bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of Recombinant Transmembrane Proteins from Mammalian Cells for Biochemical and Structural Analyses
Authors: Puthenveetil Robbins , Lee Chul‐Jin , Banerjee Anirban 
Published: June 2020

AbstractEukaryotic integral membrane proteins are key components of various biological processes. Because they are implicated in multiple diseases, it is important to understand their mechanism of action by elucidating their structure and function. Complex technical challenges associated with the generation of recombinant membrane proteins severely impair our ability to understand them using structural and biochemical methods. Here, we provide a detailed procedure to address and mitigate difficulties involved in the large‐scale heterologous overexpression and purification of eukaryotic membrane proteins using HEK293S GnTi− cells transduced with baculovirus. Two human proteins, hDHHC15 and hPORCN, are presented as examples, with step‐by‐step instructions for transient transfection and generation of baculoviruses, followed by overexpression and purification from HEK293S GnTi− cells. © 2020 Wiley Periodicals LLC.Basic Protocol 1: Small‐scale protein expression in mammalian HEK293T cellsBasic Protocol 2: Generation of baculovirus from Sf9 (insect) cellsAlternate Protocol: Enumeration‐free method for generating P2 viral stockSupport Protocol 1: Small‐scale transduction of HEK293T cells with P2 baculovirusBasic Protocol 3: Large‐scale viral transduction of HEK293S GnTi− cellsSupport Protocol 2: Large‐scale membrane preparation from HEK293S GnTi− cellsBasic Protocol 4: Large‐scale purification of membrane proteins from HEK293S GnTi− cells
Flexible task‐DAG management in PHAST library: Data‐parallel tasks and orchestration support for heterogeneous systems
Authors: Peccerillo Biagio , Bartolini Sandro 
Published: June 2020

SummaryHeterogeneous architectures proved successful in achieving unprecedented performance and energy‐efficiency. However, taking advantage of these diverse processing elements is still hard. Programmers need to code through the different approaches suitable for each target architecture and need to decide the distribution of activities on the different resources. The majority of current frameworks focuses on either performance or productivity. The former mainly provides low‐level target‐specific programming interfaces, and the latter offers high‐level tools that often fail in achieving high‐performance. In both cases, the design is usually data‐parallel, as task‐parallelism is not supported. In this work, we propose a task‐based solution within the data‐parallel heterogeneous single‐source PHAST library. Tasks can be coded in a target‐agnostic fashion, can be compiled and parallelized on multi‐core CPUs and NVIDIA GPUs automatically and support the choice of the execution platform at runtime. We evaluate the capabilities of the proposed task‐directed acyclic graph support in case of an extensive set of randomly generated task‐based applications with different sizes and characteristics. We compare it against a SYCL implementation in terms of performance and complexity metrics, highlighting that PHAST achieves about 1.56× and 2.60× speedup over SYCL for multi‐core CPU and GPU, respectively, while improving also code complexity metrics.
Crosstalk reduction in copper on‐chip interconnects with graphene barrier for ternary logic applications
Authors: Badugu Divya Madhuri , S. Sunithamani 
Published: June 2020

SummaryThis paper presents the investigations of crosstalk effects in ternary logic‐based coupled interconnects. The crosstalk analysis is investigated for coupled copper interconnects and copper‐multilayer graphene (Cu‐MLG) interconnects. In Cu‐MLG interconnects, the Cu interconnect is enclosed with MLG barrier and standard ternary inverter is used to drive the interconnect. Based on the industry standard HSPICE simulation results, the crosstalk effects such as noise peak and delay are lower compared with conventional Cu interconnects. Moreover, the Cu‐MLG interconnects show reduced power dissipation, power delay product (PDP), and energy delay product (EDP) over the Cu interconnects. From the simulation results, it is observed that the Cu‐MLG interconnects provides the performance improvements up to 30.67% compared with the Cu interconnects. Thus, the Cu‐MLG interconnects are more compatible for ternary logic integrated circuits compared with traditional Cu interconnects.
Calreticulin couples with immune checkpoints in pancreatic cancer
Authors: Huang Xing , Tang Tianyu , Wang Xun , Bai Xueli , Liang Tingbo 
Published: June 2020

