bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the genetics of transformed splenic marginal zone lymphoma
Authors: Grau Marta , López Cristina , Navarro Alba , Frigola Gerard , Nadeu Ferran , Clot Guillem , Bastidas-Mora Gabriela , Alcoceba Miguel , Baptista Maria Joao , Blanes Margarita , Colomer Dolors , Costa Dolors , Domingo-Domènech Eva , Enjuanes Anna , Escoda Lourdes , Forcada Pilar , Giné Eva , Lopez-Guerra Mónica , Ramón Olga , Rivas-Delgado Alfredo , Vicente Folch Laura , Wotherspoon Andrew , Climent Fina , Campo Elias , López-Guillermo Armando , Matutes Estella , Beà Sílvia 
Published: March 2023

Abstract
The genetic mechanisms associated with splenic marginal zone lymphoma (SMZL) transformation are not well defined. We studied 41 patients with SMZL that eventually underwent large B-cell lymphoma transformation. Tumor material was obtained either only at diagnosis (9 patients), at diagnosis and transformation (18 patients), and only at transformation (14 patients). Samples were categorized in 2 groups: (1) at diagnosis (SMZL, n = 27 samples), and (2) at transformation (SMZL-T, n = 32 samples). Using copy number arrays and a next-generation sequencing custom panel, we identified that the main genomic alterations in SMZL-T involved TNFAIP3, KMT2D, TP53, ARID1A, KLF2, 1q gains, and losses of 9p21.3 (CDKN2A/B) and 7q31-q32. Compared with SMZL, SMZL-T had higher genomic complexity, and higher incidence of TNFAIP3 and TP53 alterations, 9p21.3 (CDKN2A/B) losses, and 6p gains. SMZL and SMZL-T clones arose by divergent evolution from a common altered precursor cell that acquired different genetic alterations in virtually all evaluable cases (92%, 12 of 13 cases). Using whole-genome sequencing of diagnostic and transformation samples in 1 patient, we observed that the SMZL-T sample carried more genomic aberrations than the diagnostic sample, identified a translocation t(14;19)(q32;q13) present in both samples, and detected a focal B2M deletion due to chromothripsis acquired at transformation. Survival analysis showed that KLF2 mutations, complex karyotype, and International Prognostic Index score at transformation were predictive of a shorter survival from transformation (P = .001; P = .042; and P = .007; respectively). In summary, SMZL-T are characterized by higher genomic complexity than SMZL, and characteristic genomic alterations that could represent key players in the transformation event.
Risk factors and interventions for developing recurrent pneumonia in older adults
Authors: Takada Kazufumi , Ogawa Kazumasa , Miyamoto Atsushi , Nakahama Hiroshi , Moriguchi Shuhei , Murase Kyoko , Hanada Shigeo , Takaya Hisashi , Tamaoka Meiyo , Takai Daiya 
Published: March 2023

BackgroundPneumonia is common among older adults and often recurrent. Several studies have been conducted on the risk factors for pneumonia; however, little is known about the risk factors for recurrent pneumonia. This study aimed to identify the risk factors for developing recurrent pneumonia among older adults and to investigate methods of prevention.MethodsWe analysed the data of 256 patients aged 75 years or older who were admitted for pneumonia between June 2014 and May 2017. Moreover, we reviewed the medical records for the subsequent 3 years and defined the readmission caused by pneumonia as recurrent pneumonia. Risk factors for recurrent pneumonia were analysed using multivariable logistic regression analysis. Differences in the recurrence rate based on the types and use of hypnotics were also evaluated.ResultsOf the 256 patients, 90 (35.2%) experienced recurrent pneumonia. A low body mass index (OR: 0.91; 95% CI: 0.83‒0.99), history of pneumonia (OR: 2.71; 95% CI: 1.23‒6.13), lung disease as a comorbidity (OR: 4.73; 95% CI: 2.13‒11.60), taking hypnotics (OR: 2.16; 95% CI: 1.18‒4.01) and taking histamine-1 receptor antagonist (H1RA) (OR: 2.38; 95% CI: 1.07‒5.39) were risk factors. Patients taking benzodiazepine as hypnotics were more likely to experience recurrent pneumonia than patients not taking hypnotics (OR: 2.29; 95% CI: 1.25–4.18).ConclusionWe identified several risk factors for recurrent pneumonia. Among them, restricting the use of H1RA and hypnotics, in particular benzodiazepines, may be useful in preventing the recurrence of pneumonia in adults aged 75 years or older.
Occupational exposures and small airway obstruction in the UK Biobank Cohort
Authors: Feary Johanna , Quintero-Santofimio Valentina , Potts James , Vermeulen Roel , Kromhout Hans , Knox-Brown Ben , Amaral Andre F.S. 
Published: March 2023

