bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of biomedical knowledge for recurrent glioblastoma using natural language processing deep learning models
Authors: Jang Bum-Sup , Park Andrew J. , Kim In Ah 
Published: October 2022

AbstractBackgroundEfficient exploration of knowledge for the treatment of recurrent glioblastoma (GBM) is critical for both clinicians and researchers. However, due to the large number of clinical trials and published articles, searching for this knowledge is very labor-intensive. In the current study, using natural language processing (NLP), we analyzed medical research corpora related to recurrent glioblastoma to find potential targets and treatments.MethodsWe fine-tuned the ‘SAPBERT’, which was pretrained on biomedical ontologies, to perform question/answering (QA) and name entity recognition (NER) tasks for medical corpora. The model was fine-tuned with the SQUAD2 dataset and multiple NER datasets designed for QA task and NER task, respectively. Corpora were collected by searching the terms “recurrent glioblastoma” and “drug target”, published from 2000 to 2020 in the Web of science (N = 288 articles). Also, clinical trial corpora were collected from ‘clinicaltrial.gov’ using the searching term of ‘recurrent glioblastoma” (N = 587 studies).ResultsFor the QA task, the model showed an F1 score of 0.79. For the NER task, the model showed F1 scores of 0.90 and 0.76 for drug and gene name recognition, respectively. When asked what the molecular targets were promising for recurrent glioblastoma, the model answered that RTK inhibitors or LPA-1 antagonists were promising. From collected clinical trials, the model summarized them in the order of bevacizumab, temozolomide, lomustine, and nivolumab. Based on published articles, the model found the many drug-gene pairs with the NER task, and we presented them with a circus plot and related summarization (https://github.com/bigwiz83/NLP_rGBM).ConclusionUsing NLP deep learning models, we could explore potential targets and treatments based on medical research and clinical trial corpora. The knowledge found by the models may be used for treating recurrent glioblastoma.
Characterization of pyruvate metabolism and citric acid cycle patterns predicts response to immunotherapeutic and ferroptosis in gastric cancer
Authors: Wang Xu , Xu Bing , Du Jing , Xia Jun , Lei Guojie , Zhou Chaoting , Hu Jiayu , Zhang Yinhao , Chen Sufeng , Shao Fangchun , Yang Jiyun , Li Yanchun 
Published: October 2022

Abstract
Background
Gastric cancer is one of the most common malignancies of the digestive system with a high lethal rate. Studies have shown that inherited and acquired mutations in pyruvate metabolism and citric acid cycle (P-CA) enzymes are involved in tumorigenesis and tumor development. However, it is unclear how different P-CA patterns affect the tumor microenvironment (TME), which is critical for cancer progression.

Methods
This study mainly concentrated on investigating the role of the P-CA patterns in multicellular immune cell infiltration of GC TME. First, the expression levels of P-CA regulators were profiled in GC samples from The Cancer Genome Atlas and Gene Expression Omnibus cohorts to construct a consensus clustering analysis and identify three distinct P-CA clusters. GSVA was conducted to reveal the different biological processes in three P-CA clusters. Subsequently, 1127 cluster-related differentially expressed genes were identified, and prognostic-related genes were screened using univariate Cox regression analysis. A scoring system was then set up to quantify the P-CA gene signature and further evaluate the response of the patients to the immunotherapy.

Results
We found that GC patients in the high P-CA score group had a higher tumor mutational burden, higher microsatellite instability, and better prognosis. The opposite was observed in the low P-CA score group. Interestingly, we demonstrated P-CA gene cluster could predict the sensitivity to immunotherapy and ferroptosis-induced therapy.

Conclusion
Collectively, the P-CA gene signature in this study exhibits potential roles in the tumor microenvironment and predicts the response to immunotherapeutic. The identification of these P-CA patterns may significantly accelerate the strategic development of immunotherapy for GC.
Impact of baseline renal function on the efficacy and safety of different Anticoagulants in Atrial Fibrillation Patients – A cohort study
Authors: Lee Wei-Chieh , Liao Ting-Wei , Fang Hsiu-Yu , Wu Po-Jui , Fang Yen-Nan , Chen Huang-Chung , Lin Yu-Sheng , Chang Shang-Hung , Liu Ping-Yen , Chen Mien-Cheng 
Published: October 2022

Abstract
Background
Vitamin K antagonists and different direct oral anticoagulants (DOACs) have different renal clearance rates. However, the impact of different stages of chronic renal impairment on the efficacy and safety of warfarin, dabigatran, rivaroxaban, apixaban, and edoxaban in atrial fibrillation (AF) patients remains unclear.

