bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamically-enhanced strain in atomically thin resonators
Authors: Zhang Xin , Makles Kevin , Colombier Léo , Metten Dominik , Majjad Hicham , Verlot Pierre , Berciaud Stéphane 
Published: November 2020

AbstractGraphene and related two-dimensional (2D) materials associate remarkable mechanical, electronic, optical and phononic properties. As such, 2D materials are promising for hybrid systems that couple their elementary excitations (excitons, phonons) to their macroscopic mechanical modes. These built-in systems may yield enhanced strain-mediated coupling compared to bulkier architectures, e.g., comprising a single quantum emitter coupled to a nano-mechanical resonator. Here, using micro-Raman spectroscopy on pristine monolayer graphene drums, we demonstrate that the macroscopic flexural vibrations of graphene induce dynamical optical phonon softening. This softening is an unambiguous fingerprint of dynamically-induced tensile strain that reaches values up to ≈4 × 10−4 under strong non-linear driving. Such non-linearly enhanced strain exceeds the values predicted for harmonic vibrations with the same root mean square (RMS) amplitude by more than one order of magnitude. Our work holds promise for dynamical strain engineering and dynamical strain-mediated control of light-matter interactions in 2D materials and related heterostructures.
Efficient energy transfer mitigates parasitic light absorption in molecular charge-extraction layers for perovskite solar cells
Authors: Eggimann Hannah J. , Patel Jay B. , Johnston Michael B. , Herz Laura M. 
Published: November 2020

AbstractOrganic semiconductors are commonly used as charge-extraction layers in metal-halide perovskite solar cells. However, parasitic light absorption in the sun-facing front molecular layer, through which sun light must propagate before reaching the perovskite layer, may lower the power conversion efficiency of such devices. Here, we show that such losses may be eliminated through efficient excitation energy transfer from a photoexcited polymer layer to the underlying perovskite. Experimentally observed energy transfer between a range of different polymer films and a methylammonium lead iodide perovskite layer was used as basis for modelling the efficacy of the mechanism as a function of layer thickness, photoluminescence quantum efficiency and absorption coefficient of the organic polymer film. Our findings reveal that efficient energy transfer can be achieved for thin (≤10 nm) organic charge-extraction layers exhibiting high photoluminescence quantum efficiency. We further explore how the morphology of such thin polymer layers may be affected by interface formation with the perovskite.
All-optical adaptive control of quantum cascade random lasers
Authors: Schönhuber S. , Bachelard N. , Limbacher B. , Kainz M. A. , Andrews A. M. , Detz H. , Strasser G. , Darmo J. , Rotter S. , Unterrainer K. 
Published: November 2020

AbstractSpectral fingerprints of molecules are mostly accessible in the terahertz (THz) and mid-infrared ranges, such that efficient molecular-detection technologies rely on broadband coherent light sources at such frequencies. If THz Quantum Cascade Lasers can achieve octave-spanning bandwidth, their tunability and wavelength selectivity are often constrained by the geometry of their cavity. Here we introduce an adaptive control scheme for the generation of THz light in Quantum Cascade Random Lasers, whose emission spectra are reshaped by applying an optical field that restructures the permittivity of the active medium. Using a spatial light modulator combined with an optimization procedure, a beam in the near infrared (NIR) is spatially patterned to transform an initially multi-mode THz random laser into a tunable single-mode source. Moreover, we show that local NIR illumination can be used to spatially sense complex near-field interactions amongst modes. Our approach provides access to new degrees of freedom that can be harnessed to create broadly-tunable sources with interesting potential for applications like self-referenced spectroscopy.
Fast mode decomposition in few-mode fibers
Authors: Manuylovich Egor S. , Dvoyrin Vladislav V. , Turitsyn Sergei K. 
Published: November 2020