BackgroundSmall airways obstruction (SAO) is a key feature of both COPD and asthma, which have been associated with workplace exposures. Whether SAO, which may occur early in the development of obstructive lung disease and without symptoms, also associates with occupational exposures is unknown.MethodsUsing UK Biobank data, we derived measurements of SAO from the 65 145 participants with high-quality spirometry and lifetime occupational histories. The ALOHA+ Job Exposure Matrix was used to assign lifetime occupational exposures to each participant. The association between SAO and lifetime occupational exposures was evaluated using a logistic regression model adjusted for potential confounders. A second logistic regression model was also run to account for potential co-exposures.ResultsSAO was present in varying proportions of the population depending on definition used: 5.6% (forced expiratory flow between 25 and 75% of the forced vital capacity (FEF25–75) < lower limit of normal (LLN)) and 21.4% (forced expiratory volume in 3 s (FEV3)/forced expiratory volume in 6 s (FEV6) <LLN). After adjustment for confounders and co-exposures, people in the highest category of exposure to pesticides were significantly more likely to have SAO (FEV3/FEV6<LLN: OR 1.24, 95% CI 1.06–1.44). The association between pesticides and SAO showed an exposure-response pattern. SAO was also less likely among people in the highest exposure categories of aromatic solvents (FEV3/FEV6<LLN: OR 0.85, 95% CI 0.73–0.99) and metals (FEV3/FEV6<LLN: OR 0.77, 95% CI 0.62–0.94).ConclusionOur findings suggest that occupational exposure to pesticides play a role in the SAO. However, further work is needed to determine causality, and identify the specific component(s) responsible and the underlying mechanisms involved.
Lung microhaemorrhage drives oxidative/inflammatory damage in α1-antitrypsin deficiency
Authors: Saltini Cesare , Mohammad Naweed , Xin Yan , Alvarado Rodolfo , Ghio Andrew J. , Moneypenny Craig G. , Riva Alberto , Fu Dongtao , Flagg Tammy , Saltini Giovanni F.A. , Arisi Ivan , Fredenburg Kristianna M. , Zhang Yang , Lascano Jorge E. , Brantly Mark 
Published: March 2023

BackgroundAnimal models using intratracheal instillation show that elastase, unopposed by α1-antitrypsin (AAT), causes alveolar damage and haemorrhage associated with emphysematous changes. The aim of the present study was to characterise any relationship between alveolar haemorrhage and human AAT deficiency (AATD) using bronchoalveolar lavage (BAL) and lung explant samples from AATD subjects.MethodsBAL samples (17 patients, 15 controls) were evaluated for free haem (iron protoporphyrin IX) and total iron concentrations. Alveolar macrophage activation patterns were assessed using RNA sequencing and validatedin vitrousing haem-stimulated, monocyte-derived macrophages. Lung explants (seven patients, four controls) were assessed for iron sequestration protein expression patterns using Prussian blue stain and ferritin immunohistochemistry, as well as ferritin iron imaging and elemental analysis by transmission electron microscopy. Tissue oxidative damage was assessed using 8-hydroxy-2′-deoxyguanosine immunohistochemistry.ResultsBAL collected from AATD patients showed significantly elevated free haem and total iron concentrations. Alveolar and interstitial macrophages in AATD explants showed elevated iron and ferritin accumulation in large lysosomes packed by iron oxide cores with degraded ferritin protein cages. BAL macrophage RNA sequencing showed innate pro-inflammatory activation, replicatedin vitroby haemin exposure, which also triggered reactive oxygen species generation. AATD explants showed massive oxidative DNA damage in both lung epithelial cells and macrophages.ConclusionsBAL and tissue markers of alveolar haemorrhage, together with molecular and cellular evidence of macrophage innate pro-inflammatory activation and oxidative damage, are consistent with free haem stimulation. Overall, this initial study provides evidence for a pathogenetic role of elastase-induced alveolar haemorrhage in AATD emphysema.
Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis
Authors: Gijs Pieter-Jan , Daccord Cécile , Bernasconi Eric , Brutsche Martin , Clarenbach Christian F. , Hostettler Katrin , Guler Sabina A. , Mercier Louis , Ubags Niki , Funke-Chambour Manuela , von Garnier Christophe 
Published: March 2023

