bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions
Authors: Liu Chen , Wang Yijin , Zhou Zeyuan , Wang Shimei , Wei Zhong , Ravanbakhsh Mohammadhossein , Shen Qirong , Xiong Wu , Kowalchuk George A , Jousset Alexandre 
Published: September 2024

Abstract
Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top–down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.
Use of echinocandin outpatient parenteral antimicrobial therapy for the treatment of infection caused by Candida spp.: utilization, outcomes and impact of a change to weekly dosing
Authors: Clarke Fiona , Grenfell Adelaide , Chao Sarah , Richards Helen , Korman Tony , Rogers Benjamin 
Published: September 2024

Abstract

Background
Outpatient parenteral antimicrobial therapy (OPAT) can deliver extended parenteral treatment of fungal infections in an ambulatory setting, whilst minimizing treatment burden and cost. The extended dosing interval of rezafungin may potentiate the benefits of OPAT.

Methods
This retrospective cohort study includes all adult patients who received echinocandin therapy in a large OPAT programme between 2012 and 2022. Patient characteristics, treatment and outcomes were studied. Data were analysed to determine the effects of replacing daily dosing with weekly dosing of echinocandin.

Results
Across the study period, 11% (44/386) of all patients in our Health Service treated with ≥7 days of echinocandin were managed via OPAT. All were Candida and related ‘yeast-like’ species infections. Nakaseomyces glabrata (20/41; 49%) was the most common pathogen, fungaemia the most common presentation (17/41; 41%) and azole resistance the most frequent indication for echinocandin use (21/41; 51%).
In total, 633 days of echinocandin were administered as OPAT. Thirteen patients (13/41; 32%) received concurrent parenteral antibacterials. Treatment success was achieved in 30/41 (73%) patients. If daily echinocandin dosing was replaced with weekly dosing, a potential 52% (633 to 326) reduction in the total number of treatments (for any therapy) delivered by the OPAT team is possible. The ongoing need for daily antibacterial administration mitigated the benefit in some of this cohort.

Conclusions
Echinocandin therapy can be safely delivered via OPAT with outcomes equivalent to bed-based care. The extended dosing interval of rezafungin will allow for a substantial reduction in the number of treatments required across the patient cohort.
Establishing data elements and exchange standards to support long COVID healthcare and research
Authors: Dolin Gay , Saitwal Himali , Bertodatti Karen , Mueller Savanah , Bierman Arlene S , Suls Jerry , Brandt Katie , Camara Djibril S , Leppry Stephanie , Jones Emma , Gallego Evelyn , Carlson Dave , Norton Jenna 
Published: September 2024

Abstract

Objective
The Multiple Chronic Conditions (MCCs) Electronic Care (e-Care) Plan project aims to establish care planning data standards for individuals living with MCCs. This article reports on the portion of the project focused on long COVID and presents the process of identifying and modeling data elements using the HL7 Fast Healthcare Interoperability Resources (FHIR) standard.

Materials and Methods
Critical data elements for managing long COVID were defined through a consensus-driven approach involving a Technical Expert Panel (TEP). This involved 2 stages: identifying data concepts and establishing electronic exchange standards.

Results
The TEP-identified and -approved long COVID data elements were mapped to the HL7 US Core FHIR profiles for syntactic representation, and value sets from standard code systems were developed for semantic representation of the long COVID concepts.

Discussion
Establishing common long COVID data standards through this process, and representing them with the HL7 FHIR standard, facilitates interoperable data collection, benefiting care delivery and patient-centered outcomes research (PCOR) for long COVID. These standards may support initiatives including clinical and pragmatic trials, quality improvement, epidemiologic research, and clinical and social interventions.
By building standards-based data collection, this effort accelerates the development of evidence to better understand and deliver effective long COVID interventions and patient and caregiver priorities within the context of MCCs and to advance the delivery of coordinated, person-centered care.

