cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11907930.v1
title: Leaving the fish bowl: the ornamental trade as a global vector for freshwater fish invasions

description: Despite its social and economic benefits, the trade in ornamental species (henceforth, ‘ornamental trade’) has become a major source of non-native fish introductions into freshwater ecosystems. However, the ornamental trade as a vector for introductions of non-native freshwater fishes is not well defined. We developed a framework incorporating elements of the biological invasion process and a typical ornamental fish trade supply chain to fill this gap. Records of non-native ornamental fishes introduced to freshwater environments of Australia, Belgium (Flanders), Canada (British Columbia), China (Guangdong), the Philippines, Poland, Singapore, the United Kingdom (England), and the United States of America (Florida) were reviewed to explore the pervasiveness of these introduced fishes in the wild. These regional case studies confirmed the prominence of the ornamental trade as a global vector for freshwater fish introductions beyond their natural range. Additionally, we examined freshwater fishes associated with the ornamental trade to identify ‘risky’ species that could establish in recipient regions based on climate match. All regions assessed were at risk of new fish introductions via the ornamental trade, with the number of ‘risky’ species ranging from seven to 256. Further, there appears to be taxonomic bias in the freshwater ornamental fish trade, with 74% of the species belonging to just 10 families (of 67). Current prevention and management approaches and associated polices, regulations and legislation on aquatic non-native species within assessed regions fit five general categories: import controls, risk assessment, whitelist, blacklist, and release ban. However, these prevention/management efforts may not be sufficient to reduce the invasion risk associated with the ornamental fish trade. Recommendations including species- and vector-based risk assessments, better recording of species import consignments, increased public education and industry engagement, and early detection and rapid response are discussed in this review.
DOI: 10.6084/m9.figshare.12432215.v1
title: Additional file 3 of Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

description: Data file S3. Dataset of negative edges.
DOI: 10.6084/m9.figshare.19767851
title: Additional file 3 of Prognostic significance of different molecular typing methods and immune status based on RNA sequencing in HR-positive and HER2-negative early-stage breast cancer

description: Additional file 3.
DOI: 10.6084/m9.figshare.11907936.v1
title: A review of freshwater fish introductions to the Guangdong province, China

description: In the last few decades, non-native freshwater fishes have been introduced all over the world for economic purposes, including aquaculture and aquarium trade, as well as improvement for wild stocks resulting in adverse environmental and socio-economic effects. The Guangdong province of China is at a high risk of fish invasions owing to its warm and humid climate, abundance of water courses, flourishing aquaculture and ornamental fish trade, and extensive sea ports. A total of 160 non-native freshwater species were introduced in the Guangdong province and 71.9% of them were imported for aquarium purposes. Fourteen species have established self-sustaining populations and 21 species were found in the main river basin of the Guangdong province. Propagule pressure, rapid evolution and abundant resources in the environment were the factors likely to contribute to successful invasion by non-native fishes. The invasion of non-native fishes in the Guangdong province has already resulted in economic losses, decline of native species, as well as negative impacts on the functional diversity of native fish assemblages. To mitigate these effects and prevent future non-native fish invasions, scientists, policy makers and stakeholders should collaborate on the management of non-native fish introductions by developing risk assessments, statutory regulations, public education and scientific research.
DOI: 10.6084/m9.figshare.19767869.v1
title: Additional file 1 of 2D-DIGE based proteome analysis of wheat-Thinopyrum intermedium 7XL/7DS translocation line under drought stress

description: Additional file 1.
DOI: 10.6084/m9.figshare.11907936
title: A review of freshwater fish introductions to the Guangdong province, China

description: In the last few decades, non-native freshwater fishes have been introduced all over the world for economic purposes, including aquaculture and aquarium trade, as well as improvement for wild stocks resulting in adverse environmental and socio-economic effects. The Guangdong province of China is at a high risk of fish invasions owing to its warm and humid climate, abundance of water courses, flourishing aquaculture and ornamental fish trade, and extensive sea ports. A total of 160 non-native freshwater species were introduced in the Guangdong province and 71.9% of them were imported for aquarium purposes. Fourteen species have established self-sustaining populations and 21 species were found in the main river basin of the Guangdong province. Propagule pressure, rapid evolution and abundant resources in the environment were the factors likely to contribute to successful invasion by non-native fishes. The invasion of non-native fishes in the Guangdong province has already resulted in economic losses, decline of native species, as well as negative impacts on the functional diversity of native fish assemblages. To mitigate these effects and prevent future non-native fish invasions, scientists, policy makers and stakeholders should collaborate on the management of non-native fish introductions by developing risk assessments, statutory regulations, public education and scientific research.
DOI: 10.6084/m9.figshare.17150824
title: Comprehensive analysis of matrix metalloproteinases and their inhibitors in head and neck squamous cell carcinoma

