bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling multiphase gases in cosmological simulations using compressible multifluid hydrodynamics
Authors: Weinberger R , Hernquist L 
Published: December 2022

ABSTRACT
The diffuse medium in and around galaxies can exist in a multiphase state: small, cold gas clouds contributing significantly to the total mass embedded in pressure equilibrium with a hotter, more diffuse volume-filling component. Modelling this multiphase state in cosmological simulations poses a significant challenge due to the requirements to spatially resolve the clouds and consequently the interactions between the phases. In this paper, we present a novel method to model this gas state in cosmological hydrodynamical simulations. We solve the compressible two-fluid hydrodynamic equations using a moving-mesh finite-volume method and define mass, momentum, and energy exchange terms between the phases as operator-split source terms. Using a stratified flow model, our implementation is able to maintain volume fraction discontinuities in pressure equilibrium to machine precision, allowing for the treatment of both resolved and unresolved multiphase fluids. The solver remains second order accurate on smooth hydrodynamics problems. We use the source and sink terms of an existing two-phase model for the interstellar medium to demonstrate the value of this type of approach in simulations of galaxy formation, compare it to its effective equation of state implementation, and discuss its advantages in future large-scale simulations of galaxy formation.
The interconnection between galaxy mergers, AGN activity, and rapid quenching of star formation in simulated post-merger galaxies
Authors: Quai Salvatore , Byrne-Mamahit Shoshannah , Ellison Sara L , Patton David R , Hani Maan H 
Published: December 2022

ABSTRACT
We investigate the role of galaxy mergers on supermassive black hole (SMBH) accretion and star formation quenching in three state-of-the-art cosmological simulations with contrasting physics models: EAGLE, Illustris, and IllustrisTNG (TNG). We find that recently coalesced ‘post-mergers’ in all three simulations have elevated SMBH accretion rates by factors of ∼2–5. However, rapid (within 500 Myr of coalescence) quenching of star formation is rare, with incidence rates of $0.4{{\ \rm per\ cent}}$ in Illustris, $4.5{{\ \rm per\ cent}}$ in EAGLE, and $10{{\ \rm per\ cent}}$ in TNG. The rarity of quenching in post-mergers results from substantial gas reservoirs that remain intact after the merger. The post-mergers that do successfully quench tend to be those that had both low pre-merger gas fractions as well as those that experience the largest gas losses. Although rare, the recently quenched fraction of post-mergers is still elevated compared to a control sample of non-mergers by factors of two in TNG and 11 in EAGLE. Conversely, quenching is rarer in Illustris post-mergers than in their control. Recent observational results by Ellison et al. have found rapid quenching to be at least 30 times more common in post-mergers, a significantly higher excess than found in any of the simulations. Our results therefore indicate that whilst merger-induced SMBH accretion is a widespread prediction of the simulation, its link to quenching depends sensitively on the physics models, and that none of the subgrid models of the simulations studied here can fully capture the connection between mergers and rapid quenching seen in observations.
Constraints on clumps in the representative wind of the WN8 Wolf–Rayet star HD 96548 = WR 40 with simultaneous broad-band light and linear-polarization variability
Authors: Ignace R , Moffat A F J , Robert C , Drissen L 
Published: December 2022

ABSTRACT
We report precision ground-based broad-band optical intensity and linear-polarization light curves for the sky’s brightest WN8 star, WR 40. WN8 stars are notorious for their high level of variability, stemming from stochastic clumps in their strong winds that are slower and less hot than the winds of most other Wolf–Rayet (WR) stars. We confirm previous results that many WR stars display an amplitude of variability that is an order of magnitude higher in photometry than in polarimetry. For the first time, the unique nature of near simultaneity of our photometric and polarimetric observations of WR 40 allows us to check whether the two types of variability show correlated behaviour, of which we find none. Assuming simple temporal functions for the brightness and polarization of individual clumps, a model for simulated light curves is found to reproduce the properties of the observations, specifically the absence of correlation between photometric and polarimetric variations, the ratio of standard deviations for photometric and polarimetric variability, and the ratio of the average intrinsic polarization relative to its standard deviation. Mapping the solution for time variability to a spatial coordinate suggests that the wind clumps of WR 40 are free-free emitting in addition to light scattering.
CHD8suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing
Authors: Kerschbamer Emanuela , Arnoldi Michele , Tripathi Takshashila , Pellegrini Miguel , Maturi Samuele , Erdin Serkan , Salviato Elisa , Di Leva Francesca , Sebestyén Endre , Dassi Erik , Zarantonello Giulia , Benelli Matteo , Campos Eric , Basson M Albert , Gusella James F , Gustincich Stefano , Piazza Silvano , Demichelis Francesca , Talkowski Michael E , Ferrari Francesco , Biagioli Marta 
Published: December 2022

