bluuebunny/crossref_metadata_2025_split huggingface dataset:
A retrospective study of postoperative targeted therapy in ALK-positive lung cancer
Authors: Wang Bin , Song Yang , Chen Zhuo , Su Xiaona , Yang Xin , Wei Zhi , Chen Junxia , Chen Chuan , Li Mengxia 
Published: May 2023

AbstractIn this study, we aim to investigate the therapeutic effect and safety of ALK inhibitor in ALK-positive lung cancer patients. 59 patients with ALK-positive lung cancer from August 2013 to August 2022 were retrospectively recruited. The basic information, pathological type, clinical stage and treatment strategy were collected. These patients were divided into two groups, including 29 patients of conventional adjuvant chemotherapy, and 30 cases of targeted therapy. The patients in the targeted therapy group underwent adjuvant targeted therapy with crizotinib for 2 years. The observation indicators include curative effects and adverse events. The disease-free survival (DFS) and overall survival (OS) were also analyzed. We analyzed the pathological stages after adjuvant chemotherapy and targeted therapy in lung cancer, no significant difference in the p stage N and T was found between the two therapeutic groups. However, the DFS events, DFS median time and OS median time showed significant improvement in the targeted therapy group when compared with adjuvant chemotherapy (all P < 0.05). Besides, the patients under both therapeutic regimens presented some adverse events, among them elevated aspartate transaminase/alanine aminotransferase was the most common adverse event in all the patients, followed by nausea and vomiting. Our study identified that crizotinib-based postoperative targeted therapy helps improve the prognosis of patients with ALK-positive lung cancer, confirming that postoperative targeted therapy can be considered an effective and feasible therapeutic alternative.
Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation
Authors: Sharon Itai , Schmeing T. Martin 
Published: May 2023

AbstractCyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.
A quadratic time-dependent quantum harmonic oscillator
Authors: Onah F. E. , García Herrera E. , Ruelas-Galván J. A. , Juárez Rangel G. , Real Norzagaray E. , Rodríguez-Lara B. M. 
Published: May 2023

AbstractWe present a Lie algebraic approach to a Hamiltonian class covering driven, parametric quantum harmonic oscillators where the parameter set—mass, frequency, driving strength, and parametric pumping—is time-dependent. Our unitary-transformation-based approach provides a solution to our general quadratic time-dependent quantum harmonic model. As an example, we show an analytic solution to the periodically driven quantum harmonic oscillator without the rotating wave approximation; it works for any given detuning and coupling strength regime. For the sake of validation, we provide an analytic solution to the historical Caldirola–Kanai quantum harmonic oscillator and show that there exists a unitary transformation within our framework that takes a generalized version of it onto the Paul trap Hamiltonian. In addition, we show how our approach provides the dynamics of generalized models whose Schrödinger equation becomes numerically unstable in the laboratory frame.
Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma
Authors: Megremis Spyridon , Constantinides Bede , Xepapadaki Paraskevi , Yap Chuan Fu , Sotiropoulos Alexandros G. , Bachert Claus , Finotto Susetta , Jartti Tuomas , Tapinos Avraam , Vuorinen Tytti , Andreakos Evangelos , Robertson David L. , Papadopoulos Nikolaos G. 
Published: May 2023

AbstractAsthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome “dysbiosis” appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.
Sexual dimorphisms in serum calcium and phosphate concentrations in the Rotterdam Study
Authors: Bosman Ariadne , Koek W. Nadia H. , Campos-Obando Natalia , van der Eerden Bram C. J. , Ikram M. A. , Uitterlinden André G. , van Leeuwen Johannes P. T. M. , Zillikens M. C. 
Published: May 2023