description: <b>Objective:</b> This study aimed to explore the association of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) with cancer progression and prognosis in head and neck squamous cell carcinoma (HNSCC). <b>Methods:</b> Differentially expressed genes (DEGs) were identified by LIMMA package using R software. The correlation between the expression levels of MMPs and TIMPs in HNSCC cancer samples and adjacent normal tissue samples was performed using Pearson correlation analysis. The Kruskal-Wallis test (H-test) was used to determine the association between the expression level of MMPs/TIMPs and HNSCC clinical stage. The survival result was expressed as a KM curve, and the log-rank test was used for statistical analysis. Lasso regression and multivariate Cox regression analyses were used to examine whether the gene signature based on MMPs and TIMPs was an independent prognostic factor in patients with HNSCC. <b>Results:</b> Among the top 10 most up-regulated genes in HNSCC cancer tissues when compared with normal tissues, six genes belonged to the MMPs. Spearman correlation analysis revealed that only MMP11 and MMP23B were positively correlated with tumor stage. Survival analysis showed that patients with a high expression of MMP14, MMP20, TIMP1, and TIMP4 had a worse prognosis than low expression patients. Additionally, a novel five-gene (MMP3, MMP17, MMP19, MMP24, and TIMP1) signature was constructed and significantly associated with prognosis as an independent prognostic signature. <b>Conclusions:</b> Our data show that the accuracy of a single gene of MMP or TIMP as predictors of progression and prognosis of HNSCC is limited, although some studies have proposed that MMPs act as driving factors for cancer progression. The prediction performance of the five-gene signature prediction model was much better than that of the gene signatures based on every single gene in prognosis prediction.
DOI: 10.6084/m9.figshare.12432197
title: Additional file 1 of Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

description: Data file S1. Dataset of literature validation records.
DOI: 10.6084/m9.figshare.19767851.v1
title: Additional file 3 of Prognostic significance of different molecular typing methods and immune status based on RNA sequencing in HR-positive and HER2-negative early-stage breast cancer

description: Additional file 3.
DOI: 10.6084/m9.figshare.21345244
title: Prediction of immune subtypes and overall survival in lung squamous cell carcinoma

description: Lung squamous cell carcinoma (LUSC), one of the most common subtypes of lung cancer, is a leading cause of cancer-caused deaths in the world. It has been well demonstrated that a deep understanding of the tumor environment in cancer would be helpful to predict the prognosis of patients. This study aimed to evaluate the tumor environment in LUSC, and to construct an efficient prognosis model involved in specific subtypes. Four expression files were downloaded from the Gene Expression Omnibus (GEO) database. Three datasets (GSE19188, GSE2088, GSE6044) were considered as the testing group and the other dataset (GSE11969) was used as the validation group. By performing LUSC immune subtype consensus clustering (CC), LUSC patients were separated into two immune subtypes comprising subtype 1 (S1) and subtype 2 (S2). Weighted gene co-expression network (WGCNA) and least absolute shrinkage and selection operator (LASSO) were performed to identify and narrow down the key genes among subtype 1 related genes that were closely related to the overall survival (OS) of LUSC patients. Using immune subtype related genes, a prognostic model was also constructed to predict the OS of LUSC patients. It showed that LUSC patients in the S1 immune subtype exhibited a better OS than in the S2 immune subtype. WGCNA and LASSO analyses screened out important immune subtype related genes in specific modules that were closely associated with LUSC prognosis, followed by construction of the prognostic model. Both the testing datasets and validation dataset confirmed that the prognostic model could be efficiently used to predict the OS of LUSC patients in subtype 1. We explored the tumor environment in LUSC and established a risk prognostic model that might have the potential to be applied in clinical practice.
DOI: 10.6084/m9.figshare.21345244.v1
title: Prediction of immune subtypes and overall survival in lung squamous cell carcinoma