Methods
This study enrolled AF patients from the Chang Gung Research Database. The study endpoints included thromboembolic events, major/fatal bleeding, gastrointestinal (GI) bleeding and intracranial hemorrhage (ICH). The risks of time to study endpoints between groups were compared using a Cox proportional hazards regression model with adjustment.

Results
This study enrolled 3525 patients with moderate renal impairment (30 ≤ creatinine clearance (CrCl) < 60 mL/min), 2846 patients with mild renal impairment (60 ≤ CrCl < 90 mL/min) and 1153 patients with CrCl ≥ 90 mL/min. Over the 3.3 ± 0.9 years follow-up period, the cumulative thromboembolic events rates and the cumulative event rates of major/fatal bleeding and ICH did not differ among the warfarin and different DOAC groups at different stages of chronic renal impairment. The annual incidences of thromboembolic events, major/fatal bleeding, GI bleeding, and ICH were similar among the warfarin and different DOAC groups at different stages of renal impairment.

Conclusion
There did not appear to be major differences in bleeding or thromboembolic risk compared to warfarin in AF patients across a range of degree of renal failure when appropriate dose reductions of the DOACs are made.
ARID1A deficiency reverses the response to anti-PD(L)1 therapy in EGFR-mutant lung adenocarcinoma by enhancing autophagy-inhibited type I interferon production
Authors: Sun Dantong , Qian Haili , Wang Jinsong , Xie Tongji , Teng Fei , Li Junling , Xing Puyuan 
Published: October 2022

Abstract
Introduction
EGFR mutations in non-small cell lung cancer (NSCLC) are associated with a poor response to immune checkpoint inhibitors (ICIs), and only 20% of NSCLC patients harboring EGFR mutations benefit from immunotherapy. Novel biomarkers or therapeutics are needed to predict NSCLC prognosis and enhance the efficacy of ICIs in NSCLC patients harboring EGFR mutations, especially lung adenocarcinoma (LUAD) patients, who account for approximately 40–50% of all NSCLC cases.

Methods
An ARID1A-knockdown (ARID1A-KD) EGFR-mutant LUAD cell line was constructed using lentivirus. RNA-seq and mass spectrometry were performed. Western blotting and IHC were used for protein expression evaluation. Effects of 3-MA and rapamycin on cells were explored. Immunofluorescence assays were used for immune cell infiltration examination.

Results
ARID1A expression was negatively associated with immune cell infiltration and immune scores for ICIs in LUAD with EGFR mutations. In vitro experiments suggested that ARID1A-KD activates the EGFR/PI3K/Akt/mTOR pathway and inhibits autophagy, which attenuates the inhibition of Rig-I-like receptor pathway activity and type I interferon production in EGFR-mutant LUAD cells. In addition, 3-MA upregulated production of type I interferon in EGFR-mutant LUAD cells, with an similar effect to ARID1A-KD. On the other hand, rapamycin attenuated the enhanced production of type I interferon in ARID1A-KD EGFR-mutant LUAD cells. ARID1A function appears to influence the tumor immune microenvironment and response to ICIs.

Conclusion
ARID1A deficiency reverses response to ICIs in EGFR-mutant LUAD by enhancing autophagy-inhibited type I interferon production.
Management after initial surgery of nonfunctioning pituitary adenoma: surveillance, radiotherapy or surgery?
Authors: Charleux Thomas , Vendrely Véronique , Huchet Aymeri , Trouette Renaud , Ferrière Amandine , Tabarin Antoine , Jecko Vincent , Loiseau Hugues , Dupin Charles 
Published: October 2022

Abstract
Introduction
The first line of treatment for nonfunctioning pituitary adenoma (NFPA) is surgery. Adjuvant radiotherapy or surveillance and new treatment (second surgical operation or salvage radiotherapy) in case of recurrence are options discussed at the multidisciplinary tumor board. The purpose of this study was to evaluate the therapeutic outcome for each option.

