bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of the immunohistochemical score based on four markers in head and neck squamous cell carcinoma
Authors: Xu Qing-Qing , Li Qing-Jie , Xu Zhen , Lan Li-Long , Hou Zan , Liu Juan , Lu LiXia , Chen Yuan-Yuan , Chen Run-Zhe , Wen Xin 
Published: February 2023

PurposeHead and neck squamous cell carcinoma (HNSCC) ranks sixth among all cancers globally regarding morbidity, and it has a poor prognosis, high mortality, and highly aggressive properties. In this study, we established a model for predicting prognosis based on immunohistochemical (IHC) scores.MethodsData on 402 HNSCC cases were collected, the glmnet Cox proportional hazards model was used, risk factors were analyzed for predicting the prognosis of survival, and the IHC score was established. We used the IHC score to predict disease-free survival (DFS) using training and independent validation cohorts, including 264 cases in total. Additionally, the accuracy of the IHC score and the TNM system (8th edition) was compared. A DFS prediction nomogram was established by combining the prognostic factors.ResultsThe IHC scores included CK, Ki-67, p16, and p40 staining intensity. The concordance index and the Kaplan-Meier survival analysis showed that the IHC scores had high predictive power for HNSCC. Our results showed that the IHC score is an independent factor that can predict prognosis in a multivariate Cox regression analysis. When predicting DFS, the IHC score had a significantly higher value for the area under the ROC curve (AUC) than that of the TNM system. A nomogram was established and included the IHC score, age, tumor location, and the TNM stage. The calibration curves exhibited high consistency between the prognosis predicted by our nomogram and the actual prognosis.ConclusionsThe IHC score was more accurate than the eighth edition of the TNM system in predicting HNSCC prognosis. Therefore, combining the two methods can facilitate individualized patient consultation and care.
Salivary IgA subtypes as novel disease biomarkers in systemic lupus erythematosus
Authors: Romero-Ramírez Sandra , Sosa-Hernández Víctor A. , Cervantes-Díaz Rodrigo , Carrillo-Vázquez Daniel A. , Meza-Sánchez David E. , Núñez-Álvarez Carlos , Torres-Ruiz Jiram , Gómez-Martín Diana , Maravillas-Montero José L. 
Published: February 2023

IntroductionImmunoglobulin A (IgA) is the main antibody isotype in body fluids such as tears, intestinal mucous, colostrum, and saliva. There are two subtypes of IgA in humans: IgA1, mainly present in blood and mucosal sites, and IgA2, preferentially expressed in mucosal sites like the colon. In clinical practice, immunoglobulins are typically measured in venous or capillary blood; however, alternative samples, including saliva, are now being considered, given their non-invasive and easy collection nature. Several autoimmune diseases have been related to diverse abnormalities in oral mucosal immunity, such as rheumatoid arthritis, Sjogren’s syndrome, and systemic lupus erythematosus (SLE).MethodsWe decided to evaluate the levels of both IgA subtypes in the saliva of SLE patients. A light chain capture-based ELISA measured specific IgA1 and IgA2 levels in a cohort of SLE patients compared with age and gender-matched healthy volunteers.ResultsSurprisingly, our results indicated that in the saliva of SLE patients, total IgA and IgA1 subtype were significantly elevated; we also found that salivary IgA levels, particularly IgA2, positively correlate with anti-dsDNA IgG antibody titers. Strikingly, we also detected the presence of salivary anti-nucleosome IgA antibodies in SLE patients, a feature not previously reported elsewhere.ConclusionsAccording to our results and upon necessary validation, IgA characterization in saliva could represent a potentially helpful tool in the clinical care of SLE patients with the advantage of being a more straightforward, faster, and safer method than manipulating blood samples.
Identification and validation of immune and oxidative stress-related diagnostic markers for diabetic nephropathy by WGCNA and machine learning
Authors: Xu Mingming , Zhou Hang , Hu Ping , Pan Yang , Wang Shangren , Liu Li , Liu Xiaoqiang 
Published: February 2023