description: Lung squamous cell carcinoma (LUSC), one of the most common subtypes of lung cancer, is a leading cause of cancer-caused deaths in the world. It has been well demonstrated that a deep understanding of the tumor environment in cancer would be helpful to predict the prognosis of patients. This study aimed to evaluate the tumor environment in LUSC, and to construct an efficient prognosis model involved in specific subtypes. Four expression files were downloaded from the Gene Expression Omnibus (GEO) database. Three datasets (GSE19188, GSE2088, GSE6044) were considered as the testing group and the other dataset (GSE11969) was used as the validation group. By performing LUSC immune subtype consensus clustering (CC), LUSC patients were separated into two immune subtypes comprising subtype 1 (S1) and subtype 2 (S2). Weighted gene co-expression network (WGCNA) and least absolute shrinkage and selection operator (LASSO) were performed to identify and narrow down the key genes among subtype 1 related genes that were closely related to the overall survival (OS) of LUSC patients. Using immune subtype related genes, a prognostic model was also constructed to predict the OS of LUSC patients. It showed that LUSC patients in the S1 immune subtype exhibited a better OS than in the S2 immune subtype. WGCNA and LASSO analyses screened out important immune subtype related genes in specific modules that were closely associated with LUSC prognosis, followed by construction of the prognostic model. Both the testing datasets and validation dataset confirmed that the prognostic model could be efficiently used to predict the OS of LUSC patients in subtype 1. We explored the tumor environment in LUSC and established a risk prognostic model that might have the potential to be applied in clinical practice.
DOI: 10.6084/m9.figshare.5092312
title: Thermoresponsive nanocomposite gel for local drug delivery to suppress the growth of glioma by inducing autophagy

description: Although the treatments of malignant glioma include surgery, radiotherapy and chemotherapy by oral drug administration, the prognosis of patients with glioma remains very poor. We developed a polyethylene glycol-dipalmitoylphosphatidyle- thanoiamine (mPEG-DPPE) calcium phosphate nanoparticles (NPs) injectable thermoresponsive hydrogel (nanocomposite gel) that could provide a sustained and local delivery of paclitaxel (PTX) and temozolomide (TMZ). In addition, the proportion of PTX and TMZ for the optimal synergistic antiglioma effect on C6 cells was determined to be 1:100 (w/w) by the Chou and Talalay method. Our results clearly indicated that the autophagy induced by PTX:TMZ NPs plays an important role in regulating tumor cell death, while autophagy inhibition dramatically reverses the antitumor effect of PTX:TMZ NPs, suggesting that antiproliferative autophagy occurs in response to PTX:TMZ NPs treatment. The antitumor efficacy of the PTX:TMZ NP-loaded gel was evaluated in situ using C6 tumor-bearing rats, and the PTX:TMZ NP-loaded gel exhibited superior antitumor performance. The antitumor effects of the nanocomposite gel in vivo were shown to correlate with autophagic cell death in this study. The in vivo results further confirmed the advantages of such a strategy. The present study may provide evidence supporting the development of nanomedicine for potential clinical application.
DOI: 10.6084/m9.figshare.12432209.v1
title: Additional file 2 of Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

description: Data file S2. Dataset of edge frequency.
DOI: 10.6084/m9.figshare.12432215
title: Additional file 3 of Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

description: Data file S3. Dataset of negative edges.
DOI: 10.6084/m9.figshare.17150973.v2
title: Supplemental Tables 4-10 from Agonism and grooming behaviour explain social status effects on physiology and gene regulation in rhesus macaques

description: Variation in social status predicts molecular, physiological and life-history outcomes across a broad range of species, including our own. Experimental studies indicate that some of these relationships persist even when the physical environment is held constant. Here, we draw on datasets from one such study—experimental manipulation of dominance rank in captive female rhesus macaques—to investigate how social status shapes the lived experience of these animals to alter gene regulation, glucocorticoid physiology and mitochondrial DNA phenotypes. We focus specifically on dominance rank-associated dimensions of the social environment, including both competitive and affiliative interactions. Our results show that simple summaries of rank-associated behavioural interactions are often better predictors of molecular and physiological outcomes than dominance rank itself. However, while measures of immune function are best explained by agonism rates, glucocorticoid-related phenotypes tend to be more closely linked to affiliative behaviour. We conclude that dominance rank serves as a useful summary for investigating social environmental effects on downstream outcomes. Nevertheless, the behavioural interactions that define an individual's daily experiences reveal the proximate drivers of social status-related differences and are especially relevant for understanding why individuals who share the same social status sometimes appear physiologically distinct.This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.
DOI: 10.6084/m9.figshare.19767943
title: Additional file 3 of Diabetes risk loci-associated pathways are shared across metabolic tissues

description: Additional file 3: Table S2. eQTLs associated with T2D SNPs.
DOI: 10.6084/m9.figshare.17150973.v1
title: Supplemental Tables 4-10 from Agonism and grooming behaviour explain social status effects on physiology and gene regulation in rhesus macaques

