bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of simultaneous interaction prediction approach (SiPA) for the expansion of interaction network of traditional Chinese medicine
Authors: Rui Mengjie , Pang Hui , Ji Wei , Wang Siqi , Yu Xuefei , Wang Lilong , Feng Chunlai 
Published: August 2020

Abstract
Background
Due to the lack of enough interaction data among compositions, targets and diseases, it is difficult to construct a complete network of Traditional Chinese Medicine (TCM) that comprehensively reflects active compositions and their synergistic network in terms of specific diseases. Therefore, mapping of the full spectrum of interaction between compounds and their targets is of central importance when we use network pharmacology approach to explore the therapeutic potential of the TCM.

Methods
To address this challenge, we developed a large-scale simultaneous interaction prediction approach (SiPA) integrated one interaction network based simple inference model (SIM), focusing on ‘logical relevance’ between compounds, proteins or diseases, and another compound-target correlation space based interaction prediction model (CTCS-IPM) that was built on the basis of the canonical correlation analysis (CCA) to estimate the position of compounds (or targets) in compound-protein correlated space. Then SiPA was applied to discover reliable multiple interactions for interaction network expansion of a TCM, compound Salvia miltiorrhiza. By means of network analysis, potential active compounds and their related network synergy underlying cardiovascular diseases were evaluated between expanded and original interaction networks. Part of new interactions were validated with existing experimental evidence and molecular docking.

Results
As evaluated with known test dataset, the established combination approach was proved to make highly accurate prediction, showing a well prediction performance for the SIM and a high recall rate of 85.2% for the CTCS-IPM. Then 710 pairs of new compound-target interactions, 24 pairs of new compound-cardiovascular disease interactions and 294 pairs of new cardiovascular disease-protein interactions were predicted for compound Salvia miltiorrhiza. Results of network analysis suggested the network expansion could dramatically improve the completeness and effectiveness of the network. Validation results of literature and molecular docking manifested that inferred interactions had good reliability.

Conclusions
We provided a practical and efficient way for large-scale inference of multiple interactions of TCM ingredients, which was not limited by the lack of negative samples, sample size and target 3D structures. SiPA could help researchers more accurately prioritize the effective compounds and more completely explore network synergy of TCM for treating specific diseases, indicating a potential way for effectively identifying candidate compound (or target) in drug discovery.
Early management of sight threatening retinopathy in incontinentia pigmenti
Authors: Michel Sarah , Reynaud Clothilde , Daruich Alejandra , Hadj-Rabia Smail , Bremond-Gignac Dominique , Bodemer Christine , Robert Matthieu P. 
Published: August 2020

Abstract
Background
Early blindness secondary to incurable retinal detachment is one of the main complications of incontinentia pigmenti (IP). The efficiency of ophthalmological management for preventing such evolution has not been proven.
The objective of this retrospective study was to report a screening and treatment strategy of the vascular retinopathy in newborns and infants with IP.

Results
All files of patients diagnosed with IP within the two first months of life in a single tertiary referral center, between 2010 and 2015, were retrospectively included. The minimum follow-up duration was three years.
Patients had undergone systematic indirect ophthalmoscopy examination, looking for signs of peripheric retinal vasculopathy, according to a standardized schedule: at diagnosis, at age 1, 2, 3, 6, 9, 12, 18 and 24 months, and then once a year. Urgent laser therapy was performed under anesthesia in case of signs of retinal ischemia.
Nineteen children files (17 girls) were studied. Median age at IP diagnosis was 1 day [0–44]; median age at first retinal evaluation was 25 days. Retinal manifestations occurred in 7 patients (n = 10/38 eyes, 26.3%); they were diagnosed at median age 19 days [3–59]. These patients underwent one or two ablative session per eye (mean 1.7, median 2), under general anaesthesia. No retinal detachment or fold occurred during the follow-up (median 6 years [3–9.8]).

