bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeat controlled human malaria infection of healthy UK adults with blood-stage Plasmodium falciparum: Safety and parasite growth dynamics
Authors: Salkeld Jo , Themistocleous Yrene , Barrett Jordan R. , Mitton Celia H. , Rawlinson Thomas A. , Payne Ruth O. , Hou Mimi M. , Khozoee Baktash , Edwards Nick J. , Nielsen Carolyn M. , Sandoval Diana Muñoz , Bach Florian A. , Nahrendorf Wiebke , Ramon Raquel Lopez , Baker Megan , Ramos-Lopez Fernando , Folegatti Pedro M. , Quinkert Doris , Ellis Katherine J. , Poulton Ian D. , Lawrie Alison M. , Cho Jee-Sun , Nugent Fay L. , Spence Philip J. , Silk Sarah E. , Draper Simon J. , Minassian Angela M. 
Published: August 2022

In endemic settings it is known that natural malaria immunity is gradually acquired following repeated exposures. Here we sought to assess whether similar acquisition of blood-stage malaria immunity would occur following repeated parasite exposure by controlled human malaria infection (CHMI). We report the findings of repeat homologous blood-stage Plasmodium falciparum (3D7 clone) CHMI studies VAC063C (ClinicalTrials.gov NCT03906474) and VAC063 (ClinicalTrials.gov NCT02927145). In total, 24 healthy, unvaccinated, malaria-naïve UK adult participants underwent primary CHMI followed by drug treatment. Ten of these then underwent secondary CHMI in the same manner, and then six of these underwent a final tertiary CHMI. As with primary CHMI, malaria symptoms were common following secondary and tertiary infection, however, most resolved within a few days of treatment and there were no long term sequelae or serious adverse events related to CHMI. Despite detectable induction and boosting of anti-merozoite serum IgG antibody responses following each round of CHMI, there was no clear evidence of anti-parasite immunity (manifest as reduced parasite growth in vivo) conferred by repeated challenge with the homologous parasite in the majority of volunteers. However, three volunteers showed some variation in parasite growth dynamics in vivo following repeat CHMI that were either modest or short-lived. We also observed no major differences in clinical symptoms or laboratory markers of infection across the primary, secondary and tertiary challenges. However, there was a trend to more severe pyrexia after primary CHMI and the absence of a detectable transaminitis post-treatment following secondary and tertiary infection. We hypothesize that this could represent the initial induction of clinical immunity. Repeat homologous blood-stage CHMI is thus safe and provides a model with the potential to further the understanding of naturally acquired immunity to blood-stage infection in a highly controlled setting.Clinical Trial RegistrationClinicalTrials.gov, identifier NCT03906474, NCT02927145.
Development and validation of an interpretable 3 day intensive care unit readmission prediction model using explainable boosting machines
Authors: Hegselmann Stefan , Ertmer Christian , Volkert Thomas , Gottschalk Antje , Dugas Martin , Varghese Julian 
Published: August 2022

BackgroundIntensive care unit (ICU) readmissions are associated with mortality and poor outcomes. To improve discharge decisions, machine learning (ML) could help to identify patients at risk of ICU readmission. However, as many models are black boxes, dangerous properties may remain unnoticed. Widely used post hoc explanation methods also have inherent limitations. Few studies are evaluating inherently interpretable ML models for health care and involve clinicians in inspecting the trained model.MethodsAn inherently interpretable model for the prediction of 3 day ICU readmission was developed. We used explainable boosting machines that learn modular risk functions and which have already been shown to be suitable for the health care domain. We created a retrospective cohort of 15,589 ICU stays and 169 variables collected between 2006 and 2019 from the University Hospital Münster. A team of physicians inspected the model, checked the plausibility of each risk function, and removed problematic ones. We collected qualitative feedback during this process and analyzed the reasons for removing risk functions. The performance of the final explainable boosting machine was compared with a validated clinical score and three commonly used ML models. External validation was performed on the widely used Medical Information Mart for Intensive Care version IV database.ResultsThe developed explainable boosting machine used 67 features and showed an area under the precision-recall curve of 0.119 ± 0.020 and an area under the receiver operating characteristic curve of 0.680 ± 0.025. It performed on par with state-of-the-art gradient boosting machines (0.123 ± 0.016, 0.665 ± 0.036) and outperformed the Simplified Acute Physiology Score II (0.084 ± 0.025, 0.607 ± 0.019), logistic regression (0.092 ± 0.026, 0.587 ± 0.016), and recurrent neural networks (0.095 ± 0.008, 0.594 ± 0.027). External validation confirmed that explainable boosting machines (0.221 ± 0.023, 0.760 ± 0.010) performed similarly to gradient boosting machines (0.232 ± 0.029, 0.772 ± 0.018). Evaluation of the model inspection showed that explainable boosting machines can be useful to detect and remove problematic risk functions.ConclusionsWe developed an inherently interpretable ML model for 3 day ICU readmission prediction that reached the state-of-the-art performance of black box models. Our results suggest that for low- to medium-dimensional datasets that are common in health care, it is feasible to develop ML models that allow a high level of human control without sacrificing performance.
A study protocol for an observational cohort investigating cardiac transthyretin amyloidosis flow reserve before and after Tafamidis treatment: The AMYTRE study
Authors: Vançon Bastien , Bisson Arnaud , Courtehoux Maxime , Bernard Anne , Bailly Matthieu 
Published: August 2022

