bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ameliorating the stability of erbium-doped fiber laser using saturable absorber fabricated by the pulsed laser deposition technique
Authors: Asghar Haroon , Ahmed Rizwan , Ajmal Rizwan , Umar Zeshan A. , McInerney John. G. , Baig M. Aslam 
Published: November 2022

AbstractIn this paper, we present the performance and stability of an erbium-doped fiber laser (EDFL) based on ZnO saturable-absorber (SA) prepared using two schemes: solution method (SM) and pulsed laser deposition technique (PLDT). It was observed that EDFL with ZnO-SA prepared using SM emits at 1561.25 nm under a pump power of 230 mW. As the pump power is increased from 22.2 mW to 75.3 mW, the pulse duration decreases from 24.91 to 10.69 µs, and the pulse repetition rates increase from 11.59 to 40.91 kHz. Besides at pump power of 75.3 mW, the peak power, pulse energy, and average output power are measured as 0.327 mW, 2.86 nJ, and 0.18 mW, respectively. However, when PLDT-based SA was incorporated into the ring cavity, the emission wavelength is noticed at 1568.21 nm at a pump power of 230 mW. With the increase in pump power from 22.2 mW to 418 mW, the pulse repetition rates increase from 10.79 to 79.37 kHz and the pulse width decreases from 23.58 to 5.6 µs. Furthermore, the peak power, pulse energy, and average output power are observed to be 10.9 mW, 74 nJ, and 5.35 mW, respectively. The stability of EDFL based on SAs prepared using SM and PLDT has also been investigated. To the best of the author's knowledge, it is the first comparison of performance and long-term stability of EDFL based on two experimental techniques SM and PLDT-based SAs. These findings suggest that PLDT-based SAs provides optimum stability over a long period and enhanced the performance of fiber lasers compared to the SAs prepared using the conventional SM technique. This study paves the way for the development of ultra-stable SAs for their potential applications in pulsed laser sources and photonic devices.
Influence of bisphenol A on growth and metabolism of Vicia faba ssp. minor seedlings depending on lighting conditions
Authors: Kaźmierczak Andrzej , Kornaś Andrzej , Mościpan Małgorzata , Łęcka Justyna 
Published: November 2022

AbstractThe effect of one of anthropogenic pollutants, i.e., 4,4′-isopropylidenediphenol, called 2,2-bis (4-hydroxyphenyl) propane (BPA), at 30 and 120 mg L−1 concentrations in the darkness (DK) or dark/light (DK/LT) on growth and selected elements of metabolism of seedlings and leaf discs of Vicia faba ssp. minor was studied. Treatment with 120 mg L−1 BPA had greater effects which were reflected by increase in the number of necrotic changes in roots and stems as well as in leaf discs and reduction of the length of roots DK and DK/LT, and volume of roots in the DK group. However, minimal and no influence on the fresh and dry weight of roots and stems in plants growing under both types of lighting conditions were observed. In both DK and DK/LT groups these effects were correlated with reduced amounts of storage and cell wall-bound sugars as well as of proteins while in the DK/LT additionally with reduced soluble sugar levels in the roots and increased amounts of hydrogen peroxide and phenols in roots and stems as well as in treatment solutions, where these compounds were released. We suggest that endogenous phenols and BPA can be metabolised in roots and stems to quinones. It seems that TB-1,4-BQ, is the one of that of the five studied quinones. We expect that the results of this paper will help to answer the following question: does the phytomeliorative and phytosanitative V. faba ssp. minor plant is enough to be resistant on negative effects, and to be useful to reduce increasing amount of BPA in the environment?
The nuclear factor of activated T cells 5 (NFAT5) contributes to the renal corticomedullary differences in gene expression
Authors: Chernyakov Dmitry , Fischer Annika , Brandau Max , Petrillo Federica , Fenton Robert A. , Edemir Bayram 
Published: November 2022

