bluuebunny/crossref_metadata_2025_split huggingface dataset:
GraphSynergy: Network Inspired Deep Learning Model for
Anti–Cancer Drug Combination Prediction
Authors: Yang Jiannan , Xu Zhongzhi , Wu William , Chu Qian , Zhang Qingpeng 
Published: March 2021

Abstract
Compared with monotherapy, anti-cancer drug combination can provide effective therapy with less toxicity in cancer treatment. Recent studies found that the topological positions of protein modules related to the drugs and the cancer cell lines in the protein-protein interaction (PPI) network may reveal the effects of drugs. However, due to the size of the combinatorial space, identifying synergistic combinations of drugs from PPI network is computationally difficult. To address this challenge, we propose an end-to-end deep learning framework, namely Graph Convolutional Network for Drug Synergy (GraphSynergy), to make synergistic drug combination predictions. GraphSynergy adapts a spatial-based Graph Convolutional Network component to encode the high-order structure information of protein modules targeted by a pair of drugs, as well as the protein modules associated with a specific cancer cell line in the PPI network. The pharmacological effects of drug combinations are explicitly evaluated by their therapy and toxic scores. By introducing an attention component to automatically allocate contribution weights to the proteins, we show the ability of GraphSynergy to capture the pivotal proteins that play a part in both PPI network and biomolecular interactions between drug combinations and cancer cell lines. Experiments on two latest drug combination datasets demonstrate that GraphSynergy outperforms the state-of-the-art in predicting synergistic drug combinations. This study sheds light on using machine learning to discover effective combination therapies for cancer and other complex diseases.
Prediction of the Risk of C5 Palsy After Posterior Laminectomy and Fusion With Cervical Myelopathy Using Support Vector Machine: an Analysis of 184 Consecutive Patients
Authors: Wang Haosheng , Tang Zhi-Ri , Li Wenle , Fan Tingting , Zhao Jianwu , Kang Mingyang , Dong Rongpeng , Qu Yang 
Published: March 2021

Abstract
Background: This study aimed to predict the C5 palsy (C5P) after posterior laminectomy and fusion (PLF) with cervical myelopathy (CM) from routinely available variables by using support vector machine (SVM) method.Methods: We conducted a retrospective investigation based on 184 consecutive patients with CM after PLF, and data was collected from March 2013 to December 2019. Clinical and imaging variables were obtained and imported into univariable and multivariable logistics regression analysis to identify risk factors for C5P. According to published reports and clinical experience, a series of variables was selected to develop an SVM machine learning model to predict C5P. The accuracy (ACC), area under the receiver operating characteristic curve (AUC) and confusion matrices were used to evaluate the performance of the prediction model.Results: Among the total 184 consecutive patients, C5P occurred in 26 patients (14.13%). Multivariate analyses demonstrated the following 4 independent factors associated with C5P: electromyogram abnormal (odds ratio [OR] = 7.861), JOA recovery rate (OR = 1.412), modified Pavlov ratio (OR = 0.009), and presence of foraminal stenosis C4-C5 (OR = 15.492). The SVM model achieved an area under receiver operating characteristic curve (AUC) of 0.923 and ACC of 0.918. Meanwhile, the confusion matrix shown the classification results of the discriminant analysis. Conclusions: The designed SVM model presented a satisfied performance in predicting C5P from routinely available variables. However, future external validation is needed.
Based on Network Pharmacology to Explore the Active Ingredients and Molecular Targets of Zuojin Pill for the Treatment of Ulcerative Colitis
Authors: Wei Ying , Ren Sichen , Wang Ruilin , Jing Manyi , Liu Honghong , Wang Min , Song Hongtao , Zhao Yanling 
Published: March 2021

