bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian regulation of the GLYCINE-RICH RNA-BINDING PROTEIN gene by the master clock protein CIRCADIAN CLOCK-ASSOCIATED 1 is important for plant innate immunity
Authors: Gao Min , Zhang Chong , Angel William , Kwak Owen , Allison Jessica , Wiratan Linda , Hallworth Amelia , Wolf Julie , Lu Hua 
Published: November 2022

Abstract
Recent studies have demonstrated the importance of temporal regulation of pathogen defense by the circadian clock. However, our understanding of the molecular basis underlying this role of the circadian clock is still in its infancy. We report here the mechanism by which the Arabidopsis master clock protein CCA1 regulates an output target gene GRP7 for its circadian expression and function in pathogen defense. Our data firmly establish that CCA1 physically associates with the GRP7 promoter via the predicted CCA1-binding motif, evening element (EE). A site-directed mutagenesis study showed that while individual EE motifs differentially contribute to robust circadian expression of GRP7, abolishing all four EE motifs in the proximal GRP7 promoter disrupts rhythmicity of GRP7 expression and results in misalignment of defense signaling mediated by GRP7 and altered pathogen responses. This study provides a mechanistic link of the circadian regulation of an output gene to its biological function in pathogen defense, underscoring the importance of temporal control of plant innate immunity.
Neuron-periphery mitochondrial stress communication in aging and diseases
Authors: Li Jiasheng , Cui Jimeng , Tian Ye 
Published: November 2022

Abstract
The nervous system is the central hub of the body, detecting environmental and internal stimuli to regulate organismal metabolism via communications to the peripheral tissues. Mitochondria play an essential role in neuronal activity by supplying energy, maintaining cellular metabolism, and buffering calcium levels. A variety of mitochondrial conditions are associated with aging and age-related neurological disorders. Beyond regulating individual neuron cells, mitochondria also coordinate signaling in tissues and organs during stress conditions to mediate systemic metabolism and enable organisms to adapt to such stresses. In addition, peripheral organs and immune cells can also produce signaling molecules to modulate neuronal function. Recent studies have found that mitokines released upon mitochondrial stresses affect metabolism and the physiology of different tissues and organs at a distance. Here, we summarize recent advances in understanding neuron-periphery mitochondrial stress communication and how mitokine signals contribute to the systemic regulation of metabolism and aging with potential implications for therapeutic strategies.
Estimating the warm dark matter mass from strong lensing images with truncated marginal neural ratio estimation
Authors: Anau Montel Noemi , Coogan Adam , Correa Camila , Karchev Konstantin , Weniger Christoph 
Published: November 2022

ABSTRACT
Precision analysis of galaxy–galaxy strong gravitational lensing images provides a unique way of characterizing small-scale dark matter haloes, and could allow us to uncover the fundamental properties of dark matter’s constituents. Recently, gravitational imaging techniques made it possible to detect a few heavy subhaloes. However, gravitational lenses contain numerous subhaloes and line-of-sight haloes, whose subtle imprint is extremely difficult to detect individually. Existing methods for marginalizing over this large population of subthreshold perturbers to infer population-level parameters are typically computationally expensive, or require compressing observations into hand-crafted summary statistics, such as a power spectrum of residuals. Here, we present the first analysis pipeline to combine parametric lensing models and a recently developed neural simulation-based inference technique called truncated marginal neural ratio estimation (TMNRE) to constrain the warm dark matter halo mass function cut-off scale directly from multiple lensing images. Through a proof-of-concept application to simulated data, we show that our approach enables empirically testable inference of the dark matter cut-off mass through marginalization over a large population of realistic perturbers that would be undetectable on their own, and over lens and source parameter uncertainties. To obtain our results, we combine the signal contained in a set of images with Hubble Space Telescope resolution. Our results suggest that TMNRE can be a powerful approach to put tight constraints on the mass of warm dark matter in the multi-keV regime, which will be relevant both for existing lensing data and in the large sample of lenses that will be delivered by near-future telescopes.
Quality over quantity: Optimizing pulsar timing array analysis for stochastic and continuous gravitational wave signals
Authors: Speri Lorenzo , Porayko Nataliya K , Falxa Mikel , Chen Siyuan , Gair Jonathan R , Sesana Alberto , Taylor Stephen R 
Published: November 2022