AbstractThe corticomedullary osmotic gradient between renal cortex and medulla induces a specific spatial gene expression pattern. The factors that controls these differences are not fully addressed. Adaptation to hypertonic environment is mediated by the actions of the nuclear factor of activated T-cells 5 (NFAT5). NFAT5 induces the expression of genes that lead to intracellular accumulation of organic osmolytes. However, a systematical analysis of the NFAT5-dependent gene expression in the kidneys was missing. We used primary cultivated inner medullary collecting duct (IMCD) cells from control and NFAT5 deficient mice as well as renal cortex and inner medulla from principal cell specific NFAT5 deficient mice for gene expression profiling. In primary NFAT5 deficient IMCD cells, hyperosmolality induced changes in gene expression were abolished. The majority of the hyperosmolality induced transcripts in primary IMCD culture were determined to have the greatest expression in the inner medulla. Loss of NFAT5 altered the expression of more than 3000 genes in the renal cortex and more than 5000 genes in the inner medulla. Gene enrichment analysis indicated that loss of NFAT5 is associated with renal inflammation and increased expression of kidney injury marker genes, like lipocalin-2 or kidney injury molecule-1. In conclusion we show that NFAT5 is a master regulator of gene expression in the kidney collecting duct and in vivo loss of NFAT function induces a kidney injury like phenotype.
A continuous-time stochastic Boolean model provides a quantitative description of the budding yeast cell cycle
Authors: Laomettachit Teeraphan , Kraikivski Pavel , Tyson John J. 
Published: November 2022

AbstractThe cell division cycle is regulated by a complex network of interacting genes and proteins. The control system has been modeled in many ways, from qualitative Boolean switching-networks to quantitative differential equations and highly detailed stochastic simulations. Here we develop a continuous-time stochastic model using seven Boolean variables to represent the activities of major regulators of the budding yeast cell cycle plus one continuous variable representing cell growth. The Boolean variables are updated asynchronously by logical rules based on known biochemistry of the cell-cycle control system using Gillespie’s stochastic simulation algorithm. Time and cell size are updated continuously. By simulating a population of yeast cells, we calculate statistical properties of cell cycle progression that can be compared directly to experimental measurements. Perturbations of the normal sequence of events indicate that the cell cycle is 91% robust to random ‘flips’ of the Boolean variables, but 9% of the perturbations induce lethal mistakes in cell cycle progression. This simple, hybrid Boolean model gives a good account of the growth and division of budding yeast cells, suggesting that this modeling approach may be as accurate as detailed reaction-kinetic modeling with considerably less demands on estimating rate constants.
Ancestral social environments plus nonlinear benefits can explain cooperation in human societies
Authors: Kristensen Nadiah P. , Ohtsuki Hisashi , Chisholm Ryan A. 
Published: November 2022

AbstractHuman cooperation (paying a cost to benefit others) is puzzling from a Darwinian perspective, particularly in groups with strangers who cannot repay nor are family members. The beneficial effects of cooperation typically increase nonlinearly with the number of cooperators, e.g., increasing returns when cooperation is low and diminishing returns when cooperation is high. Such nonlinearity can allow cooperation between strangers to persist evolutionarily if a large enough proportion of the population are already cooperators. However, if a lone cooperator faces a conflict between the group’s and its own interests (a social dilemma), that raises the question of how cooperation arose in the first place. We use a mathematically tractable evolutionary model to formalise a chronological narrative that has previously only been investigated verbally: given that ancient humans interacted mostly with family members (genetic homophily), cooperation evolved first by kin selection, and then persisted in situations with nonlinear benefits as homophily declined or even if interactions with strangers became the norm. The model also predicts the coexistence of cooperators and defectors observed in the human population (polymorphism), and may explain why cooperators in behavioural experiments prefer to condition their contribution on the contributions of others (conditional cooperation in public goods games).
Enhanced Arctic moisture transport toward Siberia in autumn revealed by tagged moisture transport model experiment
Authors: Sato Tomonori , Nakamura Tetsu , Iijima Yoshihiro , Hiyama Tetsuya 
Published: November 2022