IntroductionAnginal symptoms and signs of ischemia have been reported in some patients with cardiac transthyretin amyloidosis (ATTR) without obstructive epicardial coronary artery disease (CAD). Few studies found that coronary microvascular dysfunction was highly prevalent in subjects with cardiac amyloidosis, even in the absence of epicardial CAD. The purpose of this study is to confirm the coronary microvascular dysfunction, and to go further with evaluation of the effect of Tafamidis on microvascular dysfunction after 24 months of treatment.Methods and analysisThis study is a multicentric, prospective, observational cohort study. Adult patients with confirmed ATTR cardiomyopathy seen in the nuclear medicine departments of three large referral centers and treated with Tafamidis will be included. At baseline, patients will have a clinical and echocardiography evaluation. They will undergo a dynamic rest/stress cardiac scintigraphy with flow and reserve measurements before and 24 months after Tafamidis introduction. The primary outcome of this study will be the variation of stress and rest myocardial blood flow and flow reserve between baseline and 24 months after treatment. The effect of Tafamidis will be assessed by an intention to treat analysis.Ethics and disseminationThe study has received the following approvals: Orleans Hospital Research Committee (CHRO-2021-05) and Sud-Mediterranée IV Regional Ethics Committee (21 06 02). Results will be made available to physicians, the funders, and other researchers.Clinical trial registration[https://clinicaltrials.gov/ct2/show/NCT05103943], identifier [NCT05103943].
Dry eye disease in patients with type II diabetes mellitus: A retrospective, population-based cohort study in Taiwan
Authors: Pan Li-Yen , Kuo Yu-Kai , Chen Tien-Hsing , Sun Chi-Chin 
Published: August 2022

PurposeTo investigate the risk and protective factors of dry eye disease (DED) in patients with type II diabetes mellitus (DM).DesignA retrospective cohort study using Chang- Gung research database collecting data from 2005 to 2020.MethodsPatients with type II DM were included, and those with previous ocular diseases were excluded. Ten thousand twenty nine developed DED (DED group), and 142,491 didn't (non-DED group). The possible risk and protective factors were compared and analyzed using the logistic regression model.ResultsA majority of the DED group were female with significantly higher initial and average glycated hemoglobin levels, and higher incidence of diabetic neuropathy and retinopathy. In conditional logistic regression model, advanced age was a risk factor. After adjusting for sex, age, and DM duration; average glycated hemoglobin level, diabetic neuropathy, retinopathy, and nephropathy with eGFR 30 ~ 59 and intravitreal injection, vitrectomy, pan-retinal photocoagulation, and cataract surgery were contributing factors of DED. Considering antihyperglycemic agents, DPP4 inhibitor, SGLT2 inhibitor, GLP-1 agonist, and insulin monotherapy and dual medications combining any two of the aforementioned agents were protective factors against DED compared with metformin alone. In the monotherapy group, SLGT2 inhibitor had the lowest odds ratio, followed by GLP1 agonist, DPP4 inhibitor, and insulin.ConclusionsDED in patients with DM is associated with female sex, advanced age, poor diabetic control, microvascular complications and receiving ocular procedures. GLP-1 agonist, SGLT-2 inhibitor, DPP4 inhibitor, and insulin are superior to metformin alone in preventing DM-related DED. A prospective randomized control trial is warranted to clarify our results.
PTBPs: An immunomodulatory-related prognostic biomarker in pan-cancer
Authors: Chen Chen , Shang Anquan , Gao Yuting , Huang Jingjuan , Liu Gege , Cho William C. , Li Dong 
Published: August 2022

