bluuebunny/crossref_metadata_2025 huggingface dataset:
Antimicrobial activity and enzymatic analysis of endophytes isolated from Codonopsis pilosula
Authors: Lodi Rathna Silviya , Dong Xiaodan , Jiang Chunhui , Sun Zhou , Deng Peng , Sun Sujun , Wang Xinkun , Wang Hengzhen , Mesa Arundathi , Huang Xiaopeng , Peng Lizeng , Peng Chune
Published: June 2023

The roots of the medicinal plant Codonopsis pilosula (Franch.) Nannf (C. pilosula) possess most medicinal supplements. In current research on C. pilosula root endophytes were isolated, identified, and evaluated for their antimicrobial activity against human pathogens such as Escherichia coli, Staphylococcus aureus, Bacillus subtilis, Salmonella typhi, and Pseudomonas aeruginosa and the fungi Candida albicans and Aspergillus niger. Endophytes C.P-8 and C.P-20 exhibited very significant antimicrobial activity, the secondary metabolite of C.P-8 registered at retention time 24.075 by HPLC analysis. Significant minimum inhibitory concentration (MIC) of C.P-8 was exhibited at 250 µg/ml against S. aureus and 500 µg/ml against B. subtilis. Qualitative, quantitative analyses, and partial purification of enzymes and purity was analysed by molecular weight determined by SDS‒PAGE of enzymes produced by C.P-20, amylase—64 kDa, protease—64 kDa, chitinase—30 kDa, and cellulase—54 kDa. Optimum pH and temperature of the partially purified enzymes, was carried out. The partially purified enzymes from C.P-20 displayed maximum activity at pH 6–7 and temperatures of 40°C–45°C. Moreover, the above endophytes will be useful tools for producing active enzymes and active bioantimicrobial agents against human pathogens.
Role of DevR phosphorylation in nitric oxide homeostasis and signaling ofStreptomyces coelicolorA3(2) M145
Authors: Honma Sota , Ito Shinsaku , Yajima Shunsuke , Sasaki Yasuyuki
Published: June 2023

Our previous studies revealed that a two-component system (TCS), DevS, and DevR, regulate both nitric oxide (NO) signaling and NO homeostasis in the actinobacterium Streptomyces coelicolor A3(2) M145, suggesting a reasonable system for NO-dependent metabolism. In this study, sequence alignment of DevR and DevR homologs found Asp66 (D66) and Thr196 (T196) as predicted phosphorylation sites of DevR. Phos-tag gel electrophoretic mobility shift assay suggested that D66 and T196 are involved in the phosphorylation of DevR. The respective point mutations of D66 and T196 significantly decreased the transcriptional activity of DevR, which affected nitrite production and aerial mycelium formation. These results suggested that both D66 and T196 of DevR are important for the regulation of NO homeostasis and signaling in S. coelicolor A3(2) M145.
Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues
Authors: Crespo-Piazuelo Daniel , Acloque Hervé , González-Rodríguez Olga , Mongellaz Mayrone , Mercat Marie-José , Bink Marco C A M , Huisman Abe E , Ramayo-Caldas Yuliaxis , Sánchez Juan Pablo , Ballester Maria
Published: June 2023

Background

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.

Results

More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3′UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5′-GATCCNGYGTTGCYG-3′ and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.

Conclusions

The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.
5-Aminolevulinic acid bypasses mitochondrial complex I deficiency and corrects physiological dysfunctions in Drosophila
Authors: Nozawa Naoko , Noguchi Marie , Shinno Kanako , Saito Taro , Asada Akiko , Ishii Takuya , Takahashi Kiwamu , Ishizuka Masahiro , Ando Kanae
Published: June 2023

Complex I (CI) deficiency in mitochondrial oxidative phosphorylation (OXPHOS) is the most common cause of mitochondrial diseases, and limited evidence-based treatment options exist. Although CI provides the most electrons to OXPHOS, complex II (CII) is another entry point of electrons. Enhancement of this pathway may compensate for a loss of CI; however, the effects of boosting CII activity on CI deficiency are unclear at the animal level. 5-Aminolevulinic acid (5-ALA) is a crucial precursor of heme, which is essential for CII, complex III, complex IV (CIV) and cytochrome c activities. Here, we show that feeding a combination of 5-ALA hydrochloride and sodium ferrous citrate (5-ALA-HCl + SFC) increases ATP production and suppresses defective phenotypes in Drosophila with CI deficiency. Knockdown of sicily, a Drosophila homolog of the critical CI assembly protein NDUFAF6, caused CI deficiency, accumulation of lactate and pyruvate and detrimental phenotypes such as abnormal neuromuscular junction development, locomotor dysfunctions and premature death. 5-ALA-HCl + SFC feeding increased ATP levels without recovery of CI activity. The activities of CII and CIV were upregulated, and accumulation of lactate and pyruvate was suppressed. 5-ALA-HCl + SFC feeding improved neuromuscular junction development and locomotor functions in sicily-knockdown flies. These results suggest that 5-ALA-HCl + SFC shifts metabolic programs to cope with CI deficiency.

