bluuebunny/crossref_metadata_2025 huggingface dataset:
Population III star formation in an X-ray background – I. Critical halo mass of formation and total mass in stars
Authors: Park Jongwon , Ricotti Massimo , Sugimura Kazuyuki
Published: October 2021

The first luminous objects forming in the universe produce radiation backgrounds in the far-ultraviolet and X-ray bands that affect the formation of Population III stars. Using a grid of cosmological hydrodynamics zoom-in simulations, we explore the impact of the Lyman–Warner (LW) and X-ray radiation backgrounds on the critical dark matter (DM) halo mass for Population III star formation and the total mass in stars per halo. We find that the LW radiation background lowers the H2 fraction and delays the formation of the Population III stars. On the other hand, X-ray irradiation anticipates the redshift of collapse and reduces the critical halo mass, unless the X-ray background is too strong and gas heating shuts down gas collapse into the haloes and prevents star formation. Therefore, an X-ray background can increase the number of DM haloes forming Population III stars by about a factor of 10, but the total mass in stars forming in each halo is reduced. This is because X-ray radiation increases the molecular fraction and lowers the minimum temperature of the collapsing gas (or equivalently the mass of the quasi-hydrostatic core) and therefore slows down the accretion of the gas on to the central protostar.
Population III star formation in an X-ray background – II. Protostellar discs, multiplicity, and mass function of the stars
Authors: Park Jongwon , Ricotti Massimo , Sugimura Kazuyuki
Published: October 2021

Disc fragmentation plays an important role in determining the number of primordial stars (Pop III stars), their masses, and hence the initial mass function. In this second paper of a series, we explore the effect of uniform far-ultraviolet H2-photodissociating and X-ray radiation backgrounds on the formation of Pop III stars using a grid of high-resolution zoom-in simulations. We find that, in an X-ray background, protostellar discs have lower surface density and higher Toomre Q parameter, so they are more stable. For this reason, X-ray irradiated discs undergo fewer fragmentations and typically produce either binary systems or low-multiplicity systems. In contrast, the cases with weak or no X-ray irradiation produce systems with a typical multiplicity of 6 ± 3. In addition, the most massive protostar in each system is smaller by roughly a factor of 2 when the disc is irradiated by X-rays, due to lower accretion rate. With these two effects combined, the initial mass function of fragments becomes more top-heavy in a strong X-ray background and is well described by a power law with slope 1.53 and high-mass cutoff of 61 M⊙. Without X-rays, we find a slope 0.49 and cutoff mass of 229 M⊙. Finally, protostars migrate outward after their formation likely due to the accretion of high-angular momentum gas from outside and the migration is more frequent and significant in absence of X-ray irradiation.
A multimission catalogue of ultraluminous X-ray source candidates
Authors: Walton D J , Mackenzie A D A , Gully H , Patel N R , Roberts T P , Earnshaw H P , Mateos S
Published: October 2021

We present a new, multimission catalogue of ultraluminous X-ray source (ULX) candidates, based on recent data releases from each of the XMM–Newton, Swift, and Chandra observatories (the 4XMM-DR10, 2SXPS, and CSC2 catalogues, respectively). This has been compiled by cross-correlating each of these X-ray archives with a large sample of galaxies primarily drawn from the HyperLEDA archive. Significant efforts have been made to clean the sample of known non-ULX contaminants (e.g. foreground stars, background active galactic nuclei, supernovae), and also to identify ULX candidates that are common to the different X-ray catalogues utilized, allowing us to produce a combined ‘master’ list of unique sources. Our sample contains 1843 ULX candidates associated with 951 different host galaxies, making it the largest ULX catalogue compiled to date. Of these, 689 sources are catalogued as ULX candidates for the first time. Our primary motivation is to identify new sources of interest for detailed follow-up studies, and within our catalogue we have already found one new extreme ULX candidate that has high S/N data in the archive: NGC 3044 ULX1. This source has a peak luminosity of LX,peak ∼ 1040 erg s−1, and the XMM–Newton spectrum of the source while at this peak flux is very similar to other, better-studied extreme ULXs that are now understood to be local examples of super-Eddington accretion. This likely indicates that NGC 3044 ULX1 is another source accreting at super-Eddington rates. We expect that this catalogue will be a valuable resource for planning future observations of ULXs – both with our current and future X-ray facilities – to further improve our understanding of this enigmatic population.
Sgr B2 hard X-ray emission with INTEGRAL after 2009: still detectable?
Authors: Kuznetsova Ekaterina , Krivonos Roman , Lutovinov Alexander , Clavel Maïca
Published: October 2021

