cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1263588.v2
title: An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

description: Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Moreover, a signature of DNA methylation and gene expression separated the samples based on training and gender. Differential DNA methylation was predominantly observed in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. We identified transcriptional regulator binding motifs of MRF, MEF2 and ETS proteins in the proximity of the changing sites. A transcriptional network analysis revealed modules harboring distinct ontologies and, interestingly, the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus.
DOI: 10.6084/m9.figshare.1263587.v2
title: Genome-wide DNA methylation analysis in precursor B-cells

description: DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
DOI: 10.6084/m9.figshare.1263558
title: Π-Rich σ<sup>2</sup>P-Ligands: Unusual Coordination Behavior of <i>1H</i>-1,3-Benzazaphospholes Toward Late Transition Metals

description: GRAPHICAL ABSTRACT
DOI: 10.6084/m9.figshare.1263558.v2
title: Π-Rich σ<sup>2</sup>P-Ligands: Unusual Coordination Behavior of <i>1H</i>-1,3-Benzazaphospholes Toward Late Transition Metals

description: GRAPHICAL ABSTRACT
DOI: 10.6084/m9.figshare.1263558.v1
title: π-Rich σ<sup>2</sup>P-Ligands: Unusual Coordination Behavior of <i>1H</i>-1,3-Benzazaphospholes towards Late Transition Metals

description: Coordination chemical studies of 1H-1,3-benzazaphospholes, π-excess aromatic σ<sup>2</sup>P-ligands, demonstrate similar ligand properties to those of phosphabenzenes towards M<sup>VI</sup>(CO)<sub>n</sub> but marked differences towards non-zerovalent transition metals. Benzazaphosphole d<sup>8</sup>-metal halide complexes are more strongly destabilized and undergo consecutive reactions, whereas benzazaphosphole coinage metal halide and HgCl<sub>2</sub> complexes generally display μ<sub>2</sub>P- and/or bent η<sup>1</sup>P-coordination with π-P donor bond contribution, contrasting with the preference of phosphinine CuX complexes for η<sup>1</sup>P-coordination within the ring plane.
DOI: 10.6084/m9.figshare.1263554
title: Early spring warming as one of the factors responsible for expansion of aquatic fern <i>Salvinia natans</i> (L.) All. in the Vistula delta (south Baltic Sea coast)

description: From the mid-19th century to the end of the 20th century, <i>Salvinia natans</i> (L.) All. occurred very rarely in the Vistula Delta (northern Poland), but from the beginning of the 21st century it was present in almost every watercourse and had formed very abundant populations. We examined the influence of temperature on the abundance of this plant and the efficiency of macrospore germination. Field work was carried out in 10 permanent plots every 14 days for 5 years. Macrospores germinate at water temperature of 12.4 ± 0.2°C or higher; at 20°C they develop more effectively than at 15°C. Usually, ice cover on the rivers melts in the second half of March. At this time, macro- and microspores emerge on the water surface and germinate in April. They occur in the water surface film at 15.1 ± 2.4°C and massively die during spring frost. After 1989, March and April mean temperature in the Vistula Delta rose by 1.6°C versus 1901–1988, and by 1.9°C versus 1851–1988. In 1951–1988, the mean temperature for March and April was +4.6°C and was characterized by considerable interannual variation (SD = 1.64), whereas in 1989–2009, it rose to +5.7°C and the variation range narrowed (SD = 1.24). We found that macrospores are active earlier during the warm and mild summers, germination is more effective, survival of young stages is higher, the growing season is longer, and the number of vegetative offsprings in a year is larger.
DOI: 10.6084/m9.figshare.1263554.v2
title: Early spring warming as one of the factors responsible for expansion of aquatic fern <i>Salvinia natans</i> (L.) All. in the Vistula delta (south Baltic Sea coast)

description: From the mid-19th century to the end of the 20th century, <i>Salvinia natans</i> (L.) All. occurred very rarely in the Vistula Delta (northern Poland), but from the beginning of the 21st century it was present in almost every watercourse and had formed very abundant populations. We examined the influence of temperature on the abundance of this plant and the efficiency of macrospore germination. Field work was carried out in 10 permanent plots every 14 days for 5 years. Macrospores germinate at water temperature of 12.4 ± 0.2°C or higher; at 20°C they develop more effectively than at 15°C. Usually, ice cover on the rivers melts in the second half of March. At this time, macro- and microspores emerge on the water surface and germinate in April. They occur in the water surface film at 15.1 ± 2.4°C and massively die during spring frost. After 1989, March and April mean temperature in the Vistula Delta rose by 1.6°C versus 1901–1988, and by 1.9°C versus 1851–1988. In 1951–1988, the mean temperature for March and April was +4.6°C and was characterized by considerable interannual variation (SD = 1.64), whereas in 1989–2009, it rose to +5.7°C and the variation range narrowed (SD = 1.24). We found that macrospores are active earlier during the warm and mild summers, germination is more effective, survival of young stages is higher, the growing season is longer, and the number of vegetative offsprings in a year is larger.
DOI: 10.6084/m9.figshare.1263554.v1
title: Early spring warming as one of the factors responsible for expansion of aquatic fern <i>Salvinia natans</i> (L.) All. in the Vistula delta (south Baltic Sea coast)