Methods
The records of 256 patients followed with NFPA between 2007 and 2018 were retrospectively reviewed. Mean age at initial surgery was 55 years [18–86]. Post-operative MRI found a residual tumor in 87% of patients. Mean follow-up was 12.1 years [0.8–42.7].

Results
After initial surgery, 40 patients had adjuvant radiotherapy. At 5, 10 and 15 years progression-free survival (PFS) was significantly different after surgery alone (77%, 58% and 40%) compared to surgery and adjuvant radiotherapy (84%, 78% and 78%) (HR = 0.24 [0–0.53] p < 0.0005). Overall, after first, second or third surgical operation, 69 patients had adjuvant radiotherapy and 41 salvage radiotherapy. Five-year PFS was similar for adjuvant (90%) and salvage radiotherapy (97%) (p = 0.62). After a second surgical operation, 62% and 71% of patients were irradiated after 2 and 5 years respectively. The risk of corticotropic and thyrotropic deficiency rates were 38% and 59% after second or third surgical operation and 40% and 73% after radiotherapy. Brain tumors occurred in 4 patients: 1 meningioma present at initial surgery, and after radiotherapy, 1 neurinoma which appeared at 5 years, 1 glioblastoma at 13 years and 1 meningioma at 20 years.

Conclusion
Among patients treated by surgery for NFPA, a “wait-and-see” attitude should be an option since adjuvant radiotherapy is not superior to salvage radiotherapy. However, in case of recurrence or progression, the authors recommended delivery of salvage radiotherapy to avoid a second surgical operation.
Long-term survival after pulmonary metastasectomy in patients with esophageal squamous cell carcinoma with lung metastasis
Authors: Lo Chien-Ming , Chuang Kai-Hao , Lai Hsing-Hua , Chen Yu , Chen Li-Chun , Lu Hung-I , Chen Yen-Hao , Li Shau-Hsuan 
Published: October 2022

Abstract
Objectives
Esophageal squamous cell carcinoma with pulmonary metastasis has a poor prognosis, and the only treatment modality is systemic therapy such as chemotherapy. Previous studies showed that pulmonary metastasectomy may provide benefits and has been suggested in selected patients with colorectal cancer, renal cancer, and sarcoma. However, there were few literatures evaluating the impact and treatment outcome of pulmonary metastasectomy in esophageal squamous cell carcinoma patients with isolated lung metastases. Therefore, we conducted this study.

Methods
We retrospectively reviewed our patients with esophageal squamous cell carcinoma with pulmonary metastasis. Patients with extrapulmonary metastasis were excluded. We categorized them into two groups - the pulmonary resection group and the systemic treatment only group. We compared the overall survival and progression-free survival between groups, and also analyzed the surgical modality, which includes single or multiple port surgery.

Results
The analysis included 44 esophageal squamous cell carcinoma patients with lung metastasis. Among these 44 patients, 14 patients have received pulmonary metastasectomy, and 30 patients received systemic treatment only. Patients who received pulmonary metastasectomy had significantly better overall survival (p < 0.0001) and progression-free survival (p = 0.038) than those who received only systemic treatment. The one-year overall survival and progression-free survival were 100% and 48% in patients receiving pulmonary metastatectomy, and 49% and 33% in patients receiving only systemic treatment. Among 14 patients receiving pulmonary metastatectomy, 10 patients underwent single port surgery. There were no postoperative complications in these 14 patients.

Conclusion
Esophageal squamous cell carcinoma patients with lung metastasis who can receive pulmonary metastasectomy have better prognosis, and some patients can achieve long-term survival. Our findings suggest that aggressive pulmonary metastasectomy is suggested in esophageal squamous cell carcinoma patients with if no contraindication.

Visual Abstract
Key question: How about the role of pulmonary metastasectomy in esophageal squamous cell carcinoma patients with isolated lung metastasis?

Key findings
Patients who received pulmonary metastasectomy had better overall survival and progression-free survival than those who received only systemic treatment.