BackgroundHigh bacterial burden in the lung microbiota predicts progression of idiopathic pulmonary fibrosis (IPF). Azithromycin (AZT) is a macrolide antibiotic known to alter the lung microbiota in several chronic pulmonary diseases, and observational studies have shown a positive effect of AZT on mortality and hospitalisation rate in IPF. However, the effect of AZT on the lung microbiota in IPF remains unknown.MethodsWe sought to determine the impact of a 3-month course of AZT on the lung microbiota in IPF. We assessed sputum and oropharyngeal swab specimens from 24 adults with IPF included in a randomised controlled crossover trial of oral AZT 500 mg 3 times per week. 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) were performed to assess bacterial communities. Antibiotic resistance genes (ARGs) were assessed using real-time qPCR.ResultsAZT significantly decreased community diversity with a stronger and more persistent effect in the lower airways (sputum). AZT treatment altered the temporal kinetics of the upper (oropharyngeal swab) and lower airway microbiota, increasing community similarity between the two sites for 1 month after macrolide cessation. Patients with an increase in ARG carriage had lower bacterial density and enrichment of the genusStreptococcus. In contrast, patients with more stable ARG carriage had higher bacterial density and enrichment inPrevotella.ConclusionsAZT caused sustained changes in the diversity and composition of the upper and lower airway microbiota in IPF, with effects on the temporal and spatial dynamics between the two sites.
Global survey of physician testing practices for nontuberculous mycobacteria
Authors: Loebinger Michael R. , van der Laan Roald , Obradovic Marko , van Ingen Jakko 
Published: March 2023

BackgroundCertain patients are at greater risk of developing nontuberculous mycobacterial pulmonary disease (NTM-PD), including those with lung conditions such as bronchiectasis. Testing for nontuberculous mycobacteria (NTM) in patients at risk is necessary to identify NTM-PD and start appropriate management. The aim of this survey was to evaluate current testing practices for NTM and identify testing triggers.MethodsPhysicians (n=455) who see at least one patient with NTM-PD in a typical 12-month period and test for NTM as part of practice from Europe, USA, Canada, Australia, New Zealand and Japan participated in a 10-min anonymised survey on NTM testing practices.ResultsBronchiectasis, COPD and use of immunosuppressants were the factors most likely to prompt testing among physicians in this survey (90%, 64% and 64%, respectively), with radiological findings the most common reason leading to considering NTM testing in patients with bronchiectasis and COPD (62% and 74%, respectively). Macrolide monotherapy in patients with bronchiectasis and inhaled corticosteroid use in patients with COPD were not important triggers for testing (15% and 9% of physicians, respectively). Persistent cough and weight loss triggered testing in >75% of physicians. Testing triggers were markedly different for physicians in Japan, with cystic fibrosis prompting testing in fewer physicians compared with other regions.ConclusionsTesting for NTM is influenced by underlying disease, clinical symptoms or radiological changes, but clinical practice varies considerably. Adherence to guideline recommendations for NTM testing is limited in certain patient subgroups and varies across regions. Clear recommendations on NTM testing are needed.
Unique characteristics of residual stress distribution of large-diameter keyaki (Zelkova serrata) logs and examination of their measurement method
Authors: Kameyama Naohisa , Matsuo-Ueda Miyuki , Chen Shuoye , Jiang Zhuoting , Ichiyanagi Tatsuya , Yoshida Masato , Yamamoto Hiroyuki 
Published: March 2023

AbstractLarge-diameter keyaki (Zelkova serrata Makino) logs have long been used in Japan as high-quality material especially for traditional construction and furniture. However, unlike other major wood species in Japan, keyaki has been practically considered as a wood species of high difficulty when processing. Keyaki frequently shows processing defects due to sawing, such as warping, cracking, and so forth, which often reduces the production yield of logs. Furthermore, there are drastic differences in those behaviors between individual logs, so causing unexpected processing defects. A scientific approach is required to improve this situation, but data on the material characteristics of keyaki were scarce. This study aimed to characterize the radial pattern of the residual stress as one of the processing-related characteristics. The measurement method was also examined. This study used diametral planks obtained from large-diameter keyaki logs to measure released strain of residual stress from pith to the bark sides. The results showed the distribution of released strain often showed peculiar zig-zag patterns characterized with localized residual stress, unlike the smooth bell curve pattern seen in typical logs of other species. Because of the unique characteristics, some practical points related to the measuring methodology were investigated. The extent of influence of this residual stress in the longitudinal direction was limited to within 30 cm from the site of measurement of the strain. In addition, the length of log necessary to measure the released strain without being affected by crosscutting was more than four times the log diameter—greater than the diameter ratio theorized by previous studies.
Parametric modelling and analysis to optimize adsorption of Atrazine by MgO/Fe3O4-synthesized porous carbons in water environment
Authors: George Lartey-Young , Ma Limin , Zhang Weiwei , Yao Guodong 
Published: March 2023

Abstract
Background
Pesticide contamination to water, continues to raise ecotoxicological and human concerns. Studying the application of green adsorbents for removing pesticides from water can significantly reduce ecotoxicological impacts and sustain reclamation of water bodies.