Abstract
Background: Zuojin Pill (ZJP), a classic prescription, has the potential to prevent ulcerative colitis (UC). However, the active component and mechanism of ZJP is still arcane. Objective: This study aims to use a network pharmacology approach to find the bioactive compounds and potential action mechanisms of ZJP in the treatment of UC.Methods: Firstly, the components and putative targets of ZJP were collected based on the herbal medicine target database, and a network containing the interaction between the putative targets of ZJP and the potential therapeutic targets of UC was established. Then topological parameters were calculated to identify the key targets in the network and the key targets were imported into David database to perform path enrichment analysis.Results: 7 potential therapeutic components of ZJP and 26 key targets were obtained. These targets were related to signal transduction, response to drug, cellular response to lipopolysaccharide, MAPK cascade, inflammatory response, immune response, transcription from RNA polymerase II promoter, apoptotic process, regulation of sequence-specific DNA binding transcription factor activity and lipopolysaccharide-mediated signaling pathway. Moreover, PI3K-Akt signaling pathway, MAPK signaling pathway and Toll-like receptor signaling pathway were predicted to participate in the treatment of UC, which directly regulated by 7 active components of ZJP. Quercetin and isorhamnetin have great development value in the treatment of UC. Moupinamide and palmidin A are of great value for exploration because of their safety and innovation.Conclusion: ZJP mainly were directly involved in UC through inflammation and immune regulation by PI3K-Akt signaling pathway and MAPK signaling pathway.
Rapid On-Site Evaluation, As a Diagnostic Method for PCP in a Patient with Nephrotic Syndrome
Authors: Weng Xiangwen , An Xing , Chen Xian , gao peiyang , Zhi Lijia 
Published: March 2021

Abstract
Background: Pneumocystis jirovecii pneumonia (PCP) is a common illness of the patients receiving long-term immunosuppressive treatment for which therapy is currently available. Early and prompt diagnosis of this pulmonary infection is a matter of great practical importance. Clinical presentation and radiology are not enough to confirm a diagnosis of PCP. Microscopic examination is available.Case presentation: Here we report a 63-year-old man with nephrotic syndrome,who was transferred to ICU due to unexplained aggravation of infection. The cause of pulmonary infection was identified by Rapid on-site evaluation (ROSE) finally and targeted treatment was given.Conclusions: ROSE can be a diagnostic approach for PCP, which is suitable for clinicians.
Interleukin 37 Expression was Negatively Associated with Pathological Grading in Human Gliomas
Authors: Liu Sheng , Ba Ying , Li Chenglong , Xing Mengyang , Zhang Tao , Liu Yongliang , Gao Yang , Xu Guangming 
Published: March 2021

Abstract
Background: Little is known about the roles of interleukin 37 (IL-37), a newly identified cytokine, in the pathogenesis of cancer. In this study, we aimed to determine the expression of IL-37 in gliomas with different pathological grades and evaluated its effects on survival. Methods: Ninety-five participants with different pathological grades of glioma were included in this study, which were classified into grade I-II (n=27), grade III (n=30), and grade IV (n=38). Ten normal brain tissues that were resected for intracranial decompression after traumatic brain injuries served as control group. The expression of IL-37 mRNA and protein in glioma tissues was determined using Real-time PCR and immunohistochemical techniques. The association between IL-37 expression and various clinicopathologic factors was evaluated. Results: IL-37 mRNA was expressed in normal tissues and tumor tissues, and the expression of IL-37 in tumor tissues were significantly higher than normal brain tissue (p<0.05). IL-37 expression showed decline with the increase of grade level. The expression of IL-37 was significantly lower in glioma tissues of a high malignancy compared with the glioma tissues of a low malignancy. Patients with low IL-37 expression showed a shorter survival time. Conclusions: Low IL-37 expression was negatively correlated with pathological grade, rather than pathological type. Low IL-37 was positively correlated with survival time. Thus, IL-37 maybe plays an inhibitory role in glioma progression.
Calcifying pseudoneoplasm of the neuraxis (CAPNON) associated with neurenteric cyst: an autopsy case showing unusual fatal outcome
Authors: Ichimata Shojiro , Hata Yukiko , Aikawa Akane , Ishizawa Shin , Sato Daisuke , Akai Takuya , Nishida Naoki 
Published: March 2021

Abstract
Background

Calcifying pseudoneoplasm of the neuraxis (CAPNON) is a rare calcified tumefactive lesion that can occur in the brain or spine. Although the aetiology and natural course of CAPNON has not yet been fully established, recent study reported that many CAPNON cases have dual pathology, which may be associated with its aetiology.
Case presentation

A 53-year-old man with a history of an untreated brain mass was taken to a hospital by emergency transport. A computed tomography scan revealed an intracranial hypo-attenuated mass exhibiting mass effect. Several calcified foci were observed around the lesion. He suddenly showed tonic seizure after admission, therefore an emergency craniotomy was performed. However, he unfortunately died due to advanced cerebral oedema. Microscopic findings of the surgically obtained materials were consistent with neurenteric cyst (NC). Intracranial hard masses were found adjacent to NCs and the masses were composed of fibrous cartilage-like matrix with massive linear calcification and surrounding round-to-oval epithelioid cells.
Conclusion