BackgroundDiabetic nephropathy (DN) is the primary cause of end-stage renal disease, but existing therapeutics are limited. Therefore, novel molecular pathways that contribute to DN therapy and diagnostics are urgently needed.MethodsBased on the Gene Expression Omnibus (GEO) database and Limma R package, we identified differentially expressed genes of DN and downloaded oxidative stress-related genes based on the Genecard database. Then, immune and oxidative stress-related hub genes were screened by combined WGCNA, machine learning, and protein-protein interaction (PPI) networks and validated by external validation sets. We conducted ROC analysis to assess the diagnostic efficacy of hub genes. The correlation of hub genes with clinical characteristics was analyzed by the Nephroseq v5 database. To understand the cellular clustering of hub genes in DN, we performed single nucleus RNA sequencing through the KIT database.ResultsUltimately, we screened three hub genes, namely CD36, ITGB2, and SLC1A3, which were all up-regulated. According to ROC analysis, all three demonstrated excellent diagnostic efficacy. Correlation analysis revealed that the expression of hub genes was significantly correlated with the deterioration of renal function, and the results of single nucleus RNA sequencing showed that hub genes were mainly clustered in endothelial cells and leukocyte clusters.ConclusionBy combining three machine learning algorithms with WGCNA analysis, this research identified three hub genes that could serve as novel targets for the diagnosis and therapy of DN.
Autoimmune pancreatitis: A bibliometric analysis from 2002 to 2022
Authors: Zhang Xian-Da , Zhang Yao , Zhao Yi-Zhou , Zhou Chun-Hua , Zou Duo-Wu 
Published: February 2023

Background/ObjectivesAutoimmune pancreatitis (AIP) is a distinct form of pancreatic inflammatory disease that responds well to glucocorticoid therapy. Knowledge on AIP has rapidly evolved over the past two decades. Based on bibliometric analysis, this study aimed to assess the research status of AIP over the past two decades and determine the research focus and emerging topics.MethodsAIP-related publications published between January 1, 2002, and June 6, 2022, were retrieved from the Web of Science Core Collection. Bibliometric data were analyzed using HisCite, VOSviewer, CiteSpace, and bibliometrix package. Annual output, leading countries/regions, active institutions and authors, core journals and references, and keywords of AIP were evaluated.ResultsOverall, 1,772 publications were retrieved from 501 journals by 6,767 authors from 63 countries/regions. Japan published articles on AIP the most (n=728, 41.1%), followed by the United States (n=336, 19%), Germany (n=147, 8.3%), China (n=127, 7%), and Italy (n=107, 6%). The top three most prolific authors were Terumi Kamisawa from Tokyo Metropolitan Komagome Hospital (n=117), Kazuichi Okazaki from Kansai Medical University (n=103), and Shigeyuki Kawa from Matsumoto Dental University (n=94). Pancreas was the most productive journal regarding AIP research (n=95), followed by the Journal of Gastroenterology (n=67), Internal Medicine (n=66), Pancreatology (n=63), and World Journal of Gastroenterology (n=62). “Diagnosis” was the most mentioned keyword. “Risk,” “malignancy,” “outcome,” “22-gauge needle,” and “fine-needle aspiration” were recognized as emerging topics.ConclusionJapan was the leading country in AIP research. Research papers were mainly published in specialized journals. Diagnosis was the research focus. Long-term outcomes and pancreatic tissue acquisition were recognized as research frontiers for AIP.
Patients’ experiences with virtual group gut-directed hypnotherapy: A qualitative study
Authors: Gerson Jessica , Tawde Prianca , Ghiasian Ghoncheh , Salwen-Deremer Jessica K. 
Published: February 2023