AbstractRetrieval of the optical phase information from measurement of intensity is of a high interest because this would facilitate simple and cost-efficient techniques and devices. In scientific and industrial applications that exploit multi-mode fibers, a prior knowledge of spatial mode structure of the fiber, in principle, makes it possible to recover phases using measured intensity distribution. However, current mode decomposition algorithms based on the analysis of the intensity distribution at the output of a few-mode fiber, such as optimization methods or neural networks, still have high computational costs and high latency that is a serious impediment for applications, such as telecommunications. Speed of signal processing is one of the key challenges in this approach. We present a high-performance mode decomposition algorithm with a processing time of tens of microseconds. The proposed mathematical algorithm that does not use any machine learning techniques, is several orders of magnitude faster than the state-of-the-art deep-learning-based methods. We anticipate that our results can stimulate further research on algorithms beyond popular machine learning methods and they can lead to the development of low-cost phase retrieval receivers for various applications of few-mode fibers ranging from imaging to telecommunications.
Parallel evolution in the emergence of highly pathogenic avian influenza A viruses
Authors: Escalera-Zamudio Marina , Golden Michael , Gutiérrez Bernardo , Thézé Julien , Keown Jeremy Russell , Carrique Loic , Bowden Thomas A. , Pybus Oliver G. 
Published: November 2020

AbstractParallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs evolve independently from low-pathogenic ancestors via acquisition of polybasic cleavage sites. Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the viral genome. We combine phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein structure. Our resulting mutational panel may help to reveal new links between virulence evolution and other traits, and raises the possibility of predicting aspects of AIV evolution.
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction
Authors: Shi Honglue , Rangadurai Atul , Abou Assi Hala , Roy Rohit , Case David A. , Herschlag Daniel , Yesselman Joseph D. , Al-Hashimi Hashim M. 
Published: November 2020

AbstractBiomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands of conformations far exceeds that of experimental measurements. We addressed this data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformation library. Refinement of this library with NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model accuracy was independently supported by comparisons to quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through designed ensemble redistribution via atomic mutagenesis. Applications to TAR bulge variants and more complex tertiary RNAs support the generality of this approach and the potential to make the determination of atomic-resolution RNA ensembles routine.
Measurement of genetic diseases as a cause of mortality in infants receiving whole genome sequencing
Authors: Kingsmore Stephen F. , Henderson Audrey , Owen Mallory J. , Clark Michelle M. , Hansen Christian , Dimmock David , Chambers Christina D. , Jeliffe-Pawlowski Laura L. , Hobbs Charlotte 
Published: November 2020

AbstractUnderstanding causes of infant mortality shapes public health policy and prioritizes diseases for investments in surveillance, intervention and medical research. Rapid genomic sequencing has created a novel opportunity to decrease infant mortality associated with treatable genetic diseases. Herein, we sought to measure the contribution of genetic diseases to mortality among infants by secondary analysis of babies enrolled in two clinical studies and a systematic literature review. Among 312 infants who had been admitted to an ICU at Rady Children’s Hospital between November 2015 and September 2018 and received rapid genomic sequencing, 30 (10%) died in infancy. Ten (33%) of the infants who died were diagnosed with 11 genetic diseases. The San Diego Study of Outcomes in Mothers and Infants platform identified differences between in-hospital and out-of-hospital causes of infant death. Similarly, in six published studies, 195 (21%) of 918 infant deaths were associated with genetic diseases by genomic sequencing. In 195 infant deaths associated with genetic diseases, locus heterogeneity was 70%. Treatment guidelines existed for 70% of the genetic diseases diagnosed, suggesting that rapid genomic sequencing has substantial potential to decrease infant mortality among infants in ICUs. Further studies are needed in larger, comprehensive, unbiased patient sets to determine the generalizability of these findings.
Using a Bayesian modelling approach (INLA-SPDE) to predict the occurrence of the Spinetail Devil Ray (Mobular mobular)
Authors: Lezama-Ochoa Nerea , Pennino Maria Grazia , Hall Martin A. , Lopez Jon , Murua Hilario 
Published: November 2020

AbstractTo protect the most vulnerable marine species it is essential to have an understanding of their spatiotemporal distributions. In recent decades, Bayesian statistics have been successfully used to quantify uncertainty surrounding identified areas of interest for bycatch species. However, conventional simulation-based approaches are often computationally intensive. To address this issue, in this study, an alternative Bayesian approach (Integrated Nested Laplace Approximation with Stochastic Partial Differential Equation, INLA-SPDE) is used to predict the occurrence of Mobula mobular species in the eastern Pacific Ocean (EPO). Specifically, a Generalized Additive Model is implemented to analyze data from the Inter-American Tropical Tuna Commission’s (IATTC) tropical tuna purse-seine fishery observer bycatch database (2005–2015). The INLA-SPDE approach had the potential to predict both the areas of importance in the EPO, that are already known for this species, and the more marginal hotspots, such as the Gulf of California and the Equatorial area which are not identified using other habitat models. Some drawbacks were identified with the INLA-SPDE database, including the difficulties of dealing with categorical variables and triangulating effectively to analyze spatial data. Despite these challenges, we conclude that INLA approach method is an useful complementary and/or alternative approach to traditional ones when modeling bycatch data to inform accurately management decisions.
Role of a schistosoma haematobium specific microRNA as a predictive and prognostic tool for bilharzial bladder cancer in Egypt
Authors: Gaber Dalia A. , Wassef Rita M. , El-Ayat Wael M. , El-Moazen Mohamed I. , Montasser Karim A. , Swar Sherif A. , Amin Hebat Allah A. 
Published: November 2020

