bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploratory analysis of radiomic as prognostic biomarkers in 18F-FDG PET/CT scan in uterine cervical cancer
Authors: Alencar Nadja Rolim Gonçalves de , Machado Marcos Antônio Dórea , Mourato Felipe Alves , Oliveira Mércia Liane de , Moraes Thauan Fernandes , Mattos Junior Luiz Alberto Reis , Chang Tien-Man Cabral , Azevedo Carla Rameri Alexandre Silva de , Brandão Simone Cristina Soares 
Published: December 2022

ObjectiveTo evaluate the performance of 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET/CT) radiomic features to predict overall survival (OS) in patients with locally advanced uterine cervical carcinoma.MethodsLongitudinal and retrospective study that evaluated 50 patients with cervical epidermoid carcinoma (clinical stage IB2 to IVA according to FIGO). Segmentation of the 18F-FDG PET/CT tumors was performed using the LIFEx software, generating the radiomic features. We used the Mann–Whitney test to select radiomic features associated with the clinical outcome (death), excluding the features highly correlated with each other with Spearman correlation. Subsequently, ROC curves and a Kaplan–Meier analysis were performed. A p-value &lt; 0.05 were considered significant.ResultsThe median follow-up was 23.5 months and longer than 24 months in all surviving patients. Independent predictors for OS were found–SUVpeak with an AUC of 0.74, sensitivity of 77.8%, and specificity of 72.7% (p = 0.006); and the textural feature gray-level run-length matrix GLRLM_LRLGE, with AUC of 0.74, sensitivity of 72.2%, and specificity of 81.8% (p = 0.005). When we used the derived cut-off points from these ROC curves (12.76 for SUVpeak and 0.001 for GLRLM_LRLGE) in a Kaplan–Meier analysis, we can see two different groups (one with an overall survival probability of approximately 90% and the other with 30%). These biomarkers are independent of FIGO staging.ConclusionBy radiomic 18F-FDG PET/CT data analysis, SUVpeak and GLRLM_LRLGE textural feature presented the best performance to predict OS in patients with cervical cancer undergoing chemo-radiotherapy and brachytherapy.
Manual and semi-automated approaches to MIBG myocardial scintigraphy in patients with Parkinson’s disease
Authors: Boccalini Cecilia , Carli Giulia , Vanoli Emilia Giovanna , Cocco Antoniangela , Albanese Alberto , Garibotto Valentina , Perani Daniela 
Published: December 2022

ObjectiveThis study investigates the effects of manual and semi-automatic methods for assessing MIBG semi-quantitative indices in a clinical setting.Materials and methodsWe included 123I-MIBG scans obtained in 35 patients with idiopathic Parkinson’s Disease. Early and late heart-to-mediastinum (H/M) ratios were calculated from 123I-MIBG images using regions of interest (ROIs) placed over the heart and the mediastinum. The ROIs were derived using two approaches: (i) manually drawn and (ii) semi-automatic fixed-size ROIs using anatomical landmarks. Expert, moderate-expert, and not expert raters applied the ROIs procedures and interpreted the 123I-MIBG images. We evaluated the inter and intra-rater agreements in assessing 123I-MIBG H/M ratios.ResultsA moderate agreement in the raters’ classification of pathological and non-pathological scores emerged regarding early and late H/M ratio values (κ = 0.45 and 0.69 respectively), applying the manual method, while the early and late H/M ratios obtained with the semi-automatic method reached a good agreement among observers (κ = 0.78). Cohen-Kappa values revealed that the semi-automatic method improved the agreement between expert and inexpert raters: the agreement improved from a minimum of 0.29 (fair, for early H/M) and 0.69 (substantial, in late H/M) with the manual method, to 0.90 (perfect, in early H/M) and 0.87 (perfect, in late H/M) with the semi-automatic method.ConclusionThe use of the semi-automatic method improves the agreement among raters in classifying’ H/M ratios as pathological or non-pathological, namely for inexpert readers. These results have important implications for semi-quantitative assessment of 123I-MIBG images in clinical routine.
Real-time reverse transcription recombinase polymerase amplification for rapid detection of murine hepatitis virus
Authors: Wang Xiao , Sui Xin , Ma Yueyu , Li Ming , Zhang Xu , Fei Dongliang , Ma Mingxiao 
Published: December 2022