AbstractAlthough immune checkpoint blockade is considered to be the dominant approach in future cancer immunotherapy, whether it will apply to pancreatic cancer remains largely unknown. To address this issue, pancreatic cancer–associated datasets were individually collected by Gene Expression Profiling Interactive Analysis 2 (GEPIA2), cBioPortal, and Tumor and Immune System Interaction Database (TISIDB), and subsequently subjected to prognostic, genomic, and immunologic analyses of all well‐established immune checkpoints. The results indicate that immune checkpoints might not be ideal targets for pancreatic cancer therapy. Intriguingly, the genomic alteration of calreticulin, the key mediator of chemotherapy‐induced cancer immunogenic cell death, was found to couple with immune checkpoints in pancreatic cancer. Moreover, calreticulin was observed to be highly expressed in pancreatic adenocarcinoma, and high calreticulin expression significantly favors both overall survival and disease‐free survival of patients with pancreatic adenocarcinoma. Importantly, calreticulin was further revealed to be closely related to anti‐tumor immunity in pancreatic adenocarcinoma, including multiple immune effector molecules and T‐cell signatures. Taken together, calreticulin‐based therapy may represent a more promising prospect for pancreatic cancer immunotherapy than immune checkpoint blockade therapy.
The distribution of immune cells within combined hepatocellular carcinoma and cholangiocarcinoma predicts clinical outcome
Authors: Zheng Bo‐Hao , Ma Jia‐Qiang , Tian Ling‐Yu , Dong Liang‐Qing , Song Guo‐He , Pan Jiao‐Men , Liu Yu‐Ming , Yang Shuai‐Xi , Wang Xiao‐Ying , Zhang Xiao‐Ming , Zhou Jian , Fan Jia , Shi Jie‐Yi , Gao Qiang 
Published: June 2020

AbstractBackgroundThis study aimed to investigate the clinical relevance of the immune microenvironment in patients with combined hepatocellular carcinoma and cholangiocarcinoma (cHCC‐ICC).Patients and MethodsThe density of tumor‐infiltrating CD3+, CD8+, CD163+, and Foxp3+ immune cells, as well as Programmed cell death 1, Programmed cell death‐ligand 1, and Tumor necrosis factor receptor superfamily member 4, was measured in the peritumor liver, tumor invasive margin, and intratumor subregions of 56 cHCC‐ICC by immunohistochemistry. The immune index was established to stratify patients. Prognostic significance of immune cell subsets and immune indices was evaluated.ResultsThe distribution of immune cells was highly heterogeneous among different subregions of cHCC‐ICC. As compared with the hepatocellular carcinoma (HCC) component, the lower density of CD8+ T cells and higher intensity of Foxp3+ Tregs and immune checkpoints in the intrahepatic cholangiocarcinoma (ICC) component may indicate a stronger immune evasive ability of ICC. Based on clustering classification or a combination of random forest and lasso‐cox, two models of immune indices were established and both were identified as independent prognostic factors for cHCC‐ICC patients. The selected immune variables in the immune prognostic models derived from both HCC and ICC subregions, indicating that the prognosis of cHCC‐ICC patients was a complex interaction of both components.ConclusionsThe immune contexture was heterogeneous among different subregions of cHCC‐ICC patients and contributed differently to patient prognosis. Immune score based on the densities of immune cells might serve as a promising prognostic predictor for cHCC‐ICC patients.
ATPase copper transporter A, negatively regulated by miR‐148a‐3p, contributes to cisplatin resistance in breast cancer cells
Authors: Yu Ze , Cao Weifan , Ren Yuan , Zhang Qijia , Liu Jia 
Published: June 2020