Bullet outline 5-Aminolevulinic acid (5-ALA-HCl + SFC) increases ATP production in flies with complex I deficiency.5-ALA-HCl + SFC increases the activities of complexes II and IV.5-ALA-HCl + SFC corrects metabolic abnormalities and suppresses the detrimental phenotypes caused by complex I deficiency.
Non-Bilaterians as Model Systems for Tissue Mechanics
Authors: Gooshvar Setareh , Madhu Gopika , Ruszczyk Melissa , Prakash Vivek N
Published: June 2023

Synopsis

In animals, epithelial tissues are barriers against the external environment, providing protection against biological, chemical, and physical damage. Depending on the organism’s physiology and behavior, these tissues encounter different types of mechanical forces and need to provide a suitable adaptive response to ensure success. Therefore, understanding tissue mechanics in different contexts is an important research area. Here, we review recent tissue mechanics discoveries in three early divergent non-bilaterian systems—Trichoplax adhaerens, Hydra vulgaris, and Aurelia aurita. We highlight each animal’s simple body plan and biology and unique, rapid tissue remodeling phenomena that play a crucial role in its physiology. We also discuss the emergent large-scale mechanics in these systems that arise from small-scale phenomena. Finally, we emphasize the potential of these non-bilaterian animals to be model systems in a bottom-up approach for further investigation in tissue mechanics.
20-hydroxyecdysone Upregulates Ecdysone Receptor (ECR) Gene to Promote Pupation in the Honeybee, Apis mellifera Ligustica
Authors: Yu Jing , Song Hongyu , Wang Ying , Liu Zhenguo , Wang Hongfang , Xu Baohua
Published: June 2023

Synopsis

A heterodimeric complex of two nuclear receptors, the ecdysone receptor (ECR) and ultraspiracle (USP), transduces 20-hydroxyecdysone (20E) signaling to modulate insect growth and development. Here, we aimed to determine the relationship between ECR and 20E during larval metamorphosis and also the specific roles of ECR during larval–adult transition in Apis mellifera. We found that ECR gene expression peaked in the 7-day-old larvae, then decreased gradually from the pupae stage. 20E slowly reduced food consumption and then induced starvation, resulting in small-sized adults. In addition, 20E induced ECR expression to regulate larval development time. Double-stranded RNAs (dsRNAs) were prepared using common dsECR as templates. After dsECR injection, larval transition to the pupal stage was delayed, and 80% of the larvae showed prolonged pupation beyond 18 h. Moreover, the mRNA levels of shd, sro, nvd, and spo, and ecdysteroid titers were significantly decreased in ECR RNAi larvae compared with those in GFP RNAi control larvae. ECR RNAi disrupted 20E signaling during larval metamorphosis. We performed rescuing experiments by injecting 20E in ECR RNAi larvae and found that the mRNA levels of ECR, USP, E75, E93, and Br-c were not restored. 20E induced apoptosis in the fat body during larval pupation, while RNAi knockdown of ECR genes reduced apoptosis. We concluded that 20E induced ECR to modulate 20E signaling to promote honeybee pupation. These results assist our understanding of the complicated molecular mechanisms of insect metamorphosis.
Mechanosensory Feedback in Lamprey Swimming Models and Applications in the Field of Spinal Cord Regeneration
Authors: Katz Hilary R , Hamlet Christina L
Published: June 2023

Synopsis

The central pattern generator (CPG) in anguilliform swimming has served as a model for examining the neural basis of locomotion. This system has been particularly valuable for the development of mathematical models. As our biological understanding of the neural basis of locomotion has expanded, so too have these models. Recently, there have been significant advancements in our understanding of the critical role that mechanosensory feedback plays in robust locomotion. This work has led to a push in the field of mathematical modeling to incorporate mechanosensory feedback into CPG models. In this perspective piece, we review advances in the development of these models and discuss how newer complex models can support biological investigation. We highlight lamprey spinal cord regeneration as an area that can both inform these models and benefit from them.
In situ reconstruction of an infected infrarenal aortic pseudoaneurysm and arteriovenous fistula with self-made pericardium graft
Authors: Yang Guangmin , Sun Tao , Chen Hongwei , Zhang Leiyang
Published: June 2023

Infectious aortic disease is a challenging life-threatening disease in cardiovascular surgery. A 70-year-old man patient presented with an infected infrarenal aortic pseudoaneurysm and right iliac artery- left iliac vein fistula (arteriovenous fistula). He underwent total infected tissues excision, debridement, in situ reconstructions of the aorta using a self-made pericardium graft with omental coverage and arteriovenous fistula patch repair to prevent leakage. One-year follow-up revealed the absence of clinically relevant infection with patency of the graft and the absence of biochemical inflammatory markers.
Medicines use issues perceived by Arabic-speaking patients living in English-speaking countries: A systematic review
Authors: Sawalha Rawan , Hosseinzadeh Hassan , Bajorek Beata
Published: June 2023

Objectives

Quality use of medicines, or rational medicines use, requires patients’ adherence to the quality principles of medication use. There is a limited number of reviews about quality medication use among migrant patients. This review aims to fill this gap by exploring medication-related issues experienced by Arabic-speaking patients living in English-speaking countries.