AbstractRapid Arctic warming has altered the regional hydrological cycle through reduction in Arctic sea ice. Observational and modeling efforts provided evidence that the enhanced evaporation from the Arctic Ocean could increase snowfall over high latitude terrestrial zones. However, questions remain regarding the amount of equatorward moisture transport and its change over the decadal timescale. Here we show that the transport of atmospheric moisture to Siberia that originated from Arctic Ocean evaporation has increased significantly in autumn to early winter during 1981–2019 when substantial sea ice retreat was observed. The enhanced Arctic moisture content is found in western Siberia in September, consistent with the observed increase in snow cover investigated in earlier studies. Meanwhile, the annual maximum daily amount of Arctic moisture shows a sharp increase in eastern Siberia during October–December associated with cyclonic activities along coastal regions. Our results suggest the importance of monitoring equatorward moisture transport during snow accumulation seasons because it could enhance local snowstorms as evaporation from the Arctic Ocean increases in the near future.
Poly ADP-ribosylation of SET8 leads to aberrant H4K20 methylation in mammalian nuclear genome
Authors: Estève Pierre-Olivier , Sen Sagnik , Vishnu Udayakumar S. , Ruse Cristian , Chin Hang Gyeong , Pradhan Sriharsa 
Published: November 2022

AbstractIn mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle-dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised, and degradation via ubiquitylation pathway. Knockdown of PARP1 led to an increase of SET8 protein levels, leading to aberrant H4K20me1 and H4K20me3 domains in the genome. H4K20me1 is associated with higher gene transcription levels while the increase of H4K20me3 levels was predominant in DNA repeat elements. Hence, SET8 mediated chromatin remodeling in mammalian cells are modulated by poly ADP-ribosylation by PARP1.
Offshore wind farms are projected to impact primary production and bottom water deoxygenation in the North Sea
Authors: Daewel Ute , Akhtar Naveed , Christiansen Nils , Schrum Corinna 
Published: November 2022

AbstractThe wind wake effect of offshore wind farms affects the hydrodynamical conditions in the ocean, which has been hypothesized to impact marine primary production. So far only little is known about the ecosystem response to wind wakes under the premisses of large offshore wind farm clusters. Here we show, via numerical modeling, that the associated wind wakes in the North Sea provoke large-scale changes in annual primary production with local changes of up to ±10% not only at the offshore wind farm clusters, but also distributed over a wider region. The model also projects an increase in sediment carbon in deeper areas of the southern North Sea due to reduced current velocities, and decreased dissolved oxygen inside an area with already low oxygen concentration. Our results provide evidence that the ongoing offshore wind farm developments can have a substantial impact on the structuring of coastal marine ecosystems on basin scales.
Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape
Authors: Iwata Michio , Mutsumine Hiroaki , Nakayama Yusuke , Suita Naomasa , Yamanishi Yoshihiro 
Published: November 2022

AbstractGenome-wide identification of single-cell transcriptomic responses of drugs in various human cells is a challenging issue in medical and pharmaceutical research. Here we present a computational method, tensor-based imputation of gene-expression data at the single-cell level (TIGERS), which reveals the drug-induced single-cell transcriptomic landscape. With this algorithm, we predict missing drug-induced single-cell gene-expression data with tensor imputation, and identify trajectories of regulated pathways considering intercellular heterogeneity. Tensor imputation outperformed existing imputation methods for data completion, and provided cell-type-specific transcriptomic responses for unobserved drugs. For example, TIGERS correctly predicted the cell-type-specific expression of maker genes for pancreatic islets. Pathway trajectory analysis of the imputed gene-expression profiles of all combinations of drugs and human cells identified single-cell-specific drug activities and pathway trajectories that reflect drug-induced changes in pathway regulation. The proposed method is expected to expand our understanding of the single-cell mechanisms of drugs at the pathway level.
Nature-inspired architected materials using unsupervised deep learning
Authors: Shen Sabrina Chin-yun , Buehler Markus J. 
Published: November 2022