The molecular cloud Sgr B2 is a natural Compton mirror in the Central Molecular Zone. It is believed that the observed fading of the Sgr B2 X-ray emission in continuum and the Fe Kα 6.4 keV line indicates past X-ray flare activity of the supermassive black hole Sgr A⋆. Sgr B2 was investigated by the INTEGRAL observatory in the hard X-ray in 2003–2009, showing clear decay of its hard X-ray emission. In this work, we present a long-term time evolution of the Sgr B2 hard X-ray continuum after 2009, associated with the hard X-ray source IGR J17475−2822 as observed by INTEGRAL. The 30–80 keV sky maps, obtained in 2009–2019, demonstrate a significant excess spatially consistent with IGR J17475−2822. The observed 2003–2019 light curve of IGR J17475−2822 is characterized by a linear decrease by a factor of ∼2 until 2011, after which it reaches a constant level of ∼1 mCrab. The source spectrum above 17 keV is consistent with a power-law model with Γ = 1.4 and a high-energy cut-off at ∼43 keV. The Sgr B2 residual emission after ∼2011 shows a good correspondence with models of X-ray emission due to the irradiation of the molecular gas by hard X-rays and low-energy cosmic ray ions. We discuss the possible origin of the residual Sgr B2 emission after 2011 within these models, including theoretically predicted multiply scattered emission.
Polycyclic aromatic hydrocarbons and the ionized gas in galaxies with active nuclei
Authors: Silva-Ribeiro A , Krabbe A C , Canelo C M , Monteiro A F , Sales Dinalva A , Hernandez-Jimenez J A , Andrade D P P
Published: October 2021

We present a study for a sample of galaxies with active nuclei to characterize the main type of PAH molecules present in these objects and the local physical conditions of their irradiating sources, as well as the characteristics of the residing ionized gas, by combining optical and infrared data. Photoionization models were built with the cloudy code to reproduce optical emission line ratios in combination with PAH intensity ratios. We find that the species containing 10−82 carbon atoms are the most abundant in the sample. We suggest that family of species with only two or three fused rings of and a nitrogen hanging, such as small aromatic amides are important targets worthy of consideration in future experimental/theoretical as well as observational studies. We find that the AGN photoionization models reproduce most of the observational data in the log (6.2/11.3) versus log ([${\rm N\, {\small II}}$] λ6584/H α) diagram with the optical to X-ray spectral index of αox = −1.4. The flux of small PAH, as well as the flux of ionized PAHs and PANH, decrease as the logarithm of the ionization parameter (log U) increases. The 6.2/11.3 PAH intensity ratio presents an anti correlation between the oxygen abundance and log U.Finally, we found that the ionization degree of PAH species increases with the decreasing of the 11.3/7.7 ratio and the log U, in agreement with the models proposed by Draine & Li.
Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants
Authors: Jongepier Evelien , Séguret Alice , Labutin Anton , Feldmeyer Barbara , Gstöttl Claudia , Foitzik Susanne , Heinze Jürgen , Bornberg-Bauer Erich
Published: October 2021

The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-making ants are social parasites that exploit the work force of closely related ant species for social behaviors such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in insect societies. We investigated the evolutionary fate of these chemoreceptors and found that slave-making ant genomes harbored only half as many gustatory receptors as their hosts’, potentially mirroring the outsourcing of foraging tasks to host workers. In addition, parasites had fewer odorant receptors and their loss shows striking patterns of convergence across independent origins of parasitism, in particular in orthologs often implicated in sociality like the 9-exon odorant receptors. These convergent losses represent a rare case of convergent molecular evolution at the level of individual genes. Thus, evolution can operate in a way that is both repeatable and reversible when independent ant lineages lose important social traits during the transition to a parasitic lifestyle.
Hypoxia-inducible factor-1β is essential for upregulation of the hypoxia-induced FLT1 gene in placental trophoblasts
Authors: Sasagawa Tadashi , Nagamatsu Takeshi , Yanagisawa Manami , Fujii Tomoyuki , Shibuya Masabumi
Published: October 2021