Results
The current study investigated the adsorption capacity of MgO/Fe3O4 modified coconut shell biochar (MCSB) towards Atrazine removal in water. The prepared adsorbents were structurally constricted and obtained relative amount of mesopore spaces filled by nanoparticles which equally provided active occupancy/binding sites for Atrazine molecule deposition. Equilibrium isotherm studies under temperature regimes of 300 K, 318 K and 328 K were best described by the Freundlich isotherm (R2 = 0.95–0.97) with highest adsorption capacity corresponding to the highest temperature range (328 K) at (KF = 9.60 L mg−1). The kinetics modelling was best fitted to the pseudo second-order kinetic (R2 = 0.90–0.98) reaction pathways revealing that Atrazine uptake and removal occurred majorly over non-homogenous surfaces and high influence of surface functional groups in the process. Atrazine uptake by the adsorbent were mostly efficient within pH ranges of 2–6. Thermodynamics values of free energy ΔG° were negative ranging (ΔG° = − 27.50 to − 29.77 kJ mol−1) across the varying reaction temperature indicating an exothermic reaction, while enthalpy (ΔH°) (34.59 kJ mol) and entropy (ΔS°) (90.88 JK−1/mol) values were positive revealing a degree of spontaneity which facilitated Atrazine uptake. The adsorbents regeneration capacities over five cycles were observed to decrease proportionally with maximum yields up to 50–60%. Optimization of the adsorption condition by response surface modelling (RSM) and Central Composite Design (CCD) could reveal optimum conditions for Atrazine removal through interaction of different variables at pH = 12, adsorbate initial concentration at 12 mg L−1, adsorbate dosage at 0.5 g and reaction temperature at 54 °C. The overall mechanisms of the adsorption could be contributed by availability of surface functional groups on the MCSB surface through increase in hydrophilicity facilitating easy Atrazine molecule attachment via hydrogen bonding and improved surface complexation.

Conclusions
The as-synthesized MCSB adsorbent could uptake and remove Atrazine in water. A high pH, low concentration, low adsorbent dosage and high reaction temperature could be optimized conditions to attain highest Atrazine removal by the synthesized adsorbent.

Graphical Abstract
Association between preoperative anxiety and postoperative delirium in older patients: a systematic review and meta-analysis
Authors: Yang Ke-Lu , Detroyer Elke , Van Grootven Bastiaan , Tuand Krizia , Zhao Dan-Ni , Rex Steffen , Milisen Koen 
Published: March 2023

Abstract
Background
Postoperative delirium (POD) is a common postoperative complication associated with multiple adverse consequences on patient outcomes and higher medical expenses. Preoperative anxiety has been suggested as a possible precipitating factor for the development of POD. As such, we aimed to explore the association between preoperative anxiety and POD in older surgical patients.

Methods
Electronic databases including MEDLINE (via PubMed), EMBASE (via Embase.com), Web of Science Core Collection, Cumulative Index to Nursing and Allied Health Literature (CINAHL Complete; via EBSCOhost) and clinical trial registries were systematically searched to identify prospective studies examining preoperative anxiety as a risk factor for POD in older surgical patients. We used Joanna Briggs Institute Critical Appraisal Checklist for Cohort Studies to assess the quality of included studies. The association between preoperative anxiety and POD was summarized with odds ratios (ORs) and 95% confidence intervals (CIs) using DerSimonian-Laird random-effects meta-analysis.

Results
Eleven studies were included (1691 participants; mean age ranging between 63.1–82.3 years). Five studies used a theoretical definition for preoperative anxiety, with the Anxiety subscale of Hospital Anxiety and Depression Scale (HADS-A) as the instrument being most often used. When using dichotomized measures and within the HADS-A subgroup analysis, preoperative anxiety was significantly associated with POD (OR = 2.17, 95%CI: 1.01–4.68, I2 = 54%, Tau2 = 0.4, n = 5; OR = 3.23, 95%CI: 1.70–6.13, I2 = 0, Tau2 = 0, n = 4; respectively). No association was observed when using continuous measurements (OR = 0.99, 95%CI: 0.93–1.05, I2 = 0, Tau2 = 0, n = 4), nor in the subgroup analysis of STAI-6 (six-item version of state scale of Spielberger State-Trait Anxiety Inventory, OR = 1.07, 95%CI: 0.93–1.24, I2 = 0, Tau2 = 0, n = 2). We found the overall quality of included studies to be moderate to good.