Conclusion
The open, collaborative, and consensus-based approach used in this project will enable the sharing of long COVID-related health concerns, interventions, and outcomes for patient-centered care coordination across diverse clinical settings and will facilitate the use of real-world data for long COVID research.
The NRF2 inducer CDDO-2P-Im provokes a reduction in amyloid β levels in Alzheimer’s disease model mice
Authors: Uruno Akira , Kadoguchi-Igarashi Shiori , Saito Ritsumi , Koiso Shohei , Saigusa Daisuke , Chu Ching-Tung , Suzuki Takafumi , Saito Takashi , Saido Takaomi C , Cuadrado Antonio , Yamamoto Masayuki 
Published: September 2024

Abstract
Alzheimer’s disease (AD) is the most common aetiology of dementia. The transcription factor NF-E2-related factor 2 (NRF2) induces the expression of genes encoding phase II detoxification and antioxidant genes. NRF2 is regulated by Kelch-like ECH-associated protein 1 (KEAP1), and the KEAP1-NRF2 system is the key regulatory system involved in cytoprotection. To examine whether pharmacological induction of NRF2 expression alleviates AD phenotypes in vivo, we employed two AD mouse models, i.e. App NL-G-F/NL-G-F (AppNLGF) and APPV717I::TAUP301L (APP/TAU) mice. As the synthetic oleanane triterpenoid 1-[2-cyano-3,12-dioxooleana-1,9(11-dien-28-oyl)] (CDDO)-4(−pyridin-2-yl)-imidazole (CDDO-2P-Im) exhibits strong NRF2-inducing activity, we treated AD model mice with CDDO-2P-Im. We found that Aβ42 levels were markedly greater in the brains of AppNLGF mice than in those of APP/TAU mice. CDDO-2P-Im treatment significantly decreased Aβ42 levels, but not Aβ40 levels, in APP/TAU mice. Consequently, CDDO-2P-Im also decreased the ratio of Aβ42/Aβ40, a vital marker of amyloid plaque formation. LC–MS/MS analyses revealed that CDDO-2P-Im was delivered to the brains of the APP/TAU mice. CDDO-2P-Im induced the expression of detoxification and antioxidant gene targets of NRF2 and elevated reduced glutathione (GSH) levels in the mouse brain. These results support the notion that CDDO-2P-Im ameliorates AD-related pathologic changes.
Computational Modelling and Simulations to Study the Thermal Enhancement in Nanofluid Flow in Undulating Wavy Cavity of a Cylinder: Finite Element Analysis
Authors: Fayz-Al-Asad Md , Iqbal Zahoor , Hasan Md Shamim , Eljaneid Nidal H E , Alam Sarker Md Manirul , Alhazmi Sharifah E , Shah Jaffer , Alqarni M M , Awwad Tarek M , Elnaqeeb Thanaa 
Published: September 2024

Abstract
The goal of this present work is to produce a computational model to discover the Cu – water nanofluid flow patterns and heat transfer features through a wavy chamber via a different cross-section cylinder. A finite element method based on the Galerkin weighted residual technique solves the nonlinear governing equations for the current computational model. We have conducted a parametric exploration to investigate the influence of Rayleigh number (103 ≤ Ra ≤ 106), several angles of an elliptical cylinder (0° ≤ θ ≤ 90°), aspect ratios (1 ≤ AR ≤ 3), and varied nanofluid volume fractions (0 ≤ φ ≤ 0.1). The graphical representation of the numerical results, such as streamlines, isotherm contours, the angle of elliptical cylinders, and the average Nusselt number as it relates to the rate of heat transfer. The present research and a prior publication agree strongly. The results show that the heat transfer rate increases with the angle of orientation and aspect ratio for each value. The vertical direction of an elliptical cylinder significantly enhanced the rate of heat transfer. The result indicates that for mutually pure water and nanoparticles, the maximum heat transmission rate appears at θ = 90°, AR = 3.0, λ = 5, φ = 4%, and Ra = 106. The undulation effectiveness reaches its highest at an undulation number of 5.
Case report of the combination of a TRAM flap, lipofilling, and 3-D tattooing after failed implant-based reconstruction: improving aesthetic results
Authors: Damin Andrea Pires , Tiellet Bibiana Quatrin , de Melo Marcia Portela , Zucatto Angela E , Cericatto Rodrigo , Biazus Jorge Villanova 
Published: September 2024