Placental hypoxia and increased levels of maternal blood anti-angiogenic protein, soluble fms-like tyrosine kinase-1 (sFLT1), are associated with the pathogenesis of pre-eclampsia. We have demonstrated that hypoxia-inducible factor (HIF)-2α mediates the upregulation of the hypoxia-induced FLT1 gene in trophoblasts and their cell lines. Here, we investigated the involvement of HIF-1β, which acts as a dimerization partner for HIF-α, in the upregulation of the FLT1 gene via hypoxia. We confirmed the interactions between HIF-1β and HIF-2α in the nuclei of BeWo, JAR and JEG-3 cells under hypoxia via co-immunoprecipitation. We found that hypoxia-induced upregulation of the FLT1 gene in BeWo cells and secretion of sFLT1 in human primary trophoblasts were significantly reduced by siRNAs targeting HIF-1β. Moreover, the upregulation of the FLT1 gene in BeWo cells induced by dimethyloxaloylglycine (DMOG) was also inhibited by silencing either HIF-2α or HIF-1β mRNA. It was recently shown that DNA demethylation increases both basal and hypoxia-induced expression levels of the FLT1 gene in three trophoblast-derived cell lines. In the demethylated BeWo cells, siRNAs targeting HIF-2α and HIF-1β suppressed the further increase in the expression levels of the FLT1 gene due to hypoxia or treatment with DMOG. However, luciferase reporter assays and bisulfite sequencing revealed that a hypoxia response element (−966 to −962) of the FLT1 gene is not involved in hypoxia or DMOG-induced upregulation of the FLT1 gene. These findings suggest that HIF-1β is essential for the elevated production of sFLT1 in the hypoxic trophoblasts and that the HIF-2α/HIF-1β complex may be a crucial therapeutic target for pre-eclampsia.
What Is Cosmopsychism?
Authors: Ganeri Jonardon , Shani Itay
Published: October 2021

With the deepening crisis of physicalism and the decline in its status as a sustainable research programme, philosophers of mind have begun to investigate the alternative idea—now commonly designated panpsychism—that consciousness is a fundamental feature of nature, and that the mental states, properties, and events exhibited by human beings are metaphysically grounded in the conscious actuality of reality’s most basic entities. Cosmopsychism is the thesis that the cosmos as a whole displays psychological properties, cosmopsychological properties as we might call them, and that the mental states of human beings, and indeed human beings themselves as individual subjects of experience, are metaphysically grounded in the cosmopsychological properties of the cosmos. Richly sophisticated varieties of cosmopsychism can be found in the ancient Sanskrit classics, the Upaniṣads, and more particularly in those Vedānta philosophers who provide interpretations of these texts. The papers in this issue are explorations of the connections and explanatory potential between contemporary work on cosmopsychism and arguments from the Sanskrit tradition.
The Playful Self-Involution of Divine Consciousness: Sri Aurobindo’s Evolutionary Cosmopsychism and His Response to the Individuation Problem
Authors: Medhananda Swami
Published: October 2021

This article argues that the Indian philosopher-mystic Sri Aurobindo (1872–1950) espoused a sophisticated form of cosmopsychism that has great contemporary relevance. After first discussing Aurobindo’s prescient reflections on the “central problem of consciousness” and his arguments against materialist reductionism, I explain how he developed a panentheistic philosophy of “realistic Adwaita” on the basis of his own spiritual experiences and his intensive study of the Vedāntic scriptures. He derived from this realistic Advaita philosophy a highly original doctrine of evolutionary cosmopsychism, according to which the Divine Saccidānanda is “involved” in everything in the universe and gradually manifests itself at each stage of the evolutionary process from matter to life to mind, and ultimately, to Supermind—the final stage that is yet to come, upon the attainment of which we will attain knowledge of our true divine nature as Saccidānanda. I then reconstruct Aurobindo’s novel solution to the individuation problem, according to which the Divine Saccidānanda individuates into various distinct consciousnesses by playfully limiting itself through a process of “exclusive concentration.” Finally, I highlight the continued relevance of Aurobindo’s evolutionary cosmopsychism by bringing him into conversation with Itay Shani, a contemporary proponent of cosmopsychism.
A Buddhist Response to the Quality-Combination Problem for Panpsychism
Authors: Chadha Monima
Published: October 2021

Abhidharma Buddhist philosophy presents a version of what is now often called “panprotopsychism.” The most pressing group of problems for the Abhidharma panprotopsychism, like all other panpsychist views, is what Seager calls “the combination problem.” There are at least three versions of the problem: the subject-combination problem; the quality-combination problem; and the structure-combination problem. I begin with the Abhidharma Buddhist version of panprotopsychism and its account of conscious experience. The main focus of this paper is to show that Abhidharma panprotopsychist account of conscious experience solves the quality-combination problem. In the last and closing Section, I look at other versions of the combination problem, primarily the subject-combination problem and the structural problem and provide a sketch of the Abhidharma Buddhist response to these.
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs
Authors: Cai Li , Xuan Jiajia , Lin Qiao , Wang Junhao , Liu Shurong , Xie Fangzhou , Zheng Lingling , Li Bin , Qu Lianghu , Yang Jianhua
Published: October 2021

