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4. Construction of a Prognostic Signature of 10 Autophagy-Related lncRNAs in Gastric Cancer

Author

Wang W, Pei Q, Wang L, Mu T, and Feng H

Subjects
gastric cancer, autophagy, tcga, prognostic signature, immunotherapy, Medicine (General), R5-920
Abstract

Wenwen Wang,1,2 Qingshan Pei,1 Lifen Wang,1 Tong Mu,1 Hua Feng1 1Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China; 2Shandong Provincial Engineering and Technological Research Center for Liver Diseases Prevention and Control, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of ChinaCorrespondence: Hua Feng, Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jing 5 Road, Jinan, Shandong, 250021, People’s Republic of China, Tel +86 531-68773293, Fax +86 531-87906348, Email fenghua198104@163.comBackground: Autophagy plays a double-edged sword role in cancers. LncRNAs could regulate cancer initiation and development at various levels. However, the role of autophagy-related lncRNAs (ARlncs) in gastric cancer (GC) remains indistinct.Methods: GC gene expression profile and clinical data were acquired from the Cancer Genome Atlas (TCGA). The prognostic signature composed of ARlncs was established via cox regression analysis. Kaplan–Meier (K-M) survival curve was adopted to show overall survival (OS). Independence and reliability of risk signature were visualized by cox regression analysis and ROC curve. A nomogram was constructed and the reliability was analyzed by ROC curve. Immune infiltrating cells and check points were also analyzed.Results: A prognostic signature was constructed which stratified GC patients into high- and low-risk groups according to risk score calculated via the 10 ARlncs including LINC01094, AC068790.7, AC090772.1, AC005165.1, PVT1, LINC00106, AC026368.1, AC090912.3, AC013652.1, UICLM. Patients in high-risk group showed a poor prognosis (p< 0.001). Cox regression analysis showed signature was an independent prognostic factor (p< 0.001). Areas under curves (AUC) of ROC for risk signature for predicting OS outweighed age, gender, grade, T, M and N, which suggested the reliability of the signature. A nomogram was constructed with risk signature, T, M, N and age and its AUC of ROC for 1-, 3-, and 5-year was 0.700, 0.730, 0.757 respectively, which showed good reliability. Macrophage M2, T cell CD8+ and T cell CD4+ memory resting had greatest difference between the two risk groups according to CIBERSORE-ABS algorithm (p< 0.001). CD274 (PD-L1), PDCD1 (PD-1) and PDCD1LG2 (PD-L2) were expressed higher in the high-risk group (p< 0.05), which implied that immunotherapy may be a good choice for these patients.Conclusion: The risk signature based on 10 ARlncs can serve as an efficacious prognostic predictor and guide the immunotherapies and precise treatment for GC patients.Keywords: gastric cancer, autophagy, TCGA, prognostic signature, immunotherapy

Published
2022

7. Importance of habitat heterogeneity in tidal flats to the conservation of migratory shorebirds

Author

Cai, S., Mu, T., Peng, H.-B., Ma, Z., Wilcove, D.S., Cai, S., Mu, T., Peng, H.-B., Ma, Z., and Wilcove, D.S.

Abstract

Understanding species distribution patterns and what determines them is critical for effective conservation planning and management. In the case of shorebirds migrating along the East Asian-Australasian Flyway (EAAF), the loss of stopover habitat in the Yellow Sea region is thought to be the primary reason for the precipitous population declines. However, the rates of decline vary considerably among species, and it remains unclear how such differences could arise within a group of closely related species using apparently similar habitats at the same locales. We mapped the spatial distributions of foraging shorebirds, as well as biotic (benthic invertebrates consumed by migrating shorebirds) and abiotic (sediment characteristics) environmental factors, at a key stopover site in eastern China. Five of the six sediment characteristics showed significant spatial variation with respect to distance along the shoreline or distance from the seawall in the same tidal flat. The biomasses of four of the six most abundant benthic invertebrates were concentrated in the upper or middle zones of the tidal flat. The distribution patterns of all three focal shorebird species on the tidal flat were best explained jointly by this heterogeneity of sediment characteristics and invertebrate prey. These results suggest that the loss of tidal flats along the Yellow Sea, which is typically concentrated at the upper and middle zones, may not only reduce the overall amount of staging habitat, but also disproportionately affect the most resource-rich portions for the birds. Effective conservation of shorebird staging areas along the EAAF and likely elsewhere must consider the subtle habitat heterogeneity that characterizes these tidal flats, prioritizing the protection of those portions richest in food resources, most frequently used by focal bird species, and most vulnerable to anthropogenic threats.

