bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction in PLANT DEFENSIN 1 expression in Arabidopsis thaliana results in increased resistance to pathogens and zinc toxicity
Authors: Nguyen Ngoc Nga , Lamotte Olivier , Alsulaiman Mohanad , Ruffel Sandrine , Krouk Gabriel , Berger Nathalie , Demolombe Vincent , Nespoulous Claude , Dang Thi Minh Nguyet , Aimé Sébastien , Berthomieu Pierre , Dubos Christian , Wendehenne David , Vile Denis , Gosti Françoise 
Published: June 2023

Abstract
Ectopic expression of defensins in plants correlates with their increased capacity to withstand abiotic and biotic stresses. This applies to Arabidopsis thaliana, where some of the seven members of the PLANT DEFENSIN 1 family (AtPDF1) are recognised to improve plant responses to necrotrophic pathogens and increase seedling tolerance to excess zinc (Zn). However, few studies have explored the effects of decreased endogenous defensin expression on these stress responses. Here, we carried out an extensive physiological and biochemical comparative characterization of (i) novel artificial microRNA (amiRNA) lines silenced for the five most similar AtPDF1s, and (ii) a double null mutant for the two most distant AtPDF1s. Silencing of five AtPDF1 genes was specifically associated with increased aboveground dry mass production in mature plants under excess Zn conditions, and with increased plant tolerance to different pathogens — a fungus, an oomycete and a bacterium, while the double mutant behaved similarly to the wild type. These unexpected results challenge the current paradigm describing the role of PDFs in plant stress responses. Additional roles of endogenous plant defensins are discussed, opening new perspectives for their functions.
Ubiquitin negatively regulates ABA responses by inhibiting SnRK2.2 and SnRK2.3 kinase activity in Arabidopsis
Authors: Shao Zhengyu , Yang Shuhua , Gu Yinghui , Guo Yan , Zhou Huapeng , Yang Yongqing 
Published: June 2023

Abstract
Abscisic acid (ABA) is an essential phytohormone for plant responses to complex and variable environmental conditions. The molecular basis of the ABA signaling pathway has been well elucidated. SnRK2.2 and SnRK2.3 are key protein kinases participating in ABA responses, and the regulation of their activity plays an important role in signaling. Previous mass spectroscopy analysis of SnRK2.3 suggested that ubiquitin and homologous proteins may bind directly to the kinase. Ubiquitin typically recruits E3 ubiquitin ligase complexes to target proteins, marking them for degradation by the 26S proteasome. Here, we show that SnRK2.2 and SnRK2.3 interact with ubiquitin but are not covalently attached to the protein, resulting in the suppression of their kinase activity. The binding between SnRK2.2, SnRK2.3, and ubiquitin is weakened under prolonged ABA treatment. Overexpression of ubiquitin positively regulated the growth of seedlings exposed to ABA. Our results thus demonstrate a novel function for ubiquitin, which negatively regulates ABA responses by directly inhibiting SnRK2.2 and SnRK2.3 kinase activity.
Clinical characteristics of central nervous system phaeohyphomycosis: A brief report of 20 years’ experience
Authors: Chesdachai Supavit , Yetmar Zachary A , Tabaja Hussam , Wengenack Nancy L , Abu Saleh Omar M 
Published: June 2023

Abstract
Central nervous system (CNS) phaeohyphomycosis is a rare and often fatal fungal infection. Our study reported a case series of eight CNS phaeohyphomycosis cases at our institution over the past 20 years. We did not observe the common pattern of risk factors, abscess location, or number of abscesses among them. Most patients were immunocompetent without classic risk factors for fungal infection. Early diagnosis and aggressive management with surgical intervention and prolonged antifungal therapy can lead to a favorable outcome. The study highlights the need for further research to better understand the pathogenesis and optimal management of this challenging rare infection.
Rapid population synthesis of black hole high-mass X-ray binaries: implications for binary stellar evolution
Authors: Romero-Shaw Isobel , Hirai Ryosuke , Bahramian Arash , Willcox Reinhold , Mandel Ilya 
Published: June 2023