AbstractDisruptive mutations in the chromodomain helicase DNA-binding protein 8 gene (CHD8) have been recurrently associated with autism spectrum disorders (ASDs). Here we investigated how chromatin reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes and correlates with altered alternative splicing patterns of 462 genes implicated in ‘regulation of RNA splicing’ and ‘mRNA catabolic process’. Mass spectrometry analysis uncovered a novel interaction between CHD8 and the splicing regulator heterogeneous nuclear ribonucleoprotein L (hnRNPL), providing the first mechanistic insights to explain the CHD8 suppression-derived splicing phenotype, partly implicating SETD2, a H3K36me3 methyltransferase. In summary, our results point toward broad molecular consequences of CHD8 suppression, entailing altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD.
Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells
Authors: Luo Wentian , Hickman Alison B , Genzor Pavol , Ghirlando Rodolfo , Furman Christopher M , Menshikh Anna , Haase Astrid , Dyda Fred , Wilson Matthew H 
Published: December 2022

Abstract
DNA transposon systems are widely used in mammalian cells for genetic modification experiments, but their regulation remains poorly understood. We used biochemical and cell-based assays together with AlphaFold modeling and rational protein redesign to evaluate aspects of piggyBac transposition including the previously unexplained role of the transposase N-terminus and the need for asymmetric transposon ends for cellular activity. We found that phosphorylation at predicted casein kinase II sites in the transposase N-terminus inhibits transposition, most likely by preventing transposase–DNA interactions. Deletion of the region containing these sites releases inhibition thereby enhancing activity. We also found that the N-terminal domain promotes transposase dimerization in the absence of transposon DNA. When the N-terminus is deleted, the transposase gains the ability to carry out transposition using symmetric transposon left ends. This novel activity is also conferred by appending a second C-terminal domain. When combined, these modifications together result in a transposase that is highly active when symmetric transposon ends are used. Our results demonstrate that transposase N-terminal phosphorylation and the requirement for asymmetric transposon ends both negatively regulate piggyBac transposition in mammalian cells. These novel insights into the mechanism and structure of the piggyBac transposase expand its potential use for genomic applications.
Australian genome-wide association study confirms higher female risk for adult glioma associated with variants in the region of CCDC26
Authors: Alpen Karen , Vajdic Claire M , MacInnis Robert J , Milne Roger L , Koh Eng-Siew , Hovey Elizabeth , Harrup Rosemary , Bruinsma Fiona , Nguyen Tuong L , Li Shuai , Joseph David , Benke Geza , Dugué Pierre-Antoine , Southey Melissa C , Giles Graham G , Rosenthal Mark , Drummond Katharine J , Nowak Anna K , Hopper John L , Kapuscinski Miroslaw , Makalic Enes 
Published: December 2022

Abstract

Background
Glioma accounts for approximately 80% of malignant adult brain cancer and its most common subtype, glioblastoma, has one of the lowest 5-year cancer survivals. Fifty risk-associated variants within 34 glioma genetic risk regions have been found by genome-wide association studies (GWAS) with a sex difference reported for 8q24.21 region. We conducted an Australian GWAS by glioma subtype and sex.

Methods
We analyzed genome-wide data from the Australian Genomics and Clinical Outcomes of Glioma (AGOG) consortium for 7 573 692 single nucleotide polymorphisms (SNPs) for 560 glioma cases and 2237 controls of European ancestry. Cases were classified as glioblastoma, non-glioblastoma, astrocytoma or oligodendroglioma. Logistic regression analysis was used to assess the associations of SNPs with glioma risk by subtype and by sex.

