Table1_New progress in the role of microRNAs in the diagnosis and prognosis of triple negative breast cancer.DOCX

Triple negative breast cancer is distinguished by its high malignancy, aggressive invasion, rapid progression, easy recurrence, and distant metastases. Additionally, it has a poor prognosis, a high mortality, and is unresponsive to conventional endocrine and targeted therapy, making it a challenging problem for breast cancer treatment and a hotspot for scientific research. Recent research has revealed that certain miRNA can directly or indirectly affect the occurrence, progress and recurrence of TNBC. Their expression levels have a significant impact on TNBC diagnosis, treatment and prognosis. Some miRNAs can serve as biomarkers for TNBC diagnosis and prognosis. This article summarizes the progress of miRNA research in TNBC, discusses their roles in the occurrence, invasion, metastasis, prognosis, and chemotherapy of TNBC, and proposes a treatment strategy for TNBC by interfering with miRNA expression levels.</p

Image_1_Analysis of serum antioxidant capacity and gut microbiota in calves at different growth stages in Tibet.pdf

IntroductionThe hypoxic environment at high altitudes poses a major physiological challenge to animals, especially young animals, as it disturbs the redox state and induces intestinal dysbiosis. Information about its effects on Holstein calves is limited.MethodsHere, serum biochemical indices and next-generation sequencing were used to explore serum antioxidant capacity, fecal fermentation performance, and fecal microbiota in Holstein calves aged 1, 2, 3, 4, 5, and 6 months in Tibet.Results and DiscussionSerum antioxidant capacity changed with age, with the catalase and malondialdehyde levels significantly decreasing (p  0.05) in total volatile fatty acid levels were noted between the groups. In all groups, Firmicutes, Bacteroidetes, and Actinobacteria were the three most dominant phyla in the gut. Gut microbial alpha diversity significantly increased (p < 0.05) with age. Principal coordinate analysis plot based on Bray–Curtis dissimilarity revealed significant differences (p = 0.001) among the groups. Furthermore, the relative abundance of various genera changed dynamically with age, and the serum antioxidant capacity was associated with certain gut bacteria. The study provides novel insights for feeding Holstein calves in high-altitude regions.</p

Image_2_Analysis of serum antioxidant capacity and gut microbiota in calves at different growth stages in Tibet.png

IntroductionThe hypoxic environment at high altitudes poses a major physiological challenge to animals, especially young animals, as it disturbs the redox state and induces intestinal dysbiosis. Information about its effects on Holstein calves is limited.MethodsHere, serum biochemical indices and next-generation sequencing were used to explore serum antioxidant capacity, fecal fermentation performance, and fecal microbiota in Holstein calves aged 1, 2, 3, 4, 5, and 6 months in Tibet.Results and DiscussionSerum antioxidant capacity changed with age, with the catalase and malondialdehyde levels significantly decreasing (p  0.05) in total volatile fatty acid levels were noted between the groups. In all groups, Firmicutes, Bacteroidetes, and Actinobacteria were the three most dominant phyla in the gut. Gut microbial alpha diversity significantly increased (p < 0.05) with age. Principal coordinate analysis plot based on Bray–Curtis dissimilarity revealed significant differences (p = 0.001) among the groups. Furthermore, the relative abundance of various genera changed dynamically with age, and the serum antioxidant capacity was associated with certain gut bacteria. The study provides novel insights for feeding Holstein calves in high-altitude regions.</p

Data_Sheet_1_Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers.docx

<p>Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.</p

Image_2_Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers.TIF

<p>Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.</p

Data_Sheet_2_Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers.xlsx

<p>Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.</p

Clinic pathologic characteristics of patients with breast cancer.

a<p>According to the AJCC (American Joint Committee on Cancer) staging system <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103270#pone.0103270-Edge1" target="_blank">[42]</a>.</p

The position of lincRNAs and neighboring genes in chromosome.

<p>(A) The position of lincRNA-BC2 and neighboring genes in chromosome 5. (B) The position of lincRNA-BC4 and neighboring genes in chromosome 15. (C) The position of lincRNA-BC5 and neighboring genes in chromosome X. (D) The position of lincRNA-BC8 and neighboring genes in chromosome 13.</p

Global overview of polyA-minus RNA sequencing in breast cancer tissues and matched adjacent cancer tissues.

<p>The pie charts on the left display ploy-A minus transcript distribution in breast cancer tissues (upper) and adjacent tissues to cancer (lower). The pie charts on the right display novel ncRNA categorized as sense (intronic RNA and lincRNA) and antisense transcript.</p

The expression of selected lincRNAs in breast cancer tissues and matched adjacent tissues to cancer using semi-quantitative RT-PCR.

<p>The expression of selected lincRNAs in breast cancer tissues and matched adjacent tissues to cancer using semi-quantitative RT-PCR.</p