bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deterministic all-optical magnetization writing facilitated by non-local transfer of spin angular momentum
Authors: van Hees Youri L. W. , van de Meugheuvel Paul , Koopmans Bert , Lavrijsen Reinoud 
Published: July 2020

AbstractEver since its discovery around a decade ago, all-optical magnetization switching (AOS) using femtosecond laser pulses has shown potential for future data storage and logic devices. In particular, single pulse helicity independent AOS in certain ferrimagnetic alloys and multilayers is highly efficient and ultrafast. However, in most cases it is a toggle mechanism, which is not desirable for applications. Here we experimentally demonstrate conversion from toggle switching to a deterministic mechanism by biasing AOS in a Co/Gd bilayer with a spin polarized current which is optically generated in an adjacent ferromagnetic reference layer. We show deterministic writing of an ‘up’ and ‘down’ state using a sequence of one or two pulses, respectively, and demonstrate the non-local origin by varying the magnitude of the generated spin current. Our demonstration of deterministic magnetization writing could provide an essential step towards the implementation of future optically addressable spintronic memory devices.
Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation
Authors: Koripella Ravi Kiran , Sharma Manjuli R. , Bhargava Kalpana , Datta Partha P. , Kaushal Prem S. , Keshavan Pooja , Spremulli Linda L. , Banavali Nilesh K. , Agrawal Rajendra K. 
Published: July 2020

AbstractThe mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68–3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1mt) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1mt in mitochondrial tRNA (tRNAmt) translocation. In particular, the mito-specific C-terminal extension in EF-G1mt is directly involved in translocation of the acceptor arm of the A-site tRNAmt. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane.
Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases
Authors: Uzun Maria , Alekseeva Lolita , Krutkina Maria , Koziaeva Veronika , Grouzdev Denis 
Published: July 2020

AbstractMagnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.
Dynamics of entangled networks of the quantum Internet
Authors: Gyongyosi Laszlo 
Published: July 2020

AbstractEntangled quantum networks are a fundamental of any global-scale quantum Internet. Here, a mathematical model is developed to quantify the dynamics of entangled network structures and entanglement flow in the quantum Internet. The analytical solutions of the model determine the equilibrium states of the entangled quantum networks and characterize the stability, fluctuation attributes, and dynamics of entanglement flow in entangled network structures. We demonstrate the results of the model through various entangled structures and quantify the dynamics.
Can increasing years of schooling reduce type 2 diabetes (T2D)?: Evidence from a Mendelian randomization of T2D and 10 of its risk factors
Authors: Adams Charleen D. , Boutwell Brian B. 
Published: July 2020

AbstractA focus in recent decades has involved examining the potential causal impact of educational attainment (schooling years) on a variety of disease and life-expectancy outcomes. Numerous studies have broadly revealed a link suggesting that as years of formal schooling increase so too does health and wellbeing; however, it is unclear whether the associations are causal. Here we use Mendelian randomization, an instrumental variables technique, with a two-sample design, to probe whether more years of schooling are causally linked to type 2 diabetes (T2D) and 10 of its attendant risk factors. The results revealed a protective effect of more schooling years against T2D (odds ratio = 0.39; 95% confidence interval: 0.26, 0.58; P = 3.89 × 10–06), which in turn might be partly mediated by more years of schooling being protective against the following: having a father with T2D, being overweight, having higher blood pressure and higher levels of circulating triglycerides, and having lower levels of HDL cholesterol. More schooling years had no effect on risk for gestational diabetes or polycystic ovarian syndrome and was associated with a decreased likelihood of moderate physical activity. These findings imply that strategies to retain adults in higher education may help reduce the risk for a major source of metabolic morbidity and mortality.
Cleavage of proteoglycans, plasma proteins and the platelet-derived growth factor receptor in the hemorrhagic process induced by snake venom metalloproteinases
Authors: Asega Amanda F. , Menezes Milene C. , Trevisan-Silva Dilza , Cajado-Carvalho Daniela , Bertholim Luciana , Oliveira Ana K. , Zelanis André , Serrano Solange M. T. 
Published: July 2020

