bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seedling responses to moderate and severe herbivory: a field‐clipping experiment with a keystone Mediterranean palm
Authors: Garrote P. J. , Bugalho M. N. , Fedriani J. M. 
Published: September 2023

Abstract
Plant–ungulate interactions are critical in shaping the structure of Mediterranean plant communities. Nevertheless, there is a dearth of knowledge on how plant intrinsic and extrinsic factors mediate the sign and strength of plant–ungulate interactions. This is most relevant when addressing natural or assisted restoration of plant communities in human‐disturbed areas.
We conducted field‐clipping experiments simulating how different intensities of ungulate herbivory may affect the natural regeneration and establishment of the Mediterranean dwarf palm (Chamaerops humilis), a keystone species in Mediterranean ecosystems. We quantified seedling survival and size in two human‐disturbed sites (SW Spain) where wild and domestic ungulates exert high herbivory pressure on vegetation.
Severe clipping and seedling aging reduced rates of seedling survival. In contrast, moderate clipping did not affect seedling survival, suggesting a certain degree of C. humilis tolerance to herbivory. Severe clipping reduced seedling height strongly but not seedling diameter, and these effects seem to have decreased seedling survival. Nurse shrubs increased seedling size, which likely improved seedling survival. We also found seedling compensatory growth which varied between study sites.
Field‐clipping experiments can help disentangle effects of plant extrinsic and intrinsic factors on the sign and strength of plant–ungulate interactions and their ecological consequences on the dynamics of human‐disturbed ecosystems. We call attention to the importance of appropriately managing scenarios of severe herbivory and summer droughts, particularly frequent in Mediterranean ecosystems, as synergic effects of such key drivers can negatively affect the structure and dynamics of plant communities and endanger their conservation.
The Nationalization of Patriotism in Russian Literature during the Crimean War: Institutions, Everyday Nationalism, and Images of Peasants
Authors: Vdovin Alexey 
Published: September 2023

AbstractThis article explores the issue of Russian imperial nationalism in the early phase of its formation, namely the nationalization of patriotism in literature during the Crimean War, 1853–56. Using historical studies and theories of nationalism, the author shows how and why an acute discourse of a nationalistic experience of community uniting the elite with the common people arose in St. Petersburg society, theater, and literature. Drawing on many published and archival materials, the article describes the institutions of escalating nationalism (thick journals, newspapers, the Maritime Ministry, theater, salons, and circles), everyday rituals (wearing “Russian” clothes), and the images of peasants, who in the fiction of Aleksei Potekhin, Aleksei Pisemskii, Ivan Gorbunov, Ivan Turgenev, and Dmitrii Grigorovich acted as bearers of authentic “Russianness.” The growing popularity of these writers’ texts can be explained by the fact that they demonstratively linked the psychology and subjectivity of peasant characters with their ethnic identity. Contrary to official propaganda that portrayed peasants as loyal to the tsar, faith, and Fatherland, the new representation satisfied the demand of the elite and socially diverse theater audience for images of unity within a single national community and compensated for the disappointment of defeats at the front.
Isolation and sequencing of the spoilage yeast
Kregervanrija delftensis
Authors: Collins Joseph H. , Cosio Amparo , Brogan Garrett , Chico Lucas , Rozen Alexandra , Thomson Ellen , Young Eric M. 
Published: September 2023

ABSTRACT

New sequencing workflows can enable the genomics of microbes isolated from craft beverages. Here, we use hybrid, short, and long-read sequencing to assemble the genome of a yeast isolated from cider,
Kregervanrija delftensis
NCC-J. The
Kregervanrija
genus has few genomes available; thus, this contributes to yeast genomics.
Four complete genomes of human parvovirus B19 from amniotic fluid specimens
Authors: Alidjinou Enagnon Kazali , De Coninck Lander , Swinnen Jill , Lazrek Mouna , Hober Didier , Matthijnssens Jelle 
Published: September 2023

