bluuebunny/crossref_metadata_2025_split huggingface dataset:
DriverRWH: Discovering Cancer Driver Genes By Random Walk On a Gene Mutation Hypergraph
Authors: Wang Chenye , Shi Junhan , Cai Jiansheng , Zhang Yusen , Zheng Xiaoqi , Zhang Naiqian 
Published: December 2021

Abstract
Background: Recent advances in next-generation sequencing technologies have helped investigators generate massive amounts of cancer genomic data. A critical challenge in cancer genomics is identification of a few driver mutation genes from a much larger number of passenger mutation genes. However, majority of existing computational approaches underuse the co-occurrence information of the individuals, which deems to be important in tumorigenesis and tumor progression. Driver gene list predicted from these tools are prone to be false positive, recent research is far from achieving the ultimate goal of discovering a complete catalog of driver genes. Results: To make full use of co-mutation information, we present a random walk algorithm referred to as DriverRWH on a weighted gene mutation hypergraph model, using somatic mutation data and molecular interaction network data to prioritize candidate driver genes. Applied to tumor samples of different cancer types from The Cancer Genome Atlas (TCGA), DriverRWH shows significantly better performance than state-of-art prioritization methods in terms of the area under the curve (AUC) scores and the cumulative number of known driver genes recovered in top-ranked candidate genes. DriverRWH recovers approximately 50% known driver genes in the top 30 ranked candidate genes for more than half of the cancer types. In addition, DriverRWH is also highly robust to perturbations in the mutation data and gene functional network data. Conclusion: DriverRWH is effective among various cancer types in prioritizes cancer driver genes and provides considerable improvement over other tools with a better balance of precision and sensitivity. It can be a useful tool for detecting potential driver genes and facilitate targeted cancer therapies.
Association of Triglyceride–Glucose Index and the Presence of Sarcopenia in Type 2 Diabetes Patients
Authors: Hu Wenchao , Xing Dongming 
Published: December 2021

Abstract
Objective: Triglyceride–glucose index (TyG index) has been used in healthy individuals as a marker of insulin resistance. Type 2 diabetes mellitus (T2DM) showed an increased risk of developing sarcopenia compared to control subjects. This study is performed to determine the association of TyG index with the presence of sarcopenia in T2DM patients. Method: This study included 1098 T2DM patients who were recruited from the inpatients in Qilu Hospital (Qingdao). Skeletal muscle index (SMI) was measured using dual energy X-ray absorptiometry. Serum triglyceride (TG) and fasting plasma glucose (FPG) were measured and used to calculate TyG index.Result: 119 male subjects (20.2%) had sarcopenia, while 72 female subjects (14.1%) had sarcopenia in T2DM patients. TyG index was correlated with a decreased risk of sarcopenia in both male and female T2DM groups. TyG index was found to be positively correlated with SMI after multivariate adjustment in male subjects. When TyG index was ≤9.5, TyG index was positively correlated with SMI. However, when TyG index was >9.5, there was not a significant association between TyG index and SMI. Moreover, TyG index was not correlated with SMI after multivariate analysis in female subjects. However, TyG index was positively correlated with SMI when TyG index was ≤9. When TyG index was >9, TyG index was negatively correlated with SMI, however, the correlation was not statistically significant. Conclusion: TyG index is inversely correlated with the presence of sarcopenia in type 2 diabetes patients.
Anti-Inflammatory Effects of Novel P2X4 Receptor Antagonists, NC-2600 and NP-1815-PX, in a Murine Model of Colitis
Authors: D’Antongiovanni Vanessa , Pellegrini Carolina , Benvenuti Laura , Fornai Matteo , Salvo Clelia Di , Natale Gianfranco , Ryskalin Larisa , Bertani Lorenzo , Lucarini Elena , Mannelli Lorenzo Di Cesare , Ghelardini Carla , Nemeth Zoltan H. , Haskó György , antonioli luca 
Published: December 2021