Methods

The searched databases included WebMD, EMBASE, Scopus, CINHAL, PubMed/Medline and Web of science.

Key findings

The initial search retrieved 2071 publications and 23 publications met the inclusion criteria. Our review found that the most frequently reported medication-related issues among Arabic-speaking patients residing in English-speaking countries were problems related to decision-making regarding treatment options, inappropriate counselling and lack of information about medicines and diseases, lack of monitoring and follow-up, and intentional and unintentional medication non-adherence. Informed by the bio-psycho-socio-systems model, contributing factors to the medication issues included used coping strategies, ethno-cultural and religious beliefs and ineffective relationships with healthcare providers.

Conclusions

Our review suggests that cultural factors can significantly influence individuals’ perceptions and actions around the use of medication. Thus, healthcare providers need to be mindful of the specific cultural affiliations of ethnic minorities and exhibit cultural sensitivity when prescribing medication to migrant patients to foster a better relationship between patients and healthcare providers. Applying a patient-centred approach using shared decision-making can help. Our findings also suggest that pharmacy practice is critical in improving medication safety among Arabic-speaking patients.
Disease and Dissent: Epidemics as a Catalyst for Social Unrest
Authors: Cordell Rebecca , Wood Reed M , Wright Thorin M
Published: June 2023

We identify a set of potential theoretical mechanisms that link the outbreak and spread of communicable diseases to temporal and spatial patterns of social unrest. Despite the proliferation of research since 2020 analyzing the social impact of the Covid-19 pandemic, we examine the broader relationship between less severe epidemic outbreaks and their social consequences. Epidemics, as well as the policies that governments implement to tackle them, often generate acute grievances among the public and create new opportunities for collective dissent, the combination of which promotes unrest. Nonetheless, perceived opportunities for unrest are influenced by the scale and scope of the disease outbreak, and particularly lethal disease outbreaks may therefore offset the incentives for collective mobilization. We examine these relationships using sub-national data on communicable disease outbreaks and geo-located social unrest events data in 60 African and Latin American countries from 1990 to 2017 and find support for our argument. However, we observe a curvilinear relationships between the severity of the epidemic and the incidence of unrest.
Mapping and Unpacking Global Governance Bodies: A Cross Sectional and Cross Organizational Analysis
Authors: Saz-Carranza Angel , Maggetti Martino , Yesilkagit Kutsal , Coen David
Published: June 2023

Several recent studies have pointed to the increasing relevance of relatively informal, non-treaty-based global governance bodies (GGBs). Yet, a systematic fine-grained assessment of these bodies and their implications for global governance are still pending. To what extent, do non-treaty-based GGBs constitute a truly novel type of governance body, distinct from traditional treaty-based international organizations (IOs)? How do the distinctive features of GGBs affect their role in global governance? To what extent are GGB’s patterns of emergence and development specific to policy sectors? This article tackles these questions, drawing on an original dataset on GGBs in five distinct policy areas (banking and finance, energy, global health, Internet, and migration policy). We combine a micro-organizational perspective with a meso-level network approach to unpack the main features of non-treaty-based GGBs vis-à-vis, traditional IOs. Our results provide support to the general expectation that non-treaty-based GGBs offer distinctive opportunities for global governance with respect to traditional IOs. However, importantly, this relationship is not dichotomous. We find that GGBs exist on a continuum of fit-to-purpose designs ranging from hard, formal, and intergovernmental models to a soft, informal, and multistakeholder-based form of governance. Lastly, we also find notable variations across policy areas, where global health stands out given its decentralized network structure.
Speaking of Epistemic Injustice: A Reply
Authors: Hopman Marieke Janne , Jama Guleid Ahmed , Zvonareva Olga , Hoļavins Artūrs ,   Anonymous
Published: June 2023

In this article, we reply to ‘Ethics and Epistemic Injustice in the Global South’ (Kaur et al. 2023), a response to the original article ‘Covert Qualitative Research as a Method to Study Human Rights Under Authoritarian Regimes’ (Hopman 2022). Our reply is written by authors who have expertise and direct experience with the issues at stake (authoritarianism, Global North/Global South relations, covert research methods, epistemic injustice). We show that while there are some interesting points raised in the response article, in general, it does not do justice to the arguments presented in the original article. Instead it constructs a ‘straw man’ by misrepresenting claims in the original article, attributing to it assumptions that were not there, and lumping together notions such as authoritarian zones and Global South, that were not equated in the original article. After providing arguments for this position and discussing the main topics of the critique, we present two new elements: first, a contribution by someone from Moroccan controlled Western Sahara (MCWS), who experienced covert research as a research participant. Second, an overview of lessons learned from this exchange. These include: 1) instead of authoritarian zones, ‘authoritarian situations’ is a more appropriate concept; 2) projects using covert research should strive to include overt and participatory elements; 3) a response article alleging epistemic injustice should create space for the people concerned to speak for themselves.
Effects of sample collection and storage methods on fecal bacterial diversity in California ground squirrels (Otospermophilus beecheyi)
Authors: Person Erin S , von Maydell Kianna P , Baldoza Jada E , Lacey Eileen A , Smith Jennifer E
Published: June 2023