BackgroundHypnotherapy is a useful treatment for a variety of gastrointestinal conditions. While there is strong evidence for delivering other treatments virtually and in groups, there is no research thus far on delivering hypnotherapy in this format. Given the growth of both psychogastroenterology and telehealth, these methods should be explored as they have great potential for increasing access and cost-effectiveness of intervention.AimsThis qualitative study was developed to help understand patients experiences in virtual, group-based, gut-directed hypnotherapy (GDH) in two different institutions.MethodsAuthors developed a qualitative interview with the assistance of two patient partners and then recruited patients from New York University and Dartmouth Health to participate. Interviews were completed one-on-one with patients who started and then completed GDH (≥5 visits) and who did not complete GDH (≤3 visits). Data were coded and then analyzed using thematic analysis.ResultsTwenty-one patients from NYU and Dartmouth participated in qualitative interviews. Broadly, patients reported coming to GDH because they believed in the importance of the mind-body connection or were desperate for treatment. Regardless of why patients came to GDH, they generally reported positive outcomes for GI symptoms and for other physical and mental health conditions. Most patients appreciated the group and virtual formats, though some concerns about inflexible schedules and lack of anonymity were voiced. Despite these concerns, there was broad support for virtual, group-based GDH and general excitement for behavioral health programming.ConclusionVirtual, group-based GDH is an acceptable treatment for patients from rural and urban settings. Given the possible improvements in access and cost-effectiveness that this treatment modality can provide, GI practices may want to consider it in lieu of or in addition to the traditional one-on-one treatment format. Barriers and facilitators and recommendations for practice are discussed.
Composition and biodiversity of soil and root-associated microbiome in Vitis vinifera cultivar Lambrusco distinguish the microbial terroir of the Lambrusco DOC protected designation of origin area on a local scale
Authors: Nanetti Enrico , Palladino Giorgia , Scicchitano Daniel , Trapella Giulia , Cinti Nicolò , Fabbrini Marco , Cozzi Alice , Accetta Giovanni , Tassini Carlo , Iannaccone Luigi , Candela Marco , Rampelli Simone 
Published: February 2023

IntroductionWines produced from the same grape cultivars but in different locations possess distinctive qualities leading to different consumer’s appreciation, preferences, and thus purchase choices. Here, we explore the possible importance of microbiomes at the soil–plant interface as a determinant of the terroir properties in grapevine production, which confer specific growth performances and wine chemo-sensory properties at the local scale.MethodsIn particular, we investigated the variation in microbial communities associated with the roots of Vitis vinifera cultivar Lambrusco, as well as with surrounding bulk soils, in different vineyards across the “Consorzio Tutela Lambrusco DOC” protected designation of origin area (PDO, Emilia Romagna, Italy), considering viticultural sites located both inside and outside the consortium in two different seasons (June and November 2021).ResultsAccording to our findings, rhizospheric and soil microbiomes show significant structural differences in relation to the sampling site, regardless of seasonality, while endophytic microbiomes seem to be completely unaffected by such variables. Furthermore, a deeper insight into the microbial terroir of PDO areas highlighted the presence of some rhizospheric microorganisms enriched inside the consortium and characterizing the PDO regardless of both sampling season and farming strategy. These include Bacillus, Paenibacillus, and Azospirillum, which are all well-known plant growth-promoting bacteria.DiscussionTaken together, our results suggest a connection between soil and root microbiomes of V. vinifera cultivar Lambrusco and the local designation of origin, emphasizing the potential role of PDO-enriched plant growth-promoting bacteria in vine growing and final quality of the Lambrusco DOC wine.
Using the Jurkat reporter T cell line for evaluating the functionality of novel chimeric antigen receptors
Authors: Jahan Farhana , Koski Jan , Schenkwein Diana , Ylä-Herttuala Seppo , Göös Helka , Huuskonen Sini , Varjosalo Markku , Maliniemi Pilvi , Leitner Judith , Steinberger Peter , Bühring Hans-Jörg , Vettenranta Kim , Korhonen Matti 
Published: February 2023