ABSTRACT
We report the sequences of four complete genomes of parvovirus B19, extracted from human amniotic fluid specimens collected from pregnant women with abnormal ultrasound features in France. The genome sequences are 5,596 nucleotides long and include long terminal repeats. Several amino acid substitutions were observed in nonstructural protein (NS1).
The gut microbiota composition is linked to subsequent occurrence of ventilator-associated pneumonia in critically ill patients
Authors: Orieux Arthur , Enaud Raphaël , Imbert Sébastien , Boyer Philippe , Begot Erwan , Camino Adrian , Boyer Alexandre , Berger Patrick , Gruson Didier , Delhaes Laurence , Prevel Renaud 
Published: September 2023

ABSTRACT

Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critically ill-ventilated patients. Oropharyngeal and lung microbiota have been demonstrated to be associated with VAP occurrence, but the involvement of gut microbiota has not been investigated so far. Therefore, the aim of this study is to compare the composition of the gut microbiota between patients who subsequently develop VAP and those who do not. A rectal swab was performed at admission of every consecutive patient into the intensive care unit (ICU) from October 2019 to March 2020. After DNA extraction, V3-V4 and internal transcribed spacer 2 regions deep-sequencing was performed on MiSeq sequencer (Illumina) and data were analyzed using Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline. Among 255 patients screened, 42 (16%) patients with invasive mechanical ventilation for more than 48 h were included, 18 (43%) with definite VAP and 24 without (57%). Patients who later developed VAP had similar gut bacteriobiota and mycobiota α-diversities compared to those who did not develop VAP. However, gut mycobiota was dissimilar (β-diversity) between these two groups. The presence of
Megasphaera massiliensis
was associated with the absence of VAP occurrence, whereas the presence of the fungal genus
Alternaria
sp. was associated with the occurrence of VAP. The composition of the gut microbiota, but not α-diversity, differs between critically ill patients who subsequently develop VAP and those who do not. This study encourages large multicenter cohort studies investigating the role of gut-lung axis and oropharyngeal colonization in the development of VAP in ICU patients. Trial registration number: NCT04131569, date of registration: 18 October 2019.

IMPORTANCE
The composition of the gut microbiota, but not α-diversity, differs between critically ill patients who subsequently develop ventilator-associated pneumonia (VAP) and those who do not. Investigating gut microbiota composition could help to tailor probiotics to provide protection against VAP.
Bibliometric analysis of the uveitis literature and research trends over the past two decades
Authors: Gao Tingxiao , Monson Hayley , Felfeli Tina 
Published: September 2023

ObjectiveThis study aimed to examine the publication patterns and present a current view of the field of uveitis using a bibliometric analysis.DesignBibliometric analysis.Methods and analysisA comprehensive search of three databases including MEDLINE, EMBASE and Cochrane was conducted from 1 January 2000 to 31 December 2022. Search results from all three databases were subjected to analysis by Bibliometrix, an R programme that analyses large literature dataset with statistical and mathematical models. Visualisation of collaboration networks and relevance between countries was presented with VOSviewer.ResultsA total of 26 296 articles were included in the analysis. The field of uveitis has undergone a significant exponential growth since 2000, with an average growth rate of 4.14%. The most substantial annual growth was between the years 2021 and 2022 (36%). According to the corresponding author’s countries, the three most productive countries were Turkey (3288, 12.6%), the USA (3136, 12%) and Japan (1981, 7.6%). The USA (243, 31.4%), England (117, 15%) and Germany (62, 8%) are the top three countries that contributed to clinical trials. The average international collaboration of all countries was 2.5%.ConclusionsUveitis literature has undergone significant growth in the past two decades. The demographic factors of publishing countries lead to their various productivity and types of these uveitis studies, which is closely associated with the countries’ scientific research resources and patient populations.
Design of a phase III, double-blind, randomised, placebo-controlled trial of BI 1015550 in patients with progressive pulmonary fibrosis (FIBRONEER-ILD)
Authors: Maher Toby M , Assassi Shervin , Azuma Arata , Cottin Vincent , Hoffmann-Vold Anna-Maria , Kreuter Michael , Oldham Justin M , Richeldi Luca , Valenzuela Claudia , Wijsenbeek Marlies S , Coeck Carl , Schlecker Christina , Voss Florian , Wachtlin Daniel , Martinez Fernando J 
Published: September 2023

