bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimated Breeding Values of Beef Sires Can Predict Performance of Beef-Cross-Dairy Progeny
Authors: Martín Natalia , Coleman Lucy , López-Villalobos Nicolás , Schreurs Nicola , Morris Stephen , Blair Hugh , McDade Julie , Back Penny , Hickson Rebecca
Published: September 2021

On average, half of the animal’s estimated breeding value (EBV) is passed on to their progeny. However, it is not known how the performance of beef-cross-dairy cattle relates to the EBV of their beef sire. Such information is required to determine the genetic potential of beef sires selected based on existing EBV to be used on dairy cows in New Zealand. This study evaluated the relationship between the EBV of 30 Angus and 34 Hereford sires and the performance of their progeny for birth, growth, and carcass traits, via progeny testing of 975 beef-cross-dairy offspring born to dairy cows and grown on hill country pasture. Overall, BREEDPLAN EBV did predict progeny performance of the beef-cross-dairy cattle from this study. Gestation length and birthweight increased with increasing sire EBV (mean 0.37–0.62days and 0.52–0.64kg, respectively, p<0.05). Age at weaning decreased with increasing sire EBV for liveweight at 200days (0.17–0.21days per extra kilo of sire EBV, p<0.05) but sire EBV for liveweight at 200days had no effect on the liveweight of the progeny at 200days for either breed (p>0.05). Liveweight increased with sire EBV for liveweight at 400, 600, and 800days, by a similar amount for both breeds (between 0.23 and 0.42kg increase in progeny liveweight per extra kilo of sire EBV, p<0.05). The relationships were more inconsistent for carcass traits. For Hereford, carcass weight and eye muscle area increased with increasing sire EBV (0.27kg and 0.70cm2, respectively, p<0.05). For Angus, marble score increased by 0.10 with 1% extra in sire EBV for intramuscular fat (p<0.05). Rib fat depth tended to increase with sire EBV for both breeds (p<0.1). EBV derived from beef-breed data work in dairy-beef systems but maybe slightly less than the expected 0.5units of performance per unit of EBV. New Zealand farmers should consider BREEDPLAN EBV when selecting sires to mate dairy cows or when buying beef-cross-dairy calves for beef production, to ensure the resulting calves are born safely and on time and then grow well to produce carcasses of suitable meat and fat composition.
Prognostic Value of Immune-Related Multi-IncRNA Signatures Associated With Tumor Microenvironment in Esophageal Cancer
Authors: Pang Jingjing , Pan He , Yang Chunxiu , Meng Pei , Xie Wen , Li Jiahao , Li Yueying , Xiao Shu-Yuan
Published: September 2021

Esophageal cancer is the eighth most common cancer and the sixth leading cause of cancer death worldwide. Hence, for a better understanding of tumor microenvironment and to seek for novel molecular targets for esophageal cancer, we performed related studies on two histopathological subtypes of esophageal cancer: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). Bioinformatic analyses were conducted based on the RNA-seq, genomic mutation, and clinical data from TCGA and GEO cohorts. We clustered patients into high-immunity and low-immunity groups through the ssGSEA results. The ESTIMATE algorithm was used to evaluate the tumor microenvironment. Patients with high immunity in both ESCC and EAC had lower tumor purity and poor survival. Subsequently, CIBERSORT was performed to learn about the detailed difference of tumor-infiltrating lymphocytes (TILs) between high- and low-immunity patients. Specific increase of M2 macrophages and decrease of activated dendric cells can be observed in ESCC and EAC, respectively. The most enriched functions and pathways of high-immunity patients were immunoglobulin complex, MHC class II protein complex, and allograft rejection according to the GO terms and KEGG. Two prognostic immune-related multi-lncRNA risk models were constructed and validated by ROC curve and PCA in ESCC and EAC. High-risk patients in both subtypes had poor survival, advanced clinical characteristics, and higher drug susceptibility except cisplatin and sorafenib. In addition, the tumor mutation burden (TMB) was positively correlated with the risk level in the ESCC and EAC and showed distinct differences between the two subtypes. In summary, we comprehensively analyzed the tumor microenvironment for two subtypes of esophageal cancer, identified two multi-lncRNA signatures predictive for the prognosis, and explored the possibility of the signatures to forecast drug susceptibility as well as TMB for the first time. The findings may serve as a conceptual basis for innovative strategy of individualized immunotherapy for esophageal cancer.
Clinicopathological and Prognostic Significance of Long Non-coding RNA MIAT in Human Cancers: A Review and Meta-Analysis
Authors: Wang Yongfeng , Fu Liangyin , Lu Tingting , Zhang Guangming , Zhang Jiawei , Zhao Yuanbin , Jin Haojie , Yang Kehu , Cai Hui
Published: September 2021

Background: Although the treatment of cancer has made evident progress, its morbidity and mortality are still high. A tumor marker is a critical indicator for early cancer diagnosis, and timely cancer detection can efficiently help improve the prognosis of patients. Therefore, it is necessary to identify novel markers associated with cancer. LncRNA myocardial infarction associated transcript (MIAT) is a newly identified tumor marker, and in this study, we aimed to explore the relationship between MIAT and clinicopathological features and patient prognosis.

Methods: We searched PubMed, Embase, Web of Science, and The Cochrane Library from inception to September 2020 to identify correlational studies. Then, we extracted valid data and used Stata software to make forest plots. We used the hazard ratio (HR) or odds ratio (OR) with 95% CI to evaluate the relationship between aberrant expression of MIAT and patients' prognosis and clinicopathological features.

