bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunophenotypic features of molecular subtypes of breast cancer
Authors: Chulkova S. V. , Sholokhova E. N. , Poddubnaya I. V. , Artamonova E. V. , Semyanikhina A. V. , Stylidi I. S. , Tupitsyn N. N. 
Published: November 2022

Introduction. Currently, immunotropic drugs are used in the modern strategy of cancer treatment. Importance is given to immunological markers of the tumor, which may be associated with the prognosis of the disease, the effectiveness of treatment. Therefore, the study of tumor immunophenotype is one of the leading scientific directions. Of particular interest is the study of the immunophenotypic characteristics of breast cancer depending on its biological subtype.Purpose. To evaluate the frequency of expression of HLA-I, HLA-II, CD71, MUC1, Pgp170 molecules by breast cancer cells and determine their relationship with the molecular biological subtype of the tumor.Materials and methods. This study included 120 patients with breast cancer who received treatment at the National Medical Research Centre of Oncology n. a. N. N. Blokhin (Moscow, Russia). Tumor stages II and III prevailed: 56.7 % and 33.4 %, respectively. A moderate degree of differentiation (G2) was more often noted. The luminal subtype was 58.3 % (n = 70), non-luminal – in 41.7 % (n = 50). Immunophenotyping of the primary tumor was performed by immunofluorescence on cryostat sections. The reaction was evaluated using a Zeiss luminescent microscope (Axioskop, Germany). The frequency of expression of HLA-I and class II molecules was studied depending on the clinical and morphological characteristics of breast cancer. The frequency of expression of HLA-I, HLA-II, CD71, MUC1, Pgp170 molecules depending on the molecular subtype of breast cancer was studied.Results. The absence of molecules of the major histocompatibility complex of class I and II on breast cancer cells was found in 89.6 % of the samples. The monomorphic expression was observed in 23.4 % of cases. In the luminal subtype, HLA-II class molecules were expressed more often: in total, mosaic and monomorphic types of reactions were observed in 30.5 % (20/65) of cases. With non-luminal – 20.0 % (10/47) of cases. The frequency of expression of the transferrin receptor is significantly higher in the luminal subtype than in the non-luminal subtype: 85.9 % (n = 5) and 65.2 % (n = 30), p = 0.011. Luminal breast cancer cells express transferrin receptors predominantly monomorphically: 75.4 % (n = 49) vs 43.5 % (n = 20) in the non-luminal subtype, p = 0.003. The MUC 1 expressing monomorphically tumors is higher in luminal cancer: 83.3 % (n = 35) versus 65 % (n = 26) in the non-luminal subtype. Monomorphic expression of Pgp170 is more often observed in luminal breast cancer.Conclusion. Luminal breast cancer is characterized by unfavorable prognostic immunophenotypic features. In the luminal subtype, expression of CD71 is more often observed, predominantly monomorphic. In the non-luminal subtype, expression of Pgp170 is observed less frequently. No statistically significant differences between the molecular subtypes in terms of the level of expression of HLA-I and class II molecules were found.
Impact of multiple drug-resistant Gram-negative bacterial bacteraemia on infected pancreatic necrosis patients
Authors: Wu Di , Jia Yan , Cai Wenhao , Huang Yilin , Kattakayam Arjun , Latawiec Diane , Sutton Robert , Peng Jie 
Published: November 2022

IntroductionMultiple drug-resistant Gram-negative bacterial (MDR-GNB) bacteraemia poses a serious threat to patients in hospital. Infected pancreatic necrosis (IPN) patients are a vulnerable population to infectious complications during hospitalization. This study aims to evaluate the impact of MDR Gram-negative bacteraemia on IPN patients.MethodsA case–control study was performed with data collected from 1 January 2016 to 1 July 2022 in a Chinese tertiary teaching hospital. Clinical data of the IPN patients with MDR-GNB bacteraemia were analyzed and compared to those of a matched control group without MDR-GNB bacteraemia (case–control ratio of 1:2). Comparisons were performed between with/without MDR-GNB bacteraemia and different severities of acute pancreatitis (AP). Independent predictors of overall mortality were identified via univariate and multivariate binary logistic regression analyses.ResultsMDR-GNB bacteraemia was related to a higher mortality rate (62.5% vs. 8.3%, p &lt; 0.001). Severe AP combined with MDR-GNB bacteraemia further increased mortality up to 81.3% (p = 0.025). MDR-GNB bacteraemia (odds ratio (OR) = 8.976, 95% confidence interval (CI) = 1.805 –44.620, p = 0.007) and severe AP (OR = 9.414, 95% CI = 1.742 –50.873, p = 0.009) were independent predictors of overall mortality. MDR- Klebsiella pneumoniae was the most common causative pathogen.ConclusionA higher mortality rate in IPN patients was related to MDR-GNB bacteraemia and further increased in severe AP patients combined with MDR-GNB bacteraemia.
Changed cerebral function and morphology serve as neuroimaging evidence for subclinical type 2 diabetic polyneuropathy
Authors: Zhao Lin-Mei , Chen Xin , Zhang You-Ming , Qu Min-Li , Selvarajah Dinesh , Tesfaye Solomon , Yang Fang-Xue , Ou Chu-Ying , Liao Wei-Hua , Wu Jing 
Published: November 2022