Results
We replicated the previously reported glioma risk associations in the regions of 2q33.3 C2orf80, 2q37.3 D2HGDH, 5p15.33 TERT, 7p11.2 EGFR, 8q24.21 CCDC26, 9p21.3 CDKN2BAS, 11q21 MAML2, 11q23.3 PHLDB1, 15q24.2 ETFA, 16p13.3 RHBDF1, 16p13.3 LMF1, 17p13.1 TP53, 20q13.33 RTEL, and 20q13.33 GMEB2 (P &lt; .05). We also replicated the previously reported sex difference at 8q24.21 CCDC26 (P = .0024) with the association being nominally significant for both sexes (P &lt; .05).

Conclusions
Our study supports a stronger female risk association for the region 8q24.21 CCDC26 and highlights the importance of analyzing glioma GWAS by sex. A better understanding of sex differences could provide biological insight into the cause of glioma with implications for prevention, risk prediction and treatment.
Gradual transitions in genetics and songs between coastal and inland populations of Setophaga townsendi
Authors: Ore Madelyn J , Wang Silu , Irwin Darren E 
Published: December 2022

Abstract
Setophaga townsendi is a species of wood warbler (family Parulidae) in northwestern North America that has geographic structure in the mitochondrial and nuclear genomes: while interior populations have differentiated mitonuclear ancestry from the sister species S. occidentalis, coastal populations have a mix of inland and S. occidentalis mitonuclear ancestries. This coastal to inland transition in genomic ancestry raises the possibility of similar geographic structure in phenotypic traits, especially those involved in mate choice. Using qualitative and multivariate approaches, we investigated whether there is a sharp transition between coastal and inland populations in both song and in nuclear DNA. We find there is a shallow geographic cline in Type I song but not in Type II song. Nuclear DNA shows a gradient between coast and inland. There is little correlation between variation in song and the isolation-by-distance pattern in the nuclear DNA. Learned songbird song is shaped by both genetic and cultural processes. There has been a debate on whether song learning promotes or slows down population differentiation. By comparing the within-species variation in song and genetic structures, we can expand our understanding of the dynamic interplay between mating signals and population differentiation.
Reconstructing Extinct Hominin Diets
Authors: Grine Frederick E. 
Published: December 2022

AbstractKnowledge of the dietary habits of extinct hominin species and ancient human populations is central to any understanding of their ecology. Owing to the importance of diet in both biological and cultural realms, multifarious approaches have been employed in its elucidation: archaeology, dental calculus, pathology, functional morphology, dental microwear, biogeochemistry, and genetics and genomics. Some of these paradigms have deep historical roots, while others are owing to more recent technical advances. Some produce data that are indirectly related to the object of discovery, resulting in hypothetical dietary inferences. A number provide more direct evidence about the foods that were consumed. Each method of discovery has strengths and limitations that should be recognized when the resultant data are employed in diet retrodiction. Not all approaches are equally relevant to the temporal scale of the hominin evolutionary record. Seven avenues of dietary investigation are reviewed, several of which have been employed in tandem. Reconstructions that combine data from different methods will inevitably provide more complete depictions of palaeodietary ecology.
The added value of predictive biomarkers in treat-to-target strategies for rheumatoid arthritis patients: a conceptual modelling study
Authors: Wientjes Maike H M , Ulijn Evy , Kievit Wietske , Landewé Robert B M , Meek Inger , den Broeder Nathan , van Herwaarden Noortje , van den Bemt Bart J F , Verhoef Lise M , den Broeder Alfons A 
Published: December 2022

Abstract

Objectives
To quantify the additional value of a hypothetical biomarker predicting response to treatment for RA regarding efficacy and costs by using a modelling design.

Methods
A Markov model was built comparing a usual care T2T strategy with a biomarker-steered strategy for RA patients starting biologic therapy. Outcome measures include time spent in remission or low disease activity (LDA) and costs. Four additional scenario analyses were performed by varying biomarker or clinical care characteristics: (i) costs of the biomarker; (ii) sensitivity and specificity of the biomarker; (iii) proportion of eligible patients tapering; and (iv) medication costs.