Take Home Message
Esophageal cancer with isolated pulmonary metastasis can be treated aggressively with pulmonary metastasectomy if no contraindication.
Combining deep sequencing and conventional molecular approaches reveals broad diversity and distribution of fleas and Bartonella in rodents and shrews from Arctic and Subarctic ecosystems
Authors: Buhler Kayla J. , Fernando Champika , Hill Janet E. , Galloway Terry , Carriere Suzanne , Fenton Heather , Fauteux Dominique , Jenkins Emily J. 
Published: October 2022

Abstract
Background
Bartonella are intracellular bacteria that are transmitted via animal scratches, bites and hematophagous arthropods. Rodents and their associated fleas play a key role in the maintenance of Bartonella worldwide, with > 22 species identified in rodent hosts. No studies have addressed the occurrence and diversity of Bartonella species and vectors for small mammals in Arctic and Subarctic ecosystems, which are increasingly impacted by invasive species and climate change.

Methods
In this study, we characterized the diversity of rodent fleas using conventional PCR targeting the mitochondrial cytochrome c oxidase II gene (COII) and Bartonella species in rodents and shrews (n = 505) from northern Canada using conventional PCR targeting the ITS (intergenic transcribed spacer) region and gltA (citrate synthase) gene. Metagenomic sequencing of a portion of the gltA gene was completed on a subset of 42 rodents and four rodent flea pools.

Results
Year, total summer precipitation the year prior to sampling, average minimum spring temperature and small mammal species were significant factors in predicting Bartonella positivity. Occurrence based on the ITS region was more than double that of the gltA gene and was 34% (n = 349) in northern red-backed voles, 35% (n = 20) in meadow voles, 37% (n = 68) in deer mice and 31% (n = 59) in shrews. Six species of Bartonella were identified with the ITS region, including B. grahamii, B. elizabethae, B. washoensis, Candidatus B. rudakovii, B. doshiae, B. vinsonii subsp. berkhoffii and subsp. arupensis. In addition, 47% (n = 49/105) of ITS amplicons had < 97% identity to sequences in GenBank, possibly due to a limited reference library or previously unreported species. An additional Bartonella species (B. heixiaziensis) was detected during metagenomic sequencing of the gltA gene in 6/11 rodents that had ITS sequences with < 97% identity in GenBank, highlighting that a limited reference library for the ITS marker likely accounted for low sequence similarity in our specimens. In addition, one flea pool from a northern red-backed vole contained multiple species (B. grahamii and B. heixiaziensis).

Conclusion
Our study calls attention to the usefulness of a combined approach to determine the occurrence and diversity of Bartonella communities in hosts and vectors.

Graphical Abstract
Prediction models for breast cancer-related lymphedema: a systematic review and critical appraisal
Authors: Lin Qiu , Yang Tong , Yongmei Jin , Die Ye Mao 
Published: October 2022

Abstract
Purpose
The development of risk prediction models for breast cancer lymphedema is increasing, but few studies focus on the quality of the model and its application. Therefore, this study aimed to systematically review and critically evaluate prediction models developed to predict breast cancer-related lymphedema.

Methods
PubMed, Web of Science, Embase, MEDLINE, CNKI, Wang Fang DATA, Vip Database, and SinoMed were searched for studies published from 1 January 2000 to 1 June 2021. And it will be re-run before the final analysis. Two independent investigators will undertake the literature search and screening, and discrepancies will be resolved by another investigator. The Prediction model Risk Of Bias Assessment Tool will be used to assess the prediction models’ risk of bias and applicability.

Results
Seventeen studies were included in the systematic review, including 7 counties, of which 6 were prospective studies, only 7 models were validation studies, and 4 models were externally validated. The area under the curve of 17 models was 0.680~0.908. All studies had a high risk of bias, primarily due to the participants, outcome, and analysis. The most common predictors included body mass index, radiotherapy, chemotherapy, and axillary lymph node dissection.

Conclusions
The predictive factors’ strength, external validation, and clinical application of the breast cancer lymphedema risk prediction model still need further research. Healthcare workers should choose prediction models in clinical practice judiciously.

Systematic review registration
PROSPERO CRD42021258832
Complex event processing for physical and cyber security in datacentres - recent progress, challenges and recommendations
Authors: Alaghbari Khaled A. , Saad Mohamad Hanif Md , Hussain Aini , Alam Muhammad Raisul 
Published: October 2022

