Miracle-dz/UniFAR-FTUs huggingface dataset:
Compressive deformation of Fe nanopillar : Modalities of dislocation dynamics

Unlike the tensile mode, compressive deformation of a bcc metallic nanostructure is mediated by the glide of screw dislocation. Although the bcc screw dislocations are well known to possess unusual attributes, it is still unclear how these unique effects manifest in a nanoscale solid. In the present study, atomistic simulations render a close look at the dislocation activities underlying the compressive deformation of bcc iron nanopillars. It is found that instead of performing simple glide motion, the line defects exhibit a host of complex features. In this regard, the temperature is observed to have a pronounced effect on the dislocation mechanisms and consequently, on the overall plastic response of the material. Additionally, statistical features of the load-strain data have been explored.
Constraining neutrino mass and extra relativistic degrees of freedom in dynamical dark energy models using Planck 2015 data in combination with low-redshift cosmological probes: basic extensions to ΛCDM cosmology

We investigate how the properties of dark energy affect the cosmological measurements of neutrino mass and extra relativistic degrees of freedom. We limit ourselves to the most basic extensions of $\Lambda$ cold dark matter (CDM) model, i.e. the $w$CDM model with one additional parameter $w$, and the $w_{0}w_{a}$CDM model with two additional parameters, $w_{0}$ and $w_{a}$. In the cosmological fits, we employ the 2015 cosmic microwave background temperature and polarization data from the Planck mission, in combination with low-redshift measurements such as the baryon acoustic oscillations, Type Ia supernovae and the Hubble constant ($H_{0}$). Given effects of massive neutrinos on large-scale structure, we further include weak lensing, redshift space distortion, Sunyaev--Zeldovich cluster counts and Planck lensing data. We show that, though the cosmological constant $\Lambda$ is still consistent with the current data, a phantom dark energy ($w -1$) is slightly more favoured by current observations, which leads to the fact that in both $w$CDM and $w_0w_a$CDM models we obtain a larger upper limit of $\sum m_\nu$. We also show that in the three dark energy models, the constraints on $N_{\rm eff}$ are in good accordance with each other, all in favour of the standard value 3.046, which indicates that the dark energy parameters almost have no impact on constraining $N_{\rm eff}$. Therefore, we conclude that the dark energy parameters can exert a significant influence on the cosmological weighing of neutrinos, but almost cannot affect the constraint on dark radiation.
Cultivating "Generational Blessings": Graduate School Aspirations and Intergenerational Uplift Among Women of Color

Abstract:Upward social mobility is often framed in research in ways that may disguise the unique journeys that Women of Color travel in college and as they aspire toward graduate degrees. This assets-based approach to a multisite case study explored how undergraduate Women of Color who aspire toward graduate education viewed the meaning of their potential degrees for their families and how these women described the role of family background relative to their aspirations for graduate study. Findings indicated that for these Women of Color, educational attainment was a form of aspirational capital, cultivating "generational blessings," a vital part of upward mobility. Graduate degrees were part of honoring the obligations they felt toward their families and communities (familial capital). In activating familial and aspirational capital in graduate education, participants were able to bridge the field (social context) of their families and that of graduate education.
Attractors, Statefinders and Observational Measurement for Chameleonic Brans--Dicke Cosmology

We investigate chameleonic Brans-Dicke model applied to the FRW universes. A framework to study stability and attractor solutions in the phase space is developed for the model. We show that depending on the matter field and stability conditions, it is possible to realize phantom-like behavior without introducing phantom filed in the model while the stability is fulfilled and phantom crossing occurs. The statefinder parameters to the model for different kinds of matter interacting with the chameleon scalar field are studied. We also compare our model with present day observations.
THERMAL INSTABILITY WITH ANISOTROPIC THERMAL CONDUCTION AND ADIABATIC COSMIC RAYS: IMPLICATIONS FOR COLD FILAMENTS IN GALAXY CLUSTERS

