Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporal gene expression atlas of the extremophyte Schrenkiella parvula

Extremophytes are naturally selected to survive environmental stresses, but scarcity of genetic resources for them developed with spatiotemporal resolution limit their use in stress biology. Schrenkiella parvula is one of the leading extremophyte models with initial molecular genomic resources developed to study its tolerance mechanisms to high salinity. Here we present a transcriptome atlas for S. parvula with subsequent analyses to highlight its diverse gene expression networks associated with salt responses. We included spatiotemporal expression profiles, expression specificity of each gene, and co-expression and functional gene networks representing 115 transcriptomes sequenced from 35 tissue and developmental stages examining their responses before and after 27 salt treatments in our current study. The highest number of tissue-preferentially expressed genes were found in seeds and siliques while genes in seedlings showed the broadest expression profiles among developmental stages. Seedlings had the highest magnitude of overall transcriptomic responses to salinity compared to mature tissues and developmental stages. Differentially expressed genes in response to salt were largely mutually exclusive but shared common stress response pathways spanning across tissues and developmental stages. Our foundational dataset created for S. parvula representing a stress-adapted wild plant lays the groundwork for future functional, comparative, and evolutionary studies using extremophytes aiming to uncover novel stress tolerant mechanisms. SIGNIFICANCE STATEMENT Concerted transcriptomic responses coordinated across developmental stages and tissues are required to complete a plant lifecycle under salt stress. Transcriptomic resources created with spatiotemporal resolution for plants are rare and for stress-adapted plants rarer. We present a transcriptome atlas enabling discovery of genes and networks evolved as adaptations to salt stress in a model extremophyte, Schrenkiella parvula. The spatiotemporally resolved gene expression networks are largely non-overlapping but functionally connected through synergistic stress responsive pathways.
Mercury in the free troposphere and bidirectional atmosphere–vegetation exchanges – insights from Maïdo mountain observatory in the Southern Hemisphere tropics

Abstract. Atmospheric mercury (Hg) observations in the lower free troposphere (LFT) can give important insights into Hg redox chemistry and can help constrain Hg background concentrations on a regional level. Relatively continuous sampling of LFT air, inaccessible to most ground-based stations, can be achieved at high-altitude observatories. However, such high-altitude observatories are rare, especially in the Southern Hemisphere (SH), and atmospheric Hg in the SH LFT is unconstrained. To fill this gap, we continuously measured gaseous elemental mercury (GEM; hourly) and reactive mercury (RM; integrated over ∼ 6–14 d) for 9 months at Maïdo mountain observatory (2160 m a.s.l.) on remote Réunion Island (21.1∘ S, 55.5∘ E) in the tropical Indian Ocean. GEM exhibits a marked diurnal variation characterized by a midday peak (mean: 0.95 ng m−3; SD: 0.08 ng m−3) and a nighttime low (mean: 0.78 ng m−3; SD: 0.11 ng m−3). We find that this diurnal variation is likely driven by the interplay of important GEM photo-reemission from the islands' vegetated surfaces (i.e. vegetation + soil) during daylight hours (8–22 ng m−2 h−1), boundary layer influences during the day, and predominant LFT influences at night. We estimate GEM in the LFT based on nighttime observations in particularly dry air masses and find a notable seasonal variation, with LFT GEM being lowest from December to March (mean 0.66 ng m−3; SD: 0.07 ng m−3) and highest from September to November (mean: 0.79 ng m−3; SD: 0.09 ng m−3). Such a clear GEM seasonality contrasts with the weak seasonal variation reported for the SH marine boundary layer but is in line with modeling results, highlighting the added value of continuous Hg observations in the LFT. Maïdo RM is 10.6 pg m−3 (SD: 5.9 pg m−3) on average, but RM in the cloud-free LFT might be about twice as high, as weekly–biweekly sampled RM observations are likely diluted by low-RM contributions from the boundary layer and clouds.
Boundaries of synchronization in oscillator networks

We analyze the final state sensitivity of nonlocal networks with respect to initial conditions of their units. By changing the initial conditions of a single network unit, we perturb an initially synchronized state. Depending on the perturbation strength, we observe the existence of two possible network long-term states: (i) The network neutralizes the perturbation effects and returns to its synchronized configuration. (ii) The perturbation leads the network to an alternative desynchronized state. By computing uncertainty exponents of a two-dimensional cross section of the state space, we find the existence of fractal basin boundaries separating synchronized solutions from desynchronized ones. We attribute these features to an unstable chaotic set in which trajectories persist for times indefinitely long in the network.
Climate response to off-equatorial stratospheric sulfur injections in three Earth system models – Part 2: Stratospheric and free-tropospheric response