IntroductionProgressive pulmonary fibrosis (PPF) includes any diagnosis of progressive fibrotic interstitial lung disease (ILD) other than idiopathic pulmonary fibrosis (IPF). However, disease progression appears comparable between PPF and IPF, suggesting a similar underlying pathology relating to pulmonary fibrosis. Following positive results in a phase II study in IPF, this phase III study will investigate the efficacy and safety of BI 1015550 in patients with PPF (FIBRONEER-ILD).Methods and analysisIn this phase III, double-blind, placebo-controlled trial, patients are being randomised 1:1:1 to receive BI 1015550 (9 mg or 18 mg) or placebo twice daily over at least 52 weeks, stratified by background nintedanib use. Patients must be diagnosed with pulmonary fibrosis other than IPF that is progressive, based on predefined criteria. Patients must have forced vital capacity (FVC) ≥45% predicted and haemoglobin-corrected diffusing capacity of the lung for carbon monoxide ≥25% predicted. Patients must be receiving nintedanib for at least 12 weeks, or not receiving nintedanib for at least 8 weeks, prior to screening. Patients on stable treatment with permitted immunosuppressives (eg, methotrexate, azathioprine) may continue their treatment throughout the trial. Patients with clinically significant airway obstruction or other pulmonary abnormalities, and those using immunosuppressives that may confound FVC results (cyclophosphamide, tocilizumab, mycophenolate, rituximab) or high-dose steroids will be excluded. The primary endpoint is absolute change from baseline in FVC (mL) at week 52. The key secondary endpoint is time to the first occurrence of any acute ILD exacerbation, hospitalisation for respiratory cause or death, over the duration of the trial.Ethics and disseminationThe trial is being carried out in accordance with the ethical principles of the Declaration of Helsinki, the International Council on Harmonisation Guideline for Good Clinical Practice and other local ethics committees. The study results will be disseminated at scientific congresses and in peer-reviewed publications.Trial registration numberNCT05321082.
Liquefaction triggering and post-triggering behavior of biocemented loose sand
Authors: Lee Minyong , Gomez Michael G. 
Published: September 2023

Biocementation is a biomediated ground improvement technique that can improve the engineering behavior of granular soils. The process has received significant attention as an earthquake-induced liquefaction mitigation technique; however, critical gaps have remained in our understanding of how liquefaction behaviors may shift with differences in loading magnitudes and cementation levels. In this study, direct simple shear tests were performed to examine the undrained shearing behaviors of biocemented loose Ottawa F-65 sand prepared to varying cementation levels corresponding to Vs increases up to 523 m/s. Significant increases in liquefaction triggering resistances were observed with added cementation across a broad range of loading magnitudes (CSR = 0.1–1.75) and exceeded improvements obtainable through densification alone. Following triggering, modest improvements in post-triggering strain accumulation and reconsolidation behaviors were observed that could be primarily attributed to the densification of specimens from added mineral solids at low cementation levels (Δ Vs < 150 m/s). At higher cementation magnitudes, however, post-triggering behavioral enhancements exceeded those that would be expected from densification alone. Outcomes from this study improve our understanding of the liquefaction behaviors of biocemented soils, the metrics by which these behaviors can be effectively characterized, and the mechanisms responsible for behavioral enhancements, ultimately furthering our understanding of how the technology may be employed for liquefaction mitigation.
Agata characterisation and pulse shape analysis
Authors: Boston A. J. , Crespi F. C. L. , Duchêne G. , Désesquelles P. , Gerl J. , Holloway F. , Judson D. S. , Korichi A. , Harkness-Brennan L. , Ljungvall J. , Quintana-Arnés B. , Reiter P. , Stezowski O. 
Published: September 2023