ABSTRACT
We conduct binary population synthesis to investigate the formation of wind-fed high-mass X-ray binaries containing black holes (BH-HMXBs). We evolve multiple populations of high-mass binary stars and consider BH-HMXB formation rates, masses, spins, and separations. We find that systems similar to Cygnus X-1 likely form after stable Case A mass transfer (MT) from the main-sequence progenitors of BHs, provided such MT is characterized by low accretion efficiency, β ≲ 0.1, with modest orbital angular momentum losses from the non-accreted material. Additionally, efficient BH-HMXB formation relies on a new simple treatment for Case A MT that allows donors to retain larger core masses compared to traditional rapid population-synthesis assumptions. At solar metallicity, our Preferred model yields $\mathcal {O}(1)$ observable BH-HMXBs in the Galaxy today, consistent with observations. In this simulation, 8 per cent of BH-HMXBs go on to merge as binary black holes or neutron star-black hole binaries within a Hubble time; however, none of the merging binaries have BH-HMXB progenitors with properties similar to Cygnus X-1. With our preferred settings for core mass growth, mass transfer efficiency, and angular momentum loss, accounting for an evolving metallicity, and integrating over the metallicity-specific star formation history of the Universe, we find that BH-HMXBs may have contributed ≈2–5 BBH merger signals to detections reported in the third gravitational-wave transient catalogue of the LIGO–Virgo–KAGRA Collaboration. We also suggest MT efficiency should be higher during stable Case B MT than during Case A MT.
Searching for signatures of H α spicule-like features in the solar transition region
Authors: Vilangot Nhalil Nived , Shetye Juie , Doyle J Gerry 
Published: June 2023

ABSTRACT
New instruments and telescopes covering the optical and ultraviolet spectral regions have revealed a range of small-scale dynamic features, many which may be related. For example, the range of spicule-like features hints towards a spectrum of features and not just two types; however, direct observational evidence in terms of tracking spicules across multiple wavelengths is needed in order to provide further insight into the dynamics of the Sun’s outer atmosphere. This paper uses H α data obtained with the CRisp Imaging SpectroPolarimeter instrument on the Swedish 1-m Solar Telescope, and in the transition region using the Interface Region Imaging Spectrograph with the SJI 1400 Å channel plus spectral data via the Si iv 1394 Å line to track spicules termed rapid blueshifted excursions (RBEs). The RBEs as seen in the H α blue wing images presented here can be subdivided into two categories: a single or multithreaded feature. Based on the H α spectra, the features can be divided into events showing broadening and line core absorption, events showing broadening and line core emission, events with a pure blueshifted H α profile without any absorption in the red wing, and broadened line profile with the absorption in the blue stronger compared to the red wing. From the RBE-like events that have a Si iv 1394 Å line profile, 78 per cent of them show a Si iv line flux increase. Most of these features show a second broadened Si iv component that is slightly blueshifted.
Relativistic binary systems in scale-independent energy–momentum squared gravity
Authors: Akarsu Özgür , Nazari Elham , Roshan Mahmood 
Published: June 2023

ABSTRACT
In this paper, we study the gravitational-wave (GW) radiation and radiative behaviour of relativistic compact binary systems in the scale-independent energy–momentum squared gravity (EMSG). The field equations of this theory are solved approximately. The gravitational potential of a gravitational source is then obtained by considering two matter Lagrangian densities that both describe a perfect fluid in general relativity (GR). We derive the GW signals emitted from a compact binary system. The results are different from those obtained in GR. It is shown that the relevant non-GR corrections modify the wave amplitude and leave the GW polarizations unchanged. Interestingly, this modification depends on the choice of the matter Lagrangian density. This means that for different Lagrangian densities, this theory presents different predictions for the GW radiation. In this case, the system loses energy to modified GWs. This leads to a change in the secular variation of the Keplerian parameters of the binary system. In this work, we investigate the non-GR effects on the radiative parameter, that is, the first time derivative of the orbital period. Next, applying these results together with GW observations from the relativistic binary systems, we constrain/test the scale-independent EMSG theory in the strong-field regime. After assuming that GR is the valid gravity theory, as a priori expectation, we find that the free parameter of the theory is of the order 10−5 from the direct GW observation, the GW events GW190425 and GW170817, as well as the indirect GW observation, the double pulsar PSR J0737−3039A/B experiment.
Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota
Authors: Perez-Lamarque Benoît , Sommeria-Klein Guilhem , Duret Loréna , Morlon Hélène 
Published: June 2023