ABSTRACT
The search for gravitational waves using Pulsar Timing Arrays (PTAs) is a computationally expensive complex analysis that involves source-specific noise studies. As more pulsars are added to the arrays, this stage of PTA analysis will become increasingly challenging. Therefore, optimizing the number of included pulsars is crucial to reduce the computational burden of data analysis. Here, we present a suite of methods to rank pulsars for use within the scope of PTA analysis. First, we use the maximization of the signal-to-noise ratio as a proxy to select pulsars. With this method, we target the detection of stochastic and continuous gravitational wave signals. Next, we present a ranking that minimizes the coupling between spatial correlation signatures, namely monopolar, dipolar, and Hellings & Downs correlations. Finally, we also explore how to combine these two methods. We test these approaches against mock data using frequentist and Bayesian hypothesis testing. For equal-noise pulsars, we find that an optimal selection leads to an increase in the log-Bayes factor two times steeper than a random selection for the hypothesis test of a gravitational wave background versus a common uncorrelated red noise process. For the same test but for a realistic European PTA (EPTA) data set, a subset of 25 pulsars selected out of 40 can provide a log-likelihood ratio that is 89 % of the total, implying that an optimally selected subset of pulsars can yield results comparable to those obtained from the whole array. We expect these selection methods to play a crucial role in future PTA data combinations.
Stellar population analysis of MaNGA early-type galaxies: IMF dependence and systematic effects
Authors: Bernardi M , Sánchez H Domínguez , Sheth R K , Brownstein J R , Lane R R 
Published: November 2022

ABSTRACT
We study systematics associated with estimating simple stellar population (SSP) parameters – age, metallicity [M/H], α-enhancement [α/Fe], and initial mass function (IMF) shape – and associated M*/L gradients, of elliptical slow rotators (E-SRs), fast rotators (E-FRs), and S0s from stacked spectra of galaxies in the MaNGA survey. These systematics arise from (i) how one normalizes the spectra when stacking; (ii) having to subtract emission before estimating absorption line strengths; (iii) the decision to fit the whole spectrum or just a few absorption lines; (iv) SSP model differences (e.g. isochrones, enrichment, IMF). The MILES+Padova SSP models, fit to the Hβ, 〈Fe〉, TiO2SDSS, and [MgFe] Lick indices in the stacks, indicate that out to the half-light radius Re: (a) ages are younger and [α/Fe] values are lower in the central regions but the opposite is true of [M/H]; (b) the IMF is more bottom-heavy in the center, but is close to Kroupa beyond about Re/2; (c) this makes M*/L about 2 × larger in the central regions than beyond Re/2. While the models of Conroy et al. return similar [M/H] and [α/Fe] profiles, the age and (hence) M*/L profiles can differ significantly even for solar abundances and a Kroupa IMF; different responses to non-solar abundances and IMF parametrization further compound these differences. There are clear (model independent) differences between E-SRs, E-FRs, and S0s: younger ages and less enhanced [α/Fe] values suggest that E-FRs and S0s are not SSPs, but relaxing this assumption is unlikely to change their inferred M*/L gradients significantly.
Host defense functions of the epididymal amyloid matrix
Authors: Myers Caitlyn , Hastert Mary Catherine , Cornwall Gail A 
Published: November 2022

AbstractThe epididymal lumen is an immunologically distinct environment. It maintains tolerance for the naturally antigenic spermatozoa to allow their maturation into functional cells while simultaneously defending against pathogens that can ascend the male tract and cause infertility. We previously demonstrated that a nonpathological amyloid matrix that includes several cystatin-related epididymal spermatogenic (CRES) subgroup family members is distributed throughout the mouse epididymal lumen but its function was unknown. Here, we reveal a role for the epididymal amyloid matrix in host defense and demonstrate that the CRES amyloids and CD-1 mouse epididymal amyloid matrix exhibit potent antimicrobial activity against bacterial strains that commonly cause epididymal infections in men. We show the CRES and epididymal amyloids use several defense mechanisms including bacterial trapping, disruption of bacterial membranes and promotion of unique bacterial ghost-like structures. Remarkably, these antimicrobial actions varied depending on the bacterial strain indicating CRES amyloids and the epididymal amyloids elicit strain-specific host defense responses. We also demonstrate that the CRES monomer and immature assemblies of the epididymal amyloid transitioned into advanced structures in the presence of bacteria, suggesting their amyloid-forming/shape-shifting properties allows for a rapid reaction to a pathogen and provides an inherent plasticity in their host defense response. Together, our studies reveal new mechanistic insight into how the male reproductive tract defends against pathogens. Future studies using a mouse model for human epididymitis are needed to establish the epididymal amyloid responses to pathogens in vivo. Broadly, our studies provide an example of why nature has maintained the amyloid fold throughout evolution.
Clinical utility of plasma cell-free DNA in gliomas
Authors: Carpenter Erica L , Bagley Stephen J 
Published: November 2022