description: From the mid-19<sup>th</sup> century to the end of the 20<sup>th</sup> century, <i>Salvinia natans</i> (L.) All. occurred very rarely in the Vistula Delta (northern Poland), but from the beginning of the 21<sup>st</sup> century it was present in almost every watercourse and had formed very abundant populations. We examined the influence of temperature on the abundance of this plant and the efficiency of macrospore germination. Field work was carried out in 10 permanent plots every 14 days for 5 years. Macrospores germinate at water temperature of 12.4 ± 0.2°C or higher; at 20°C they develop more effectively than at 15°C. Usually, ice cover on the rivers melts in the second half of March. At this time, macro- and microspores emerge on the water surface and germinate in April. They occur in the water surface film at 15.1 ± 2.4°C and massively die during spring frost. After 1989, March and April mean temperature in the Vistula Delta rose by 1.6°C versus 1901–1988, and by 1.9°C versus 1851–1988. In 1951–1988 the mean temperature for March and April was +4.6°C and was characterized by considerable interannual variation (SD = 1.64), whereas in 1989–2009 it rose to +5.7°C and the variation range narrowed (SD = 1.24). We found that macrospores are active earlier during the warm and mild summers, germination is more effective, survival of young stages is higher, the growing season is longer, and the number of vegetative offspring in year is larger.
DOI: 10.6084/m9.figshare.1263545
title: Trends in tagging of marine mammals: a review of marine mammal biologging studies

description: The number of scientific papers resulting from biologging instruments deployed on marine mammals is increasing as improved technologies result in smaller devices and improved sensor-, storage- and transmission capabilities. I undertook a comprehensive review of papers resulting from biologging deployments on free-ranging marine mammals between 1965 and 2013 (<i>n</i> = 620) to summarise where (e.g. on which species, as well as in which geographic areas) deployment efforts were focused, the impacts of the resulting papers, and where there are shortcomings in the literature. Species-, sex- and age-class biases were evident in terms of animals instrumented. Also, large proportions of the papers resulted from deployments on a small number of species (particularly among the pinnipeds) and were more often on adult females than other demographic classes. The mean impact of papers (as assessed using journal impact factors and numbers of citations) was consistent over time, and was influenced by the number of species studied, sample sizes and instrument capabilities. I found a paucity of papers addressing device influences on animals, as well as studies with explicit conservation and/or management implications. This review aims to increase awareness of marine mammal biologging data already collected, stimulate appropriate further studies, and encourage the reuse of existing data.
DOI: 10.6084/m9.figshare.1263531
title: <i>RASSF6</i> exhibits promoter hypermethylation in metastatic melanoma and inhibits invasion in melanoma cells

description: Brain metastasis is a major contributor to cancer mortality, yet, the genetic changes underlying the development of this capacity remain poorly understood. RASSF proteins are a family of tumor suppressors that often suffer epigenetic inactivation during tumorigenesis. However, their epigenetic status in brain metastases has not been well characterized. We have examined the promoter methylation of the classical RASSF members (<i>RASSF1A-RASSF6</i>) in a panel of metastatic brain tumor samples. <i>RASSF1A</i> and <i>RASSF2</i> have been shown to undergo promoter methylation at high frequency in primary lung and breast tumors and in brain metastases. Other members exhibited little or no methylation in these tumors. In examining melanoma metastases, however, we found that RASSF6 exhibits the highest frequency of inactivation in melanoma and in melanoma brain metastases. Most melanomas are driven by an activating mutation in <i>B-Raf</i>. Introduction of RASSF6 into a B-Raf<sup>V600E</sup>-containing metastatic melanoma cell line inhibited its ability to invade through collagen and suppressed MAPK pathway activation and AKT. RASSF6 also appears to increase the association of mutant B-Raf and MST1, providing a potential mechanism by which RASSF6 is able to suppress MAPK activation. Thus<b>,</b> we have identified a novel potential role for RASSF6 in melanoma development. Promoter methylation leading to reduced expression of RASSF6 may play an important role in melanoma development and may contribute to brain metastases.
DOI: 10.6084/m9.figshare.1263545.v1
title: Trends in tagging of marine mammals: a review of marine mammal biologging studies

