bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 26-year time series of mortality and growth of the Pacific oyster C. gigas recorded along French coasts
Authors: Mazaleyrat Anna , Normand Julien , Dubroca Laurent , Fleury Elodie 
Published: July 2022

AbstractWe used a compiled data set from a monitoring network of oyster production coordinated by IFREMER (the French Research Institute for the Exploitation of the Sea). This network monitors the growth and mortality of the Pacific oyster Crassostrea gigas along French coasts since 1993. The archive, although publicly available, has been challenging to use due to changes in protocols and little information on metadata. Here, we describe data collection for almost 30 years, cleaning and processing. For 13 locations, we modeled growth and mortality of spat (less than one-year-old individuals) and half-grown oysters (between one and two-year-old individuals) as a function of time to cope with changes in data acquisition frequency, and produced standardized annual growth and cumulative mortality indicators to improve data usability. This improved database is expected to be used by ecologists interested in the evolution of life-cycle indicators of a marine species under the influence of climate change. It can also be valuable for epidemiologists because mortality data traces the emergence and spread of a massive epizootic.
Country Compendium of the Global Register of Introduced and Invasive Species
Authors: Pagad Shyama , Bisset Stewart , Genovesi Piero , Groom Quentin , Hirsch Tim , Jetz Walter , Ranipeta Ajay , Schigel Dmitry , Sica Yanina V. , McGeoch Melodie A. 
Published: July 2022

AbstractThe Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien species, along with a designation of those species with evidence of impact at a country level. The Compendium provides a baseline for monitoring the distribution and invasion status of all major taxonomic groups, and can be used for the purpose of global analyses of introduced (alien, non-native, exotic) and invasive species (invasive alien species), including regional, single and multi-species taxon assessments and comparisons. It enables exploration of gaps and inferred absences of species across countries, and also provides one means for updating individual GRIIS Checklists. The Country Compendium is, for example, instrumental, along with data on first records of introduction, for assessing and reporting on invasive alien species targets, including for the Convention on Biological Diversity and Sustainable Development Goals. The GRIIS Country Compendium provides a baseline and mechanism for tracking the spread of introduced and invasive alien species across countries globally.

Design Type(s)
Data integration objective ● Observation design

Measurement Type(s)
Alien species occurrence ● Evidence of impact invasive alien species assessment objective

Technology Type(s)
Agent expert ● Data collation

Factor Type(s)
Geographic location ● Origin / provenance ● Habitat

Sample Characteristics - Organism
Animalia ● Bacteria ● Chromista ● Fungi ● Plantae ● Protista (Protozoa) ● Viruses

Sample Characteristics - Location
Global countries
Learning transport processes with machine intelligence
Authors: Miniati Francesco , Gregori Gianluca 
Published: July 2022

AbstractTransport processes ruled by complex micro-physics and impractical to theoretical investigation may exhibit emergent behavior describable by mathematical expressions. Such information, while implicitly contained in the results of microscopic-scale numerical simulations close to first principles or experiments is not in a form suitable for macroscopic modelling. Here we present a machine learning approach that leverages such information to deploy micro-physics informed transport flux representations applicable to a continuum mechanics description. One issue with deep neural networks, arguably providing the most generic of such representations, is their noisiness which is shown to break the performance of numerical schemes. The matter is addressed and a methodology suitable for schemes characterised by second order convergence rate is presented. The capability of the methodology is demonstrated through an idealized study of the long standing problem of heat flux suppression relevant to fusion and cosmic plasmas. Symbolic representations, although potentially less generic, are straightforward to use in numerical schemes and theoretical analysis, and can be even more accurate as shown by the application to the same problem of an advanced symbolic regression tool. These results are a promising initial step to filling the gap between micro and macro in this important area of modeling.
Implementation intentions to express gratitude increase daily time co-present with an intimate partner, and moderate effects of variation in CD38
Authors: Chang Yen-Ping , Way Baldwin M. , Sheeran Paschal , Kurtz Laura E. , Baucom Donald H. , Algoe Sara B. 
Published: July 2022

