cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5926723.v2
title: Minimizing Flow Completion Times using Adaptive Routing over Inter-Datacenter Wide Area Networks

description: Inter-datacenter networks connect dozens of geographically dispersed datacenters and carry traffic flows with highly variable sizes and different classes. Adaptive flow routing can improve efficiency and performance by assigning paths to new flows according to network status and flow properties. A popular approach widely used for traffic engineering is based on current bandwidth utilization of links. We propose an alternative that reduces bandwidth usage by up to at least 50% and flow completion times by up to at least 40% across various scheduling policies and flow size distributions.
DOI: 10.6084/m9.figshare.5926714
title: Transcriptome analysis of colouration-related genes in two white-fleshed nectarine varieties and their yellow-fleshed mutants

description: Nectarine, a variety of peach is rich in bioactive and antioxidant compounds, and both white- and yellow-fleshed nectarine fruits are commercially popular. However, although anthocyanin (flavonoid) and carotenoid biosynthetic pathways play important roles in plant colouration, the molecular basis of fruit flesh colouration remains largely unknown. Accordingly, we performed an RNA sequencing-based transcriptome analysis of two white-fleshed nectarines, Zhongyou9 (ZY9) and Zhongyou13 (ZY13-W), and their yellow-fleshed mutants, Hongyu (HY) and Zhongyou13-Y (ZY13-Y). To differentiate the impact of ripening on gene expression, we also compared ZY9 and HY at two different time points, namely, before and after fruit ripening. We found that the yellow-fleshed HY may accumulate flavonoids through the generation of more flavonoid biosynthesis precursors, as well as through the overexpression of flavonoid synthase genes. In addition, we also found that HY could impede carotenoid degradation <i>via</i> beta-carotene 3-hydroxylase and carotenoid cleavage dioxygenase genes. Meanwhile, ZY13-Y may regulate its yellow colouration through overexpression of chalcone synthase genes, in order to accumulate flavonoids, as well as through the underexpression of flavonol 3-O-methyltransferase and carotenoid cleavage dioxygenase genes, in order to slow flavonoid and carotenoid degradation. As demonstrated by the multiple transcription factors that were differentially expressed in the yellow- and white-fleshed varieties, it is clear that the regulation of peach and nectarine colouration is a complex process. Furthermore, we also identified several other genes that are potentially related to fruit colouration. Thus, our results provide a valuable advancement in the elucidation of the molecular basis of flesh colouration in nectarine.
DOI: 10.6084/m9.figshare.5926714.v1
title: Transcriptome analysis of colouration-related genes in two white-fleshed nectarine varieties and their yellow-fleshed mutants

description: Nectarine, a variety of peach is rich in bioactive and antioxidant compounds, and both white- and yellow-fleshed nectarine fruits are commercially popular. However, although anthocyanin (flavonoid) and carotenoid biosynthetic pathways play important roles in plant colouration, the molecular basis of fruit flesh colouration remains largely unknown. Accordingly, we performed an RNA sequencing-based transcriptome analysis of two white-fleshed nectarines, Zhongyou9 (ZY9) and Zhongyou13 (ZY13-W), and their yellow-fleshed mutants, Hongyu (HY) and Zhongyou13-Y (ZY13-Y). To differentiate the impact of ripening on gene expression, we also compared ZY9 and HY at two different time points, namely, before and after fruit ripening. We found that the yellow-fleshed HY may accumulate flavonoids through the generation of more flavonoid biosynthesis precursors, as well as through the overexpression of flavonoid synthase genes. In addition, we also found that HY could impede carotenoid degradation <i>via</i> beta-carotene 3-hydroxylase and carotenoid cleavage dioxygenase genes. Meanwhile, ZY13-Y may regulate its yellow colouration through overexpression of chalcone synthase genes, in order to accumulate flavonoids, as well as through the underexpression of flavonol 3-O-methyltransferase and carotenoid cleavage dioxygenase genes, in order to slow flavonoid and carotenoid degradation. As demonstrated by the multiple transcription factors that were differentially expressed in the yellow- and white-fleshed varieties, it is clear that the regulation of peach and nectarine colouration is a complex process. Furthermore, we also identified several other genes that are potentially related to fruit colouration. Thus, our results provide a valuable advancement in the elucidation of the molecular basis of flesh colouration in nectarine.
DOI: 10.6084/m9.figshare.5926690
title: Double gene targeting PCR assay for the detection of <i>Crocodylus porosus</i> in commercial products