AbstractThe AGATA and GRETA spectrometers are large arrays of highly segmented HPGe detectors that use the technique of gamma ray tracking to reconstruct the scattering path of gamma rays interacting within the active material. A basic requirement is a precise reconstruction of the individual interaction locations within the detectors. This is possible through the use of pulse shape analysis which has to be conducted in real time due to the high data rates generated by the spectrometer. The methodologies that have been evaluated to perform this for AGATA are discussed along with the approaches used to calculate the pulse shape databases required by these algorithms. Finally, the performance and limitations of the existing approaches are reviewed.
Hp(3) vs TLD-100 for eye lens dosimetry in interventional radiology procedures: a preliminary study
Authors: Manna Francesco , De Nardellis Gianleonardo , Carmosino Patrizio Antonio , Ambrosino Fabrizio , Caruso Umberto , Correra Marco , Fiore Francesco , La Verde Giuseppe , Tarotto Luca , Pugliese Mariagabriella 
Published: September 2023

AbstractFollowing the 2013/59/EURATOM Directive, the Italian 101/2020 Decree Law lowered the annual limit on the equivalent dose to eye lens from 150 to 20 mSv for exposed workers, in order to limit the risk of radiation-induced cataract. Such a drastic reduction makes it very important to perform accurate dose monitoring for medical staff that works with ionizing radiation as interventional radiologists and cardiologists. The standard for occupational eye lens dosimetry consists into Hp(3) calibrated dosimeters placed on physicians glasses, next to the eyes. However, this dosimetry system suffers calibration issues, and therefore, the dose is usually extrapolated from extremity or whole body measurements, leading to low accuracy. Chips of thermoluminescent dosimeters TLD-100 and dedicated Hp(3) calibrated dosimeters were placed over a plexiglas (PMMA) phantom to measure the Entrance Surface Air Kerma (Ke) and the eye lens equivalent dose (H) to physician, respectively, during simulated interventional radiology procedures. Values were all below the regulatory limit. Our results show that TLD-100’s response seems to be correlated with Hp(3) according to the relationship Ke = F × H, with an average factor F = 3.9 mGy/mSv, opening the possibility of using both dosimeters for accurate radiation protection of exposed workers.
DPP9 Stabilizes NRF2 to Suppress Ferroptosis and Induce Sorafenib Resistance in Clear Cell Renal Cell Carcinoma
Authors: Chang Kun , Chen Yingji , Zhang Xuanzhi , Zhang Wei , Xu Ning , Zeng Bohan , Wang Yue , Feng Tao , Dai Bo , Xu Fujiang , Ye Dingwei , Wang Chenji 
Published: September 2023

Abstract

The KEAP1-NRF2 axis is the principal regulator of cellular responses to oxidative and electrophilic stressors. NRF2 hyperactivation is frequently observed in many types of cancer and promotes cancer initiation, progression, metastasis, and resistance to various therapies. Here, we determined that dipeptidyl peptidase 9 (DPP9) is a regulator of the KEAP1-NRF2 pathway in clear cell renal cell carcinoma (ccRCC). DPP9 was markedly overexpressed at the mRNA and protein levels in ccRCC, and high DPP9 expression levels correlated with advanced tumor stage and poor prognosis in patients with ccRCC. Protein affinity purification to identify functional partners of DPP9 revealed that it bound to KEAP1 via a conserved ESGE motif. DPP9 disrupted KEAP1-NRF2 binding by competing with NRF2 for binding to KEAP1 in an enzyme-independent manner. Upregulation of DPP9 led to stabilization of NRF2, driving NRF2-dependent transcription and thereby decreasing cellular reactive oxygen species levels. Moreover, DPP9 overexpression suppressed ferroptosis and induced resistance to sorafenib in ccRCC cells, which was largely dependent on the NRF2 transcriptional target SLC7A11. Collectively, these findings indicate that the accumulation of DPP9 results in hyperactivation of the NRF2 pathway to promote tumorigenesis and intrinsic drug resistance in ccRCC.