AbstractHow host-associated microbial communities evolve as their hosts diversify remains equivocal: how conserved is their composition? What was the composition of ancestral microbiota? Do microbial taxa covary in abundance over millions of years? Multivariate phylogenetic models of trait evolution are key to answering similar questions for complex host phenotypes, yet they are not directly applicable to relative abundances, which usually characterize microbiota. Here, we extend these models in this context, thereby providing a powerful approach for estimating phylosymbiosis (the extent to which closely related host species harbor similar microbiota), ancestral microbiota composition, and integration (evolutionary covariations in bacterial abundances). We apply our model to the gut microbiota of mammals and birds. We find significant phylosymbiosis that is not entirely explained by diet and geographic location, indicating that other evolutionary-conserved traits shape microbiota composition. We identify main shifts in microbiota composition during the evolution of the two groups and infer an ancestral mammalian microbiota consistent with an insectivorous diet. We also find remarkably consistent evolutionary covariations among bacterial orders in mammals and birds. Surprisingly, despite the substantial variability of present-day gut microbiota, some aspects of their composition are conserved over millions of years of host evolutionary history.
Mono- and binuclear complexes of copper(II) with dimethylaminomethyl derivatives of 2-naphthol and 6-quinolinol: synthesis and in vitro study of antitumor properties
Authors: Akhmetova Vnira R , Galimova El'miraM , Mescheryakova Ekaterina S , Dzhemileva Lilya U , Dzhemilev Usein M , D'yakonov Vladimir A 
Published: June 2023

Abstract
1-(Dimethylamino)methyl-6-quinolinol scaffold, a structural moiety of the molecule of anticancer drug topotecan, was modified into copper-containing products to study cytotoxic properties. New mononuclear and binuclear Cu(II) complexes with 1-(N,N-dimethylamino)methyl-6-quinolinol were synthesized for the first time. The same way Cu(II) complexes with 1-(dimethylamino)methyl-2-naphtol ligand were synthesized. The structures of mono- and binuclear Cu(II) complexes with 1-aminomethyl-2-naphtol were confirmed by X-ray diffraction. The obtained compounds were examined for in vitro cytotoxic activity against Jurkat, K562, U937, MDA-MB-231, MCF7, T47D, and HEK293 cells. The induction of apoptosis and the effect of novel Cu complexes on the cell cycle were investigated. The cells showed a higher sensitivity to mononuclear Cu(II) complex with 1-(N,N-dimethylamino)methyl-6-quinolinolligand. All synthesized Cu(II) complexes had higher antitumor activity than the drugs topotecan, camptothecin, and platinum containing cisplatin.
Genotoxicity of cytokines at chemotherapy-induced ‘storm’ concentrations in a model of the human bone marrow
Authors: Asurappulige Harshini S H , Thomas Adam D , Morse H Ruth 
Published: June 2023

Abstract
Donor cell leukaemia (DCL) is a complication of haematopoietic stem cell transplantation where donated cells become malignant within the patient’s bone marrow. As DCL predominates as acute myeloid leukaemia, we hypothesized that the cytokine storm following chemotherapy played a role in promoting and supporting leukaemogenesis. Cytokines have also been implicated in genotoxicity; thus, we explored a cell line model of the human bone marrow (BM) to secrete myeloid cytokines following drug treatment and their potential to induce micronuclei. HS-5 human stromal cells were exposed to mitoxantrone (MTX) and chlorambucil (CHL) and, for the first time, were profiled for 80 cytokines using an array. Fifty-four cytokines were detected in untreated cells, of which 24 were upregulated and 10 were downregulated by both drugs. FGF-7 was the lowest cytokine to be detected in both untreated and treated cells. Eleven cytokines not detected at baseline were detected following drug exposure. TNFα, IL6, GM-CSF, G-CSF, and TGFβ1 were selected for micronuclei induction. TK6 cells were exposed to these cytokines in isolation and in paired combinations. Only TNFα and TGFβ1 induced micronuclei at healthy concentrations, but all five cytokines induced micronuclei at storm levels, which was further increased when combined in pairs. Of particular concern was that some combinations induced micronuclei at levels above the mitomycin C positive control; however, most combinations were less than the sum of micronuclei induced following exposure to each cytokine in isolation. These data infer a possible role for cytokines through chemotherapy-induced cytokine storm, in the instigation and support of leukaemogenesis in the BM, and implicate the need to evaluate individuals for variability in cytokine secretion as a potential risk factor for complications such as DCL.
CREEPY: CRISPR-mediated editing of synthetic episomes in yeast
Authors: Zhao Yu , Coelho Camila , Lauer Stephanie , Majewski Miłosz , Laurent Jon M , Brosh Ran , Boeke Jef D 
Published: June 2023