Abstract
Noninvasive molecular profiling of tumors using plasma-based next-generation sequencing (NGS) is increasingly used to aid in diagnosis, treatment selection, and disease monitoring in oncology. In patients with glioma, however, the plasma cell-free DNA (cfDNA) tumor fraction, defined as the fractional proportion of circulating tumor-derived DNA (ctDNA) relative to total cfDNA, is especially low, in large part due to the blood-brain barrier. As a result, commercial plasma-based NGS assays, designed to screen for a small number of actionable genomic alterations, are not sensitive enough to guide the management of patients with glioma. As this has been long recognized in neuro-oncology, significant research efforts have been undertaken to improve the sensitivity of plasma ctDNA detection in patients with glioma and to understand the biology and clinical relevance of non-tumor-derived cfDNA, which makes up most of the total cfDNA pool. Here, we review key recent advances in the field of plasma cfDNA analysis in patients with glioma, including (1) the prognostic impact of pre-treatment and on-treatment total plasma cfDNA concentrations, (2) use of tumor-guided sequencing approaches to improve the sensitivity of ctDNA detection in the plasma, and (3) the emergence of plasma cfDNA methylomics for detection and discrimination of glioma from other primary intracranial tumors.
Liquid biopsy—from bench to bedside
Authors: Ray Amitava , Vohra Tarang K 
Published: November 2022

AbstractOver the last decade, molecular markers have become an integral part in the management of Central Nervous System (CNS) tumors. Somatic mutations that identify and prognosticate tumors are also detected in the bio-fluids especially the serum and CSF; the sampling of which is known as liquid biopsy (LB). These tumor-derived biomarkers include plasma circulating tumor cells (CTCs), cell-free DNA (cf/ctDNAs), circulating cell-free microRNAs (cfmiRNAs), circulating extracellular vesicles, or exosomes (EVs), proteins, and tumor educated platelets. Established in the management of other malignancies, liquid biopsy is becoming an important tool in the management of CNS tumors as well. This review presents a snapshot of the current state of LB research its potential and the possible pitfalls.
Advances in molecular biomarkers and liquid biopsy in gliomas
Authors: Mathios Dimitrios , Phallen Jillian 
Published: November 2022

Abstract
There have been significant strides toward understanding the molecular landscape of brain cancer. These advances have been focused on analyses of the tumor microenvironment and have recently expanded to include liquid biopsies to identify molecular biomarkers noninvasively. Moving from tissue to liquid-based analyses of molecular biomarkers has been challenging and currently, there are no approved noninvasive tests that are clinically useful. However, the emerging field of molecular liquid biopsy assay development in the neuro-oncology space has great potential to revolutionize the detection and monitoring of patients with brain cancer.
The Impact of the Danish National Smoking Ban From 2007 on the Incidence of Eight Smoking-related Diseases: A Nationwide Register-based Interrupted Time Series Analysis
Authors: Jarlstrup Nanna Schneekloth , Thygesen Lau Caspar , Grønbæk Morten Klöcker , Rod Morten Hulvej , Tolstrup Janne Schurmann 
Published: November 2022