Results: The study included 21 studies, containing 2,048 patients. Meta-analysis showed that overexpression of lncRNA MIAT was associated with poor overall survival (OS) (HR = 1.60, 95% CI, 1.31–1.96, p < 0.001). In addition, high expression of MIAT could forecast tumor size (OR = 2.26, 95% CI 1.34–3.81, p = 0.002), distant metastasis (OR = 2.54, 95% CI 1.84–3.50, p < 0.001), TNM stage (OR = 2.38, 95% CI 1.36–4.18, p = 0.002), lymph node metastasis (OR = 2.59, 95% CI 1.25–5.36, p = 0.011), and the degree of differentiation (OR = 2.65, 95% CI 1.54–4.58, p < 0.001). However, other clinicopathological features, including age (OR = 1.07, 95% CI 0.87–1.32, p = 0.516), gender (OR = 0.95, 95% CI 0.77–1.19, p = 0.668), and histology (OR = 0.72, 95% CI 0.48–1.10, p = 0.128) were not significantly different from high expression of MIAT.

Conclusions: Our study showed that overexpression of MIAT is related to poor overall survival and clinicopathological features. MIAT can be considered a novel tumor marker to help diagnose tumors earlier and improve patient prognosis.
Identifying Risk Factors for Secondary Infection Post-SARS-CoV-2 Infection in Patients With Severe and Critical COVID-19
Authors: Guo Mingquan , Gao Menglu , Gao Jing , Zhang Tengfei , Jin Xin , Fan Jian , Wang Qianying , Li Xin , Chen Jian , Zhu Zhaoqin
Published: September 2021

Emerging evidence has unveiled the secondary infection as one of the mortal causes of post-SARS-CoV-2 infection, but the factors related to secondary bacterial or fungi infection remains largely unexplored. We here systematically investigated the factors that might contribute to secondary infection. By clinical examination index analysis of patients, combined with the integrative analysis with RNA-seq analysis in the peripheral blood mononuclear cell isolated shortly from initial infection, this study showed that the antibiotic catabolic process and myeloid cell homeostasis were activated while the T-cell response were relatively repressed in those with the risk of secondary infection. Further monitoring analysis of immune cell and liver injury analysis showed that the risk of secondary infection was accompanied by severe lymphocytopenia at the intermediate and late stages and liver injury at the early stages of SARS-CoV-2. Moreover, the metagenomics analysis of bronchoalveolar lavage fluid and the microbial culture analysis, to some extent, showed that the severe pneumonia-related bacteria have already existed in the initial infection.
Normal T and B Cell Responses Against SARS-CoV-2 in a Family With a Non-Functional Vitamin D Receptor: A Case Report
Authors: Kongsbak-Wismann Martin , Al-Jaberi Fatima A. H. , Schmidt Jonas Damgård , Ghanizada Mustafa , Hansen Cecilie Bo , Lopez Daniel Villalba , Woetmann Anders , Ødum Niels , Bonefeld Charlotte Menné , Stryhn Anette , Garred Peter , Buus Søren , Geisler Carsten
Published: September 2021

The coronavirus disease 2019 (COVID-19) pandemic has severely impacted daily life all over the world. Any measures to slow down the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to decrease disease severity are highly requested. Recent studies have reported inverse correlations between plasma levels of vitamin D and susceptibility to SARS-CoV-2 infection and COVID-19 severity. Therefore, it has been proposed to supplement the general population with vitamin D to reduce the impact of COVID-19. However, by studying the course of COVID-19 and the immune response against SARS-CoV-2 in a family with a mutated, non-functional vitamin D receptor, we here demonstrate that vitamin D signaling was dispensable for mounting an efficient adaptive immune response against SARS-CoV-2 in this family. Although these observations might not directly be transferred to the general population, they question a central role of vitamin D in the generation of adaptive immunity against SARS-CoV-2.
Enhanced Spin Accumulation in Semiconductor at Room Temperature Using Ni0.65Zn0.35Fe2O4(NZFO) as Spin Injector in NZFO/MgO/p-Si Device
Authors: Maji Nilay , Shit Subhasis , Nath T. K.
Published: September 2021

In this article, the fabrication of a Ni0.65Zn0.35Fe2O4/MgO/p-Si heterostructure device has been optimized using the pulsed laser deposition (PLD) technique, and a detailed investigation of its structural, electrical, and magnetic features has been performed experimentally. The electronic and magneto-transport characteristics have been explored in the temperature range of 100–300 K. The current-voltage (I-V) characteristics of the heterojunction have been recorded, which displayed an excellent rectifying magnetic tunnel diode-like behavior throughout that temperature regime. The application of an external magnetic field parallel to the plane of the NZFO film causes the current (I) across the junction to decrease, clearly indicating positive junction magnetoresistance (JMR) of the heterostructure. The root of displaying positive magnetoresistance in our heterojunction has been well justified using the standard spin injection model. The electrical injection of spin-polarized carriers and its accumulation and detection in a p-Si channel have been demonstrated using the NZFO/MgO tunnel contact using a three-terminal (3-T) Hanle device. The parameters such as spin lifetime (99 ps), spin diffusion length (276 nm), and spin polarization (0.44) have been estimated from the Hanle curve detected in our heterostructure at room temperature, making the Ni0.65Zn0.35Fe2O4/MgO/p-Si device a very favorable promising junction structure in the field of spintronics for several device appliances in the future.
Artificial Intelligence for COVID-19: A Systematic Review
Authors: Wang Lian , Zhang Yonggang , Wang Dongguang , Tong Xiang , Liu Tao , Zhang Shijie , Huang Jizhen , Zhang Li , Chen Lingmin , Fan Hong , Clarke Mike
Published: September 2021

Background: Recently, Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome virus 2 (SARS-CoV-2), has affected more than 200 countries and lead to enormous losses. This study systematically reviews the application of Artificial Intelligence (AI) techniques in COVID-19, especially for diagnosis, estimation of epidemic trends, prognosis, and exploration of effective and safe drugs and vaccines; and discusses the potential limitations.