Murine hepatitis virus (MHV) is a highly infectious murine coronavirus that has a high potential for causing harm to host animals. This study aimed to develop a real-time reverse transcription recombinase polymerase amplification (RT-RPA) method for rapid detection of MHV in laboratory mice.MethodsSpecific primers and probes for RT-RPA assay were designed targeting the conserved region in the M gene of the MHV reference strain (accession no. FJ6647223) according to the TwistDx manual instructions. The specificity, sensitivity, and reproducibility of the RT-RPA method were evaluated and compared with those of the standard RT-qPCR method. The clinical applicability of this assay was evaluated using 68 field samples.ResultsAmplification using the newly developed RT-RPA assay was completed within 20 min at 37°C, while that using the RT-qPCR method required nearly 60 min. The RT-RPA method exhibited an obvious time-saving advantage. Both RT-RPA and RT-PCR methods had the same limit of detection, which was 4.45 × 101 copies/μL. The specificity was indicated by a lack of cross-reaction with MHV, pneumonia virus of mice, Sendai virus, hantavirus, minute virus of mice, and reovirus type III. The MHV detection rate of RT-RPA assays was 13.63% (9/66) and RT-qPCR assays was 15.15% (10/66). Cohen’s “kappa” (κ) analysis results exhibited a very good agreement between two methods with the value of κ ≥ 0.750(since κ = 0.939) and p &lt; 0.0005 (since p = 0.000).ConclusionThe RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of MHV in laboratory mice and has significant potential for application in laboratories.
Factors associated with antidepressant responses to repetitive transcranial magnetic stimulation in antidepressant-resistant depression
Authors: Li Cheng-Ta , Su Tung-Ping , Cheng Chih-Ming , Chen Mu-Hong , Bai Ya-Mei , Tsai Shih-Jen 
Published: December 2022

BackgroundA significant proportion of patients with major depressive disorder (MDD) failed to respond to antidepressant medications. Repetitive transcranial magnetic stimulation (rTMS) is an effective option for treating such treatment-resistant patients with MDD (TRD). Reliable clinical predictors for antidepressant responses to rTMS remain elusive.MethodsIn total, 212 patients with MDD who failed to respond to at least one adequate antidepressant trial and had a detailed evaluation before rTMS were recruited for chart review. Demographic data, clinical characteristics, psychiatric comorbidities, symptom ratings [e.g., objective and subjective depression, life stress, depression refractoriness by Maudsley Staging Method (MSM)], and antidepressant treatment responses were analyzed.ResultsMSM-subitem1 (duration of current depressive episode; Beta = 0.209, p = 0.004), MSM-subitem5 (a history of ECT treatment; Beta = –0.210, p = 0.004), and psychiatric admissions (Beta = 0.241, p = 0.001) predicted antidepressant response of rTMS treatment. ECT was underutilized (only 3.3%). Psychiatric admissions [Exp(B) = 1.382, p = 0.021], a comorbidity of OCD [0.047, 0.005], and life stress level [0.984, 0.029] predicted the history of ECT treatment.ConclusionSeveral clinical variables (e.g., number of psychiatric admissions, OCD as a comorbidity, and life stress level) were reliable clinical factors associated with antidepressant responses of rTMS treatment and may be utilized in combination with MSM subitems to evaluate levels of TRD.
Patients with dysphagia: How to supply nutrition through non-tube feeding
Authors: Shen Zhean , Hou Yingze , Huerman Ayideng , Ma Aiqin 
Published: December 2022

ObjectiveDysphagia has become one of the important factors that cause malnutrition in the whole age group. At present, tube feeding is still the mainstream means to solve the problem of dysphagia. However, tube feeding has physical and mental harm to people, and the ways of non-tube feeding are relatively diversified. The significance of the thickening mechanism described in some articles to solve the problem of dysphagia is not clear.Setting and participantsAll patients with dysphagia worldwide, including oropharyngeal dysphagia (OD) and non-oropharyngeal dysphagia.MethodsWe searched the literature in Pubmed, Web of Science and Cochrane Library and initially browsed the titles and abstracts. We reviewed the full text of the articles that met our topic, and the language of the article was limited to English.ResultsWe found that food thickening to a certain degree (350–1,750 cP) can reduce the complications of choking, aspiration, reflux, and other complications in patients with dysphagia, and reduce the social disorder, anxiety, and other psychological problems caused by catheterization and surgery. Significantly, food science engineers should invite clinicians to intervene in the development of specialty foods from different perspectives such as clinical pathophysiology and fluid mechanics.Conclusion and implicationsIt is necessary to develop special foods for patients with dysphagia, which requires scientists from different disciplines to work together.
3D vs. 2D MRI radiomics in skeletal Ewing sarcoma: Feature reproducibility and preliminary machine learning analysis on neoadjuvant chemotherapy response prediction
Authors: Gitto Salvatore , Corino Valentina D. A. , Annovazzi Alessio , Milazzo Machado Estevāo , Bologna Marco , Marzorati Lorenzo , Albano Domenico , Messina Carmelo , Serpi Francesca , Anelli Vincenzo , Ferraresi Virginia , Zoccali Carmine , Aliprandi Alberto , Parafioriti Antonina , Luzzati Alessandro , Biagini Roberto , Mainardi Luca , Sconfienza Luca Maria 
Published: December 2022

