Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin architectural alterations due to null mutation of a major CG methylase in rice.

Associations between 3D chromatin architectures and epigenetic modifications have been characterized in animals. However, any impact of DNA methylation on chromatin architecture in plants is understudied, which is confined to Arabidopsis thaliana. Because plant species differ in genome size, composition, and overall chromatin packing, it is unclear to what extent findings from A. thaliana hold in other species. Moreover, the incomplete chromatin architectural profiles and the low-resolution Hi-C (high-throughput chromosome conformation capture) data from A. thaliana have hampered characterizing its subtle chromatin structures and their associations with DNA methylation. We constructed a high-resolution Hi-C interaction map for the null OsMET1-2 (the major CG methyltransferase in rice) mutant (osmet1-2) and isogenic wild-type rice (WT). Chromatin structural changes occurred in osmet1-2, including intra-/inter-chromosomal interactions, compartment transition, and TAD (topologically associated domains) variations. Our findings provide novel insights into the potential function of DNA methylation in TAD formation in rice and confirmed DNA methylation plays similar essential roles in chromatin packing in A. thaliana and rice. This article is protected by copyright. All rights reserved.
Caspase-8 and FADD prevent spontaneous ZBP1 expression and necroptosis

Significance Caspase-8 and Fas-associated death domain (FADD) play key roles in the regulation of cell death by necroptosis. The absence of either protein results in early embryonic lethality due to the activation of the kinase receptor interacting protein kinase-3 (RIPK3) and its phosphorylation of the necroptosis executioner, mixed-lineage kinase-like (MLKL). We genetically engineered and characterized a mouse model to monitor MLKL phosphorylation in the absence of necroptosis in vivo. Ablation of caspase-8 or FADD resulted in the transcriptional upregulation in several tissues of Z-DNA binding protein-1 (ZBP1), a cytosolic nucleic acid sensor capable of activating RIPK3, and ZBP1 was required for spontaneous phosphorylation of MLKL. Our findings provide a mechanism by which the FADD/Caspase-8 complex prevents necroptosis.
Bereaved Caregiver Perspectives on the End of Life in Pediatric Patients With Ventricular Assist Devices

OBJECTIVES: Ventricular assist devices (VADs) are increasingly used in pediatric heart failure as bridges to heart transplantation, although 25% will die with VADs. Family experiences in this population are not well-described. The objective is to understand bereaved families’ perspectives on VAD and end-of-life decision-making. DESIGN: Semistructured interviews with bereaved caregivers of pediatric VAD patients. SETTING: Tertiary children’s hospital. PATIENTS: Families of six pediatric VAD patients who died from 2014 to 2020. INTERVENTIONS: Not available. MEASUREMENTS AND MAIN RESULTS: Applying a grounded theory framework, interviews were coded by two independent readers using qualitative software. Themes were discussed in iterative multidisciplinary meetings. Participants were interviewed at a median 2.4 years after their child died. Three major themes emerged: 1) “lack of regret” for VAD implantation despite the outcome; 2) “caregiver-child accord” (via patient’s verbal assent or physical cues) at implantation and end-of-life was important in family decision-making; and 3) development of a “local surrogate family” (medical team and peer families) provided powerful support. CONCLUSIONS: Bereaved families’ perspectives provide insight into quality decision-making for major interventions and end-of-life care in pediatric patients with chronic illness who face decisions regarding technology dependence.
Binary Lenses in OGLE-III EWS Database. Seasons 2006--2008

We present 27 binary lens candidates from OGLE-III Early Warning System database for the seasons 2006--2008. The candidates have been selected by visual light curves inspection. Our sample of binary lens events consists now of 78 stellar systems and 7 extrasolar planets of OGLE-III published elsewhere. Examining the distribution of stellar binaries we find that the number of systems per logarithmic mass ratio interval increases with mass ratio q, in contradiction with our previous findings. Stellar binaries belong to the region 0.03<q<1 and there is a gap between them and a separate population of planets.
Iraqi Muslim Women and Primary Healthcare Providers’ Perspectives and Experiences in the Clinic Visit in the Western United States