RNA polymerase III (Pol III) transcribes hundreds of non-coding RNA genes (ncRNAs), which involve in a variety of cellular processes. However, the expression, functions, regulatory networks and evolution of these Pol III-transcribed ncRNAs are still largely unknown. In this study, we developed a novel resource, Pol3Base (http://rna.sysu.edu.cn/pol3base/), to decode the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. The current release of Pol3Base includes thousands of regulatory relationships between ∼79 000 ncRNAs and transcription factors by mining 56 ChIP-seq datasets. By integrating CLIP-seq datasets, we deciphered the interactions of these ncRNAs with >240 RNA binding proteins. Moreover, Pol3Base contains ∼9700 RNA modifications located within thousands of Pol III-transcribed ncRNAs. Importantly, we characterized expression profiles of ncRNAs in >70 tissues and 28 different tumor types. In addition, by comparing these ncRNAs from human and mouse, we revealed about 4000 evolutionary conserved ncRNAs. We also identified ∼11 403 tRNA-derived small RNAs (tsRNAs) in 32 different tumor types. Finally, by analyzing somatic mutation data, we investigated the mutation map of these ncRNAs to help uncover their potential roles in diverse diseases. This resource will help expand our understanding of potential functions and regulatory networks of Pol III-transcribed ncRNAs.
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Authors: Pratt Henry E , Andrews Gregory R , Phalke Nishigandha , Huey Jack D , Purcaro Michael J , van der Velde Arjan , Moore Jill E , Weng Zhiping
Published: October 2021

The human genome contains ∼2000 transcriptional regulatory proteins, including ∼1600 DNA-binding transcription factors (TFs) recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX, and in vivo, using techniques including ChIP-seq. We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. Factorbook is publicly available at www.factorbook.org; we will continue to expand the resource as ENCODE Phase IV data are released.
Functional asymmetry and chemical reactivity of CsoR family persulfide sensors
Authors: Fakhoury Joseph N , Zhang Yifan , Edmonds Katherine A , Bringas Mauro , Luebke Justin L , Gonzalez-Gutierrez Giovanni , Capdevila Daiana A , Giedroc David P
Published: October 2021

CstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.
ImmReg: the regulon atlas of immune-related pathways across cancer types
Authors: Jiang Tiantongfei , Zhou Weiwei , Chang Zhenghong , Zou Haozhe , Bai Jing , Sun Qisen , Pan Tao , Xu Juan , Li Yongsheng , Li Xia
Published: October 2021

Immune system gene regulation perturbation has been found to be a major cause of the development of various types of cancer. Numbers of mechanisms contribute to gene expression regulation, thus, systematically identification of potential regulons of immune-related pathways is critical to cancer immunotherapy. Here, we comprehensively chart the landscape of transcription factors, microRNAs, RNA binding proteins and long noncoding RNAs regulation in 17 immune-related pathways across 33 cancers. The potential immunology regulons are likely to exhibit higher expressions in immune cells, show expression perturbations in cancer, and are significantly correlated with immune cell infiltrations. We also identify a panel of clinically relevant immunology regulons across cancers. Moreover, the regulon atlas of immune-related pathways helps prioritizing cancer-related genes (i.e. ETV7, miR-146a-5p, ZFP36 and HCP5). We further identified two molecular subtypes of glioma (cold and hot tumour phenotypes), which were characterized by differences in immune cell infiltrations, expression of checkpoints, and prognosis. Finally, we developed a user-friendly resource, ImmReg (http://bio-bigdata.hrbmu.edu.cn/ImmReg/), with multiple modules to visualize, browse, and download immunology regulation. Our study provides a comprehensive landscape of immunology regulons, which will shed light on future development of RNA-based cancer immunotherapies.
Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones
Authors: Popova Liudmila V , Nagarajan Prabakaran , Lovejoy Callie M , Sunkel Benjamin D , Gardner Miranda L , Wang Meng , Freitas Michael A , Stanton Benjamin Z , Parthun Mark R
Published: October 2021

A central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
Evaluation of severity of delayed graft function in kidney transplant recipients
Authors: Schrezenmeier Eva , Müller Mia , Friedersdorff Frank , Khadzhynov Dmytro , Halleck Fabian , Staeck Oliver , Dürr Michael , Zhang Kun , Eckardt Kai-Uwe , Budde Klemens , Lehner Lukas J
Published: October 2021

Background

The most common definition of delayed graft function (DGF) relies on dialysis during the first week post-transplant and does not consider DGF severity. The impact of DGF severity on long-term graft outcome remains controversial.

Methods

We analysed 627 deceased-donor kidney transplant recipients (KTRs) transplanted in 2005–2015 at our centre for DGF severity, associated risk factors and long-term consequences of DGF.

Results

We found 349 (55.7%) KTRs with DGF, which were classified into four groups according to DGF duration (0–1, 2–7, 8–14, >14 days) and were compared with KTR with no DGF. A longer duration of DGF was associated with progressive worsening of 10-year death-censored graft survival {no DGF: 88.3% [95% confidence interval (CI) 82.4–94.2]; 0–1 day: 81.3% [95% CI 68.2–94.4], 2–7 days: 61.5% [95% CI 43.1.1–79.9], 8–14 days: 66.6% [95% CI 47.4–85.8], >14 days: 51.2% [95% CI 33–69.4]; P < 0.001}. In kidneys with a Kidney Donor Profile Index (KDPI) ≥85%, all DGF severity groups demonstrated reduced graft survival. However, in the <85% KDPI kidneys, only >14 days DGF duration showed worse outcomes.

