispecific IgG format containing four independent antigen binding sites
Authors: Ljungars Anne , Schiött Torbjörn , Mattson Ulrika , Steppa Jessica , Hambe Björn , Semmrich Monika , Ohlin Mats , Tornberg Ulla-Carin , Mattsson Mikael 
Published: January 2020

AbstractBispecific antibodies come in many different formats, including the particularly interesting two-in-one antibodies, where one conventional IgG binds two different antigens. The IgG format allows these antibodies to mediate Fc-related functionality, and their wild-type structure ensures low immunogenicity and enables standard methods to be used for development. It is however difficult, time-consuming and costly to generate two-in-one antibodies. Herein we demonstrate a new approach to create a similar type of antibody by combining two different variable heavy (VH) domains in each Fab arm of an IgG, a tetra-VH IgG format. The VHs are used as building blocks, where one VH is placed at its usual position, and the second VH replaces the variable light (VL) domain in a conventional IgG. VH domains, binding several different types of antigens, were discovered and could be rearranged in any combination, offering a convenient “plug and play” format. The tetra-VH IgGs were found to be functionally tetravalent, binding two antigens on each arm of the IgG molecule simultaneously. This offers a new strategy to also create monospecific, tetravalent IgGs that, depending on antigen architecture and mode-of-action, may have enhanced efficacy compared to traditional bivalent antibodies.
Retinitis Pigmentosa Due to Rp1 Biallelic Variants
Authors: Silva Rita Sousa , Salles Mariana Vallim , Motta Fabiana Louise , Sallum Juliana Maria Ferraz 
Published: January 2020

AbstractIn the present study, we screened 529 Brazilian individuals affected by inherited retinal disorders. A total of seven unrelated and nonsyndromic patients with RP1 biallelic variants (OMIM # 180100) were diagnosed in our centre and included in the study. They had classic retinitis pigmentosa with diagnosis at the first decade of life. The visual acuities were severely affected at a young age. The fundus aspects were similar among all patients. An atrophic ring was present around the fovea in several cases. All patients had molecular diagnosis, with six different RP1 variants. This study reports two new pathogenic variants - two frameshift duplications (c.1234dupA p.Met412Asnfs*7 and c.1265dupC p.Ala423Cysfs*2) and reinforces other four known pathogenic variants – two frameshift deletions (c.469delG p.Val157Trpfs*16 and c.3843delT p.Pro1282Leufs*12) and two stop gain mutations (c.1186 C > T p.Arg396* and c.1625C > G p.Ser542*). These findings broaden the spectrum of RP1 variants. This study also reviewed the fundus characteristics that clinically could raise the hypothesis of a retinitis pigmentosa due to RP1 gene. It is worthwhile to try to identify the disease-causing variants in each patient since it can provide prognostic information and be useful in genetic consultation and diagnosis in the future.
Isolation and characterization of nutrient dependent pyocyanin from Pseudomonas aeruginosa and its dye and agrochemical properties
Authors: DeBritto Savitha , Gajbar Tanzeembanu D. , Satapute Praveen , Sundaram Lalitha , Lakshmikantha Ramachandra Yarappa , Jogaiah Sudisha , Ito Shin-ichi 
Published: January 2020

AbstractPyocyanin is a blue green phenazine pigment produced in large quantities by active cultures of Pseudomonas aeruginosa, with advantageous applications in medicine, agriculture and for the environment. Hence, in the present study, a potent bacterium was isolated from agricultural soil and was identified morphologically and by 16S rRNA sequencing as P. aeruginosa (isolate KU_BIO2). When the influence of nutrient supplements in both King’s A and Nutrient media as amended was investigated, an enhanced pyocyanin production of 2.56 µg ml−1 was achieved in King’s A medium amended with soya bean followed by 1.702 µg ml−1 of pyocyanin from the nutrient medium amended with sweet potato. Purified pyocyanin was characterized by UV-Vis Spectrophotometer and Fourier-Transform Infrared spectroscopy (FTIR). Furthermore, Liquid Chromatography Mass Spectrum (LCMS) and Nuclear Magnetic Resonance (NMR) confirmed its mass value at 211 and as N-CH3 protons resonating at 3.363 ppm as a singlet respectively. The isolated pyocyanin displayed remarkable dye property by inducing color change in cotton cloth from white to pink. Lastly, the antifungal activity of test pyocyanin showed inhibition of growth of rice blast fungus, Magnaporthe grisea and bacterial blight of rice, Xanthomonas oryzae at concentrations of 150 and 200 ppm, respectively. Thus, this investigation provides evidence for diverse actions of pyocyanin which are nutrient dependent and are capable of acting on a large scale, by utilizing microbes existing in agriculture wastes, and thus could be used as an alternative source in the making of natural textile dyes with strong durability and a broad spectrum of ecofriendly agrochemicals.
Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta
Authors: Guan Yiming , Chen Meili , Ma Yingying , Du Zhenglin , Yuan Na , Li Yu , Xiao Jingfa , Zhang Yayu 
Published: January 2020

AbstractIlyonectria robusta causes rusty root rot, the most devastating chronic disease of ginseng. Here, we for the first time report the high-quality genome of the I. robusta strain CD-56. Time-course (36 h, 72 h, and 144 h) dual RNA-Seq analysis of the infection process was performed, and many genes, including candidate effectors, were found to be associated with the progression and success of infection. The gene expression profile of CD-56 showed a trend of initial inhibition and then gradually returned to a profile similar to that of the control. Analyses of the gene expression patterns and functions of pathogenicity-related genes, especially candidate effector genes, indicated that the stress response changed to an adaptive response during the infection process. For ginseng, gene expression patterns were highly related to physiological conditions. Specifically, the results showed that ginseng defenses were activated by CD-56 infection and persisted for at least 144 h thereafter but that the mechanisms invoked were not effective in preventing CD-56 growth. Moreover, CD-56 did not appear to fully suppress plant defenses, even in late stages after infection. Our results provide new insight into the chronic pathogenesis of CD-56 and the comprehensive and complex inducible defense responses of ginseng root to I. robusta infection.
The origin and current situation of Fusarium oxysporum f. sp. cubense tropical race 4 in Israel and the Middle East
Authors: Maymon Marcel , Sela Noa , Shpatz Uri , Galpaz Navot , Freeman Stanley 
Published: January 2020

AbstractFusarium oxysporum f.sp. cubense (Foc) is considered one of the most devastating soilborne fungal pathogens of banana worldwide. Foc causing mortality to Cavendish group bananas, and belonging to the unique vegetative compatibility group (VCG) 01213/16 has been termed tropical race 4 (TR4) and has currently been renamed F. odoratissimum. The pathogen that was first detected approximately 50 years ago in South East Asia, has since spread to countries within the greater Mekong subregion and to Australia. Recently, the pathogen disseminated to India, Pakistan, Oman and Mozambique (Africa) and was identified in the South American continent in Colombia in 2019. In the Middle East, TR4 was first reported from Jordan and Lebanon, and later from Israel in 2016. In Israel, the pathogen was identified as TR4 by VCG tests, pathogenicity assays and molecular verification. The complete genomes of five representative TR4 isolates including two from Israel, one from Jordan, one from the Philippines, and one from Indonesia were sequenced, and single nucleotide polymorphisms (SNPs) analyses were conducted. SNPs were compared to 11 additional sequenced TR4 isolates, to determine the origin of the Israeli isolates. SNP detection and phylogeographical analyses determined that the Middle Eastern isolates are closely related, indicating that the pathogen most likely spread to Israel from Jordan, while those from Colombia are related to a representative isolate from Indonesia.