Abstract
The pharmacological blockade of P2X4 receptors has shown potential benefits in the management of several immune/inflammatory diseases. However, data regarding the involvement of P2X4 receptors in the pathophysiological mechanisms of action in intestinal inflammation are not well defined. We aimed to evaluate the anti-inflammatory effects of two novel and selective P2X4 receptor antagonists, NC-2600 and NP-1815-PX, and characterize the molecular mechanisms of their action in a murine model of 2,4-dinitrobenzene sulfonic acid (DNBS)-induced colitis. These two drugs and dexamethasone (DEX) were administered orally for 6 days, immediately after the manifestation of DNBS. The body weight decrease, resulting from colitis, was attenuated by NC-2600 and NP-1815-PX, but not DEX. However, all three drugs attenuated the increase in spleen weight and ameliorated macroscopic and microscopic colonic tissue damage. Furthermore, all three compounds decreased tissue IL-1β levels and caspase-1 expression and activity. Colonic tissue increase of tumor necrosis factor was downregulated by DEX, while both NC-2600 and NP-1815-PX were ineffective The reduction of occludin associated with colitis was ameliorated by NC-2600 and NP-1815-PX, but not DEX. In THP-1 cells, lipopolysaccharide and ATP upregulated IL-1β release and NLRP3, caspase-1, caspase-5 and caspase-8 activity, but not of caspase-4. These changes were prevented by NC-2600 and NP-1815-PX treatment. For the first time, the above findings show that the selective inhibition of P2X4 receptors represents a viable approach to manage bowel inflammation via the inhibition of NLRP3 inflammasome signaling pathways.
High Performance of UiO-66 Metal-Organic Framework Modified with Melamine for Uptaking of Lead and Cadmium from Aqueous Solutions
Authors: Abdelmoaty alaaS , El-Wakeel Shaimaa , Fathy Nady , Hanna AdlyA 
Published: December 2021

Abstract
In this paper, UiO-66 metal-organic framework (MOF) was prepared by a hydrothermal method and modified consequently with melamine (MUiO-66), as so as enhance the adsorption properties of these materials in liquid-phase adsorption. With respect to this, the adsorption of lead and cadmium divalent ions was performed under varying conditions of pH, metal ion concentration, contact time, adsorbent dose and temperature. Morphology, texture properties, functional groups, crystallinity and thermal properties of both MOFs were examined. UiO-66 composed of sphere-like particles and covered by layers of melamine with enhancing in crystallinity and active sites as well as the total surface area increased from 1080 to 1160 m2/g. The modified UiO-66 with melamine (MUiO-66) showed a notable adsorption capacity of 177.5 and 146.6 mg/g for Pb and Cd (II) ions, respectively. Adsorption of both metals fitted well with the pseudo-second-order kinetic and Langmuir models and controlled by a physisorption mechanism at pH of 5. Also, adsorption process is an endothermic in nature and desorption is achieved well for three cycles by MUiO-66. Therefore, UiO-66 and MUiO-66 obtained in this work have a great promise in adsorption of heavy metals such as Pb and Cd(II) ions from wastewater.
An Optimized and Well-Characterized Niosome-Based Nanocarrier for Letrozole: A Brand- New Hybrid Therapy for Breast Cancer
Authors: Ahmadi Saeedeh , Akbarzadeh Iman , Chiani Mohsen , Seraj Mahmoud , Noorbazargan Hassan , Saffar Samaneh , Quazi Sameer , Far Bahareh Farasati 
Published: December 2021