Immigrants to the U.S. are subject to healthcare disparities due to differences in language, culture, religion, and gender. Clinic visits are particularly challenging for both health providers and patients due to communication barriers, expectations of the visit that are informed by past experiences, strongly held values, and gender. This qualitative study used critical ethnography and postcolonial feminism to explore perceptions and experiences of 15 Iraqi Muslim women with refugee backgrounds and 10 primary healthcare providers as they shared about their clinical encounters. Semi-structured interviews and field notes were analyzed with a postcolonial feminist framework that highlighted perspectives of health providers and Iraqi Muslim women in regard to representation, gender, and values. Health providers were aware of the need for gender-concordant care and preservation of modesty for Muslim patients. Gaps in care stemmed from a need for greater understanding of values and expectations. Improvement in the quality of care requires a venue for open discourse between providers, staff, and patients to improve mutual understanding.
Policy interventions and competing management paradigms shape the long-term distribution of forest harvesting across the landscape

Significance Humans have dramatically affected ecosystems and stocks of natural resources worldwide, often by sequentially harvesting the most profitable components of the environment. Although research has examined historical harvesting patterns in forests and broad issues of resource depletion, little has investigated how “high grading” along gradients of productivity and accessibility has changed the forest landscape over time. Analysis of a dataset from coastal British Columbia, Canada shows a tendency to log down the value chain when management choices are unconstrained and the potential of government policy to impose a greater stewardship ethic on harvesting behavior. This history of serial depletion of profitable environmental components has left a legacy of reduced value in the forest, with implications for intergenerational and intercommunity equity.
Outer Rotation Curve of the Galaxy with VERA I: Trigonometric Parallax of IRAS 05168+3634

We report measurement of trigonometric parallax of IRAS 05168+3634 with VERA. The parallax is 0.532 ± 0.053 mas, corresponding to a distance of 1.88 −0.17 kpc. This result is significantly smaller than the previous distance estimate of 6 kpc based on kinematic distance. This drastic change in the source distance revises not only physical parameters of IRAS 05168+3634, but also its location of the source, placing it in the Perseus arm rather than the Outer arm. We also measure proper motions of the source. A combination of the distance and the proper motions with systemic velocity yields rotation velocity (Θ) of 227 −11 km s −1 at the source, assuming Θ0 = 240 km s. Our result combined with previous VLBI results for six sources in the Perseus arm indicates that the sources rotate systematically slower than the Galactic rotation velocity at the LSR. In fact, we show observed disk peculiar motions averaged over the seven sources in the Perseus arm as (Umean, Vmean) = (11 ± 3, −17 ± 3) km s, indicating that these seven sources are systematically moving toward the Galactic center, and lag behind the Galactic rotation.
Guided Internet-Delivered Treatment for Depression: Scoping Review

Background Studies on guided internet-delivered treatment have demonstrated promising results for patients with depressive disorder. Objective The aim of this study was to provide an overview of this research area and identify potential gaps in the research. Methods In this scoping review, web-based databases were used to identify research papers published between 2010 and 2022 where guided internet-delivered treatment was administered to participants with depressive disorders, a standardized rating scale of depressive symptoms was used as the primary outcome measure, and the treatment was compared with a control condition. Results A total of 111 studies were included, and an overview of the studies was provided. Several gaps in the research were identified regarding the design of the studies, treatments delivered, participant representation, and treatment completion. Conclusions This review provides a comprehensive overview of the research area, and several research gaps were identified. The use of other designs and active control conditions is recommended. Future studies should provide access to treatment manuals, and more replications should be conducted. Researchers should aim to include underrepresented populations and provide reports of comorbidities. Definitions of adequate dosage, reports of completion rates, and reasons for treatment dropout are recommended for future studies.
AN HST SURVEY OF THE HIGHEST-VELOCITY EJECTA IN CASSIOPEIA A