Background: The polypyrimidine tract-binding protein (PTBP) nuclear ribonucleoprotein family of proteins, including PTBP1, PTBP2 and PTBP3, regulate the process of cell proliferation, differentiation, apoptosis and carcinogenesis. PTBPs exhibit oncogenic effects in certain tumors. However, the role of PTBPs in pan-cancer remains unclear. Our study examined the clinical significance and mechanism of PTBPs in pan-cancer.Methods: We compared the expression of PTBPs in paired and unpaired tissue samples from the Cancer Genome Atlas (TCGA) database. Univariate and multivariate Cox regression, Kaplan–Meier curves, and time-dependent receiver operating characteristic (ROC) curves were used to assess the prognostic significance of PTBPs in pan-cancer. The cBioPortal database also identified genomic abnormalities in PTBPs. TISIDB, TCGA, and Cellminer were used to investigate the relationship between PTBP expression and immune subtypes, immune checkpoint (ICP) genes, tumor mutational burden (TMB), microsatellite instability (MSI), tumor-infiltrating immune cells, and chemosensitivity. cBioPortal was used to search for PTBP co-expressing genes in pan-cancer, and GO and KEGG enrichment analyses were performed to search for PTBP-related signaling pathways.Results:PTBPs were shown to be widely upregulated in human tumor tissues. PTBP1 showed good prognostic value in ACC, KIRP, and LGG; PTBP2 in ACC and KICH; and PTBP3 in ACC, LGG, and PAAD, with AUC &gt;0.7. PTBPs were differentially expressed in tumor immune subtypes and had a strong correlation with tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment (TME). In addition, PTBP expressions were related to ICP, TMB, and MSI, suggesting that these three PTBPs may be potential tumor immunotherapeutic targets and predict the efficacy of immunotherapy. Enrichment analysis of co-expressed genes of PTBPs showed that they may be involved in alternative splicing, cell cycle, cellular senescence, and protein modification.Conclusion: PTBPs are involved in the malignant progression of tumors. PTBP1, PTBP2 and PTBP3 may be potential biomarkers for prognosis and immunotherapy in pan-cancer and may be novel immunotherapeutic targets.
Trimethylamine N-oxide promotes demyelination in spontaneous hypertension rats through enhancing pyroptosis of oligodendrocytes
Authors: Ji Xiaotan , Tian Long , Niu Shenna , Yao Shumei , Qu Chuanqiang 
Published: August 2022

BackgroundHypertension is a leading risk factor for cerebral small vessel disease (CSVD), a brain microvessels dysfunction accompanied by white matter lesions (WML). Trimethylamine N-oxide (TMAO), a metabolite of intestinal flora, is correlated with cardiovascular and aging diseases. Here, we explored the effect of TMAO on the demyelination of WML.MethodsSpontaneous hypertension rats (SHRs) and primary oligodendrocytes were used to explore the effect of TMAO on demyelination in vivo and in vitro. T2-weighted magnetic resonance imaging (MRI) was applied to characterize the white matter hyperintensities (WMH) in rats. TMAO level was evaluated using LC-MS/MS assay. The histopathological changes of corpus callosum were measured by hematoxylin-eosin and luxol fast blue staining. And the related markers were detected by IHC, IF and western blot assay. Mito Tracker Red probe, DCFH-DA assay, flow cytometry based on JC-1 staining and Annexin V-FITC/PI double staining were conducted to evaluate the mitochondrial function, intracellular ROS levels and cell apoptosis.ResultsSHRs exhibited stronger WMH signals and a higher TMAO level than age-matched normotensive Wistar-kyoto rats (WKY). The corpus callosum region of SHR showed decreased volumes and enhanced demyelination when treated with TMAO. Furthermore, TMAO significantly elevated ROS production and induced NLRP3 inflammasome and impairment of mitochondrial function of oligodendrocytes. More importantly, TMAO enhanced the pyroptosis-related inflammatory death of oligodendrocytes.ConclusionTMAO could cross the blood-brain barrier (BBB) and promote oligodendrocytes pyroptosis via ROS/NLRP3 inflammasome signaling and mitochondrial dysfunction to promote demyelination, revealing a new diagnostic marker for WML under hypertension.
Comprehensive germline and somatic genomic profiles of Chinese patients with biliary tract cancer
Authors: Yu Haipeng , Xu Yan , Gao Wei , Li Mei , He Ji’an , Deng Xiaoqian , Xing Wenge 
Published: August 2022