Abstract
This study aimed to improve the anticancer activity of letrozole through a niosomal formulation. Optimized niosomal formulation of letrozole was achieved by response surface methodology (RSM). The niosomes were well-characterized by several methods. The anticancer activity and its mechanism were studied in MCF-7 and MDA-MB-231 breast cancer cells. The release of the drug from the niosomes was according to the Kors Meyer-Peppa kinetic model. The niosomes were stable with high encapsulation efficiency. Significant higher anticancer activity and more induction of apoptosis were obtained for niosomal letrozole. Results indicated that niosomes could be a promising drug carrier for delivery of letrozole to breast cancer cells.
External Validation Study On The Value of Deep Learning Algorithm For The Prediction of Hematoma Expansion From Noncontrast CT Scans
Authors: Guo Dong Chuang , Gu Jun , He Jian , Chu Hai Rui , Dong Na , Zheng Yi Feng 
Published: December 2021

Abstract
Background: Hematoma expansion is an independent predictor of patient outcome and mortality. The early diagnosis of hematoma expansion is crucial for selecting clinical treatment options This study aims to explore the value of a deep learning algorithm for the prediction of hematoma expansion from noncontrast Computed tomography（NCCT） scan through external validation.Methods: 102 NCCT images of Hypertensive intracerebral hemorrhage (HICH) patients diagnosed in our hospital were retrospectively reviewed. The initial Computed tomography (CT) scan images were evaluated by a commercial Artificial intelligence (AI) software using deep learning algorithm and radiologists respectively to predict hematoma expansion and the corresponding sensitivity and specificity of the two groups were calculated and compared, Pair-wise comparisons were conducted among gold standard hematoma expansion diagnosis time, AI software diagnosis time and doctors’ reading time.Results: Among 102 HICH patients, The sensitivity, specificity and accuracy of predicting hematoma expansion in the AI group were higher than those in the doctor group（80.0% vs 66.7%,73.6% vs 58.3%,75.5% vs 60.8%）,with statistically significant difference (p<0.05).The AI diagnosis time (2.8 ± 0.3s) and the doctors’ diagnosis time (11.7 ± 0.3s) were both significantly shorter than the gold standard diagnosis time (14.5 ± 8.8h) (p <0.05), AI diagnosis time was significantly shorter than that of doctors (p<0.05).Conclusions: Deep learning algorithm could effectively predict hematoma expansion at an early stage from the initial CT scan images of HICH patients after onset with high sensitivity and specificity and greatly shortened diagnosis time, which provides a new, accurate, easy-to-use and fast method for the early prediction of hematoma expansion.
Mental and Psycho-social Health and Quality-of-Life Before and After Cardiac Rehabilitation: A Prospective Cohort Study With Comparison to Specific Population Norms
Authors: Angst Felix , Giger Raoul D. , Lehmann Susanne , Sandor Peter , Teuchmann Peter , Csordas Adam 
Published: December 2021

Abstract
Background. Data on mental health improvement after cardiac rehabilitation (CR) are contradicting. The aim was to examine the mental and psycho-social health of patients admitted to our rehabilitation center following hospital treatment for acute coronary syndrome, before and after multidisciplinary CR.Methods. Outcome was measured at admission and discharge by the 36-Item Short Form Survey (SF-36), the Symptom Checklist-90 Revised (SCL-90R), the Coping Strategy Questionnaire (CSQ) and the 6-minute-walking distance test. The patients’ health status was compared with norms of sex-, age- and comorbidity-matched data from the German general population. Score differences from norms were measured by standardized mean differences (SMDs); health changes were quantified by standardized effect sizes (ESs). Their importance for comprehensive assessment was quantified by explorative factor analysis.Results. Of n=70 patients followed-up (male: 79%; mean age: 66.6 years), 79% had ≥3 comorbidities. At baseline, SF-36 Physical functioning (SMD=–0.75), Role physical (–0.90), Social functioning (SMD=–0.44), and Role emotional (SMD=–0.45) were significantly worse than the norm. After CR, almost all scores significantly improved by ES=0.23 (SCL-90R Interpersonal sensitivity) to 1.04 (SF-36 Physical functioning). The strongest factor (up to 41.1% explained variance) for health state and change was the mental health domain, followed by function&pain (up to 26.3%).Conclusions. Normative deficits in physical and psycho-social health were reported at baseline. After CR, at follow-up, all scores, except phobia, showed significant improvement. The comprehensive measurement of bio-psycho-social health should not be limited to depression and anxiety but include, especially, the somatization and social participation dimensions.
Effect of Remediation Reagents on Bacterial Composition and Ecological Function in Black-Odorous Water Sediments
Authors: Xia Dong , Zhao Hanbin , Kobayashi Sohei , Mi Qi , Hao Aimin , Iseri Yasushi 
Published: December 2021