Conclusions
An unclear association between preoperative anxiety and POD in older surgical patients was found in our study. Given the ambiguity in conceptualization and measurement instruments used for preoperative anxiety, more research is warranted in which a greater emphasis should be placed on how preoperative anxiety is operationalized and measured.
Comparison of paraspinal muscle composition measurements using IDEAL fat–water and T2-weighted MR images
Authors: Masi Sara , Rye Meaghan , Roussac Alexa , Naghdi Neda , Rosenstein Brent , Bailey Jeannie F. , Fortin Maryse 
Published: March 2023

Abstract
Purpose
The purpose of this study was to evaluate the agreement between paraspinal muscle composition measurements obtained from fat–water images using % fat-signal fraction (%FSF) in comparison to those obtained from T2-weighted magnetic resonance images (MRI) using a thresholding method.

Methods
A sample of 35 subjects (19 females, 16 males; 40.26 ± 11.3 years old) was selected from a cohort of patients with chronic low back pain (LBP). Axial T2-weighted and IDEAL (Lava-Flex, 2 echo sequence) fat and water MR images were obtained using a 3.0 Tesla GE scanner. Multifidus, erector spinae, and psoas major muscle composition measurements were acquired bilaterally at L4–L5 and L5–S1 using both imaging sequences and related measurement methods. All measurements were obtained by the same rater, with a minimum of 7 days between each method. Intra-class correlation coefficients (ICCs) were calculated to assess intra-rater reliability. Pearson Correlation and Bland–Altman 95% limits of agreement were used to assess the agreement between both measurement methods.

Results
The intra-rater reliability was excellent for all measurements with ICCs varying between 0.851 and 0.997. Strong positive correlations indicating a strong relationship between composition measurements were obtained from fat–water and T2-weighted images for bilateral multifidus and erector spinae muscles at both spinal levels and the right psoas major muscle at L4–L5, with correlation coefficient r ranging between 0.67 and 0.92. Bland–Altman plots for bilateral multifidus and erector spinae muscles at both levels revealed excellent agreement between the two methods, however, systematic differences between both methods were evident for psoas major fat measurements.

Conclusion
Our findings suggest that utilizing fat–water and T2-weighted MR images are comparable for quantifying multifidus and erector spinae muscle composition but not of the psoas major. While this suggests that both methods could be used interchangeably for the multifidus and erector spinae, further evaluation is required to expand and confirm our findings to other spinal levels.
CD248 promotes migration and metastasis of osteosarcoma through ITGB1-mediated FAK-paxillin pathway activation
Authors: Lu Shiqi , Lu Tong , Zhang Jiayu , Gan Lunbiao , Wu Xinjie , Han Donghui , Zhang Keying , Xu Chao , Liu Shaojie , Qin Weijun , Yang Fa , Wen Weihong 
Published: March 2023

Abstract
Background
Osteosarcoma (OS) is the most common malignant bone tumor with a high incidence in children and adolescents. Frequent tumor metastasis and high postoperative recurrence are the most common challenges in OS. However, detailed mechanism is largely unknown.

Methods
We examined the expression of CD248 in OS tissue microarrays by immunohistochemistry (IHC) staining. We studied the biological function of CD248 in cell proliferation, invasion and migration of OS cells by CCK8 assay, transwell and wound healing assay. We also studied its function in the metastasis of OS in vivo. At last, we explored the potential mechanism how CD248 promotes OS metastasis by using RNA-seq, western blot, immunofluorescence staining and co-immunoprecipitation using CD248 knockdown OS cells.

Results
CD248 was highly expressed in OS tissues and its high expression was correlated with pulmonary metastasis of OS. Knockdown of CD248 in OS cells significantly inhibited cell migration, invasion and metastasis, while had no obvious effect on cell proliferation. Lung metastasis in nude mice was significantly inhibited when CD248 was knocked down. Mechanistically, we found that CD248 could promote the interaction between ITGB1 and extracellular matrix (ECM) proteins like CYR61 and FN, which activated the FAK-paxillin pathway to promote the formation of focal adhesion and metastasis of OS.

Conclusion
Our data showed that high CD248 expression is correlated with the metastatic potential of OS. CD248 may promote migration and metastasis through enhancing the interaction between ITGB1 and certain ECM proteins. Therefore, CD248 is a potential marker for diagnosis and effective target for the treatment of metastatic OS.