Methods: We report this systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched PubMed, Embase and the Cochrane Library from inception to 19 September 2020 for published studies of AI applications in COVID-19. We used PROBAST (prediction model risk of bias assessment tool) to assess the quality of literature related to the diagnosis and prognosis of COVID-19. We registered the protocol (PROSPERO CRD42020211555).

Results: We included 78 studies: 46 articles discussed AI-assisted diagnosis for COVID-19 with total accuracy of 70.00 to 99.92%, sensitivity of 73.00 to 100.00%, specificity of 25 to 100.00%, and area under the curve of 0.732 to 1.000. Fourteen articles evaluated prognosis based on clinical characteristics at hospital admission, such as clinical, laboratory and radiological characteristics, reaching accuracy of 74.4 to 95.20%, sensitivity of 72.8 to 98.00%, specificity of 55 to 96.87% and AUC of 0.66 to 0.997 in predicting critical COVID-19. Nine articles used AI models to predict the epidemic of the COVID-19, such as epidemic peak, infection rate, number of infected cases, transmission laws, and development trend. Eight articles used AI to explore potential effective drugs, primarily through drug repurposing and drug development. Finally, 1 article predicted vaccine targets that have the potential to develop COVID-19 vaccines.

Conclusions: In this review, we have shown that AI achieved high performance in diagnosis, prognosis evaluation, epidemic prediction and drug discovery for COVID-19. AI has the potential to enhance significantly existing medical and healthcare system efficiency during the COVID-19 pandemic.
Potential Triggers for Thrombocytopenia and/or Hemorrhage by the BNT162b2 Vaccine, Pfizer-BioNTech
Authors: Okada Yusuke , Sakai Ryota , Sato-Fitoussi Marie , Nodera Marika , Yoshinaga Shoichi , Shibata Akiko , Kurasawa Takahiko , Kondo Tsuneo , Amano Koichi
Published: September 2021

Immune thrombocytopenia is an autoimmune disease that can cause bleeding in severe cases. Although available published data do not associate the BNT162b2 vaccine (Pfizer-BioNTech) with the risk of developing thrombocytopenia, the ChAdOx1 nCov-19 vaccine has raised concerns about its potential link with thrombosis and thrombocytopenia. We would like to clarify whether the BNT162b2 vaccine administration may interfere with pre-existing conditions and whether it may cause a risk of thrombocytopenia. Herein, we report three cases of post-vaccine thrombocytopenia among patients with rheumatoid arthritis (RA); one case in which a causal relationship cannot be ruled out with the BNT162b2 vaccine was officially announced. Furthermore, we reviewed reports of adverse events and death cases with a focus on thrombocytopenia and hemorrhages, following vaccination with BNT162b2 in Japan between February 17, 2021 and July 16, 2021, as reported by the Ministry of Health, Labour, and Welfare within the general population. The three cases in this report share the common features of old age, RA, chronic renal failure or hypertension, and pre-existing mild thrombocytopenia at baseline. A total of 746 death cases were reported during this time period, with death by bleeding accounting for 8.8% of the total deaths, of which 84.8% were cranial and statistically higher in young women than among elderly women. The risk-benefit ratio of the vaccine needs to be reconsidered based on high- and low-risk population types and ethnicity. To do so, the expansion of the pharmacovigilance system for BNT162b2 vaccination is urgently required worldwide.
Primary Cilia in Glial Cells: An Oasis in the Journey to Overcoming Neurodegenerative Diseases
Authors: Ki Soo Mi , Jeong Hui Su , Lee Ji Eun
Published: September 2021

Many neurodegenerative diseases have been associated with defects in primary cilia, which are cellular organelles involved in diverse cellular processes and homeostasis. Several types of glial cells in both the central and peripheral nervous systems not only support the development and function of neurons but also play significant roles in the mechanisms of neurological disease. Nevertheless, most studies have focused on investigating the role of primary cilia in neurons. Accordingly, the interest of recent studies has expanded to elucidate the role of primary cilia in glial cells. Correspondingly, several reports have added to the growing evidence that most glial cells have primary cilia and that impairment of cilia leads to neurodegenerative diseases. In this review, we aimed to understand the regulatory mechanisms of cilia formation and the disease-related functions of cilia, which are common or specific to each glial cell. Moreover, we have paid close attention to the signal transduction and pathological mechanisms mediated by glia cilia in representative neurodegenerative diseases. Finally, we expect that this field of research will clarify the mechanisms involved in the formation and function of glial cilia to provide novel insights and ideas for the treatment of neurodegenerative diseases in the future.
Much Ado About Missingness: A Demonstration of Full Information Maximum Likelihood Estimation to Address Missingness in Functional Magnetic Resonance Imaging Data
Authors: Nelson Timothy D. , Brock Rebecca L. , Yokum Sonja , Tomaso Cara C. , Savage Cary R. , Stice Eric
Published: September 2021