IntroductionCentral and peripheral nervous systems are all involved in type 2 diabetic polyneuropathy mechanisms, but such subclinical changes and associations remain unknown. This study aims to explore subclinical changes of the central and peripheral and unveil their association.MethodsA total of 55 type-2 diabetes patients consisting of symptomatic (n = 23), subclinical (n = 12), and no polyneuropathy (n = 20) were enrolled in this study. Cerebral morphology, function, peripheral electrophysiology, and clinical information were collected and assessed using ANOVA and post-hoc analysis. Gaussian random field correction was used for multiple comparison corrections. Pearson/Spearman correlation analysis was used to evaluate the association of the cerebral with the peripheral.ResultsWhen comparing the subclinical group with no polyneuropathy groups, no statistical differences were shown in peripheral evaluations except amplitudes of tibial nerves. At the same time, functional connectivity from the orbitofrontal to bilateral postcentral and middle temporal cortex increased significantly. Gray matter volume of orbitofrontal and its functional connectivity show a transient elevation in the subclinical group compared with the symptomatic group. Besides, gray matter volume in the orbitofrontal cortex negatively correlated with the Neuropathy Symptom Score (r = -0.5871, p &lt; 0.001), Neuropathy Disability Score (r = -0.3682, p = 0.009), and Douleur Neuropathique en 4 questions (r = -0.4403, p = 0.003), and also found correlated positively with bilateral peroneal amplitude (r &gt; 0.4, p &lt; 0.05) and conduction velocities of the right sensory sural nerve(r = 0.3181, p = 0.03). Similarly, functional connectivity from the orbitofrontal to the postcentral cortex was positively associated with cold detection threshold (r = 0.3842, p = 0.03) and negatively associated with Neuropathy Symptom Score (r = -0.3460, p = 0.01).DiscussionFunction and morphology of brain changes in subclinical type 2 diabetic polyneuropathy might serve as an earlier biomarker. Novel insights from subclinical stage to investigate the mechanism of type 2 diabetic polyneuropathy are warranted.
The ADRENAL score: A comprehensive scoring system for standardized evaluation of adrenal tumor
Authors: Zhou Xiaochen , Li Xuwen , Fu Bin , Liu Weipeng , Zhang Cheng , Xia Yu , Gong Honghan , Zhu Lingyan , Lei Enjun , Kaplan Joshua , Deng Yaoliang , Eun Daniel , Wang Gongxian 
Published: November 2022

ObjectivesTo propose an original and standardized scoring system to quantify the functional and anatomical characteristics of adrenal tumor.Materials and methodsFour groups of consecutive adrenalectomies (n = 458) with heterogeneity in tumor characteristics and surgical approaches, including 212 laparoscopic cases (Group 1) and 105 robotic cases (Group 2) from The First Affiliated Hospital of Nanchang University, 28 robotic cases from Temple University Hospital (Group 3) and 113 laparoscopic cases from The First Affiliated Hospital of Guangxi Medical University (Group 4). All patients were followed up for 4.5 to 5.5 years. Six parameters including functional status or suspicion of malignancy, tumor size, relationship to adjacent organs, intratumoral enhancement on CT, nearness of the tumor to major vessels and body mass index were assessed and scored on a 0, 1 and 2 points scale. Correlation between the sum of the 6 scores and tumor laterality (ADRENAL score) verse operative time (OT), estimated blood loss (EBL), perioperative complications, transfusion, conversion and length of hospital stay was analyzed.ResultsADRENAL score was a strong predictor of both OT and EBL in all four groups (p &lt; 0.05 for all tests). In Group 2 and 4, higher ADRENAL score seemed to correlate with longer hospital stay. No statistically significant correlation between ADRENAL score and complication, transfusion or conversion was noted yet.ConclusionsADRENAL score appears to be a valid predictor of surgical outcomes. It may provide a common reference for adrenal surgery training program, preoperative risk assessment and stratified comparative analysis of adrenal surgeries via different techniques and approaches.
In patients with primary Sjögren’s syndrome innate-like MAIT cells display upregulated IL-7R, IFN-γ, and IL-21 expression and have increased proportions of CCR9 and CXCR5-expressing cells
Authors: Hinrichs Anneline C. , Kruize Aike A. , Leavis Helen L. , van Roon Joel A. G. 
Published: November 2022