AbstractClose social connections drive mental and physical health and promote longevity. Positive, other-focused behavior like expressing gratitude may be a key mechanism for increasing close bonds. Existing evidence consistent with this claim is predominantly correlational, likely driven by challenges in causally influencing and sustaining behavior change in the context of ongoing relationships. This 5-week field experiment with daily data from couples provides the first evidence for a brief, low-cost behavioral technique to increase everyday expressed gratitude to a romantic partner. Random assignment to the gratitude expression treatment (GET) increased the amount of time couples spent co-present in everyday life, from the weeks before GET to the weeks after, relative to the control condition. This effect was mediated by the change in expressed gratitude. Voluntary co-presence is an important behavioral indicator of close bonds in non-human animals. Further analyses with a functional genotype related to the oxytocin system (rs6449182) suggest a neurochemical pathway involved in the effects of expressing gratitude. Together, this evidence bridges animal and human research on bonding behavior and sets up future experiments on biopsychosocial mechanisms linking close bonds to health.
Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster
Authors: Ortega-Yáñez Andrea , Cruz-Ruiz Samantha , Vázquez Martha , Zurita Mario 
Published: July 2022

AbstractTranscription factors (TFs) activate gene expression by binding to elements close to promoters or enhancers. Some TFs can bind to heterochromatic regions to initiate gene activation, suggesting that if a TF is able to bind to any type of heterochromatin, it can activate transcription. To investigate this possibility, we used the CRISPRa system based on dCas9-VPR as an artificial TF in Drosophila. dCas9-VPR was targeted to the TAHRE telomeric element, an example of constitutive heterochromatin, and to promoters and enhancers of the HOX Ultrabithorax (Ubx) and Sex Combs Reduced (Scr) genes in the context of facultative heterochromatin. dCas9-VPR robustly activated TAHRE transcription, showing that although this element is heterochromatic, dCas9-VPR was sufficient to activate its expression. In the case of HOX gene promoters, although Polycomb complexes epigenetically silence these genes, both were ectopically activated. When the artificial TF was directed to enhancers, we found that the expression pattern was different compared to the effect on the promoters. In the case of the Scr upstream enhancer, dCas9-VPR activated the gene ectopically but with less expressivity; however, ectopic activation also occurred in different cells. In the case of the bxI enhancer located in the third intron of Ubx, the presence of dCas9-VPR is capable of increasing transcription initiation while simultaneously blocking transcription elongation, generating a lack of functional phenotype. Our results show that CRISPRa system is able to activate transcription in any type of heterochromatin; nevertheless, its effect on transcription is subject to the intrinsic characteristics of each gene or regulatory element.
Environmental stability and phenotypic plasticity benefit the cold-water coral Desmophyllum dianthus in an acidified fjord
Authors: Beck Kristina K. , Schmidt-Grieb Gertraud M. , Laudien Jürgen , Försterra Günter , Häussermann Verena , González Humberto E. , Espinoza Juan Pablo , Richter Claudio , Wall Marlene 
Published: July 2022

AbstractThe stratified Chilean Comau Fjord sustains a dense population of the cold-water coral (CWC)Desmophyllum dianthusin aragonite supersaturated shallow and aragonite undersaturated deep water. This provides a rare opportunity to evaluate CWC fitness trade-offs in response to physico-chemical drivers and their variability. Here, we combined year-long reciprocal transplantation experiments along natural oceanographic gradients with an in situ assessment of CWC fitness. Following transplantation, corals acclimated fast to the novel environment with no discernible difference between native and novel (i.e. cross-transplanted) corals, demonstrating high phenotypic plasticity. Surprisingly, corals exposed to lowest aragonite saturation (Ωarag < 1) and temperature (T < 12.0 °C), but stable environmental conditions, at the deep station grew fastest and expressed the fittest phenotype. We found an inverse relationship between CWC fitness and environmental variability and propose to consider the high frequency fluctuations of abiotic and biotic factors to better predict the future of CWCs in a changing ocean.
Bioinspired enzymatic compartments constructed by spatiotemporally confined in situ self-assembly of catalytic peptide
Authors: Wang Yaling , Pan Tiezheng , Wei Xuewen , Su Fangcui , Li Ang , Tai Yifan , Wei Tingting , Zhang Qian , Kong Deling , Zhang Chunqiu 
Published: July 2022