Significance:
DPP9 overcomes oxidative stress and suppresses ferroptosis in ccRCC by binding to KEAP1 and promoting NRF2 stability, which drives tumor development and sorafenib resistance.
Intratumoral Bacteria as Mediators of Cancer Immunotherapy Response
Authors: Sfanos Karen S. 
Published: September 2023

AbstractMultiple lines of evidence spanning from animal models to human clinical trials indicate that the microbiome influences cancer immunotherapy response. Whereas initial studies focused exclusively on the gastrointestinal (gut) microbiota–tumor axis, more recent studies have examined the possibility that bacteria located within tumor cells or within the tumor microenvironment mediate cancer treatment response. Strikingly, this phenomenon has been demonstrated in cancers that arise in anatomic locations that are traditionally thought to be devoid of resident microbiota. In this issue of Cancer Research, Wu and colleagues examine the effects of intratumoral bacterial signatures on treatment response in the setting of neoadjuvant chemotherapy combined with immunotherapy (NACI) in the treatment of esophageal squamous cell carcinoma (ESCC). The study reports that intratumoral Streptococcus, presumably due to bacterial translocation from the gut, predicts the treatment efficacy of NACI in murine models as well as individuals with ESCC. These new findings further highlight the possibility that the presence of intratumoral microbes as well as their associated metabolites influence both the tumor immune microenvironment and immunotherapy efficacy. These findings also raise the intriguing possibility of cross-reactivity between tumor and bacterial antigens. Given that the gut microbiome is potentially a modifiable factor via diet, prebiotics/probiotics, and fecal microbiota transplantation, among other strategies, further exploration into the mechanisms by which gut and/or intratumoral bacteria influence antitumor immunity is certainly warranted.See related article by Wu et al., p. 3131
BACH1 Loss Exerts Antitumor Effects on Mantle Cell Lymphoma Cells via Inducing a Tumor-Intrinsic Innate Immune Response and Cell-Cycle Arrest
Authors: Li Guilan , Feng Min , Zhang Ziting , Liu Jiangyuan , Zhang Han 
Published: September 2023

Abstract

BTB and CNC homology 1 (BACH1) is a transcription repressor that regulates multiple physiological processes, including intracellular heme homeostasis and immune responses. Increasing lines of evidence indicate that BACH1 reshapes metastasis and metabolism of human solid tumors. However, its potential roles in mantle cell lymphoma (MCL) remain largely unknown. Here, we found that silencing BACH1 in MCL cells induced markedly cell-cycle arrest and cell apoptosis, whereas overexpression of BACH1 exhibited the opposite patterns. Increased BACH1 levels not only promoted tumor growth and dispersal in xenografts, but also conferred a long-term poor prognosis in patients with MCL. Interestingly, RNA sequencing analysis revealed noncanonical function of BACH1 in regulation of type I interferon (IFNI) response, DNA replication and repair, and cell cycle. Mechanistically, zinc finger and BTB domain containing 20 (ZBTB20) and HMG-box transcription factor 1 (HBP1) were for the first time identified as two novel downstream targets repressed by BACH1 in MCL cells. Further double-knockdown functional assays confirmed that loss of BACH1 induced ZBTB20-mediated IFNα production and HBP1-mediated cell-cycle arrest, indicating that BACH1-centered regulatory network may be a novel targetable vulnerability in MCL cells.

Implications:
BACH1 serves as a pleotropic regulator of tumor-intrinsic innate immune response and cell-cycle progression, disruption of which may offer a promising therapeutic strategy for MCL treatment.
Abstract IA12: Fluorescence guided surgery: Rapidly evolving applications
Authors: Rosenthal Eben L. , Hom Marisa L. , Lu Goulan 
Published: September 2023

Abstract
Despite advances in operative technology, intraoperative methods have not improved cancer detection during surgery in the past 30 years. We propose to test the combination of high-resolution/depth-limited imaging properties of optical imaging agents with the low-resolution/tissue penetrating properties of nuclear agents for detection of primary tumors and regional lymph nodes. We propose that combined optical and nuclear imaging can detect tumor fragments less than 1 mm3 in vivo during removal of head and neck cancers. In fact, nuclear PET imaging alone may be highly successful - The current standard of care for evaluation and surveillance of regional and metastatic disease in head and neck squamous cell carcinoma (HNSCC) is FDG-PET/CT scan, which is highly sensitive but not specific. To address this, we show that a head and neck cancer, tumor-specific PET radiopharmaceutical can improve diagnostic specificity in this patient population.
Citation Format: Eben L. Rosenthal, Marisa L. Hom, Goulan Lu. Fluorescence guided surgery: Rapidly evolving applications [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr IA12.