AbstractEnvenoming by viperid snakes results in a complex pattern of tissue damage, including hemorrhage, which in severe cases may lead to permanent sequelae. Snake venom metalloproteinases (SVMPs) are main players in this pathogenesis, acting synergistically upon different mammalian proteomes. Hemorrhagic Factor 3 (HF3), a P-III class SVMP from Bothrops jararaca, induces severe local hemorrhage at pmol doses in a murine model. Our hypothesis is that in a complex scenario of tissue damage, HF3 triggers proteolytic cascades by acting on a partially known substrate repertoire. Here, we focused on the hypothesis that different proteoglycans, plasma proteins, and the platelet derived growth factor receptor (PDGFR) could be involved in the HF3-induced hemorrhagic process. In surface plasmon resonance assays, various proteoglycans were demonstrated to interact with HF3, and their incubation with HF3 showed degradation or limited proteolysis. Likewise, Western blot analysis showed in vivo degradation of biglycan, decorin, glypican, lumican and syndecan in the HF3-induced hemorrhagic process. Moreover, antithrombin III, complement components C3 and C4, factor II and plasminogen were cleaved in vitro by HF3. Notably, HF3 cleaved PDGFR (alpha and beta) and PDGF in vitro, while both receptor forms were detected as cleaved in vivo in the hemorrhagic process induced by HF3. These findings outline the multifactorial character of SVMP-induced tissue damage, including the transient activation of tissue proteinases, and underscore for the first time that endothelial glycocalyx proteoglycans and PDGFR are targets of SVMPs in the disruption of microvasculature integrity and generation of hemorrhage.
An efficient coral survey method based on a large-scale 3-D structure model obtained by Speedy Sea Scanner and U-Net segmentation
Authors: Mizuno Katsunori , Terayama Kei , Hagino Seiichiro , Tabeta Shigeru , Sakamoto Shingo , Ogawa Toshihiro , Sugimoto Kenichi , Fukami Hironobu 
Published: July 2020

AbstractOver the last 3 decades, a large portion of coral cover has been lost around the globe. This significant decline necessitates a rapid assessment of coral reef health to enable more effective management. In this paper, we propose an efficient method for coral cover estimation and demonstrate its viability. A large-scale 3-D structure model, with resolutions in the x, y and z planes of 0.01 m, was successfully generated by means of a towed optical camera array system (Speedy Sea Scanner). The survey efficiency attained was 12,146 m2/h. In addition, we propose a segmentation method utilizing U-Net architecture and estimate coral coverage using a large-scale 2-D image. The U-Net-based segmentation method has shown higher accuracy than pixelwise CNN modeling. Moreover, the computational cost of a U-Net-based method is much lower than that of a pixelwise CNN-based one. We believe that an array of these survey tools can contribute to the rapid assessment of coral reefs.
A systematic approach to alkaline-surfactant-foam flooding of heavy oil: microfluidic assessment with a novel phase-behavior viscosity map
Authors: Vavra Eric , Puerto Maura , Biswal Sibani L. , Hirasaki George J. 
Published: July 2020

AbstractThe apparent viscosity of viscous heavy oil emulsions in water can be less than that of the bulk oil. Microfluidic flooding experiments were conducted to evaluate how alkali-surfactant-foam enhanced oil recovery (ASF EOR) of heavy oil is affected by emulsion formation. A novel phase-behavior viscosity map—a plot of added salinity vs. soap fraction combining phase behavior and bulk apparent viscosity information—is proposed as a rapid and convenient method for identifying suitable injection compositions. The characteristic soap fraction, $${X}_{soap}^{Sor}$$XsoapSor, is shown to be an effective benchmark for relating information from the phase-viscosity map to expected ASF flood test performance in micromodels. Characteristically more hydrophilic cases were found to be favorable for recovering oil, despite greater interfacial tensions, due to wettability alteration towards water-wet conditions and the formation of low apparent-viscosity oil-in-water (O/W) macroemulsions. Wettability alteration and bubble-oil pinch-off were identified as contributing mechanisms to the formation of these macroemulsions. Conversely, characteristically less hydrophilic cases were accompanied by a large increase in apparent viscosity due to the formation of water-in-oil (W/O) macroemulsions.
Effects of combining exercise with long-chain polyunsaturated fatty acid supplementation on cognitive function in the elderly: a randomised controlled trial
Authors: Tokuda Hisanori , Ito Mika , Sueyasu Toshiaki , Sasaki Hideyuki , Morita Satoshi , Kaneda Yoshihisa , Rogi Tomohiro , Kondo Sumio , Kouzaki Motoki , Tsukiura Takashi , Shibata Hiroshi 
Published: July 2020