Results
In the base model, patients spent 2.9 months extra in LDA or remission in the biomarker strategy compared with usual care T2T over 48 months. Total costs were €43 301 and €42 568 for, respectively, the usual care and biomarker strategy, and treatment costs accounted for 91% of total costs in both scenarios. Cost savings were driven due to patients in the biomarker strategy experiencing remission or LDA earlier, and starting tapering sooner. Cost-effectiveness was not so much driven by costs or test characteristics of the biomarker (scenario 1/2), but rather by the level of early and proactive tapering and drug costs (scenarios 3/4).

Conclusions
The use of a biomarker for prediction of response to b/tsDMARD treatment in RA can be of added value to current treat-to-target clinical care. However, gains in efficacy are modest and cost gains are depending on a combination of early proactive tapering and high medication costs.
Envisioning translational hyperscanning: how applied neuroscience might improve family-centered care
Authors: Provenzi Livio , Roberti Elisa , Capelli Elena 
Published: December 2022

AbstractFrom the very beginning of their life, human beings are immersed in a social and interactive environment that contributes to shaping their social and cognitive development under typical and at-risk conditions. In order to understand human development in its bidirectional relationship with the social environment, we need to develop a ‘complexity-sensitive’ approach in neuroscience. Recent advances have started to do so with the application of hyperscanning techniques which involve recording adult and child neural activity simultaneously and highlighting the presence of similar patterns of brain activity in the dyad. Numerous studies focused on typically developing children have been published in recent years with the application of this technique to different fields of developmental research. However, hyperscanning techniques could also be extremely beneficial and effective in studying development in atypical and clinical populations. Such application, namely translational hyperscanning, should foster the transition toward a two-brain translational neuroscience. In this paper, we envision how the application of hyperscanning to atypical and clinical child populations can inform family-centered care for children and their parents.
6K1, NIa-VPg, NIa-Pro, and CP of Wheat Streak Mosaic Virus Are Collective Determinants of Wheat Streak Mosaic Disease in Wheat
Authors: Tatineni Satyanarayana , Alexander Jeffrey , Nunna Haritha 
Published: December 2022

Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) is the causal agent of the most economically important wheat streak mosaic disease of wheat ( Triticum aestivum) in the Great Plains region of the United States. WSMV determinants responsible for wheat streak mosaic disease in wheat are unknown. Triticum mosaic virus (TriMV), a wheat-infecting virus, was used as an expression vector for the transient expression of each of the WSMV-encoded cistrons in wheat. WSMV-encoded 6K1, NIa-VPg, NIa-Pro, and CP cistrons in TriMV elicited symptoms specific to different stages of wheat streak mosaic disease without significantly affecting the genomic RNA accumulation. WSMV 6K1 produced early wheat streak mosaic disease-like symptoms of severe chlorotic streaks and patches. NIa-VPg and CP caused severe chlorotic streaks, followed by moderate stunting (only with NIa-VPg) of wheat, mimicking early- and mid-stage symptoms of wheat streak mosaic disease. WSMV NIa-Pro caused mild chlorotic streaks, followed by dark green leaves with severe stunting, representing the late symptoms of wheat streak mosaic disease. Collectively, these data suggest that cumulative effects of WSMV-encoded 6K1, NIa-VPg, NIa-Pro, and CP are responsible for different stages of wheat streak mosaic disease symptoms in wheat. Furthermore, deletion analysis of wheat streak mosaic disease determinants revealed that complete 6K1 and NIa-Pro, amino acids 3 to 60 and 121 to 197 of NIa-VPg, and amino acids 101 to 294 of CP are responsible for wheat streak mosaic disease-like symptoms in wheat. This study suggests that management strategies for wheat streak mosaic disease in wheat should target WSMV determinants of the disease phenotype.
Accelerated Healing from Severe Radiation Dermatitis Using Noncontact, Low-frequency Ultrasound-assisted Saline Wash Therapy
Authors: Luu Yen , Han Joseph , Owji Shayan , Kamat Samir , Luu Chuc , Ungar Jonathan , Gulati Nicholas 
Published: December 2022