AbstractUrinary bladder cancer is a common malignancy in Egypt, thus reliable methodologies are required for screening and early detection. In this study, we analyzed the gene expression of a Schistosoma hematobium specific microRNA “Sha-miR-71a” and mitogen-associated protein kinase-3 (MAPK-3) in the urine samples of 50 bladder cancer patients and 50 patients with benign bilharzial cystitis. Fifty control subjects were also tested. Indirect hemagglutination test (IHA) diagnosed 70% of studied cancer cases as bilharzial associated bladder cancer (BBC), while histopathological examination detected only 18%. Urinary Sha-miR-71a & MAPK-3 revealed enhanced expression in BBC (p-value = 0.001) compared to non-bilharzial bladder cancer (NBBC) cases. Patients with chronic bilharzial cystitis exhibited a significant increase in gene expression compared to those with acute infection (p-value = 0.001). Sha-miR-71a and MAPK-3 showed good sensitivity and specificity in the diagnosis of BBC when analyzed by the receiver operating characteristic (ROC) curve. They were also prognostic regarding malignancy grade. Both biomarkers showed a positive correlation. Our results revealed that IHA is a reliable test in the diagnosis of bilharziasis associated with bladder cancer, and that Sha-miR-71a and MAPK-3 provide non-invasive specific biomarkers to diagnose BBC, as well as a potential role in testing bilharzial patients for risk to develop cancer.
Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics
Authors: da Silva Alexandre Freitas , Machado Laís Ceschini , de Paula Marcia Bicudo , da Silva Pessoa Vieira Carla Júlia , de Morais Bronzoni Roberta Vieira , de Melo Santos Maria Alice Varjal , Wallau Gabriel Luz 
Published: November 2020

AbstractMosquitoes are insects of medical importance due their role as vectors of different pathogens to humans. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquito species. Here we characterized the mitogenomes of mosquito species through low-coverage whole genome sequencing and data mining. A total of 37 draft mitogenomes of different species were assembled from which 16 are newly-sequenced species. We datamined additional 49 mosquito mitogenomes, and together with our 37 mitogenomes, we reconstructed the evolutionary history of 86 species including representatives from 15 genera and 7 tribes. Our results showed that most of the species clustered in clades with other members of their own genus with exception of Aedes genus which was paraphyletic. We confirmed the monophyletic status of the Mansoniini tribe including both Coquillettidia and Mansonia genus. The Aedeomyiini and Uranotaeniini were consistently recovered as basal to other tribes in the subfamily Culicinae, although the exact relationships among these tribes differed between analyses. These results demonstrate that low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge and hence generate basic fundamental information that will help in the understanding of the role of these species as pathogen vectors.
Potential and efficiency of statistical learning closely intertwined with individuals’ executive functions: a mathematical modeling study
Authors: Park Jungtak , Yoon Hee-Dong , Yoo Taehyun , Shin Minho , Jeon Hyeon-Ae 
Published: November 2020

AbstractStatistical learning (SL) is essential in enabling humans to extract probabilistic regularities from the world. The ability to accomplish ultimate learning performance with training (i.e., the potential of learning) has been known to be dissociated with performance improvement per amount of learning time (i.e., the efficiency of learning). Here, we quantified the potential and efficiency of SL separately through mathematical modeling and scrutinized how they were affected by various executive functions. Our results showed that a high potential of SL was associated with poor inhibition and good visuo-spatial working memory, whereas high efficiency of SL was closely related to good inhibition and good set-shifting. We unveiled the distinct characteristics of SL in relation to potential and efficiency and their interaction with executive functions.
High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)
Authors: Martin Sara L. , Benedict Leshawn , Wei Wei , Sauder Connie A. , Beckie Hugh J. , Hall Linda M. 
Published: November 2020

AbstractKochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = − 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species’ genetic variation or limit the species’ ability to respond to further selection pressure.
Proteomic identification of the proteins related to cigarette smoke-induced cardiac hypertrophy in spontaneously hypertensive rats
Authors: Kitamura Yuki , Mise Nathan , Mori Yurie , Suzuki Yuka , Ohashi Tomoki , Tada-Oikawa Saeko , Tokisu Masaki , Zong Cai , Oikawa Shinji , Ichihara Sahoko 
Published: November 2020

AbstractSmoking increases the risk of cardiovascular diseases. The present study was designed to determine the effects of 2-month exposure to cigarette smoke (CS) on proteins in the left ventricles of spontaneously hypertensive rats (SHR) and to identify the molecular targets associated with the pathogenesis/progression of CS-induced cardiac hypertrophy. SHR and Wistar Kyoto rats (WKY) were exposed to CS at low (2 puffs/min for 40 min) or high dose (2 puffs/min for 120 min), 5 days a week for 2 months. Using the two-dimensional fluorescence difference gel electrophoresis combined with MALDI-TOF/TOF tandem mass spectrometry, we compared differences in the expression levels of proteins in the whole left ventricles induced by long-term smoking. High-dose CS mainly caused cardiac hypertrophy in SHR, but not WKY, but no change in blood pressure. Proteomic analysis identified 30 protein spots with significant alterations, with 14 up-regulated and 16 down-regulated proteins in the left ventricles of CS-exposed SHR, compared with control SHR. Among these proteins, two members of the heat shock proteins (HSP70 and HSP20) showed significant up-regulation in the left ventricles of CS high-dose SHR, and the results were confirmed by western blot analysis. Our findings suggested that HSPs play an important role in regulation of CS-induced cardiac hypertrophy.
Effects of high-fat diet and Apoe deficiency on retinal structure and function in mice
Authors: Cao Xiupeng , Guo Yatu , Wang Yuchuan , Wang Hao , Liu Dong , Gong Yibo , Wang Jue , Chen Xia , Zhang Wei 
Published: November 2020

AbstractTo investigate the effects of a high-fat diet (HFD) and apolipoprotein E (Apoe) deficiency on retinal structure and function in mice. Apoe KO mice and wild-type C57BL/6J mice were given a low-fat diet (LFD) or a HFD for 32 weeks. Blood glucose, serum lipids, body weight and visceral fat weight were evaluated. Retinal sterol quantification was carried out by isotope dilution gas chromatography-mass spectrometry. The cholesterol metabolism related genes SCAP-SREBP expressions were detected by qRT-PCR. Retinal function was recorded using an electroretinogram. The thickness of each layer of the retina was measured by optical coherence tomography. Fundus fluorescein angiography was performed to detect retinal vasculature changes. Immunohistochemical staining was used to determine the expression of NF-κB, TNF-α and VEGFR2 in the retina among HFD, HFD Apoe−/−, LFD Apoe−/− and WT mice retinas. HFD feeding caused the mice to gain weight and develop hypercholesterinemia, while Apoe−/− abnormalities also affected blood lipid metabolism. Both HFD and Apoe deficiency elevated retinal cholesterol, especially in the HFD Apoe−/− mice. No up-regulated expression of SCAP-SREBP was observed as a negative regulator. Impaired retinal functions, thinning retinas and abnormal retinal vasculature were observed in the peripheral retinas of the HFD and Apoe−/− mice compared with those in the normal chow group, particularly in the HFD Apoe−/− mice. Moreover, the expression of NF-κB in the retinas of the HFD and Apoe−/− mice was increased, together with upregulated TNF-α mRNA levels and TNF-α expression in the layer of retinal ganglion cells of the peripheral retina. At the same time, the expression level of VEGFR2 was elevated in the intervention groups, most notably in HFD Apoe−/− mice. HFD or Apoe gene deletion had certain adverse effects on retinal function and structure, which were far below the combined factors and induced harm to the retina. Furthermore, HFD caused retinal ischemia and hypoxia. Additionally, Apoe abnormality increased susceptibility to ischemia. These changes upregulated NF-κB expression in ganglion cells and activated downstream TNF-α. Simultaneously, they activated VEGFR2, accelerating angiogenesis and vascular permeability. All of the aforementioned outcomes initiated inflammatory responses to trigger ganglion cell apoptosis and aggravate retinal neovascularization.