Background: T cells that are genetically modified with chimeric antigen receptor (CAR) hold promise for immunotherapy of cancer. Currently, there are intense efforts to improve the safety and efficacy of CAR T cell therapies against liquid and solid tumors. Earlier we designed a novel CAR backbone (FiCAR) where the spacer is derived from immunoglobulin (Ig) -like domains of the signal-regulatory protein alpha (SIRPα). However, the analysis of novel CAR using primary T cells is slow and laborious.Methods: To explore the versatility of the CAR backbone, we designed a set of variant FiCARs with different spacer lengths and targeting antigens. To expedite the analysis of the novel CARs, we transduced the FiCAR genes using lentiviruses into Jurkat reporter T cells carrying fluorescent reporter genes. The expression of fluorescent markers in response to FiCAR engagement with targets was analyzed by flow cytometry, and cytotoxicity was evaluated using killing assays. Furthermore, the killing mechanisms that are employed by FiCAR-equipped Jurkat T cells were investigated by flow cytometry, and the intracellular pathways involved in signaling by FiCAR were analyzed by phosphoproteomic analysis using mass spectrometry.Results: Seven different CARs were designed and transduced into Jurkat reporter cells. We show that the SIRPα derived FiCARs can be detected by flow cytometry using the SE12B6A4 antibody recognizing SIRPα. Furthermore, FiCAR engagement leads to robust activation of NFκβ and NFAT signaling, as demonstrated by the expression of the fluorescent reporter genes. Interestingly, the Jurkat reporter system also revealed tonic signaling by a HER-2 targeting FiCAR. FiCAR-equipped Jurkat T cells were cytotoxic in cocultures with target cells and target cell engagement lead to an upregulation of CD107a on the Jurkat reporter T cell surface. Phosphoproteomic analyses confirmed signal transduction via the intracellular CD28/CD3ζ sequences upon the interaction of the FiCAR1 with its antigen. In addition, downstream signaling of CD3ζ/ZAP70- SLP-76-PLCγ, PI3K–AKT–NFκB pathways and activation of NFAT and AP-1 were observed.Conclusion: We conclude that the FiCAR backbone can be shortened and lengthened at will by engineering it with one to three SIRPα derived Ig-like domains, and the FiCARs are functional when equipped with different single chain variable fragment target binding domains. The Jurkat reporter system expedites the analysis of novel CARs as to their expression, signaling function, evaluation of tonic signaling issues and cytotoxic activity.
Correlation between retinal structure and brain multimodal magnetic resonance imaging in patients with Alzheimer’s disease
Authors: Hao Xiaoli , Zhang Weiwei , Jiao Bin , Yang Qijie , Zhang Xinyue , Chen Ruiting , Wang Xin , Xiao Xuewen , Zhu Yuan , Liao Weihua , Wang Dongcui , Shen Lu 
Published: February 2023

BackgroundThe retina imaging and brain magnetic resonance imaging (MRI) can both reflect early changes in Alzheimer’s disease (AD) and may serve as potential biomarker for early diagnosis, but their correlation and the internal mechanism of retinal structural changes remain unclear. This study aimed to explore the possible correlation between retinal structure and visual pathway, brain structure, intrinsic activity changes in AD patients, as well as to build a classification model to identify AD patients.MethodsIn the study, 49 AD patients and 48 healthy controls (HCs) were enrolled. Retinal images were obtained by optical coherence tomography (OCT). Multimodal MRI sequences of all subjects were collected. Spearman correlation analysis and multiple linear regression models were used to assess the correlation between OCT parameters and multimodal MRI findings. The diagnostic value of combination of retinal imaging and brain multimodal MRI was assessed by performing a receiver operating characteristic (ROC) curve.ResultsCompared with HCs, retinal thickness and multimodal MRI findings of AD patients were significantly altered (p &lt; 0.05). Significant correlations were presented between the fractional anisotropy (FA) value of optic tract and mean retinal thickness, macular volume, macular ganglion cell layer (GCL) thickness, inner plexiform layer (IPL) thickness in AD patients (p &lt; 0.01). The fractional amplitude of low frequency fluctuations (fALFF) value of primary visual cortex (V1) was correlated with temporal quadrant peripapillary retinal nerve fiber layer (pRNFL) thickness (p &lt; 0.05). The model combining thickness of GCL and temporal quadrant pRNFL, volume of hippocampus and lateral geniculate nucleus, and age showed the best performance to identify AD patients [area under the curve (AUC) = 0.936, sensitivity = 89.1%, specificity = 87.0%].ConclusionOur study demonstrated that retinal structure change was related to the loss of integrity of white matter fiber tracts in the visual pathway and the decreased LGN volume and functional metabolism of V1 in AD patients. Trans-synaptic axonal retrograde lesions may be the underlying mechanism. Combining retinal imaging and multimodal MRI may provide new insight into the mechanism of retinal structural changes in AD and may serve as new target for early auxiliary diagnosis of AD.
Flow diverters in the treatment of unruptured vertebral artery dissecting aneurysm: A single-center experience
Authors: Lu Xiaoyang , Zhang Yuansheng , Zhou Hu , Jian Lipeng , Yin Shi , Li Tao , Huang Wei 
Published: February 2023