AbstractBackgroundPrevious research has documented the effect of comprehensive smoking bans on preventing various adverse health outcomes in the years post-ban. In 2007, Denmark implemented a national smoking ban that prohibited indoor smoking in workplaces and public settings, although only partial restrictions applied in specific premises such as small bars, one-person offices, and in psychiatric units. We tested the hypothesis that the implementation of the national smoking ban was associated with a decrease in incidence of smoking-related morbidity in the Danish population compared to the pre-ban period.MethodsInterrupted time series analyses including the entire Danish population (≥30 years) was conducted. Information of hospitalizations and cause-specific mortality due to acute myocardial infarction, heart failure, hemorrhagic stroke, ischemic stroke, chronic obstructive pulmonary disease, cancer in bronchus and lung, cancer in lip, mouth, oral cavity, and pharynx, and bladder cancer were obtained from population-based registers. Poisson regression models accounting for seasonal variations and secular trends quantified immediate changes in incidence rates occurring at the time of the smoking ban as well as changes in the post-ban trend compared to pre-ban levels.ResultsOverall, we observed no consistent declines in incidence of cardiovascular diseases, chronic obstructive pulmonary disease, or the specific types of cancer in the post-ban period compared with the pre-ban period.ConclusionNo consistent reduction in incidence of smoking-related diseases was observed after the smoking ban was introduced in Denmark. This probably reflects that the Danish smoking ban included several exemptions, resulting in a less comprehensive ban compared to those introduced in other countries.ImplicationsIn this study, we found that the Danish national smoking ban from 2007 did not consistently reduced the incidence of eight smoking-related outcomes in the post-ban period compared to pre-ban levels. We argue that due to the exemptions in the smoking ban, which for example allowed smoking in specific premises of the care and nursing sector, in one-person offices, and small bars, the ban was not sufficiently comprehensive to influence smoking behavior and thereof the incidence of smoking-related morbidity. Our findings highlight the importance of introducing comprehensive legislative measures to yield largest health benefits at a population level.
Predictors of SARS-CoV-2 RNA From Nasopharyngeal Swabs and Concordance With Other Compartments in Nonhospitalized Adults With Mild to Moderate COVID-19
Authors: Moser Carlee , Li Jonathan Z , Eron Joseph J , Aga Evgenia , Daar Eric S , Wohl David A , Coombs Robert W , Javan Arzhang Cyrus , Bender Ignacio Rachel A , Jagannathan Prasanna , Ritz Justin , Sieg Scott F , Parikh Urvi M , Hughes Michael D , Currier Judith S , Smith Davey M , Chew Kara W ,   ACTIV-2/A5401 Study Team, Hosey Lara , Roa Jhoanna , Patel Nilam , Degli-Angeli Emily , Goecker Erin , Daza Glenda , Harb Socorro , Dragavon Joan , Aldrovandi Grace , Murtaugh William , Cooper Marlene , Gutzman Howard , Knowles Kevin , Bowman Rachel , Erhardt Bill , Adams Stacey 
Published: November 2022

Abstract

Background
Identifying characteristics associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding may be useful to understand viral compartmentalization, disease pathogenesis, and risks for viral transmission.

Methods
Participants were enrolled August 2020 to February 2021 in ACTIV-2/A5401, a placebo-controlled platform trial evaluating investigational therapies for mild-to-moderate coronavirus disease 2019 (COVID-19), and underwent quantitative SARS-CoV-2 RNA testing on nasopharyngeal and anterior nasal swabs, oral wash/saliva, and plasma at entry (day 0, pretreatment) and days 3, 7, 14, and 28. Concordance of RNA levels (copies/mL) across compartments and predictors of nasopharyngeal RNA levels were assessed at entry (n = 537). Predictors of changes over time were evaluated among placebo recipients (n = 265) with censored linear regression models.

Results
Nasopharyngeal and anterior nasal RNA levels at study entry were highly correlated (r = 0.84); higher levels of both were associated with greater detection of RNA in plasma and oral wash/saliva. Older age, White non-Hispanic race/ethnicity, lower body mass index (BMI), SARS-CoV-2 immunoglobulin G seronegativity, and shorter prior symptom duration were associated with higher nasopharyngeal RNA at entry. In adjusted models, body mass index and race/ethnicity associations were attenuated, but the association with age remained (for every 10 years older, mean nasopharyngeal RNA was 0.27 log10 copies/mL higher; P &lt; .001). Examining longitudinal viral RNA levels among placebo recipients, women had faster declines in nasopharyngeal RNA than men (mean change, −2.0 vs −1.3 log10 copies/mL, entry to day 3; P &lt; .001).