AbstractEnzymatic compartments, inspired by cell compartmentalization, which bring enzymes and substrates together in confined environments, are of particular interest in ensuring the enhanced catalytic efficiency and increased lifetime of encapsulated enzymes. Herein, we constructed bioinspired enzymatic compartments (TPE-Q18H@GPs) with semi-permeability by spatiotemporally controllable self-assembly of catalytic peptide TPE-Q18H in hollow porous glucan particles (GPs), allowing substrates and products to pass in/out freely, while enzymatic aggregations were retained. Due to the enrichment of substrates and synergistic effect of catalytic nanofibers formed in the confined environment, the enzymatic compartments exhibited stronger substrate binding affinity and over two-fold enhancement of second-order kinetic constant (kcat/Km) compared to TPE-Q18H nanofibers in disperse system. Moreover, GPs enabled the compartments sufficient stability against perturbation conditions, such as high temperature and degradation. This work opens an intriguing avenue to construct enzymatic compartments using porous biomass materials and has fundamental implications for constructing artificial organelles and even artificial cells.
Observation of bulk-edge correspondence in topological pumping based on a tunable electric circuit
Authors: Yatsugi Kenichi , Yoshida Tsuneya , Mizoguchi Tomonari , Kuno Yoshihito , Iizuka Hideo , Tadokoro Yukihiro , Hatsugai Yasuhiro 
Published: July 2022

AbstractIn topological phases, localized edge states protected by the bulk topological number appear. This phenomenon is known as the bulk-edge correspondence, which has been theoretically established in various topological systems including topological pumping. There have been experimental works on topological edge states. However, direct observation of bulk topological numbers remains challenging. Here, we experimentally observe both topological edge states and bulk Chern numbers near the topological phase transition in a tunable electric circuit system. The admittance matrix of the system is accurately engineered by using variable capacitors, leading to the implementation of classical analogue of the quantum Hall phase and the topological transition. The topological numbers of the edge states are determined experimentally, where the locations of the edge states are flipped in the topological transition. The corresponding bulk Chern numbers are determined by the Středa’s formula to the impedance spectrum. Our electric circuit scheme is a promising platform to provide a crucial understanding of topological phenomena, and opens up the possibility toward functional energy transfer mechanisms.
Deep learning for the rare-event rational design of 3D printed multi-material mechanical metamaterials
Authors: Pahlavani Helda , Amani Muhamad , Saldívar Mauricio Cruz , Zhou Jie , Mirzaali Mohammad J. , Zadpoor Amir A. 
Published: July 2022

AbstractEmerging multi-material 3D printing techniques enables the rational design of metamaterials with not only complex geometries but also arbitrary distributions of multiple materials within those geometries, yielding unique combinations of elastic properties. However, discovering the rare designs that lead to highly unusual combinations of material properties, such as double-auxeticity and high elastic moduli, remains a non-trivial crucial task. Here, we use computational models and deep learning algorithms to identify rare-event designs. In particular, we study the relationship between random distributions of hard and soft phases in three types of planar lattices and the resulting mechanical properties of the two-dimensional networks. By creating a mapping from the space of design parameters to the space of mechanical properties, we are able to reduce the computational time required for evaluating each design to ≈2.4 × 10−6 s, and to make the process of evaluating different designs highly parallelizable. We then select ten designs to be 3D printed, mechanically test them, and characterize their behavior using digital image correlation to validate the accuracy of our computational models. Our simulation results show that our deep learning-based algorithms can accurately predict the mechanical behavior of the different designs and that our modeling results match experimental observations.
Neutrophils incite and macrophages avert electrical storm after myocardial infarction
Authors: Grune Jana , Lewis Andrew J. M. , Yamazoe Masahiro , Hulsmans Maarten , Rohde David , Xiao Ling , Zhang Shuang , Ott Christiane , Calcagno David M. , Zhou Yirong , Timm Kerstin , Shanmuganathan Mayooran , Pulous Fadi E. , Schloss Maximillian J. , Foy Brody H. , Capen Diane , Vinegoni Claudio , Wojtkiewicz Gregory R. , Iwamoto Yoshiko , Grune Tilman , Brown Dennis , Higgins John , Ferreira Vanessa M. , Herring Neil , Channon Keith M. , Neubauer Stefan ,   Oxford Acute Myocardial Infarction (OxAMI) Study, Shanmuganathan Mayooran , Ferreira Vanessa M. , Channon Keith M. , Sosnovik David E. , Milan David J. , Swirski Filip K. , King Kevin R. , Aguirre Aaron D. , Ellinor Patrick T. , Nahrendorf Matthias 
Published: July 2022