ObjectiveTo evaluate the efficacy and safety of flow diverters (FD) in the treatment of vertebral artery dissecting aneurysm (VADA).MethodsA total of 16 patients with 17 unruptured VADAs treated with FD from January 2017 to May 2021 were included. Data of clinical outcomes and radiographic examination were collected and assessed by the modified Rankin Scale (mRS) and O'Kelly-Marotta (OKM) grading scale.ResultsAll patients were treated with a single FD. No perioperative complications occurred. The mean age was 55.1 years old. The mean size of the aneurysm was 10.4 mm. All patients had a favorable occlusion (OKM D + C3) result and the complete occlusion rate in the 6th month was 66.7% (OKM D). The mean clinical follow-up time was 7.8 months, and all patients had a good clinical outcome (mRS = 0). No procedure-related complication occurred at the last follow-up time.ConclusionFD is an effective and safe tool for treating unruptured VADA. Long-term prospective studies with a large sample are still needed to confirm these findings in the future.
The clinical and neurocognitive functional changes with awake brain mapping for gliomas invading eloquent areas: Institutional experience and the utility of The Montreal Cognitive Assessment
Authors: Wang Yuan , Guo Shaochun , Wang Na , Liu Jinghui , Chen Fan , Zhai Yulong , Wang Yue , Jiao Yang , Zhao Wenjian , Fan Chao , Xue Yanrong , Gao GuoDong , Ji Peigang , Wang Liang 
Published: February 2023

ObjectiveAwake craniotomy with intraoperative brain functional mapping effectively reduces the potential risk of neurological deficits in patients with glioma invading the eloquent areas. However, glioma patients frequently present with impaired neurocognitive function. The present study aimed to investigate the neurocognitive and functional outcomes of glioma patients after awake brain mapping and assess the experience of a tertiary neurosurgical center in China over eight years.MethodsThis retrospective study included 80 patients who underwent awake brain mapping for gliomas invading the eloquent cortex between January 2013 and December 2021. Clinical and surgical factors, such as the extent of resection (EOR), perioperative Karnofsky Performance Score (KPS), progression-free survival (PFS), and overall survival (OS), were evaluated. We also used the Montreal Cognitive Assessment (MoCA) to assess the neurocognitive status changes.ResultsThe most frequently observed location of glioma was the frontal lobe (33/80, 41.25%), whereas the tumor primarily invaded the language-related cortex (36/80, 45%). Most patients had supratotal resection (11/80, 13.75%) and total resection (45/80, 56.25%). The median PFS was 43.2 months, and the median OS was 48.9 months in our cohort. The transient (less than seven days) neurological deficit rate was 17.5%, whereas the rate of persistent deficit (lasting for three months) was 15%. At three months of follow-up, most patients (72/80, 90%) had KPS scores &gt; 80. Meanwhile, compared to the preoperative baseline tests, the changes in MoCA scores presented significant improvements at discharge and three months follow-up tests.ConclusionAwake brain mapping is a feasible and safe method for treating glioma invading the eloquent cortex, with the benefit of minimizing neurological deficits, increasing EOR, and extending survival time. The results of MoCA test indicated that brain mapping plays a critical role in preserving neurocognitive function during tumor resection.
Humoral Effect of SARS-CoV-2 mRNA vaccination with booster dose in solid tumor patients with different anticancer treatments
Authors: Piubelli Chiara , Valerio Matteo , Verzè Matteo , Nicolis Fabrizio , Mantoan Carlotta , Zamboni Sonia , Perandin Francesca , Rizzi Eleonora , Tais Stefano , Degani Monica , Caldrer Sara , Gobbi Federico Giovanni , Bisoffi Zeno , Gori Stefania 
Published: February 2023

IntroductionCancer patients are at risk for serious complications in case of SARS-CoV-2 infection. In these patients SARS-CoV-2 vaccination is strongly recommended, with the preferential use of mRNA vaccines. The antibody response in cancer patients is variable, depending on the type of cancer and antitumoral treatment. In solid tumor patients an antibody response similar to healthy subjects has been confirmed after the second dose. Only few studies explored the duration of immunization after the two doses and the effect of the third dose.MethodsIn our study we explored a cohort of 273 solid tumor patients at different stages and treated with different anticancer therapies.Results and DiscussionOur analysis demonstrated that the persistence of the neutralizing antibody and the humoral response after the booster dose of vaccine was not dependent on either the tumor type, the stage or type of anticancer treatment.