We present Hubble Space Telescope WFC3/IR images of the Cassiopeia A supernova remnant that survey its high-velocity, S-rich debris in the NE jet and SW counterjet regions through [S iii] λλ9069, 9531 and [S ii] λλ10,287–10,370 line emissions. We identify nearly 3400 sulfur emitting knots concentrated in ∼120° wide opposing streams, almost triple the number previously known. The vast majority of these ejecta knots lie at projected distances well out ahead of the remnant’s forward blast wave and main shell ejecta, extending to angular distance of 320 ″ ? > to the NE and 260 ″ ? > to the SW from the center of expansion. Such angular distances imply undecelerated ejecta knot transverse velocities of 15,600 and 12,700 km s−1, respectively, assuming an explosion date ≈ 1670 ? > AD and a distance of 3.4 kpc. Optical spectra of knots near the outermost tip of the NE ejecta stream show strong emission lines of S, Ca, and Ar. We estimate a total mass ∼0.1 M ⊙ ? > and a kinetic energy of at least ∼ 1 × 10 50 ? > erg for S-rich ejecta in the NE jet and SW counterjet. Although their broadness and kinetic energy argue against the Cas A SN being a jet-induced explosion, the jets are kinematically and chemically distinct from the rest of the remnant. This may reflect an origin in a jet-like mechanism that accelerated interior material from a Si-, S-, Ar-, and Ca-rich region near the progenitor’s core up through the mantle and H-, He-, N-, and O-rich outer layers with velocities that greatly exceeded that of the rapidly expanding photosphere.
eta/s at finite coupling

We compute the ratio of the coefficient of shear viscosity to entropy density at finite coupling and at zero chemical potential using holographic duality, up to ten derivative terms in the low energy effective five-dimensional action, of a specific kind, which may or may not be connected to the supersymmetric completion of type IIB theory. The result suggests that this ratio can be positive only for the 8th derivative term even with the form of that term in the action as C{sup ij}{sub kl}C{sup kl}{sub mn}C{sup mn}{sub rs}C{sup rs}{sub ij}, where C is the Weyl tensor.
HST+COS spectra of the double white dwarf CSS 41177 place the secondary inside the pulsational instability strip

We present Hubble Space Telescope + Cosmic Origins Spectrograph (HST+COS) data of the eclipsing double white dwarf binary CSS 41177. Due to the temperature difference between the two white dwarfs, the HST+COS far-ultraviolet data are dominated by the hot, primary white dwarf and allow us to precisely measure its temperature (T1). Using eclipse observations, we also tightly constrain the temperature of the cooler secondary white dwarf (T2). Our results, where T1 = 22 439 ± 59 K and T2 = 10 876 ± 32 K, with the uncertainties being purely statistical, place the secondary inside and close to the blue edge of the empirical instability strip for low-temperature hydrogen-atmosphere white dwarfs. Dedicated high-speed photometry is encouraged to probe for the presence of pulsations, which will constrain the border of the instability strip as well as probe a new region of low gravity within the strip.
The Relationship Among Autistic Traits, Impulsivity, and Functionality in Patients With Obsessive-Compulsive Disorder

Abstract Obsessive-compulsive disorder (OCD) is a chronic mental disorder that causes disabilities. This study investigated the relationship among impulsivity, autistic traits, and disabilities in patients with OCD. We included 88 patients with OCD and 90 healthy volunteers without any mental disorders. The participants were evaluated using the Yale-Brown Obsessive-Compulsive Scale, Autism Spectrum Quotient (AQ), Barratt Impulsiveness Scale-11 (BIS-11), and World Health Organization Disability Assessment Schedule (WHODAS 2.0). Regression analyses revealed that AQ-attention switching and BIS-attentional subscale scores were associated with WHODAS-overall score in the OCD group (p = 0.017 and p = 0.034, respectively). In the OCD group, AQ total, social skills, and communication subdomain scores partially mediated the relationship between impulsivity and disability. BIS total, attentional, and nonplanning subscale scores partially mediated the relationship between autistic traits and disability. Developing new treatment strategies for cognitive recovery, in addition to traditional treatment approaches in patients with OCD, may help increase functionality in patients with OCD.
Functional characterization of enhancer activity during a long terminal repeat's evolution

Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1- and CEBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences revealed that LTR18A elements have generally lost regulatory activity over time through sequence changes, with the largest effects occurring owing to mutations in the AP-1 and CEBP motifs. We observed that the two motifs are conserved at higher rates than expected based on neutral evolution. Finally, we identified LTR18A elements as potential enhancers in the human genome, primarily in epithelial cells. Together, our results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements.
Berry Phase Physics in Free and Interacting Fermionic Systems

Berry phase plays an important role in many non-trivial phenomena over a broad range of many-body systems. In this thesis we focus on the Berry phase due to the change of the particles' momenta, and study its effects in free and interacting fermionic systems. We start with reviewing the semi-classical kinetic theory with Berry phase for a non-interacting ensemble of fermions -- a Berry Fermi gas -- which might be far-from-equilibrium. We particularly review the famous Berry phase contribution to the anomalous Hall current. We then provide a concrete and general path integral derivation for the semi-classical theory. Then we turn to the specific example of Weyl fermion, which exhibits the profound quantum phenomenon of chiral anomaly; we review how this quantum effect, and its closely related chiral magnetic effect and chiral vortical effect, arise from Berry phase in the semi-classical kinetic theory. We also discuss how Lorentz symmetry in the kinetic theory of Weyl fermion, seemly violated by the Berry phase term, is realized non-trivially; we provide a physical interpretation for this non-trivial realization, and discuss its mathematical foundation in Wigner translation. Next, we turn towards interacting fermionic systems. We consider Fermi liquid near equilibrium, and propose the Berry Fermi liquid theory -- the extension to Landau Fermi liquid theory incorporating Berry phase (and other) effects. In our proposed Berry Fermi liquid theory, we can show the Berry phase is a Fermi surface property, qualitatively unmodified by interactions. But there also arise new effects from interactions, most notably the emergent electric dipole moment which contributes to the anomalous Hall current in addition to the usual Berry phase contribution. We prove our proposed Berry Fermi liquid theory from quantum field theory to all orders in Feynman diagram expansion under very general assumptions.
Escape from breast tumor dormancy: The convergence of obesity and menopause

Significance Postmenopausal (PM) obesity is associated with an increased risk of, and a poor prognosis for, breast cancer (BC); however, clinically relevant therapeutic strategies for obesity-associated PM BC are currently nonexistent. We report that PM obesity promotes the escape from tumor dormancy via the early acquisition of the switch to the vascular phenotype (SVP) and initiates aggressive tumor growth via increased neovascularization. Finally, we show that targeting neovascularization via a multikinase angiogenesis inhibitor delayed the obesity-mediated SVP, prolonged tumor latency, reduced tumor frequency, and increased tumor-free survival in obese PM mice.
Beliefs and attitudes of drug and alcohol clinicians when considering referral of Aboriginal clients to involuntary drug and alcohol treatment: A qualitative study