Observations of the cores of nearby galaxy clusters show Hα and molecular emission-line filaments. We argue that these are the result of local thermal instability in a globally stable galaxy cluster core. We present local, high-resolution, two-dimensional magnetohydrodynamic simulations of thermal instability for conditions appropriate to the intracluster medium (ICM); the simulations include anisotropic thermal conduction along magnetic field lines and adiabatic cosmic rays. Thermal conduction suppresses thermal instability along magnetic field lines on scales smaller than the Field length (≳10 kpc for the hot, diffuse ICM). We show that the Field length in the cold medium must be resolved both along and perpendicular to the magnetic field in order to obtain numerically converged results. Because of negligible conduction perpendicular to the magnetic field, thermal instability leads to fine scale structure in the perpendicular direction. Filaments of cold gas along magnetic field lines are thus a natural consequence of thermal instability with anisotropic thermal conduction. This is true even in the fully nonlinear regime and even for dynamically weak magnetic fields. The filamentary structure in the cold gas is also imprinted on the diffuse X-ray-emitting plasma in the neighboring hot ICM. Nonlinearly, filaments of cold (∼104 K) gas should have lengths (along the magnetic field) comparable to the Field length in the cold medium ∼10−4 pc! Observations show, however, that the atomic filaments in clusters are far more extended, ∼10 kpc. Cosmic-ray pressure support (or a small-scale turbulent magnetic pressure) may resolve this discrepancy: even a small cosmic-ray pressure in the diffuse ICM, ∼10−4 of the thermal pressure, can be adiabatically compressed to provide significant pressure support in cold filaments. This is qualitatively consistent with the large population of cosmic rays invoked to explain the atomic and molecular line ratios observed in filaments.
DISK RADII AND GRAIN SIZES IN HERSCHEL-RESOLVED DEBRIS DISKS

The radii of debris disks and the sizes of their dust grains are important tracers of the planetesimal formation mechanisms and physical processes operating in these systems. Here we use a representative sample of 34 debris disks resolved in various Herschel Space Observatory (Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA) programs to constrain the disk radii and the size distribution of their dust. While we modeled disks with both warm and cold components, and identified warm inner disks around about two-thirds of the stars, we focus our analysis only on the cold outer disks, i.e., Kuiper-belt analogs. We derive the disk radii from the resolved images and find a large dispersion for host stars of any spectral class, but no significant trend with the stellar luminosity. This argues against ice lines as a dominant player in setting the debris disk sizes, since the ice line location varies with the luminosity of the central star. Fixing the disk radii to those inferred from the resolved images, we model the spectral energy distribution to determine the dust temperature and the grain size distribution for each target. While the dust temperature systematically increases toward earlier spectral types, the ratio of the dust temperature to the blackbody temperature at the disk radius decreases with the stellar luminosity. This is explained by a clear trend of typical sizes increasing toward more luminous stars. The typical grain sizes are compared to the radiation pressure blowout limit sblow that is proportional to the stellar luminosity-to-mass ratio and thus also increases toward earlier spectral classes. The grain sizes in the disks of G- to A-stars are inferred to be several times sblow at all stellar luminosities, in agreement with collisional models of debris disks. The sizes, measured in the units of sblow, appear to decrease with the luminosity, which may be suggestive of the disk's stirring level increasing toward earlier-type stars. The dust opacity index β ranges between zero and two, and the size distribution index q varies between three and five for all the disks in the sample.
Measurement of differential magnification

In gravitational lensing, the magnification effect changes the luminosity and size of a background galaxy. If the image sizes are not small compared to the scale over which the magnification and shear vary, higher-order distortions occur which are termed differential magnification. We give an approximation of the magnification gradient for several halo models. Assuming a symmetric distribution of source brightness, estimates for the differential magnification are obtained and then tested with simulations. One of the main uncertainties of our estimators comes from the finite resolution of the image. We study the strength of our method with the resolution of current and future telescopes. We point out that out method is a potential approach to estimate the first flexion, and can be used to study galaxy and cluster mass profil es.
ReS2‐Based Field‐Effect Transistors and Photodetectors