Measures of fecal bacterial abundance and taxonomic composition are commonly used as proxies for gut microbial diversity in studies of free-living mammals. Because methods of sample collection and storage may affect measures of bacterial diversity, we evaluated the effects of several procedures on fecal bacterial diversity in a free-living population of California ground squirrels (Otospermophilus beecheyi). Replicate fecal samples from 12 adult female squirrels were collected either from the soil beneath traps in which individuals had been captured or from tubs placed under squirrels during handling. Samples were then either frozen immediately in liquid nitrogen or stored on ice for several hours before being transferred to a −80°C freezer. Sequencing of the bacterial 16s RNA gene revealed no differences among methods with regard to sequence read depth (number of sequences recovered per animal) or alpha (within-individual) diversity of bacterial taxa. While our collection-storage procedures had a significant effect on one of the metrics of beta (among-individual) bacterial diversity examined, this effect was small compared to that of individual identity. Date of sample collection affected alpha and beta diversity; samples collected only 1 week apart differed significantly in bacterial diversity. Overall, these findings suggest that the collection and storage methods employed yield generally comparable information and are capable of capturing potentially important patterns of fecal bacterial composition and diversity in free-living mammals.
Efficacy of aural detection methods for detecting Northern Pika (Ochotona hyperborea) occupancy in rocky and densely vegetated habitats
Authors: Sakiyama Tomoki , García Molinos Jorge
Published: June 2023

Wildlife monitoring plays a key role in species conservation, with growing importance under the threat of climate change. The Northern Pika (Ochotona hyperborea) is a cold-adapted species found in Hokkaido, Japan, presumably vulnerable to such threats. However, its high elusiveness hinders detailed population surveys, and visual detection methods—often used for other pika species—are not applicable to its densely vegetated habitats. In this study, we assessed the efficacy of aural detection methods to survey the occupancy of Northern Pika through their distinct vocalizations. We conducted two types of point-count surveys—auditory observation and playback—during 2021 at 18 sites in and around Daisetsuzan National Park. We then assessed the efficacy of these methods in detecting presence and compared time until first detection of the animal. The Northern Pika was present at 11 of all surveyed sites, with a predominance at higher elevations. Our results suggest that both auditory observation and playback are effective at detecting presence, but playback is more time-efficient. We discuss the advantages and disadvantages of each method given these results. In conclusion, our results demonstrate that both survey methods are applicable for Northern Pika population surveys—even in densely vegetated habitats—representing valid and affordable survey methods that can help to improve current monitoring and conservation efforts, and will be of increasing value given potentially negative effects of climate change on persistence of the species.
Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes
Authors: Feng Cibo , Wang Jin , Chu Xiakun
Published: June 2023

The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression. When the cell changes its identity in the cell-fate decision-making process, extensive rearrangements of chromosome structures occur accompanied by large-scale adaptations of gene expression, underscoring the importance of chromosome dynamics in shaping genome function. Over the last two decades, rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of chromosomes. In parallel, these enormous data offer valuable opportunities for developing quantitative computational models. Here, we review a variety of large-scale polymer models developed to investigate the structures and dynamics of chromosomes. Different from the underlying modeling strategies, these approaches can be classified into data-driven (‘top-down’) and physics-based (‘bottom-up’) categories. We discuss their contributions to offering valuable insights into the relationships among the structures, dynamics, and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.
Revealing ‘invisible’ poetry by W. H. Auden through computer vision: Using photometric stereo to visualize indented impressions
Authors: Brenner Simon , Frühwirth Timo , Mayer Sandra
Published: June 2023

This article explores the use of computer-vision technologies in the context of digitally editing and researching letters and literary papers by the British-American poet W. H. Auden. Two documents in the previously inaccessible ‘Auden Musulin Papers’ contain colourless indented typewriter impressions of poetry. These impressions result from the papers’ original use as ‘backing sheets’, inserted into a typewriter below those sheets of paper on which Auden typed his poetry. Subsequently, these backing sheets were reused in the poet’s ‘working correspondence’ to Welsh-Austrian writer Stella Musulin. While standard image-digitization technologies fail to capture these 3D indented impressions, they can successfully be represented by means of Photometric Stereo, which has been fruitfully employed in the research of 3D cultural-heritage objects. Following a detailed outline of this method, this article demonstrates how Photometric Stereo can help to reconstruct poetry that has survived only in the form of indented impressions. Thus, the case study illustrates how computer vision can contribute to our understanding both of ‘poetic’ practices of composition and revision as well as of ‘material’ writing practices. It also has wide-ranging implications for re-conceptualizing sheets of paper as 3D objects in the research of literary documents from the twentieth century.
A subarcsec localized fast radio burst with a significant host galaxy dispersion measure contribution
Authors: Caleb M , Driessen L N , Gordon A C , Tejos N , Bernales L , Qiu H , Chibueze J O , Stappers B W , Rajwade K M , Cavallaro F , Wang Y , Kumar P , Majid W A , Wharton R S , Naudet C J , Bezuidenhout M C , Jankowski F , Malenta M , Morello V , Sanidas S , Surnis M P , Barr E D , Chen W , Kramer M , Fong W , Kilpatrick C D , Prochaska J Xavier , Simha S , Venter C , Heywood I , Kundu A , Schussler F
Published: June 2023