description: The number of scientific papers resulting from biologging instruments deployed on marine mammals is increasing as improved technologies result in smaller devices and improved sensor-, storage- and transmission capabilities. I undertook a comprehensive review of papers resulting from biologging deployments on free-ranging marine mammals between 1965 and 2013 (<i>n</i> = 620) to summarise where (e.g. on which species, as well as in which geographic areas) deployment efforts were focused, the impacts of the resulting papers, and where there are shortcomings in the literature. Species-, sex- and age-class biases were evident in terms of animals instrumented. Also, large proportions of the papers resulted from deployments on a small number of species (particularly among the pinnipeds) and were more often on adult females than other demographic classes. The mean impact of papers (as assessed using journal impact factors and numbers of citations) was consistent over time, and was influenced by the number of species studied, sample sizes and instrument capabilities. I found a paucity of papers addressing device influences on animals, as well as studies with explicit conservation and/or management implications. This review aims to increase awareness of marine mammal biologging data already collected, stimulate appropriate further studies, and encourage the reuse of existing data.
DOI: 10.6084/m9.figshare.1263545.v3
title: Trends in tagging of marine mammals: a review of marine mammal biologging studies

description: The number of scientific papers resulting from biologging instruments deployed on marine mammals is increasing as improved technologies result in smaller devices and improved sensor-, storage- and transmission capabilities. I undertook a comprehensive review of papers resulting from biologging deployments on free-ranging marine mammals between 1965 and 2013 (<i>n</i> = 620) to summarise where (e.g. on which species, as well as in which geographic areas) deployment efforts were focused, the impacts of the resulting papers, and where there are shortcomings in the literature. Species-, sex- and age-class biases were evident in terms of animals instrumented. Also, large proportions of the papers resulted from deployments on a small number of species (particularly among the pinnipeds) and were more often on adult females than other demographic classes. The mean impact of papers (as assessed using journal impact factors and numbers of citations) was consistent over time, and was influenced by the number of species studied, sample sizes and instrument capabilities. I found a paucity of papers addressing device influences on animals, as well as studies with explicit conservation and/or management implications. This review aims to increase awareness of marine mammal biologging data already collected, stimulate appropriate further studies, and encourage the reuse of existing data.
DOI: 10.6084/m9.figshare.1263545.v2
title: Trends in tagging of marine mammals: a review of marine mammal biologging studies

description: The number of scientific papers resulting from biologging instruments deployed on marine mammals is increasing as improved technologies result in smaller devices and improved sensor-, storage- and transmission capabilities. I undertook a comprehensive review of papers resulting from biologging deployments on free-ranging marine mammals between 1965 and 2013 (<i>n</i> = 620) to summarise where (e.g. on which species, as well as in which geographic areas) deployment efforts were focused, the impacts of the resulting papers, and where there are shortcomings in the literature. Species-, sex- and age-class biases were evident in terms of animals instrumented. Also, large proportions of the papers resulted from deployments on a small number of species (particularly among the pinnipeds) and were more often on adult females than other demographic classes. The mean impact of papers (as assessed using journal impact factors and numbers of citations) was consistent over time, and was influenced by the number of species studied, sample sizes and instrument capabilities. I found a paucity of papers addressing device influences on animals, as well as studies with explicit conservation and/or management implications. This review aims to increase awareness of marine mammal biologging data already collected, stimulate appropriate further studies, and encourage the reuse of existing data.
DOI: 10.6084/m9.figshare.1263531.v1
title: <i>RASSF6</i> exhibits promoter hypermethylation in metastatic melanoma and inhibits invasion in melanoma cells

description: ABSTRACTBrain metastasis is a major contributor to cancer mortality; yet, the genetic changes underlying the development of this capacity remain poorly understood. RASSF proteins are a family of tumor suppressors that often suffer epigenetic inactivation during tumorigenesis. However, their epigenetic status in brain metastases has not been well characterized. We have examined the promoter methylation of the classical RASSF members (<i>RASSF1A-RASSF6</i>) in a panel of metastatic brain tumor samples. <i>RASSF1A</i> and <i>RASSF2</i> have been shown to undergo promoter methylation at high frequency in primary lung and breast tumors and in brain metastases. Other members exhibited little or no methylation in these tumors. In examining melanoma metastases, however, we found that RASSF6 exhibits the highest frequency of inactivation in melanoma and in melanoma brain metastases. Most melanomas are driven by an activating mutation in <i>B-Raf</i>. Introduction of RASSF6 into a B-Raf<sup>V600E</sup>-containing metastatic melanoma cell line inhibited its ability to invade through collagen and suppressed MAPK pathway activation and AKT. RASSF6 also appears to increase the association of mutant B-Raf and MST1, providing a potential mechanism by which RASSF6 is able to suppress MAPK activation. Thus<b>,</b> we have identified a novel potential role for RASSF6 in melanoma development. Promoter methylation leading to reduced expression of RASSF6 may play an important role in melanoma development and may contribute to brain metastases.
DOI: 10.6084/m9.figshare.1263528
title: The importance of vertical habitat gradients on zooplankton distribution in an enclosed marine environment (South Adriatic Sea)