ABSTRACTRadiotherapy (RT) is a modality for cancer management that frequently causes critical injury to tissues adjacent to the targeted cancer site. Acute radiation dermatitis (RD) is one of the most common adverse effects of RT and may lead to secondary infection, disfigurement, and discontinuation of therapy. The authors report the efficacy of a multidisciplinary collaboration between radiation oncology, dermatology, and wound care teams in the management of severe, acute RD. This case report describes the use of noncontact, low-frequency ultrasound (NCLFU)-assisted saline wash therapy leading to accelerated healing of severe RD in an older man treated with RT for scalp squamous cell carcinoma. Although NCLFU-assisted saline wash therapy provides gentle debridement of wound surfaces and has demonstrated efficacy in the management of chronic wounds, the potential role for NCLFU therapy in RD management has not yet been explored.
A Novel Classification for Diabetic Foot Ulcers of the First Ray
Authors: Tamir Eran , Rabau Oded , Beer Yiftah , Smorgick Yossi , Kaufman Hanna , Finestone Aharon S. 
Published: December 2022

ABSTRACTOBJECTIVEDiabetic foot ulcers of the first ray result from several distinct biomechanical mechanisms related to anatomical deformities, which must be addressed if surgical offloading is contemplated. The objective of this study was to create a classification of the anatomical deformities of first-ray ulcers that could lead to better standardization of treatment and reporting.METHODSThe authors performed a file review of patients with diabetic neuropathy diagnosed with first-ray ulcers over a period of 3 years in an outpatient setting. Anatomical deformities were diagnosed clinically and reported with ulcer location. The primary classification was the metatarsophalangeal joint, the interphalangeal joint, and the distal phalanx.RESULTSRecords for 59 patients (mean age, 62 years) with University of Texas A1 and A2 ulcers were reviewed. Mean ulcer duration was 2 months. The more common deformities were hallux valgus (41%), hallux valgus interphalangeus (14%), and hallux malleus (20%), and these were primarily associated with metatarsophalangeal, interphalangeal joint, and tip-of-toe ulcers, respectively (P< .0001).CONCLUSIONSBy classifying ulcer locations, the relevant corrective surgery may be chosen. Although some prophylactic procedures may be safe and effective, prophylactic hallux valgus correction in the diabetic foot requires further study.
Implementing a Trauma-Informed Approach at a Student-Run Clinic for Individuals Seeking Asylum
Authors: Jaradeh Katrin , Sergi Francesco , Kivlahan Coleen , Nava Gonzales Cesar , Cury Mar , DeFries Triveni 
Published: December 2022

Problem
Health care professionals complete forensic medical evaluations (FMEs) to corroborate evidence of persecution among individuals seeking asylum. Many FMEs are conducted at student-run clinics for individuals seeking asylum (or student-run asylum clinics; SRACs). Trauma-informed care (TIC) recognizes that trauma is pervasive and seeks to mitigate reexposure to trauma in health care interactions. Given that FMEs involve recalling trauma, TIC is an ideal model for supporting the individuals involved in an FME.

Approach
The authors operationalized TIC principles in an SRAC model (the Human Rights Cooperative) at the University of California, San Francisco. Between April 2019 and April 2022, the SRAC provided 3 to 10 pro bono FMEs per month, as well as community referrals for individuals seeking asylum, clinician and medical student training on FMEs and TIC, and research on FMEs. This report describes the SRAC operations, organized by the 10 implementation domains of the Substance Abuse and Mental Health Services Administration guidance to organizations for implementing a trauma-informed approach.

Outcomes
Between April 2019 and April 2022, the SRAC completed 160 FMEs. Sixty-nine clinicians performed FMEs, and 119 first-year medical students participated in the accompanying elective. Qualitative survey responses by clinicians, lawyers, students, and clients (individuals seeking asylum) highlighted the trauma-informed principles of safety; trustworthiness and transparency; empowerment, voice, and choice; peer support; collaboration and mutuality; and cultural, historical, and gender issues. All students who acted as leaders sustained their engagement with the SRAC over time.

Next Steps
Future research should use validated tools to assess secondary trauma and resilience within SRACs. The SRAC concept, which engages medical students and experienced clinicians in learning skills that can be used in the pursuit of health justice and equity, should be expanded and supported in U.S. medical schools across the country, which is facing unprecedented levels of migration.