Conclusion
Ocular screening should be performed in all cases of IP as soon as possible after diagnosis. A strict ophthalmological monitoring and prophylactic treatment of retinal vasculopathy can efficiently prevent the early blinding complications of the disease.
Roles of METTL3 in cancer: mechanisms and therapeutic targeting
Authors: Zeng Chengwu , Huang Wanxu , Li Yangqiu , Weng Hengyou 
Published: August 2020

AbstractN6-methyladenosine (m6A) is the most abundant mRNA modification and is catalyzed by the methyltransferase complex, in which methyltransferase-like 3 (METTL3) is the sole catalytic subunit. Accumulating evidence in recent years reveals that METTL3 plays key roles in a variety of cancer types, either dependent or independent on its m6A RNA methyltransferase activity. While the roles of m6A modifications in cancer have been extensively reviewed elsewhere, the critical functions of METTL3 in various types of cancer, as well as the potential targeting of METTL3 as cancer treatment, have not yet been highlighted. Here we summarize our current understanding both on the oncogenic and tumor-suppressive functions of METTL3, as well as the underlying molecular mechanisms. The well-documented protein structure of the METTL3/METTL14 heterodimer provides the basis for potential therapeutic targeting, which is also discussed in this review.
CircRNA hsa_circ_0002577 accelerates endometrial cancer progression through activating IGF1R/PI3K/Akt pathway
Authors: Wang Yu , Yin Lili , Sun Xiaofei 
Published: August 2020

Abstract
Background
Endometrial cancer (EC) is a common gynecologic malignancy worldwide. This study investigated the regulatory effects of circular RNA (circRNA) hsa_circ_0002577 on the tumorigenesis of EC.

Methods
Tumor samples and adjacent normal tissues were obtained from 84 EC patients. Recombinant lentiviral vectors expressing hsa_circ_0002577 (Lv-circRNA), short hairpin RNAs against hsa_circ_0002577 (sh-circRNA), miR-625-5p mimics, miR-625-5p inhibitor, lentiviral vectors expressing insulin-like growth factor 1 receptor (IGF1R) and their corresponding controls were transfected into EC cells as designated. A mouse xenograft model was established in BALB/c mice by inoculating Ishikawa cells transfected with sh-circRNA or control sequence.

Results
Hsa_circ_0002577 was upregulated in EC tissue samples and cells as compared to normal controls. EC patients with higher expression of hsa_circ_0002577 showed poorer overall survival and more advanced tumor stage. EC cells transfected with Lv-circRNA showed promoted proliferation, migration, and invasion, whereas the delivery of sh-circRNA exerted an opposite effect. Further analyses showed that hsa_circ_0002577 acted as a miR-625-5p sponge in EC cells. IGF1R was a potential downstream target of miR-625-5p. The expression of IGF1R in EC tissues was significantly higher than that in matched controls. Hsa_circ_0002577 accelerated EC development by inducing IGF1R expression and activating PI3K/Akt signaling pathway. Also, the knockdown of hsa_circ_0002577 delayed tumor growth and metastasis in the inoculated mice.

Conclusion
Our study showed that circRNA hsa_circ_002577 accelerated EC progression by acting as a miR-625-5p sponge, upregulating IGF1R and activating the PI3K/Akt pathway, suggesting the potential therapeutic use of hsa_circ_002577 in EC treatment.

Trial registration
Not Applicable.
KIAA1522 potentiates TNFα-NFκB signaling to antagonize platinum-based chemotherapy in lung adenocarcinoma
Authors: Wang Boshi , Jing Tiantian , Jin Weilin , Chen Jinnan , Wu Chengsi , Wang Mingrong , Liu Yizhen 
Published: August 2020

Abstract
Background
The platinum-based chemotherapy is the first-line regimen for the treatment of Non-small cell lung cancer (NSCLC). However, the therapeutic efficiency is largely limited by tenacious chemo-insensitivity that results in inferior prognosis in a cohort of patients. It has been known that KIAA1522 is aberrantly expressed and implicated in several types of solid tumors including NSCLC. Nowadays, knowledge about this gene is quite limited. Here, we aimed to identify the role of KIAA1522 in lung adenocarcinomas, and the molecular events that underlie KIAA1522-mediated chemoresistance to the platinum.

Methods
Immunohistochemistry were used to detect KIAA1522 expression in clinical NSCLC samples. Then, the survival analyses were performed to assess the link between KIAA1522 expression and overall survival or therapeutic outcome. In vivo depletion of KIAA1522 in adenocarcinoma cells were achieved by adeno-associated virus-mediated sgRNA/Cre delivery into the conditional KrasG12D/Cas9 expressed mice, which were designated to identify the roles of KIAA1522 in tumorigenesis and/or chemotherapy responses. The effects of KIAA1522 and downstream molecular events were studied by pharmacology in mice model and assays using in vitro cultured cells. The clinical relevance of our findings was examined by data-mining of online datasets from multiple cohorts.