IntroductionMucosal-associated invariant T (MAIT) cells might play a role in B cell hyperactivity and local inflammation in primary Sjögren’s syndrome (pSS), just like previously studied mucosa-associated CCR9+ and CXCR5+ T helper cells. Here, we investigated expression of CCR9, CXCR5, IL-18R and IL-7R on MAIT cells in pSS, and assessed the capacity of DMARDs to inhibit the activity of MAIT cells.MethodsCirculating CD161+ and IL-18Rα+ TCRVα7.2+ MAIT cells from pSS patients and healthy controls (HC) were assessed using flow cytometry, and expression of CCR9, CXCR5, and IL-7R on MAIT cells was studied. Production of IFN-γ and IL-21 by MAIT cells was measured upon IL-7 stimulation in the presence of leflunomide (LEF) and hydroxychloroquine (HCQ).ResultsThe numbers of CD161+ and IL-18Rα+ MAIT cells were decreased in pSS patients compared to HC. Relative increased percentages of CD4 MAIT cells in pSS patients caused significantly higher CD4/CD8 ratios in MAIT cells. The numbers of CCR9 and CXCR5-expressing MAIT cells were significantly higher in pSS patients. IL-7R expression was higher in CD8 MAIT cells as compared to all CD8 T cells, and changes in IL-7R expression correlated to several clinical parameters. The elevated production of IL-21 by MAIT cells was significantly inhibited by LEF/HCQ treatment.ConclusionCirculating CD161+ and IL-18Rα+ MAIT cell numbers are decreased in pSS patients. Given their enriched CCR9/CXCR5 expression this may facilitate migration to inflamed salivary glands known to overexpress CCL25/CXCL13. Given the pivotal role of IL-7 and IL-21 in inflammation in pSS this indicates a potential role for MAIT cells in driving pSS immunopathology.
High-resolution variability of dissolved and suspended organic matter in the Cape Verde Frontal Zone
Authors: Campanero Rubén , Burgoa Nadia , Fernández-Castro Bieito , Valiente Sara , Nieto-Cid Mar , Martínez-Pérez Alba M. , Gelado-Caballero María Dolores , Hernández-Hernández Nauzet , Marrero-Díaz Ángeles , Machín Francisco , Rodríguez-Santana Ángel , Hernández-García Inés , Delgado-Huertas Antonio , Martínez-Marrero Antonio , Arístegui Javier , Álvarez-Salgado Xosé Antón 
Published: November 2022

Distributions of dissolved (DOM) and suspended (POM) organic matter, and their chromophoric (CDOM) and fluorescent (FDOM) fractions, are investigated at high resolution (&lt; 10 km) in the Cape Verde Frontal Zone (CVFZ) during fall 2017. In the epipelagic layer (&lt; 200 m), meso- and submesoscale structures (meanders, eddies) captured by the high resolution sampling dictate the tight coupling between physical and biogeochemical parameters at the front. Remarkably, fluorescent humic-like substances show relatively high fluorescence intensities between 50 and 150 m, apparently not related to local mineralization processes. We hypothesize that it is due to the input of Sahara dust, which transports highly re-worked DOM with distinctive optical properties. In the mesopelagic layer (200-1500 m), our results suggest that DOM and POM mineralization occurs mainly during the transit of the water masses from the formation sites to the CVFZ. Therefore, most of the local mineralization seems to be due to fast-sinking POM produced in situ or imported from the Mauritanian upwelling. These local mineralization processes lead to the production of refractory CDOM, an empirical evidence of the microbial carbon pump mechanism. DOM released from these fast-sinking POM is the likely reason behind the observed columns of relatively high DOC surrounded by areas of lower concentration. DOM and POM dynamics in the CVFZ has turned out to be very complex, in parallel to the complexity of meso- and submesoscale structures present in the area. On top of this high resolution variability, the input of Sahara dust or the release of DOM from sinking particles have been hypothesized to explain the observed distributions.
Understanding the impact of environmental variability and fisheries on the red sea urchin population in Baja California
Authors: Medellín–Ortiz Alfonso , Montaño–Moctezuma Gabriela , Álvarez–Flores Carlos , Santamaría-del-Ángel Eduardo , García–Nava Hector , Beas–Luna Rodrigo , Cavanaugh Kyle 
Published: November 2022