Conclusions

DGF had a duration-dependent effect on graft survival, which varied depending on the KDPI. Of note, 0- to 1-day DGF showed comparable results to no DGF in the whole cohort.
Global Implementation of Tobacco Demand Reduction Measures Specified in Framework Convention on Tobacco Control
Authors: Hiilamo Heikki , Glantz Stanton
Published: October 2021

Introduction

The world’s first global health treaty, WHO Framework Convention on Tobacco Control (FCTC) aims to reduce tobacco product demand by focusing on tobacco taxes, smoking bans, health warning labels, and tobacco advertising bans. Previous studies almost unanimously suggest that FCTC has prompted countries to implement more effective tobacco demand reduction policies.

Aims and Methods

By taking into account the pre-FCTC status, country income level, and state capacity we studied if ratifying FCTC was associated with tobacco demand reduction measures in 2018/2019. We used logistic regression to assess the association of FCTC ratification with adoption demand reduction measures, accounting for years since ratification, baseline status, and other covariates.

Results

Except for taxes, state of tobacco policy implementation before FCTC ratification did not predict adoption of FCTC policies. Time since FCTC ratification was associated with implementing smoking bans and pictorial HWLs. In contrast, while the tax rate prior to FCTC ratification was positively associated with increased taxes after FCTC ratification, time since FCTC ratification was marginally negatively associated with increases in tobacco taxes.

Conclusions

While the FCTC was followed by implementation of compliant demand reduction policies, there are still many parties that have not implemented the FCTC, particularly increasing taxes and ending tobacco advertising and promotions.

Implications

We assessed changes in tobacco demand reductions measures over 22 years in 193 countries. By using internal tobacco industry documents, we were able establish a baseline before the FCTC negotiations. Unlike previous studies, we included four tobacco demand reductions measures: tobacco taxes, smoking bans, health warning labels, and tobacco advertising ban. The limitation of the study is that we do not have data to describe if demand reduction measures are actually enforced or what their effect on tobacco consumption is.
Are systematic reviews addressing nutrition for cancer prevention trustworthy? A systematic survey of quality and risk of bias
Authors: Zajac Joanna F , Storman Dawid , Swierz Mateusz J , Koperny Magdalena , Weglarz Paulina , Staskiewicz Wojciech , Gorecka Magdalena , Skuza Anna , Wach Adam , Kaluzinska Klaudia , Bochenek-Cibor Justyna , Johnston Bradley C , Bala Malgorzata M
Published: October 2021

Context

The last 30 years have yielded a vast number of systematic reviews and/or meta-analyses addressing the link between nutrition and cancer risk.

Objective

The aim of this survey was to assess overall quality and potential for risk of bias in systematic reviews and meta-analyses (SRMAs) that examined the role of nutrition in cancer prevention.

Data Sources

MEDLINE, Embase, and the Cochrane Library databases were searched (last search performed November 2018).

Study Selection

Studies identified as SRMAs that investigated a nutritional or dietary intervention or exposure for cancer prevention in the general population or in people at risk of cancer and in which primary studies had a comparison group were eligible for inclusion. Screening, data extraction, and quality assessment were conducted independently by 2 reviewers.

Data Extraction

Altogether, 101 studies were randomly selected for analysis. The methodological quality and risk of bias were evaluated using the AMSTAR-2 and ROBIS tools, respectively.

Results

Most SRMAs included observational studies. Less than 10% of SRMAs reported a study protocol, and only 51% of SRMAs assessed the risk of bias in primary studies. Most studies conducted subgroup analyses, but only a few reported tests of interaction or specified subgroups of interest a priori. Overall, according to AMSTAR-2, only 1% of SRMAs were of high quality, while 97% were of critically low quality. Only 3% had a low risk of bias, according to ROBIS.

Conclusions

This systematic survey revealed substantial limitations with respect to quality and risk of bias of SRMAs. SRMAs examining nutrition and cancer prevention cannot be considered trustworthy, and results should be interpreted with caution. Peer reviewers as well as users of SRMAs should be advised to use the AMSTAR-2 and/or ROBIS instruments to help to determine the overall quality and risk of bias of SRMAs.