CAPNON associated with NC was considered to be most appropriate diagnosis of present case. To the best of our knowledge, this is the first report of such case. The present case suggests that delay of treatment may cause a poor outcome, at least in CAPNON associated with NC. Careful investigation, including of the underlying pathology, may be essential for deciding treatment strategies for CAPNON.
Esophageal Granular Cell Tumor and Eosinophils: A Multicenter Experience
Authors: Reddi Deepti , Chandler Christropher , Cardona Diana , Schild Michael , Westerhoff Maria , McMullen Emily , Tomizawa Yutaka , Clinton Lani , Swanson Paul E. 
Published: March 2021

Abstract
Background: Esophageal granular cell tumor (eGCT) is rare, and the recent literature suggests a link between eosinophilic esophagitis (EoE) and eGCT. The aim of our study was to determine if EoE or other disorders associated with eosinophilia are consistently associated with eGCT. Methods: We retrospectively searched pathology databases of three academic institutions from 1999 to 2018 for eGCTs. The archived slides and medical records were reviewed.Results: From 294,855 esophagogastroduodenoscopy procedures, 45 patients (17 males and 28 females) with eGCTs were identified. The patients were 30-73 years in age (median 50) had eGCT (0.2 – 2.0 cm, average 0.71). Thirteen had a history of gastroesophageal reflux disease, 5 had Barrett esophagus/goblet cell metaplasia and 1 had EoE. Thirty-four eGCTs had intralesional eosinophils (14 with peak >10 eosinophils/400x hpf); of these, 21 also had eosinophils in lamina propria (9 with peak >10 eosinophils/hpf). eGCT with atypical features (including nuclear enlargement and prominent nucleoli) were more likely to have increased eosinophils in non-epithelial compartments than those without atypia. Pleomorphism and spindled cells were seen in 3 eGCT cases (mean peak intralesional eosinophils: 43 per hpf); 2 of these had goblet cell metaplasia. We found no association between EoE and eGCT, p= 0.5966, (95% C.I. 0.0276, 6.5389, Fisher’s exact test). Instead, most patients had gastroesophageal reflux disease or Barrett esophagus.Conclusion: Eosinophilia, common in eGCT and adjacent stroma, likely drives atypical/reactive histologic features, but a pathogenic relationship between eosinophil rich inflammatory conditions and eGCT has not yet been established.
An analysis of histopathological features of Crohn’s disease in surgical specimens
Authors: Fu Yujuan , Liu Xiuli , Xu Jiaqi , Zhong Tingting , Jiang Junchang , Cao Qian , Fu Tianhong , Jiang Zhinong 
Published: March 2021

Abstract
Background

The diagnosis of Crohn’s disease is challenging. This study aimed to compare the histological features of Crohn’s disease and non-Crohn’s disease (i.e., other intestinal inflammatory diseases) in surgical specimens to identify histologic features for differential diagnosis.
Methods

We evaluated patients who were diagnosed with Crohn’s disease (n = 171) and non-Crohn’s disease (n = 215) between 2010 and 2015 and underwent surgical bowel resection. The frequency of histological features in surgical resection specimens were compared between these two patient groups.
Results

Transmural inflammation, subserosal lymphoid aggregates, fissures or sinus-like structures, granulomas or granuloma-like nodules, abnormalities of the enteric nervous system, and mucosa structure alterations (i.e., muscularis mucosae thickening or mucosal atrophy with pseudopyloric gland metaplasia) were more frequent in Crohn’s disease than non-Crohn’s disease (p < 0.001 for all). A set of 3 of the above pathological features had a specificity of 93.5% for Crohn’s disease. Some of the above histologic features were further grouped as chronic inflammatory change that includes granulomas or granuloma-like nodules, lymphoid aggregates in the muscularis propria or subserosa, fissures or sinus-like structures, and architectural abnormality (i.e., the presence of abnormal enteric nervous system and/or mucosa structure alterations). A combination of transmural inflammation, chronic inflammatory change, and architectural abnormality had a sensitivity of 92.4% and a specificity of 97.7% for Crohn’s disease.
Conclusions