description: The demand for crocodile meat is quickly growing because of its exotic and organoleptic appeal and also the low content of cholesterol and lipids. Moreover, crocodile oil and blood have been used in alternative medicines for treating asthma and several other ailments since ancient times. Furthermore, crocodile hides have great demand in leather industries. All of these have collectively contributed to the extensive hunting, illegal trading and consequent decline of crocodiles in most parts of the world. To keep space with the growing demands, some crocodile species such as <i>Crocodylus porosus</i> have been raised in farms and its commercial trades have been legalised. However, demand for wild crocodiles in foods and medicines has continued in high gear. Recently, several DNA-based methods have been proposed for crocodile detection, but those assays are based on single gene and longer-sized amplicon targets that break down during extensive processing. To address this gap, here we developed and validated a highly stable double gene targeted multiplex PCR assay for the identification of <i>C. porosus</i> materials in commercial products. The assay involved two short sites from <i>C. porosus</i> atp6 (77 bp) and cytb (127 bp) genes and a universal internal control (99 bp) for eukaryotes. The PCR primers were cross-tested against 18 species and validated under pure and mixed matrices under extensive boiling, autoclaving and microwave cooking conditions. Finally, it was used to identify five crocodile-based commercial products. The lower limits of detection for atp6 and cytb genes were 0.001 ng and 0.01 ng DNA, respectively, in pure meat and 1% under mixed matrices. Some inherent features, such as 77–127 bp amplicon sizes, exceptional stability and superior sensitivity, suggested the assay could be used for the identification of <i>C. porosus</i> in any forensic specimen.
DOI: 10.6084/m9.figshare.5926690.v1
title: Double gene targeting PCR assay for the detection of <i>Crocodylus porosus</i> in commercial products

description: The demand for crocodile meat is quickly growing because of its exotic and organoleptic appeal and also the low content of cholesterol and lipids. Moreover, crocodile oil and blood have been used in alternative medicines for treating asthma and several other ailments since ancient times. Furthermore, crocodile hides have great demand in leather industries. All of these have collectively contributed to the extensive hunting, illegal trading and consequent decline of crocodiles in most parts of the world. To keep space with the growing demands, some crocodile species such as <i>Crocodylus porosus</i> have been raised in farms and its commercial trades have been legalised. However, demand for wild crocodiles in foods and medicines has continued in high gear. Recently, several DNA-based methods have been proposed for crocodile detection, but those assays are based on single gene and longer-sized amplicon targets that break down during extensive processing. To address this gap, here we developed and validated a highly stable double gene targeted multiplex PCR assay for the identification of <i>C. porosus</i> materials in commercial products. The assay involved two short sites from <i>C. porosus</i> atp6 (77 bp) and cytb (127 bp) genes and a universal internal control (99 bp) for eukaryotes. The PCR primers were cross-tested against 18 species and validated under pure and mixed matrices under extensive boiling, autoclaving and microwave cooking conditions. Finally, it was used to identify five crocodile-based commercial products. The lower limits of detection for atp6 and cytb genes were 0.001 ng and 0.01 ng DNA, respectively, in pure meat and 1% under mixed matrices. Some inherent features, such as 77–127 bp amplicon sizes, exceptional stability and superior sensitivity, suggested the assay could be used for the identification of <i>C. porosus</i> in any forensic specimen.
DOI: 10.6084/m9.figshare.5926690.v3
title: Double gene targeting PCR assay for the detection of <i>Crocodylus porosus</i> in commercial products