AbstractBackgroundBreast cancer is the leading cause of death among women. Cisplatin is an effective drug for breast cancer, but resistance often develops during long term chemotherapy. While the mechanism of chemotherapy resistance is still not fully understood.MethodsSurvival analyses of ATP7A and ATP7B were used to evaluate their effects on the development of Breast invasive carcinoma (BRCA). Immunostaining, flow cytometry, and IC50 assay were utilized to examine the effects of ATP7A‐siRNA combined with cisplatin on apoptosis in breast cancer cells. Q‐PCR, western blotting, and dual‐luciferase assay were employed to confirm ATP7A is a novel target gene of miR‐148a‐3p.ResultsIn this current study, we identified knocking‐down ATP7A could enhance cytotoxicity treatment of cisplatin in breast cancer cells. We also demonstrated miR‐148a‐3p overexpression in BRCA cells increased the sensitivity to cisplatin, and subsequently enhanced DNA damage and apoptosis. Moreover, we found ATP7A is a novel target gene of miR‐148a‐3p. In brief, our results showed miR‐148a could accelerate chemotherapy induced‐apoptosis in breast cancer cells by inhibiting ATP7A expression.ConclusionsOur results highlight that inhibition of ATP7A is a potential strategy for targeting breast cancer resistant to cisplatin, and we provided an interesting method to compare the involvement of various genes in the assessment of cisplatin resistance.
Erythrocyte microRNAs show biomarker potential and implicate multiple sclerosis susceptibility genes
Authors: Groen Kira , Maltby Vicki E. , Scott Rodney J. , Tajouri Lotti , Lechner‐Scott Jeannette 
Published: June 2020

AbstractBackgroundMultiple sclerosis is a demyelinating autoimmune disease, for which there is no blood‐borne biomarker. Erythrocytes may provide a source of such biomarkers as they contain microRNAs. MicroRNAs regulate protein translation through complementary binding to messenger RNA. As erythrocytes are transcriptionally inactive, their microRNA profiles may be less susceptible to variation. The aim of this study was to assess the biomarker potential of erythrocyte microRNAs for multiple sclerosis and assess the potential contribution of erythrocyte‐derived extracellular vesicle microRNAs to pathology.MethodsErythrocytes were isolated from whole blood by density gradient centrifugation. Erythrocyte microRNAs of a discovery cohort (23 multiple sclerosis patients and 22 healthy controls) were sequenced. Increased expression of miR‐183 cluster microRNAs (hsa‐miR‐96‐5p, hsa‐miR‐182‐5p and hsa‐miR‐183‐5p) was validated in an independent cohort of 42 patients and 45 healthy and pathological (migraine) controls. Erythrocyte‐derived extracellular vesicles were created ex vivo and their microRNAs were sequenced. Targets of microRNAs were predicted using miRDIP.ResultsHsa‐miR‐182‐5p and hsa‐miR‐183‐5p were able to discriminate relapsing multiple sclerosis patients from migraine patients and/or healthy controls with 89‐94% accuracy and around 90% specificity. Hsa‐miR‐182‐5p and hsa‐miR‐183‐5p expression correlated with measures of physical disability and hsa‐miR‐96‐5p expression correlated with measures of cognitive disability in multiple sclerosis. Erythrocytes were found to selectively package microRNAs into extracellular vesicles and 34 microRNAs were found to be differentially packaged between healthy controls and multiple sclerosis patients. Several gene targets of differentially expressed and packaged erythrocyte microRNAs overlapped with multiple sclerosis susceptibility genes. Gene enrichment analysis indicated involvement in nervous system development and histone H3‐K27 demethylation.ConclusionsErythrocyte miR‐183 cluster members may be developed into specific multiple sclerosis biomarkers that could assist with diagnosis and disability monitoring. Erythrocyte and their extracellular microRNAs were shown to target multiple sclerosis susceptibility genes and may be contributing to the pathophysiology via previously identified routes.
Prostate‐specific antigen modulates the osteogenic differentiation of MSCs via the cadherin 11‐Akt axis
Authors: Wu Longxiang , Xiang Shiqi , Hu Xiheng , Mo Miao , Zhao Cheng , Cai Yi , Tong Shiyu , Jiang Huichuan , Chen Linxiao , Wang Zhi , Xiong Wei , Ou Zhenyu 
Published: June 2020