A combination of transmural inflammation, chronic inflammatory change, and architectural abnormality in surgical bowel resection specimens is diagnostic for Crohn’s disease.
Atmospheric scattering of energetic electrons from near-Earth space
Authors: Angelopoulos Vassilis , Tsai Ethan , Wilkins Colin , Zhang Xiaojia , Artemyev Anton , Liu Jiang , Runov Andrei , Iglesias Laura , Turner Drew , Strangeway Robert , Wirz Richard , Li Wen , Adair Lydia , Caron Ryan , Chung Maxwell , Cruce Patrick , Grimes Eric , Hector Kathryn , Lawson Michael , Leneman David , Masongsong Emmanuel , Norris Austin , Russell Cynthia , Shaffer Christopher , Wu Jiashu , Jha Sharvani , King James , Kumar Suyash , Nguyen Kelly , Nguyen Michelle , Palla Akhil , Roosnovo Alexa , Xie Erica , Yap Rebecca , Young Chanel , Blake J. B. , Adair Nick , Allen Matthew , Anderson Michael , Arreola-Zamora Michael , Artinger Jessica , Asher Jeffrey , Branchevsky Donna , Capitelli Michael , Castro Rommel , Chao Gary , Chung Nathan , Cliffe Micah , Colton Kyle , Costello Cian , Depe Danny , Domae Benjamin , Eldin Sarah , Fitgibbon Lauren , Flemming Alex , Fox Ian , Frederick Duncan , Gilbert Alex , Gildemeister Anthony , Gonzalez Alexander , Hesford Brayden , Krieger Renee , Lian Kevin , Mao Jason , McKinney Emmons , Miller Jordan , Nuesca Matt , Park Elisa , Pedersen Carter , Qu Ziyuan , Rozario Reuben , Rye Erik , Seaton Ryan , Subramanian Akshaya , Sundin Stephen , Tan Aysen , Turner Wynne , Villegas Austin , Wasden Matt , Wing Graham , Wong Cass , Zarifian Anais , Zhang Gary 
Published: March 2021

Abstract
In near-Earth space, the magnetosphere, energetic electrons (tens to thousands of kiloelectron volts) orbit around Earth, forming the radiation belts. When scattered by magnetospheric processes, these electrons precipitate to the upper atmosphere, where they deplete ozone, a radiatively active gas, modifying global atmospheric circulation. Relativistic electrons (those above a few hundred kiloelectron volts), can reach the lowest altitudes and have the strongest effects on the upper atmosphere; their loss from the magnetosphere is also important for space weather. Previous models have only considered magnetospheric scattering and precipitation of energetic electrons; atmospheric scattering of such electrons has not been adequately considered, principally due to lack of observations. Here we report the first observations of this process. We find that atmospherically-scattered energetic (relativistic) electrons form a low-intensity, persistent “drizzle”, whose integrated energy flux is comparable to (greater than) that of the more intense but ephemeral precipitation by magnetospheric scattering. Thus, atmospheric scattering of energetic electrons is important for global atmospheric circulation, radiation belt flux evolution, and the repopulation of the magnetosphere with lower-energy, secondary electrons.
Zonal Wave 3 Pattern in the Southern Hemisphere generated by tropical convection
Authors: Goyal Rishav , Jucker Martin , Gupta Alex Sen , Hendon Harry , England Matthew 
Published: March 2021

Abstract
A distinctive feature of the Southern Hemisphere (SH) extratropical atmospheric circulation is the quasi-stationary zonal wave 3 (ZW3) pattern, characterized by three high and three low-pressure centers around the SH extratropics. This feature is present in both the mean atmospheric circulation and its variability on daily, seasonal and interannual timescales. While the ZW3 pattern has significant impacts on meridional heat transport and Antarctic sea ice extent, the reason for its existence remains uncertain, although it has long been assumed to be linked to the existence of three major land masses in the SH extratropics. Here we use an atmospheric general circulation model to show that the stationery ZW3 pattern is instead driven by zonal asymmetric deep atmospheric convection in the tropics, with little to no role played by the orography or land masses in the extratropics. Localized regions of deep convection in the tropics form a local Hadley cell which in turn creates a wave source in the subtropics that excites a poleward and eastward propagating wave train which forms stationary waves in the SH high latitudes. Our findings suggest that changes in tropical deep convection, either due to natural variability or climate change, will impact the zonal wave 3 pattern, with implications for Southern Hemisphere climate, ocean circulation, and sea-ice.
In Vitro Callus Culture of Dianthus Chinensis L. for Assessment of Flavonoid Related Gene Expression Profile
Authors: Sreelek R. , Siril Elenjikkal A 
Published: March 2021