The current paper leveraged a large multi-study functional magnetic resonance imaging (fMRI) dataset (N = 363) and a generated missingness paradigm to demonstrate different approaches for handling missing fMRI data under a variety of conditions. The performance of full information maximum likelihood (FIML) estimation, both with and without auxiliary variables, and listwise deletion were compared under different conditions of generated missing data volumes (i.e., 20, 35, and 50%). FIML generally performed better than listwise deletion in replicating results from the full dataset, but differences were small in the absence of auxiliary variables that correlated strongly with fMRI task data. However, when an auxiliary variable created to correlate r = 0.5 with fMRI task data was included, the performance of the FIML model improved, suggesting the potential value of FIML-based approaches for missing fMRI data when a strong auxiliary variable is available. In addition to primary methodological insights, the current study also makes an important contribution to the literature on neural vulnerability factors for obesity. Specifically, results from the full data model show that greater activation in regions implicated in reward processing (caudate and putamen) in response to tastes of milkshake significantly predicted weight gain over the following year. Implications of both methodological and substantive findings are discussed.
Food and Feed Safety of NS-B5ØØ27-4 Omega-3 Canola (Brassica napus): A New Source of Long-Chain Omega-3 Fatty Acids
Authors: MacIntosh Susan C. , Shaw Megan , Connelly Michael , Yao Zhuyun June
Published: September 2021

DHA canola, a genetically engineered Brassica napus (OECD Unique Identifier NS-B5ØØ27-4), has been developed as one of the first land-based production systems for omega-3 long-chain polyunsaturated fatty acids (LCPUFA), whose health benefits are well-established. Yet, the marine sources of these nutrients are under high pressures due to over-fishing and increasing demand. DHA canola is a plant-based source for these essential fatty acids that produces a high level of docosahexaenoic acid (DHA). This terrestrial system allows for sustainable, scalable and stable production of omega-3 LCPUFA that addresses not only the increasing market demand, but also the complex interplay of agriculture, aquaculture, and human nutrition. The vector used to produce the desired oil profile in DHA canola contains the expression cassettes of seven genes in the DHA biosynthesis pathway and was specifically designed to convert oleic acid to DHA in canola seed. The characterization and safety evaluation of food and feed produced from DHA canola are described and supported by a detailed nutritional analysis of the seed, meal, and oil. Aside from the intended changes of the fatty acid profile, none of the other compositional analytes showed biologically meaningful differences when compared to conventional canola varieties. In addition, the meal from DHA canola is compositionally equivalent to conventional canola meal. Further evidence of nutritional value and safety of DHA canola oil have been confirmed in fish feeding studies. Given that most human populations lack sufficient daily intakes of omega-3 LCPUFA, a dietary exposure assessment is also included. In conclusion, the results from these studies demonstrate it is safe to use products derived from DHA canola in human foods, nutraceuticals, or animal feeds.
Fibroglandular Tissue and Background Parenchymal Enhancement on Breast MR Imaging Correlates With Breast Cancer
Authors: Hu Xiaoxin , Jiang Luan , You Chao , Gu Yajia
Published: September 2021

Objectives

To evaluate the association of breast cancer with both the background parenchymal enhancement intensity and volume (BPEI and BPEV, respectively) and the amount of fibroglandular tissue (FGT) using an automatic quantitative assessment method in breast magnetic resonance imaging (MRI).

Materials and Methods

Among 17,274 women who underwent breast MRI, 132 normal women (control group), 132 women with benign breast lesions (benign group), and 132 women with breast cancer (cancer group) were randomly selected and matched by age and menopausal status. The area under the receiver operating characteristic curve (AUC) was compared in Cancer vs Control and Cancer vs Benign groups to assess the discriminative ability of BPEI, BPEV and FGT.

Results

Compared with the control groups, the cancer group showed a significant difference in BPEV with a maximum AUC of 0.715 and 0.684 for patients in premenopausal and postmenopausal subgroup, respectively. And the cancer group showed a significant difference in BPEV with a maximum AUC of 0.622 and 0.633 for patients in premenopausal and postmenopausal subgroup, respectively, when compared with the benign group. FGT showed no significant difference when breast cancer group was compared with normal control and benign lesion group, respectively. Compared with the control groups, BPEI showed a slight difference in the cancer group. Compared with the benign group, no significant difference was seen in cancer group.

Conclusion

Increased BPEV is correlated with a high risk of breast cancer While FGT is not.
Influencing Factors and Cumulative Risk Analysis of Cervical Lymph Node Metastasis of Papillary Thyroid Microcarcinoma
Authors: Yin Yirong , Xu Xiang , Shen Liyan , Zhao Wenjuan , Diao Hongcui , Li Chengqian
Published: September 2021

Objective

To explore the influencing factors and cumulative risk of lymph node metastasis (LNM) in papillary thyroid microcarcinoma (PTMC) patients.

Methods

607 patients confirmed PTMC pathologically after thyroidectomy were enrolled in this retrospective study. The rate of LNM was calculated. Different clinicopathological characteristics were compared in PTMC patients with and without LNM and in different subgroups of LNM, respectively. Correlation between clinicopathological characteristics and LNM was analyzed and the cumulative risk of LNM according to different clinicopathological characteristics was calculated.