AbstractSex differences in serum phosphate and calcium have been reported but the exact nature and underlying regulatory mechanisms remain unclear. We aimed to compare calcium and phosphate concentrations between sexes, and explore potential covariates to elucidate underlying mechanisms of sex differences in a prospective, population-based cohort study. Pooled data of subjects > 45 years from three independent cohorts of the Rotterdam Study (RS) were used: RS-I-3 (n = 3623), RS-II-1 (n = 2394), RS-III-1 (n = 3241), with separate analyses from an additional time point of the first cohort RS-I-1 (n = 2688). Compared to men, women had significantly higher total serum calcium and phosphate concentrations which was not explained by BMI, kidney function nor smoking. Adjustment for serum estradiol diminished sex differences in serum calcium while adjustment for serum testosterone diminished sex differences in serum phosphate. Adjustment for vitamin D and alkaline phosphatase did not change the association between sex and calcium or phosphate in RS-I-1. In the sex-combined group, both serum calcium and phosphate decreased with age with a significant interaction for sex differences for serum calcium but not phosphate. In sex-stratified analyses, serum estradiol but not testosterone was inversely associated with serum calcium in both sexes. Serum estradiol was inversely associated with serum phosphate in both sexes to a similar degree, while serum testosterone was inversely associated with serum phosphate in both sexes with an apparent stronger effect in men than in women. Premenopausal women had lower serum phosphate compared to postmenopausal women. Serum testosterone was inversely associated with serum phosphate in postmenopausal women only. In conclusion, women > 45 years have higher serum calcium and phosphate concentrations compared to men of similar age, not explained by vitamin D or alkaline phosphatase concentrations. Serum estradiol but not testosterone was inversely associated with serum calcium while serum testosterone was inversely associated with serum phosphate in both sexes. Serum testosterone may in part explain sex differences in serum phosphate while estradiol could partly explain sex differences in serum calcium.
The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage
Authors: Paukszto Łukasz , Górski Piotr , Krawczyk Katarzyna , Maździarz Mateusz , Szczecińska Monika , Ślipiko Monika , Sawicki Jakub 
Published: May 2023

AbstractOrganellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts—109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.
An enhanced view on the Mediterranean Sea crust from potential fields data
Authors: Sampietro Daniele , Capponi Martina , Thébault Erwan , Gailler Lydie 
Published: May 2023

AbstractThe Earth’s crust is exceptionally important to understand the geological evolution of our planet and to access natural resources as minerals, critical raw materials, geothermal energy, water, hydrocarbons, etc.. However, in many regions of the world it is still poorly modelled and understood. Here we present the latest advance on three-dimensional modelling of the Mediterranean Sea crust based on freely available global gravity and magnetic field models. The proposed model, based on the inversion of gravity and magnetic field anomalies constrained by available a-priori information (such as interpreted seismic profiles, previous studies, etc.), provides, with an unprecedented spatial resolution of 15 km, the depths of the main modelled geological horizons (Plio-Quaternary, Messinian and Pre-Messinian sediments, crystalline crust and upper mantle), coherent with the known available constraints, together with the three-dimensional distribution of density and magnetic susceptibility. The inversion is carried out by means of a Bayesian algorithm, which allows to modify at the same time the geometries and the three dimensional distributions of density and magnetic susceptibility, always respecting the constraints introduced by the initial information. In addition to unveil the structure of the crust beneath the Mediterranean Sea, the present study also shows the informative content of freely available global gravity and magnetic models, thus putting the base for the development of future high resolution models of the Earth crust at global level.
AZD5438 a GSK-3a/b and CDK inhibitor is antiapoptotic modulates mitochondrial activity and protects human neurons from mitochondrial toxins
Authors: Shi Gongyu , Scott Helen , Azhar Nur Izzah Farhana Mohamad , Gialeli Andriana , Clennell Benjamin , Lee Keng Siang , Hurcombe Jenny , Whitcomb Daniel , Coward Richard , Wong Liang-Fong , Cordero-Llana Oscar , Uney James B. 
Published: May 2023