Abstract
Black-odorous urban water bodies and sediments pose a serious environmental problem. Herein, we conducted microcosm batch experiments to investigate the effect of remediation reagents (magnesium hydroxide and calcium nitrate) on native bacterial communities and their ecological functions in the black-odorous sediment of urban water. The dominant phyla (Proteobacteria, Actinobacteria, Chloroflexi, and Planctomycetes) and classes (Alpha-, Beta-, and Gamma-proteobacteria, Actinobacteria, Anaerolineae, and Planctomycetia) were determined under calcium nitrate and magnesium hydroxide treatments. Functional groups related to aerobic metabolism, including aerobic chemoheterotrophy, dark sulfide oxidation, and correlated dominant genera (Thiobacillus, Lysobacter, Gp16, and Gaiella) became more abundant under calcium nitrate treatment, whereas functional genes potentially involved in dissimilatory sulfate reduction became less abundant. The relative abundance of chloroplasts, fermentation, and correlated genera (Desulfomonile and unclassified Cyanobacteria) decreased under magnesium hydroxide treatment. These results indicated that calcium nitrate addition improved hypoxia-related reducing conditions in the sediment and promoted aerobic chemoheterotrophy.
The Effect of Mindfulness-Based Cognitive Therapy On Rumination and Intrusive Thoughts in Patients With Bipolar Disorder: Secondary Analyses From a Randomized Controlled Trial
Authors: Lubbers Jelle , Geurts Dirk , Hanssen Imke , Huijbers Marloes , Spijker Jan , Speckens Anne , Cladder-Micus Mira 
Published: December 2021

Abstract
Background: Preliminary evidence suggests that Mindfulness-Based Cognitive Therapy (MBCT) is a promising treatment for bipolar disorder (BD). One of the proposed working mechanisms of MBCT in attenuating depressive symptoms is through the reduction of depressive rumination. In BD the effect of MBCT on rumination is less well studied. The primary aim of this study was to investigate the effect of MBCT on self-reported trait depressive rumination and an experimental state measure of negative intrusive thoughts. On an exploratory note, we investigated the effect of MBCT on positive rumination and positive intrusive thoughts.Methods: The study population consisted of a subsample of bipolar type I or II patients participating in a multicenter randomized controlled trial comparing MBCT + treatment as usual (TAU) (N = 25) to TAU alone (N = 24). Trait depressive rumination (RRS brooding subscale) and negative intrusive thoughts (breathing focus task (BFT)) were assessed at baseline and post-treatment. During the BFT, participants were asked to report negative, positive and neutral intrusive thoughts while focusing on their breathing. Results: Compared to TAU alone, MBCT + TAU resulted in a significant pre- to post-treatment reduction of trait depressive rumination (R2 = 0.16, F(1, 28) = 5.30, p = .029; medium effect size (f2 = 0.19)) and negative intrusive thoughts on the BFT (R2 = .15, F(1, 28) = 4.88, p = .036; medium effect size (f2 = 0.17)). MBCT did not significantly change positive rumination or positive intrusive thoughts on the BFT.Conclusions: MBCT might be a helpful additional intervention to reduce depressive rumination in BD which might reduce risk of depressive relapse or recurrence. Future research is required to replicate our findings and to explore whether this reduction in rumination following MBCT indeed mediates a reduction in depressive symptoms and leads to relapse prevention in BD.
CAR T Cells Equipped With a Fully Human scFv Targeting Trop2 Can Be Used to Treat Pancreatic Cancer
Authors: Zhu Hong Jia , Jia Yujie , Tan Jingwen , Fang Xiaoyan , Ye Jing , Tuhin Israth Jahan , Xu Nan , Kang Liqing , Li Minghao , Lou XiaoYan , Zhou Jing-e , Wang Yiting , Yan Zhiqiang , Yu Lei 
Published: December 2021