Abstract. The paper constitutes Part 2 of a study performing a first systematic inter-model comparison of the atmospheric responses to stratospheric aerosol injection (SAI) at various single latitudes in the tropics, as simulated by three state-of-the-art Earth system models – CESM2-WACCM6, UKESM1.0, and GISS-E2.1-G. Building on Part 1 (Visioni et al., 2023) we demonstrate the role of biases in the climatological circulation and specific aspects of the model microphysics in driving the inter-model differences in the simulated sulfate distributions. We then characterize the simulated changes in stratospheric and free-tropospheric temperatures, ozone, water vapor, and large-scale circulation, elucidating the role of the above aspects in the surface SAI responses discussed in Part 1. We show that the differences in the aerosol spatial distribution can be explained by the significantly faster shallow branches of the Brewer–Dobson circulation in CESM2, a relatively isolated tropical pipe and older tropical age of air in UKESM, and smaller aerosol sizes and relatively stronger horizontal mixing (thus very young stratospheric age of air) in the two GISS versions used. We also find a large spread in the magnitudes of the tropical lower-stratospheric warming amongst the models, driven by microphysical, chemical, and dynamical differences. These lead to large differences in stratospheric water vapor responses, with significant increases in stratospheric water vapor under SAI in CESM2 and GISS that were largely not reproduced in UKESM. For ozone, good agreement was found in the tropical stratosphere amongst the models with more complex microphysics, with lower stratospheric ozone changes consistent with the SAI-induced modulation of the large-scale circulation and the resulting changes in transport. In contrast, we find a large inter-model spread in the Antarctic ozone responses that can largely be explained by the differences in the simulated latitudinal distributions of aerosols as well as the degree of implementation of heterogeneous halogen chemistry on sulfate in the models. The use of GISS runs with bulk microphysics demonstrates the importance of more detailed treatment of aerosol processes, with contrastingly different stratospheric SAI responses to the models using the two-moment aerosol treatment; however, some problems in halogen chemistry in GISS are also identified that require further attention. Overall, our results contribute to an increased understanding of the underlying physical mechanisms as well as identifying and narrowing the uncertainty in model projections of climate impacts from SAI.
Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics

In this paper we establish a new efficient method for simulating polymer–solvent systems which combines a lattice Boltzmann approach for the fluid with a continuum molecular-dynamics (MD) model for the polymer chain. The two parts are coupled by a simple dissipative force while the system is driven by stochastic forces added to both the fluid and the polymer. Extensive tests of the new method for the case of a single polymer chain in a solvent are performed. The dynamic and static scaling properties predicted by analytical theory are validated. In this context, the influence of the finite size of the simulation box is discussed. While usually the finite size corrections scale as L−1 (L denoting the linear dimension of the box), the decay rate of the Rouse modes is only subject to an L−3 finite size effect. Furthermore, the mapping to an existing MD simulation of the same system is done so that all physical input values for the new method can be derived from pure MD simulation. Both methods can thus be com.
The Comparative Effects of Modified Augmentative and The Comparative Effects of Modified Augmentative and Alternative Communication Modalities on Requesting for a Child Alternative Communication Modalities on Requesting for a Child with Autism and Visual Impairments with Autism and Visual Impairment

The present study used a multiple probe across behaviors design, with an embedded alternating treatments design to compare the effects of two modified communication systems, the Picture Exchange Communication System (PECS) and a speech generating device, on requesting for a child with multiple disabilities, including autism and visual impairments. Both modalities were taught across the first three phases of PECS instruction (simple request, distance and persistence, and discrimination). During baseline the participant demonstrated little to no requesting across all three phases for either modality. During intervention requesting increased to proficient levels across all three phases for both modalities. Modified PECS, however, yielded noticeably faster results in the distance and persistence phase. Social validity and preference for each modality were also assessed. Both communication systems were found to be acceptable. Both the parent and participant showed preference for the modified PECS. The importance of social validity and modality preference is discussed.
The Role of Social Capital in the Transition to Postsecondary Education of Students Who Are Deaf or Hard of Hearing

Abstract:Social capital can positively influence students' postsecondary aspirations and their postschool transitions to higher education and employment. Educators, families, and young people themselves can play an active role in generating and developing adolescents' social capital. A targeted focus on developing robust social capital could play an important role in the transition planning and support provided to secondary students who are deaf or hard of hearing (DHH) and contribute to their success in postsecondary education and employment. A qualitative study gaining the perspectives of DHH young adults attending universities in Australia investigated the role of social capital in assisting DHH students in their attainment of postsecondary education. Ten DHH university students who communicated primarily through spoken English participated in semistructured interviews. Thematic analysis identified social capital facilitator themes on four levels: community, school, family, and individual. In addition, two barrier themes were identified.
Angular momentum of light