Atomically thin 2D layered transition metal dichalcogenides (TMDs) have been extensively studied in recent years because of their appealing electrical and optical properties. Here, the fabrication of ReS2 field‐effect transistors is reported via the encapsulation of ReS2 nanosheets in a high‐κ Al2O3 dielectric environment. Low‐temperature transport measurements allow to observe a direct metal‐to‐insulator transition originating from strong electron–electron interactions. Remarkably, the photodetectors based on ReS2 exhibit gate‐tunable photoresponsivity up to 16.14 A W−1 and external quantum efficiency reaching 3168%, showing a competitive device performance to those reported in graphene, MoSe2, GaS, and GaSe‐based photodetectors. This study unambiguously distinguishes ReS2 as a new candidate for future applications in electronics and optoelectronics.
LONG-TERM OPTICAL OBSERVATIONS OF THE Be/X-RAY BINARY X PER

We present optical spectroscopic observations of X Per from 1999 to 2013 with the 2.16 m telescope at Xinglong Station and the 2.4 m telescope at Lijiang Station, National Astronomical Observatories of China. Combining these observations with the public optical photometric data, we find certain epochs of anti-correlations between the optical brightness and the intensity of the Hα and He i 6678 lines, which may be attributed to the mass ejections from the Be star; however, alternative explanations are also possible. The variability of the Fe ii 6317 line in the spectra of X Per might also be caused by the shocked waves formed after the mass ejections from the Be star. The X-ray activities of the system might also be connected with the mass ejection events from the Be star. When the ejected materials were transported from the surface of the Be star to the orbit of the neutron star, an X-ray flare could be observed in its X-ray light curves. We use the neutron star as a probe to constrain the motion of the ejected material in the circumstellar disk. With the diffusion time of the ejected material from the surface of the Be star to the orbit of neutron star, the viscosity parameter α of the circumstellar disk is estimated to be 0.39 and 0.28 for the different times, indicating that the disk around the Be star may be truncated by the neutron star at the 2:1 resonance radius and that a Type I X-ray outburst is unlikely to be observed in X Per.
On the structural theory of $\rm II_1$ factors of negatively curved groups

Ozawa showed that for any i.c. c. , hyperbolic group, the associated group factor is solid. Developing a new approach that combines some methods of Peterson, Ozawa and Popa, and Ozawa, we strengthen this result by showing that these factors are strongly solid. Using our methods in cooperation with a cocycle superrigidity result of Ioana, we show that profinite actions of lattices in Sp(n,1), n>1, are virtually W*-superrigid.
Auditory cortex encodes lipreading information through spatially distributed activity

Watching a speaker’s face improves speech perception accuracy. These benefits are owed, in part, to implicit lipreading abilities present in the general population. While it is established that lipreading can alter the perception of a heard word, it is unknown how information that is extracted from lipread words is transformed into a neural code that the auditory system can use. One influential, but untested, hypothesis is that visual speech modulates the population coded representations of phonetic and phonemic features in the auditory system. This model is largely supported by data showing that silent lipreading evokes activity in auditory cortex, but these activations could alternatively reflect general effects of arousal or attention, or the encoding of non-linguistic features such as visual timing information. This gap limits our understanding of how vision supports speech perception processes. To test the hypothesis that the auditory system encodes visual speech information, we acquired fMRI data from healthy adults and intracranial recordings from electrodes implanted in patients with epilepsy during auditory and visual speech perception tasks. Across both methods, linear classifiers successfully decoded the identity of silently lipread words using the spatial pattern of auditory cortex responses. Examining the time-course of classification using intracranial recordings, lipread words were classified at significantly earlier time-points relative to heard words, suggesting a predictive mechanism for facilitating speech. These results support a model in which the auditory system combines the joint neural distributions evoked by heard and lipread words to generate a more precise estimate of what was said. Significance Statement When we listen to someone speak in a noisy environment, watching their face can help us understand them better, largely due to automatic lipreading abilities. However, it unknown how lipreading information is transformed into a neural code that the auditory system can use. We used fMRI and intracranial recordings in patients to study how the brain processes silently lipread words and found that the auditory system encodes the identity of lipread words through spatially distributed activity. These results suggest that the auditory system combines information from both lipreading and hearing to generate more precise estimates of what is said, potentially by both activating the corresponding representation of the heard word and suppressing incorrect phonemic representations.
Microbial diversity estimation and hill number calculation using the hierarchical Pitman-Yor process