Abstract
We present a complex case of a patient diagnosed with bilateral breast cancer. The patient initially underwent bilateral skin-sparing mastectomy and immediate subpectoral implant-base breast reconstruction. She had an uncomplicated postoperative recovery. However, three months later, she developed a severe and persistent local infection during adjuvant chemotherapy, resulting in the loss of the breast implants and the formation of massive deforming scars in the chest area. To address this, the patient underwent a series of reconstructive procedures. Lipofilling was used on the chest wall to improve skin quality, followed by a late bilateral transverse rectus abdominis myocutaneous flap for breast reconstruction. Additionally, the final aesthetic result was enhanced by applying a 3-D tattoo. This case highlights the use of a sequence of reconstructive procedures as a feasible alternative to manage complex and extensive scars after failure of primary breast reconstruction.
The sucrose signalling route controls Flavescence dorée phytoplasma load in grapevine leaves
Authors: Morabito Cristina , Pagliarani Chiara , Lovisolo Claudio , Ripamonti Matteo , Bosco Domenico , Marzachì Cristina , Roitsch Thomas , Schubert Andrea 
Published: September 2024

Abstract
Flavescence dorée (FD) is a phytoplasma disease transmitted by insects, causing severe damage in vineyards across Europe. Since there is no effective treatment, infected plants must be removed to prevent further spread. There is variation in susceptibility to FD among different grapevine cultivars, and some exhibit symptom remission, known as recovery, although the mechanisms behind this are unclear. Diseased plants accumulate soluble sugars, including sucrose, which influences the concentration of trehalose-6-phosphate (T6P), a signalling molecule affecting plant growth and stress responses. It is hypothesized that sucrose-mediated signalling via T6P could trigger defence mechanisms, reducing FD pathogen load and increasing plant recovery. To test this hypothesis, two grapevine genotypes with different susceptibility to FD were compared, revealing increased sucrose level and trehalose-6-phosphate synthase (TPS) activity in the more tolerant cultivar. However, FD-infected plants showed inhibited sucrose-cleaving enzymes and no activation of TPS expression. Attempts to enhance sucrose levels through trunk infusion and girdling promoted sucrose metabolism, T6P biosynthesis, and defence gene expression, facilitating symptom recovery. Girdling particularly enhanced T6P biosynthesis and expression of defence genes above the treatment point, reducing FD pathogen presence and promoting recovery. These findings indicate that elevated sucrose levels, possibly signalling through T6P, may limit FD pathogen spread, aiding in plant recovery.
Isotopic abundance of carbon in the DLA towards QSO B1331+170
Authors: Milaković Dinko , Webb John K , Molaro Paolo , Lee Chung-Chi , Jethwa Prashin , Cupani Guido , Murphy Michael T , Welsh Louise , D’Odorico Valentina , Cristiani Stefano , Génova Santos Ricardo , Martins Carlos J A P , Nunes Nelson J , Schmidt Tobias M , Pepe Francesco A , Zapatero Osorio Maria Rosa , Alibert Yann , González Hernández J I , Di Marcantonio Paolo , Palle Enric , Rebolo Rafael , Santos Nuno C , Sousa Sérgio G , Suárez Mascareño Alejandro 
Published: September 2024

ABSTRACT
Chemical evolution models predict a gradual build-up of 13C in the Universe, based on empirical nuclear reaction rates and assumptions on the properties of stellar populations. However, old metal-poor stars within the Galaxy contain more 13C than is predicted, suggesting that further refinements to the models are necessary. Gas at high-redshift provides important supplementary information at metallicities $-2\lesssim \left[{\rm Fe/H}\right]\lesssim -1$, for which there are only a few measurements in the Galaxy. We obtained new, high-quality, VLT/ESPRESSO observations of the QSO B1331$+$170 and used them to measure 12C/13C in the damped Lyman-$\alpha$ system (DLA) at $z_{\rm abs}=1.776$, with $\left[{\rm Fe/H}\right]$ = −1.27. ai-vpfit, an artificial intelligence tool based on genetic algorithms and guided by a spectroscopic information criterion, was used to explore different possible kinematic structures of the carbon gas. Three hundred independent ai-vpfit models of the absorption system were produced using pre-set 12C/13C values, ranging from 4 to 500. Our results show that ${\rm ^{12}C / ^{13}C}=28.5^{+51.5}_{-10.4}$, suggesting a possibility of 13C production at low metallicity.
CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver
Authors: Li Hong-Yu , Wang Min , Jiang Xiaoyu , Jing Yaobin , Wu Zeming , He Yifang , Yan Kaowen , Sun Shuhui , Ma Shuai , Ji Zhejun , Wang Si , Belmonte Juan Carlos Izpisua , Qu Jing , Zhang Weiqi , Wei Taotao , Liu Guang-Hui 
Published: September 2024

