bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fibrosis-4 index is a prognostic factor for cholangiocarcinoma patients who received immunotherapy
Authors: Zhang Zhiwei , Zhang Jingzhao , Cai Ming , Huang Xiaorui , Guo Xinyi , Zhu Dengsheng , Guo Tong , Yu Yahong 
Published: May 2024

BackgroundResearch of immunotherapy for cholangiocarcinoma has yielded some results, but more clinical data are needed to prove its efficacy and safety. Moreover, there is a need to identify accessible indexes for selecting patients who may benefit from such treatments.MethodsThe medical records of 66 cholangiocarcinoma patients who underwent immunotherapy were retrospectively collected. The effectiveness of immunotherapy was assessed by tumor response, progression-free survival (PFS), and overall survival (OS), while safety was evaluated by adverse events during treatment. Univariate and multivariate Cox regression analyses were performed to identify prognostic risk factors for PFS and OS, and Kaplan-Meier curves of potential prognostic factors were drawn.ResultsOverall, in this study, immunotherapy achieved an objective response rate of 24.2% and a disease control rate of 89.4% for the included patients. The median PFS was 445 days, and the median OS was 772.5 days. Of the 66 patients, 65 experienced adverse events during treatment, but none had severe consequences. Multivariate Cox analysis indicated that tumor number is a prognostic risk factor for disease progression following immunotherapy in cholangiocarcinoma patients, while tumor differentiation and the fibrosis-4 (FIB-4) index are independent risk factors for OS.ConclusionIn general, immunotherapy for cholangiocarcinoma is safe, with adverse events remaining within manageable limits, and it can effectively control disease progression in most patients. The FIB-4 index may reflect the potential benefit of immunotherapy for patients with cholangiocarcinoma.
Consolidation therapy with autologous stem cell transplantation after remission of induction chemotherapy prolongs the survival of patients with peripheral T-cell lymphoma
Authors: Fulati Wulipan , Ma Jiexian , Wu Min , Qian Wensi , Chen Pingping , Hu Yingwei , Chen Mingyue , Xu Yu , Huang Zilan , Zhang Hongdi , Xie Yanhui , Shen Lin 
Published: May 2024

BackgroundThere was little evidence of autologous stem cell transplantation (ASCT) as consolidation therapy after remission of induction for patients with Peripheral T-cell lymphoma (PTCL). In this study, we conducted a comparative analysis of real-world survival outcomes between consolidation therapy and observation in patients with PTCL.MethodsA total of 92 patients with peripheral T-cell lymphoma (PTCL) who were admitted to the Department of Hematology, Huadong Hospital Affiliated with Fudan University from January 2013 to April 2019 were divided into two groups based on whether they were treated with high-dose therapy (HDT) followed by autologous hematopoietic stem cell transplantation (ASCT): ASCT as consolidation therapy (n=30) and observation (n=62). Clinical characteristics, treatment patterns, and survival outcomes were analyzed between the two groups. Univariate and Cox multivariate regression analyses were also performed to detect prognostic factors of survival.ResultsWith a median follow-up time of 41 months, the median overall survival (OS) of peripheral T-cell lymphoma patients treated with ASCT was not reached; the median progression-free survival (PFS) was 77.0 months, which was much higher than that of patients without ASCT (p&lt;0.003 for OS, p=0.015 for PFS). Subgroup analysis found that patients with high risks benefited more from ASCT. Combination with hemophagocytic lymphohistiocytosis (HLH) (p&lt;0.001), clinical stage more than III (p=0.014), IPI score above 3 (p=0.049), and bone marrow involvement (p=0.010) were the independent prognostic factors significantly associated with worse OS and PFS. Additionally, pegylated liposomal doxorubicin (PLD)–containing chemotherapy regimen could bring a higher overall response rate (ORR) and prolong the survival of patients with PTCL who underwent ASCT.ConclusionASCT may improve the long-term survival of patients with PTCL as consolidation therapy after achieving complete or partial remission of induction treatment, particularly for those with high risks. The chemotherapy regimen containing pegylated liposomal doxorubicin may induce deeper remission than traditional doxorubicin in PTCL. It is crucial to identify the specific groups most likely to benefit from upfront ASCT.
Pharmacodynamic monitoring by residual gene expression of the nuclear factor of activated T cell-regulated genes in lung transplant recipients and its correlation with tacrolimus blood levels
Authors: Boada-Pérez Meritxell , Ruiz de Miguel Victoria , Erro Marta , Ussetti Piedad , Aguilar Myriam , Castejón Raquel , Rosado Silvia , Escobar-Fornieles Roser , Revilla-López Eva , Bravo Carlos , Sáez-Giménez Berta , Zapata-Ortega Marta , Villena-Ortiz Yolanda , Vima-Bofarull Jaume , Monforte Víctor , Gómez-Ollés Susana 
Published: May 2024