AbstractWe previously reported that kenpaullone, which inhibits GSK-3a/b and CDKs inhibited CCCP mediated mitochondrial depolarisation and augments the mitochondrial network. To investigate the actions of this class of drug further, we compared the ability of kenpaullone, alsterpaullone, 1-azakenapaullone, AZD5438, AT7519 (CDK and GSK-3a/b inhibitors) and dexpramipexole and olesoxime (mitochondrial permeability transition pore inhibitors) to prevent CCCP mediated mitochondrial depolarisation and found that AZD5438 and AT7519, were the most effective. Furthermore, treatment with AZD5438 alone increased the complexity of the mitochondrial network. We also found that AZD5438 prevented the rotenone induced decrease in PGC-1alpha and TOM20 levels and that it mediated powerful anti-apoptotic effects and promoted glycolytic respiration. Importantly, experiments in human iPSC derived cortical and midbrain neurons showed AZD5438 mediated significant protective effects, preventing the neuronal cell death, and collapse in the neurite and mitochondrial network associated with rotenone treatment. These results suggest drugs that target GSK-3a/b and CDKs should be developed and assessed further as they may have significant therapeutic potential.
Eight-year tillage in black soil, effects on soil aggregates, and carbon and nitrogen stock
Authors: Wang Ling , Qi Shengjie , Gao Wenfang , Luo Yang , Hou Yunpeng , Liang Yao , Zheng Hongbing , Zhang Shuimei , Li Ruiping , Wang Meng , Zheng Jinyu , Gao Zhiwei 
Published: May 2023

AbstractThe effects of different tillage management practices on the soil aggregates, soil carbon stock (STCS), and soil nitrogen stock (STNS) are key issues in agricultural research. We conducted an 8-year field experiment to evaluate the effects of different tillage methods: stubble cleaning and ridging (CK), no-tillage with stubble retention (NT), plow tillage (PT), and width lines (WL) on soil aggregates, STCS, and STNS in the black soil corn continuous cropping area of Northeast China. Different tillage methods predominantly affected the soil aggregates in the 2–0.25 mm and 0.25–0.053 mm size classes. The PT methods increased the proportion of macroaggregates and improved the quality of the soil aggregates. PT methods significantly increased the soil organic carbon content at the 0–30 cm layer by changing the number of soil macroaggregates. The PT practices are better strategies for enhancing soil carbon sinks, and the WL method increased the total amount of N in the soil pool. Our results suggest that the PT and WL methods are the best strategies for improving the quality of soil aggregates and preventing/reducing depletion of soil C and N in a black soil area of Northeast China.
Mechanism modeling and application of Salvia miltiorrhiza percolation process
Authors: Wang Wanying , Ding Feng , Qu Haibin , Gong Xingchu 
Published: May 2023

AbstractPercolation is a common extraction method of food processing industry. In this work, taking the percolation extraction of salvianolic acid B from Salvia miltiorrhiza (Salviae Miltiorrhizae Radix et Rhizoma) as an example, the percolation mechanism model was derived. The volume partition coefficient was calculated according to the impregnation. experiment. The bed layer voidage was measured by single-factor percolation experiment and the internal mass transfer coefficient was calculated by the parameters obtained by fitting the impregnation kinetic model. After screening, the Wilson and Geankoplis, and Koch and Brady formulas were used to calculate the external mass transfer coefficient and the axial diffusion coefficient, respectively. After substituting each parameter into the model, the process of percolation of Salvia miltiorrhiza was predicted, and the coefficient of determination R2 was all greater than 0.94. Sensitivity analysis was used to show that all the parameters studied had a significant impact on the prediction effect. Based on the model, the design space including the range of raw material properties and process parameters was established and successfully verified. At the same time, the model was applied to the quantitative extraction and endpoint prediction of the percolation process.
Complex implementation factors demonstrated when evaluating cost-effectiveness and monitoring racial disparities associated with [18F]DCFPyL PET/CT in prostate cancer men
Authors: Subramanian Kritika , Martinez Juana , Huicochea Castellanos Sandra , Ivanidze Jana , Nagar Himanshu , Nicholson Sean , Youn Trisha , Nauseef Jones T. , Tagawa Scott , Osborne Joseph R. 
Published: May 2023