Results

(1) There were 228 cases (37.56%) of PTMC combined with LNM. Compared with the non-lymph node metastasis group, the proportion of age <55 years, male, multiple foci, bilateral foci, diameter>0.5cm, extracapsular invasion, HT and intermediate-to-high risk stratification for recurrence of the LNM group was significantly increased (all p<0.05);(2) Multivariate logistic regression analysis showed that age <55years, male, multiple foci, diameter>0.5cm,HT were independently positively correlated with LNM (all p <0.05); (3) Subgroup analysis showed that women aged <55 years combined with HT and aged≥55 years combined with BMI≥25 kg/m2 were independently positively associated with LNM; (4) With the increase of the tumor diameter, the cumulative risk of LNM in group of age <55 years, males, and multiple foci increased gradually, and was higher than those of age≥55 years, females and single foci, respectively. (5) Among the 228 cases of LNM, the proportion of lymph nodes (LN) >5 and the positive rate of LN were both higher in male group than that in the female group. The proportion of multiple foci and HT in LLNM group was higher than that in CLNM group (all P<0.05).

Conclusion

Age <55 years, males, multiple foci, diameter >0.5cm and HT were independent risk factors of LNM; HT was an independent risk factor for LNM in female <55 years old, and BMI≥25 kg/m2 was an independent risk factor for LNM in female ≥55 years old; The increase of tumor diameter in age <55 years, males, multiple foci, and bilateral foci increased the cumulative risk of LNM, respectively; The number of LNM and the positive rate of LNM were both higher in male, and patients with multiple foci or HT were more likely to develop into LLNM.
Identification of Hub Genes Associated With Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis
Authors: Huang Hao , Zhu Ling , Huang Chao , Dong Yi , Fan Liangliang , Tao Lijian , Peng Zhangzhe , Xiang Rong
Published: September 2021

Background

Clear cell renal cell carcinoma (ccRCC) is a common genitourinary cancer type with a high mortality rate. Due to a diverse range of biochemical alterations and a high level of tumor heterogeneity, it is crucial to select highly validated prognostic biomarkers to be able to identify subtypes of ccRCC early and apply precision medicine approaches.

Methods

Transcriptome data of ccRCC and clinical traits of patients were obtained from the GSE126964 dataset of Gene Expression Omnibus and The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) database. Weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) screening were applied to detect common differentially co-expressed genes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes analysis, survival analysis, prognostic model establishment, and gene set enrichment analysis were also performed. Immunohistochemical analysis results of the expression levels of prognostic genes were obtained from The Human Protein Atlas. Single-gene RNA sequencing data were obtained from the GSE131685 and GSE171306 datasets.

Results

In the present study, a total of 2,492 DEGs identified between ccRCC and healthy controls were filtered, revealing 1,300 upregulated genes and 1,192 downregulated genes. Using WGCNA, the turquoise module was identified to be closely associated with ccRCC. Hub genes were identified using the maximal clique centrality algorithm. After having intersected the hub genes and the DEGs in GSE126964 and TCGA-KIRC dataset, and after performing univariate, least absolute shrinkage and selection operator, and multivariate Cox regression analyses, ALDOB, EFHD1, and ESRRG were identified as significant prognostic factors in patients diagnosed with ccRCC. Single-gene RNA sequencing analysis revealed the expression profile of ALDOB, EFHD1, and ESRRG in different cell types of ccRCC.

Conclusions

The present results demonstrated that ALDOB, EFHD1, and ESRRG may act as potential targets for medical therapy and could serve as diagnostic biomarkers for ccRCC.
The Non-Coding RNAs Inducing Drug Resistance in Ovarian Cancer: A New Perspective for Understanding Drug Resistance
Authors: Li Gaofeng , Gong Jun , Cao Shulong , Wu Zhaoyang , Cheng Dong , Zhu Jia , Huang Xuqun , Tang Jingyi , Yuan Yuning , Cai Wenqi , Zhang Haiyuan
Published: September 2021

Ovarian cancer, a common malignant tumor, is one of the primary causes of cancer-related deaths in women. Systemic chemotherapy with platinum-based compounds or taxanes is the first-line treatment for ovarian cancer. However, resistance to these chemotherapeutic drugs worsens the prognosis. The underlying mechanism of chemotherapeutic resistance in ovarian cancer remains unclear. Non-coding RNAs, including long non-coding RNAs, microRNAs, and circular RNAs, have been implicated in the development of drug resistance. Abnormally expressed non-coding RNAs can promote ovarian cancer resistance by inducing apoptosis inhibition, protective autophagy, abnormal tumor cell proliferation, epithelial-mesenchymal transition, abnormal glycolysis, drug efflux, and cancer cell stemness. This review summarizes the role of non-coding RNAs in the development of chemotherapeutic resistance in ovarian cancer, including their mechanisms, targets, and potential signaling pathways. This will facilitate the development of novel chemotherapeutic agents that can target these non-coding RNAs and improve ovarian cancer treatment.
Prediction of Biochemical Recurrence After Radical Prostatectomy Based on Preoperative 68Ga-PSMA-11 PET/CT
Authors: Qiu Xuefeng , Chen Mengxia , Yin Haoli , Zhang Qing , Li Haoyang , Guo Suhan , Fu Yao , Zang Shiming , Ai Shuyue , Wang Feng , Guo Hongqian
Published: September 2021

Purpose

This study was designed to investigate the prognostic role of preoperative 68Ga-PSMA-11 PET/CT in predicting biochemical recurrence (BCR) of localized prostate cancer (PCa) after radical prostatectomy (RP).