AbstractMultifactorial lifestyle intervention is known to be more effective for ameliorating cognitive decline than single factor intervention; however, the effects of combining exercise with long-chain polyunsaturated fatty acids (LCPUFA) on the elderlies' cognitive function remain unclear. We conducted a randomised, single-masked placebo-controlled trial in non-demented elderly Japanese individuals. Participants were randomly allocated to the exercise with LCPUFA, placebo, or no exercise with placebo (control) groups. Participants in the exercise groups performed 150 min of exercise per week, comprised resistance and aerobic training, for 24 weeks with supplements of either LCPUFA (docosahexaenoic acid, 300 mg/day; eicosapentaenoic acid, 100 mg/day; arachidonic acid, 120 mg/day) or placebo. Cognitive functions were evaluated by neuropsychological tests prior to and following the intervention. The per-protocol set analysis (n = 76) revealed no significant differences between the exercise and the control groups in changes of neuropsychological tests. Subgroup analysis for participants with low skeletal muscle mass index (SMI) corresponding to sarcopenia cut-off value showed changes in selective attention, while working memory in the exercise with LCPUFA group was better than in the control group. These findings suggest that exercise with LCPUFA supplementation potentially improves attention and working memory in the elderly with low SMI.
Fractionation of carbon and hydrogen isotopes of TSR-altered gas products under closed system pyrolysis
Authors: Liu Quanyou , Peng Weilong , Meng Qingqiang , Zhu Dongya , Jin Zhijun , Wu Xiaoqi 
Published: July 2020

AbstractThermochemical sulfate reduction (TSR) is common in marine carbonate gas reservoirs, leading to complicated isotope characteristics of TSR-altered gas. This study aims to better understand how TSR affects the geochemical and isotopic compositions of alkanes in pyrolysis products. Pyrolysis of TSR were conducted with crude oil, nonane (C9) and methylnaphthalene (MN) in the presence of MgSO4 solution at temperatures of 350 °C, 360 °C, and 370 °C for different durations of 4–219 h in a closed system. Results show that carbon and hydrogen isotope compositions of alkane gas resulting from TSR (pyrolysis with crude oil and MgSO4) became heavier with increasing carbon number, i.e., δ13C1 < δ13C2 < δ13C3 and δ2H–C1 < δ2H–C2 < δ2H–C3. Compared with the δ13C1, δ13C2 and δ13C3 increased in a much wider range as heating continued. Carbon and hydrogen isotopes of alkane gas produced by TSR became heavier with increasing gas souring index. Values for δ13C1–δ13C2 and δ2H–C1– δ2H–C2 typically decreased as oil and C9 underwent thermal cracking. Comparative experiments using C9 in the presence of MgSO4 produced partially reversed carbon isotope series (δ13C1 > δ13C2), which, for the first time, confirmed the ability of TSR to cause isotopic reversal from pyrolysis. The residual heavy alkanes gradually became 13C-enriched during TSR, which increased δ13C2 values and changed the partially reversed isotope sequence to a positive sequence (δ13C1 < δ13C2). The discovery of a partial reversal of the carbon isotope series of alkane gases through pyrolysis will further deepen the understanding of TSR-altered natural gas.
Crystal structure of the Rab33B/Atg16L1 effector complex
Authors: Metje-Sprink Janina , Groffmann Johannes , Neumann Piotr , Barg-Kues Brigitte , Ficner Ralf , Kühnel Karin , Schalk Amanda M. , Binotti Beyenech 
Published: July 2020