AbstractProstate cancer (PC) staging with conventional imaging often includes multiparametric magnetic resonance (MR) of the prostate, computed tomography (CT) of the chest, abdomen, and pelvis, and whole-body bone scintigraphy. The recent development of highly sensitive and specific prostate specific membrane antigen (PSMA) positron emission tomography (PET) has suggested that prior imaging techniques may be insufficiently sensitive or specific, particularly when evaluating small pathologic lesions. As PSMA PET/CT is considered to be superior for multiple clinical indications, it is being deployed as the new multidisciplinary standard-of-care. Given this, we performed a cost-effectiveness analysis of [18F]DCFPyL PSMA PET/CT imaging in the evaluation of PC relative to conventional imaging and anti-3-[18F]FACBC (18F-Fluciclovine) PET/CT. We also conducted a single institution review of PSMA PET/CT scans performed primarily for research indications from January 2018 to October 2021. Our snapshot of this period of time in our catchment demonstrated that PSMA PET/CT imaging was disproportionately accessed by men of European ancestry (EA) and those residing in zip codes associated with a higher median household income. The cost-effectiveness analysis demonstrated that [18F]DCFPyL PET/CT should be considered as an alternative to anti-3-[18F]FACBC PET/CT and standard of care imaging for prostate cancer staging. [18F]DCFPyL PET/CT is a new imaging modality to evaluate PC patients with higher sensitivity and specificity in detecting disease than other prostate specific imaging studies. Despite this, access may be inequitable. This discrepancy will need to be addressed proactively as the distribution network of the radiotracer includes both academic and non-academic sites nationwide.
In-silico investigations of haemodynamic parameters for a blunt thoracic aortic injury case
Authors: Dadras Rezvan , Jabbari Alireza , Asl Narges Kamaei , Soltani Madjid , Rafiee Farnaz , Parsaee Mozhgan , Golchin Shadi , Pouraliakbar Hamidreza , Sadeghipour Parham , Alimohammadi Mona 
Published: May 2023

AbstractAccounting for 1.5% of thoracic trauma, blunt thoracic aortic injury (BTAI) is a rare disease with a high mortality rate that nowadays is treated mostly via thoracic endovascular aortic repair (TEVAR). Personalised computational models based on fluid–solid interaction (FSI) principals not only support clinical researchers in studying virtual therapy response, but also are capable of predicting eventual outcomes. The present work studies the variation of key haemodynamic parameters in a clinical case of BTAI after successful TEVAR, using a two-way FSI model. The three-dimensional (3D) patient-specific geometries of the patient were coupled with three-element Windkessel model for both prior and post intervention cases, forcing a correct prediction of blood flow over each section. Results showed significant improvement in velocity and pressure distribution after stenting. High oscillatory, low magnitude shear (HOLMES) regions require careful examination in future follow-ups, since thrombus formation was confirmed in some previously clinically reported cases of BTAI treated with TEVAR. The strength of swirling flows along aorta was also damped after stent deployment. Highlighting the importance of haemodynamic parameters in case-specific therapies. In future studies, compromising motion of aortic wall due to excessive cost of FSI simulations can be considered and should be based on the objectives of studies to achieve a more clinical-friendly patient-specific CFD model
Long-term risk of major adverse cardiovascular events following ischemic stroke or TIA
Authors: Carlsson Andreas , Irewall Anna-Lotta , Graipe Anna , Ulvenstam Anders , Mooe Thomas , Ögren Joachim 
Published: May 2023

AbstractData are scarce on long-term outcomes after ischemic stroke (IS) or transient ischemic attack (TIA). In this prospective cohort study, we examined the cumulative incidence of major adverse cardiovascular events (MACE) after IS and TIA using a competing risk model and factors associated with new events using a Cox-proportional hazard regression model. All patients discharged alive from Östersund Hospital with IS or TIA between 2010 and 2013 (n = 1535) were followed until 31 December 2017. The primary endpoint was a composite of IS, type 1 acute myocardial infarction (AMI), and cardiovascular (CV) death. Secondary endpoints were the individual components of the primary endpoint, in all patients and separated in IS and TIA subgroups. The cumulative incidence of MACE (median follow-up: 4.4 years) was 12.8% (95% CI: 11.2–14.6) within 1 year after discharge and 35.6% (95% CI: 31.8–39.4) by the end of follow-up. The risk of MACE and CV death was significantly increased in IS compared to TIA (p-values < 0.05), but not the risk of IS or type 1 AMI. Age, kidney failure, prior IS, prior AMI, congestive heart failure, atrial fibrillation, and impaired functional status, were associated with an increased risk of MACE. The risk of recurring events after IS and TIA is high. IS patients have a higher risk of MACE and CV death than TIA patients.