AbstractBackgroundA high prevalence of osteoblastic bone metastases is characteristic of prostate cancer. Prostate‐specific antigen (PSA) is a serine protease uniquely produced by prostate cancer cells and is an important serological marker for prostate cancer. However, whether PSA modulates the osteogenic process remains largely unknown. In this study, we explored the effect of PSA on modulating the osteoblastic differentiation of mesenchymal stem cells (MSCs). In this study, we used flow cytometry, CCK‐8 assay, Alizarin red S (ARS) staining and quantification, alkaline phosphatase (ALP) activity and staining, Western blotting, and quantitative real‐time PCR (qRT‐PCR) to explore the effect of PSA on osteogenic differentiation of MSCs.ResultsWe first demonstrated that although PSA did not affect the proliferation, morphology, or phenotype of MSCs, it significantly promoted the osteogenic differentiation of MSCs in a concentration‐dependent manner. Furthermore, we demonstrated that PSA promoted the osteogenic differentiation of MSCs by elevating the expression of Cadherin 11 in MSCs and, thus, activating the Akt signaling pathway.ConclusionsIn conclusion, we demonstrated that PSA could promote the osteogenesis of MSCs through Akt signaling pathway activation by elevating the expression of cadherin‐11 in MSCs. These findings imply a possible role of PSA in osteoblastic bone metastases in prostate cancer.
Prognostic validation and therapeutic decision‐making of the AJCC eighth pathological prognostic staging for T3N0 breast cancer after mastectomy
Authors: Wu San‐Gang , Wang Jun , Lei Jian , Lian Chen‐Lu , Hua Li , Zhou Juan , He Zhen‐Yu 
Published: June 2020

AbstractBackgroundT3N0 breast cancer might be a distinct clinical and biological entity, with higher heterogeneity and presenting diverse responses to locoregional and systemic therapy. The aim of the current study was to validate the prognostic effect and assess the treatment decision‐making of the American Joint Committee on Cancer (AJCC) eighth pathological prognostic staging in T3N0 breast cancer after mastectomy.MethodsWe retrospectively included 2465 patients with stage T3N0 breast cancer who had undergone mastectomy between 2010 and 2014 using the data from Surveillance, Epidemiology, and End Results program. The primary endpoint of this study was breast cancer–specific survival (BCSS).ResultsOf the entire cohort, 76.0% of patients in the seventh AJCC staging system were restaged to the eighth AJCC pathological prognostic staging system. A total of 1431 (58.1%) and 1175 (47.7%) of them received chemotherapy and postmastectomy radiotherapy (PMRT), respectively. Pathological staging was an independent prognostic factor for BCSS. Using pathological prognostic stage IA as the reference, BCSS gradually became worse with increased hazard ratios. The 5‐years BCSS was 96.9%, 95.5%, 91.1%, 85.6%, and 75.5% in pathological prognostic stage IA, IB, IIA, IIB, and IIIA breast cancers, respectively (P < .001). In pathological prognostic stage IA, IB, and IIA breast cancers, the receipt of PMRT or chemotherapy was not correlated with better BCSS. However, PMRT was correlated with better BCSS in pathological prognostic stage IIB disease (P = .006), but not in pathological prognostic IIIA disease. Moreover, chemotherapy was correlated with better BCSS in pathological prognostic stage IIIA disease (P = .006), but not in pathological prognostic stage IIB disease.ConclusionsThe eighth AJCC pathological prognostic staging system provides more risk stratification of T3N0 breast cancers after mastectomy and might affect individualized decision‐making for chemotherapy and PMRT in this patient subset.
Classification of gastric cancer by EBV status combined with molecular profiling predicts patient prognosis
Authors: He Cai‐Yun , Qiu Miao‐Zhen , Yang Xin‐Hua , Zhou Da‐Lei , Ma Jiang‐Jun , Long Ya‐Kang , Ye Zu‐Lu , Xu Bo‐Heng , Zhao Qi , Jin Ying , Lu Shi‐Xun , Wang Zhi‐Qiang , Guan Wen‐Long , Zhao Bai‐Wei , Zhou Zhi‐Wei , Shao Jian‐Yong , Xu Rui‐Hua 
Published: June 2020