IntroductionThe red sea urchin fishery is one of the most important fisheries in Baja California and the only urchin fishery in México; yet little is known on understanding how local, regional, and oceanic environmental variability may affect red sea urchin populations. MethodsWe analyzed how food availability, predator abundance and environmental variability could affect red sea urchin populations developing generalized linear models under different temperature conditions: Pre-heat wave, heat wave, and post–heatwave, including sites where sea surface temperature was above, below, and on average. Models included: a) biological variables: Macrocystis pyrifera (kelp) biomass, red sea urchin (Mesocentrotus franciscanus) density, sheephead (Semicossyphus pulcher), kelp bass (Paralabrax clathratus) and spiny lobster (Panulirus interruptus) catches, and b) oceanographic variables: sea surface temperature, wave power, upwelling index, multivariate El Niño index and North Pacific Gyre Oscillation index. ResultsBetween 65 and 82% of the variability observed in red sea urchin populations was explained by different combinations of variables, depending on the thermal condition analyzed. We observed that local environmental variability, such as food availability and predator harvest are highly important factors in determining red sea urchin population changes, compared to regional and oceanic scale variables such as upwelling, El Niño, or the North Pacific Gyre Oscillation. Results show that the relative importance of these variables changed depending on the spatial and temporal scale being analyzed, meaning that under “normal or average” conditions one set of variables is important, compared to extreme environmental conditions such as El Niño or “the Blob” when a different set of variables explained the observed variability. Urchin predators’ catches were correlated with urchin density during the pre-heatwave scenario, suggesting that under “average temperature” conditions the effect of fishing on predators, and consequently on urchin density is higher than local temperature, the most important variable during warm conditions. DiscussionThis study suggests that in Baja California, red sea urchin harvest has become the most important red sea urchin population control, so efforts should be encouraged and supported by state and federal agencies to promote more resilient ecosystems in the face of environmental uncertainty. Improving management of the commercial species that inhabit kelp forest, could yield benefits for the entire ecosystem, fishers, and the red sea urchin population in Mexico.
Serum IL-12p40: A novel biomarker for early prediction of minimal change disease relapse following glucocorticoids therapy
Authors: Bai Mengqiu , Zhang Jian , Su Xinwan , Yao Xi , Li Heng , Cheng Jun , Mao Jianhua , Li Xiayu , Chen Jianghua , Lin Weiqiang 
Published: November 2022

BackgroundMinimal change disease (MCD) has a high recurrence rate, but currently, no biomarker can predict its recurrence. To this end, this study aimed at identifying potential serum cytokines as valuable biomarkers for predicting the risk of MCD recurrence.Materials and methodsRaybiotech 440 cytokine antibody microarray was used to detect the serum samples of eight relapsed, eight non-relapsed MCD patients after glucocorticoid treatment, and eight healthy controls. The differentially expressed cytokines were confirmed by enzyme-linked immunosorbent assay (ELISA) with serum samples from 29 non-relapsed and 35 relapsed MCD patients. The study used the receiver operating characteristic (ROC) curve analysis to investigate the sensitivity and specificity of a serum biomarker for predicting the MCD relapse.ResultsSerum IL-12p40 levels increased significantly in the relapsed group. The Area Under the ROC Curve (AUC) of IL-12p40 was 0.727 (95%CI: 0.597–0.856; P &lt; 0.01). The RNA-sequencing analysis and qPCR assay performed on the IL-12 treated mouse podocytes and the control group showed increased expression of podocyte damage genes, such as connective tissue growth factor (CTGF), matrix metallopeptidase 9 (MMP9), secreted phosphoprotein 1 (SPP1), and cyclooxygenase-2 (COX-2) in the former group.ConclusionIL-12p40 may serve as a new biomarker for predicting the risk of MCD recurrence after glucocorticoid treatment, and it may be involved in the pathogenesis and recurrence of MCD.
Identification of diagnostic gene biomarkers related to immune infiltration in patients with idiopathic pulmonary fibrosis based on bioinformatics strategies
Authors: Dai Xiangdong , Yang Zhihua , Zhang Wenjing , Liu Shuai , Zhao Qianru , Liu Tao , Chen Lu , Li Lin , Wang Yi , Shao Rui 
Published: November 2022