description: The spatio-temporal patterns of a zooplankton community structure in a strongly stratified enclosed marine environment were studied over a one-year period. Copepods were by far the most abundant group, accounting for 69–91% of the total zooplankton, with a numerical dominance of the genus <i>Oithona</i>. Cluster analysis revealed four different groups of samples and a comparison was made of the hydrographical and biological properties of the resulting groups. Water temperature was the main force discriminating the zooplankton community. The strongest vertical separation was recorded in summer, while a salinity impact was noted during the autumn after a strong intrusion of open sea water. Most of the dominant zooplankters exhibited a distinct vertical separation over the study period, where thermophilic taxa (Cladocera, <i>Centropages kröyeri, C. typicus, Oikopleura fusiformis, O. longicauda, Euterpina acutifrons</i>) kept to the surface and cryophilic species (<i>Diaixis pygmaea, Mesaiokeras hurei, Calanus helgolandicus, Parasagitta setosa</i>) were concentrated below the thermocline layer (20 m depth) for most of the year. Due to the unique physical, chemical and biological properties of the study site, this research is an important step towards better understanding the distribution of zooplankton during stratified conditions.
DOI: 10.6084/m9.figshare.1263531.v3
title: <i>RASSF6</i> exhibits promoter hypermethylation in metastatic melanoma and inhibits invasion in melanoma cells

description: Brain metastasis is a major contributor to cancer mortality, yet, the genetic changes underlying the development of this capacity remain poorly understood. RASSF proteins are a family of tumor suppressors that often suffer epigenetic inactivation during tumorigenesis. However, their epigenetic status in brain metastases has not been well characterized. We have examined the promoter methylation of the classical RASSF members (<i>RASSF1A-RASSF6</i>) in a panel of metastatic brain tumor samples. <i>RASSF1A</i> and <i>RASSF2</i> have been shown to undergo promoter methylation at high frequency in primary lung and breast tumors and in brain metastases. Other members exhibited little or no methylation in these tumors. In examining melanoma metastases, however, we found that RASSF6 exhibits the highest frequency of inactivation in melanoma and in melanoma brain metastases. Most melanomas are driven by an activating mutation in <i>B-Raf</i>. Introduction of RASSF6 into a B-Raf<sup>V600E</sup>-containing metastatic melanoma cell line inhibited its ability to invade through collagen and suppressed MAPK pathway activation and AKT. RASSF6 also appears to increase the association of mutant B-Raf and MST1, providing a potential mechanism by which RASSF6 is able to suppress MAPK activation. Thus<b>,</b> we have identified a novel potential role for RASSF6 in melanoma development. Promoter methylation leading to reduced expression of RASSF6 may play an important role in melanoma development and may contribute to brain metastases.
DOI: 10.6084/m9.figshare.1263531.v2
title: <i>RASSF6</i> exhibits promoter hypermethylation in metastatic melanoma and inhibits invasion in melanoma cells

description: Brain metastasis is a major contributor to cancer mortality, yet, the genetic changes underlying the development of this capacity remain poorly understood. RASSF proteins are a family of tumor suppressors that often suffer epigenetic inactivation during tumorigenesis. However, their epigenetic status in brain metastases has not been well characterized. We have examined the promoter methylation of the classical RASSF members (<i>RASSF1A-RASSF6</i>) in a panel of metastatic brain tumor samples. <i>RASSF1A</i> and <i>RASSF2</i> have been shown to undergo promoter methylation at high frequency in primary lung and breast tumors and in brain metastases. Other members exhibited little or no methylation in these tumors. In examining melanoma metastases, however, we found that RASSF6 exhibits the highest frequency of inactivation in melanoma and in melanoma brain metastases. Most melanomas are driven by an activating mutation in <i>B-Raf</i>. Introduction of RASSF6 into a B-Raf<sup>V600E</sup>-containing metastatic melanoma cell line inhibited its ability to invade through collagen and suppressed MAPK pathway activation and AKT. RASSF6 also appears to increase the association of mutant B-Raf and MST1, providing a potential mechanism by which RASSF6 is able to suppress MAPK activation. Thus<b>,</b> we have identified a novel potential role for RASSF6 in melanoma development. Promoter methylation leading to reduced expression of RASSF6 may play an important role in melanoma development and may contribute to brain metastases.