Published
2023

8. Achievements, challenges, and recommendations for waterbird conservation in China's coastal wetlands

Author

Ma, Z., Choi, C.-Y., Gan, X., Li, J., Liu, Y., Melville, D.S., Mu, T., Piersma, T., Zhang, Z., Ma, Z., Choi, C.-Y., Gan, X., Li, J., Liu, Y., Melville, D.S., Mu, T., Piersma, T., and Zhang, Z.

Abstract

China's coastal wetlands provide breeding, migration stopover, and wintering habitats for about 230 waterbird species, which is more than a quarter of all waterbirds in the world. Large-scale and high intensity human activities have resulted in serious loss and degradation of coastal wetlands over the past half century, causing population declines in many waterbirds. Through a literature review and expert surveys, this article reviews conservation measures taken in recent decades to protect waterbirds in China's coastal wetlands and provides recommendations for future conservation action from three aspects: policy and administration, habitat conservation and management, and multiparty participation. Over the past decades, many conservation legislation, regulations and action plans at the national level and more site-specific measures and interventions have been implemented, with notable improvement in the effectiveness in policy making and multi-stakeholder participation. Accordingly, some threats to waterbirds have been mitigated and many key sites for waterbirds have been designated as strictly protected nature reserves. However, some critical issues still remain, mostly related to habitat conservation and management, such as coastal wetland restoration, control of invasive Spartina alterniflora, control of environmental pollution, and improvement of artificial habitat quality. We highlight that protecting natural tidal wetlands and improving habitat quality are critical for the conservation of coastal waterbirds, especially those highly dependent on the intertidal wetlands. China has demonstrated strong commitment to ecological conservation and restoration for the future, in terms of both funding and policies for biodiversity and wetland ecosystems. It is important that this commitment to conserve coastal waterbirds is supported continuously by science- and evidence-based decisions and actions.

Published
2023

14. Evaluating staging habitat quality to advance the conservation of a declining migratory shorebird, Red Knot Calidris canutus

Author

Mu, T., Cai, S., Peng, H., Hassell, C.J., Boyle, A., Zhang, Z., Piersma, T., Wilcove, D.S., Mu, T., Cai, S., Peng, H., Hassell, C.J., Boyle, A., Zhang, Z., Piersma, T., and Wilcove, D.S.

Abstract

1. Identifying where and when population “bottlenecks” occur is critical to the conservation of migratory species, many of which are declining precipitously worldwide. Especially challenging is the evaluation of changes to staging sites. These sites are indispensable links in the migratory cycle but are typically used only briefly. 2. We devised a field-based approach to assess the quality and carrying capacity of a critical staging site in Nanpu, China, for the declining, migratory Red Knot (Calidris canutus rogersi & C. c. piersmai) during northward migration. The Nanpu tidal flat supports 50,000-100,000 Red Knotsannually, and while there, the knots feed almost exclusively on the bivalve Potamocorbula laevis. We simultaneously monitored changes in the abundance of Red Knots and bivalves across the entire staging site in spring 2018. 3. After taking into account potential competition with other shorebird species, we estimated that the Nanpu tidal flat was capable of supporting approximately 1.46-1.70 times the current observed level of usage of the site by Red Knots, and therefore is operating below, but close, to carrying capacity with respect to food resources for Red Knots. This result suggests that any further development of this site could harm the EAAF Red Knot population. 4. Synthesis and applications: Quantitative monitoring and evaluation of habitat quality of staging sites are essential to successfully conserve declining migratory species. In particular, researchers and conservation practitioners should incorporate both population size and staging duration in order to more accurately assess the importance of different sites and to quantify how changes in staging habitat quality may translate into changes in migrant population sizes at both local and global scales.

Published
2022

16. Barriers to Accessing Addiction Treatment for Women at Risk of Homelessness.

Author

Rizzo, D, Mu, T, Cotroneo, S, Arunogiri, S, Rizzo, D, Mu, T, Cotroneo, S, and Arunogiri, S

Abstract

Women remain under-represented in addiction treatment, comprising less than a third of clients in treatment services. Shame, stigma, and fear of legal and social repercussions (e.g., child protection involvement) are major barriers impacting on treatment-seeking for women. This is compounded for women at risk of homelessness, with practical and logistical reasons for not engaging in treatment. We conducted a qualitative study with both clinicians and service-providers, and women with lived experience of addiction and at risk of homelessness, to identify barriers to access and help-seeking within this vulnerable population. Adult women with lived experience of homelessness and addiction were invited to participate in an online focus group. Interviews were transcribed and analyzed using framework analysis. Analysis resulted in the identification of barriers to access in three areas. These were system-related, socio-cultural, and emotional barriers. We also present findings from the focus group recorded in real-time, using the novel method of digital illustration. This study highlights key factors impacting on help-seeking and access to treatment for addiction faced by women at risk of homelessness. The findings of this study highlight important areas of consideration for clinicians and service-providers working with women who experience addiction, as well as informing future research directions for this priority population. Findings are discussed in the context of exigent literature.