Methods

A total of 77 biopsy-confirmed PCa patients with 68Ga-PSMA-11 PET/CT prior to RP were included. A PSMA-ligand PET/CT-based risk model with SUVmax, maximum diameter of the index tumor and T stage was developed for prediction of 2-year BCR using Cox regression analysis. Also, the efficacy of the developed risk model was compared with European Association of Urology risk stratification (D’Amico) and the Cancer of the Prostate Risk Assessment (CAPRA) score. C-index and calibration plot were used to assess discrimination and calibration with internal validation.

Results

With a median follow-up of 25 months, 23 (29.9%) patients experienced BCR within 2 years after RP. Patients experienced BCR had a significant higher PSA at diagnosis (p<0.001), a higher ISUP grade of biopsy (p=0.044), as well as a higher ISUP grade (p=0.001), a higher possibility of T3 diseases (p=0.001) and positive margin (p=0.008) on postoperative pathology. SUVmax, maximum diameter of the index tumor and T stage on preoperative PSMA-ligand PET/CT were significantly associated with BCR (all p<0.01). PSMA-ligand PET/CT-based risk model had a superior discrimination (c-index 78.5%) and good calibration at internal validation. The efficacy of this model in predicting 2-year BCR after RP was better, compared with CAPRA (c-index 66.3%) and D’Amico (c-index 66.2%). The addition of the PSMA-ligand PET/CT-derived variables also improved the efficacy of the existing models in predicting 2-year BCR (C-index of 78.9% for modified CAPRA and 79.3% for modified D’Amico, respectively).

Conclusion

A PSMA-ligand PET/CT-based risk model showed good efficacy in predicting 2-year BCR after RP, which needed to be validated by further prospective studies.
Choroid Plexus Carcinomas With TP53 Germline Mutations: Management and Outcome
Authors: Li Yanong , Liu Hailong , Li Tandy , Feng Jin , He Yanjiao , Chen Li , Li Chunde , Qiu Xiaoguang
Published: September 2021

Background

Choroid plexus carcinomas (CPCs) are rare pediatric tumors commonly associated with Li-Fraumeni syndrome (LFS), which involves a germline mutation of the tumor suppressor gene TP53.

Materials and Methods

We retrospectively analyzed the corresponding information of 12 cases, including the effects of surgery and radiotherapy and TP53 germline mutations, to analyse the management strategies. Kaplan-Meier curves and the log-rank test were used to evaluate the progression-free survival (PFS).

Results

Twelve CPC patients were included, of which TP53 germline mutations were found in eight cases. All patients underwent surgical resection, and six patients received radiotherapy following with operation after initial diagnosis, one patient received radiotherapy following relapse. It was significantly different (P=0.012 and 0.028) that patients with TP53 germline mutation receiving the gross total resection (GTR) without radiotherapy showed survival advantages. Without TP53 germline mutations also showed survival advantages, but there is no statistical significance (P=0.063)

Conclusions

These findings provide evidence for the therapeutic strategy that radiotherapy should not be considered for patients with TP53 germline mutations.
High Abdominal Perfusion Pressure Using Umbilical Cord Flap in the Management of Gastroschisis
Authors: Arafa Mohamed Ahmed , Elshimy Khalid Mohamed , Shehata Mohamed Ali , Elbatarny Akram , Almetaher Hisham Almohamady , Seleim Hamed Mahmoud
Published: September 2021

Background: Gastroschisis management remains a controversy. Most surgeons prefer reduction and fascial closure. Others advise staged reduction to avoid a sudden rise in intra-abdominal pressure (IAP). This study aims to evaluate the feasibility of using the umbilical cord as a flap (without skin on the top) for tension-free repair of gastroschisis.

Methods: In a prospective study of neonates with gastroschisis repaired between January 2018 to October 2020 in Tanta University Hospital, we used the umbilical cord as a flap after the evacuation of all its blood vessels and suturing the edges of the cord with the skin edges of the defect. They were guided by monitoring abdominal perfusion pressure (APP), peak inspiratory pressure (PIP), central venous pressure (CVP), and urine output during 24 and 48 h postoperatively. The umbilical cord flap is used for tension-free closure of gastroschisis if PIP > 24 mmHg, IAP > 20 cmH2O (15 mmHg), APP <50 mmHg, and CVP > 15cmH2O.

Results: In 20 cases that had gastroschisis with a median age of 24 h, we applied the umbilical cord flap in all cases and then purse string (Prolene Zero) with daily tightening till complete closure in seven cases, secondary suturing after 10 days in four cases, and leaving skin creeping until complete closure in nine cases. During the trials of closure, the range of APP was 49–52 mmHg. The range of IAP (IVP) was 15–20 cmH2O (11–15 mmHg), the range of PIP was 22–25 cmH2O, the range of CVP was 13–15 cmH2O, and the range of urine output was 1–1.5 ml/kg/h.