We present the discovery of FRB 20210410D with the MeerKAT radio interferometer in South Africa, as part of the MeerTRAP commensal project. FRB 20210410D has a dispersion measure DM = 578.78 ± 2 ${\rm pc \, cm^{-3}}$ and was localized to subarcsec precision in the 2 s images made from the correlation data products. The localization enabled the association of the FRB with an optical galaxy at z = 0.1415, which when combined with the DM places it above the 3σ scatter of the Macquart relation. We attribute the excess DM to the host galaxy after accounting for contributions from the Milky Way’s interstellar medium and halo, and the combined effects of the intergalactic medium and intervening galaxies. This is the first FRB that is not associated with a dwarf galaxy to exhibit a likely large host galaxy DM contribution. We do not detect any continuum radio emission at the FRB position or from the host galaxy down to a 3σ rms of 14.4 $\mu$Jy beam−1. The FRB has a scattering delay of $29.4^{+2.8}_{-2.7}$ ms at 1 GHz, and exhibits candidate subpulses in the spectrum, which hint at the possibility of it being a repeating FRB. Although not constraining, we note that this FRB has not been seen to repeat in 7.28 h at 1.3 GHz with MeerKAT, 3 h at 2.4 GHz with Murriyang, and 5.7 h at simultaneous 2.3 GHz and 8.4 GHz observations with the Deep Space Network. We encourage further follow-up to establish a possible repeating nature.
New evidence for the precession of tilted disc in SDSS J081256.85+191157.8
Authors: Sun Qi-Bin , Qian Sheng-Bang , Zhu Li-Ying , Liao Wen-Ping , Zhao Er-Gang , Li Fu-Xing , Shi Xiang-Dong , Li Min-Yu
Published: June 2023

Superorbital signals and negative superhumps are thought to be related to the reverse precession of the nodal line in a tilted disc, but the evidence is lacking. Our results provide new evidence for the precession of the tilted disc. Based on the TESS and K2 photometry, we investigate the superorbital signals, negative superhumps, positive superhumps, and eclipse characteristics of the long-period eclipsing cataclysmic variable star SDSS J0812. We find superorbital signals, negative superhumps, and positive superhumps with periods of 3.0451(5) d, 0.152047(2) d, and 0.174686 (7) d, respectively, in the K2 photometry, but all disappear in the TESS photometry, where the positive superhumps are present only in the first half of the same campaign, confirming that none of them is permanently present in SDSS J0812. In addition, we find for the first time a cyclic variation of the O-C of minima, eclipse depth, and negative superhumps amplitudes for 3.045 (8) d, 3.040(6) d, and 3.053 (8) d in SDSS J0812, respectively, and all reach the maximum at ∼0.75 precession phases of the tilted disc, which provides new evidence for the precession of the tilted disc. We suggest that the O-C and eclipse depth variations may come from a shift of the brightness centre of the precession tilted disc. Our first finding on the periodic variation of negative superhumps amplitude with the superorbital signals is significant evidence that the origin of negative superhumps is related to the precession of the tilted disc.
The Cosmic Ultraviolet Baryon Survey (CUBS) – VI. Connecting physical properties of the cool circumgalactic medium to galaxies at z ≈ 1
Authors: Qu Zhijie , Chen Hsiao-Wen , Rudie Gwen C , Johnson Sean D , Zahedy Fakhri S , DePalma David , Boettcher Erin , Cantalupo Sebastiano , Chen Mandy C , Cooksey Kathy L , Faucher-Giguère Claude-André , Li Jennifer I-Hsiu , Lopez Sebastian , Schaye Joop , Simcoe Robert A
Published: June 2023