Abstract
Purpose: Chimeric antigen receptor (CAR) T cell therapy has demonstrated clinical success in treating haematologic malignancies but has not been effective against solid tumours thus far. Trop2 is a tumour-related antigen broadly overexpressed on a variety of tumours and has been reported as a promising target for pancreatic cancers. Our study aimed to determine whether CAR T cells designed with a fully human Trop2-specific single-chain fragment variable (scFv) can be used in the treatment of Trop2-positive pancreatic tumours.Methods: We designed Trop2-targeted chimeric antigen receptor engineered T cells with a novel human anti-Trop2 scFv (2F11) and then investigated the cytotoxicity, degranulation, and cytokine secretion profiles of the anti-Trop2 CAR T cells when they were exposed to Trop2+ cancer cells in vitro. We also studied the antitumour efficacy and toxicity of Trop2-specific CAR T cells in vivo using a BxPC-3 pancreatic xenograft model.Results: Trop2-targeted CAR T cells designed with 2F11 effectively killed Trop2-positive pancreatic cancer cells and produced high levels of cytotoxic cytokines in vitro. In addition, Trop2-targeted CAR T cells, which persistently circulate in vivo and efficiently infiltrate into tumour tissues, significantly blocked and even eliminated BxPC-3 pancreatic xenograft tumour growth without obvious deleterious effects observed after intravenous injection into NSG mice. Moreover, disease-free survival was efficiently prolonged.Conclusion: These results show that Trop2-targeted CAR T cells equipped with a fully human anti-Trop2 scFv could be a potential treatment strategy for pancreatic cancer and could be useful for clinical evaluation.
Assessment of Therapeutic Outcome and Role of Reirradiation in Patients With Radiation-induced Glioma
Authors: Ohno Makoto , Miyakita Yasuji , Takahashi Masamichi , Yanagisawa Shunsuke , Tamura Yukie , Kawauchi Daisuke , Kikuchi Miyu , Igaki Hiroshi , Yoshida Akihiko , Satomi Kaishi , Matsushita Yuko , Ichimura Koichi , Narita Yoshitaka 
Published: December 2021