Published
2022

20. ESTIMATING THE PLANT NITROGEN CONTENT OF FOXTAIL MILLET (SETARIA ITALICA L.) BASED ON CONTINUOUS WAVELET ANALYSIS.

Author

XIA, F., FENG, M. C., ZHU, S. A., WANG, C., MU, T. T., XIAO, L. J., YANG, W. D., ZHANG, M. J., SONG, X. Y., YANG, H., and QIN, M. X.

Subjects
NITROGEN content of plants, FOXTAIL millet, WAVELETS (Mathematics), SUPPORT vector machines, WAVELET transforms
Abstract

The variation in the plant nitrogen content (PNC) directly characterizes the growth of foxtail millet, and estimation of the PNC using hyperspectral techniques is important for effective evaluating the growth of this species. Effective statistical modeling methods can improve the accuracy and reliability of PNC estimates. In this study, field experiments were conducted under different gradients of organic fertilizer to develop an estimation model for determining the PNC in foxtail millet. The continuous wavelet transform (CWT) was used to process the collected reflection spectra and construct partial least square regression (PLSR), random forest (RF) and support vector machine (SVM) estimation models. Among the common wavelet families, Daubechies (db5), Coiflets (coif3), Biorthogonal (bior1.5), Symlets (sym8), haar and rbio3.1 were selected to analyze the correlation with the PNC, and all the wavelet functions had a good correlation with the PNC. The correlation coefficients were 0.834, -0.835, -0.973, -0.784, -0.789 and -0.770, respectively. The CWT technique can significantly improve the prediction accuracy of the PNC. The best PNC estimate was obtained using db5 (R²cal = 0.859, RMSEcal = 3.415), and the best decomposition scale was 24. In addition, the validation data indicate that db5-RF can be used to estimate the PNC (R²val = 0.935, RMSE: = 1.311, RPDval = 3.32). This study provides a reference for the practical application of PNC analysis in foxtail millet. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Reaching, Engaging and Advancing Research (REAR); An Assessment of Health Managers’ Skills and Knowledge in Data Management, Analysis, Utilization, and Dissemination Kenya, Tanzania and Rwanda

Author

Madhavaram S, Owour K, Remera E, Dawson S, Kumalija C, Muhula S, Ah Mu T, Funk H, Ngunu C, Memiah P, Oyore Jp, Cook C, Majigo M, Kingori C, Mwangi W, Mwangi M, Nsanzimana S, Sebeza J, and Mochache

Subjects
general_medical_research, Tanzania, Evidence-based practice, biology, Health professionals, business.industry, Data management, education, Capacity building, Business, Public relations, Workforce development, biology.organism_classification
Abstract

The objective of the study was to investigate the gap between data and evidence-based decisions among healthcare professionals considering the enormous amount of individual and aggregate data collected. Our study assessed the capacity, skills, and knowledge of the Ministry of Health leadership staff to understand data management, analysis, utilization, and dissemination. Three key components were assessed: 1) Knowledge through true/false questions, 2) Level of Skill (and Competency) using a Likert scale, and 3) Understanding of Key Concepts and Tools based on a Likert scale. The 183 study respondents were diverse healthcare professionals from Kenya, Tanzania, and Rwanda. Majority of respondents had not received any training on data management, analysis, interpretation, and utilization techniques, further there was a significant difference between those who had received training versus those who had not(p=0.005). The respondents were competent in work-related experiences but lacked skills and knowledge on: data concepts and tools, study designs, and types of data analysis. These findings explain the gap between data management, analysis, utilization, and dissemination among health professional’s cadre. To enhance service delivery and optimal provision of health care, it is imperative to have all health care professionals receive a well-designed training on data management, analysis, interpretation, and utilization.

Published
2018

31. LncRNA LINC00958 promotes tumor progression through miR-4306/CEMIP axis in osteosarcoma.

Author

ZHOU, Y. and MU, T.