IntroductionTrough blood levels (C0) of tacrolimus are used to adjust drug dosage, but they do not consistently correlate with clinical outcomes. Measurement of residual gene expression of nuclear factor of activated T cell (NFAT)-regulated genes (NFAT-RGE) has been proposed as a pharmacodynamic biomarker to assess the degree of immunosuppression in certain solid organ transplantations, but little is known regarding lung transplant recipients (LTR). Our primary objective is to correlate tacrolimus blood levels with NFAT-RGE.MethodsNFAT-RGE and tacrolimus C0 and peak (C1.5) levels were determined in 42 patients at three, six and 12 months post-transplantation.ResultsTacrolimus C0 did not exhibit a correlation with NFAT-RGE, whereas C1.5 did. Besides, over 20% of measurements indicated high levels of immunosuppression based on the below 30% NFAT-RGE threshold observed in many studies. Among those measurements within the therapeutic range, 19% had an NFAT-RGE&lt;30%.ConclusionConsequently, a subset of patients within the tacrolimus therapeutic range may be more susceptible to infection or cancer, potentially benefiting from NFAT-RGE and tacrolimus peak level monitoring to tailor their dosage. Further quantitative risk assessment studies are needed to elucidate the relationship between NFAT-RGE and the risk of infection, cancer, or rejection.
The prognostic value of preoperative systemic inflammatory response index in predicting outcomes of acute type A aortic dissection patients underwent surgical treatment
Authors: Xie Lin-feng , Xie Qi-gui , Gao Wen-ping , Wu Qing-song , Lin Xin-fan , Qiu Zhi-huang , Chen Liang-wan 
Published: May 2024

BackgroundThe systemic inflammatory response index (SIRI) is a novel inflammatory-immune biological marker that has prognostic value in various cardiovascular diseases. This study aims to investigate the relationship between SIRI and short-term and long-term prognosis in patients with acute type A aortic dissection (AAAD) underwent surgical treatment.MethodsWe conducted a retrospective analysis of patients with AAAD who underwent emergency surgical treatment at our center. Through multifactorial logistics regression analysis and cox proportional hazards regression analysis, we identified SIRI as an independent risk factor for major adverse events (MAEs) and long-term aorta-related adverse events (ARAEs) post-surgery. The optimal cutoff value of preoperative SIRI was determined using receiver operating characteristic (ROC) curve analysis, and patients were divided into low SIRI group and high SIRI group. The prognostic outcomes at different time points post-surgery for the two groups of patients were analyzed using Kaplan-Meier survival analysis, and the significance was determined by log-rank test.ResultsA total of 691 AAAD patients were included in this study. Among them, 50 patients (7.2%) died within 30 days post-surgery, and 175 patients (25.3%) experienced MAEs. A total of 641 patients were followed up, with an average follow-up time of 33.5 ± 17.5 months, during which 113 patients (17.6%) experienced ARAEs. The results of multifactorial logistics regression analysis and cox proportional hazards regression analysis showed that SIRI was an independent risk factor for postoperative MAEs (OR=3.148, 95%CI[1.650-6.006], p&lt;0.001) and ARAEs (HR=2.248, 95%CI[1.050-4.809], p&lt;0.037). Kaplan-Meier analysis demonstrated that the MAEs-free survival in the high SIRI group was significantly lower than that in the low SIRI group, and a similar trend was observed in the ARAEs-free survival during follow-up (log-rank test, p&lt;0.001).ConclusionPreoperative SIRI is significantly associated with the short-term and long-term prognosis of AAAD patients underwent emergency open surgery, demonstrating its valuable prognostic value. Therefore, preoperative SIRI is a reliable biological marker that can serve as a valuable tool for preoperative risk stratification and decision management.
Prognostic role of circulating cytokines and inflammation indexes for avelumab maintenance in metastatic urothelial carcinoma
Authors: Maiorano Brigida Anna , Schinzari Giovanni , Carbone Carmine , Piro Geny , Rossi Ernesto , Di Maio Massimo , Di Giacomo Annamaria , Maiello Evaristo 
Published: May 2024