Results
The clinical evidences reveal that KIAA1522 independently predicts both the overall survival and the outcome of platinum-based chemotherapy in lung adenocarcinomas. By using a KrasG12D-driven murine lung adenocarcinoma model and performing in vitro assays, we demonstrated that KIAA1522 is a critical positive regulator of lung adenocarcinoma and a modulator of cisplatin response. KIAA1522 potentiates the TNFα-TNFR2-NFκB signaling which in turn intensifies recalcitrance to cisplatin treatment. These results were further manifested by integrative bioinformatic analyses of independent datasets, in which KIAA1522 is tightly associated with the activity of TNFα-NFκB pathway and the cisplatin-resistant gene signatures. More strikingly, overexpression of KIAA1522 counteracts the cisplatin-induced tumor growth arrest in vivo, and this effect can be remarkably diminished by the disruption of NFκB activity.

Conclusion
High expression of KIAA1522 is turned out to be an indicator of dismal effectiveness of platinum-based therapy in lung adenocarcinomas. KIAA1522 hyperactivates TNFα-NFκB signaling to facilitate resistance to platinum reagents. Targeting NFκB signaling through small molecule inhibitors may be a rational strategy to conquer chemoresistance and synergize platinum-based chemotherapy in KIAA1522 overexpressed lung adenocarcinomas.
A systematic evaluation of single-cell RNA-sequencing imputation methods
Authors: Hou Wenpin , Ji Zhicheng , Ji Hongkai , Hicks Stephanie C. 
Published: August 2020

AbstractBackgroundThe rapid development of single-cell RNA-sequencing (scRNA-seq) technologies has led to the emergence of many methods for removing systematic technical noises, including imputation methods, which aim to address the increased sparsity observed in single-cell data. Although many imputation methods have been developed, there is no consensus on how methods compare to each other.ResultsHere, we perform a systematic evaluation of 18 scRNA-seq imputation methods to assess their accuracy and usability. We benchmark these methods in terms of the similarity between imputed cell profiles and bulk samples and whether these methods recover relevant biological signals or introduce spurious noise in downstream differential expression, unsupervised clustering, and pseudotemporal trajectory analyses, as well as their computational run time, memory usage, and scalability. Methods are evaluated using data from both cell lines and tissues and from both plate- and droplet-based single-cell platforms.ConclusionsWe found that the majority of scRNA-seq imputation methods outperformed no imputation in recovering gene expression observed in bulk RNA-seq. However, the majority of the methods did not improve performance in downstream analyses compared to no imputation, in particular for clustering and trajectory analysis, and thus should be used with caution. In addition, we found substantial variability in the performance of the methods within each evaluation aspect. Overall, MAGIC, kNN-smoothing, and SAVER were found to outperform the other methods most consistently.
The effect of psychoeducational intervention, based on a self-regulation model on menstrual distress in adolescents: a protocol of a randomized controlled trial
Authors: Asgari Somayeh , Alimoardi Zainab , Soleimani Mohammad Ali , Allen Kelly-Ann , Bahrami Nasim 
Published: August 2020

Abstract
Introduction
Menstrual distress caused by primary dysmenorrhea is associated with physical and psychological symptoms—before, after, and during menstruation. Leventhal’s self-regulation educational model is based on the cognitive and emotional experiences of threat responses to symptoms and relates to coping responses. This study aims to investigate the effect of the implementation of a psychoeducational intervention, based on the self-regulation model of menstrual distress in adolescents.

Methods/design
In this randomized controlled trial, 120 adolescent girls with moderate to severe menstrual pain (based on visual analog scale (VAS) ≥ 4) from twelve randomly selected high schools in Qazvin City will be enrolled in the study and will be randomly assigned to either a 3-session psychoeducational intervention (n = 60) or control (n = 60) groups. The sessions will be between 60 and 90 min apiece, and they will run for three consecutive weeks (one session per week). The data collection tools will include questionnaire eliciting menstrual information and demographics, the VAS, the Moos Menstrual Distress Questionnaire, and the illness perception questionnaire. One month prior to the intervention, both groups will participate in an initial assessment to assess the severity of their pain and level of menstrual distress. Finally, all questionnaires will be completed for three consecutive months after the intervention is completed.

Discussion
It is anticipated that findings of this study will provide evidence for the effectiveness of the Leventhal self-regulation model. Implications for improved practice, understanding, and treatment for menstrual distress may also arise.