Abstract

OBJECTIVE: To investigate the mechanism by which LINC00958 affects osteosarcoma progression through miR-4306/CEMIP axis. PATIENTS AND METHODS: The microarray data (GSE66673) for gene expression in osteosarcoma cells were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes were analyzed by bioinformatics tools. Real-time quantitative PCR (RT-qPCR) was performed to detect the expression levels of LINC00958, miR-4306, and CEMIP in osteosarcoma tissues and cell lines. Western blot was performed to detect the expression levels of CEMIP. Subcellular fractionation analysis and RNA Fluorescence in situ hybridization (FISH) assay were performed to analyze the subcellular localization of LINC00958. The target relationship between LINC00958, CEMIP, and miR- 4306 was verified by public bioinformatics database and dual-luciferase reporter assay. RNA immunoprecipitation (RIP) assay was performed to detect LINC00958 and miR-4306 bound to AGO2. The biological functions of LINC00958 and miR-205 on proliferation, cell cycle, apoptosis, migration, and invasion of osteosarcoma cells were evaluated by gain-of-function and loss-of-function experiments. Tumorigenic and metastatic abilities of cells in vivo were detected by xenograft tumor experiments and tumor metastasis assays in nude mice. Correlation between miR-4306 and LINC00958 or CEMIP expression in osteosarcoma tissues was analyzed using Pearson correlation analysis. Kaplan-Meier analysis was performed to assess the relationship between LINC00958 expression and overall survival of osteosarcoma patients. RESULTS: LINC00958 expression levels significantly increased in osteosarcoma tissues while miR-4306 expression levels significantly decreased, and the expression of these two genes was negatively correlated. Subcellular fractionation analysis and RNA FISH assay demonstrated that LINC00958 was mainly localized in the cytoplasm. Dual-luciferase reporter gene assay verified that LINC00958 competitively bound miR-4306 and repressed its expression. Silencing of LINC00958 inhibited proliferation, cell cycle, metastasis, and invasion of osteosarcoma cells while inducing cellular apoptosis. The introduction of miR-4306 inhibitors reversed the tumor-suppressing effect of silencing LINC00958. miR-4306 binds to CEMIP and suppressed its expression. Xenograft tumor experiments and tumor metastasis assays in nude mice demonstrated that silencing LINC00958 inhibited osteosarcoma cells’ growth and metastasis while inhibiting miR-4306 reversed this effect. Kaplan-Meier analysis showed that high expression of LINC00958 was significantly associated with poor prognosis of osteosarcoma patients. CONCLUSIONS: LINC0095 promotes tumorigenesis and metastasis in osteosarcoma by competitively inhibiting miR-4306 expression, leading to elevated expression of CEMIP. [ABSTRACT FROM AUTHOR]

Published
2021

33. Loss of habitat leads to loss of birds: reflections on the Jiangsu, China, coastal development plans

Author

Piersma, T., Chan, Y.-C, Mu, T., Hassell, C.J., Melville, D.S., Peng, H.-B., Ma, Z., Zhang, Z., Wilcove, D.S., Piersma, T., Chan, Y.-C, Mu, T., Hassell, C.J., Melville, D.S., Peng, H.-B., Ma, Z., Zhang, Z., and Wilcove, D.S.

Abstract

Prompted by the realization that parts of the coast of southern Jiangsu Province, China, are under threat of reclamation, we here summarize evidence that loss of intertidal habitats around the Yellow Sea and at other parts along the Chinese and Korean coasts has already led to severe population declines of migratory shorebirds, including multiple endangered species. All the evidence currently at hand suggest that the plans to reclaim (develop) additional intertidal habitat in this region poses a substantial threat to the remaining shorebird populations. We recommend that new Environmental Impact Assessments are warranted before further reductions in the extent of mudflats take place.

Published
2017

38. Analysis of gluconate metabolism for pyruvate production in engineered Escherichia coli based on genome-wide transcriptomes.

Author

Yang, M., Mu, T., Zhong, W., Olajuyin, A.M., and Xing, J.