AbstractNature-inspired material design is driven by superior properties found in natural architected materials and enabled by recent developments in additive manufacturing and machine learning. Existing approaches to push design beyond biomimicry typically use supervised deep learning algorithms to predict and optimize properties based on experimental or simulation data. However, these methods constrain generated material designs to abstracted labels and to “black box” outputs that are only indirectly manipulable. Here we report an alternative approach using an unsupervised generative adversarial network (GAN) model. Training the model on unlabeled data constructs a latent space free of human intervention, which can then be explored through seeding, image encoding, and vector arithmetic to control specific parameters of de novo generated material designs and to push them beyond training data distributions for broad applicability. We illustrate this end-to-end with new materials inspired by leaf microstructures, showing how biological 2D structures can be used to develop novel architected materials in 2 and 3 dimensions. We further utilize a genetic algorithm to optimize generated microstructures for mechanical properties, operating directly on the latent space. This approach allows for transfer of information across manifestations using the latent space as mediator, opening new avenues for exploration of nature-inspired materials.
Bio-inspired color-changing and self-healing hybrid hydrogels for wearable sensors and adaptive camouflage
Authors: Liu Han , Yu Long , Zhao Bingqian , Ni Yezhou , Gu Peng , Qiu Hua , Zhang Wan , Chen Kunlin 
Published: November 2022

A novel color-changing and self-healing hybrid hydrogel was prepared by mixing the thermochromic dye microcapsules and photochromic dye microcapsules with the multi-branched polyacrylate.
The VLT-FLAMES Tarantula Survey
Authors: Sana H. , Ramírez-Agudelo O. H. , Hénault-Brunet V. , Mahy L. , Almeida L. A. , de Koter A. , Bestenlehner J. M. , Evans C. J. , Langer N. , Schneider F. R. N. , Crowther P. A. , de Mink S. E. , Herrero A. , Lennon D. J. , Gieles M. , Maíz Apellániz J. , Renzo M. , Sabbi E. , van Loon J. Th. , Vink J. S. 
Published: November 2022

Context. The origin of massive runaway stars is an important unsolved problem in astrophysics. Two main scenarios have been proposed, namely: dynamical ejection or release from a binary at the first core collapse. However, their relative contribution remains heavily debated.
Aims. Taking advantage of two large spectroscopic campaigns towards massive stars in 30 Doradus, we aim to provide observational constraints on the properties of the O-type runaway population in the most massive active star-forming region in the Local Group.
Methods. We used radial velocity measurements of the O-type star populations in 30 Doradus obtained by the VLT-FLAMES Tarantula Survey and the Tarantula Massive Binary Monitoring to identify single and binary O-type runaways. Here, we discuss the rotational properties of the detected runaways and qualitatively compare the observations with expectations of ejection scenarios.
Results. We identified 23 single and one binary O-type runaway objects, most of them located outside the main star-forming regions in 30 Doradus. We find an overabundance of rapid rotators (ve sin i > 200 km s−1) among the runaway population, thus providing an explanation for the observed overabundance of rapidly rotating stars in the 30 Doradus field. Considerations of the projected rotation rates and runaway line-of-sight velocities reveal a conspicuous absence of rapidly rotating (ve sin i > 210 km s−1), fast-moving (vlos > 60 km s−1) runaway stars in our sample, strongly suggesting the presence of two different populations of runaway stars: a population of rapidly spinning but slowly moving runaway stars and a population of fast-moving but slowly rotating ones. These are detected with a ratio close to 2:1 in our sample.
Conclusions. We argue that slowly moving but rapidly spinning runaway stars result from binary ejections, while rapidly moving but slowly spinning runaways could result from dynamical ejections. Given that detection biases will more strongly impact the slow-moving runaway population, our results suggest that the binary evolution scenario dominates the current massive runaway star population in 30 Doradus.
MASAVE: A mobile test system for audio-visual experiments at home
Authors: Strasser Ewald , Brand Thomas , Rennies Jan 
Published: November 2022