ObjectiveThe study aims to identify potential diagnostic markers of idiopathic pulmonary fibrosis (IPF) and analyze the significance of immune cell infiltration in this pathology.Materials and methodsDownload two publicly available gene expression profiles (GSE10667 and GSE24206 datasets) from the GEO database including 48 Idiopathic pulmonary fibrosis (IPF) samples and 21 human control samples and select for distinctly expressed genes (DEG) from them. Lasso regression model and support vector machine recursive feature elimination S,V,R,F analysis were used to check candidate biomarkers. The area under the subject’s work characteristic curve (AUC) value is used to evaluate its recognition ability. The GSE53845 dataset (40 IPF patients and 8 controls) continue to validate the expression level and diagnostic value of biomarkers in IPF. Comprehensive analysis of immune infiltrated cells of IPF was performed using R software and immune cell infiltration estimation analysis tool- deconvolution algorithm (CIBERSORT).Results43 DEGs were identified in total. The identified DEGs mostly involve pneumonia, lung disease, collagen disease, obstructive pulmonary disease and other diseases. The activation of IL-17 signaling pathways, amoebic disease, interaction of viral proteins with cytokines and cytokine receptors, protein digestion and absorption, and flaccid hormone signaling pathways in IPF were different from the control group. The expression degree of CRTAC1, COL10A1, COMP, RPS4Y1, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 in IPF tissue were prominently higher than the normal group. Immune cell infiltration analysis showed that CRTAC1, COL10A1, COMP, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 were associated with monocytes, plasma cells, neutrophils, and regulatory (treg) T cells.ConclusionCRTAC1, COL10A1, COMP, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 can be used as diagnostic markers for IPF, providing new ideas for the future study of IPF occurrence and molecular mechanisms.
Genomic analysis of methicillin-resistant Staphylococcus aureus clonal complex 239 isolated from Danish patients with and without an international travel history
Authors: Coppens Jasmine , Xavier Basil Britto , Vlaeminck Jelle , Larsen Jesper , Lammens Christine , Van Puyvelde Sandra , Goossens Herman , Larsen Anders Rhod , Malhotra-Kumar Surbhi 
Published: November 2022

IntroductionInternational travel has been a major determinant for the introduction of pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) into naïve geographic areas. MRSA clonal complex 239 (CC239) is a highly virulent clone that is predominant in Asia. The objective of this study was to determine the geographic origin of MRSA CC239 isolates recovered from Danish cases with or without a history of international travel during 2004–2016.Materials and methodsHuman MRSA isolates with spa types t030 and t037 (n = 60) were obtained from the National Reference Laboratory for Antimicrobial Resistance. For each case, the following data were collected from notification forms: sex, age, isolation year, specimen source (screening swab or clinical sample), infection type, and international travel history. All isolates were whole-genome sequenced, and a comparative genome and phylogenetic analysis was performed.ResultsThe majority of isolates originated from skin and soft tissue (SST) infections and screening swabs. In 31 out of 60 cases reported international travel to different parts of the world. Fifty-four isolates belonged to CC239, including sequence type 239 (ST239) (n = 43), ST241 (n = 5), ST4377 (n = 2), ST4378 (n = 1), ST1465 (n = 1), ST343 (n = 1), and ST592 (n = 1). The majority of the CC239 MRSA isolates (40/54) belonged to well-known geographic clades, including the Asian (n = 12), Serbian (n = 11), South American (n = 2), and Turkish (n = 15). Most MRSA ST239 isolates belonging to the highly virulent Asian clade carried sasX and were recovered from individuals who had travelled to Asia, Africa and the Middle East.ConclusionOur data reveal multiple introductions of MRSA CC239 into Denmark through international travel, which highlights the importance of continued genomic surveillance of MRSA in persons returning from international travel to areas where MRSA is endemic.