Background The human microbiome comprises the microorganisms that inhabit the various locales of the human body and plays a vital role in human health. The composition of a microbial population is often quantified through measures of species diversity, which summarize the number of species along with their relative abundances into a single value. In a microbiome sample there will certainly be species missing from the target population which will affect the diversity estimates. Methods We employ a model based on the hierarchical Pitman-Yor (HPY) process to model the species abundance distributions over multiple populations. The model parameters are estimated using a Gibbs sampler. We also derive estimates of species diversity, conditional and unconditional on the observed data, as a function of the HPY parameters Finally, we derive a general formula for the Hill numbers in the HPY context. Results We show that the Gibbs sampler for the HPY model performs well in simulations. We also show that the conditional estimates of diversity from the HPY model improve over naïve estimates when species are missing. Similarly the conditional HPY estimates tend to perform better than the naïve estimates especially when the number of individuals sampled from a population is small.
Failure to replicate long-range tunable attractions in colloidal system

Recently, a temperature-sensitive long-range attraction colloidal system exhibiting melting and pre-melting of colloidal crystals has been reported by Li et al.[1]. If it is true, it would be an ideal system to simulate a board range of phase transitions happening in atomic systems. We have reanalyzed their data in [1] and have discovered great inconsistency in their radial distribution functions g(r) and pair potentials u(r). We have tried to reproduce their experimental results but failed to find the temperature-sensitive long rang attraction as reported by Li et al. Based on our experimental observations, We conclude that the melting and premelting reported in their paper are non-equilibrium phenomena caused by non-uniform temperature in the samples of Li et al.
Protein Unfolding—Thermodynamic Perspectives and Unfolding Models

Protein unfolding is a dynamic cooperative process with many short-lived intermediates. Cooperativity means that similar molecular elements act dependently on each other. The thermodynamics of protein unfolding can be determined with differential scanning calorimetry (DSC). The measurement of the heat capacity provides the temperature profiles of enthalpy, entropy and free energy. The thermodynamics of protein unfolding is completely determined with these thermodynamic properties. We emphasise the model-independent analysis of the heat capacity. The temperature profiles of enthalpy H(T), entropy S(T) and free energy G(T) can be obtained directly by a numerical integration of Cp(T). In evaluating different models for protein unfolding. It is essential to simulate all thermodynamic properties, not only the heat capacity. A chemical equilibrium two-state model is a widely used approximation to protein unfolding. The model assumes a chemical equilibrium between only two protein conformations, the native protein (N) and the unfolded protein (U). The model fits the heat capacity Cp(T) quite well, but fails in simulating the other thermodynamic properties. In this review we propose a modification of the chemical equilibrium two-state model, which removes these inconsistencies. We also propose a new statistical-mechanical two-state model based on a simple, two-parameter partition function Z(T), from which all thermodynamic parameters can be derived. The thermodynamic predictions of the new models are compared to published DSC-experiments obtained with lysozyme, a globular protein, and β-lactoglobulin, a β-barrel protein. Good fits to all thermodynamic properties are obtained. In particular, the models predict a zero free energy for the native protein, which is confirmed experimentally by DSC. This is in contrast to the often-cited chemical equilibrium two-state model, which predict a positive free energy for the native protein. Two-state models use macroscopic fit parameters, the conformational enthalpy and the heat capacity difference between native and unfolded protein. These simulations provide no molecular insight. The review therefore includes a recently published multistate cooperative model based on physicality well-defined molecular parameters only.
Systematic mining and genetic characterization of regulatory factors for wheat spike development