Abstract
Dianthus chinensis L. is an edible, ornamental herb used to prepare the Dianthi Herba, a Chinese traditional rejuvenating medicine. Owing to the rapid proliferation of callus tissues, in vitro production of flavonoids has their own specific importance. Callus cultures raised followed by auxin directed biosynthesis of flavonoid through related transcript profile were carried out. Murashige and Skoog (MS) medium fortified with 2,4- Dichlorophenoxy acetic acid (2,4- D) or picloram induced formation of friable callus from internode derived cultures of D. chinensis. Culture medium containing 2,4- D (10 µM) produced the highest flavonoid content, 4.44 mg quercetin equivalent per gram (QE g− 1) under incubation in continuous dark condition, while maximum dry weight yield (0.38 g/ culture) was obtained from 10 µM 2,4- D under 16 h light / 8 h dark condition (50 µmol m− 2 s− 1 irradiance) at 60 days of incubation. The callus raised in light condition in 10 µM 2,4- D selected to analyze flavonoid related gene expression profile viz., chalcone synthase (CHS), chalcone isomerase (CHI), flavanone-3-hydroxylase (F3H), and flavonol synthase (FLS) at specific time intervals. The transcript abundance of CHS, F3H, or FLS gene was higher at 60 days old callus cultures and reaching 11.59, 48.31, and 114.63-fold relative expression than that of initial callus tissues respectively. These understandings are critical for the regulation of targeted phytochemicals as well as their wide exploitation in the field of biological research.
Effect of Drosophila suzukii on blueberry VOCs: chemical cues for a pupal parasitoid, Trichopria anastrephae
Authors: Vega Gerardo de la , Triñanes Federico , González Andres 
Published: March 2021

Abstract
Biocontrol agents such as parasitic wasps use long-range volatiles and host-associated cues from lower trophic levels to find their hosts. Although, this chemical landscape may be altered by the invasion of exotic insect species. The spotted-wing drosophila (SWD), Drosophila suzukii (Diptera: Drosophilidae), is a highly polyphagous fruit pest native to eastern Asia and recently arrived in South America. The aim of our study was to characterize the effect of SWD attack on the volatile organic compounds (VOCs) of blueberries, a common host fruit, and to correlate these odor changes with the olfactory-mediated behavioral response of resident populations of Trichopria anastrephae parasitoids. Using fruit VOC chemical characterization followed by multivariate analyses of the odor blends of SWD-attacked blueberries, we showed that the development of SWD immature stages inside the fruit generates a different odor profile than control fruits (physically damaged and free of damage). These differences can be explained by the diversity, frequency and amounts of fruit VOCs. The behavioral response of female parasitic wasps showed that T. anastrephae has an innate attraction to volatile cues from infested host fruits, which may lead to successful location of their insect host. Since resident parasitoids are able locate this novel potential host, biological control programs using local populations may be plausible as a SWD control strategy.
Expression Status and Prognostic Roles of m6A-related Genes in Multiple Myeloma: YTHDF2 as the independent prognostic factor
Authors: Liu Rui , Shen Ying , Wang Xiaman , Wu Dong , Zhai Meng , He Aili , Bai Ju 
Published: March 2021

Abstract
Background: N6-methyladenosine is the most abundant RNA modification, which plays a prominent role in multiple biology processes, including tumorigenesis. Multiple myeloma (MM) is the second most frequent hematological cancer. However, the expression status and value of m6A-related genes in multiple myeloma remain elusive.Methods: m6A-related gene expression data and clinical information of MM patients were obtained from the Gene Expression Omnibus (GEO) database. Based on differentially expressed analysis, protein-protein interaction (PPI) analysis, Pearson correlation analysis, Kaplan-Meier survival analysis and Cox regression analysis, the prognostic m6A-associated genes were identified. The receiver operation characteristic (ROC) curves were used to verify the prognostic and diagnostic efficiency. The molecular mechanisms were investigated by differentially expressed mRNA and microRNA analyses with the help of online database ENCORI and POSTAR.Results: Among 22 m6A-related genes, HNRNPC, RBM15B, RBM15, YTHDF3, YTHDF2, HNRNPA2B1 and IGF2BP2 were significantly upregulated, while ZC3H13, FTO, IGF2BP3, ALKBH5 and YTHDC1 were significantly downregulated in MM patients. The high expression of HNRNPC, HNRNPA2B1, YTHDF2 and the low expression of ZC3H13 were associated with adverse survival. Furthermore, the expression level of YTHDF2 was the independent prognostic factor of MM. ROC curves suggested the great prediction performance for MM patients. Differentially expressed mRNA and microRNA analyses indicated the probable involvement of miR-205/YTHDF2/EGR1 axis.Conclusions: Our study first systematically analyzed the expression status of m6A-related genes in multiple myeloma, identified HNRNPC, HNRNPA2B1, YTHDF2 and ZC3H13 that could be the potential prognostic biomarkers, especially YTHDF2, which may be implicated in the miR-205/YTHDF2/EGR1 axis.