Abstract
Background: We retrospectively reviewed the clinical characteristics and treatment outcomes to clarify the optimal therapeutic strategy, especially the role of reirradiation in patients with radiation-induced glioma (RIG). Methods: We identified patients with high-grade glioma who satisfied Cahan’s criteria for RIG in our database during 2001–2021 and analyzed the outcomes.Results: We identified 11 patients with RIG. The primary diseases included germinomas (n=2), acute lymphoblastic lymphomas (n=2), medulloblastomas (n=3), diffuse astrocytoma with isocitrate dehydrogenase (IDH) 2 mutant (n=1), pilocytic astrocytoma (n=1), pituitary adenoma (n=1), and a metastatic tumor from lung cancer (n=1). The median latency period was 17 years (range: 9–30 years). The RIGs included glioblastoma with IDH 1/2 wild-type (n=7), glioblastoma not otherwise specified (n=2), anaplastic astrocytoma with IDH1/2 wild-type (n=1), and anaplastic astrocytoma not otherwise specified (n=1). All patients underwent tumor removal or biopsy, 5 patients postoperatively received reirradiation combined with chemotherapy, and 6 patients were treated with chemotherapy alone. The median progression-free and overall survival times were 11.3 and 28.3 months, respectively. The median progression-free survival time of patients treated with reirradiation and chemotherapy (n=5) tended to be longer than that of patients that received chemotherapy alone (n=6) (17.0 vs 8.1 months; p=0.45); the median survival time was similar (29.6 vs 27.4 months; p=0.28). Local recurrences were observed less frequently in patients who received reirradiation combined with chemotherapy (50%) than in those who received chemotherapy alone (100%; p=0.046). None of the patients developed radiation necrosis. In one case, the different IDH2 mutational states between the primary and secondary tumors were useful for diagnosing the secondary tumor as RIG. Conclusions: RIG can occur more than 20 years after successful treatment of the primary disease using radiotherapy; thus, follow-up times should be extended to 30 years. Reirradiation combined with chemotherapy appears to be feasible and have favorable outcomes. Identifying the IDH1/2 mutational status can have a diagnostic effect on establishing RIG in recurrent gliomas.
Safety and Long-term Improvement of Mesenchymal Stromal Cell Infusion in Critically COVID-19 Patients: A Randomized Clinical Trial.
Authors: Rebelatto Carmen Kuniyoshi , Senegaglia Alexandra Cristina , Franck Claudio Luciano , Daga Debora Regina , Shigunov Patrícia , Stimamiglio Marco Augusto , Marsaro Daniela Boscaro , Schaidt Bruna , Micosky Andressa , de Azambuja Ana Paula , Leitão Cleverson Alex , Petterle Ricardo Rasmussen , Jamur Valderez Ravaglio , Vaz Isadora May , Mallmann Antônio Paulo , Junior Hipólito Carraro , Ditzel Eduardo , Brofman Paulo Roberto Slud , Correa Alejandro 
Published: December 2021

Abstract
Background: COVID-19 is a multisystem disease that presents acute and persistent symptoms, the PostAcute Sequelae (PASC). Long-term symptoms may be due to consequences from organ or tissue injury caused by SARS-CoV-2, associated clotting or inflammatory processes during acute COVID-19. Various strategies are being chosen for by clinicians to prevent severe cases of COVID-19; however, a single treatment would not be efficient in treating such a complex disease. Mesenchymal stromal cells (MSCs) are known for their immunomodulatory properties and regeneration ability; therefore, they are a promising tool for treating disorders involving immune dysregulation and extensive tissue damage, as is the case with COVID-19. This study aimed to assess the safety and explore the long-term efficacy of three intravenous doses of UC-MSCs (umbilical cord-MSCs) as an adjunctive therapy in the recovery and postacute sequelae reduction caused by COVID-19. To our knowledge, this is the first report that presents the longest follow-up after MSC treatment in COVID-19 patients. Methods: This was a phase I/II, prospective, single-center, randomized, double-blind, placebo-controlled clinical trial. Seventeen patients diagnosed with COVID-19 who require intensive care surveillance and invasive mechanical ventilation – critically ill patients – were included. The patient infusion was three doses of 5x105 cells/kg UC-MSCs, with a dosing interval of 48 hours (n=11) or placebo (n=6). These evaluations consisted of a clinical assessment, viral load, laboratory testing, including blood count, serologic, biochemical, cell subpopulation, cytokines and CT scan. Results: The results revealed that in the UC-MSC group, there was a reduction in the levels of ferritin, IL-6 and MCP1-CCL2 on the fourteen day. In the second month, a decrease in the levels of reactive C-protein, D-dimer, and neutrophils and an increase in the numbers of TCD3, TCD4 and NK lymphocytes were observed. A decrease in lung extension was observed at the fourth month. The improvement in all these parameters was maintained until the end of patient follow-up. Conclusions: UC-MSCs infusion is safe and can play an important role as an adjunctive therapy, both in the early stages, preventing severe complications and in the chronic phase with postacute sequelae reduction in critically ill COVID-19 patients. Trial registration: Brazilian Registry of Clinical Trials (ReBEC), UTN code - U1111-1254-9819. Registered 31 October 2020 - Retrospectively registered, https://ensaiosclinicos.gov.br/rg/RBR-3fz9yr