By means of the Helmholtz theorem on the decomposition of vector fields, the angular momentum of the classical electromagnetic field is decomposed, in a general and manifestly gauge invariant manner, into a spin component and an orbital component. The method is applied to linearly and circularly polarized plane waves in their classical and quantum forms.
Isospin-Asymmetry Dependence of the Thermodynamic Nuclear Equation of State in Many-Body Perturbation Theory

In this work, the thermodynamic nuclear equation of state is computed using chiral nuclear interactions in many-body perturbation theory. The generalization of many-body perturbation theory to finite temperatures is carefully investigated. The liquid-gas instability of isospin-asymmetric nuclear matter is studied, and the dependence of the equation of state on the isospin asymmetry is examined in detail.
Leading Modes of East Asian Winter Climate Variability and Their Predictability: An Assessment of th

The variability and predictability of the East Asian (EA) winter climate has been studied, based on observed datasets and multi-model ensemble (MME) hindcast experiments archived at the APEC Climate Center (APCC). The focus is on the leading modes of wintertime variability over the eastern to northeastern part of Asia, which are identified based on multivariate EOF analysis of the monthly 850 hPa wind and temperature. The leading EA climate mode is characterized by continental-scale temperature anomalies covering a broad region from the northwestern flank of the Siberian high to northeast Asia. The second mode is associated with fluctuations of temperature and monsoon northerlies over the EA locations of Korea, Japan and eastern coastal China. Moreover, the first mode is found to be influenced by the Scandinavian (SCA) pattern, while the second mode is closely associated with the Eurasia (EU) pattern. In general, the dominant circulation patterns of the EA wintertime variability from each MME member model compare well with their observational counterparts. However, the temporal variations of these modes are difficult to reproduce in the model simulations. The variation of the leading mode is found to be better predicted by most models, which leads to better predictions of the winter climate over continental northeast Asia, compared to the second mode. The MME performance is further assessed in the context of circulation changes during ENSO. It is found that most models have difficulty in capturing both the timing and strength of the observed second EA climate mode variations. Analysis based on observations shows that there is Rossby wave activity from Eurasia in early boreal winter during ENSO years. The Eurasian wave train, however, is either too weak or absent in the model simulations. Overall, these results highlight the difficulties in forecasting EA winter climate in the current framework of seasonal climate prediction. Corresponding author: Soo-Jin Sohn, APEC Climate Center (APCC), 1463 U-dong, Haeundae-gu, Busan 612020, Repub-
Entropy generation at the multi-fluid MHD solar wind termination shock

In a series of earlier papers, we have developed expressions for ion and electron velocity distribution functions and theirvelocity moments at the passage over the solar wind termination shock. As we have shown there, with introduction of appropriate particle invariants and the use of Liouville`s theorem one can get explicit solutions for the resulting total downstream pressure adding up from partial pressure contributions of solar wind protons, solar wind electrons and pick-up protons. These expressions deliver in a first step the main contributions to the total plasma pressure in the downstream plasma flow and consistently determine the shock compression ratio. Here now we start out from these individual fluid pressures downstream of the shock and thereafter evaluate for the first time the shock-induced entropy production of the different fluids, when they are passing over the shock to the downstream side. As is shown here, the resulting ion entropy production substantially deviates from earlier calculations using a pseudo-polytropic reaction of the ions to the shock compression, with polytropies selected to describe fluid-specific reactions at the shock passage similar to those seen by the VOYAGERs. From these latter models ion entropy jumps are derived that depend on the pick-up ion abundance, while our calculations, to the opposite, deliver an abundance-independent ion entropy production which only depends on the shock compression ratio and the tilt angle between the upstream magnetic field and the shock surface normal. We also do show here that only when including the strongly heated electrons into the entropy balance one then arrives at the total entropy production that just fulfills the thermodynamically permitted limit.
INVERSIONS FOR AVERAGE SUPERGRANULAR FLOWS USING FINITE-FREQUENCY KERNELS

I analyze the maps recording the travel-time shifts caused by averaged plasma anomalies under an “average supergranule,” constructed by means of statistical averaging over 5582 individual supergranules with large divergence signals detected in two months of Helioseismic and Magnetic Imager Dopplergrams. By utilizing a three-dimensional validated time–distance inversion code, I measure a peak vertical velocity of 117 ± 2 m s−1 at depths around 1.2 Mm in the center of the supergranule and a root-mean-square vertical velocity of 21 m s−1 over the area of the supergranule. A discrepancy between this measurement and the measured surface vertical velocity (a few m s−1) can be explained by the existence of the large-amplitude vertical flow under the surface of supergranules with large divergence signals, recently suggested by Duvall & Hanasoge.
Transport gap in side-gated graphene constrictions

We present measurements on side-gated graphene constrictions of different geometries. We characterize the transport gap by its width in back-gate voltage and compare this to an analysis based on Coulomb blockade measurements of localized states. We study the effect of an applied side-gate voltage on the transport gap and show that high side-gate voltages lift the suppression of the conductance. Finally we study the effect of an applied magnetic field and demonstrate the presence of edge states in the constriction.
THE AKARI DEEP FIELD SOUTH: PUSHING TO HIGH REDSHIFT