BackgroundAvelumab maintenance after first-line platinum-based chemotherapy represents a cornerstone for the treatment of metastatic urothelial carcinoma (mUC). However, identifying prognostic biomarkers is paramount for optimizing patients’ benefits while minimizing toxicity. Cytokines represent circulating mediators of the complex interaction between cancer, the immune system, and inflammation. Inflammation, a hallmark of cancer, can be expressed by circulating factors. In different tumor subtypes, peripheral blood biomarkers, such as circulating cytokines, and systemic inflammatory indexes, have been addressed as potential prognostic factors for immune checkpoint inhibitors. However, their role in mUC still needs to be determined.MethodsBetween February 2021 and April 2023, we prospectively collected plasma cytokines and inflammation indexes in 28 patients with mUC before starting avelumab as first-line maintenance. The primary endpoint was the relationship between baseline cytokines and inflammatory indexes with the clinical benefit (CB), defined as the number of Responders. Secondary endpoints included the correlation of baseline cytokines and inflammatory indexes with progression-free survival (PFS), overall survival (OS), and the number and grade of immune-related adverse events.ResultsHigh pre-treatment levels of interferon (IFN)-γ and interleukin (IL)-2, and low levels of IL-6, IL-8, neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), and systemic-inflammation index (SII) were associated with clinical benefit and longer survival. In the multivariate analysis, low IL-8, NLR, and SII levels maintained a positive prognostic value for OS.ConclusionOur data suggest that, in mUC patients receiving avelumab, pre-treatment levels of plasma cytokines and inflammatory indexes may serve as potential prognostic biomarkers for response and efficacy. In particular, patients with signs of pre-therapeutic inflammation showed a significantly lower response and survival to avelumab. On the contrary, low systemic inflammation and high levels of cytokines characterized responders and longer survivors.
Application of two-sample Mendelian randomization method to assess the causal relationship between rheumatoid arthritis and osteoporotic fracture
Authors: Zhenyu Cai , Le Chang , Shiyong Zeng , Jinding Lin , Mingzhong Liu , Haifeng Tang , Rongdong Zeng 
Published: May 2024

BackgroundThe association between rheumatoid arthritis (RA) and osteoporotic fracture has garnered considerable attention; however, the causal relationships between diseases remain uncertain. Therefore, this study employed Mendelian randomization (MR) analysis to investigate the causal effects of RA on osteoporotic fracture.MethodsThe summary data for RA and osteoporotic fracture were extracted from the genome-wide association studies (GWAS) catalog and the Finn Biobank database. The database provides information about diseased and health control subjects. We searched the database for the following conditions: RA, osteoporosis (OP), and osteoporotic fractures. Entries were published by investigating centers, which had established definitions and diagnostic criteria. We downloaded and processed the data to obtain the single-nucleotide polymorphisms (SNPs) strongly associated with RA, OP, and osteoporotic fracture. RA genetic associations were obtained from the GWAS catalog, including 1961 cases and 454,387 controls. The osteoporosis of the GWAS catalog involved 991 cases and 455,357 controls, and the data of the Finn Biobank involved 8,017 cases and 391,037 controls. Genetic associations for osteoporotic fracture were taken from the Finn Biobank of 1822 cases and 311,210 controls. Independent SNPs that are significantly associated with meeting the criteria of p &lt; 5 × 10–8, r2 &lt; 0.001, and kb = 10,000 were selected for MR analysis. The inverse variance-weighted (IVW) method along with other MR methods was employed for analysis, while sensitivity analyses were conducted to assess reliability and stability.ResultsThe results provided strong evidence that RA was causally and positively associated with osteoporosis from the GWAS catalog (OR = 1.16590; 95% CI: 1.04067–1.30619; p = 0.00811) and the Finn Biobank database (OR = 1.07314; 95% CI: 1.03455–1.11317; p = 0.00016). Moreover, a positive causal relationship was detected between RA and osteoporotic fracture (OR = 1.10132; 95% CI: 1.00506–1.20680; p = 0.03863). The results were robust according to sensitivity tests.ConclusionThis study showed positive causal relationships between RA and osteoporotic fracture. These results should be considered in further studies and public health measures on osteoporosis prevention strategies.
Evaluating sarcopenia prevalence and SARC-F effectiveness in elderly Spanish women with RA: a comparative study of EWGSOP criteria
Authors: Valencia-Muntalà Lidia , Gómez-Vaquero Carmen , Mora Maribel , Berbel-Arcobé Laura , Benavent Diego , Narváez Javier , Juanola Xavier , Nolla Joan M. 
Published: May 2024