ObjectiveThe extent of response to neoadjuvant chemotherapy predicts survival in Ewing sarcoma. This study focuses on MRI radiomics of skeletal Ewing sarcoma and aims to investigate feature reproducibility and machine learning prediction of response to neoadjuvant chemotherapy.Materials and methodsThis retrospective study included thirty patients with biopsy-proven skeletal Ewing sarcoma, who were treated with neoadjuvant chemotherapy before surgery at two tertiary sarcoma centres. 7 patients were poor responders and 23 were good responders based on pathological assessment of the surgical specimen. On pre-treatment T1-weighted and T2-weighted MRI, 2D and 3D tumour segmentations were manually performed. Features were extracted from original and wavelet-transformed images. Feature reproducibility was assessed through small geometrical transformations of the regions of interest mimicking multiple manual delineations, and intraclass correlation coefficient &gt;0.75 defined feature reproducibility. Feature selection also consisted of collinearity and significance analysis. After class balancing in the training cohort, three machine learning classifiers were trained and tested on unseen data using hold-out cross-validation.Results1303 (77%) 3D and 620 (65%) 2D radiomic features were reproducible. 4 3D and 4 2D features passed feature selection. Logistic regression built upon 3D features achieved the best performance with 85% accuracy (AUC=0.9) in predicting response to neoadjuvant chemotherapy.ConclusionCompared to 2D approach, 3D MRI radiomics of Ewing sarcoma had superior reproducibility and higher accuracy in predicting response to neoadjuvant chemotherapy, particularly when using logistic regression classifier.
Detection of somatic copy number deletion of the CDKN2A gene by quantitative multiplex PCR for clinical practice
Authors: Tian Yuan , Zhou Jing , Qiao Juanli , Liu Zhaojun , Gu Liankun , Zhang Baozhen , Lu Youyong , Xing Rui , Deng Dajun 
Published: December 2022

BackgroundA feasible method to detect somatic copy number deletion (SCND) of genes is still absent to date.MethodsInterstitial base-resolution deletion/fusion coordinates for CDKN2A were extracted from published articles and our whole genome sequencing (WGS) datasets. The copy number of the CDKN2A gene was measured with a quantitative multiplex PCR assay P16-Light and confirmed with whole genome sequencing (WGS).ResultsEstimated common deletion regions (CDRs) were observed in many tumor suppressor genes, such as ATM, CDKN2A, FAT1, miR31HG, PTEN, and RB1, in the SNP array-based COSMIC datasets. A 5.1 kb base-resolution CDR could be identified in &gt;90% of cancer samples with CDKN2A deletion by sequencing. The CDKN2A CDR covers exon-2, which is essential for P16INK4A and P14ARF synthesis. Using the true CDKN2A CDR as a PCR target, a quantitative multiplex PCR assay P16-Light was programmed to detect CDKN2A gene copy number. P16-Light was further confirmed with WGS as the gold standard among cancer tissue samples from 139 patients.ConclusionThe 5.1 kb CDKN2A CDR was found in &gt;90% of cancers containing CDKN2A deletion. The CDKN2A CDR was used as a potential target for developing the P16-Light assay to detect CDKN2A SCND and amplification for routine clinical practices.
Immunogenicity of SARS-CoV-2 vaccination in patients undergoing autologous stem cell transplantation. A multicentric experience
Authors: Autore Francesco , Stirparo Luca , Innocenti Idanna , Papa Elena , Marchesi Francesco , Togni Chiara , Mariani Sabrina , Torrieri Lorenzo , Salvatori Martina , Fazio Francesca , Metafuni Elisabetta , Giammarco Sabrina , Sora Federica , Falcucci Paolo , Ferrari Antonella , Trisolini Silvia Maria , Capria Saveria , Tafuri Agostino , Chiusolo Patrizia , Sica Simona , Laurenti Luca 
Published: December 2022