Conclusion: The umbilical cord flap is an easy, feasible, and cheap method for tension-free closure of gastroschisis with limiting the PIP ≤ 24 mmHg, IAP ≤ 20 cmH2O (15 mmHg), APP > 50 mmHg, and CVP ≤ 15cmH2O.
Electron and Photon Energy Spectra Outside of 6 MV X-ray Small Radiotherapy Field Edges Produced by a Varian iX Linac
Authors: Xicohténcatl-Hernández Nahum , Moreno-Ramirez Adriana , Massillon-JL Guerda
Published: September 2021

Due to the increase in the survival probability for patients treated with modern radiotherapy techniques to live enough for experimenting the late radiation effect, low dose outside the treatment volume becomes a concern. However, besides the absorbed dose, the beam quality outside the field edge should be taken into account. This work aimed at investigating the photon and electron fluence spectra outside the field edges for several small radiotherapy fields for determining the quality of the beams in order to better evaluate the secondary effect after modern radiotherapy treatments. Phase-space files of a 6 MV X-ray beam produced by a Varian iX linac for eight small fields of 0.7 × 0.7 cm2, 0.9 × 0.9 cm2, 1.8 × 1.8 cm2, 2.2 × 2.2 cm2, 2.7 × 2.7 cm2, 3.1 × 3.1 cm2, 3.6 × 3.6 cm2, and 4.5 × 4.5 cm2 and for the reference 10 × 10 cm2 field at SSD = 100 cm were generated using the BEAMnrc code. The photon and electron fluences in each field were calculated at 0.15, 1.35, and 9.85 cm water depth and several off-axis distances using FLURZnrc. The number of low-energy electrons between 1 and 10 keV at 2 cm outside the field edge increases by 60% compared to the central axis. Due to the relatively high linear energy transfer (LET) of these electrons, the results of this work should help to better evaluate the possible late effect of secondary radiation on healthy organs close to the tumor volume after radiotherapy treatment. We also observed high-energy electrons outside the field edge that are attributed to the leakage of the primary electron beam from the head of the linac. From a standpoint of radiological protection, these electrons should be taken into account when evaluating the dose delivered to the patient’s skin.
Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability
Authors: Zhao Yue , Miao Yulu , Zhi Fengdong , Pan Yue , Zhang Jianguo , Yang Xuepeng , Zhang John Z. H. , Zhang Lujia
Published: September 2021

Enzyme thermostability is an important parameter for estimating its industrial value. However, most naturally produced enzymes are incapable of meeting the industrial thermostability requirements. Software programs can be utilized to predict protein thermostability. Despite the fast-growing number of programs designed for this purpose; few provide reliable applicability because they do not account for thermodynamic weaknesses. Aspartic proteases are widely used in industrial processing; however, their thermostability is not able to meet the large-scale production requirements. In this study, through analyzing structural characteristics and modifying thermostability using prediction software programs, we improved the thermostability of pepsin, a representative aspartic protease. Based on the structural characteristics of pepsin and the experimental results of mutations predicted by several energy-based prediction software programs, it was found that the majority of pepsin’s thermodynamic weaknesses lie on its flexible regions on the surface. Using computational design, mutations were made based on the predicted sites of thermodynamic weakness. As a result, the half-lives of mutants D52N and S129A at 70°C were increased by 200.0 and 66.3%, respectively. Our work demonstrated that in the effort of improving protein thermostability, identification of structural weaknesses with the help of computational design, could efficiently improve the accuracy of protein rational design.
Late Blight Resistance Evaluation and Genome-Wide Assessment of Genetic Diversity in Wild and Cultivated Potato Species
Authors: Duan Yanfeng , Duan Shaoguang , Xu Jianfei , Zheng Jiayi , Hu Jun , Li Xiaochuan , Li Baoju , Li Guangcun , Jin Liping
Published: September 2021

Late blight, caused by the oomycete Phytophthora infestans, is the most devastating disease in potato-producing regions of the world. Cultivation of resistant varieties is the most effective and environmentally friendly way to control potato late blight disease, and identification of germplasms with late blight resistance and clarification their genetic relationship would promote the development of the resistant varieties. In this study, a diverse population of 189 genotypes with potential late blight resistance, consisting of 20 wild species and cultivated Solanum tuberosum Andigenum group and Chilotanum group, was screened for the presence of late blight resistance by performing challenge inoculation with four Phytophthora infestans isolates including one 13_A2 isolate, CN152. Ten elite resources with broad-spectrum resistance and 127 with isolate-specific resistance against P. infestans were identified. To improve the available gene pool for future potato breeding programs, the population was genotyped using 30 simple sequence repeat (SSR) markers covering the entire potato genome. A total of 173 alleles were detected with an average of 5.77 alleles per locus. Structure analysis discriminated the 189 potato genotypes into five populations based on taxonomic classification and genetic origin with some deviations. There was no obvious clustering by country of origin, ploidy level, EBN (endosperm balance number) value, or nuclear clade. Analysis of molecular variance showed 10.08% genetic variation existed among populations. The genetic differentiation (Fst) ranged from 0.0937 to 0.1764, and the nucleotide diversity (π) was 0.2269 across populations with the range from 0.1942 to 0.2489. Further genotyping of 20K SNP array confirmed the classification of SSRs and could uncover the genetic relationships of Solanum germplasms. Our results indicate that there exits abundant genetic variation in wild and cultivated potato germplasms, while the cultivated S. tuberosum Chilotanum group has lower genetic diversity. The phenotypic and genetic information obtained in this study provide a useful guide for hybrid combination and resistance introgression from wild gene pool into cultivated species for cultivar improvement, as well as for germplasm conservation efforts and resistance gene mining.
A New Curve of Critical Leaf Potassium Concentration Based on the Maximum Root Dry Matter for Diagnosing Potassium Nutritional Status of Sweet Potato
Authors: Lv Zunfu , Lu Guoquan
Published: September 2021