Abstract
Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal protein L22 (RPL22) as the foremost RAG whose deficiency mitigates the effects of cellular senescence. Consequently, absence of RPL22 delays hMPCs from becoming senescent, while an excess of RPL22 accelerates the senescence process. Mechanistically, we found in senescent hMPCs, RPL22 accumulates within the nucleolus. This accumulation triggers a cascade of events, including heterochromatin decompaction with concomitant degradation of key heterochromatin proteins, specifically heterochromatin protein 1γ (HP1γ) and heterochromatin protein KRAB-associated protein 1 (KAP1). Subsequently, RPL22-dependent breakdown of heterochromatin stimulates the transcription of ribosomal RNAs (rRNAs), triggering cellular senescence. In summary, our findings unveil a novel role for nucleolar RPL22 as a destabilizer of heterochromatin and a driver of cellular senescence, shedding new light on the intricate mechanisms underlying the aging process.
Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization
Authors: Wu Yiran , Adeel Muhammad Muzammal , Xia Dian , Sancar Aziz , Li Wentao 
Published: September 2024

Abstract
Aflatoxin B1 (AFB1), a potent mycotoxin, is one of the environmental risk factors that cause liver cancer. In the liver, the bioactivated AFB1 intercalates into the DNA double helix to form a bulky DNA adduct which will lead to mutation if left unrepaired. Here, we adapted the tXR-seq method to measure the nucleotide excision repair of AFB1-induced DNA adducts at single-nucleotide resolution on a genome-wide scale, and compared it with repair data obtained from conventional UV-damage XR-seq. Our results showed that transcription-coupled repair plays a major role in the damage removal process. We further analyzed the distribution of nucleotide excision repair sites for AFB1-induced DNA adducts within the 3D human genome organization. Our analysis revealed a heterogeneous AFB1–dG repair across four different organization levels, including chromosome territories, A/B compartments, TADs, and chromatin loops. We found that chromosomes positioned closer to the nuclear center and regions within A compartments have higher levels of nucleotide excision repair. Notably, we observed high repair activity around both TAD boundaries and loop anchors. These findings provide insights into the complex interplay between AFB1-induced DNA damage repair, transcription, and 3D genome organization, shedding light on the mechanisms underlying AFB1-induced mutagenesis.
Antibody-mediated rejection diagnosed in early protocol biopsies in high immunological risk kidney transplant recipients
Authors: Arana Carolt , Hermida Evelyn , Rovira Jordi , Caro José Luis , Cucchiari David , Larque Ana Belén , Palou Eduard , Torres Juan , Montagud-Marrahi Enrique , Cuadrado-Páyan Elena , Rodriguez Diana , Cacho Judit , Gonzalez Angela , Reinoso Johanna , Nicolau Carlos , Esforzado Nuria , Torregrosa Vicente , Piñeiro Gastón , Revuelta Ignacio , Cofan Federico , Diekmann Fritz , Ventura-Aguiar Pedro , Oppenheimer Federico 
Published: September 2024

ABSTRACT

Background
Renal transplant recipients with donor-specific anti-HLA antibodies are at an increased risk of antibody-mediated rejection (ABMR). Early protocolized renal biopsies may serve as a strategy to improve diagnosis in this patient population.

Methods
We evaluated 155 highly sensitized renal transplant recipients with cPRA class I + II &gt;90% pre-transplant from 2015 to 2022. Patients with protocol biopsies within the first 2 weeks post-transplant were included.