20 Spike architecture largely affects grain number embraced, which is a key factor 21 influencing wheat grain yield. Here, we systematically explore the genetic regulation 22 network governing wheat spike development by integration of multi-omic data with 23 population genetics. Transcriptome and epigenome profile of shoot apex at eight 24 developmental stages were generated. Gain-of-chromatin accessibility and changes of 25 H3K27me3 coordinately associate with the progressive transcriptome alteration for 26 flowering. A core transcriptional regulation network (TRN) that likely drives various 27 meristematic cell identities transition to form spike was constructed. Integration of the 28 . CC-BY-NC-ND 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 11, 2022. ; https://doi.org/10.1101/2022.11. 11.516122 doi: bioRxiv preprint
Transcription-independent hold of the G1/S transition is exploited to cope with DNA replication stress

RB1 (retinoblastoma) members control the G1/S commitment as transcriptional repressors in eukaryotic cells. Here we uncover that an extra copy of RB1 equivalent (WHI7 or WHI5) is sufficient to bypass the indispensability of the central genomic checkpoint kinases Mec1ATR-Rad53CHK1 in Saccharomyces cerevisiae. Mec1-Rad53 directly phosphorylate Whi7/5, antagonizing their nuclear export or protein turnover upon replication stress. Through in vitro reconstitution, we show that Whi7 C-terminus directly binds and hinders S-CDK-Cks1 from processively phosphorylating Sic1. By microfluidic single-cell real-time quantitative imaging, we demonstrate that both Whi7 and Whi5 are required to flatten the degradation curve of the major S-CDK inhibitor Sic1 in vivo. These findings reveal an eclipsed transcription-independent role of Whi7 homologs, which is highlighted by genome integrity checkpoints to hold the G1/S transition instantly as a rapid response to unforeseeable replication threats. Key points Whi7 overexpression bypasses the essential function of Mec1 and Rad53 in a transcription-independent way. Whi7 is stabilized by checkpoint-mediated phosphorylation. Whi7 binds and hinders S-CDK-Cks1 from multi-phosphorylation of Sci1, thereby prolonging Sic1 degradation and G1/S transition.
SEN1 is responsible for molybdate transport into nodule symbiosomes for nitrogen fixation in Lotus japonicus

Symbiotic nitrogen fixation (SNF) in legume root nodules requires a steady supply of molybdenum (Mo) for synthesis of the iron-Mo cofactor for nitrogenase in bacteroids. For this nutrient to be exported by the host plant it must cross the peribacteroid membrane (PBM), however, the molybdate transporter responsible has not yet been identified. A Lotus japonicus symbiotic mutant, sen1, forms nodules that do not fix nitrogen; it has nodule defects and bacteroid degradation. The biochemical function and subcellular localization of SEN1 protein remains to be elucidated. Here, we found a new phenotype in which the SEN1 mutation resulted in increased Mo accumulation in the nodule host fractions but decreased Mo accumulation in the bacteroids at 10 days post inoculation. We identified the molybdate efflux transport activity of SEN1 via heterologous expression in yeast. SEN1 was expressed exclusively in nodules, and its expression was stable in response to varying Mo supply in nutrient solution. In situ immunostaining verified that the SEN1 protein is localized, in part, to the PBM in the rhizobium-infected cells. Taken together, these results confirmed that SEN1 is responsible for mediating molybdate efflux from the cytosol of nodule host cells to the symbiosomes for SNF. Furthermore, SEN1 mutation reduced the expression of nifD and nifK, suggesting that SEN1 may be pertinent to iron-Mo-cofactor assembly. This work fills the knowledge gap regarding how molybdate is allocated from the host plant to the bacteroids; such knowledge is critical for developing new SNF biological systems in non-legume plants. One-sentence summary SEN1 is localized partly in the peribacteroid membrane of nodule cells and mediates the molybdate exportation from the host plant cytosol to the symbiosomes for symbiotic nitrogen fixation.