AbstractSudden cardiac death, arising from abnormal electrical conduction, occurs frequently in patients with coronary heart disease. Myocardial ischemia simultaneously induces arrhythmia and massive myocardial leukocyte changes. In this study, we optimized a mouse model in which hypokalemia combined with myocardial infarction triggered spontaneous ventricular tachycardia in ambulatory mice, and we showed that major leukocyte subsets have opposing effects on cardiac conduction. Neutrophils increased ventricular tachycardia via lipocalin-2 in mice, whereas neutrophilia associated with ventricular tachycardia in patients. In contrast, macrophages protected against arrhythmia. Depleting recruited macrophages in Ccr2−/− mice or all macrophage subsets with Csf1 receptor inhibition increased both ventricular tachycardia and fibrillation. Higher arrhythmia burden and mortality in Cd36−/− and Mertk−/− mice, viewed together with reduced mitochondrial integrity and accelerated cardiomyocyte death in the absence of macrophages, indicated that receptor-mediated phagocytosis protects against lethal electrical storm. Thus, modulation of leukocyte function provides a potential therapeutic pathway for reducing the risk of sudden cardiac death.
The dynamic power allocation to maximize the achievable sum rate for massive MIMO‐NOMA systems
Authors: Amirifar Zahra , Abouei Jamshid 
Published: July 2022

AbstractThe demand of mobile networks and quality of service have recently increased to higher Spectral Efficiency (SE) or Energy Efficiency (EE) and massive connectivity for 5G wireless communications. The concept of beamforming Multiple‐Input Multiple‐Output (MIMO) is capable of significantly reducing the amount of required Radio Frequency Chains (RFCs) used by massive MIMO systems without remarkable performance loss. However, in existing beamformed MIMO, the amount of supported devices cannot be higher than the amount of RFCs using the same time‐frequency resources, and it is the basic limit for these systems. To address this issue, non‐orthogonal multiple access (NOMA) has been recently recommended, which can accommodate higher covered using via non‐orthogonal resource allocation. Nevertheless, power allocation is a core factor of the NOMA scheme. However, maximizing the sum rate problem based on power allocation in Massive MIMO‐NOMA scenarios is non‐convex and non‐linear, which creates a very challenging situation to acquire the closed‐form approach. Thus, in this paper, an approach to this difficulty is outlined for Massive MIMO‐NOMA systems to maximize the sum rate as a convex and linear problem. Simulation results of the suggested Beamformed MIMO‐NOMA (BMN) algorithm show that a higher achievable sum rate is achieved compared with the usual beamformed MIMO.
Governor controller improvement to enhance SSSG performance in presence of electrical arc furnace
Authors: Bekhradian Reza , Sanaye‐Pasand Majid , Davarpanah Mahdi , Kor Yashar 
Published: July 2022