IntroductionThe European Working Group on Sarcopenia in Older People (EWGSOP) has put forward two key proposals for diagnosing sarcopenia: the EWGSOP1 in 2010 and the EWGSOP2 in 2019. These proposals are currently the most widely used guidelines for diagnosing sarcopenia. However, data on the prevalence of sarcopenia in patients with rheumatoid arthritis (RA) based on EWGSOP criteria are limited. This study aimed to: (a) establish the prevalence of sarcopenia in an elderly Spanish cohort of women with RA using both EWGSOP1 and EWGSOP2 criteria; and (b) evaluate the effectiveness of the SARC-F questionnaire in detecting sarcopenia.MethodsIn this observational, cross-sectional study, 67 women aged over 65 years who met the ACR 2010 criteria for RA were consecutively recruited from a tertiary university hospital. Assessments included: (a) demographic and anthropometric data; (b) RA-related variables (disease history, analytical evaluation, activity, disability, quality of life); and (c) sarcopenia-related variables (muscle strength, gait speed, skeletal muscle mass, and SARC-F questionnaire). The prevalence of sarcopenia was determined using both EWGSOP1 and EWGSOP2 criteria. Furthermore, the effectiveness of the SARC-F questionnaire for detecting sarcopenia were calculated.ResultsThe prevalence of sarcopenia was 43% according to the EWGSOP1 criteria and 16% according to the EWGSOP2 criteria. Patients diagnosed with sarcopenia based on the latter criteria also met the EWGSOP1's criteria for sarcopenia. Agreement between the two sets of EWGSOP criteria was poor. The SARC-F questionnaire demonstrated an inherently high sensitivity (100%) as well as good specificity (75%) and diagnostic accuracy (79%) in detecting sarcopenia according to EWGSOP2 criteria.ConclusionsThe prevalence rate of sarcopenia among elderly Spanish women with RA varies significantly depending on whether EWGSOP1 or EWGSOP2 criteria are applied. The SARC-F questionnaire is effective for predicting sarcopenia when used in conjunction with the EWGSOP2 criteria, which is currently the most accepted standard in clinical practice.
Evaluation of fecal sample collection methods for feline gut microbiome profiling: fecal loop vs. litter box
Authors: Ma Xiaolei , Brinker Emily , Lea Christopher R. , Delmain Diane , Chamorro Erin D. , Martin Douglas R. , Graff Emily C. , Wang Xu 
Published: May 2024

IntroductionMicrobial population structures within fecal samples are vital for disease screening, diagnosis, and gut microbiome research. The two primary methods for collecting feline fecal samples are: (1) using a fecal loop, which retrieves a rectal sample using a small, looped instrument, and (2) using the litter box, which collects stool directly from the litter. Each method has its own advantages and disadvantages and is suitable for different research objectives.Methods and resultsWhole-genome shotgun metagenomic sequencing were performed on the gut microbiomes of fecal samples collected using these two methods from 10 adult cats housed in the same research facility. We evaluated the influence of collection methods on feline microbiome analysis, particularly their impact on DNA extraction, metagenomic sequencing yield, microbial composition, and diversity in subsequent gut microbiome analyses. Interestingly, fecal sample collection using a fecal loop resulted in a lower yield of microbial DNA compared to the litterbox method (p = 0.004). However, there were no significant differences between the two groups in the proportion of host contamination (p = 0.106), virus contamination (p = 0.232), relative taxonomy abundance of top five phyla (Padj &gt; 0.638), or the number of microbial genes covered (p = 0.770). Furthermore, no significant differences were observed in alpha-diversity, beta-diversity, the number of taxa identified at each taxonomic level, and the relative abundance of taxonomic units.DiscussionThese two sample collection methods do not affect microbial population structures within fecal samples and collecting fecal samples directly from the litterbox within 6 hours after defecation can be considered a reliable approach for microbiome research.
Development and biological characterization of an infectious cDNA clone of NADC34-like PRRSV
Authors: Lin Yafang , Zhou Lujia , Xiao Changguang , Li Zongjie , Liu Ke , Li Beibei , Shao Donghua , Qiu Yafeng , Ma Zhiyong , Wei Jianchao 
Published: May 2024