description: The demand for crocodile meat is quickly growing because of its exotic and organoleptic appeal and also the low content of cholesterol and lipids. Moreover, crocodile oil and blood have been used in alternative medicines for treating asthma and several other ailments since ancient times. Furthermore, crocodile hides have great demand in leather industries. All of these have collectively contributed to the extensive hunting, illegal trading and consequent decline of crocodiles in most parts of the world. To keep space with the growing demands, some crocodile species such as <i>Crocodylus porosus</i> have been raised in farms and its commercial trades have been legalised. However, demand for wild crocodiles in foods and medicines has continued in high gear. Recently, several DNA-based methods have been proposed for crocodile detection, but those assays are based on single gene and longer-sized amplicon targets that break down during extensive processing. To address this gap, here we developed and validated a highly stable double gene targeted multiplex PCR assay for the identification of <i>C. porosus</i> materials in commercial products. The assay involved two short sites from <i>C. porosus</i> atp6 (77 bp) and cytb (127 bp) genes and a universal internal control (99 bp) for eukaryotes. The PCR primers were cross-tested against 18 species and validated under pure and mixed matrices under extensive boiling, autoclaving and microwave cooking conditions. Finally, it was used to identify five crocodile-based commercial products. The lower limits of detection for atp6 and cytb genes were 0.001 ng and 0.01 ng DNA, respectively, in pure meat and 1% under mixed matrices. Some inherent features, such as 77–127 bp amplicon sizes, exceptional stability and superior sensitivity, suggested the assay could be used for the identification of <i>C. porosus</i> in any forensic specimen.
DOI: 10.6084/m9.figshare.5926690.v2
title: Double gene targeting PCR assay for the detection of <i>Crocodylus porosus</i> in commercial products

description: The demand for crocodile meat is quickly growing because of its exotic and organoleptic appeal and also the low content of cholesterol and lipids. Moreover, crocodile oil and blood have been used in alternative medicines for treating asthma and several other ailments since ancient times. Furthermore, crocodile hides have great demand in leather industries. All of these have collectively contributed to the extensive hunting, illegal trading and consequent decline of crocodiles in most parts of the world. To keep space with the growing demands, some crocodile species such as <i>Crocodylus porosus</i> have been raised in farms and its commercial trades have been legalised. However, demand for wild crocodiles in foods and medicines has continued in high gear. Recently, several DNA-based methods have been proposed for crocodile detection, but those assays are based on single gene and longer-sized amplicon targets that break down during extensive processing. To address this gap, here we developed and validated a highly stable double gene targeted multiplex PCR assay for the identification of <i>C. porosus</i> materials in commercial products. The assay involved two short sites from <i>C. porosus</i> atp6 (77 bp) and cytb (127 bp) genes and a universal internal control (99 bp) for eukaryotes. The PCR primers were cross-tested against 18 species and validated under pure and mixed matrices under extensive boiling, autoclaving and microwave cooking conditions. Finally, it was used to identify five crocodile-based commercial products. The lower limits of detection for atp6 and cytb genes were 0.001 ng and 0.01 ng DNA, respectively, in pure meat and 1% under mixed matrices. Some inherent features, such as 77–127 bp amplicon sizes, exceptional stability and superior sensitivity, suggested the assay could be used for the identification of <i>C. porosus</i> in any forensic specimen.
DOI: 10.6084/m9.figshare.5926681
title: Midbond basis functions for weakly bound complexes

description: Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.
DOI: 10.6084/m9.figshare.5926681.v1
title: Midbond basis functions for weakly bound complexes

description: Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.
DOI: 10.6084/m9.figshare.5926675
title: MicroRNA meta-signature of oral cancer: evidence from a meta-analysis