BackgroundBiliary tract cancer (BTC) is an uncommon but highly lethal malignancy with poor clinical outcomes. To promote the development of precision medicine for BTC, uncovering its genomic profile becomes particularly important. However, studies on the genomic feature of Chinese BTC patients remain insufficient.MethodsA total of 382 Chinese patients with BTC were enrolled in this study, including 71 with intrahepatic cholangiocarcinoma (ICC), 194 with extrahepatic cholangiocarcinoma (ECC), and 117 with gallbladder carcinoma (GBC). Genetic testing was performed by utilizing the next-generation sequencing (NGS) of 499 cancer-related genes and the results were compared to those of Western BTC patients (MSKCC cohorts).ResultsThe most prevalent genes were TP53 (51.6%), ARID1A (25.9%), KMT2C (24.6%), NCOR1 (17%), SMAD4 (15.2%), KRAS (14.9%), KMT2D (14.9%), ATM (14.1%), and APC (13.9%) in Chinese BTC patients. TP53, SMAD4, and APC were more prevalent in GBC, ECC, and ICC, respectively. In addition, 10.5% of Chinese BTC patients harbored pathogenic or likely pathogenic (P/LP) germline alterations in 41 genes, which were mainly related to DNA damage repair (DDR). Additionally, the genomic features of Chinese and Western BTC tumors were similar, with the exception of the notable difference in the prevalence of TP53, KRAS, IDH1, KMT2C, and SMAD4. Notably, Chinese BTC patients had high prevalence (57.1%) of actionable alterations, especially for those with ECC, and half (192/382) of them had somatic DDR alterations, with the prevalence of deleterious ones being significantly higher than their Western counterparts. Twenty-three percent of patients had a higher tumor mutational burden (TMB-H, over 10 mutations/MB), and TMB was significantly higher in those with deleterious DDR alterations and/or microsatellite instability-high. The most common mutational signature in BTC patients was Signature 1, and interestingly, Signatures 1, 4, and 26 were significantly associated with higher TMB level, but not with the survival of patients who had received immunotherapy in pan-cancer.ConclusionOur study elaborated the distinct germline and somatic genomic characteristics of Chinese BTC patients and identified clinically actionable alterations, highlighting the possibility for the development and application of precision medicine.
A cuproptosis and copper metabolism–related gene prognostic index for head and neck squamous cell carcinoma
Authors: Zhang Shuaiyuan , Zhang Lujin , Lu Huanzi , Yao Yihuan , Liu Xiaoyong , Hou Jingsong 
Published: August 2022

BackgroundThe purpose of this study was to identify the prognostic value of cuproptosis and copper metabolism–related genes, to clarify their molecular and immunological characteristics, and to elucidate their benefits in head and neck squamous cell carcinoma (HNSCC).MethodsThe details of human cuproptosis and copper metabolism–related genes were searched and filtered from the msigdb database and the latest literature. To identify prognostic genes associated with cuproptosis and copper metabolism, we used least absolute shrinkage and selection operator regression, and this coefficient was used to set up a prognostic risk score model. HNSCC samples were divided into two groups according to the median risk. Afterwards, the function and immune characteristics of these genes in HNSCC were analyzed.ResultsThe 14-gene signature was constructed to classify HNSCC patients into low-risk and high-risk groups according to the risk level. In the The Cancer Genome Atlas (TCGA) cohort, the overall survival (OS) rate of the high-risk group was lower than that of the low-risk group (P &lt; 0.0001). The area under the curve of the time-dependent Receiver Operator Characteristic (ROC) curve assessed the good performance of the genetic signature in predicting OS and showed similar performance in the external validation cohort. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment assays and Protein-Protein Interaction (PPI) protein networks have been used to explore signaling pathways and potential mechanisms that were markedly active in patients with HNSCC. Furthermore, the 14 cuproptosis and copper metabolism-related genes were significantly correlated with the immune microenvironment, suggesting that these genes may be linked with the immune regulation and development of HNSCC.ConclusionsOur results emphasize the significance of cuproptosis and copper metabolism as a predictive biomarker for HNSCC, and its expression levels seem to be correlated with immune- related features; thus, they may be a possible biomarker for HNSCC prognosis.
LncRNA-ENST00000543604 exerts a tumor-promoting effect via miRNA 564/AEG-1 or ZNF326/EMT and predicts the prognosis of and chemotherapeutic effect in colorectal cancer
Authors: Wang Weimin , Zhou Zhen , Dai Xiaojun , Wang Haibo , Jin Jun , Min Ke , Wang Yunfan , Lv Mengying , Liu Yanqing , Zhou Yan 
Published: August 2022