Abstract Introduction Involuntary drug and alcohol treatment occurs in many countries and its role is often controversial. This can be a particular concern in relation to First Nations or other culturally distinct populations. This study explores beliefs and attitudes of drug and alcohol clinicians when considering referral of Aboriginal Australians to involuntary drug and alcohol treatment in New South Wales (NSW), Australia. Methods The Involuntary Drug and Alcohol Treatment program (IDAT) is legislated by the NSW Drug and Alcohol Treatment Act 2007. There are two IDAT units—in urban (Sydney, four beds) and regional NSW (Orange, eight beds). NSW Health drug and alcohol clinicians who had referred clients to IDAT between 2016 and 2018 were invited to participate in a semi‐structured 1:1 interview. Eleven clinicians (n = 2, male) from six local health districts (urban through to remote) agreed to participate. A descriptive qualitative analysis of responses was conducted. Results Two key themes summarised the beliefs and attitudes that clinicians reported influencing them when considering referral of Aboriginal Australians to involuntary drug and alcohol treatment in NSW: (i) dilemma between saving someone's life and being culturally safe; and (ii) need for holistic wrap‐around care. Discussion and Conclusions Almost all clinicians were worried that being in IDAT would further erode their Aboriginal client's autonomy and be retraumatising. Strategies are needed to support the involvement of Aboriginal‐specific services in IDAT processes and ensure local support options for clients on discharge. Future research should examine the effectiveness, acceptability and feasibility of involuntary drug and alcohol treatment programs.
Host galaxy colour gradients and accretion disc obscuration in AEGIS z ∼ 1 X-ray-selected active galactic nuclei

We describe the effect of active galactic nucleus (AGN) light on host galaxy optical and UV-optical colours, as determined from X-ray-selected AGN host galaxies at z ∼ 1, and compare the AGN host galaxy colours to those of a control sample matched to the AGN sample in both redshift and stellar mass. We identify as X-ray-selected AGNs 8.7 +4 ―3 per cent of the red-sequence control galaxies, 9.8 ± 3 per cent of the blue-cloud control galaxies and 14.7 +4 ―3 per cent of the green-valley control galaxies. The nuclear colours of AGN hosts are generally bluer than their outer colours, while the control galaxies exhibit redder nuclei. AGNs in blue-cloud host galaxies experience less X-ray obscuration, while AGNs in red-sequence hosts have more, which is the reverse of what is expected from general considerations of the interstellar medium. Outer and integrated colours of AGN hosts generally agree with the control galaxies, regardless of X-ray obscuration, but the nuclear colours of unobscured AGNs are typically much bluer, especially for X-ray luminous objects. Visible point sources are seen in many of these, indicating that the nuclear colours have been contaminated by AGN light and that obscuration of the X-ray radiation and visible light are therefore highly correlated. Red AGN hosts are typically slightly bluer than red-sequence control galaxies, which suggests that their stellar populations are slightly younger. We compare these colour data to current models of AGN formation. The unexpected trend of less X-ray obscuration in blue-cloud galaxies and more in red-sequence galaxies is problematic for all AGN feedback models, in which gas and dust is thought to be removed as star formation shuts down. A second class of models involving radiative instabilities in hot gas is more promising for red-sequence AGNs but predicts a larger number of point sources in red-sequence AGNs than is observed. Regardless, it appears that multiple AGN models are necessary to explain the varied AGN host properties discussed in the current work. Finally, we find that integrated optical and UV - optical colours are not strongly affected by X-ray-selected AGNs except in rare cases (< 10 per cent), where the AGN is very luminous, unobscured and/or visible as a point source.
First-principles simulations of a graphene-based field-effect transistor

We improvise a novel approach to carry out first-principles simulations of graphene-based vertical field effect tunneling transistors that consist of a graphene$|${\it h}-BN$|$graphene multilayer structure. Within the density functional theory framework, we exploit the effective screening medium (ESM) method to properly treat boundary conditions for electrostatic potentials and investigate the effect of gate voltage. The distribution of free carriers and the band structure of both top and bottom graphene layers are calculated self-consistently. The dielectric properties of {\it h}-BN thin films sandwiched between graphene layers are computed layer-by-layer following the theory of microscopic permittivity. We find that the permittivities of BN layers are very close to that of crystalline {\it h}-BN. The effect of interface with graphene on the dielectric properties of {\it h}-BN is weak, according to an analysis on the interface charge redistribution.