Abstract
Use of synthetic genomics to design and build ‘big’ DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, introducing designer variations to episomal assemblies with high efficiency and fidelity remains challenging. Here we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, a method for rapid engineering of large synthetic episomal DNA constructs. We demonstrate that CRISPR editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes. We optimize CREEPY for efficient and precise multiplex editing of &gt;100 kb yeast episomes, providing an expanded toolkit for synthetic genomics.
Structural insights into CodY activation and DNA recognition
Authors: Hainzl Tobias , Bonde Mari , Almqvist Fredrik , Johansson Jörgen , Sauer-Eriksson A Elisabeth 
Published: June 2023

Abstract
Virulence factors enable pathogenic bacteria to infect host cells, establish infection, and contribute to disease progressions. In Gram-positive pathogens such as Staphylococcus aureus (Sa) and Enterococcus faecalis (Ef), the pleiotropic transcription factor CodY plays a key role in integrating metabolism and virulence factor expression. However, to date, the structural mechanisms of CodY activation and DNA recognition are not understood. Here, we report the crystal structures of CodY from Sa and Ef in their ligand-free form and their ligand-bound form complexed with DNA. Binding of the ligands—branched chain amino acids and GTP—induces conformational changes in the form of helical shifts that propagate to the homodimer interface and reorient the linker helices and DNA binding domains. DNA binding is mediated by a non-canonical recognition mechanism dictated by DNA shape readout. Furthermore, two CodY dimers bind to two overlapping binding sites in a highly cooperative manner facilitated by cross-dimer interactions and minor groove deformation. Our structural and biochemical data explain how CodY can bind a wide range of substrates, a hallmark of many pleiotropic transcription factors. These data contribute to a better understanding of the mechanisms underlying virulence activation in important human pathogens.
Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain
Authors: Bascunana Virginie , Pelletier Audrey , Gouhier Arthur , Bemmo Amandine , Balsalobre Aurelio , Drouin Jacques 
Published: June 2023

Abstract
Pioneer factors are transcription factors (TFs) that have the unique ability to recognise their target DNA sequences within closed chromatin. Whereas their interactions with cognate DNA is similar to other TFs, their ability to interact with chromatin remains poorly understood. Having previously defined the modalities of DNA interactions for the pioneer factor Pax7, we have now used natural isoforms of this pioneer as well as deletion and replacement mutants to investigate the Pax7 structural requirements for chromatin interaction and opening. We show that the GL+ natural isoform of Pax7 that has two extra amino acids within the DNA binding paired domain is unable to activate the melanotrope transcriptome and to fully activate a large subset of melanotrope-specific enhancers targeted for Pax7 pioneer action. This enhancer subset remains in the primed state rather than being fully activated, despite the GL+ isoform having similar intrinsic transcriptional activity as the GL– isoform. C-terminal deletions of Pax7 lead to the same loss of pioneer ability, with similar reduced recruitments of the cooperating TF Tpit and of the co-regulators Ash2 and BRG1. This suggests complex interrelations between the DNA binding and C-terminal domains of Pax7 that are crucial for its chromatin opening pioneer ability.
Distribution, preparedness and management of Ukrainian adult refugees on dialysis—an international survey by the Renal Disaster Relief Task Force of the European Renal Association
Authors: Pawłowicz-Szlarska Ewa , Vanholder Raymond , Sever Mehmet S , Tuğlular Serhan , Luyckx Valerie , Eckardt Kai-Uwe , Gallego Daniel , Ivanov Dmytro , Nistor Ionut , Shroff Rukshana , Škoberne Andrej , Stuard Stefano , Gellert Ryszard , Noruišiene Edita , Sekkarie Mohamed , Wiecek Andrzej ,   the Renal Disaster Relief Task Force of the ERA, Tuglular Serhan , Eckardt Kai-Uwe , Gallego Daniel , Ivanov Dimitri , Klis Anna , Loboda Yelena , Luyckx Valerie , Noruišiene Edita , Nistor Ionut , Pawłowicz-Szlarska Ewa , Shroff Rukshana , Skoberne Andrej , Stuard Stefano , Sever Mehmet Sukru , Vanholder Raymond , Więcek Andrzej 
Published: June 2023