AbstractPurposeTo identify how Epstein‐Barr virus (EBV) status combined with molecular profiling predicts the prognosis of gastric cancer patients and their associated clinical actionable biomarkers.Experimental DesignA next‐generation sequencing assay targeting 295 cancer‐related genes was performed in 73 EBV‐associated gastric cancer (EBVaGC) and 75 EBV‐negative gastric cancer (EBVnGC) specimens and these results were compared with overall survival (OS).ResultsPIK3CA, ARID1A, SMAD4, and PIK3R1 mutated significantly more frequently in EBVaGC compared with their corresponding mutation rate in EBVnGC. As the most frequently mutated gene in EBVnGC (62.7%), TP53 also displayed a mutation rate of 15.1% in EBVaGC. PIK3R1 was revealed as a novel mutated gene (11.0%) associated almost exclusively with EBVaGC. PIK3CA, SMAD4, PIK3R1, and BCOR were revealed to be unique driver genes in EBVaGC. ARID1A displayed a significantly large proportion of inactivated variants in EBVaGC. A notable finding was that integrating the EBV status with tumor mutation burden (TMB) and large genomic instability (LGI) categorized the tumors into four distinct molecular subtypes and optimally predicted patient prognosis. The corresponding median OSs for the EBV+/TMB‐high, EBV+/TMB‐low, EBV‐/LGI‐, and EBV‐/LGI+ subtypes were 96.2, 75.3, 44.4, and 20.2 months, respectively. The different subtypes were significantly segregated according to distinct mutational profiles and pathways.ConclusionsNovel mutations in PIK3R1 and TP53 genes, driver genes such as PIK3CA, SMAD4, PIK3R1, BCOR, and ARID1A, and distinguished genomic profiles from EBVnGC were identified in EBVaGC tumors. The classification of gastric cancer by EBV, TMB, and LGI could be a good prognostic indicator, and provides distinguishing, targetable markers for treatment.
Molecular mechanisms, off‐target activities, and clinical potentials of genome editing systems
Authors: Zheng Nannan , Li Liyang , Wang Xiangdong 
Published: June 2020

AbstractMethodologies of genome editing are rapidly developing with the improvement of gene science and technology, mechanism‐based understanding, and urgent needs. In addition to the specificity and efficiency of on‐target sites, one of the most important issues is to find and avoid off‐targets before clinical application of gene editing as a therapy. Various algorithms, modified nucleases, and delivery vectors are developed to localize and minimize off‐target sites. The present review aimed to clarify off‐targets of various genome editing and explore potentials of clinical application by understanding structures, mechanisms, clinical applications, and off‐target activities of genome editing systems, including CRISPR/Cas9, CRISPR/Cas12a, zinc finger nucleases, transcription activator‐like effector nucleases, meganucleases, and recent developments. Current genome editing in cancer therapy mainly targeted immune systems in tumor microenvironment by ex vivo modification of the immune cells in phases I/II of clinical trials. We believe that genome editing will be the critical part of clinical precision medicine strategy and multidisciplinary therapy strategy by integrating gene sequencing, clinical transomics, and single cell biomedicine. There is an urgent need to develop on/off‐target‐specific biomarkers to monitor the efficacy and side‐effects of gene therapy. Thus, the genome editing will be an alternative of clinical therapies for cancer with the rapid development of methodology and an important part of clinical precision medicine strategy.
HK3 is correlated with immune infiltrates and predicts response to immunotherapy in non‐small cell lung cancer
Authors: Tuo Zhan , Zheng Xin , Zong Yan , Li Jie , Zou Chunyan , Lv Yi , Liu Jun 
Published: June 2020