AbstractA datacentre stores information and manages data access in fast and reliable manner. Failure of datacentre operation is not an option and can be catastrophic. Internet of things (IoT) devices in datacentre can automate management tasks and reduce human intervention and error. IoT devices can be used to manage many datacentre routine tasks such as monitoring physical infrastructure, updating software and configuration, monitoring network traffic, and automating alerting reports to respective authorities. The physical and cyber security of the datacentre can be handled by IoT technology by intrusion detection methods. By 2025, more than 25 billion things will be connected to the internet network, therefore massive data will be generated by different heterogeneous sources, and powerful processing engines such as complex event processing (CEP) are needed to handle such a fast and continuous stream of big data. The integration of machine learning (ML) and deep learning (DL) can enhance CEP by introducing new features such as automated rule extraction and self-healing mechanism. This study aims to provide an overview of CEP, as well as its features and potential for integration with IoT applications and ML/DL techniques. We provide a review of recent research works to highlight the capability and applicability of CEP technology to monitor physical facilities and cyber security in detail. This review also highlights several issues and challenges, and provides suggestions for future research. The highlighted insights and recommendations in this paper could raise efforts toward the development of future datacentres based on CEP technology.
Post-lockdown changes in diet in Italy and the USA: Return to old habits or structural changes?
Authors: Scozzafava Gabriele , Contini Caterina , Gerini Francesca , Casini Leonardo 
Published: October 2022

AbstractThis study analyses the impacts of the COVID-19 pandemic on food consumption at the end of the first lockdown in the New York State (USA) and in Italy (spring 2020). The results of our study show that important changes occurred in food habits in these two countries, in which lockdown was very similar. Three models of response to the shock of the lockdown were noted in both countries. The first model (40%) includes individuals who largely increased their food consumption, the second model (26%) showed a more virtuous and responsible behaviour, while the third model (34%) displayed no change in food consumption. Diet quality in terms of healthiness and sustainability declined in the USA, while in Italy, approximately one-third of the sample showed an improvement in diet in these same areas. The use of sociodemographic, motivational, and behavioural variables to profile subjects who adhered to each food model has made it possible to obtain information that can be used to develop communication campaigns and policies for a healthier and more sustainable diet.
Dietary supplementation of Macleaya cordata extract and Bacillus in combination improve laying performance by regulating reproductive hormones, intestinal microbiota and barrier function of laying hens
Authors: Wang Fei , Zou Peng , Xu Shujie , Wang Qi , Zhou Yuanhao , Li Xiang , Tang Li , Wang Baikui , Jin Qian , Yu Dongyou , Li Weifen 
Published: October 2022

Abstract
Background
This study aimed to investigate whether the combination of Macleaya cordata extract (MCE) and Bacillus could improve the laying performance and health of laying hens better.

Methods
A total of 360 29-week-old Jingbai laying hens were randomly divided into 4 treatments: control group (basal diet), MCE group (basal diet + MCE), Probiotics Bacillus Compound (PBC) group (basal diet + compound Bacillus), MCE + PBC group (basal diet + MCE + compound Bacillus). The feeding experiment lasted for 42 d.

Results
The results showed that the laying rate and the average daily egg mass in the MCE + PBC group were significantly higher than those in the control group (P < 0.05) and better than the MCE and PBC group. Combination of MCE and Bacillus significantly increased the content of follicle-stimulating hormone (FSH) in the serum and up-regulated the expression of related hormone receptor gene (estrogen receptor-β, FSHR and luteinizing hormone/choriogonadotropin receptor) in the ovary of laying hens (P < 0.05). In the MCE + PBC group, the mRNA expressions of zonula occluden-1, Occludin and mucin-2 in jejunum was increased and the intestinal epithelial barrier detected by transmission electron microscopy was enhanced compared with the control group (P < 0.05). In addition, compared with the control group, combination of MCE and Bacillus significantly increased the total antioxidant capacity and catalase activity (P < 0.05), and down-regulated the mRNA expressions of inflammation-related genes (interleukin-1β and tumor necrosis factor-α) as well as apoptosis-related genes (Caspase 3, Caspase 8 and P53) (P < 0.05). The concentration of acetic acid and butyric acid in the cecum content of laying hens in the MCE + PBC group was significantly increased compared with the control group (P < 0.05).

Conclusions
Collectively, dietary supplementation of 600 μg/kg MCE and 5 × 108 CFU/kg compound Bacillus can improve laying performance by improving microbiota to enhance antioxidant capacity and intestinal barrier, regulate reproductive hormones and the concentration of cecal short-chain fatty acids of laying hens, and the combined effect of MCE and Bacillus is better than that of single supplementation.