COVID-19 disease has a strong impact on hematological patients; those receiving autologous hematopoietic stem cell transplantation (aHSCT) represent a particularly vulnerable group, in which the effectiveness of vaccination is very variable. Chiarucci et al. showed that patients affected by non-Hodgkin lymphoma (NHL) and treated with rituximab experienced a lower rate of immunization against SARS-CoV-2 (54%), as well as significantly lower IgG antibody titers. In our multicenter retrospective observational study, we included 82 patients who underwent aHSCT, divided into two groups: 58 patients vaccinated after aHSCT (group A) and 24 vaccinated before getting transplantation (group B). In group A, 39 (67%) patients had positive serology, and the rate of positivity increased with time after aHSCT. In the subgroup of patients with NHL, the administration of rituximab predicted negative serology, particularly when administered in the 6 months before vaccination (13% response rate). Patients affected by plasma cells had a higher rate of positivity (83% overall), independently of the time to aHSCT. In group B, no patient who initially showed positive serology became negative after transplantation, so the aHSCT did not affect the response to the vaccination. Our study confirmed the role of rituximab as a negative predictor of response to SARS-CoV-2 vaccination, whereas the conditioning and transplantation procedure itself seemed to be less important.
Immune-based treatment re-challenge in renal cell carcinoma: A systematic review and meta-analysis
Authors: Papathanassiou Maria , Tamposis Ioannis , Exarchou-Kouveli Kalliopi K. , Kontou Panagiota I. , de Paz Anna Tzortzi , Mitrakas Lampros , Samara Maria , Bagos Pantelis G. , Tzortzis Vassilios , Vlachostergios Panagiotis J. 
Published: December 2022

IntroductionThe use of immune checkpoint inhibitors (ICIs) as a front-line treatment for metastatic renal cell carcinoma (RCC) has significantly improved patient’ outcome. However, little is known about the efficacy or lack thereof of immunotherapy after prior use of anti-PD1/PD-L1 or/and anti-CTLA monoclonal antibodies.MethodsElectronic databases, including PubMed, EMBASE, Medline, Web of Science, and Cochrane Library, were comprehensively searched from inception to July 2022. Objective response rates (ORR), progression-free survival (PFS), and ≥ grade 3 adverse events (AEs) were assessed in the meta-analysis, along with corresponding 95% confidence intervals (CIs) and publication bias.ResultsTen studies which contained a total of 500 patients were included. The pooled ORR was 19% (95% CI: 10, 31), and PFS was 5.6 months (95% CI: 4.1, 7.8). There were ≥ grade 3 AEs noted in 25% of patients (95% CI: 14, 37).ConclusionThis meta-analysis on different second-line ICI-containing therapies in ICI-pretreated mRCC patients supports a modest efficacy and tolerable toxicity.
Human matters in asthma: Considering the microbiome in pulmonary health
Authors: Marathe Sandesh J. , Snider Mark A. , Flores-Torres Armando S. , Dubin Patricia J. , Samarasinghe Amali E. 
Published: December 2022

Graphical AbstractExogenous factors that influence the microbiome and asthma pathogenesis. External factors including a well-balanced diet and clean air support a healthy gut microbiome that releases metabolites and short-chain fatty acids (SCFA) that promote a healthy pulmonary immune system that remains non-inflammatory thereby protecting against the development of asthma or asthma exacerbations (left panel). An unhealthy diet, dirty air, and some pharmaceutical agents on the other hand can induce dysbiosis in the gut and lung microbial communities through induction of co-morbid states like obesity and aberrant immune activation. Additional confounders including modes of delivery and feeding, use of antibiotics during pregnancy and childhood also have an impact on the airway microbial homeostasis and asthma onset and pathogenesis (right panel). Figure prepared on BioRender.
Understanding inter-individual variability in pharmacokinetics/pharmacodynamics of aripiprazole in children with tic disorders: Individualized administration based on physiological development and CYP2D6 genotypes
Authors: Xin Yingying , Gao Liuliu , Tuo Yali , Nie Gang , Mei Yan , Chen Chen , Wang Jun , Li Sichan , Sun Dan , Qian Qiaoqiao , Fu Yongli , Wang Yang , Liu Zhisheng 
Published: December 2022