ABSTRACT

Background
Due to the Russian–Ukrainian war, some of the about 10 000 adults requiring dialysis in Ukraine fled their country to continue dialysis abroad. To better understand the needs of conflict-affected dialysis patients, the Renal Disaster Relief Task Force of the European Renal Association conducted a survey on distribution, preparedness and management of adults requiring dialysis who were displaced due to the war.

Methods
A cross-sectional online survey was sent via National Nephrology Societies across Europe and disseminated to their dialysis centers. Fresenius Medical Care shared a set of aggregated data.

Results
Data were received on 602 patients dialyzed in 24 countries. Most patients were dialyzed in Poland (45.0%), followed by Slovakia (18.1%), Czech Republic (7.8%) and Romania (6.3%). The interval between last dialysis and the first in the reporting center was 3.1 ± 1.6 days, but was ≥4 days in 28.1% of patients. Mean age was 48.1 ± 13.4 years, 43.5% were females. Medical records were carried by 63.9% of patients, 63.3% carried a list of medications, 60.4% carried the medications themselves and 44.0% carried their dialysis prescription, with 26.1% carrying all of these items and 16.1% carrying none. Upon presentation outside Ukraine, 33.9% of patients needed hospitalization. Dialysis therapy was not continued in the reporting center by 28.2% of patients until the end of the observation period.

Conclusions
We received information about approximately 6% of Ukrainian dialysis patients, who had fled their country by the end of August 2022. A substantial proportion were temporarily underdialyzed, carried incomplete medical information and needed hospitalization. The results of our survey may help to inform policies and targeted interventions to respond to the special needs of this vulnerable population during wars and other disasters in the future.
Community-sourced sightings of atypical birds can be used to understand the evolution of plumage color and pattern
Authors: Aguillon Stepfanie M , Shultz Allison J 
Published: June 2023

AbstractBirds are known for their brilliant colors and extraordinary patterns. Sightings of individuals with atypical plumage often cause considerable excitement in the birding public, but receive little attention beyond reporting one-off sightings by the scientific community. In this Perspective, we argue that sightings of individuals with atypical plumage submitted to community science platforms hold the potential to further our understanding of the evolution of plumage color and patterning in birds. As a demonstration, we outline two examples using sightings of leucistic individuals—those that lack melanin across the body or in certain feather patches. First, we discuss the potential for understanding carotenoid pigmentation with these sightings. Leucism influences melanins, but not carotenoids, and so the extent and distribution of carotenoids across the body are unmasked. In a leucistic individual, carotenoids may or may not be more extensive than what is typically visible and this could help to understand the energetic costs and constraints involved in obtaining, processing, and depositing carotenoids in different species. Second, we discuss how partial leucism could provide insights into plumage pattern evolution. We demonstrate that one can use the many observations present on community science platforms to identify repeated patterns in different partially leucistic individuals of the same species, and match these to patches present in related species. These patterns could be the result of shared underlying genetic variation that controls plumage patterning in birds over long evolutionary timescales. With these examples, we outline a few potential lines of inquiry possible with atypical sightings submitted to community science platforms and note that other plumage aberrations provide additional opportunities. We encourage researchers to take full advantage of these chance sightings when they occur and database managers to make it possible to more easily tag photos of individuals with atypical plumage or other traits.