This paper presents a newly established sample of 19 unique galaxies and galaxy groups at redshift z = 0.89–1.21 in six QSO fields from the Cosmic Ultraviolet Baryon Survey (CUBS), designated as the CUBSz1 sample. In this sample, nine galaxies or galaxy groups show absorption features, while the other 10 systems exhibit 2σ upper limits of $\log N (\rm{He\,{\small I}})/\mbox{${\rm cm^{-2}}$}\lesssim 13.5$ and $\log N (\rm{O\,{\small V}})/\mbox{${\rm cm^{-2}}$}\lesssim 13.3$. Environmental properties of the galaxies, including galaxy overdensities, the total stellar mass and gravitational potential summed over all neighbours, and the presence of local ionizing sources, are found to have a significant impact on the observed CGM absorption properties. Specifically, massive galaxies and galaxies in overdense regions exhibit a higher rate of incidence of absorption. The CGM absorption properties in galaxy groups appear to be driven by the galaxy closest to the QSO sightline, rather than by the most massive galaxy or by mass-weighted properties. We introduce a total projected gravitational potential ψ, defined as −ψ/G = ∑Mhalo/dproj summed over all group members, to characterize the galaxy environment. This projected gravitational potential correlates linearly with the maximum density detected in each sightline (i.e. a power-law slope of $0.95_{-0.14}^{+0.15}$), consistent with higher pressure gas being confined in deeper gravitational potential wells. In addition, we find that the radial profile of cool gas density exhibits a decline from the inner regions to the outskirts, and the amplitude is consistent with the cool gas being in pressure balance with the hot halo. Finally, we note that the ionizing flux from nearby galaxies can elevate the N(H i)/N(He i) ratio, which provides a unique diagnostic of possible local sources contributing to the ionizing radiation field.
The evolution of the internal structure of massive star-forming regions in the Milky Way as revealed by ALMA
Authors: Dib Sami
Published: June 2023

We analyse the structure of 15 protocluster forming regions in the Milky Way using their 1.3 mm continuum emission maps from the ALMA-IMF large program. The analysis of the cloud structure is performed using the delta-variance spectrum technique. The calculated spectra display a self-similar regime on small scales as well as the presence of a prominent bump on larger scales and whose physical size, Lhub, falls in the range of ≈7000–60 000 au. These scales correspond to the sizes of the most compact clumps within the protocluster forming clouds. A significant correlation is found between Lhub and the surface density of the free–free emission estimated from the integrated flux of the H41α recombination line $\left(\Sigma _{\rm H41\alpha }^{\rm free \!-\! free}\right)$ as well as a significant anticorrelation between Lhub and the ratio of the 1.3–3 mm continuum emission fluxes $\left(S_{\rm 1.3 \, mm}^{\rm cloud}/S_{\rm 3 \, mm}^{\rm cloud}\right)$. Smaller values of $\left(S_{\rm 1.3 \, mm}^{\rm cloud}/S_{\rm 3 \, mm}^{\rm cloud}\right)$ and larger values of $\Sigma _{\rm H41\alpha }^{\rm free \!-\! free}$ correspond to more advanced evolutionary stages of the protocluster forming clumps. Hence, our results suggest that the sizes of the densest regions in the clouds are directly linked to their evolutionary stage and to their star formation activity with more evolved clouds having larger protocluster forming clumps. This is an indication that gravity plays a vital role in regulating the size, mass growth, and star formation activity of these clumps with ongoing gas accretion.
The tiered radio extragalactic continuum (T-RECS) simulation II: H i emission and continuum-H i cross-correlation
Authors: Bonaldi Anna , Hartley Philippa , Ronconi Tommaso , De Zotti Gianfranco , Bonato Matteo
Published: June 2023

In this paper, we extend the Tiered Radio Extragalactic Continuum Simulation (T-RECS) to include H i emission. The H i T-RECS model is based on the most recent H i mass function estimates, combined with prescriptions to convert H i mass to total integrated H i flux. It further models source size, morphology, and kinematics, including rotational velocity and H i line width. The continuum T-RECS model is updated to improve the agreement with deeper number counts available at 150 MHz. The model for star-forming galaxies (SFGs) is also modified according to the most recent indications of a star formation rate (SFR)–radio luminosity relation, which depends primarily on stellar mass rather than redshift. We further introduce prescriptions to associate an H i mass with the T-RECS radio continuum SFG and active galactic nuclei (AGN) populations. This gives us a way to meaningfully associate counterparts between H i and continuum catalogues, thus building H i× continuum simulated observations. Clustering properties of the sources in both H i and the continuum are reproduced by associating the galaxies with dark matter haloes in a cosmological simulation. We deliver a set of mock catalogues as well as the code to produce them, which can be used for simulating observations and predicting results from radio surveys with existing and forthcoming radio facilities, such as the Square Kilometre Array (SKA).
Divergent directed evolution of a TetR-type repressor towards aromatic molecules
Authors: Nasr Mohamed A , Martin Vincent J J , Kwan David H
Published: June 2023

Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
Replication DNA polymerases, genome instability and cancer therapies
Authors: Strauss Juliet D , Pursell Zachary F
Published: June 2023

It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
Hypertension in chronic kidney disease—treatment standard 2023
Authors: Georgianos Panagiotis I , Agarwal Rajiv
Published: June 2023