Systematic Review Registration

PROSPERO registration number CRD42019121116.
Rapid Changes in Nasopharyngeal Antibiotic Resistance Gene Profiles After Short Courses of Antibiotics in a Pilot Study of Ambulatory Young Children
Authors: Howard Leigh M , Dantuluri Keerti L , Soper Nicole , Thomsen Isaac P , Grijalva Carlos G
Published: October 2021

We quantified antibiotic resistance genes before and after short antibiotic courses in nasopharyngeal specimens from ambulatory children. Carriage of certain bacteria and resistance genes was common before antibiotics. After antibiotics, we observed substantial reductions in pneumococcal and Staphylococcus aureus carriage and rapid expansion in the abundance of certain resistance genes.
Where’s Swimmy?: Mining unique color features buried in galaxies by deep anomaly detection using Subaru Hyper Suprime-Cam data
Authors: Tanaka Takumi S , Shimakawa Rhythm , Shimasaku Kazuhiro , Toba Yoshiki , Kashikawa Nobunari , Tanaka Masayuki , Inoue Akio K
Published: October 2021

We present the Swimmy (Subaru WIde-field Machine-learning anoMalY) survey program, a deep-learning-based search for unique sources using multicolored (grizy) imaging data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). This program aims to detect unexpected, novel, and rare populations and phenomena, by utilizing the deep imaging data acquired from the wide-field coverage of the HSC-SSP. This article, as the first paper in the Swimmy series, describes an anomaly detection technique to select unique populations as “outliers” from the data-set. The model was tested with known extreme emission-line galaxies (XELGs) and quasars, which consequently confirmed that the proposed method successfully selected $\sim\!\! 60\%$–$70\%$ of the quasars and $60\%$ of the XELGs without labeled training data. In reference to the spectral information of local galaxies at z = 0.05–0.2 obtained from the Sloan Digital Sky Survey, we investigated the physical properties of the selected anomalies and compared them based on the significance of their outlier values. The results revealed that XELGs constitute notable fractions of the most anomalous galaxies, and certain galaxies manifest unique morphological features. In summary, deep anomaly detection is an effective tool that can search rare objects, and, ultimately, unknown unknowns with large data-sets. Further development of the proposed model and selection process can promote the practical applications required to achieve specific scientific goals.
Origin and adaptive evolution of UV RESISTANCE LOCUS 8-mediated signaling during plant terrestrialization
Authors: Zhang Zhenhua , Xu Chenjie , Zhang Shiyu , Shi Chen , Cheng Hong , Liu Hongtao , Zhong Bojian
Published: October 2021

UV RESISTANCE LOCUS 8 (UVR8) mediates photomorphogenic responses and acclimation to UV-B radiation by regulating the transcription of a series of transcription factors (TFs). However, the origin and evolution of UVR8-mediated signaling pathways remain largely unknown. In this study, we investigated the origin and evolution of the major components of the UVR8-mediated signaling pathway (UVR8, REPRESSOR OF UV-B PHOTOMORPHOGENESIS [RUP], BRI1-EMS-SUPPRESSOR1 [BES1], BES1-INTERACTING MYC-LIKE 1 (BIM1), WRKY DNA-BINDING PROTEIN 36 (WRKY36), MYB DOMAIN PROTEIN 73/77/13 [MYB73/MYB77/MYB13], and PHYTOCHROME INTERACTING FACTOR 4/5 [PIF4 and PIF5]) using comparative genomics and phylogenetic approaches. We showed that the central regulator UVR8 presented a conservative evolutionary route during plant evolution, and the evolutionary history of downstream negative regulators and TFs was different from that of green plant phylogeny. The canonical UVR8-CONSTITUTIVELY PHOTOMORPHOGENIC 1(COP1)/SUPPRESSOR OF PHYA-105 (SPA)-ELONGATED HYPOCOTYL 5 (HY5)-RUP signaling pathway originated in chlorophytes and conferred green algae the additional ability to cope with UV-B radiation. Moreover, the emergence of multiple UVR8-mediated signaling pathways in charophytes laid the foundations for the cross-talk between UV-B signals and endogenous hormone responses. Importantly, we observed signatures that reflect plant adaptations to high UV-B irradiance in subaerial/terrestrial environments, including positive selection in UVR8 and RUPs and increased copy number of some vital TFs. These results revealed that green plants not only experienced adaptive modifications in the canonical UVR8-COP1/SPA-HY5-RUP signaling pathway, but also diversified their UV-B signal transduction mechanisms through increasing cross-talk with other pathways, such as those associated with brassinosteroids and auxin. This study greatly expands our understanding of molecular evolution and adaptive mechanisms underlying plant UV-B acclimation.
Pain-Related Post-Exertional Malaise in Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME/CFS) and Fibromyalgia: A Systematic Review and Three-Level Meta-Analysis
Authors: Barhorst Ellen E , Boruch Alexander E , Cook Dane B , Lindheimer Jacob B
Published: October 2021

Objective

Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) and fibromyalgia (FM) are two debilitating, moderately comorbid illnesses in which chronic musculoskeletal pain symptoms are prevalent. These individuals can experience post-exertional malaise (PEM), a phenomenon in which symptom severity is worsened for 24 hours or longer after physical stress, but the pain-related component of PEM is not well characterized.