description: Variation in social status predicts molecular, physiological and life-history outcomes across a broad range of species, including our own. Experimental studies indicate that some of these relationships persist even when the physical environment is held constant. Here, we draw on datasets from one such study—experimental manipulation of dominance rank in captive female rhesus macaques—to investigate how social status shapes the lived experience of these animals to alter gene regulation, glucocorticoid physiology and mitochondrial DNA phenotypes. We focus specifically on dominance rank-associated dimensions of the social environment, including both competitive and affiliative interactions. Our results show that simple summaries of rank-associated behavioural interactions are often better predictors of molecular and physiological outcomes than dominance rank itself. However, while measures of immune function are best explained by agonism rates, glucocorticoid-related phenotypes tend to be more closely linked to affiliative behaviour. We conclude that dominance rank serves as a useful summary for investigating social environmental effects on downstream outcomes. Nevertheless, the behavioural interactions that define an individual's daily experiences reveal the proximate drivers of social status-related differences and are especially relevant for understanding why individuals who share the same social status sometimes appear physiologically distinct.This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.
DOI: 10.6084/m9.figshare.19247991
title: Aeroponic evaluation identifies variation in Indian potato varieties for root morphology, nitrogen use efficiency parameters and yield traits

description: Nitrogen (N) is an essential nutrient for plant growth and tuber yield in potato. Its excess application is harmful for environment, and therefore dissecting traits involved in improving nitrogen use efficiency (NUE) and yield is essential to address them. This study was conducted to analyze variation in 56 Indian potato varieties at optimal N concentration (2 milli molar) under aeroponics for two years based on 17 different traits for root system architecture (length, surface area, diameter and volume), plant height, leaf area, root and shoot dry weight, tuber traits (number, yield and dry matter), and NUE parameters <i>viz.</i>, NUE, agronomic NUE (AgNUE), nitrogen uptake efficiency (NUpE), nitrogen utilization efficiency (NUtE), harvest index (HI) and N harvest index (NHI). Significant differences (<i>p</i> &lt; 0.05) were observed in the varieties for most traits under the investigation. The Agglomerative hierarchical clustering (AHC) analysis clearly distinguished the varieties into two main groups, and principal component analysis (PCA) analysis showed total 64.78% variability in the first two components. Significant and positive correlations were found for tuber yield with AgNUE, NUE and NUpE. On the other hand, top 10 promising varieties under aeroponics for above traits were Kufri Badshah, Kufri Frysona, Kufri Chipsona-3, Kufri Pushkar, Kufri Lalit, Kufri Ashoka, Kufri Sutlej, Kufri Jyoti, Kufri Mohan and Kufri Khyati. This study implies that a great variation exists in the Indian potato varieties including old and new categories and they can be exploited in breeding for increasing resource capture to improve NUE in potato.
DOI: 10.6084/m9.figshare.19247991.v1
title: Aeroponic evaluation identifies variation in Indian potato varieties for root morphology, nitrogen use efficiency parameters and yield traits

description: Nitrogen (N) is an essential nutrient for plant growth and tuber yield in potato. Its excess application is harmful for environment, and therefore dissecting traits involved in improving nitrogen use efficiency (NUE) and yield is essential to address them. This study was conducted to analyze variation in 56 Indian potato varieties at optimal N concentration (2 milli molar) under aeroponics for two years based on 17 different traits for root system architecture (length, surface area, diameter and volume), plant height, leaf area, root and shoot dry weight, tuber traits (number, yield and dry matter), and NUE parameters <i>viz.</i>, NUE, agronomic NUE (AgNUE), nitrogen uptake efficiency (NUpE), nitrogen utilization efficiency (NUtE), harvest index (HI) and N harvest index (NHI). Significant differences (<i>p</i> &lt; 0.05) were observed in the varieties for most traits under the investigation. The Agglomerative hierarchical clustering (AHC) analysis clearly distinguished the varieties into two main groups, and principal component analysis (PCA) analysis showed total 64.78% variability in the first two components. Significant and positive correlations were found for tuber yield with AgNUE, NUE and NUpE. On the other hand, top 10 promising varieties under aeroponics for above traits were Kufri Badshah, Kufri Frysona, Kufri Chipsona-3, Kufri Pushkar, Kufri Lalit, Kufri Ashoka, Kufri Sutlej, Kufri Jyoti, Kufri Mohan and Kufri Khyati. This study implies that a great variation exists in the Indian potato varieties including old and new categories and they can be exploited in breeding for increasing resource capture to improve NUE in potato.