Ethical considerations
The research protocol will be reviewed by the ethics committee, which is affiliated with the Qazvin University of Medical Sciences (Decree code: IR.QUMS.REC.1398.043).

Trial registration
IRCT20190625044002N1. Registration date: 2019-09-03.
Rivaroxaban compared to no treatment in ER-negative stage I–III early breast cancer patients (the TIP Trial): study protocol for a phase II preoperative window-of-opportunity study design randomised controlled trial
Authors: Castle John , Blower Emma , Bundred Nigel J. , Harvey James R. , Thachil Jecko , Marshall Andrea , Cox Karina , Cicconi Silvia , Holcombe Chris , Palmieri Carlos , Kirwan Cliona C. 
Published: August 2020

AbstractBackgroundBreast cancer patients are at a four-fold increased risk of developing a venous thromboembolism (VTE), a major cause of death in this group. Conversely, coagulation factors promote tumour growth and metastasis. This has been evidenced in preclinical models, with an inhibitory effect of anticoagulants on cancer growth through proliferative, angiogenic, apoptotic, cancer stem cell and metastatic processes. The extrinsic clotting pathway is also more upregulated in patients in the relatively poorer prognosis oestrogen receptor (ER)-negative breast cancer subgroup, with increased tumour stromal expression of the coagulation factors Tissue Factor and thrombin.Rivaroxaban (Xarelto®, Bayer AG, Leverkusen, Germany) is a direct oral anticoagulant (DOAC). It is a Factor Xa inhibitor that is routinely prescribed for the prevention of stroke in non-valvular atrial fibrillation and for both VTE prophylaxis and treatment. This trial will assess the anti-proliferative and other anti-cancer progression mechanisms of Rivaroxaban in ER-negative early breast cancer patients.MethodsThis UK-based preoperative window-of-opportunity phase II randomised control trial will randomise 88 treatment-naïve early breast cancer patients to receive 20 mg OD Rivaroxaban treatment for 11 to 17 days or no treatment. Treatment will be stopped 24 h (range 18–36 h) prior to surgery or repeat core biopsy. All patients will be followed up for 2 weeks following surgery or repeat core biopsy.The primary endpoint is change in tumour Ki67. Secondary outcome measures include tumour markers of apoptosis and angiogenesis, extrinsic clotting pathway activation and systemic markers of metastasis, tumour load and coagulation.DiscussionLaboratory evidence supports an anti-cancer role for anticoagulants; however, this has failed to translate into survival benefit when trialled in patients with metastatic disease or poor prognosis cancers, such as lung cancer. Subgroup analysis supported a potential survival benefit in better prognosis advanced disease patients. This is the first study to investigate the anti-cancer effects of anticoagulants in early breast cancer.Trial registrationUK National Research Ethics Service (NRES) approval 15/NW/0406, MHRA Clinical Trials Authorisation 48380/0003/001-0001. The sponsor is Manchester University NHS Foundation Trust, and the trial is co-ordinated by Cancer Research UK Liverpool Cancer Trials Unit (LCTU). EudraCT2014-004909-33, registered 27 July 2015.ISRCTN14785273.
Acupressure therapy and Liu Zi Jue Qigong for pulmonary function and quality of life in patients with severe novel coronavirus pneumonia (COVID-19): a study protocol for a randomized controlled trial
Authors: Zhang Shuaipan , Zhu Qingguang , Zhan Chao , Cheng Wei , Mingfang Xiao , Fang Min , Fang Lei 
Published: August 2020