Design

Systematic review and meta-analysis.

Methods

Case–control studies involving adults with ME/CFS or FM and measuring pain symptoms before and after exposure to a standardized aerobic exercise test were included. Hedges’ d effect sizes were aggregated with random-effects models, and potential moderators were explored with meta-regression analysis. Results were adjusted for nesting effects with three-level modeling.

Results

Forty-five effects were extracted from 15 studies involving 306 patients and 292 healthy controls. After adjusting for nesting effects, we observed a small to moderate effect indicating higher post-exercise pain in patients than in controls (Hedges’ d = 0.42; 95% confidence interval [CI]: 0.16–0.67). The mean effect was significantly moderated by pain measurement time point (b = –0.19, z = –2.57, P = 0.01), such that studies measuring pain 8–72 hours after exercise showed larger effects (d = 0.71, 95% CI = 0.28–1.14) than did those measuring pain 0–2 hours after exercise (d = 0.32, 95% CI = 0.10–0.53).

Conclusions

People with ME/CFS and FM experience small to moderate increases in pain severity after exercise, which confirms pain as a component of PEM and emphasizes its debilitating impact in ME/CFS and FM. Future directions include determining mechanisms of pain-related PEM and developing exercise prescriptions that minimize symptom exacerbation in these illnesses.
Precise measurement of the scintillation decay constant of the ZnWO4 crystal
Authors: Shibata M , Sekiya H , Ichimura K
Published: October 2021

The scintillation decay time constant of a ZnWO4 crystal irradiated with α-particles from 241Am was precisely investigated, and was found to depend on the incident direction of the α-particles on the crystal. The longest decay time constant (24.3 ± 0.6 μs) was obtained on the surface perpendicular to the b-axis of the crystal (surface B). On surfaces A and C, the decay constants were 20.0 and 21.3 ± 0.2 μs, respectively. The scintillation yield of ZnWO4 was also anisotropic and depended on the incident direction of the heavy particles. The maximum yield was achieved on surface B, suggesting a correlation between the light yield and the scintillation decay time constant of ZnWO4 crystals.
Embedding Population Health in Physical Therapist Professional Education
Authors: Dunleavy Kim , Mejia-Downs Anne , Guerrero Hadiya Green , Wentzell Erin , Rucker-Bussie Valerie M , Davenport Todd E , Magnusson Dawn M
Published: October 2021

The future of health care professional education is moving from a focus on the individual to embrace the health of the larger society. The COVID-19 pandemic has further highlighted the connection between social determinants and the health of populations. There are frameworks and competencies to support the delivery of population health content in the entry-level Doctor of Physical Therapy (DPT) curriculum. Three options for integrating population health content into the DPT curriculum are presented: (1) threading the content throughout the curriculum, (2) concentrating the content in 1 or 2 identified courses, and (3) offering elective courses. Each of these strategies has benefits and challenges, but threading the content throughout the curriculum provides the best opportunity to reinforce population health competencies across populations and practice settings. Experiential learning using authentic scenarios provides an ideal opportunity for students to understand population health concepts in a real-world context. Activities that incorporate interaction with other health professions broaden students’ perspectives of the role of different professions for achieving population health goals. Examples of learning activities are included in 3 competency areas, Foundations of Population Health, Prevention and Health Promotion, and Health Policy. Current societal issues provide an opportunity to enhance population health education from a meaningful perspective for students. The topic of health equity presents an opportunity to tie social and political factors of population health to social justice and health outcomes. Similarly, the COVID-19 pandemic puts issues of mental health, health disparities, and health systems front and center in our understanding of population health.

Impact

Health care practitioners are looking at health through the lens of health equity and acknowledging the impact of social and political determinants on health to address health disparities, decrease health care expenditures, and respond to changes necessitated by pandemics such as COVID-19. As health care systems and practices are rethought and reconstructed, the intentional integration of population health principles woven into the fabric of professional education is a critical component of preparing future providers. This article describes how population health concepts can be meaningfully embedded into the DPT curriculum along with providing realistic examples and activities.
Barriers and facilitators to pharmacists’ engagement in response to domestic violence: a qualitative interview study informed by the capability-opportunity-motivation-behaviour model
Authors: Lewis Natalia V , Stone Tracey , Feder Gene S , Horwood Jeremy
Published: October 2021

Background

Domestic and sexual violence and abuse (DSVA) is a global public health problem resulting in health inequalities. Community pharmacies are uniquely placed to help people affected by DSVA. We examined factors that impact pharmacists’ engagement in response to DSVA when providing public health services.

Methods

Semi-structured qualitative interviews with community pharmacists (n = 20) were analyzed thematically, with inductive themes mapped to the Capability–Opportunity–Motivation Behaviour (COM-B) model.