Hypertension is very common and remains often poorly controlled in patients with chronic kidney disease (CKD). Accurate blood pressure (BP) measurement is the essential first step in the diagnosis and management of hypertension. Dietary sodium restriction is often overlooked, but can improve BP control, especially among patients treated with an agent to block the renin–angiotensin system. In the presence of very high albuminuria, international guidelines consistently and strongly recommend the use of an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker as the antihypertensive agent of first choice. Long-acting dihydropyridine calcium channel blockers and diuretics are reasonable second- and third-line therapeutic options. For patients with treatment-resistant hypertension, guidelines recommend the addition of spironolactone to the baseline antihypertensive regimen. However, the associated risk of hyperkalemia restricts the broad utilization of spironolactone in patients with moderate-to-advanced CKD. Evidence from the CLICK (Chlorthalidone in Chronic Kidney Disease) trial indicates that the thiazide-like diuretic chlorthalidone is effective and serves as an alternative therapeutic opportunity for patients with stage 4 CKD and uncontrolled hypertension, including those with treatment-resistant hypertension. Chlorthalidone can also mitigate the risk of hyperkalemia to enable the concomitant use of spironolactone, but this combination requires careful monitoring of BP and kidney function for the prevention of adverse events. Emerging agents, such as the non-steroidal mineralocorticoid receptor antagonist ocedurenone, dual endothelin receptor antagonist aprocitentan and the aldosterone synthase inhibitor baxdrostat offer novel targets and strategies to control BP better. Larger and longer term clinical trials are needed to demonstrate the safety and efficacy of these novel therapies in the future. In this article, we review the current standards of treatment and discuss novel developments in pathophysiology, diagnosis, outcome prediction and management of hypertension in patients with CKD.
iEarth: an interdisciplinary framework in the era of big data and AI for sustainable development
Authors: Gong Peng , Guo Huadong , Chen Bin , Chen Fang , He Guojun , Liang Dong , Liu Zhonghui , Sun Zhongchang , Wu Jin , Xu Zhenci , Yan Dongmei , Zhang Hongsheng
Published: June 2023

The Intelligent Earth (iEarth) framework, composed of four major themes: iEarth data, science, analytics, and decision, is proposed to define and build an interdisciplinary and synergistic framework for research, practice, and education that simultaneously safeguards the sustainable development of our living planet.
Warming-induced phenological mismatch between trees and shrubs explains high-elevation forest expansion
Authors: Li Xiaoxia , Liang Eryuan , Camarero J Julio , Rossi Sergio , Zhang Jingtian , Zhu Haifeng , Fu Yongshuo H , Sun Jian , Wang Tao , Piao Shilong , Peñuelas Josep
Published: June 2023

Despite the importance of species interaction in modulating the range shifts of plants, little is known about the responses of coexisting life forms to a warmer climate. Here, we combine long-term monitoring of cambial phenology in sympatric trees and shrubs at two treelines of the Tibetan Plateau, with a meta-analysis of ring-width series from 344 shrubs and 575 trees paired across 11 alpine treelines in the Northern Hemisphere. Under a spring warming of +1°C, xylem resumption advances by 2–4 days in trees, but delays by 3–8 days in shrubs. The divergent phenological response to warming was due to shrubs being 3.2 times more sensitive than trees to chilling accumulation. Warmer winters increased the thermal requirement for cambial reactivation in shrubs, leading to a delayed response to warmer springs. Our meta-analysis confirmed such a mechanism across continental scales. The warming-induced phenological mismatch may give a competitive advantage to trees over shrubs, which would provide a new explanation for increasing alpine treeline shifts under the context of climate change.
Response to “Plant-based diets and postprandial hyperkalemia”
Authors: St-Jules David E , Fouque Denis
Published: June 2023

Diet therapy for hyperkalemia in people with chronic kidney disease (CKD) has shifted considerably in recent years with the observations that reported potassium intake is weakly, or not at all, associated with plasma potassium levels in this population. One of the lingering debates is whether dietary potassium presents a risk of hyperkalemia in the postprandial state. Although there is general agreement about the need for additional research, the commentary by Varshney et al contends that the available research sufficiently demonstrates that high-potassium plant foods do not pose a risk of postprandial hyperkalemia. Others argue that this remains unsettled science. Although the traditional approach of providing people with CKD lists of high-potassium foods to limit or avoid may be unnecessary, those at high risk of hyperkalemia should be encouraged to consume balanced meals and control portions, at least until some of the key research gaps in this area are resolved. This editorial critiques the analyses offered by Varshney et al and explains the rationale for a more cautious approach to care.
The predictors of paradoxical reactions, especially psoriasis, to biologic therapy—findings from the TReasure database: a 5-year follow-up study
Authors: Yagiz Burcu , Lermi Nihal , Coskun Belkis N , Dalkilic Ediz , Kiraz Sedat , Erden Abdulsamet , Ertenli Ihsan , Duran Emine , Bilgin Emre , Yılmaz Recep , Ateş Aşkın , Tufan Abdurrahman , Küçük Hamit , Mercan Ridvan , Cinaklı Haluk , Akar Servet , Yaşar Bilge Nazife Ş , Kaşifoglu Timucin , Türk Sümeyye M , Gonullu Emel Orge , Bes Cemal , Alpay Kanitez Nilufer , Emmungil Hakan , Kalyoncu Umut , Pehlivan Yavuz
Published: June 2023

Objectives

The objectives of this study were to assess the clinical characteristics, predictive factors, and practical algorithms of paradoxical reactions (PRs), specifically paradoxical psoriasis (PP).