AbstractBackgroundWith the knowledge of tumor immunobiology deepening among researchers, the breakthroughs in the field of tumor immunotherapy in recent years have provided new approaches for cancer therapy. While patients who receive treatment are all at risk of side effects, about one‐fifth of them have sustained responses. It is crucial to figure out the underlying mechanism of how the immune system regulates the nonsmall cell lung cancer (NSCLC) microenvironment to improve the benefit of immunotherapy. Regarding glucose metabolism, the initial step is to generate glucose‐6‐phosphate by phosphorylating glucose with hexokinases‐3 (HK3). According to a recent study, HK3 has a functional role in the treatment of acute promyelocytic leukemia and colorectal cancer.ResultsHere, we studied the co‐expression relationship between the glycolytic pathway gene and the immune checkpoint gene and found that the expression of HK3 in tumor tissues may be related to immune status. By analyzing The Cancer Genome Atlas (TCGA) data, we found that the expression of HK3 was closely related to the main clinical features as well as to molecular characteristics. We also predicted that cases with low expression of HK3 were usually malignant entities and were shown to be obvious genomic aberrations of driver oncogenes. At the same time, gene ontology analysis based on significantly related genes in HK3 expression showed that HK3 expression was linked to inflammatory activity and immune response. Additionally, HK3 showed a remarkable trend in predicting the efficacy of immunotherapy for patients receiving Keytruda (PD‐1 monoclonal antibody) treatment.ConclusionsThis is the first comprehensive study to characterize HK3 expression in NSCLC from molecular and clinical aspects.
Collaborated effort against SARS‐CoV‐2 outbreak in China
Authors: Yang Qiwen , Zhou Yang , Ai Jingwen , Ma Jinmin , Cao Fenglin , Cao Weifan , Zhang Wengeng , Wang Shifu , Chen Weijun , Ma Xiaoling , Zhang Wenhong , Li Weimin 
Published: June 2020

AbstractA previously unknown beta coronavirus, SARS‐CoV‐2, was discovered from a cluster of patients with pneumonia of unknown cause in Wuhan since the end of 2019. Ever since the start of COVID‐19, government administrations, academic institutions, and technology enterprises are under unprecedented cooperation in controlling this outbreak from pathogen identification, epidemic situation assessment, to outbreak containment. Timely identification, isolation, and whole‐genome sequencing of SARS‐CoV‐2 have laid the foundation for effective control of this novel infection. With the increasing case numbers worldwide, more real‐time information is emerging, changing our understandings to SARS‐CoV‐2 outbreak, and nonetheless refining the outbreak control responses. The efficient management of COVID‐19 requires global collaboration and an efficient share of information.
New focuses of clinical and translational medicine in 2020
Authors: Cheng Xin , Wu Duojiao , Cheng Yunfeng , Qiao Tiankui , Wang Xiangdong 
Published: June 2020

AbstractClinical and translational medicine is an ongoing opportunity and challenge to transition science from bench to patient, from patient to bench, and from patient to policy for scientists and clinicians. Of the many objectives, the most important one is to improve the quality of life in patients, including living duration, dignity, emotional well‐being, psychiatric and physical health, as well as independency. Emphasis and redefining concepts has allowed clinical and translational medicine to experience exciting and productive developments. Further discoveries, innovations, validations, and developments in clinical and translational medicine are expected in 2020. The present editorial aims to present the top three most discussed topics with high expectations for translation from clinical investigations and trials into practice and application.