description: <b>Aim:</b> It was the aim of the study to identify commonly deregulated miRNAs in oral cancer patients by performing a meta-analysis of previously published miRNA expression profiles in cancer and matched normal non-cancerous tissue in such patients. <b>Material and methods:</b> Meta-analysis included seven independent studies analyzed by a vote-counting method followed by bioinformatic enrichment analysis. <b>Results:</b> Amongst seven independent studies included in the meta-analysis, 20 miRNAs were found to be deregulated in oral cancer when compared with non-cancerous tissue. Eleven miRNAs were consistently up-regulated in three or more studies (miR-21-5p, miR-31-5p, miR-135b-5p, miR-31-3p, miR-93-5p, miR-34b-5p, miR-424-5p, miR-18a-5p, miR-455-3p, miR-450a-5p, miR-21-3p), and nine were down-regulated (miR-139-5p, miR-30a-3p, miR-376c-3p, miR-885-5p, miR-375, miR-486-5p, miR-411-5p, miR-133a-3p, miR-30a-5p). The meta-signature of identified miRNAs was functionally characterized by KEGG enrichment analysis. Twenty-four KEGG pathways were significantly enriched, and TGF-beta signaling was the most enriched signaling pathway. The highest number of meta-signature miRNAs was involved in the sphingolipid signaling pathway. Natural killer cell-mediated cytotoxicity was the pathway with most genes regulated by identified miRNAs. The rest of the enriched pathways in our miRNA list describe different malignancies and signaling. <b>Conclusions:</b> The identified miRNA meta-signature might be considered as a potential battery of biomarkers when distinguishing oral cancer tissue from normal, non-cancerous tissue. Further mechanistic studies are warranted in order to confirm and fully elucidate the role of deregulated miRNAs in oral cancer.
DOI: 10.6084/m9.figshare.5926675.v1
title: MicroRNA meta-signature of oral cancer: evidence from a meta-analysis

description: <b>Aim:</b> It was the aim of the study to identify commonly deregulated miRNAs in oral cancer patients by performing a meta-analysis of previously published miRNA expression profiles in cancer and matched normal non-cancerous tissue in such patients. <b>Material and methods:</b> Meta-analysis included seven independent studies analyzed by a vote-counting method followed by bioinformatic enrichment analysis. <b>Results:</b> Amongst seven independent studies included in the meta-analysis, 20 miRNAs were found to be deregulated in oral cancer when compared with non-cancerous tissue. Eleven miRNAs were consistently up-regulated in three or more studies (miR-21-5p, miR-31-5p, miR-135b-5p, miR-31-3p, miR-93-5p, miR-34b-5p, miR-424-5p, miR-18a-5p, miR-455-3p, miR-450a-5p, miR-21-3p), and nine were down-regulated (miR-139-5p, miR-30a-3p, miR-376c-3p, miR-885-5p, miR-375, miR-486-5p, miR-411-5p, miR-133a-3p, miR-30a-5p). The meta-signature of identified miRNAs was functionally characterized by KEGG enrichment analysis. Twenty-four KEGG pathways were significantly enriched, and TGF-beta signaling was the most enriched signaling pathway. The highest number of meta-signature miRNAs was involved in the sphingolipid signaling pathway. Natural killer cell-mediated cytotoxicity was the pathway with most genes regulated by identified miRNAs. The rest of the enriched pathways in our miRNA list describe different malignancies and signaling. <b>Conclusions:</b> The identified miRNA meta-signature might be considered as a potential battery of biomarkers when distinguishing oral cancer tissue from normal, non-cancerous tissue. Further mechanistic studies are warranted in order to confirm and fully elucidate the role of deregulated miRNAs in oral cancer.
DOI: 10.6084/m9.figshare.5926669.v5
title: On the Y-DNA of Jesus of Nazareth