AbstractThe Atg12-Atg5/Atg16L1 complex is recruited by WIPI2b to the site of autophagosome formation. Atg16L1 is an effector of the Golgi resident GTPase Rab33B. Here we identified a minimal stable complex of murine Rab33B(30–202) Q92L and Atg16L1(153–210). Atg16L1(153–210) comprises the C-terminal part of the Atg16L1 coiled-coil domain. We have determined the crystal structure of the Rab33B Q92L/Atg16L1(153–210) effector complex at 3.47 Å resolution. This structure reveals that two Rab33B molecules bind to the diverging α-helices of the dimeric Atg16L1 coiled-coil domain. We mutated Atg16L1 and Rab33B interface residues and found that they disrupt complex formation in pull-down assays and cellular co-localization studies. The Rab33B binding site of Atg16L1 comprises 20 residues and immediately precedes the WIPI2b binding site. Rab33B mutations that abolish Atg16L binding also abrogate Rab33B association with the Golgi stacks. Atg16L1 mutants that are defective in Rab33B binding still co-localize with WIPI2b in vivo. The close proximity of the Rab33B and WIPI2b binding sites might facilitate the recruitment of Rab33B containing vesicles to provide a source of lipids during autophagosome biogenesis.
Development of novel hybridized models for urban flood susceptibility mapping
Authors: Rahmati Omid , Darabi Hamid , Panahi Mahdi , Kalantari Zahra , Naghibi Seyed Amir , Ferreira Carla Sofia Santos , Kornejady Aiding , Karimidastenaei Zahra , Mohammadi Farnoush , Stefanidis Stefanos , Tien Bui Dieu , Haghighi Ali Torabi 
Published: July 2020

AbstractFloods in urban environments often result in loss of life and destruction of property, with many negative socio-economic effects. However, the application of most flood prediction models still remains challenging due to data scarcity. This creates a need to develop novel hybridized models based on historical urban flood events, using, e.g., metaheuristic optimization algorithms and wavelet analysis. The hybridized models examined in this study (Wavelet-SVR-Bat and Wavelet-SVR-GWO), designed as intelligent systems, consist of a support vector regression (SVR), integrated with a combination of wavelet transform and metaheuristic optimization algorithms, including the grey wolf optimizer (GWO), and the bat optimizer (Bat). The efficiency of the novel hybridized and standalone SVR models for spatial modeling of urban flood inundation was evaluated using different cutoff-dependent and cutoff-independent evaluation criteria, including area under the receiver operating characteristic curve (AUC), Accuracy (A), Matthews Correlation Coefficient (MCC), Misclassification Rate (MR), and F-score. The results demonstrated that both hybridized models had very high performance (Wavelet-SVR-GWO: AUC = 0.981, A = 0.92, MCC = 0.86, MR = 0.07; Wavelet-SVR-Bat: AUC = 0.972, A = 0.88, MCC = 0.76, MR = 0.11) compared with the standalone SVR (AUC = 0.917, A = 0.85, MCC = 0.7, MR = 0.15). Therefore, these hybridized models are a promising, cost-effective method for spatial modeling of urban flood susceptibility and for providing in-depth insights to guide flood preparedness and emergency response services.
Quantum state holography to reconstruct the molecular wave packet using an attosecond XUV–XUV pump-probe technique
Authors: González-Castrillo Alberto , Martín Fernando , Palacios Alicia 
Published: July 2020

AbstractAn attosecond molecular interferometer is proposed by using a XUV–XUV pump-probe scheme. The interferograms resulting in the photoelectron distributions enable the full reconstruction of the molecular wave packet associated to excited states using a quantum state holographic approach that, to our knowledge, has only been proposed for simple atomic targets combining attosecond XUV pulses with IR light. In contrast with existing works, we investigate schemes where one- and two-photon absorption paths contribute to ionize the hydrogen molecule and show that it is possible to retrieve the excitation dynamics even when imprinted in a minority channel. Furthermore, we provide a systematic analysis of the time-frequency maps that reveal the distinct, but tightly coupled, motion of electrons and nuclei.
Single berry reconstitution prior to RNA-sequencing reveals novel insights into transcriptomic remodeling by leafroll virus infections in grapevines
Authors: Ghaffari Sana , Reynard Jean Sébastien , Rienth Markus 
Published: July 2020