Results

Pharmacists were confident in providing public health services, but a lack of DSVA training meant there is a need to support their ‘Capability’ to respond to DSVA. Pharmacies were perceived as highly accessible healthcare providers on the high street, with sexual health consultations offering an ideal ‘Opportunity’ to enquire about DSVA in a private consultation room. Pharmacist’s ‘Motivation’ to enquire about DSVA was driven by potential positive client outcomes and a desire to be more involved in public heath interventions, but organisation- and system-level support and remuneration is needed.

Conclusions

Community pharmacy offers opportunities for integrating DSVA work in existing public health services. Pharmacists need training on DSVA, ongoing support, allocated funding for DSVA work, and awareness raising campaign for the public on their extended public health role.
Subjective Bond Returns and Belief Aggregation
Authors: Buraschi Andrea , Piatti Ilaria , Whelan Paul
Published: October 2021

This paper proposes an aggregation scheme of subjective bond return expectations based on the historical accuracy of professional interest rate forecasters. We use disaggregated survey data on bond returns and document large disagreement in the cross-sectional distribution and persistence in forecast accuracy. Our aggregate subjective belief proxy outperforms equal weighting schemes, and its dynamics are significantly different from statistical forecasting models. With this measure in hand, we study the relationship between quantities of risk and subjective expectations of excess returns and demonstrate a strong link between the two, even if such a relationship is difficult to detect using realized returns.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
A review of JAK–STAT signalling in the pathogenesis of spondyloarthritis and the role of JAK inhibition
Authors: McInnes Iain B , Szekanecz Zoltán , McGonagle Dennis , Maksymowych Walter P , Pfeil Alexander , Lippe Ralph , Song In-Ho , Lertratanakul Apinya , Sornasse Thierry , Biljan Ana , Deodhar Atul
Published: October 2021

Spondyloarthritis (SpA) comprises a group of chronic inflammatory diseases with overlapping clinical, genetic and pathophysiological features including back pain, peripheral arthritis, psoriasis, enthesitis and dactylitis. Several cytokines are involved in the pathogenesis of SpA, variously contributing to each clinical manifestation. Many SpA-associated cytokines, including IL-23, IL-17, IL-6, type I/II interferon and tumour necrosis factor signal directly or indirectly via the Janus kinase (JAK)–signal transducer and activator of transcription pathway. JAK signalling also regulates development and maturation of cells of the innate and adaptive immune systems. Accordingly, disruption of this signalling pathway by small molecule oral JAK inhibitors can inhibit signalling implicated in SpA pathogenesis. Herein we discuss the role of JAK signalling in the pathogenesis of SpA and summarize the safety and efficacy of JAK inhibition by reference to relevant SpA clinical trials.
The Impact of Undernutrition on Cognition in Children with Severe Malaria and Community Children: A Prospective 2-Year Cohort Study
Authors: Mburu Waruiru , Conroy Andrea L , Cusick Sarah E , Bangirana Paul , Bond Caitlin , Zhao Yi , Opoka Robert O , John Chandy C
Published: October 2021

Background

The frequency of recovery from undernutrition after an episode of severe malaria, and the relationship between undernutrition during severe malaria and clinical and cognitive outcomes are not well characterized.

Methods

We evaluated undernutrition and cognition in children in Kampala, Uganda 18 months to 5 years of age with cerebral malaria (CM), severe malarial anemia (SMA) or community children (CC). The Mullen Scales of Early Learning was used to measure cognition. Undernutrition, defined as 2 SDs below median for weight-for-age (underweight), height-for-age (stunting) or weight-for-height (wasting), was compared with mortality, hospital readmission and cognition over 24-month follow-up.

Results

At enrollment, wasting was more common in CM (16.7%) or SMA (15.9%) than CC (4.7%) (both p < 0.0001), and being underweight was more common in SMA (27.0%) than CC (12.8%; p = 0.001), while prevalence of stunting was similar in all three groups. By 6-month follow-up, prevalence of wasting or being underweight did not differ significantly between children with severe malaria and CC. Undernutrition at enrollment was not associated with mortality or hospital readmission, but children who were underweight or stunted at baseline had lower cognitive z-scores than those who were not {underweight, mean difference [95% confidence interval (CI)] −0.98 (−1.66, −0.31), −0.72 (−1.16, −0.27) and −0.61 (−1.08, −0.13); and stunted, −0.70 (−1.25, −0.15), −0.73 (−1.16, −0.31) and −0.61 (−0.96, −0.27), for CM, SMA and CC, respectively}.

Conclusion

In children with severe malaria, wasting and being underweight return to population levels after treatment. However, being stunted or underweight at enrollment was associated with worse long-term cognition in both CC and children with severe malaria.