description: An ancient dilemma for Christianity is that a) the Jewish Messiah must according to prophecy be a member of the house of David, and the tribe of Judah, but b) house and tribal identity are inherited only through the male line, and Jesus lacked a human father, albeit that Joseph belonged to the house of David. Here we offer a resolution of this dilemma, a resolution that arises in the context of a non-Darwinian approach to genetic genealogy.
DOI: 10.6084/m9.figshare.5926669.v6
title: On the Y-DNA of Jesus of Nazareth

description: An ancient dilemma for Christianity is that a) the Jewish Messiah must according to prophecy be a member of the house of David, and the tribe of Judah, but b) house and tribal identity are inherited only through the male line, and Jesus lacked a human father, albeit that Joseph belonged to the house of David. Here we offer a resolution of this dilemma, a resolution that arises in the context of a non-Darwinian approach to genetic genealogy.
DOI: 10.6084/m9.figshare.5926630
title: Within-species variation among populations of the <i>Carex flava</i> complex as a function of habitat conditions

description: <b><i>Background</i></b>: Variable habitat conditions contribute to morphological variability that plays a substantial part in evolution of plants. Understanding the extent of phenotypic plasticity has important implication for assigning individuals to taxa. <b><i>Aims</i></b>: I analysed morphological variability among populations within species of the <i>Carex flava</i> group and tested to what extent morphological variability was associated with habitat conditions. <b><i>Methods</i></b>: A total of 571 specimens from 20 populations of four species from the <i>C. flava</i> complex were sampled in Poland and tested by Discriminant Function Analysis (DFA). The relationship between morphological characters and habitat factors was explored by means of the redundancy analysis (RDA). <b><i>Results</i></b>: Variability of the generative and vegetative traits was fairly similar in <i>Carex lepidocarpa, C. flava</i> and <i>Carex demissa</i>, while it was somewhat higher in <i>Carex viridula</i>. The morphological traits were mostly related to soil organic matter content, calcium and carbonate, as well as to habitat fertility (C:N ratio), elevation and habitat disturbance. The results obtained do not support the separation of <i>C</i>. <i>viridula</i> var. <i>pulchella</i> from <i>C. viridula</i> var. <i>viridula</i>. <b><i>Conclusions</i></b>: Phenotypic variability in the species of the <i>C. flava</i> complex is related to habitat conditions and this can lead to the differentiation of morphotypes within species.
DOI: 10.6084/m9.figshare.5926630.v1
title: Within-species variation among populations of the <i>Carex flava</i> complex as a function of habitat conditions

description: <b><i>Background</i></b>: Variable habitat conditions contribute to morphological variability that plays a substantial part in evolution of plants. Understanding the extent of phenotypic plasticity has important implication for assigning individuals to taxa. <b><i>Aims</i></b>: I analysed morphological variability among populations within species of the <i>Carex flava</i> group and tested to what extent morphological variability was associated with habitat conditions. <b><i>Methods</i></b>: A total of 571 specimens from 20 populations of four species from the <i>C. flava</i> complex were sampled in Poland and tested by Discriminant Function Analysis (DFA). The relationship between morphological characters and habitat factors was explored by means of the redundancy analysis (RDA). <b><i>Results</i></b>: Variability of the generative and vegetative traits was fairly similar in <i>Carex lepidocarpa, C. flava</i> and <i>Carex demissa</i>, while it was somewhat higher in <i>Carex viridula</i>. The morphological traits were mostly related to soil organic matter content, calcium and carbonate, as well as to habitat fertility (C:N ratio), elevation and habitat disturbance. The results obtained do not support the separation of <i>C</i>. <i>viridula</i> var. <i>pulchella</i> from <i>C. viridula</i> var. <i>viridula</i>. <b><i>Conclusions</i></b>: Phenotypic variability in the species of the <i>C. flava</i> complex is related to habitat conditions and this can lead to the differentiation of morphotypes within species.
DOI: 10.6084/m9.figshare.5926591
title: Habia rubica sequences

description: Sequences of 5 molecular markers:ND2MUSKACOI9ODCFGB-I5