ObjectivesColorectal cancer(CRC) is a common malignant tumor. Recent studies have found that lncRNAs play an important role in the occurrence and development of colorectal cancer.MethodsBased on high-throughput sequencing results of fresh CRC tissues and adjacent tissues, we identified lncRNA-ENST00000543604 (lncRNA 604) as the research object by qRT-PCR in CRC tissues and cells. We explored the mechanism of lncRNA 604 action by using luciferin reporter, qRT-PCR and Western blot assays. Kaplan-Meier survival analysis and a Cox regression model were used to analyze the correlation of lncRNA 604 and its regulatory molecules with the prognosis of and chemotherapy efficacy in CRC patients.ResultsIn this study, we found that the expression levels of lncRNA 604 were increased in CRC. LncRNA 604 could promote CRC cell proliferation and metastasis through the miRNA 564/AEG-1 or ZNF326/EMT signaling axis in vivo and in vitro. LncRNA 604 could predict the prognosis of CRC and was an independent negative factor. LncRNA 604 exerted a synergistic effect with miRNA 564 or ZNF326 on the prognosis of CRC. LncRNA 604 could improve chemoresistance by increasing the expression of AEG-1, NF-κB, and ERCC1.ConclusionsOur study demonstrated that lncRNA 604 could promote the progression of CRC via the lncRNA 604/miRNA 564/AEG-1/EMT or lncRNA 604/ZNF326/EMT signaling axis. LncRNA 604 could improve chemoresistance by increasing drug resistance protein expression.
Surgery and chemotherapy cannot improve the survival of patients with early-stage mucosa-associated lymphoid tissue derived primary pulmonary lymphoma
Authors: Lin Huahang , Zhou Ke , Peng Zhiyu , Liang Linchuan , Cao Jie , Mei Jiandong 
Published: August 2022

BackgroundTo date, there is no treatment consensus on mucosa-associated lymphoid tissue (MALT) derived primary pulmonary lymphoma (PPL).MethodsWe identified patients with early-stage MALT-type PPL from the National Cancer Institute’s Surveillance, Epidemiology, and End Results program database. The patients were divided into four groups according to treatment modalities: None of surgery or chemotherapy (None) group, Surgery alone group, Chemotherapy alone (Chemo alone) group, and Surgery plus chemotherapy (Surgery + chemo) group. Overall survival (OS) and cancer-specific survival (CSS) were study endpoints. We performed Cox regression analyses, propensity score-matched analyses (PSM) and Kaplan-Meier (KM) survival curves to compare the survival among different groups.ResultsA total of 953 patients were included in our analysis with 302, 403, 175, and 73 cases in the None, Surgery alone, Chemo alone, and Surgery + chemo groups, respectively. In this cohort, the estimated 3-year, 5-year and 10-year OS rates were 86.95%, 78.91%, and 55.89%, respectively. Meanwhile, the estimated 3-year, 5-year and 10-year CSS rates were 96.71%, 93.73%, and 86.84%, respectively. Multivariate Cox regression analyses demonstrated that increasing age, tumors located in the lower lobe, and stage II were significant predictors of poorer OS while increasing age and tumors located in the bilateral lungs were associated with lower CSS. After PSM analyses, the KM survival curves showed no significant differences in OS or CSS among the four groups.ConclusionEarly-stage MALT-type PPL is indolent in nature. Neither surgery, chemotherapy nor a combination of surgery and chemotherapy can improve OS and CSS, suggesting that “watch and wait” may be a reasonable alternative.