Objective: This study aims to develop a combined population pharmacokinetic (PPK) model for aripiprazole (ARI) and its main active metabolite dehydroaripiprazole (DARI) in pediatric patients with tic disorders (TD), to investigate the inter-individual variability caused by physiological and genetic factors in pharmacokinetics of ARI and optimize the dosing regimens for pediatric patients.Methods: A prospective PPK research was performed in Chinese children with TD. Totally 84 patients aged 4.83–17.33 years were obtained for the pharmacokinetic analysis. 27 CYP2D6 and ABCB1 gene alleles were detected. Moreover, the clinical efficacy was evaluated according to reduction rate of Yale Global Tic Severity Scale (YGTSS) score at the 12th week comparing with the baseline. Monte Carlo simulations were used to evaluate and optimize dosing regimens.Results: The PPK model was established to predict the concentrations of ARI and DARI. Body weight and CYP2D6 genotype were the significant covariates affecting the clearance of ARI. The DARI/ARI metabolic ratios (MRs) of AUC24h, Cmin and Cmax at the steady state of results were ultra-rapid metabolizers (UMs) &gt; normal metabolizers (NMs) &gt; intermediated metabolizers (IMs). MRs could be used to distinguish UMs or IMs from other patients. The best predictor of clinical efficacy for TD was the trough concentration of ARI and the cut-off point was 101.636 ng/ml.Conclusion: The pharmacokinetics of ARI and DARI in pediatric TD were significantly influenced by body weight and CYP2D6 genotype. Individualized dosing regimens were recommended for pediatric patients with TD to ensure clinical efficacy.
The iron-modulating hormone hepcidin is upregulated and associated with poor survival outcomes in renal clear cell carcinoma
Authors: Huang Jian , Liu Wang , Song Shiqi , Li Jean C. , Gan Kaimei , Shen Chunxiao , Holzbeierlein Jeffrey , Li Benyi 
Published: December 2022

Background: Reliable biomarkers are rare for renal cell carcinoma (RCC) treatment selection. We aimed to discover novel biomarkers for precision medicine. The iron-regulating hormone hepcidin (HAMP) was reportedly increased in RCC patient sera and tissues. However, its potential implication as a prognostic biomarker remains exclusive.Methods: Multiple RNA-seq and cDNA microarray datasets were utilized to analyze gene expression profiles. Hepcidin protein expression was assessed using an ELISA assay in cell culture models. Comparisons of gene expression profiles and patient survival outcomes were conducted using the R package bioinformatics software.Results: Five (HAMP, HBS, ISCA2, STEAP2, and STEAP3) out of 71 iron-modulating genes exhibited consistent changes along with tumor stage, lymph node invasion, distal metastasis, tumor cell grade, progression-free interval, overall survival, and disease-specific survival. Of which HAMP upregulation exerted as a superior factor (AUC = 0.911) over the other four genes in distinguishing ccRCC tissue from normal renal tissue. HAMP upregulation was tightly associated with its promoter hypomethylation and immune checkpoint factors (PDCD1, LAG3, TIGIT, and CTLA4). Interleukin-34 (IL34) treatment strongly enhanced hepcidin expression in renal cancer Caki-1 cells. Patients with higher levels of HAMP expression experienced worse survival outcomes.Conclusion: These data suggest that HAMP upregulation is a potent prognostic factor of poor survival outcomes and a novel immunotherapeutic biomarker for ccRCC patients.
Effect of Burkholderia ambifaria LK-P4 inoculation on the plant growth characteristics, metabolism, and pharmacological activity of Anoectochilus roxburghii
Authors: Wang Juanying , Zhao Hanyu , Chen Ting , Lin Wenxiong , Lin Sheng 
Published: December 2022

BackgroundPlant growth-promoting bacteria (PGPB) represents a common biological fertilizer with remarkable effect in improving crop production and environmental friendliness.MethodsIn the present work, we presented a detailed characterization of plant morphology and physiology, metabolism, and pharmacological activity of A. roxburghii between Burkholderia ambifaria LK-P4 inoculation and un-inoculation (CK) treatment by routine analytical techniques (include microscopy and enzymatic activity assays and so on) coupled with metabolomics approaches.ResultsMorphological and physiological results showedthat the P4 bacteria could significantly increase plant stomatal density, freshweight, survival rate,and the content of total flavonoids in leaves but reducethe amount of free amino acid. Furthermore, metabolite data showed that fatty acids (linoleic acid, linolenic acid, stearic acid) and active substance (kyotorphin and piceatannol) were specifically up-regulated in P4 inoculation. It was also demonstrated that the differential metabolites were involved in citrate cycle, glyoxylate and dicarboxylate metabolism, and biosynthesis of unsaturated fatty acids pathway. In addition, pharmacological efficacy found that A. roxburghii under P4 inoculation can significantly decrease (p &lt; 0.05) blood glucose levels and protect the organs of mice with similar effect of Glibenclamide tablets.ConlusionOverall, it can be seen that the exogenous P4 bacteria can promote the growth and increase content of special metabolites in A. roxburghii. This study provided theoretical basis and supported for the high-yield and high-quality bionic cultivation of A. roxburghii.