We present a mobile apparatus for audio-visual experiments (MASAVE) that is easy to build with a low budget and which can run listening tests, pupillometry, and eye-tracking, e.g., for measuring listening effort and fatigue. The design goal was to keep the MASAVE at affordable costs and to enable shipping the preassembled system to the subjects for self-setup in home environments. Two experiments were conducted to validate the proposed system. In the first experiment we tested the reliability of speech perception data gathered using the MASAVE in a less controlled, rather noisy environment. Speech recognition thresholds (SRTs) were measured in a lobby versus a sound-attenuated boot. Results show that the data from both sites did not differ significantly and SRT measurements were possible even for speech levels as low as 40–45 dB SPL. The second experiment validated the usability of the preassembled system and the use of pupillometry measurements under conditions of darkness, which can be achieved by applying a textile cover over the MASAVE and the subject to block out light. The results suggest that the tested participants had no usability issues with setting up the system, that the temperature under the cover increased by several degrees only when the measurement duration was rather long, and that pupillometry measurements can be made with the proposed setup. Overall, the validations indicate that the MASAVE can serve as an alternative when lab testing is not possible, and to gather more data or to reach subject groups that are otherwise difficult to reach.
A second-order low-regularity correction of Lie splitting for the semilinear Klein–Gordon equation
Authors: Li Buyang , Schratz Katharina , Zivcovich Franco 
Published: November 2022

The numerical approximation of nonsmooth solutions of the semilinear Klein–Gordon equation in the d-dimensional space, with d = 1, 2, 3, is studied based on the discovery of a new cancellation structure in the equation. This cancellation structure allows us to construct a low-regularity correction of the Lie splitting method (i.e., exponential Euler method), which can significantly improve the accuracy of the numerical solutions under low-regularity conditions compared with other second-order methods. In particular, the proposed time-stepping method can have second-order convergence in the energy space under the regularity condition
$ (u,{\mathrm{\partial }}_tu)\in {L}^{\mathrm{\infty }}(0,T;{H}^{1+\frac{d}{4}}\times {H}^{\frac{d}{4}})$
. In one dimension, the proposed method is shown to have almost
$ \frac{4}{3}$
-order convergence in L∞(0, T; H1 × L2) for solutions in the same space, i.e., no additional regularity in the solution is required. Rigorous error estimates are presented for a fully discrete spectral method with the proposed low-regularity time-stepping scheme. The numerical experiments show that the proposed time-stepping method is much more accurate than previously proposed methods for approximating the time dynamics of nonsmooth solutions of the semilinear Klein–Gordon equation.
Evaluation of the Bio-Evolution Microsporidia generic and typing real-time PCR assays for the diagnosis of intestinal microsporidiosis
Authors: Moniot Maxime , Nourrisson Céline , Bonnin Virginie , Damiani Céline , Argy Nicolas , Bonhomme Julie , Fréalle Emilie , Angebault Cécile , Debourgogne Anne , Sitterlé Emilie , Flori Pierre , Brunet Julie , Dalle Frédéric , Favennec Loïc , Poirier Philippe ,   French Microsporidiosis Network
Published: November 2022

Cases of intestinal microsporidiosis infection are underestimated and affect both immunocompromized and immunocompetent patients. Real-time PCR is superseding microscopic examination for its diagnosis in medical analysis laboratories. However, few manufacturers include microsporidia in their PCR panel for the diagnosis of infectious gastroenteritis. Here, we evaluated the performances of the real-time PCR assays microsporidia generic and microsporidia typing (Bio-Evolution, France) on the Rotor-Gene Q real-time PCR cycler (Qiagen, France). We included 45 negative and 44 positive stool samples for Enterocytozoon bieneusi (n = 34, with various genotypes), Encephalitozoon intestinalis (n = 4), Encephalitozoon hellem (n = 4), and Encephalitozoon cuniculi (n = 2). We also studied a four-year survey of an inter-laboratory quality control program including 9 centers that used this commercial assay. Sensitivity and specificity of the microsporidia generic assay were 86.4% and 93.3%, respectively. Encephalitozoon hellem and Encephalitozoon cuniculi were detected by the microsporidia generic PCR assay but not by the microsporidia typing PCR assay. These results were consistent with the results of the inter-laboratory quality control program. In conclusion, Bio-Evolution Real-time PCR assays are useful tools for intestinal microsporidiosis, but negative results for microsporidia typing assays require supplementary analyses to confirm E. hellem or E. cuniculi infections.