The AKARI Deep Field South (ADF-S) is a large extragalactic survey field that is covered by multiple instruments, from optical to far-IR and radio. I summarise recent results in this and related fields prompted by the release of the Herschel far-IR/submm images, including studies of cold dust in nearby galaxies, the identification of strongly lensed distant galaxies, and the use of colour selection to find candidate very high redshift sources. I conclude that the potential for significant new results from the ADF-S is very great. The addition of new wavelength bands in the future, eg. from Euclid, SKA, ALMA and elsewhere, will boost the importance of this field still further.
Gas Retention and Accumulation in Stellar Clusters and Galaxies: Implications for Star Formation and Black Hole Accretion

Author(s): Naiman, Jill Palmer | Advisor(s): Ramirez-Ruiz, Enrico; Lin, Douglas C | Abstract: Star formation cannot proceed without the existence of an extensive gas reservoir. In particular, the supply of gas to form stars in dwarf galaxies and star clusters requires overcoming a variety of difficulties - namely, the effectiveness of different feedback mechanisms in removing gas from these shallow gravitational potentials. In addition, the supply of external gas to these systems is determined by the large scale galactic structure in which they reside. This thesis employs computational hydrodynamics coupled with physically realistic subgrid feedback prescriptions to resolve the interplay between the small scale feedback mechanisms and larger scale gas flows to determine the amount of gas a shallow potential can accumulate. First, we consider the flow of gas external to dwarf galaxies and star clusters into their cores as a generalized accretion process. Second, we explore the enhancement of gas accretion rates onto the compact members of young star clusters when the flow of external gas into the cluster cores is large. Third, we discuss how external gas flows initiated by the presence of a massive nuclear star cluster can enhance central massive black hole accretion rates during galaxy mergers. Fourth, we change our focus to exploring internal stellar wind retention in proto-globular clusters as a mechanism to supply gas for multiple episodes of star formation. Finally, the implications of stellar wind retention on the current gas reservoir in globular clusters is discussed.
What is the Mass of a Gap-Opening Planet?

High contrast imaging instruments such as GPI and SPHERE are discovering gap structures in protoplanetary disks at an ever faster pace. Some of these gaps may be opened by planets forming in the disks. In order to constrain planet formation models using disk observations, it is crucial to find a robust way to quantitatively back out the properties of the gap-opening planets, in particular their masses, from the observed gap properties, such as their depths and widths. Combing 2D and 3D hydrodynamics simulations with 3D radiative transfer simulations, we investigate the morphology of planet-opened gaps in near-infrared scattered light images. Quantitatively, we obtain correlations that directly link intrinsic gap depths and widths in the gas surface density to observed depths and widths in images of disks at modest inclinations under finite angular resolution. Subsequently, the properties of the surface density gaps enable us to derive the disk scale height at the location of the gap $h$, and to constrain the quantity $M_{\rm p}^2/\alpha$, where $M_{\rm p}$ is the mass of the gap-opening planet and $\alpha$ characterizes the viscosity in the gap. As examples, we examine the gaps recently imaged by VLT/SPHERE, Gemini/GPI, and Subaru/HiCIAO in HD 97048, TW Hya, HD 169142, LkCa 15, and RX J1615.3-3255. Scale heights of the disks and possible masses of the gap-opening planets are derived assuming each gap is opened by a single planet. Assuming $\alpha=10^{-3}$, the derived planet mass in all cases are roughly between 0.1-1 $M_{\rm J}$.
Dynamical cluster disruption and its implications for multiple population models in the E-MOSAICS simulations

© 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. Several models have been advanced to explain the multiple stellar populations observed in globular clusters (GCs). Most models necessitate a large initial population of unenriched stars that provide the pollution for an enriched population, and which are subsequently lost from the cluster. This scenario generally requires clusters to lose > 90 per cent of their birth mass. We use a suite of 25 cosmological zoom-in simulations of present-day Milky Way mass galaxies from the E-MOSAICS project to study whether dynamical disruption by evaporation and tidal shocking provides the necessary mass-loss. We find that GCs with present-day masses M > 105M⊙were only 2-4 times more massive at birth, in conflict with the requirements of the proposed models. This factor correlates weakly with metallicity, gas pressure at birth, or galactocentric radius, but increases towards lower GC masses. To reconcile our results with observational data, either an unphysically steep cluster mass-size relation must be assumed, or the initial enriched fractions must be similar to their present values. We provide the required relation between the initial enriched fraction and cluster mass. Dynamical cluster mass-loss cannot reproduce the high observed enriched fractions nor their trend with cluster mass.