AbstractBackgroundIn December 2019, pneumonia associated with the 2019 novel coronavirus (COVID-19) emerged in Wuhan, China. The number of cases has increased rapidly. Patients with severe disease have a poor prognosis, and there are no effective therapies for COVID-19. Only rapid advice guidelines for symptomatic supportive care have been used. A traditional Chinese medicine rehabilitation (TCMR) program consisting of acupressure therapy and Liu Zi Jue Qigong can be used as a complementary therapy for COVID-19. Hence, we designed a randomized trial to evaluate the efficacy and advantages of TCMR for treating patients with severe COVID-19.Methods/designThis is a parallel-design, two-arm, analyst assessor-blinded, randomized controlled trial. A total of 128 patients with COVID-19 aged from 20 to 80 years will be recruited and assigned randomly into a guideline therapy group and a guideline therapy plus TCMR group at a 1:1 ratio. Patients in both groups will receive guideline therapy. The patients in the intervention group will perform acupressure therapy and Liu Zi Jue Qigong exercises in addition to conventional treatments twice a day and will be persistent from admission to discharge. The primary outcome will be measured with the Modified Medical Research Council Dyspnea Scale, and the secondary outcomes will include the Activities of Daily Living Barthel Index Scale, Patient Health Questionnaire-9 Scale, and the Respiratory Symptoms Scale. The assessments of the clinical scales will be performed at three points (before treatment, the 7th day during hospitalization, and the discharge day). Adverse events will be noted and recorded for the safety evaluation.DiscussionThis trial will provide high-quality evidence of the value of TCMR, which consists of acupressure therapy and Liu Zi Jue Qigong exercises, for treating patients with severe COVID-19.Trial registrationChinese Clinical Trial RegistryChiCTR2000029994. Registered on 18 February 2020
Efficacy of Hwangryunhaedok-tang (Huang-lian-jie-du-tang, Oren-gedoku-to) for patients with hyperlipidemia: a study protocol for a randomized, double-blind, placebo-controlled, parallel, investigator-initiated clinical trial
Authors: Lee Boram , Han Kyungsun , Park Hyo-Ju , Kim Ae-Ran , Kwon O-Jin , Yang Changsop , Cho Chung-Sik 
Published: August 2020

AbstractBackgroundThe prevalence of hyperlipidemia continues to increase due to aging and lifestyle changes. Statins are currently used as the first choice for treating hyperlipidemia, but are limited by adverse reactions. Hwangryunhaedok-tang (HHT) has received attention as a promising intervention for hyperlipidemia through a few experimental and clinical trials. This study aims to explore the feasibility, effectiveness, and safety of HHT for hyperlipidemia treatment.MethodsThis is a study protocol for a randomized, double-blind, placebo-controlled, parallel, investigator-initiated, pilot clinical trial held in Daejeon, Republic of Korea. Thirty patients with hyperlipidemia will be randomly allocated to HHT or placebo granule groups in equal proportions. Participants will be administered HHT or placebo granules three times per day for 8 weeks and followed up for another 4 weeks. The primary outcome is low-density lipoprotein cholesterol at 8 weeks from the commencement of treatment. Other blood lipid parameters, biomarkers of atherosclerosis, the degree of arteriosclerosis, blood glucose parameters, blood pressure, anthropometric parameters, health-related quality of life, and the changes in the general symptoms of cold and hot patterns will be measured as secondary outcomes. Adverse events and laboratory test results will be investigated to assess the safety. Changes in the gut microbiome before and after intervention will also be assessed as an exploratory outcome through next-generation sequencing. Data will be recorded in electronic case report forms and analyzed using SAS® Version 9.4.DiscussionThis is a rigorously designed pilot clinical trial to explore the effect and safety of Hwangryunhaedok-tang compared to placebo control for patients with hyperlipidemia, thereby potentially facilitating better management of hyperlipidemia. The results of this pilot study could form the foundation for a future large-scale, confirmatory clinical trial.Trial registrationClinical Research Information ServiceKCT0004564. Registered on December 18, 2019
Zmo0994, a novel LEA-like protein from Zymomonas mobilis, increases multi-abiotic stress tolerance in Escherichia coli
Authors: Yang Jungwoo , Kim Ha Eun , Jung Young Hoon , Kim Jungyeon , Kim Do Hyoung , Walmsley Adrian R. , Kim Kyoung Heon 
Published: August 2020

Abstract
Background
Pretreatment processes and subsequent enzymatic hydrolysis are prerequisites to utilize lignocellulosic sugar for fermentation. However, the resulting hydrolysate frequently hinders fermentation processes due to the presence of inhibitors and toxic products (e.g., ethanol). Thus, it is crucial to develop robust microbes conferring multi-stress tolerance.

Results
Zmo0994, a functionally uncharacterized protein from Zymomonas mobilis, was identified and characterized for the first time. A major effect of Zmo0994 was a significant enhancement in the tolerance to abiotic stresses such as ethanol, furfural, 5′-hydroxymethylfurfural and high temperature, when expressed in Escherichia coli. Through transcriptome analysis and in vivo experiments, the cellular mechanism of this protein was revealed as due to its ability to trigger genes, involved in aerobic respiration for ATP synthesis.

Conclusions
These findings have significant implications that might lead to the development of robust microbes for the highly efficient industrial fermentation processes.