Critical leaf nutrient concentrations have often been used to diagnose the nutritional status of crops. Determining critical leaf potassium (K) concentrations for the maximum root dry matter (RDM) will provide a reliable means of linking leaf K nutrient concentrations to the yield of sweet potato. Three field experiments, using varying K application rates (0–300 kg K ha−1) and two sweet potato cultivars, were performed in the Zhejiang Province of China. A new critical leaf K curve (Kleaf) based on the maximum RDM was determined to assess K nutrition in sweet potato and described by the equation Kleaf=4.55×RDMmax-0.075. A critical root K curve (Kroot) based on the maximum RDM was also determined to assess K nutrition and described by the equation Kroot=2.36×RDMmax-0.087. The K nutrition index (KNI) was constructed to identify the situations of K-limiting and non-K-limiting treatments. The leaf KNI (KNIleaf) ranged from 0.56 to 1.17, and the root K KNI (KNIroot) ranged from 0.52 to 1.35 during the growth period of sweet potato. The results showed that the critical leaf K concentration curve can be used as an accurate leaf K status diagnostic tool at critical growth stages that connected leaf nutrient concentration and sweet potato tuber yield. This K curve will contribute to K management of sweet potato during its growth period in China.
MKK4/5-MPK3/6 Cascade Regulates Agrobacterium-Mediated Transformation by Modulating Plant Immunity in Arabidopsis
Authors: Liu Tengfei , Cao Li , Cheng Yuanyuan , Ji Jing , Wei Yongshu , Wang Chenchen , Duan Kaixuan
Published: September 2021

Agrobacterium tumefaciens is a specialized plant pathogen that causes crown gall disease and is commonly used for Agrobacterium-mediated transformation. As a pathogen, Agrobacterium triggers plant immunity, which affects transformation. However, the signaling components and pathways in plant immunity to Agrobacterium remain elusive. We demonstrate that two Arabidopsis mitogen-activated protein kinase kinases (MAPKKs) MKK4/MKK5 and their downstream mitogen-activated protein kinases (MAPKs) MPK3/MPK6 play major roles in both Agrobacterium-triggered immunity and Agrobacterium-mediated transformation. Agrobacteria induce MPK3/MPK6 activity and the expression of plant defense response genes at a very early stage. This process is dependent on the MKK4/MKK5 function. The loss of the function of MKK4 and MKK5 or their downstream MPK3 and MPK6 abolishes plant immunity to agrobacteria and increases transformation frequency, whereas the activation of MKK4 and MKK5 enhances plant immunity and represses transformation. Global transcriptome analysis indicates that agrobacteria induce various plant defense pathways, including reactive oxygen species (ROS) production, ethylene (ET), and salicylic acid- (SA-) mediated defense responses, and that MKK4/MKK5 is essential for the induction of these pathways. The activation of MKK4 and MKK5 promotes ROS production and cell death during agrobacteria infection. Based on these results, we propose that the MKK4/5-MPK3/6 cascade is an essential signaling pathway regulating Agrobacterium-mediated transformation through the modulation of Agrobacterium-triggered plant immunity.
Model Application of Entomopathogenic Fungi as Alternatives to Chemical Pesticides: Prospects, Challenges, and Insights for Next-Generation Sustainable Agriculture
Authors: Bamisile Bamisope Steve , Akutse Komivi Senyo , Siddiqui Junaid Ali , Xu Yijuan
Published: September 2021

In the past few decades, the control of pests and diseases of cultivated plants using natural and biological measures has drawn increasing attention in the quest to reduce the level of dependence on chemical products for agricultural production. The use of living organisms, predators, parasitoids, and microorganisms, such as viruses, bacteria, and fungi, has proven to be a viable and sustainable pest management technique. Among the aforementioned, fungi, most importantly the insect-pathogenic species, have been in use for more than 150years. These include the most popular strains belonging to the generaBeauveria,Metarhizium,Isaria,Hirsutella, andLecanicillium. Their application is usually through an inundative approach, which inherently involves exposure of the fungal spores to unfavorable humidity, temperature, and solar radiation conditions. These abiotic factors reduce the persistence and efficacy of these insect-pathogenic fungi. Despite these limitations, over 170 strains have been formulated as mycopesticides and are available for commercial use. In the last few decades, numerous studies have suggested that these species of entomopathogenic fungi (EPF) offer far more benefits and have broader ecological functions than hitherto presumed. For instance, aside from their roles as insect killers, it has been well established that they also colonize various host plants and, hence, provide other benefits including plant pathogen antagonism and plant growth promotion and serve as sources of novel bioactive compounds and secondary metabolites, etc. In this light, the potential of EPF as alternatives or perhaps as supplements to chemical pesticides in plant protection is discussed in this review. The paper highlights the numerous benefits associated with endophytic fungal entomopathogen and host plant associations, the mechanisms involved in mediating plant defense against pests and pathogens, and the general limitations to the use of EPF in plant protection. A deeper understanding of these plant host-fungus-insect relationships could help unveil the hidden potentials of fungal endophytes, which would consequently increase the level of acceptance and adoption by users as an integral part of pest management programs and as a suitable alternative to chemical inputs toward sustainable crop production.