Conclusions
SARS-CoV-2 RNA shedding was concordant across compartments. Age was strongly associated with viral shedding, and men had slower viral clearance than women, which could explain sex differences in acute COVID-19 outcomes.
Palliative Rehabilitation in Acute Inpatient Rehabilitation: Prognostic Factors and Functional Outcomes in Patients with Cancer
Authors: Tennison Jegy M , Asher Arash , Hui David , Javle Milind , Bassett Roland L , Bruera Eduardo 
Published: November 2022

AbstractBackgroundPrognosis has a vital role for patients with cancer undergoing palliative rehabilitation in acute inpatient rehabilitation. This study aimed to identify the proportion of patients who survived &lt;2 months after discharge and the associated prognostic factors.Materials and MethodsThis was a secondary analysis of a retrospective study of 163 consecutive patients admitted to acute inpatient rehabilitation from September 1, 2017, to February 28, 2018 at a cancer center. Baseline demographics, clinical characteristics, and putative prognostic factors, including Activity Measure for Post-Acute Care (AM-PAC) functional scores, were analyzed.ResultsOf 163 patients, 27 (17%; 95% CI, 11-23) died within 60 days of discharge. These patients were more likely to be male (OR = 2.83; 95% CI, 1.16-6.92; P = .017); have longer hospital stays (OR = 1.02; 95% CI, 1-1.04; P = .015); receive ≥ weekly packed red blood cell (OR = 5.31; 95% CI, 1.86-15.1; P = .003) or platelet (OR = 4.57; 95% CI, 1.44-14.5; P = .014) transfusions; have lower AM-PAC daily activity scores upon discharge (OR = 0.90; 95% CI, 0.83-0.97; P = .006); and have lower AM-PAC basic mobility scores upon admission (OR = 0.91; 95% CI, 0.85-0.98; P = .018) and discharge (OR = 0.88; 95% CI, 0.82-0.94; P = &lt;.001). Multivariate analysis showed that the male sex (OR = 2.71; 95% CI, 1.03-7.15; P = .037) was independently associated with ≤2 months survival, whereas AM-PAC basic mobility score at admission of &gt;33 (OR = 0.24, 95% CI, 0.07-0.79; P = .022) was less likely.ConclusionApproximately 1 in 6 patients who completed acute inpatient rehabilitation died within 2 months of discharge, had poorer baseline functional status, and were less likely to regain function than those who lived longer.
Climate change and economic activity: evidence from US states
Authors: Mohaddes Kamiar , Ng Ryan N C , Pesaran M Hashem , Raissi Mehdi , Yang Jui-Chung 
Published: November 2022

Abstract
We investigate the long-term macroeconomic effects of climate change across 48 US states over the period 1963–2016 using a novel econometric strategy that links deviations of temperature and precipitation (weather) from their long-term moving-average historical norms (climate) to various state-specific economic performance indicators at the aggregate and sectoral levels. We show that climate change has a long-lasting adverse impact on real output in various states and economic sectors, and on labour productivity and employment in the United States. Moreover, in contrast to most cross-country results, our within US estimates tend to be asymmetrical with respect to deviations of climate variables (including precipitation) from their historical norms.
Transitioning unions: what constitutes a just transition for Swedish trade unions?
Authors: Gärdebo Johan 
Published: November 2022

Abstract
The inclusion of ‘just transition’ in the Paris Agreement in 2015 has inspired subsequent attempts, and hopes, to bridge jobs versus climate divide in attempts to decarbonize industrial society. But what are the imperatives for a just tr[ansition of the workforce? And what are the nationally defined development priorities for the creation of decent work and quality jobs? Through interviews with Swedish trade union representatives from Sweden’s three largest industrial emitters (steel, petroleum refining, cement) along with representatives at the central level, this study illustrates contrasting interpretations of what constitutes a just transition. The main tensions concern the time a climate transition is allowed to take; if policies should support local inhabitants or global concerns over climate change; why allegiances are limited to the industrial town or encompass a wider trade union movement; and whether national politics or European coordination is what makes a transition ‘just’. While central levels of Swedish trade unions understand just transition in international and intergenerational terms, local level trade unions advocate for an emplaced understanding of just transition. Given the risk of growing conflicts between different segments of trade unions over the issue of climate transition policies, a progressive alliance between the labour- and climate movements is improbable as matters stand at present.