AbstractLeafroll viruses are among the most devastating pathogens in viticulture and are responsible for major economic losses in the wine industry. However, the molecular interactions underlying the effects on fruit quality deterioration are not well understood. The few molecular studies conducted on berries from infected vines, associated quality decreases with the repression of key genes in sugar transport and anthocyanin biosynthesis. Sampling protocols in these studies did however not account for berry heterogeneity and potential virus induced phenological shifts, which could have biased the molecular information. In the present study, we adopted an innovative individual berry sampling protocol to produce homogeneous batches for RNA extraction, thereby circumventing berry heterogeneity and compensating for virus induced phenological shifts. This way a characterization of the transcriptomic modulation by viral infections was possible and explain why our results differ significantly from previously reported repression of anthocyanin biosynthesis and sugar metabolism. The present study provides new insights into the berry transcriptome modulation by leafroll infection, highlighting the virus induced upregulation of plant innate immunity as well as an increased responsiveness of the early ripening berry to biotic stressors. The study furthermore emphasizes the importance of sampling protocols in physiological studies on grapevine berry metabolism.
Expression profiling of human milk derived exosomal microRNAs and their targets in HIV-1 infected mothers
Authors: Zahoor Muhammad Atif , Yao Xiao-Dan , Henrick Bethany M. , Verschoor Chris P. , Abimiku Alash’le , Osawe Sophia , Rosenthal Kenneth L. 
Published: July 2020

AbstractDespite the use of antiretroviral therapy (ART) in HIV-1 infected mothers approximately 5% of new HIV-1 infections still occur in breastfed infants annually, which warrants for the development of novel strategies to prevent new HIV-1 infections in infants. Human milk (HM) exosomes are highly enriched in microRNAs (miRNAs), which play an important role in neonatal immunity. Furthermore, HM exosomes from healthy donors are known to inhibit HIV-1 infection and transmission; however, the effect of HIV-1 on HM exosomal miRNA signatures remains unknown. In this study, we used nCounter NanoString technology and investigated miRNAs expression profiles in first week postpartum HM exosomes from HIV-1 infected and uninfected control mothers (n = 36). Our results indicated that HIV-1 perturbed the differential expression patterns of 19 miRNAs (13 upregulated and 6 downregulated) in HIV-1 infected women compared to healthy controls. DIANA-miR functional pathway analyses revealed that multiple biological pathways are involved including cell cycle, pathways in cancer, TGF-β signaling, FoxO signaling, fatty acid biosynthesis, p53 signaling and apoptosis. Moreover, the receiver operating characteristics (ROC) curve analyses of miR-630 and miR-378g yielded areas under the ROC curves of 0.82 (95% CI 0.67 to 0.82) and 0.83 (95% CI 0.67 to 0.83), respectively highlighting their potential to serve as biomarkers to identify HIV-1 infection in women. These data may contribute to the development of new therapeutic strategies in prevention of mother-to-child transmission (MTCT) of HIV-1.
Screening of safe soybean cultivars for cadmium contaminated fields
Authors: Zhi Yang , Sun Ting , Zhou Qixing , Leng Xue 
Published: July 2020

AbstractThe selection and breeding of Cd-safe cultivars (CSCs) has been used to minimize the influx of Cd into the human food chain. The pot-culture experiment combined with the field-culture experiment were conducted to screen out CSCs, i.e. the cultivars accumulating Cd at low enough level for safe consumption in their edible parts when grown in contaminated soils, were screened out and explored among the crop cultivars. We used 25 Chinese soybean cultivars in different Cd contaminated soils to assess the performance of this new method. Variations in uptake, enrichment, and translocation of Cd among these cultivars were studied to screen out soybean CSCs. The accumulation of Cd in the five soybean genotypes was lower than 0.20 mg kg−1 under 1.0 mg Cd kg−1 treatment, and the EF and TF were lower than 1.0. The field studies further identified that cultivar Shennong 10, Tiedou 36 and Liaodou 21 fit the criteria for CSCs, which were suitable to be planted in low-Cd (Cd concentration < 1.22 mg kg−1) contaminated soils. The results can provide scientific methods for screening low-Cd accumulation in soybeans and can provide a path for controlling, treating and remedying Cd-contaminated agricultural soils to make grains safe for human consumption.