Results
A total of 122 patients were included in the study. Of these, 13 (10.6%) were diagnosed with very early antibody-mediated rejection (veABMR) within the first 2 weeks post-transplant. This corresponds to 52% (13/25 patients) of all ABMR cases reported during the follow-up of this population. The graft survival rates at 1 and 3 years were significantly lower in patients with veABMR (P &lt; .001) compared with patients without rejection in the early protocol biopsy. In terms of severity, the veABMR cohort exhibited a hazard ratio (HR) of 10.33 (95% confidence interval 3.23–33.06, P &lt; .001) for graft failure. The presence of donor-specific antibodies class II on the day of transplantation and a higher percentage of eplet mismatch (EpMM), particularly EpMM DQA1, correlated with the development of veABMR.

Conclusion
Early protocol biopsies play a pivotal role in the early detection of veABMR in high-risk immunological patients. Patients with veABMR face significant risks of graft loss, despite early treatment of rejection.
Nutrigenetics and Nutritional Strategies in Systemic Arterial Hypertension: Evidence From a Scoping Review
Authors: Holzbach Luciana C , Brandão-Lima Paula N , Duarte Graziela B S , Rogero Marcelo M , Cominetti Cristiane 
Published: September 2024

Abstract
Nutrition and genetics have individual roles in systemic arterial hypertension (SAH); however, they can interact, influencing the regulation of blood pressure (BP) levels. The aim of this study was to evaluate the available evidence regarding gene–nutrient interactions in modulating BP levels in adults with SAH. The review followed the recommendations of the Joanna Briggs Institute and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Twelve studies met the inclusion criteria for this review, reporting on 20 genes and 31 single nucleotide polymorphisms (SNPs), with 19 of them associated with BP variations. The most frequently evaluated SNPs were ACE rs4646994 and AT1R rs5186. Among the nutritional interventions, dietary sodium content was the focus of most studies (n = 11). Interactions with sodium consumption were observed for the following SNPs: KDM1A rs587168, EDNRB rs5351, LSS rs2254524, IRS1 rs1801278, KCNK9 rs6997709, ACE rs4646994, GNB3 rs5443, PPARG rs4684847, EDN1 rs5370, BCAT1 rs7961152, IL18 rs5744292, NOS3 rs2070744, and AT1R rs5186. In the presence of a diet rich in fruits and vegetables, moderate alcohol consumption, and reduced sodium intake, the SNP AT2R rs11091046 was associated with a decrease in BP levels. Furthermore, the SNP MTHFR rs1801133 exhibited an interaction with riboflavin supplementation in affecting BP levels. The evidence regarding the interaction between genetics and diet on BP levels remains limited. Among the existing findings, an interaction was observed between sodium, calcium, riboflavin, and specific polymorphisms; however, the underlying mechanisms for these interactions have yet to be identified. Note: This paper is part of the Nutrition Reviews Special Collection on Precision Nutrition.
Plasma diagnostics of supernova remnant 3C 400.2 by Suzaku observations
Authors: Onuma Masataka , Nobukawa Kumiko K , Nobukawa Masayoshi , Yamauchi Shigeo , Uchiyama Hideki 
Published: September 2024

Abstract
We report on the results of plasma diagnostics of the supernova remnant (SNR) 3C 400.2, which has been reported to have a recombining plasma by previous studies. For careful background estimation, we simultaneously fitted spectra extracted from the SNR and background regions and evaluated the SNR emission contaminating the background-region spectrum as well as the background emission in the source-region spectrum. The SNR emission is explained by the collisional ionization equilibrium plasma originating from the interstellar medium and the ionizing plasma originating from the ejecta, in contrast to previous studies. In addition, we found an unidentified X-ray source near the SNR, Suzaku J1937.4$+$1718, which is accompanied by an emission line at $\sim$4.4 keV with a $2.8\sigma$ confidence level. Because there is no striking atomic line at the energy in the rest frame, Suzaku J1937.4$+$1718 could be an extragalactic object with a redshifted Fe line.