AbstractElectrical Arc Furnaces (EAFs) consume time‐varying power. This causes mechanical torque variations in the nearby small scale synchronous generators (SSSGs) and reduces their life expectancy. In this paper, an appropriate EAF model is implemented and verified by using field measurements. Moreover, an actual distribution system to which an SSSG is connected to supply industrial loads including an EAF is investigated based on time‐domain simulation studies. To enhance dynamic performance of the SSSG adjacent to an EAF load, two novel approaches are presented in this paper. The first method is utilized for proper adjustment of governor controller parameters. Analytical and simulation‐based studies are accomplished to determine proper parameters of the SSSG conventional governor controller to mitigate the mechanical oscillations caused by EAF. These comprehensive investigations reveal that the governor PI controller proportional parameter should be adjusted as small as possible to mitigate the SSSG oscillations; while, the oscillations are fairly independent of integrator parameter. Besides, the integrator parameter should be set as high as possible to improve the SSSG dynamic performance. Moreover, a new modified SSSG governor controller including steady‐state and transient control loops is developed and a novel control strategy is proposed to enhance steady‐state and transient performance of SSSG. Finally, robustness and effectiveness of the proposed controller and its parameters are investigated using field measured EAF current signals for various transients. It should be noted that the proposed strategies of this paper can be also applied to similar cases where a nonlinear time varying load is connected to an SSSG.
Atomic diffusion and turbulent mixing in solar-like stars: Impact on the fundamental properties of FG-type stars
Authors: Moedas Nuno , Deal Morgan , Bossini Diego , Campilho Bernardo 
Published: July 2022

Context. Chemical composition is an important factor that affects stellar evolution. The element abundance on the stellar surface evolves along the lifetime of the star because of transport processes, including atomic diffusion. However, models of stars with masses higher than about 1.2 M⊙ predict unrealistic variations at the stellar surface. This indicates the need for competing transport processes that are mostly computationally expensive for large grids of stellar models.
Aims. The purpose of this study is to implement turbulent mixing in stellar models and assess the possibility of reproducing the effect of radiative accelerations with turbulent mixing for elements like iron in order to make the computation of large grids possible.
Methods. We computed stellar models with the Module for Experiments in Stellar Astrophysics code and assessed the effects of atomic diffusion (with radiative acceleration) in the presence of turbulent mixing. Starting from a turbulent mixing prescription already calibrated on helium surface abundances of F-type stars as a reference, we parametrised the effect of radiative accelerations on iron with a turbulent diffusion coefficient. Finally, we tested this parametrisation by modelling two F-type stars of the Kepler Legacy sample.
Results. We found that, for iron, a parametrisation of turbulent mixing that simulates the effect of radiative acceleration is possible. This leads to an increase in the efficiency of the turbulent mixing to counteract the effect of gravitational settling. This approximation does not affect significantly the surface abundances of the other elements we studied, except for oxygen and calcium. We demonstrate that this parametrisation has a negligible impact on the accuracy of the seismic properties inferred with these models. Moreover, turbulent mixing makes the computation of realistic F-type star models including the effect atomic diffusion possible. This leads to differences of about 10% in the inferred ages compared to results obtained with models that neglect these processes.
Conclusions. The inclusion of turbulent mixing and atomic diffusion with radiative accelerations allows a more realistic characterisation of F-type stars. The parametrisation of the effect of radiative acceleration on iron opens the possibility to compute larger grids of stellar models in a reasonable amount of time, which is currently difficult when the different chemical transport mechanisms, especially radiative accelerations, are considered, although this parametrisation cannot simulate the evolution of abundances of all elements (e.g. calcium).
GaiaData Release 3
Authors: Halbwachs Jean-Louis , Pourbaix Dimitri , Arenou Frédéric , Galluccio Laurent , Guillout Patrick , Bauchet Nathalie , Marchal Olivier , Sadowski Gilles , Teyssier David 
Published: July 2022

Context.TheGaiaEarly Data Release 3 contained the positions, parallaxes, and proper motions of 1.5 billion sources, some of which did not show a good fit to the ‘single star’ model. Binarity is one of the causes of this.Aims.Four million of these stars were selected and various models were tested to detect binary stars and to derive their parameters.Methods.We used a preliminary treatment to discard the partially resolved double stars and to correct the transits for perspective acceleration. We then investigated whether the measurements show a good fit to an acceleration model with or without jerk. We tried the orbital model when the fit of any acceleration model was beyond our acceptance criteria. We also tried a Variability-Induced Mover (VIM) model when the star was photometrically variable. A final selection was made in order to keep only solutions that probably correspond to the real nature of the stars.Results.Following our analysis, 338 215 acceleration solutions, about 165 500 orbital solutions, and 869 VIM solutions were retained. In addition, formulae for calculating the uncertainties of the Campbell orbital elements from orbital solutions expressed in Thiele-Innes elements are given in an appendix.