IntroductionPorcine Reproductive and Respiratory Syndrome virus (PRRSV) causes high abortion rates in gestating sows and stillbirths, as well as high piglet mortality, seriously jeopardizing the pig industry in China and worldwide.MethodsIn this study, an infectious clone containing the full-length genome of NADC34-like PRRSV was constructed for the first time using reverse genetic techniques. The gene was amplified segmentally onto a plasmid, transfected into BHK-21 cells, and the transfected supernatant was harvested and transfected into PAM cells, which showed classical cytopathic effects (CPE).ResultsThe virus rJS-KS/2021 was successfully rescued which could be demonstrated by Western Blot and indirect immunofluorescence assays. Its growth curve was similar to the original strain. Replace the 5’UTR and 3’UTR of rJS-KS/2021 with 5’UTR and 3’UTR of HP-PRRSV (strain SH1) also failed to propagate on MARC-145.DiscussionIn this study, an infectious clone of NADC34-like was constructed by reverse genetics, replacing the UTR and changing the cellular tropism of the virus. These findings provide a solid foundation for studying the recombination of different PRRSVs and the adaption of PRRSVs on MARC-145 in the future.
Ammonium sulfate denatures transport medium less dependent on guanidinium isothiocyanate and enables SARS-CoV-2 RNA and antigen detection compatibility
Authors: Liu Ge , Xu Jiapeng , Huang Yuanyuan , Ye Wei , Li Jieyu , Yan Ran , Luo Qiting , Zhou Xinrui , Cai Yingna , Jiang Hanfang , Lu Xiujing , Zheng Kai , He Zhendan , Zhu Qinchang 
Published: May 2024

IntroductionRapid identification of infected individuals through viral RNA or antigen detection followed by effective personal isolation is usually the most effective way to prevent the spread of a newly emerging virus. Large-scale detection involves mass specimen collection and transportation. For biosafety reasons, denaturing viral transport medium has been extensively used during the SARS-CoV-2 pandemic. However, the high concentrations of guanidinium isothiocyanate (GITC) in such media have raised issues around sufficient GITC supply and laboratory safety. Moreover, there is a lack of denaturing transport media compatible with SARS-CoV-2 RNA and antigen detection.MethodsHere, we tested whether supplementing media containing low concentrations of GITC with ammonium sulfate (AS) would affect the throat-swab detection of SARS-CoV-2 or a viral inactivation assay targeting coronavirus and other enveloped and non-enveloped viruses. The effect of adding AS to the media on RNA stability and its compatibility with SARS-CoV-2 antigen detection were also tested.Results and discussionWe found that adding AS to the denaturing transport media reduced the need for high levels of GITC, improved SARS-COV-2 RNA detection without compromising virus inactivation, and enabled the denaturing transport media compatible with SARS-CoV-2 antigen detection.
Bacterial–fungal interactions and response to heavy metal contamination of soil in agricultural areas
Authors: Li Jia , Zheng Qiwen , Liu Jiangyun , Pei Shuwei , Yang Zhen , Chen Rentong , Ma Li , Niu Jingping , Tian Tian 
Published: May 2024

IntroductionLong-term heavy metal contamination of soil affects the structure and function of microbial communities. The aim of our study was to investigate the effect of soil heavy metal contamination on microorganisms and the impact of different heavy metal pollution levels on the microbial interactions.MethodsWe collected soil samples and determined soil properties. Microbial diversity was analyzed in two groups of samples using high-throughput sequencing technology. Additionally, we constructed microbial networks to analyze microbial interactions.ResultsThe pollution load index (PLI) &lt; 1 indicates that the area is not polluted. 1 &lt; PLI &lt; 2 represents moderate pollution. PLI was 1.05 and 0.14 for the heavy metal contaminated area and the uncontaminated area, respectively. Cd, Hg, Pb, Zn, and Cu were identified as the major contaminants in the contaminated area, with the contamination factors were 30.35, 11.26, 5.46, 5.19, and 2.46, respectively. The diversities and compositions of the bacterial community varied significantly between the two groups. Compared to the uncontaminated area, the co-occurrence network between bacterial and fungal species in the contaminated area was more complex. The keystone taxa of the co-occurrence network in the contaminated area were more than those in the uncontaminated area and were completely different from it.DiscussionHeavy metal concentrations played a crucial role in shaping the difference in microbial community compositions. Microorganisms adapt to long-term and moderate levels of heavy metal contamination through enhanced interactions. Bacteria resistant to heavy metal concentrations may play an important role in soils contaminated with moderate levels of heavy metals over long periods of time.