Methods

The TReasure database is a web-based prospective observational cohort comprised of patients with RA and SpA from 17 centres around Turkey since 2017. A cohort study and a case–control study nestled within the cohort were identified.

Results

In total, 2867 RA and 5316 SpA patients were evaluated. The first biologic agent was found to have caused PRs in 60% of the 136 patients (1.66%) who developed the PRs. The median time interval between the PRs and biological onset was 12 months (range 1–132 months, mean 21 months). The most common types of PP, constituting 92.6% of PRs, were pustular (60.3%) and palmoplantar (30.9%). Adalimumab (30.9%), infliximab (19%) and etanercept (17.4%) were the most common agents causing the PP. In the treatment of most PP patients (73.2%), switching biologic agents was favoured, with TNF inhibitor (TNFi) chosen in 46.03% and non-TNFi in 26.9% of cases. The three most frequently selected drugs were etanercept (24.6%), secukinumab (9.5%) and adalimumab (8.7%). Only 5.17% of patients who switched to another TNFi showed progression. The odds ratios (s) for SSZ, HCQ, and LEF use were significantly higher in RA controls than in PP patients (P = 0.033, OR = 0.15; P = 0.012, OR = 0.15; and P = 0.015, OR = 0.13, respectively). In the PP group with SpA, the number of smokers was significantly higher (P = 0.003, OR: 2.0, 95% CI: 1.05, 3.81).

Conclusion

Contrary to expectations based on earlier research suggesting that paradoxical reactions develop with the class effect of biological agents, the response of patients who were shifted to another TNFi was favourable.
Linking Polygenic Risk of Schizophrenia to Variation in Magnetic Resonance Imaging Brain Measures: A Comprehensive Systematic Review
Authors: Jameei Hadis , Rakesh Divyangana , Zalesky Andrew , Cairns Murray J , Reay William R , Wray Naomi R , Di Biase Maria A
Published: June 2023

Background and hypothesis

Schizophrenia is highly heritable, with a polygenic effect of many genes conferring risk. Evidence on whether cumulative risk also predicts alterations in brain morphology and function is inconsistent. This systematic review examined evidence for schizophrenia polygenic risk score (sczPRS) associations with commonly used magnetic resonance imaging (MRI) measures. We expected consistent evidence to emerge for significant sczPRS associations with variation in structure and function, specifically in frontal, temporal, and insula cortices that are commonly implicated in schizophrenia pathophysiology.

Study Design

In accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we searched MEDLINE, Embase, and PsycINFO for peer-reviewed studies published between January 2013 and March 2022. Studies were screened against predetermined criteria and National Institutes of Health (NIH) quality assessment tools.

Study Results

In total, 57 studies of T1-weighted structural, diffusion, and functional MRI were included (age range = 9–80 years, Nrange = 64–76 644). We observed moderate, albeit preliminary, evidence for higher sczPRS predicting global reductions in cortical thickness and widespread variation in functional connectivity, and to a lesser extent, region-specific reductions in frontal and temporal volume and thickness. Conversely, sczPRS does not predict whole-brain surface area or gray/white matter volume. Limited evidence emerged for sczPRS associations with diffusion tensor measures of white matter microstructure in a large community sample and smaller cohorts of children and young adults. These findings were broadly consistent across community and clinical populations.

Conclusions

Our review supports the hypothesis that schizophrenia is a disorder of disrupted within and between-region brain connectivity, and points to specific whole-brain and regional MRI metrics that may provide useful intermediate phenotypes.
Beyond crony capitalism: financialization, flexible actors and private power in transition economies—the case of Agrokor
Authors: Stubbs Paul , Žitko Mislav
Published: June 2023

In this article, we provide a critique of the concept of crony capitalism as the dominant explanation of change in economies in transition-based as it is on an idealized technocratic representation of ‘free markets’. We do this through an analysis of the fall of the Croatian company Agrokor, one of the most important companies in post-socialist Southeast Europe. The Agrokor case allows for an understanding of state-economy restructurings in times of crisis, and the competing temporalities and rhythms of corporate practices, political interventions and public perceptions. Agrokor can be considered as a symbol of many of the unfolding contradictions of transnational capitalism in the semi-periphery. The nature of Agrokor’s demise is understood as a result of the hyper-financialization of the firm and the rise of transnational predatory finance. The translation of liquidity and debt crises into a fundamental restructuring of the conglomerate, ushering in a shift in power and control, is the product of active work by a range of agents and an attempted resolution, partial and unfinished, of a struggle for dominance between fractions of capital.