Subjects
*METABOLISM, *BACTERIAL genetics, *ESCHERICHIA coli, *PYRUVATES, *NAD (Coenzyme), *GLYCOLYSIS, *GLYCERIN metabolism
Abstract

For pyruvate-producing strains, intracellular reduced nicotinamide adenine dinucleotide ( NADH) accumulation is the main reason for the glycolysis inhibition. Comparing with glucose, using sodium gluconate as carbon source brought a decrease in NADH production and an increase in pyruvate production in engineered strain YP211. In order to explore the metabolic advantages of gluconate, genome-wide transcriptome analysis was employed to compare the metabolic differences between the two carbon sources. The results showed that the transcription of the genes gntU, gntK, and gntT responsible for transport and phosphorylation of gluconate, and genes edd and eda belonging to the Entner-Doudoroff ( ED) pathway, was significantly enhanced. This suggested that the shortest route for the synthesis of pyruvate from gluconate was activated, and the synthesis of NADH was halved. Besides, the transcription of genes glp ABCDTKF related to the glycerol metabolism was significantly enhanced, which might be because glycerol metabolism pathways were activated in the absence of glucose. These results provided valuable information for the further design of metabolic pathways in the construction of pyruvate-producing strains. Significance and Impact of the Study Comparing with glucose, using sodium gluconate as carbon source brought a decrease in nicotinamide adenine dinucleotide and an increase in pyruvate production in engineered strain YP211. From the genome-wide transcriptome analysis, the Entner-Doudoroff pathway was activated strongly in gluconate metabolism, which innovatively provided a shorter and more effective pathway for pyruvate production. [ABSTRACT FROM AUTHOR]

Published
2017
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49. Use of medical simulation in neonatal-perinatal fellowship training programs.

Author

Johnson, L., Mu, T., and Sawyer, T.

Subjects
*MEDICAL simulation, *MEDICAL fellowships, *MEDICAL education, *PERINATOLOGY, *MEDICAL statistics, *PROFESSIONALISM
Abstract

Objective: Simulation-based training is being increasingly used in undergraduate and graduate medical education. There are no prior studies on the use of simulation-based training in Neonatal-Perinatal Medicine (NPM) fellowship programs in the U.S. We conducted this study to evaluate the current use of simulation-based training in these programs. Subjects and methods: An 18 question survey was sent to all NPM fellowship Program Directors in the U.S. The survey contained questions regarding the use of simulation-based training, details on how the training was accomplished and perceived barriers to its use. Results: 62% (60/97) of the programs surveyed responded. Eighty-one percent of responding programs reporting using simulation. Of those, 86% used mannequin-based high-fidelity simulation. The most common uses for simulation training included: neonatal resuscitation skills (86%), procedural skills (71%), airway management (69%), crisis resource management/team training (69%), and professionalism (47%). Most programs are still developing their curriculums and there was a wide range in the amount of time spent on simulation training. Common barriers included time and cost of equipment. Conclusions: The majority of NPM fellowship programs we surveyed used simulation as part of their training and most did so with the use of high-fidelity mannequins. The proportion of programs using simulation for crisis team management and professionalism suggest that these types of training are important component of simulation-based training in addition to the traditional use for resuscitation skills. Further research is needed to determine if simulation-based training in NPM fellowship provides important benefits over traditional teaching methods. [ABSTRACT FROM AUTHOR]

Published
2012
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50. Permissive hypercapnia practices among neonatologists in the United States: Results of a national survey.

Author

Mu, T. S., Sawyer, T. L., Jordan, C. P., and Uyehara, C. F. T.

Subjects
*NEONATOLOGISTS, *PEDIATRICIANS, *HYPERCAPNIA, *PHYSIOLOGICAL effects of carbon dioxide, *LUNG injuries
Abstract

Objective: There is no consensus among practicing neonatologists regarding the definition of permissive hypercapnia and yet its practice is commonly employed to prevent lung injury from excessive ventilation. The goal of this study was to determine clinical practice among neonatologists regarding a definition of permissive hypercapnia in a preterm infant based upon gestational age at birth, degree of respiratory support, and acute vs. chronic management. Methods: Surveys were e-mailed to neonatologists who are members of the AAP Section on Perinatal Pediatrics containing a link to an on-line survey company (www.surveymonkey.com). Responses were compared using Pearson X2 analyses. Results: Of 2689 individuals surveyed, 747 (28%) completed the survey. 97% of those respondents reported practicing permissive hypercapnia. Regardless of stated permissive hypercapnia practice preferences, the majority of neonatologists accept 45-55 mm Hg as their target PaCO2 levels on the first day of life and 55-65 mm Hg thereafter. Conclusions: Our data suggest most neonatologists surveyed employ a permissive hypercapnia respiratory management strategy, as they accept higher than normal PaCO2 levels for preterm infants . Our findings highlight the need for continuing studies to document whether the values of targeted PaCO2 reported here provide lung protection without compromising overall safety and long-term complications. [ABSTRACT FROM AUTHOR]

Published
2011
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